@article{11120, abstract = {The nuclear envelope (NE) is a highly specialized membrane that delineates the eukaryotic cell nucleus. It is composed of the inner and outer nuclear membranes, nuclear pore complexes (NPCs) and, in metazoa, the lamina. The NE not only regulates the trafficking of macromolecules between nucleoplasm and cytosol but also provides anchoring sites for chromatin and the cytoskeleton. Through these interactions, the NE helps position the nucleus within the cell and chromosomes within the nucleus, thereby regulating the expression of certain genes. The NE is not static, rather it is continuously remodeled during cell division. The most dramatic example of NE reorganization occurs during mitosis in metazoa when the NE undergoes a complete cycle of disassembly and reformation. Despite the importance of the NE for eukaryotic cell life, relatively little is known about its biogenesis or many of its functions. We thus are far from understanding the molecular etiology of a diverse group of NE-associated diseases.}, author = {HETZER, Martin W and Walther, Tobias C. and Mattaj, Iain W.}, issn = {1530-8995}, journal = {Annual Review of Cell and Developmental Biology}, keywords = {Cell Biology, Developmental Biology}, pages = {347--380}, publisher = {Annual Reviews}, title = {{Pushing the envelope: Structure, function, and dynamics of the nuclear periphery}}, doi = {10.1146/annurev.cellbio.21.090704.151152}, volume = {21}, year = {2005}, } @inproceedings{11698, abstract = {We give a short survey of the use of hyperlink analysis in web search engine ranking and sketch other applications of hyperlink analysis in the web space.}, author = {Henzinger, Monika H}, booktitle = {Proceedings of the 16th ACM conference on Hypertext and hypermedia}, isbn = {9781595931689}, keywords = {Hyperlink Analysis, World Wide Web}, location = {Salzburg, Austria}, pages = {1--3}, publisher = {Association for Computing Machinery}, title = {{Hyperlink analysis on the world wide web}}, doi = {10.1145/1083356.1083357}, year = {2005}, } @article{11904, 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}, issn = {1573-1413}, journal = {World Wide Web}, number = {2}, pages = {101--126}, publisher = {Springer Nature}, title = {{Query-free news search}}, doi = {10.1007/s11280-004-4870-6}, volume = {8}, year = {2005}, } @article{11763, abstract = {We present the first polylog-competitive online algorithm for the general multicast admission control and routing problem in the throughput model. The ratio of the number of requests accepted by the optimum offline algorithm to the expected number of requests accepted by our algorithm is O((log n + log log M)(log n + log M) log n), where M is the number of multicast groups and n is the number of nodes in the graph. We show that this is close to optimum by presenting an Ω(log n log M) lower bound on this ratio for any randomized online algorithm against an oblivious adversary, when M is much larger than the link capacities. Our lower bound applies even in the restricted case where the link capacities are much larger than bandwidth requested by a single multicast. We also present a simple proof showing that it is impossible to be competitive against an adaptive online adversary. As in the previous online routing algorithms, our algorithm uses edge-costs when deciding on which is the best path to use. In contrast to the previous competitive algorithms in the throughput model, our cost is not a direct function of the edge load. The new cost definition allows us to decouple the effects of routing and admission decisions of different multicast groups.}, author = {Goel, Ashish and Henzinger, Monika H and Plotkin, Serge}, issn = {0196-6774}, journal = {Journal of Algorithms}, number = {1}, pages = {1--20}, publisher = {Elsevier}, title = {{An online throughput-competitive algorithm for multicast routing and admission control}}, doi = {10.1016/j.jalgor.2004.11.001}, volume = {55}, year = {2005}, } @article{12657, abstract = {An enhanced temperature-index glacier melt model, incorporating incoming shortwave radiation and albedo, is presented. The model is an attempt to combine the high temporal resolution and accuracy of physically based melt models with the lower data requirements and computational simplicity of empirical melt models, represented by the ‘degree-day’ method and its variants. The model is run with both measured and modelled radiation data, to test its applicability to glaciers with differing data availability. Five automatic weather stations were established on Haut Glacier d’Arolla, Switzerland, between May and September 2001. Reference surface melt rates were calculated using a physically based energy-balance melt model. The performance of the enhanced temperature-index model was tested at each of the four validation stations by comparing predicted hourly melt rates with reference melt rates. Predictions made with three other temperature-index models were evaluated in the same way for comparison. The enhanced temperature-index model offers significant improvements over the other temperature-index models, and accounts for 90–95% of the variation in the reference melt rate. The improvement is lower, but still significant, when the model is forced by modelled shortwave radiation data, thus offering a better alternative to existing models that require only temperature data input.}, author = {Pellicciotti, Francesca and Brock, Ben and Strasser, Ulrich and Burlando, Paolo and Funk, Martin and Corripio, Javier}, issn = {1727-5652}, journal = {Journal of Glaciology}, number = {175}, pages = {573--587}, publisher = {Cambridge University Press}, title = {{An enhanced temperature-index glacier melt model including the shortwave radiation balance: Development and testing for Haut Glacier d’Arolla, Switzerland}}, doi = {10.3189/172756505781829124}, volume = {51}, year = {2005}, } @article{1298, abstract = {Genetically encoded fluorescent probes of neural activity represent new promising tools for systems neuroscience. Here, we present a comparative in vivo analysis of 10 different genetically encoded calcium indicators, as well as the pH-sensitive synapto-pHluorin. We analyzed their fluorescence changes in presynaptic boutons of the Drosophila larval neuromuscular junction. Robust neural activity did not result in any or noteworthy fluorescence changes when Flash-Pericam, Camgaroo-1, and Camgaroo-2 were expressed. However, calculated on the raw data, fractional fluorescence changes up to 18% were reported by synapto-pHluorin, Yellow Cameleon 2.0, 2.3, and 3.3, Inverse-Pericam, GCaMP1.3, GCaMP1.6, and the troponin C-based calcium sensor TN-L15. The response characteristics of all of these indicators differed considerably from each other, with GCaMP1.6 reporting high rates of neural activity with the largest and fastest fluorescence changes. However, GCaMP1.6 suffered from photobleaching, whereas the fluorescence signals of the double-chromophore indicators were in general smaller but more photostable and reproducible, with TN-L15 showing the fastest rise of the signals at lower activity rates. We show for GCaMP1.3 and YC3.3 that an expanded range of neural activity evoked fairly linear fluorescence changes and a corresponding linear increase in the signal-to-noise ratio (SNR). The expression level of the indicator biased the signal kinetics and SNR, whereas the signal amplitude was independent. The presented data will be useful for in vivo experiments with respect to the selection of an appropriate indicator, as well as for the correct interpretation of the optical signals.}, author = {Reiff, Dierk F and Ihring, Alexandra and Guerrero, Giovanna and Isacoff, Ehud Y and Maximilian Jösch and Nakai, Junichi and Borst, Alexander}, journal = {Journal of Neuroscience}, number = {19}, pages = {4766 -- 4778}, publisher = {Society for Neuroscience}, title = {{In vivo performance of genetically encoded indicators of neural activity in flies}}, doi = {10.1523/JNEUROSCI.4900-04.2005}, volume = {25}, year = {2005}, } @article{1447, abstract = {Building on a recent paper [8], here we argue that the combinatorics of matroids are intimately related to the geometry and topology of toric hyperkähler varieties. We show that just like toric varieties occupy a central role in Stanley’s proof for the necessity of McMullen’s conjecture (or g-inequalities) about the classification of face vectors of simplicial polytopes, the topology of toric hyperkähler varieties leads to new restrictions on face vectors of matroid complexes. Namely in this paper we will give two proofs that the injectivity part of the Hard Lefschetz theorem survives for toric hyperkähler varieties. We explain how this implies the g-inequalities for rationally representable matroids. We show how the geometrical intuition in the first proof, coupled with results of Chari [3], leads to a proof of the g-inequalities for general matroid complexes, which is a recent result of Swartz [20]. The geometrical idea in the second proof will show that a pure O-sequence should satisfy the g-inequalities, thus showing that our result is in fact a consequence of a long-standing conjecture of Stanley.}, author = {Tamas Hausel}, journal = {Open Mathematics}, number = {1}, pages = {26 -- 38}, publisher = {Central European Science Journals}, title = {{Quaternionic geometry of matroids}}, doi = {10.2478/BF02475653}, volume = {3}, year = {2005}, } @inbook{1444, abstract = {The paper surveys the mirror symmetry conjectures of Hausel-Thaddeus and Hausel-Rodriguez-Villegas concerning the equality of certain Hodge numbers of SL(n, ℂ) vs. PGL(n, ℂ) flat connections and character varieties for curves, respectively. Several new results and conjectures and their relations to works of Hitchin, Gothen, Garsia-Haiman and Earl-Kirwan are explained. These use the representation theory of finite groups of Lie-type via the arithmetic of character varieties and lead to an unexpected conjecture for a Hard Lefschetz theorem for their cohomology.}, author = {Tamas Hausel}, booktitle = {Geometric Methods in Algebra and Number Theory}, pages = {193 -- 217}, publisher = {Springer}, title = {{Mirror symmetry and Langlands duality in the non-Abelian Hodge theory of a curve}}, doi = {10.1007/0-8176-4417-2_9}, volume = {235}, year = {2005}, } @article{1463, abstract = {We study an integration theory in circle equivariant cohomology in order to prove a theorem relating the cohomology ring of a hyperkähler quotient to the cohomology ring of the quotient by a maximal abelian subgroup, analogous to a theorem of Martin for symplectic quotients. We discuss applications of this theorem to quiver varieties, and compute as an example the ordinary and equivariant cohomology rings of a hyperpolygon space.}, author = {Tamas Hausel and Proudfoot, Nicholas J}, journal = {Topology}, number = {1}, pages = {231 -- 248}, publisher = {Elsevier}, title = {{Abelianization for hyperkähler quotients}}, doi = {10.1016/j.top.2004.04.002}, volume = {44}, year = {2005}, } @article{1742, abstract = {The effects of substrate temperature, growth rate, and postgrowth annealing on the composition of Ge islands grown on Si(001) were investigated with a combination of selective wet chemical etching and atomic force microscopy. A simple kinetic model comprising only surface diffusion processes can explain all the experimentally observed compositional profiles for pyramid and dome islands grown in the 560-620°C range. From this model three-dimensional compositional maps were extracted. By performing annealing experiments a change in the composition of the domes was observed. This could be explained as the result of the islands' movement induced by alloying-driven energy minimization. Also in this case kinetically hindered bulk diffusion processes are not needed to explain the experimental observations.}, author = {Georgios Katsaros and Costantini, Giovanni and Stoffel, Mathieu and Esteban, Rubén and Bittner, Alexander M and Rastelli, Armando and Denker, Ulrich and Schmidt, Oliver G and Kern, Klaus}, journal = {Physical Review B - Condensed Matter and Materials Physics}, number = {19}, publisher = {American Physical Society}, title = {{Kinetic origin of island intermixing during the growth of Ge on Si (001)}}, doi = {10.1103/PhysRevB.72.195320}, volume = {72}, year = {2005}, } @article{1740, abstract = {A systematic study of the morphology of self-organized islands in the InAs/GaAs(0 0 1) and Ge/Si(0 0 1) systems is presented, based on high-resolution scanning tunneling microscopy measurements. We demonstrate that in both cases two main island families coexist: smaller pyramids bound by one type of shallow facets and larger multifaceted domes. Their structure and facet orientation are precisely determined, thus solving a highly debated argument in the case of InAs/GaAs(0 0 1). The comparison between the two material systems reveals the existence of striking similarities that extend even to the nature of island precursors and to the islands that form when depositing InGaAs or GeSi alloys. The implications of these observations on a possible universal description of the Stranski-Krastanow growth mode are discussed with respect to recent theoretical results.}, author = {Costantini, Giovanni and Rastelli, Armando and Manzano, Carlos and Acosta-Diaz, P and Georgios Katsaros and Songmuang, Rudeeson and Schmidt, Oliver G and Von Känel, Hans and Kern, Klaus}, journal = {Journal of Crystal Growth}, number = {1-4}, pages = {38 -- 45}, publisher = {Elsevier}, title = {{Pyramids and domes in the InAs/GaAs (0 0 1) and Ge/Si (0 0 1) systems}}, doi = {10.1016/j.jcrysgro.2004.12.047}, volume = {278}, year = {2005}, } @article{1743, abstract = {Laterally aligned multilayer GeSiSi islands grown on a patterned Si (001) substrate are disclosed by selective etching of Si in a KOH solution. This procedure allows us to visualize the vertical alignment of the islands in a three-dimensional perspective. Our technique reveals that partly coalesced double islands in the initial layer do not merge together, but instead gradually reproduce into well-separated double islands in upper layers. We attribute this effect to very thin spacer layers, which efficiently transfer the strain modulation of each island through the spacer layer to the surface. The etching rate of Si is reduced in tensile strained regions, which helps to preserve sufficient Si between the stacked islands to form a periodic array of freestanding and vertically modulated heterostructure pillars.}, author = {Zhong, Zheyang and Georgios Katsaros and Stoffel, Mathieu and Costantini, Giovanni and Kern, Klaus and Schmidt, Oliver G and Jin-Phillipp, Neng Y and Bauer, Günther}, journal = {Applied Physics Letters}, number = {26}, pages = {1 -- 3}, publisher = {American Institute of Physics}, title = {{Periodic pillar structures by Si etching of multilayer GeSi/Si islands}}, doi = {10.1063/1.2150278}, volume = {87}, year = {2005}, } @article{1744, abstract = {This paper presents optical duobinary and dicode signalling, as alternatives to the binary format, in order to improve the transmission performance in the presense of non-linear effects in a dense wavelength division multiplex (WDM) optical system. Duobinary signalling is applied to an optical system to explore the reduction of stimulated Brillouin scattering (SBS) effects. Duobinary signalling suppresses the SBS effects, and an eye-opening improvement of 0.25 to 1.2 dB is achieved relative to binary transmission over a range of input power levels. An experimental study demonstrates that duobinary modulation suppresses the four wave mixing (FWM) products of a dense WDM system by a maximum of 3 dB. The suppression is maintained over a range of channel spacings. An investigation of the impact of fibre dispersion on FWM products under binary, duobinary and dicode modulation in a dense WDM system is then performed, with interchannel spacing and optical power variation. This leads to the development of a set of guidelines for the application areas, in which it is appropriate to use duobinary or dicode modulation in WDM systems as a means of mitigating the impact of FWM.}, author = {Georgios Katsaros and Darwazeh, Izzat Z and Lane, Phil M}, journal = {IEE Proceedings - Optoelectronics}, number = {6}, pages = {344 -- 352}, publisher = {Institute of Electrical Engineers}, title = {{Non linear transmission effects in duobinary and dicode optical systems}}, doi = {10.1049/ip-opt:20045067}, volume = {152}, year = {2005}, } @article{1741, abstract = {SiGe islands move laterally on a Si(001) substrate during in situ postgrowth annealing. This surprising behavior is revealed by an analysis of the substrate surface morphology after island removal using wet chemical etching. We explain the island motion by asymmetric surface-mediated alloying. Material leaves one side of the island by surface diffusion, and mixes with additional Si from the surrounding surface as it redeposits on the other side. Thus the island moves laterally while becoming larger and more dilute.}, author = {Denker, Ulrich and Rastelli, Armando and Stoffel, Mathieu and Tersoff, Jerry and Georgios Katsaros and Costantini, Giovanni and Kern, Klaus and Jin-Phillipp, Neng Y and Jesson, David E and Schmidt, Oliver G}, journal = {Physical Review Letters}, number = {21}, publisher = {American Physical Society}, title = {{Lateral motion of SiGe islands driven by surface-mediated alloying}}, doi = {10.1103/PhysRevLett.94.216103}, volume = {94}, year = {2005}, } @article{1795, abstract = {Background: Murine leukemia virus (MLV) vector particles can be pseudotyped with a truncated variant of the human immunodeficiency virus type 1 (HIV-1) envelope protein (Env) and selectively target gene transfer to human cells expressing both CD4 and an appropriate co-receptor. Vector transduction mimics the HIV-1 entry process and is therefore a safe tool to study HIV-1 entry. Results: Using FLY cells, which express the MLV gag and pol genes, we generated stable producer cell lines that express the HIV-1 envelope gene and a retroviral vector genome encoding the green fluorescent protein (GFP). The BH10 or 89.6 P HIV-1 Env was expressed from a bicistronic vector which allowed the rapid selection of stable cell lines. A codon-usage-optimized synthetic env gene permitted high, Rev-independent Env expression. Vectors generated by these producer cells displayed different sensitivity to entry inhibitors. Conclusion: These data illustrate that MLV/HIV-1 vectors are a valuable screening system for entry inhibitors or neutralizing antisera generated by vaccines.}, author = {Sandra Siegert and Thaler, Sonja and Wagner, Ralf and Schnierle, Barbara S}, journal = {AIDS Research and Therapy}, number = {1}, publisher = {BioMed Central}, title = {{Assessment of HIV-1 entry inhibitors by MLV/HIV-1 pseudotyped vectors}}, doi = {10.1186/1742-6405-2-7}, volume = {2}, year = {2005}, } @article{1962, abstract = { Complex I of respiratory chains plays a central role in bioenergetics and is implicated in many human neurodegenerative diseases. An understanding of its mechanism requires a knowledge of the organization of redox centers. The arrangement of iron-sulfur clusters in the hydrophilic domain of complex I from Thermus thermophilus has been determined with the use of x-ray crystallography. One binuclear and six tetranuclear clusters are arranged, maximally 14 angstroms apart, in an 84-angstrom-long electron transfer chain. The binuclear cluster N1a and the tetranuclear cluster N7 are not in this pathway. Cluster N1a may play a role in the prevention of oxidative damage. The structure provides a framework for the interpretation of the large amounts of data accumulated on complex I.}, author = {Hinchliffe, Philip and Leonid Sazanov}, journal = {Science}, number = {5735}, pages = {771 -- 774}, publisher = {American Association for the Advancement of Science}, title = {{Biochemistry: Organization of iron-sulfur clusters in respiratory complex I}}, doi = {10.1126/science.1113988}, volume = {309}, year = {2005}, } @book{210, abstract = {Harold Davenport was one of the truly great mathematicians of the twentieth century. Based on lectures he gave at the University of Michigan in the early 1960s, this book is concerned with the use of analytic methods in the study of integer solutions to Diophantine equations and Diophantine inequalities. It provides an excellent introduction to a timeless area of number theory that is still as widely researched today as it was when the book originally appeared. The three main themes of the book are Waring's problem and the representation of integers by diagonal forms, the solubility in integers of systems of forms in many variables, and the solubility in integers of diagonal inequalities. For the second edition of the book a comprehensive foreword has been added in which three prominent authorities describe the modern context and recent developments. A thorough bibliography has also been added.}, author = {Davenport, Harold and Browning, Timothy D}, pages = {140}, publisher = {Cambridge University Press}, title = {{Analytic Methods for Diophantine Equations and Diophantine Inequalities}}, doi = {10.1017/CBO9780511542893}, year = {2005}, } @article{211, abstract = {Let f ∈ ℤ[x] be a polynomial of degree d. The paucity of non-trivial positive integer solutions to the equation f(x1)+f(x 2)=f(x3)+f(x4) is established, provided that d ≤ 7$. Also the corresponding situation is investigated for equal sums of three like polynomials.}, author = {Timothy Browning}, journal = {Bulletin of the London Mathematical Society}, number = {6}, pages = {801 -- 808}, publisher = {John Wiley and Sons Ltd}, title = {{Equal sums of like polynomials}}, doi = {10.1112/S0024609305004741}, volume = {37}, year = {2005}, } @article{212, abstract = {For any n ≧ 2, let F ∈ ℤ [ x 1, … , xn ] be a form of degree d≧ 2, which produces a geometrically irreducible hypersurface in ℙn–1. This paper is concerned with the number N(F;B) of rational points on F = 0 which have height at most B. For any ε > 0 we establish the estimate N(F; B) = O(B n− 2+ ε ), whenever either n ≦ 5 or the hypersurface is not a union of lines. Here the implied constant depends at most upon d, n and ε.}, author = {Timothy Browning and Heath-Brown, Roger}, journal = {Journal fur die Reine und Angewandte Mathematik}, number = {584}, pages = {83 -- 115}, publisher = {Walter de Gruyter and Co }, title = {{Counting rational points on hypersurfaces}}, doi = {https://doi.org/10.1515/crll.2005.2005.584.83}, year = {2005}, } @article{214, abstract = {Given an absolutely irreducible ternary form F, the purpose of this paper is to produce better upper bounds for the number of integer solutions to the equation F=0, that are restricted to lie in very lopsided boxes. As an application of the main result, a new paucity estimate is obtained for equal sums of two like powers.}, author = {Timothy Browning and Heath-Brown, Roger}, journal = {Mathematische Zeitschrift}, number = {2}, pages = {233 -- 247}, publisher = {Unknown}, title = {{Plane curves in boxes and equal sums of two powers}}, doi = {10.1007/s00209-004-0719-z}, volume = {251}, year = {2005}, } @article{217, abstract = {We show that the number of nontrivial rational points of height at most B, which lie on the cubic surface x1 x2 x3 = x4 (x1 + x2 + x3)2, has order of magnitude B (log B)6. This agrees with Manin's conjecture.}, author = {Timothy Browning}, journal = {Journal of Number Theory}, number = {2}, pages = {242 -- 283}, publisher = {Elsevier}, title = {{The density of rational points on a certain singular cubic surface}}, doi = {10.1016/j.jnt.2005.11.007}, volume = {119}, year = {2005}, } @article{2307, abstract = {The human norepinephrine (NE) transporter (hNET) attenuates neuronal signaling by rapid NE clearance from the synaptic cleft, and NET is a target for cocaine and amphetamines as well as therapeutics for depression, obsessive-compulsive disorder, and post-traumatic stress disorder. In spite of its central importance in the nervous system, little is known about how NET substrates, such as NE, 1-methyl-4-tetrahydropyridinium (MPP+), or amphetamine, interact with NET at the molecular level. Nor do we understand the mechanisms behind the transport rate. Previously we introduced a fluorescent substrate similar to MPP+, which allowed separate and simultaneous binding and transport measurement (Schwartz, J. W., Blakely, R. D., and DeFelice, L. J. (2003) J. Biol. Chem. 278, 9768-9777). Here we use this substrate, 4-(4-(dimethylamino)styrl)-N-methyl-pyridinium (ASP+), in combination with green fluorescent protein-tagged hNETs to measure substrate-transporter stoichiometry and substrate binding kinetics. Calibrated confocal microscopy and fluorescence correlation spectroscopy reveal that hNETs, which are homo-multimers, bind one substrate molecule per transporter subunit. Substrate residence at the transporter, obtained from rapid on-off kinetics revealed in fluorescence correlation spectroscopy, is 526 μs. Substrate residence obtained by infinite dilution is 1000 times slower. This novel examination of substrate-transporter kinetics indicates that a single ASP + molecule binds and unbinds thousands of times before being transported or ultimately dissociated from hNET. Calibrated fluorescent images combined with mass spectroscopy give a transport rate of 0.06 ASP +/hNET-protein/s, thus 36,000 on-off binding events (and 36 actual departures) occur for one transport event. Therefore binding has a low probability of resulting in transport. We interpret these data to mean that inefficient binding could contribute to slow transport rates.}, author = {Schwartz, Joel W and Gaia Novarino and Piston, David W and DeFelice, Louis J}, journal = {Journal of Biological Chemistry}, number = {19}, pages = {19177 -- 19184}, publisher = {American Society for Biochemistry and Molecular Biology}, title = {{Substrate binding stoichiometry and kinetics of the norepinephrine transporter}}, doi = {10.1074/jbc.M412923200}, volume = {280}, year = {2005}, } @book{2335, abstract = {This book contains a unique survey of the mathematically rigorous results about the quantum-mechanical many-body problem that have been obtained by the authors in the past seven years. It addresses a topic that is not only rich mathematically, using a large variety of techniques in mathematical analysis, but is also one with strong ties to current experiments on ultra-cold Bose gases and Bose-Einstein condensation. The book provides a pedagogical entry into an active area of ongoing research for both graduate students and researchers. It is an outgrowth of a course given by the authors for graduate students and post-doctoral researchers at the Oberwolfach Research Institute in 2004. The book also provides a coherent summary of the field and a reference for mathematicians and physicists active in research on quantum mechanics.}, author = {Lieb, Élliott and Seiringer, Robert and Solovej, Jan and Yngvason, Jakob}, isbn = {978-3-7643-7336-8}, pages = {VIII, 203}, publisher = {Birkhäuser Verlag}, title = {{The Mathematics of the Bose gas and its Condensation}}, doi = {10.1007/b137508}, volume = {34}, year = {2005}, } @inbook{2336, 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, and to explore new regimes not treated before. 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 2πħ2 aρ/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 N 7/5 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 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, several 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 and superfluidity as we have shown. On the frontier of experimental developments is the possibility that a dilute gas in an elongated trap will behave like a one-dimensional system; we have proved this mathematically. 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; using this we can also prove the N 7/5 formula for the ground state energy of the two-component charged Bose gas proposed by Dyson in 1967. All of this is quite recent work and it is hoped that the mathematical methodology might be useful, ultimately, to solve more complex problems connected with these interesting systems.}, author = {Lieb, Élliott H and Robert Seiringer and Solovej, Jan P and Yngvason, Jakob}, booktitle = {Perspectives in Analysis}, editor = {Benedicks, Michael and Jones, Peter W and Smirnov, Stanislav and Winckler, Björn}, pages = {97 -- 183}, publisher = {Springer}, title = {{The quantum-mechanical many-body problem: The Bose gas}}, doi = {10.1007/3-540-30434-7_9}, volume = {27}, year = {2005}, } @article{2359, abstract = {The validity of substituting a c-number z for the k = 0 mode operator a0 is established rigorously in full generality, thereby verifying one aspect of Bogoliubov's 1947 theory. This substitution not only yields the correct value of thermodynamic quantities such as the pressure or ground state energy, but also the value of |z|2 that maximizes the partition function equals the true amount of condensation in the presence of a gauge-symmetry-breaking term. This point had previously been elusive.}, author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob}, journal = {Physical Review Letters}, number = {8}, publisher = {American Physical Society}, title = {{Justification of c-number substitutions in bosonic hamiltonians}}, doi = {10.1103/PhysRevLett.94.080401}, volume = {94}, year = {2005}, } @article{2362, abstract = {Recent developments in the physics of low-density trapped gases make it worthwhile to verify old, well-known results that, while plausible, were based on perturbation theory and assumptions about pseudopotentials. We use and extend recently developed techniques to give a rigorous derivation of the asymptotic formula for the ground-state energy of a dilute gas of N fermions interacting with a short-range, positive potential of scattering length a. For spin-12 fermions, this is E∼E0+(22m)2πNa, where E0 is the energy of the noninteracting system and is the density. A similar formula holds in two dimensions (2D), with a replaced by ln(a2). Obviously this 2D energy is not the expectation value of a density-independent pseudopotential.}, author = {Lieb, Élliott H and Robert Seiringer and Solovej, Jan P}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {5}, publisher = {American Physical Society}, title = {{Ground state energy of the low density Fermi gas}}, doi = {10.1103/PhysRevA.71.053605}, volume = {71}, year = {2005}, } @article{2361, abstract = {The strong subadditivity of entropy plays a key role in several areas of physics and mathematics. It states that the entropy S[±]=- Tr(ϱlnϱ) of a density matrix ϱ123 on the product of three Hilbert spaces satisfies S[ϱ123]- S[ϱ12]≤S[ϱ23]-S[ϱ2]. We strengthen this to S[ϱ123]-S[ϱ12] ≤αnα(S[ϱ23α]-S[ϱ2α]), where the nα are weights and the ϱ23α are partitions of ϱ23. Correspondingly, there is a strengthening of the theorem that the map A|Trexp[L+lnA] is concave. As applications we prove some monotonicity and convexity properties of the Wehrl coherent state entropy and entropy inequalities for quantum gases.}, author = {Lieb, Élliott H and Robert Seiringer}, journal = {Physical Review A - Atomic, Molecular, and Optical Physics}, number = {6}, publisher = {American Physical Society}, title = {{Stronger subadditivity of entropy}}, doi = {10.1103/PhysRevA.71.062329}, volume = {71}, year = {2005}, } @inproceedings{2428, abstract = {We consider an online version of the conflict-free coloring of a set of points on the line, where each newly inserted point must be assigned a color upon insertion, and at all times the coloring has to be conflict-free, in the sense that in every interval I there is a color that appears exactly once in I. We present several deterministic and randomized algorithms for achieving this goal, and analyze their performance, that is, the maximum number of colors that they need to use, as a function of the number n of inserted points. We first show that a natural and simple (deterministic) approach may perform rather poorly, requiring Ω(√n) colors in the worst case. We then modify this approach, to obtain an efficient deterministic algorithm that uses a maximum of Θ(log 2 n) colors. Next, we present two randomized solutions. The first algorithm requires an expected number of at most O(log 2 n) colors, and produces a coloring which is valid with high probability, and the second one, which is a variant of our efficient deterministic algorithm, requires an expected number of at most O(log n log log n) colors but always produces a valid coloring. We also analyze the performance of the simplest proposed algorithm when the points are inserted in a random order, and present an incomplete analysis that indicates that, with high probability, it uses only O(log n) colors. Finally, we show that in the extension of this problem to two dimensions, where the relevant ranges are disks, n colors may be required in the worst case. The average-case behavior for disks, and cases involving other planar ranges, are still open.}, author = {Fiat, Amos and Levy, Meital B and Matoušek, Jiří and Pach, Elchanan M and Sharir, Micha and Smorodinsky, Shakhar and Uli Wagner and Welzl, Emo}, pages = {545 -- 554}, publisher = {SIAM}, title = {{Online conflict-free coloring for intervals}}, doi = {10.1137/S0097539704446682}, year = {2005}, } @article{2427, abstract = {Intersection graphs of disks and of line segments, respectively, have been well studied, because of both practical applications and theoretically interesting properties of these graphs. Despite partial results, the complexity status of the Clique problem for these two graph classes is still open. Here, we consider the Clique problem for intersection graphs of ellipses, which, in a sense, interpolate between disks and line segments, and show that the problem is APX-hard in that case. Moreover, this holds even if for all ellipses, the ratio of the larger over the smaller radius is some prescribed number. Furthermore, the reduction immediately carries over to intersection graphs of triangles. To our knowledge, this is the first hardness result for the Clique problem in intersection graphs of convex objects with finite description complexity. We also describe a simple approximation algorithm for the case of ellipses for which the ratio of radii is bounded.}, author = {Ambühl, Christoph and Uli Wagner}, journal = {Theory of Computing Systems}, number = {3}, pages = {279 -- 292}, publisher = {Springer}, title = {{The Clique problem in intersection graphs of ellipses and triangles}}, doi = {10.1007/s00224-005-1141-6}, volume = {38}, year = {2005}, } @article{2455, abstract = {Local accumulation of the plant growth regulator auxin mediates pattern formation in Arabidopsis roots and influences outgrowth and development of lateral root- and shoot-derived primordia. However, it has remained unclear how auxin can simultaneously regulate patterning and organ outgrowth and how its distribution is stabilized in a primordium-specif ic manner. Here we show that five PIN genes collectively control auxin distribution to regulate cell division and cell expansion in the primary root. Furthermore, the joint action of these genes has an important role in pattern formation by focusing the auxin maximum and restricting the expression domain of PLETHORA (PLT) genes, major determinants for root stem cell specification. In turn, PLT genes are required for PIN gene transcription to stabilize the auxin maximum at the distal root tip. Our data reveal an interaction network of auxin transport facilitators and root fate determinants that control patterning and growth of the root primordium.}, author = {Billou, Ikram and Xu, Jian and Wildwater, Marjolein and Willemsen, Viola and Paponov, Ivan A and Jirí Friml and Heldstra, Renze and Aida, Mitsuhiro and Palme, Klaus J and Scheres, Ben}, journal = {Nature}, number = {7021}, pages = {39 -- 44}, publisher = {Nature Publishing Group}, title = {{The PIN auxin efflux facilitator network controls growth and patterning in Arabidopsis roots}}, doi = {10.1038/nature03184}, volume = {433}, year = {2005}, } @inbook{2464, author = {Jirí Friml and Wiśniewska, Justyna}, booktitle = {Intercellular Communication in Plants}, editor = {Fleming, Andrew J.}, publisher = {Wiley-Blackwell}, title = {{Auxin as an intercellular signal}}, volume = {16}, year = {2005}, } @inbook{2463, author = {Dubová, J and Hejátko, Jan and Jirí Friml}, booktitle = {Encyclopedia of Molecular Cell Biology and Molecular Medicine}, editor = {Meyers, Robert A}, pages = {249 -- 295}, publisher = {Wiley-Blackwell}, title = {{Reproduction, plants}}, doi = {10.1002/3527600906}, volume = {12}, year = {2005}, } @article{2648, abstract = {Hyperpolarization-activated and cyclic nucleotide-gated (HCN) channels are involved in the control of neuronal excitability and plasticity. In this study, we used immunoblotting and immunohistochemical techniques to reveal the developmental expression and subcellular distribution of the HCN1 subunit in the cerebellar cortex. During postnatal development, the spatio-temporal expression of HCN1 correlated well with the morphological events occurring during the ontogenesis of cerebellar interneurons. Using immunoblotting techniques, HCN1 was weakly detected during the first postnatal week and continued to increase throughout postnatal development, peaking at postnatal day (P)15. At the light-microscopic level, HCN1 immunoreactivity was very weak until P7 whereas from P10-12 to adulthood it was strongly detected in the lower third of the molecular layer and in the Purkinje cell layer. HCN1 was present in axons running through the molecular layer and in the pericellular basket around Purkinje cells at P12, but in the periaxonal plexus (the pinceau) surrounding their initial segment only after P15. Using immunofluorescence, HCN1 colocalized with GAD65 and synaptophysin, demonstrating that the subunit was present in inhibitory axons and axon terminals. At the electron-microscopic level, in adulthood, HCN1 immunoparticles were detected at postsynaptic sites in basket and Purkinje cells but most immunoparticles were found at presynaptic sites in basket cell axons and in terminals. In the axon terminals, the distribution of HCN1 was relatively uniform along the extrasynaptic plasma membrane; this was confirmed using quantitative techniques. The present findings suggest that HCN1 channels may provide a significant route for modulating co-ordinated cerebellar synaptic transmission through basket cells.}, author = {Luján, Rafael and Albasanz, José L and Ryuichi Shigemoto and Juíz, José M}, journal = {European Journal of Neuroscience}, number = {8}, pages = {2073 -- 2082}, publisher = {Wiley-Blackwell}, title = {{Preferential localization of the hyperpolarization-activated cyclic nucleotide-gated cation channel subunit HCN1 in basket cell terminals of the rat cerebellum}}, doi = {10.1111/j.1460-9568.2005.04043.x}, volume = {21}, year = {2005}, } @article{2650, abstract = {Septohippocampal cholinergic neurons play key roles in learning and memory processes, and in the generation of hippocampal theta rhythm. The range of receptors for endogenous modulators expressed on these neurons is unclear. Here we describe GABAB 1a/b receptor (GABABR) and type 1 cannabinoid receptor (CB1R) expression in rat septal cholinergic [i.e. choline acetyltransferase (ChAT)-positive] cells. Using double immunofluorescent staining, we found that almost two-thirds of the cholinergic cells in the rat medial septum were GABABR positive, and that these cells had significantly larger somata than did GABABR-negative cholinergic neurons. We detected CB1R labelling in somata after axonal protein transport was blocked by colchicine. In these animals about one-third of the cholinergic cells were CB1R positive. These cells again had larger somata than CB1R-negative cholinergic neurons. The analyses confirmed that the size of GABABR-positive and CB 1R-positive cholinergic cells were alike, and all CB 1R-positive cholinergic cells were GABABR positive as well. CB1R-positive cells were invariably ChAT positive. All retrogradely labelled septohippocampal cholinergic cells were positive for GABABR and at least half of them also for CB1R. These data shed light on the existence of at least two cholinergic cell types in the medial septum: one expresses GABABR and CB1R, has large somata and projects to the hippocampus, whereas the other is negative for GABABR and CB1R and has smaller somata. The results also suggest that cholinergic transmission in the hippocampus is fine-tuned by endocannabinoid signalling.}, author = {Nyíri, Gábor and Szabadits, Eszter and Cserép, Csaba and Mackie, Ken P and Ryuichi Shigemoto and Freund, Tamás F}, journal = {European Journal of Neuroscience}, number = {11}, pages = {3034 -- 3042}, publisher = {Wiley-Blackwell}, title = {{GABAB and CB1 cannabinoid receptor expression identifies two types of septal cholinergic neurons}}, doi = {10.1111/j.1460-9568.2005.04146.x}, volume = {21}, year = {2005}, } @misc{2647, abstract = {Our understanding of the role played by neurotransmitter receptors in the developing brain has advanced in recent years. The major excitatory and inhibitory neurotransmitters in the brain, glutamate and GABA, activate both ionotropic (ligand-gated ion channels) and metabotropic (G protein-coupled) receptors, and are generally associated with neuronal communication in the mature brain. However, before the emergence of their role in neurotransmission in adulthood, they also act to influence earlier developmental events, some of which occur prior to synapse formation: such as proliferation, migration, differentiation or survival processes during neural development. To fulfill these actions in the constructing of the nervous system, different types of glutamate and GABA receptors need to be expressed both at the right time and at the right place. The identification by molecular cloning of 16 ionotropic glutamate receptor subunits, eight metabotropic glutamate receptor subtypes, 21 ionotropic and two metabotropic GABA receptor subunits, some of which exist in alternatively splice variants, has enriched our appreciation of how molecular diversity leads to functional diversity in the brain. It now appears that many different types of glutamate and GABA receptor subunits have prominent expression in the embryonic and/or postnatal brain, whereas others are mainly present in the adult brain. Although the significance of this differential expression of subunits is not fully understood, it appears that the change in subunit composition is essential for normal development in particular brain regions. This review focuses on emerging information relating to the expression and role of glutamatergic and GABAergic neurotransmitter receptors during prenatal and postnatal development.}, author = {Luján, Rafael and Ryuichi Shigemoto and López-Bendito, Guillermina}, booktitle = {Neuroscience}, number = {3}, pages = {567 -- 580}, publisher = {Elsevier}, title = {{Glutamate and GABA receptor signalling in the developing brain}}, doi = {10.1016/j.neuroscience.2004.09.042}, volume = {130}, year = {2005}, } @article{2651, abstract = {The GABAergic system, a major inhibitory regulator in the central nervous system, may also play important roles in peripheral nonneuronal tissues and cells. Recent studies showed that GABAB receptor is expressed in testis and sperm. To understand the role of the GABAergic system in spermiogenesis, we examined cellular localization of GABA and GABAB receptor subunits in rat spermatids by immunocytochemistry. Immunoreactivity for GABA was detected around acrosomal granules of spermatids during the Golgi and cap phases. GABAB(1) immunoreactivity was observed in the acrosomal vesicle of spermatids in Golgi phase, and during cap phase, this reactivity expanded to the entire region of the acrosome covering the nuclear membrane. The level of reactivity decreased gradually with maturation of spermatids. In contrast, GABAB(2) immunoreactivity was not observed in spermatids during Golgi phase but was detected in the equatorial region during cap phase. Both GABA immunoreactivity and GABAB(2) immunoreactivity were transferred to the residual cytoplasm during the release of spermatozoa. Electron microscopic immunocytochemistry revealed that, during cap phase, GABA and GABAB(1) were distributed within the whole acrosomal vesicle but not in the acrosomal granule. GABAB(2) immunoreactivity was observed in the narrow space between the inner acrosomal and nuclear membrane and was limited to the equatorial region of the spermatid head. These results indicate that the GABAergic system might be involved in regulation of spermiogenesis.}, author = {Kanbara, Kiyoto and Okamoto, Keiko and Nomura, Sakashi and Kaneko, Takeshi and Ryuichi Shigemoto and Azuma, Haruhito and Katsuoka, Yoji and Watanabe, Masahiko}, journal = {Journal of Andrology}, number = {4}, pages = {485 -- 493}, publisher = {American Society of Andrology}, title = {{Cellular localization of GABA and GABAB receptor subunit proteins during spermiogenesis in rat testis}}, doi = {10.2164/jandrol.04185}, volume = {26}, year = {2005}, } @article{2649, abstract = {The number of ionotropic receptors in synapses is an essential factor for determining the efficacy of fast transmission. We estimated the number of functional AMPA receptors at single postsynaptic sites by a combination of two-photon uncaging of glutamate and the nonstationary fluctuation analysis in immature rat Purkinje cells (PCs), which receive a single type of excitatory input from climbing fibers. Areas of postsynaptic membrane specialization at the recorded synapses were measured by reconstruction of serial ultrathin sections. The number of functional AMPA receptors was proportional to the synaptic area with a density of ∼ 1280 receptors/μm 2. Moreover, highly sensitive freeze-fracture replica labeling revealed a homogeneous density of immunogold particles for AMPA receptors in synaptic sites (910 ± 36 particles/μm 2) and much lower density in extrasynaptic sites (19 ± 2 particles/μm 2) in the immature PCs. Our results indicate that in this developing synapse, the efficacy of transmission is determined by the synaptic area.}, author = {Tanaka, Junichi and Matsuzaki, Masanori and Tarusawa, Etsuko and Momiyama, Akiko and Molnár, Elek and Kasai, Haruo and Ryuichi Shigemoto}, journal = {Journal of Neuroscience}, number = {4}, pages = {799 -- 807}, publisher = {Society for Neuroscience}, title = {{Number and density of AMPA receptors in single synapses in immature cerebellum}}, doi = {10.1523/JNEUROSCI.4256-04.2005}, volume = {25}, year = {2005}, } @article{2654, abstract = {Presynaptic metabotropic glutamate receptors (mGluRs) show a highly selective expression and subcellular location in nerve terminals modulating neurotransmitter release. We have demonstrated that alternatively spliced variants of mGluR8, mGluR8a and mGluR8b, have an overlapping distribution in the hippocampus, and besides perforant path terminals, they are expressed in the presynaptic active zone of boutons making synapses selectively with several types of GABAergic interneurons, primarily in the stratum oriens. Boutons labeled for mGluR8 formed either type I or type II synapses, and the latter were GABAergic. Some mGluR8-positive boutons also expressed mGluR7 or vasoactive intestinal polypeptide. Interneurons strongly immunopositive for the muscarinic M2 or the mGlu1 receptors were the primary targets of mGluR8-containing terminals in the stratum oriens, but only neurochemically distinct subsets were innervated by mGluR8-enriched terminals. The majority of M2-positive neurons were mGluR8 innervated, but a minority, which expresses somatostatin, was not. Rare neurons coexpressing calretinin and M2 were consistently targeted by mGluR8-positive boutons. In vivo recording and labeling of an mGluR8-decorated and strongly M2-positive interneuron revealed a trilaminar cell with complex spike bursts during theta oscillations and strong discharge during sharp wave/ripple events. The trilaminar cell had a large projection from the CA1 area to the subiculum and a preferential innervation of interneurons in the CA1 area in addition to pyramidal cell somata and dendrites. The postsynaptic interneuron type-specific expression of the high-efficacy presynaptic mGluR8 in both putative glutamatergic and in identified GABAergic terminals predicts a role in adjusting the activity of interneurons depending on the level of network activity.}, author = {Ferraguti, Francesco and Klausberger,Thomas and Cobden, Philip M and Baude, Agnès and Roberts, John D and Szűcs, Péter and Kinoshita, Ayae and Ryuichi Shigemoto and Somogyi, Péter and Dalezios, Yannis}, journal = {Journal of Neuroscience}, number = {45}, pages = {10520 -- 10536}, publisher = {Society for Neuroscience}, title = {{ Metabotropic glutamate receptor 8-expressing nerve terminals target subsets of GABAergic neurons in the hippocampus}}, doi = {10.1523/JNEUROSCI.2547-05.2005}, volume = {25}, year = {2005}, } @article{2658, abstract = {Enhanced glutamatergic neurotransmission via the subthalamopallidal or subthalamonigral projection seems crucial for developing parkinsonian motor signs. In the present study, the possible changes in the expression of metabotropic glutamate receptors (mGluRs) were examined in the basal ganglia of a primate model for Parkinson's disease. When the patterns of immunohistochemical localization of mGluRs in monkeys administered systemically with 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) were analysed in comparison with normal controls, we found that expression of mGluR1α, but not of other subtypes, was significantly reduced in the internal and external segments of the globus pallidus and the substantia nigra pars reticulata. To elucidate the functional role of mGluR1 in the control of pallidal neuron activity, extracellular unit recordings combined with intrapallidal microinjections of mGluR1-related agents were then performed in normal and parkinsonian monkeys. In normal awake conditions, the spontaneous firing rates of neurons in the pallidal complex were increased by DHPG, a selective agonist of group I mGluRs, whereas they were decreased by AIDA, a selective antagonist of group I mGluRs, or LY367385, a selective antagonist of mGluR1. These electrophysiological data strongly indicate that the excitatory mechanism of pallidal neurons by glutamate is mediated at least partly through mGluR1. The effects of the mGluR1-related agents on neuronal firing in the internal pallidal segment became rather obscure after MPTP treatment. Our results suggest that the specific down-regulation of pallidal and nigral mGluR1 ot in the parkinsonian state may exert a compensatory action to reverse the overactivity of the subthalamic nucleus-derived glutamatergic input that is generated in the disease.}, author = {Kaneda, Katsuyuki and Tachibana, Yoshihisa and Imanishi, Michiko and Kita, Hitoshi and Ryuichi Shigemoto and Nambu, Atsushi and Takada, Masahiko}, journal = {European Journal of Neuroscience}, number = {12}, pages = {3241 -- 3254}, publisher = {Wiley-Blackwell}, title = {{Down-regulation of metabotropic glutamate receptor 1α in globus pallidus and substantia nigra of parkinsonian monkeys}}, doi = {10.1111/j.1460-9568.2005.04488.x}, volume = {22}, year = {2005}, } @article{2652, abstract = {We studied neurogliaform neurons in the stratum lacunosum moleculare of the CA1 hippocampal area. These interneurons have short stellate dendrites and an extensive axonal arbor mainly located in the stratum lacunosum moleculare. Single-cell reverse transcription-PCR showed that these neurons were GABAergic and that the majority expressed mRNA for neuropeptide Y. Most neurogliaform neurons tested were immunoreactive for α-actinin-2, and many stratum lacunosum moleculare interneurons coexpressed α-actinin-2 and neuropeptide Y. Neurogliaform neurons received monosynaptic, DNQX-sensitive excitatory input from the perforant path, and 40 Hz stimulation of this input evoked EPSCs displaying either depression or initial facilitation, followed by depression. Paired recordings performed between neurogliaform neurons showed that 85% of pairs were electrically connected and 70% were also connected via GABAergic synapses. Injection of sine waveforms into neurons during paired recordings resulted in transmission of the waveforms through the electrical synapse. Unitary IPSCs recorded from neurogliaform pairs readily fatigued, had a slow decay, and had a strong depression of the synaptic response at a 5 Hz stimulation frequency that was antagonized by the GABA B antagonist (2S)-3-[[(1S)-1-(3,4-dichlorophenyl)ethyl]amino-2-hydroxypropyl](phenylmethyl) phosphinic acid (CGP55845). The amplitude of the first IPSC during the 5 Hz stimulation was also increased by CGP55845, suggesting a tonic inhibition of synaptic transmission. A small unitary GABA B-mediated IPSC could also be detected, providing the first evidence for such a component between GABAergic interneurons. Electron microscopic localization of the GABA B1 subunit at neurogliaform synapses revealed the protein in both presynaptic and postsynaptic membranes. Our data disclose a novel interneuronal network well suited for modulating the flow of information between the entorhinal cortex and CA1 hippocampus.}, author = {Price, Christopher J and Cauli, Bruno and Kovács, Endre R and Kulik, Ákos and Lambolez, Bertrand and Ryuichi Shigemoto and Capogna,Marco}, journal = {Journal of Neuroscience}, number = {29}, pages = {6775 -- 6786}, publisher = {Society for Neuroscience}, title = {{Neurogliaform neurons form a novel inhibitory network in the hippocampal CA1 area}}, doi = {10.1523/JNEUROSCI.1135-05.2005}, volume = {25}, year = {2005}, } @article{2655, abstract = {Input-dependent left-right asymmetry of NMDA receptor ε2 (NR2B) subunit allocation was discovered in hippocampal Schaffer collateral (Sch) and commissural fiber pyramidal cell synapses (Kawakami et al., 2003). To investigate whether this asymmetrical ε2 allocation is also related to the types of the postsynaptic cells, we compared postembedding immunogold labeling for ε2 in left and right Sch synapses on pyramidal cells and interneurons. To facilitate the detection of ε2 density difference, we used ε1 (NR2A) knock-out (KO) mice, which have a simplified NMDA receptor subunit composition. The labeling density for ε2 but not ζ1 (NR1) and subtype 2/3 glutamate receptor (GluR2/3) in Sch-CA1 pyramidal cell synapses was significantly different between the left and right hippocampus with opposite directions in strata oriens and radiatum; the left to right ratio of ε2 labeling density was 1:1.50 in stratum oriens and 1.44:1 in stratum radiatum. No significant difference, however, was detected in CA1 stratum radiatum between the left and right Sch-GluR4-positive (mostly parvalbumin-positive) and Sch-GluR4-negative interneuron synapses. Consistent with the anatomical asymmetry, the amplitude ratio of NMDA EPSCs to non-NMDA EPSCs in pyramidal cells was approximately two times larger in right than left stratum radiatum and vice versa in stratum oriens of ε1 KO mice. Moreover, the amplitude of long-term potentiation in the Sch-CA1 synapses of left stratum radiatum was significantly larger than that in the right corresponding synapses. These results indicate that the asymmetry of ε2 distribution is target cell specific, resulting in the left-right difference in NMDA receptor content and plasticity in Sch-CA1 pyramidal cell synapses in ε1 KO mice.}, author = {Wu, Yue and Kawakami, Ryosuke and Shinohara, Yoshiaki and Fukaya, Masahiro and Sakimura, Kenji and Mishina, Masayoshi and Watanabe, Masahiko and Ito, Isao and Ryuichi Shigemoto}, journal = {Journal of Neuroscience}, number = {40}, pages = {9213 -- 9226}, publisher = {Society for Neuroscience}, title = {{Target-cell-specific left-right asymmetry of NMDA receptor content in Schaffer collateral synapses in ε1/NR2A knock-out mice}}, doi = {10.1523/JNEUROSCI.2134-05.2005}, volume = {25}, year = {2005}, } @article{2653, abstract = {Synaptic vesicle release occurs at a specialized membrane domain known as the presynaptic active zone (AZ). Several membrane proteins are involved in the vesicle release processes such as docking, priming, and exocytotic fusion. Cytomatrix at the active zone (CAZ) proteins are structural components of the AZ and are highly concentrated in it. Localization of other release-related proteins including target soluble N-ethylmaleimide-sensitive-factor attachment protein receptor (t-SNARE) proteins, however, has not been well demonstrated in the AZ. Here, we used sodium dodecyl sulfate-digested freeze-fracture replica labeling (SDS-FRL) to analyze quantitatively the distribution of CAZ and t-SNARE proteins in the hippocampal CA3 area. The AZ in replicated membrane was identified by immunolabeling for CAZ proteins (CAZ-associated structural protein [CAST] and Bassoon). Clusters of immunogold particles for these proteins were found on the P-face of presynaptic terminals of the mossy fiber and associational/commissural (AJC) fiber. Co-labeling with CAST revealed distribution of the t-SNARE proteins syntaxin and synaptosomal-associated protein of 25 kDa (SNAP-25) in the AZ as well as in the extrasynaptic membrane surrounding the AZ (SZ). Quantitative analysis demonstrated that the density of immunoparticles for CAST in the AZ was more than 100 times higher than in the SZ, whereas that for syntaxin and SNAP-25 was not significantly different between the AZ and SZ in both the A/C and mossy fiber terminals. These results support the involvement of the t-SNARE proteins in exocytotic fusion in the AZ and the role of CAST in specialization of the membrane domain for the AZ.}, author = {Hagiwara, Akari and Fukazawa, Yugo and Deguchi-Tawarada, Maki and Ohtsuka, Toshihisa and Ryuichi Shigemoto}, journal = {Journal of Comparative Neurology}, number = {2}, pages = {195 -- 216}, publisher = {Wiley-Blackwell}, title = {{Differential distribution of release-related proteins in the hippocampal CA3 area as revealed by freeze-fracture replica labeling}}, doi = {10.1002/cne.20633}, volume = {489}, year = {2005}, } @article{2656, abstract = {Previous studies have shown that neurons in the sacral dorsal commissural nucleus (SDCN) express neurokinin-1 receptor (NK1R) and can be modulated by the co-release of GABA and glycine (Gly) from single presynaptic terminal. These results raise the possibility that GABA/Gly-cocontaining terminals might make synaptic contacts with NK1R-expressing neurons in the SDCN. In order to provide morphological evidence for this hypothesis, the triple-immunohistochemical studies were performed in the SDCN. Triple-immunofluorescence histochemical study showed that some axon terminals in close association with NK1R-immunopositive (NK1R-ip) neurons in the SDCN were immunopositive for both glutamic acid decarboxylase (GAD) and glycine transporter 2 (GlyT2). In electron microscopic dual- and triple-immunohistochemistry for GAD/GlyT2, GAD/NK1R, GlyT2/NK1R, or GAD/GlyT2/NK1R also revealed dually labeled (GAD/GlyT2-ip) synaptic terminals upon SDCN neurons, as well as GAD- and/or GlyT2-ip axon terminals in synaptic contact with NK1R-ip SDCN neurons. These results suggested that some synaptic terminals upon NK1R-expressing SDCN neurons co-released both GABA and Gly.}, author = {Feng, Yu-Peng and Li, Yun-Qing and Wang, Wen and Wu, Sheng-Xi and Chen, Tao and Ryuichi Shigemoto and Mizuno, Noboru}, journal = {Neuroscience Letters}, number = {3}, pages = {144 -- 148}, publisher = {Elsevier}, title = {{Morphological evidence for GABA/glycine-cocontaining terminals in synaptic contact with neurokinin-1 receptor-expressing neurons in the sacral dorsal commissural nucleus of the rat}}, doi = {10.1016/j.neulet.2005.06.068}, volume = {388}, year = {2005}, } @article{2744, abstract = {We study the long time evolution of a quantum particle interacting with a random potential in the Boltzmann-Grad low density limit. We prove that the phase space density of the quantum evolution defined through the Husimi function converges weakly to a linear Boltzmann equation. The Boltzmann collision kernel is given by the full quantum scattering cross-section of the obstacle potential.}, author = {Eng, David and László Erdös}, journal = {Reviews in Mathematical Physics}, number = {6}, pages = {669 -- 743}, publisher = {World Scientific Publishing}, title = {{The linear Boltzmann equation as the low density limit of a random Schrödinger equation}}, doi = {10.1142/S0129055X0500242X}, volume = {17}, year = {2005}, } @article{2743, abstract = {We consider the supersymmetric quantum mechanical system which is obtained by dimensionally reducing d = 6, N = 1 supersymmetric gauge theory with gauge group U(1) and a single charged hypermultiplet. Using the deformation method and ideas introduced by Porrati and Rozenberg [1], we present a detailed proof of the existence of a normalizable ground state for this system.}, author = {László Erdös and Hasler, David G and Solovej, Jan P}, journal = {Annales Henri Poincare}, number = {2}, pages = {247 -- 267}, publisher = {Birkhäuser}, title = {{Existence of the D0-D4 bound state: A detailed proof}}, doi = {10.1007/s00023-005-0205-0}, volume = {6}, year = {2005}, } @article{2788, abstract = {We present the results of an experimental investigation into the nature and structure of turbulent pipe flow at moderate Reynolds numbers. A turbulence regeneration mechanism is identified which sustains a symmetric traveling wave within the flow. The periodicity of the mechanism allows comparison to the wavelength of numerically observed exact traveling wave solutions and close agreement is found. The advection speed of the upstream turbulence laminar interface in the experimental flow is observed to form a lower bound on the phase velocities of the exact traveling wave solutions. Overall our observations suggest that the dynamics of the turbulent flow at moderate Reynolds numbers are governed by unstable nonlinear traveling waves.}, author = {Björn Hof and van Doorne, Casimir W and Westerweel, Jerry and Nieuwstadt, Frans T}, journal = {Physical Review Letters}, number = {21}, publisher = {American Physical Society}, title = {{Turbulence regeneration in pipe flow at moderate reynolds numbers}}, doi = {10.1103/PhysRevLett.95.214502}, volume = {95}, year = {2005}, } @article{2790, abstract = {We present the results of an experimental investigation of the effect of a magnetic field on the stability of convection in a liquid metal. A rectangular container of gallium is subjected to a horizontal temperature gradient and a uniform magnetic field is applied separately in three directions. The magnetic field suppresses the oscillation most effectively when it is applied in the vertical direction and is least efficient when applied in the direction of the temperature gradient. The critical temperature difference required for the onset of oscillations is found to scale exponentially with the magnitude of the magnetic field for all three orientations. Comparisons are made with available theory and qualitative differences are discussed.}, author = {Björn Hof and Juel, Anne and Mullin, Tom P}, journal = {Journal of Fluid Mechanics}, pages = {193 -- 201}, publisher = {Cambridge University Press}, title = {{Magnetohydrodynamic damping of oscillations in low-Prandtl-number convection}}, doi = {10.1017/S0022112005006762}, volume = {545}, year = {2005}, } @article{2789, abstract = {Transitional pipe flow is investigated in two different experimental set-ups. In the first the stability threshold and the initial growth of localized perturbations are studied. Good agreement is found with an earlier investigation of the transition threshold. The measurement technique applied in the last part of this study allows the reconstruction of the streamwise vorticity in a turbulent puff.}, author = {Björn Hof}, journal = {Fluid Mechanics and its Applications}, pages = {221 -- 231}, publisher = {Springer}, title = {{Transition to turbulence in pipe flow}}, doi = {10.1007/1-4020-4049-0_12}, volume = {77}, year = {2005}, } @article{2867, abstract = {The plant hormone auxin elicits many specific context-dependent developmental responses. Auxin promotes degradation of Aux/IAA proteins that prevent transcription factors of the auxin response factor (ARF) family from regulating auxin-responsive target genes. Aux/IAAs and ARFs are represented by large gene families in Arabidopsis. Here we show that stabilization of BDL/IAA12 or its sister protein IAA13 prevents MP/ARF5-dependent embryonic root formation whereas stabilized SHY2/IAA3 interferes with seedling growth. Although both bdl and shy2-2 proteins inhibited MP/ARF5-dependent reporter gene activation, shy2-2 was much less efficient than bdl to interfere with embryonic root initiation when expressed from the BDL promoter. Similarly, MP was much more efficient than ARF16 in this process. When expressed from the SHY2 promoter, both shy2-2 and bdl inhibited cell elongation and auxin-induced gene expression in the seedling hypocotyl. By contrast, gravitropism and auxin-induced gene expression in the root, which were promoted by functionally redundant NPH4/ARF7 and ARF19 proteins, were inhibited by shy2-2, but not by bdl protein. Our results suggest that auxin signals are converted into specific responses by matching pairs of coexpressed ARF and Aux/IAA proteins.}, author = {Weijers, Dolf and Eva Benková and Jäger, Katja E and Schlereth, Alexandra and Hamann, Thorsten and Kientz, Marika and Wilmoth, Jill C and Reed, Jason W and Jürgens, Gerd}, journal = {EMBO Journal}, number = {10}, pages = {1874 -- 1885}, publisher = {Wiley-Blackwell}, title = {{Developmental specificity of auxin response by pairs of ARF and Aux/IAA transcriptional regulators}}, doi = {10.1038/sj.emboj.7600659}, volume = {24}, year = {2005}, } @article{2895, abstract = {One of the fundamental properties of the immune system is its capacity to avoid autoimmune diseases. The mechanism underlying this process, known as self-tolerance, is hitherto unresolved but seems to involve the control of clonal expansion of autoreactive lymphocytes. This article reviews mathematical modeling of self-tolerance, addressing two specific hypotheses. The first hypothesis posits that self-tolerance is mediated by tuning of activation thresholds, which makes autoreactive T lymphocytes reversibly "anergic" and unable to proliferate. The second hypothesis posits that the proliferation of autoreactive T lymphocytes is instead controlled by specific regulatory T lymphocytes. Models representing the population dynamics of autoreactive T lymphocytes according to these two hypotheses were derived. For each model we identified how cell density affects tolerance, and predicted the corresponding phase spaces and bifurcations. We show that the simple induction of proliferative anergy, as modeled here, has a density dependence that is only partially compatible with adoptive transfers of tolerance, and that the models of tolerance mediated by specific regulatory T cells are closer to the observations.}, author = {Carneiro, Jorge and Tiago Paixao and Milutinovic, Dejan and Sousa, João and Leon, Kalet and Gardner, Rui and Faro, Jose}, journal = {Journal of Computational and Applied Mathematics}, number = {1}, pages = {77 -- 100}, publisher = {Elsevier}, title = {{Immunological self tolerance: Lessons from mathematical modeling}}, doi = {10.1016/j.cam.2004.10.025}, volume = {184}, year = {2005}, } @article{3004, abstract = {Molecular mechanisms of pattern formation in the plant embryo are not well understood. Recent molecular and cellular studies, in conjunction with earlier microsurgical, physiological, and genetic work, are now starting to define the outlines of a model where gradients of the signaling molecule auxin play a central role in embryo patterning. It is relatively clear how these gradients are established and interpreted, but how they are maintained is still unresolved. Here, we have studied the contributions of auxin biosynthesis, conjugation, and transport pathways to the maintenance of embryonic auxin gradients. Auxin homeostasis in the embryo was manipulated by region-specific conditional expression of indoleacetic acid-tryptophan monooxygenase or indoleacetic acid-lysine synthetase, bacterial enzymes for auxin biosynthesis or conjugation. Neither manipulation of auxin biosynthesis nor of auxin conjugation interfered with auxin gradients and patterning in the embryo. This result suggests a compensatory mechanism for buffering auxin gradients in the embryo. Chemical and genetic inhibition revealed that auxin transport activity, in particular that of the PIN-FORMED1 (PIN1) and PIN4 proteins, is a major factor in the maintenance of these gradients.}, author = {Weijers, Dolf and Sauer, Michael and Meurette, Olivier and Jirí Friml and Ljung, Karin and Sandberg, Göran and Hooykaas, Paul and Offringa, Remko}, journal = {Plant Cell}, number = {9}, pages = {2517 -- 2526}, publisher = {American Society of Plant Biologists}, title = {{Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis}}, doi = {10.1105/tpc.105.034637}, volume = {17}, year = {2005}, } @article{3000, abstract = {In plants, cell polarity is an issue more recurring than in other systems, because plants, due to their adaptive and flexible development, often change cell polarity postembryonically according to intrinsic cues and demands of the environment. Recent findings on the directional movement of the plant signalling molecule auxin provide a unique connection between individual cell polarity and the establishment of polarity at the tissue, organ, and whole-plant levels. Decisions about the subcellular polar targeting of PIN auxin transport components determine the direction of auxin flow between cells and consequently mediate multiple developmental events. In addition, mutations or chemical interference with PIN-based auxin transport result in abnormal cell divisions. Thus, the complicated links between cell polarity establishment, auxin transport, cytoskeleton, and oriented cell divisions now begin to emerge. Here we review the available literature on the issues of cell polarity in both plants and animals to extend our understanding on the generation, maintenance, and transmission of cell polarity in plants.}, author = {Dhonukshe, Pankaj and Kleine Vehn, Jürgen and Friml, Jirí}, journal = {Protoplasma}, number = {1-2}, pages = {67 -- 73}, publisher = {Springer}, title = {{Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first?}}, doi = {10.1007/s00709-005-0104-8}, volume = {226}, year = {2005}, } @article{3001, abstract = {One of the mechanisms by which signalling molecules regulate cellular behaviour is modulating subcellular protein translocation. This mode of regulation is often based on specialized vesicle trafficking, termed constitutive cycling, which consists of repeated internalization and recycling of proteins to and from the plasma membrane. No such mechanism of hormone action has been shown in plants although several proteins, including the PIN auxin efflux facilitators, exhibit constitutive cycling. Here we show that a major regulator of plant development, auxin, inhibits endocytosis. This effect is specific to biologically active auxins and requires activity of the Calossin-like protein BIG. By inhibiting the internalization step of PIN constitutive cycling, auxin increases levels of PINs at the plasma membrane. Concomitantly, auxin promotes its own efflux from cells by a vesicle-trafficking-dependent mechanism. Furthermore, asymmetric auxin translocation during gravitropism is correlated with decreased PIN internalization. Our data imply a previously undescribed mode of plant hormone action: by modulating PIN protein trafficking, auxin regulates PIN abundance and activity at the cell surface, providing a mechanism for the feedback regulation of auxin transport.}, author = {Paciorek, Tomasz and Zažímalová, Eva and Ruthardt, Nadia and Petrášek, Jan and Stierhof, York-Dieter and Kleine-Vehn, Jürgen and Morris, David A and Emans, Neil and Jürgens, Gerd and Geldner, Niko and Jirí Friml}, journal = {Nature}, number = {7046}, pages = {1251 -- 1256}, publisher = {Nature Publishing Group}, title = {{Auxin inhibits endocytosis and promotes its own efflux from cells}}, doi = {10.1038/nature03633}, volume = {435}, year = {2005}, } @article{3003, abstract = {Plant development displays an exceptional plasticity and adaptability that involves the dynamic, asymmetric distribution of the phytohormone auxin. Polar auxin flow, which requires polarly localized transport facilitators of the PIN family, largely contributes to the establishment and maintenance of the auxin gradients. Functionally overlapping action of PIN proteins mediates multiple developmental processes, including embryo formation, organ development and tropisms. Here we show that PIN proteins exhibit synergistic interactions, which involve cross-regulation of PIN gene expression in pin mutants or plants with inhibited auxin transport. Auxin itself positively feeds back on PIN gene expression in a tissue-specific manner through an AUX/IAA-dependent signalling pathway. This regulatory switch is indicative of a mechanism by which the loss of a specific PIN protein is compensated for by auxin-dependent ectopic: expression of its homologues. The compensatory properties of the PIN-dependent transport network might enable the stabilization of auxin gradients and potentially contribute to the robustness of plant adaptive development.}, author = {Vieten, Anne and Vanneste, Steffen and Wiśniewska, Justyna and Eva Benková and Benjamins, René and Beeckman, Tom and Luschnig, Christian and Jirí Friml}, journal = {Development}, number = {20}, pages = {4521 -- 4531}, publisher = {Company of Biologists}, title = {{Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression}}, doi = {10.1242/dev.02027}, volume = {132}, year = {2005}, } @inproceedings{3212, abstract = {The Full-Domain Hash (FDH) signature scheme [3] forms one the most basic usages of random oracles. It works with a family F of trapdoor permutations (TDP), where the signature of m is computed as f−1(h(m)) (here f ∈R F and h is modelled as a random oracle). It is known to be existentially unforgeable for any TDP family F [3], although a much tighter security reduction is known for a restrictive class of TDP’s [10,14] — namely, those induced by a family of claw-free permutations (CFP) pairs. The latter result was shown [11] to match the best possible “black-box” security reduction in the random oracle model, irrespective of the TDP family F (e.g., RSA) one might use. In this work we investigate the question if it is possible to instantiate the random oracle h with a “real” family of hash functions H such that the corresponding schemes can be proven secure in the standard model, under some natural assumption on the family F. Our main result rules out the existence of such instantiations for any assumption on F which (1) is satisfied by a family of random permutations; and (2) does not allow the attacker to invert f ∈R F on an a-priori unbounded number of points. Moreover, this holds even if the choice of H can arbitrarily depend on f. As an immediate corollary, we rule out instantiating FDH based on general claw-free permutations, which shows that in order to prove the security of FDH in the standard model one must utilize significantly more structure on F than what is sufficient for the best proof of security in the random oracle model.}, author = {Dodis, Yevgeniy and Oliveira, Roberto and Krzysztof Pietrzak}, pages = {449 -- 466}, publisher = {Springer}, title = {{On the generic insecurity of the full domain hash}}, doi = {10.1007/11535218_27}, volume = {3621}, year = {2005}, } @inproceedings{3213, abstract = {We study the question whether the sequential or parallel composition of two functions, each indistinguishable from a random function by non-adaptive distinguishers is secure against adaptive distinguishers. The sequential composition of F and G is the function G(F()), the parallel composition is F G where ⋆ is some group operation. It has been shown that composition indeed gives adaptive security in the information theoretic setting, but unfortunately the proof does not translate into the more interesting computational case. In this work we show that in the computational setting composition does not imply adaptive security: If there is a prime order cyclic group where the decisional Diffie-Hellman assumption holds, then there are functions F and G which are indistinguishable by non-adaptive polynomially time-bounded adversaries, but whose parallel composition can be completely broken (i.e. we recover the key) with only three adaptive queries. We give a similar result for sequential composition. Interestingly, we need a standard assumption from the asymmetric (aka. public-key) world to prove a negative result for symmetric (aka. private-key) systems.}, author = {Krzysztof Pietrzak}, pages = {55 -- 65}, publisher = {Springer}, title = {{Composition does not imply adaptive security}}, doi = {10.1007/11535218_4}, volume = {3621}, year = {2005}, } @inproceedings{3211, abstract = {We present an improved bound on the advantage of any q-query adversary at distinguishing between the CBC MAC over a random n-bit permutation and a random function outputting n bits. The result assumes that no message queried is a prefix of any other, as is the case when all messages to be MACed have the same length. We go on to give an improved analysis of the encrypted CBC MAC, where there is no restriction on queried messages. Letting m be the block length of the longest query, our bounds are about mq2/2n for the basic CBC MAC and mo(1)q2/2n for the encrypted CBC MAC, improving prior bounds of m2q2/2n. The new bounds translate into improved guarantees on the probability of forging these MACs.}, author = {Bellare, Mihir and Krzysztof Pietrzak and Rogaway, Phillip}, pages = {527 -- 545}, publisher = {Springer}, title = {{Improved security analyses for CBC MACs}}, doi = {10.1007/11535218_32}, volume = {3621}, year = {2005}, } @article{3426, abstract = {We discuss the formation of graded morphogen profiles in a cell layer by nonlinear transport phenomena, important for patterning developing organisms. We focus on a process termed transcytosis, where morphogen transport results from the binding of ligands to receptors on the cell surface, incorporation into the cell, and subsequent externalization. Starting from a microscopic model, we derive effective transport equations. We show that, in contrast to morphogen transport by extracellular diffusion, transcytosis leads to robust ligand profiles which are insensitive to the rate of ligand production.}, author = {Bollenbach, Mark Tobias and Kruse, Karsten and Pantazis, Periklis and González Gaitán, Marcos and Jülicher, Frank}, journal = {Physical Review Letters}, number = {1}, publisher = {American Physical Society}, title = {{Robust formation of morphogen gradients}}, doi = {10.1103/PhysRevLett.94.018103}, volume = {94}, year = {2005}, } @article{3443, abstract = {In the hippocampal CA1 area, a relatively homogenous population of pyramidal cells is accompanied by a diversity of GABAergic interneurons. Previously, we found that parvalbumin-expressing basket, axo-axonic, bistratified, and oriens-lacunosum moleculare cells, innervating different domains of pyramidal cells, have distinct firing patterns during network oscillations in vivo. A second family of interneurons, expressing cholecystokinin but not parvalbumin, is known to target the same domains of pyramidal cells as do the parvalbumin cells. To test the temporal activity of these independent and parallel GABAergic inputs, we recorded the precise spike timing of identified cholecystokinin interneurons during hippocampal network oscillations in anesthetized rats and determined their molecular expression profiles and synaptic targets. The cells were cannabinoid receptor type 1 immunopositive. Contrary to the stereotyped firing of parvalbumin interneurons, cholecystokinin-expressing basket and dendrite-innervating cells discharge, on average, with 1.7 ± 2.0 Hz during high-frequency ripple oscillations in an episode-dependent manner. During theta oscillations, cholecystokinin- expressing interneurons fire with 8.8 ± 3.3 Hz at a characteristic time on the ascending phase of theta waves (155 ± 81°), when place cells start firing in freely moving animals. The firing patterns of some interneurons recorded in drug-free behaving rats were similar to cholecystokinin cells in anesthetized animals. Our results demonstrate that cholecystokinin- and parvalbumin-expressing interneurons make different contributions to network oscillations and play distinct roles in different brain states. We suggest that the specific spike timing of cholecystokinin interneurons and their sensitivity to endocannabinoids might contribute to differentiate subgroups of pyramidal cells forming neuronal assemblies, whereas parvalbumin interneurons contribute to synchronizing the entire network. Copyright © 2005 Society for Neuroscience.}, author = {Klausberger,Thomas and Marton,Laszlo F and Joseph O'Neill and Huck, Jojanneke H and Dalezios, Yannis and Fuentealba,Pablo and Suen, Wai Yee and Papp, Edit Cs and Kaneko, Takeshi and Watanabe, Masahiko and Jozsef Csicsvari and Somogyi, Péter}, journal = {Journal of Neuroscience}, number = {42}, pages = {9782 -- 9793}, publisher = {Society for Neuroscience}, title = {{Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations}}, doi = {10.1523/JNEUROSCI.3269-05.2005}, volume = {25}, year = {2005}, } @inproceedings{3557, abstract = {A challenging problem in computer-aided geometric design is the decomposition of a surface into four-sided regions that are then represented by NURBS patches. There are various approaches published in the literature and implemented as commercially available software, but all fall short in either automation or quality of the result. At Raindrop Geomagic, we have recently taken a fresh approach based on concepts from Morse theory. This by itself is not a new idea, but we have some novel ingredients that make this work, one being a rational notion of hierarchy that guides the construction of a simplified decomposition sensitive to only the major critical points.}, author = {Herbert Edelsbrunner}, pages = {9 -- 11}, publisher = {ACM}, title = {{Surface tiling with differential topology}}, doi = {http://dx.doi.org/10.2312/SGP/SGP05/009-011}, year = {2005}, } @inbook{3589, abstract = {During zebrafish gastrulation, the interplay between patterning events and morphogenesis creates an embryo out of a seemingly unstructured blastula stage embryo, an embryo with distinct polarities along its anterior–posterior, dorsoventral and left–right axes at the end of gastrulation.}, author = {Köppen, Mathias and Heisenberg, Carl-Philipp J}, booktitle = {Encyclopedia of Life Sciences}, publisher = {Wiley-Blackwell}, title = {{Cleavage and gastrulation in zebrafish embryos}}, doi = {10.1038/npg.els.0001072}, year = {2005}, } @inbook{3588, author = {Castanon Ortega, Irinka and Heisenberg, Carl-Philipp J}, booktitle = {Cell Migration in Development and Disease}, editor = {Wedlich, Doris}, pages = {71 -- 105}, publisher = {Wiley-VCH}, title = {{Cell migration during zebrafish gastrulation}}, doi = {10.1002/3527604669}, year = {2005}, } @misc{3590, author = {Castanon Ortega, Irinka and Heisenberg, Carl-Philipp J}, booktitle = {Nature Cell Biology}, number = {1}, pages = {19 -- 19}, publisher = {Nature Publishing Group}, title = {{A stern view of gastrulation}}, doi = {10.1038/ncb0105-19}, volume = {7}, year = {2005}, } @inproceedings{3689, abstract = {Digital cameras have become almost ubiquitous and their use for fast and casual capturing of natural images is unchallenged. For making images of documents, however, they have not caught up to flatbed scanners yet, mainly because camera images tend to suffer from distortion due to the perspective and are therefore limited in their further use for archival or OCR. For images of non-planar paper surfaces like books, page curl causes additional distortion, which poses an even greater problem due to its nonlinearity. This paper presents a new algorithm for removing both perspective and page curl distortion. It requires only a single camera image as input and relies on a priori layout information instead of additional hardware. Therefore, it is much more user friendly than most previous approaches, and allows for flexible ad hoc document capture. Results are presented showing that the algorithm produces visually pleasing output and increases OCR accuracy, thus having the potential to become a general purpose preprocessing tool for camera based document capture.}, author = {Ulges, Adrian and Christoph Lampert and Breuel,Thomas M}, pages = {1001 -- 1005}, publisher = {IEEE}, title = {{Document image dewarping using robust estimation of curled text lines}}, doi = { 10.1109/ICDAR.2005.90}, volume = {2}, year = {2005}, } @inproceedings{3684, abstract = {Ever since text processors became popular, users have dreamt of handling documents printed on paper as comfortably as electronic ones, with full text search typically appearing very close to the top of the wish list. This paper presents the design of a prototype system that takes a step into this direction. The user’s desktop is continuously monitored and of each detected document a high resolution snapshot is taken using a digital camera. The resulting image is processed using specially designed dewarping and OCR algorithms, making a digital and fully searchable version of the document available to the user in real-time. These steps are performed without any user interaction. This enables the system to run as a background task without disturbing the user in her work, while at the same time offering electronic access to all paper documents that have been present on the desktop during the uptime of the system.}, author = {Christoph Lampert and Braun,Tim and Ulges, Adrian and Keysers,Daniel and Breuel,Thomas M}, pages = {79 -- 86}, publisher = {CBDAR}, title = {{Oblivious document capture and real-time retrieval}}, year = {2005}, } @article{3720, author = {Guzmán, José and Gerevich, Zoltan and Hengstler, Jan and Illes, Peter and Kleemann, Werner}, journal = {Synapse}, number = {4}, pages = {235 -- 238}, publisher = {Wiley}, title = {{P2Y1 receptors inhibit both strength and plasticity of glutamatergic synaptic neurotransmission in the rat prefrontal cortex.}}, doi = {10.1002/syn.20177}, volume = {57}, year = {2005}, } @article{3753, abstract = {Characterizing the dynamics of specific RNA levels requires real-time RNA profiling in a single cell. We show that the combination of a synthetic modular genetic system with fluorescence correlation spectroscopy allows us to directly measure in real time the activity of any specific promoter in prokaryotes. Using a simple inducible gene expression system, we found that induced RNA levels within a single bacterium of Escherichia coli exhibited a pulsating profile in response to a steady input of inducer. The genetic deletion of an efflux pump system, a key determinant of antibiotic resistance, altered the pulsating transcriptional dynamics and caused overexpression of induced RNA. In contrast with population measurements, real-time RNA profiling permits identifying relationships between genotypes and transcriptional dynamics that are accessible only at the level of the single cell.}, author = {Le,Thuc T. and Harlepp, Sébastien and Calin Guet and Dittmar,Kimberly and Emonet,Thierry and Pan,Tao and Cluzel,Philippe}, journal = {PNAS}, number = {26}, pages = {9160 -- 9164}, publisher = {National Academy of Sciences}, title = {{Real-time RNA profiling within a single bacterium}}, doi = {10.1073/pnas.0503311102}, volume = {102}, year = {2005}, } @article{3763, abstract = {The generation of realistic motion satisfying user-defined requirements is one of the most important goals of computer animation. Our aim in this paper is the synthesis of realistic, controllable motion for lightweight natural objects in a gaseous medium. We formulate this problem as a large-scale spacetime optimization with user controls and fluid motion equations as constraints. We have devised novel and effective methods to make this large optimization tractable. Initial trajectories are generated with data-driven synthesis based on stylistic motion planning. Smoothed particle hydrodynamics (SPH) is used during optimization to produce fluid simulations at a reasonable computational cost, while interesting vortex-based fluid motion is generated by recording the presence of vortices in the initial trajectories and maintaining them through optimization. Object rotations are refined as a postprocess to enhance the visual quality of the results. We demonstrate our techniques on a number of animations involving single or multiple objects.}, author = {Shi, Lin and Yu, Yizhou and Wojtan, Christopher J and Chenney, Stephen}, journal = {The Visual Computer}, number = {7}, pages = {474 -- 487}, publisher = {Springer}, title = {{Controllable motion synthesis in a gaseous medium}}, doi = {10.1007/s00371-005-0296-0}, volume = {21}, year = {2005}, } @misc{3812, abstract = {Hippocampal GABAergic interneurons show diverse molecular and morphological properties. The functional significance of this diversity for information processing is poorly understood. Here we show that cholecystokinin (CCK)-expressing interneurons in rat dentate gyrus release GABA in a highly asynchronous manner, in contrast to parvalbumin (PV) interneurons. With a gamma-frequency burst of ten action potentials, the ratio of asynchronous to synchronous release is 3:1 in CCK interneurons but is 1:5 in parvalbumin interneurons. N-type channels trigger synchronous and asynchronous release in CCK interneuron synapses, whereas P/Q-type Ca(2+) channels mediate release at PV interneuron synapses. Effects of Ca(2+) chelators suggest that both a long-lasting presynaptic Ca(2+) transient and a large distance between Ca(2+) source and sensor of exocytosis contribute to the higher ratio of asynchronous to synchronous release in CCK interneuron synapses. Asynchronous release occurs at physiological temperature and with behaviorally relevant stimulation patterns, thus generating long-lasting inhibition in the brain.}, author = {Hefft, Stefan and Peter Jonas}, booktitle = {Nature Neuroscience}, number = {10}, pages = {1319 -- 28}, publisher = {Nature Publishing Group}, title = {{Asynchronous GABA release generates long-lasting inhibition at a hippocampal interneuron-principal neuron synapse (Review)}}, doi = {10.1038/nn1542}, volume = {8}, year = {2005}, } @inproceedings{3896, abstract = {Temporal Logic Model Checking is one of the most potent tools for the verification of finite state systems. Computation Tree Logic (CTL) has gained popularity because unlike most other logics, CTL model checking of a single transition system can be achieved in polynomial time. However, in most real-life problems, specially in distributed and parallel systems, the system consist of a set of concurrent processes and the verification problem translates to model check the composition of the component processes. Since explicit composition leads to state explosion, verifying the system without actually composing the components is attractive, even for possibly restrictive class of systems. We show that the problem of compositional CTL model checking is PSPACE complete for the class of systems composed of components that are tree-like transition structure and do not interact among themselves. For the simplest forms of existential and universal CTL formulas model checking turns out to be NP complete and coNP complete, respectively. The results hold for both synchronous and asynchronous composition.}, author = {Krishnendu Chatterjee and Dasgupta, Pallab and Chakrabarti, Partha P}, pages = {89 -- 102}, publisher = {Springer}, title = {{Complexity of compositional model checking of computation tree logic on simple structures}}, doi = {10.1007/978-3-540-30536-1_13}, volume = {3326}, year = {2005}, } @inproceedings{3893, abstract = {We study infinite stochastic games played by two-players on a finite graph with goals specified by sets of infinite traces. The games are concurrent (each player simultaneously and independently chooses an action at each round), stochastic (the next state is determined by a probability distribution depending on the current state and the chosen actions), infinite (the game continues for an infinite number of rounds), nonzero-sum (the players' goals are not necessarily conflicting), and undiscounted. We show that if each player has an W-regular objective expressed as a paxity objective, then there exists an epsilon-Nash equilibrium, for every epsilon > 0. However, exact Nash equilibria need not exist. We study the complexity of finding values (payoff profile) of an epsilon-Nash equilibrium. We show that the values of an epsilon-Nash equilibrium in nonzero-sum concurrent parity games can be computed by solving the following two simpler problems: computing the values of zero-sum (the goals of the players axe strictly conflicting) concurrent parity games and computing epsilon-Nash equilibrium values of nonzero-sum concurrent games with reachability objectives. As a consequence we establish that values of an epsilon-Nash equilibrium can be computed in TFNP (total functional NP), and hence in EXPTIME.}, author = {Krishnendu Chatterjee}, pages = {413 -- 427}, publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik}, title = {{Two-player nonzero-sum ω-regular games}}, doi = {10.1007/11539452_32}, volume = {3653}, year = {2005}, } @article{3916, abstract = {Divergent reproductive interests of males and females often cause sexual conflict [1] and [2]. Males of many species manipulate females by transferring seminal fluids that boost female short-term fecundity while decreasing their life expectancy and future reproductivity [3] and [4]. The life history of ants, however, is expected to reduce sexual conflict; whereas most insect females show repeated phases of mating and reproduction, antqueens mate only during a short period early in life and undergo a lifelong commitment to their mates by storing sperm [5]. Furthermore, sexual offspring can only be reared after a sterile worker force has been built up [5]. Therefore, the males should also profit from a long female lifespan. In the antCardiocondyla obscurior, mating indeed has a positive effect on the lifetime reproductive success of queens. Queens that mated to either one fertile or one sterilized male lived considerably longer and started laying eggs earlier than virgin queens. Only queens that received viable sperm from fertile males showed increased fecundity. The lack of a trade-off between fecundity and longevity is unexpected, given evolutionary theories of aging [6]. Our data instead reveal the existence of sexual cooperation in ants.}, author = {Schrempf, Alexandra and Heinze, Jürgen and Cremer, Sylvia}, journal = {Current Biology}, number = {3}, pages = {267 -- 270}, publisher = {Cell Press}, title = {{Sexual cooperation: mating increases longevity in ant queens}}, doi = {10.1016/j.cub.2005.01.036}, volume = {15}, year = {2005}, } @article{3915, abstract = {In the ant Cardiocondyla obscurior, wingless males compete with nestmate males for access to female mating partners, leading to local mate competition (LMC). Queen number varies between colonies, resulting in variation in the strength of LMC. Cremer & Heinze (2002, Proceedings of the Royal Society of London, Series B, 269, 417–422) showed that colonies responded to increasing queen number by producing a less femalebiased sex ratio, as predicted by LMC theory. However, the proximate mechanisms responsible for this variation in the sex ratio could not be determined because the study was restricted to adult sex ratios.With LMC, the primary sex ratio (proportion of haploid eggs laid by the queen) is expected to be female biased, which lowers the conflict between queens and workers over sex allocation. We compared the primary sex ratios laid by queens in monogynous and in polygynous experimental colonies of C. obscurior. The proportion of haploid eggs laid by queens was significantly lower in single-queen than in multiple-queen colonies. Furthermore, queens rapidly adjusted their primary sex ratios to changes in colony queen number. This is the first report of an adaptive adjustment of the primary sex ratio in response to LMC by ant queens.}, author = {De Menten, Ludivine and Cremer, Sylvia and Heinze, Jürgen and Aron, Serge}, journal = {Animal Behaviour}, number = {5}, pages = {1031 -- 1035}, publisher = {Elsevier}, title = {{Primary sex ratio adjustment by ant queens in response to local mate competition}}, doi = {10.1016/j.anbehav.2004.09.005}, volume = {69}, year = {2005}, } @article{4167, abstract = {In this study, we elucidate the roles of the winged-helix transcription factor Foxa2 in ventral CNS development in zebrafish. Through cloning of monorail (mol), which we find encodes the transcription factor Foxa2, and phenotypic analysis of mol(-/-) embryos, we show that floorplate is induced in the absence of Foxa2 function but fails to further differentiate. In mol(-/-) mutants, expression of Foxa and Hh family genes is not maintained in floorplate cells and lateral expansion of the floorplate fails to occur. Our results suggest that this is due to defects both in the regulation of Hh activity in medial floorplate cells as well as cell-autonomous requirements for Foxa2 in the prospective laterally positioned floorplate cells themselves. Foxa2 is also required for induction and/or patterning of several distinct cell types in the ventral CNS. Serotonergic neurones of the raphe nucleus and the trochlear motor nucleus are absent in mol(-/-) embryos, and oculomotor and facial motoneurones ectopically occupy ventral CNS midline positions in the midbrain and hindbrain. There is also a severe reduction of prospective oligodendrocytes in the midbrain and hindbrain. Finally, in the absence of Foxa2, at least two likely Hh pathway target genes are ectopically expressed in more dorsal regions of the midbrain and hindbrain ventricular neuroepithelium, raising the possibility that Foxa2 activity may normally be required to limit the range of action of secreted Hh proteins.}, author = {Norton, Will and Mangoli, Maryam and Lele, Zsolt and Pogoda, Hans and Diamond, Brianne and Mercurio, Sara and Russell, Claire and Teraoka, Hiroki and Stickney, Heather and Rauch, Gerd and Heisenberg, Carl-Philipp J and Houart, Corinne and Schilling, Thomas and Frohnhoefer, Hans and Rastegar, Sepand and Neumann, Carl and Gardiner, R Mark and Strähle, Uwe and Geisler, Robert and Rees, Michelle and Talbot, William and Wilson, Stephen}, journal = {Development}, number = {4}, pages = {645 -- 658}, publisher = {Company of Biologists}, title = {{Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones}}, doi = {10.1242/dev.01611}, volume = {132}, year = {2005}, } @article{4183, abstract = {The spreading of an epithelial cell sheet over a substrate is a common process during embryogenesis. Typical examples include epiboly during zebrafish gastrulation and Drosophila dorsal closure. We provide evidence that in both cases, actin-based contraction of the leading edge of the epithelium is of critical importance.}, author = {Köppen, Mathias and Fernández, Beatriz and Carvalho, Lara and Jacinto, António and Heisenberg, Carl-Philipp J}, journal = {Mechanisms of Development}, number = {Supplement 1}, pages = {S112 -- S113}, publisher = {Elsevier}, title = {{Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure}}, doi = {10.1016/j.mod.2005.06.010}, volume = {122}, year = {2005}, } @inproceedings{4367, author = {Podelski,Andreas and Thomas Wies}, pages = {267 -- 282}, publisher = {Springer}, title = {{Boolean Heaps}}, doi = {1550}, year = {2005}, } @article{3143, abstract = {Two ETS transcription factors of the Pea3 subfamily are induced in subpopulations of dorsal root ganglion (DRG) sensory and spinal motor neurons by target-derived factors. Their expression controls late aspects of neuronal differentiation such as target invasion and branching. Here, we show that the late onset of ETS gene expression is an essential requirement for normal sensory neuron differentiation. We provide genetic evidence in the mouse that precocious ETS expression in DRG sensory neurons perturbs axonal projections, the acquisition of terminal differentiation markers, and their dependence on neurotrophic support. Together, our findings indicate that DRG sensory neurons exhibit a temporal developmental switch that can be revealed by distinct responses to ETS transcription factor signaling at sequential steps of neuronal maturation.}, author = {Simon Hippenmeyer and Vrieseling, Eline and Sigrist, Markus and Portmann, Thomas and Laengle, Celia and Ladle, David R and Arber, Silvia}, journal = {PLoS Biology}, number = {5}, pages = {0878 -- 0890}, publisher = {Public Library of Science}, title = {{A developmental switch in the response of DRG neurons to ETS transcription factor signaling}}, doi = {10.1371/journal.pbio.0030159}, volume = {3}, year = {2005}, } @article{3141, abstract = {The two actin-related subunits of the Arp2/3 complex, Arp2 and Arp3, are proposed to form a pseudo actin dimer that nucleates actin polymerization. However, in the crystal structure of the inactive complex, they are too far apart to form such a nucleus. Here, we show using EM that yeast and bovine Arp2/3 complexes exist in a distribution among open, intermediate and closed conformations. The crystal structure docks well into the open conformation. The activator WASp binds at the cleft between Arp2 and Arp3, and all WASp-bound complexes are closed. The inhibitor coronin binds near the p35 subunit, and all coronin-bound complexes are open. Activating and loss-of-function mutations in the p35 subunit skew conformational distribution in opposite directions, closed and open, respectively. We conclude that WASp stabilizes p35-dependent closure of the complex, holding Arp2 and Arp3 closer together to nucleate an actin filament.}, author = {Rodal, Avital A and Sokolova, Olga and Robins, Deborah B and Daugherty, Karen M and Simon Hippenmeyer and Riezman, Howard and Grigorieff, Nikolaus and Goode, Bruce L}, journal = {Nature Structural and Molecular Biology}, number = {1}, pages = {26 -- 31}, publisher = {Nature Publishing Group}, title = {{Conformational changes in the Arp2 3 complex leading to actin nucleation}}, doi = {10.1038/nsmb870}, volume = {12}, year = {2005}, } @inproceedings{3175, abstract = {This paper addresses the novel problem of automatically synthesizing an output image from a large collection of different input images. The synthesized image, called a digital tapestry, can be viewed as a visual summary or a virtual 'thumbnail' of all the images in the input collection. The problem of creating the tapestry is cast as a multi-class labeling problem such that each region in the tapestry is constructed from input image blocks that are salient and such that neighboring blocks satisfy spatial compatibility. This is formulated using a Markov Random Field and optimized via the graph cut based expansion move algorithm. The standard expansion move algorithm can only handle energies with metric terms, while our energy contains non-metric (soft and hard) constraints. Therefore we propose two novel contributions. First, we extend the expansion move algorithm for energy functions with non-metric hard constraints. Secondly, we modify it for functions with "almost" metric soft terms, and show that it gives good results in practice. The proposed framework was tested on several consumer photograph collections, and the results are presented.}, author = {Rother, Carsten and Kumar, Sanjiv and Vladimir Kolmogorov and Blake, Andrew}, pages = {589 -- 596}, publisher = {IEEE}, title = {{Digital tapestry}}, doi = {10.1109/CVPR.2005.130}, volume = {1}, year = {2005}, } @inproceedings{3176, abstract = {This paper demonstrates the high quality, real-time segmentation techniques. We achieve real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, layered dynamic programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, layered graph cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar performance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output. }, author = {Vladimir Kolmogorov and Criminisi, Antonio and Blake, Andrew and Cross, Geoffrey and Rother, Carsten}, pages = {1186 -- 1186}, publisher = {IEEE}, title = {{Bi-layer segmentation of binocular stereo video}}, doi = {10.1109/CVPR.2005.90}, year = {2005}, } @inproceedings{3183, abstract = {This paper describes two algorithms capable of real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar perfomance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output.}, author = {Vladimir Kolmogorov and Criminisi, Antonio and Blake, Andrew and Cross, Geoffrey and Rother, Carsten}, pages = {407 -- 414}, publisher = {IEEE}, title = {{Bi-layer segmentation of binocular stereo video}}, doi = {10.1109/CVPR.2005.91}, volume = {2}, year = {2005}, } @inproceedings{3182, abstract = {In the work of the authors (2003), we showed that graph cuts can find hypersurfaces of globally minimal length (or area) under any Riemannian metric. Here we show that graph cuts on directed regular grids can approximate a significantly more general class of continuous non-symmetric metrics. Using submodularity condition (Boros and Hammer, 2002 and Kolmogorov and Zabih, 2004), we obtain a tight characterization of graph-representable metrics. Such "submodular" metrics have an elegant geometric interpretation via hypersurface functionals combining length/area and flux. Practically speaking, we attend 'geo-cuts' algorithm to a wider class of geometrically motivated hypersurface functionals and show how to globally optimize any combination of length/area and flux of a given vector field. The concept of flux was recently introduced into computer vision by Vasilevskiy and Siddiqi (2002) but it was mainly studied within variational framework so far. We are first to show that flux can be integrated into graph cuts as well. Combining geometric concepts of flux and length/area within the global optimization framework of graph cuts allows principled discrete segmentation models and advances the slate of the art for the graph cuts methods in vision. In particular we address the "shrinking" problem of graph cuts, improve segmentation of long thin objects, and introduce useful shape constraints.}, author = {Vladimir Kolmogorov and Boykov, Yuri}, pages = {564 -- 571}, publisher = {IEEE}, title = {{What metrics can be approximated by geo cuts or global optimization of length area and flux}}, doi = {10.1109/ICCV.2005.252}, volume = {1}, year = {2005}, } @inproceedings{3181, abstract = {Tree-reweighted max-product (TRW) message passing [9] is a modified form of the ordinary max-product algorithm for attempting to find minimal energy configurations in Markov random field with cycles. For a TRW fixed point satisfying the strong tree agreement condition, the algorithm outputs a configuration that is provably optimal. In this paper, we focus on the case of binary variables with pairwise couplings, and establish stronger properties of TRW fixed points that satisfy only the milder condition of weak tree agreement (WTA). First, we demonstrate how it is possible to identify part of the optimal solution - i.e., a provably optimal solution for a subset of nodes - without knowing a complete solution. Second, we show that for submodular functions, a WTA fixed point always yields a globally optimal solution. We establish that for binary variables, any WTA fixed point always achieves the global maximum of the linear programming relaxation underlying the TRW method.}, author = {Vladimir Kolmogorov and Wainwright, Martin J}, pages = {316 -- 323}, publisher = {AUAI Press}, title = {{On the optimality of tree reweighted max product message passing}}, year = {2005}, } @article{3417, abstract = {Recently, direct measurements of forces stabilizing single proteins or individual receptor–ligand bonds became possible with ultra-sensitive force probe methods like the atomic force microscope (AFM). In force spectroscopy experiments using AFM, a single molecule or receptor–ligand pair is tethered between the tip of a micromachined cantilever and a supporting surface. While the molecule is stretched, forces are measured by the deflection of the cantilever and plotted against extension, yielding a force spectrum characteristic for each biomolecular system. In order to obtain statistically relevant results, several hundred to thousand single-molecule experiments have to be performed, each resulting in a unique force spectrum. We developed software and algorithms to analyse large numbers of force spectra. Our algorithms include the fitting polymer extension models to force peaks as well as the automatic alignment of spectra. The aligned spectra allowed recognition of patterns of peaks across different spectra. We demonstrate the capabilities of our software by analysing force spectra that were recorded by unfolding single transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding pathways were detected by classifying peak patterns. Deviant spectra, e.g. those with no attachment or erratic peaks, can be easily identified. The software is based on the programming language C++, the GNU Scientific Library (GSL), the software WaveMetrics IGOR Pro and available open-source at http://bioinformatics.org/fskit/.}, author = {Kuhn, Michael and Harald Janovjak and Hubain, Maurice and Mueller, Daniel J}, journal = {Journal of Microscopy}, number = {2}, pages = {125 -- 132}, publisher = {Wiley-Blackwell}, title = {{Automated alignment and pattern recognition of single-molecule force spectroscopy data}}, doi = {10.1111/j.1365-2818.2005.01478.x}, volume = {218}, year = {2005}, } @article{3416, abstract = {In the last decade atomic force microscopy has been used to measure the mechanical stability of single proteins. These force spectroscopy experiments have shown that many water-soluble and membrane proteins unfold via one or more intermediates. Recently, Li and co-workers found a linear correlation between the unfolding force of the native state and the intermediate in fibronectin, which they suggested indicated the presence of a molecular memory or multiple unfolding pathways (1). Here, we apply two independent methods in combination with Monte Carlo simulations to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show that correlation analysis of unfolding forces is very sensitive to errors in force calibration of the instrument. In contrast, a comparison of relative forces provides a robust measure for the stability of unfolding intermediates. The proposed approach detects three energetically different states of α-helices E and D in trimeric BR. These states are not observed for monomeric BR and indicate that substantial information is hidden in forced unfolding experiments of single proteins.}, author = {Harald Janovjak and Sapra, Tanuj K and Mueller, Daniel J}, journal = {Biophysical Journal}, number = {5}, pages = {37 -- 39}, publisher = {Biophysical Society}, title = {{Complex stability of single proteins explored by forced unfolding experiments}}, doi = {10.1529/biophysj.105.059774}, volume = {88}, year = {2005}, } @article{3418, abstract = {Atomic force microscopy (AFM) allows the critical forces that unfold single proteins and rupture individual receptor–ligand bonds to be measured. To derive the shape of the energy landscape, the dynamic strength of the system is probed at different force loading rates. This is usually achieved by varying the pulling speed between a few nm/s and a few mgrm/s, although for a more complete investigation of the kinetic properties higher speeds are desirable. Above 10 mgrm/s, the hydrodynamic drag force acting on the AFM cantilever reaches the same order of magnitude as the molecular forces. This has limited the maximum pulling speed in AFM single-molecule force spectroscopy experiments. Here, we present an approach for considering these hydrodynamic effects, thereby allowing a correct evaluation of AFM force measurements recorded over an extended range of pulling speeds (and thus loading rates). To support and illustrate our theoretical considerations, we experimentally evaluated the mechanical unfolding of a multi-domain protein recorded at 30 mgrm/s pulling speed.}, author = {Harald Janovjak and Struckmeier, Jens and Mueller, Daniel J}, journal = {European Biophysics Journal}, number = {1}, pages = {91 -- 96}, publisher = {Springer}, title = {{Hydrodynamic effects in fast AFM single molecule force measurements}}, doi = {10.1007/s00249-004-0430-3}, volume = {34}, year = {2005}, } @inbook{3433, author = {Jonathan Bollback}, booktitle = {Statistical methods in Molecular Evolution}, editor = {Nielsen, Rasmus}, pages = {439 -- 462}, publisher = {Springer}, title = {{Posterior mapping and posterior predictive distributions}}, doi = {10.1007/0-387-27733-1}, year = {2005}, } @misc{3509, abstract = {Methods, apparatus and computer program products can generate light weight but highly realistic and accurate colored models of three-dimensional colored objects. The colored model may be generated from a second plurality of points that define a coarse digital representation of the surface and at least one texture map containing information derived from a first plurality of colored points that define a fine digital representation of the surface. This derivation is achieved by mapping points within the texture map to the fine digital representation of the three-dimensional surface. Colored scan data may be used to construct the fine digital representation as a triangulated surface (i.e., triangulation) using a wrapping operation.}, author = {Williams, Steven and Edelsbrunner, Herbert and Fu, Ping}, title = {{Methods, apparatus and computer program products for modeling three-dimensional colored objects}}, year = {2005}, } @inproceedings{3558, abstract = {The tandem algorithm combines the marching cube algorithm for surface extraction and the edge contraction algorithm for surface simplification in lock-step to avoid the costly intermediate step of storing the entire extracted surface triangulation. Beyond this basic strategy, we introduce refinements to prevent artifacts in the resulting triangulation, first, by carefully monitoring the amount of simplification during the process and, second, by driving the simplification toward a compromise between shape approximation and mesh quality. We have implemented the algorithm and used extensive computational experiments to document the effects of various design options and to further fine-tune the algorithm.}, author = {Attali, Dominique and Cohen-Steiner, David and Herbert Edelsbrunner}, pages = {139 -- 148}, publisher = {ACM}, title = {{Extraction and simplification of iso-surfaces in tandem}}, year = {2005}, } @inbook{3576, abstract = {ears of research in biology have established that all cellular functions are deeply connected to the shape and dynamics of their molec- ular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of biomolecules. The analysis of these structures has led to the development of computational biology, whose aim is to predict from molecular simulation properties inaccessible to experimental probes. Here we focus on the representation of biomolecules used in these sim- ulations, and in particular on the hard sphere models. We review how the geometry of the union of such spheres is used to model their interactions with their environment, and how it has been included in simulations of molecular dynamics. In parallel, we review our own developments in mathematics and com- puter science on understanding the geometry of unions of balls, and their applications in molecular simulation.}, author = {Herbert Edelsbrunner and Koehl, Patrice}, booktitle = {Combinatorial and Computational Geometry}, pages = {243 -- 275}, publisher = {Cambridge University Press}, title = {{The geometry of biomolecular solvation}}, volume = {52}, year = {2005}, } @article{3612, abstract = {Left-right asymmetry in snails is intriguing because individuals of opposite chirality are either unable to mate or can only mate with difficulty, so could be reproductively isolated from each other. We have therefore investigated chiral evolution in the Japanese land snail genus Euhadra to understand whether changes in chirality have promoted speciation. In particular, we aimed to understand the effect of the maternal inheritance of chirality on reproductive isolation and gene flow. We found that the mitochondrial DNA phylogeny of Euhadra is consistent with a single, relatively ancient evolution of sinistral species and suggests either recent “single-gene speciation” or gene flow between chiral morphs that are unable to mate. To clarify the conditions under which new chiral morphs might evolve and whether single-gene speciation can occur, we developed a mathematical model that is relevant to any maternal-effect gene. The model shows that reproductive character displacement can promote the evolution of new chiral morphs, tending to counteract the positive frequency-dependent selection that would otherwise drive the more common chiral morph to fixation. This therefore suggests a general mechanism as to how chiral variation arises in snails. In populations that contain both chiral morphs, two different situations are then possible. In the first, gene flow is substantial between morphs even without interchiral mating, because of the maternal inheritance of chirality. In the second, reproductive isolation is possible but unstable, and will also lead to gene flow if intrachiral matings occasionally produce offspring with the opposite chirality. Together, the results imply that speciation by chiral reversal is only meaningful in the context of a complex biogeographical process, and so must usually involve other factors. In order to understand the roles of reproductive character displacement and gene flow in the chiral evolution of Euhadra, it will be necessary to investigate populations in which both chiral morphs coexist.}, author = {Davison, Angus and Chiba, Satoshi and Nicholas Barton and Clarke, Bernard}, journal = {PLoS Biology}, number = {9}, publisher = {Public Library of Science}, title = {{Speciation and gene flow between snails of opposing chirality}}, doi = {10.1371/journal.pbio.0030282}, volume = {3}, year = {2005}, } @article{3611, abstract = {We present two novel methods to infer mating patterns from genetic data. They differ from existing statistical methods of parentage inference in that they apply to populations that deviate from Hardy–Weinberg and linkage equilibrium, and so are suited for the study of assortative mating in hybrid zones. The core data set consists of genotypes at several loci for a number of full-sib clutches of unknown parentage. Our inference is based throughout on estimates of allelic associations within and across loci, such as heterozygote deficit and pairwise linkage disequilibrium. In the first method, the most likely parents of a given clutch are determined from the genotypic distribution of the associated adult population, given an explicit model of nonrandom mating. This leads to estimates of the strength of assortment. The second approach is based solely on the offspring genotypes and relies on the fact that a linear relation exists between associations among the offspring and those in the population of breeding pairs. We apply both methods to a sample from the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Disco glossidae) in Croatia. Consistently, both approaches provide no evidence for a departure from random mating, despite adequate statistical power. Instead, B. variegata-like individuals among the adults contributed disproportionately to the offspring cohort, consistent with their preference for the type of breeding habitat in which this study was conducted.}, author = {Nürnberger, Beate and Nicholas Barton and Kruuk, Loeske E and Vines, Timothy H}, journal = {Heredity}, number = {2}, pages = {247 -- 257}, publisher = {Nature Publishing Group}, title = {{Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes}}, doi = {10.1038/sj.hdy.6800607}, volume = {94}, year = {2005}, } @article{3613, abstract = {The extent of genetic variation in fitness is a crucial issue in evolutionary biology and yet remains largely unresolved. In Drosophila melanogaster, we have devised a method that allows the net effects on fitness of heterozygous wild-type chromosomes to be measured, by competing them against two different “balancer” chromosomes. We have applied the method to a large sample of 40 wild-type third chromosomes and have measured fitnesses of nonlethal chromosomes as well as chromosomes bearing recessive lethals. The measurements were made in the environment to which the population was adapted and did not involve inbreeding. The results show an extraordinary similarity in the behavior of replicates of the same chromosome, indicating consistent genetic effects on total fitness. Some invading chromosomes increased rapidly and some slowly, and some rose to appreciable frequency after several months, but then declined again: in every case, the same pattern was seen in each replicate. We estimated relative fitnesses, rates of change of fitness, and relative viabilities, for each chromosome. There were significant fluctuations around the fitted model, which were also highly replicable. Wild-type chromosomes varied substantially in their effects on heterozygous fitness, and these effects vary through time, most likely as a result of genotype × environment interactions.}, author = {Gardner, Michael P and Fowler, Kevin and Nicholas Barton and Patridge, Linda}, journal = {Genetics}, number = {3}, pages = {1553 -- 1571}, publisher = {Genetics Society of America}, title = {{Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns}}, doi = {10.1534/genetics.104.032367}, volume = {169}, year = {2005}, } @article{3691, abstract = {In strictly pseudoconvex domains with smooth boundary, we prove a commutator relationship between admissible integral operators, as introduced by Lieb and Range, and smooth vector fields which are tangential at boundary points. This makes it possible to gain estimates for admissible operators in function spaces which involve tangential derivatives. Examples are given under with circumstances these can be transformed into genuine Sobolev- and C k-estimates.}, author = {Christoph Lampert}, journal = {Publicacions Matemàtiques}, number = {1}, pages = {179 -- 195}, publisher = {Universitat Autònoma de Barcelona, Departament de Matemàtique}, title = {{Boundary regularity of admissible operators}}, doi = {10.5565/PUBLMAT_49105_08}, volume = {49}, year = {2005}, } @article{3721, abstract = {Recent advances in atomic force microscopy allowed globular and membrane proteins to be mechanically unfolded on a single-molecule level. Presented is an extension to the existing force spectroscopy experiments. While unfolding single bacteriorhodopsins from native purple membranes, small oscillation amplitudes (6–9nm) were supplied to the vertical displacement of the cantilever at a frequency of 3kHz. The phase and amplitude response of the cantilever-protein system was converted to reveal the elastic (conservative) and viscous (dissipative) contributions to the unfolding process. The elastic response (stiffness) of the extended parts of the protein were in the range of a few tens pN/nm and could be well described by the derivative of the wormlike chain model. Discrete events in the viscous response coincided with the unfolding of single secondary structure elements and were in the range of 1μNs/m. In addition, these force modulation spectroscopy experiments revealed novel mechanical unfolding intermediates of bacteriorhodopsin. We found that kinks result in a loss of unfolding cooperativity in transmembrane helices. Reconstructing force-distance spectra by the integration of amplitude-distance spectra verified their position, offering a novel approach to detect intermediates during the forced unfolding of single proteins.}, author = {Harald Janovjak and Mueller, Daniel J and Humphris, Andrew D}, journal = {Biophysical Journal}, number = {2}, pages = {1423 -- 1431}, publisher = {Biophysical Society}, title = {{Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins}}, doi = {10.1529/biophysj.104.052746}, volume = {88}, year = {2005}, } @article{3741, abstract = {In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here, we reformulate the clustering problem from an information theoretic perspective that avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster "prototype," does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures nonlinear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures.}, author = {Slonim,N. and Atwal,G. and Gasper Tkacik and Bialek, William S}, journal = {PNAS}, number = {51}, pages = {18297 -- 18302}, publisher = {National Academy of Sciences}, title = {{Information-based clustering}}, doi = {10.1073/pnas.0507432102}, volume = {102}, year = {2005}, } @unpublished{3746, abstract = {We address the practical problems of estimating the information relations that characterize large networks. Building on methods developed for analysis of the neural code, we show that reliable estimates of mutual information can be obtained with manageable computational effort. The same methods allow estimation of higher order, multi-information terms. These ideas are illustrated by analyses of gene expression, financial markets, and consumer preferences. In each case, information theoretic measures correlate with independent, intuitive measures of the underlying structures in the system.}, author = {Slonim,Noam and Atwal,Gurinder S and Gasper Tkacik and Bialek, William S}, booktitle = {ArXiv}, pages = {1 -- 11}, publisher = {ArXiv}, title = {{Estimating mutual information and multi-information in large networks}}, year = {2005}, } @article{3808, abstract = {Action potentials in central neurons are initiated near the axon initial segment, propagate into the axon, and finally invade the presynaptic terminals, where they trigger transmitter release. Voltage-gated Na(+) channels are key determinants of excitability, but Na(+) channel density and properties in axons and presynaptic terminals of cortical neurons have not been examined yet. In hippocampal mossy fiber boutons, which emerge from parent axons en passant, Na(+) channels are very abundant, with an estimated number of approximately 2000 channels per bouton. Presynaptic Na(+) channels show faster inactivation kinetics than somatic channels, suggesting differences between subcellular compartments of the same cell. Computational analysis of action potential propagation in axon-multibouton structures reveals that Na(+) channels in boutons preferentially amplify the presynaptic action potential and enhance Ca(2+) inflow, whereas Na(+) channels in axons control the reliability and speed of propagation. Thus, presynaptic and axonal Na(+) channels contribute differentially to mossy fiber synaptic transmission.}, author = {Engel, Dominique and Peter Jonas}, journal = {Neuron}, number = {3}, pages = {405 -- 17}, publisher = {Elsevier}, title = {{Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons}}, doi = {10.1016/j.neuron.2004.12.048 }, volume = {45}, year = {2005}, } @inproceedings{3892, abstract = {In 2-player non-zero-sum games, Nash equilibria capture the options for rational behavior if each player attempts to maximize her payoff. In contrast to classical game theory, we consider lexicographic objectives: first, each player tries to maximize her own payoff, and then, the player tries to minimize the opponent's payoff. Such objectives arise naturally in the verification of systems with multiple components. There, instead of proving that each component satisfies its specification no matter how the other components behave, it often suffices to prove that each component satisfies its specification provided that the other components satisfy their specifications. We say that a Nash equilibrium is secure if it is an equilibrium with respect to the lexicographic objectives of both players. We prove that in graph games with Borel winning conditions, which include the games that arise in verification, there may be several Nash equilibria, but there is always a unique maximal payoff profile of a secure equilibrium. We show how this equilibrium can be computed in the case of omega-regular winning conditions, and we characterize the memory requirements of strategies that achieve the equilibrium.}, author = {Krishnendu Chatterjee and Thomas Henzinger and Jurdziński, Marcin}, pages = {141 -- 161}, publisher = {Springer}, title = {{Games with secure equilibria}}, doi = {10.1007/11561163_7}, volume = {3657}, year = {2005}, } @inproceedings{3902, author = {Cremer, Sylvia and Boomsma, Jacobus}, publisher = {Elsevier}, title = {{The drawback of mobility: invasive species in a globalised world}}, year = {2005}, }