--- _id: '3004' abstract: - lang: eng text: 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: - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Olivier full_name: Meurette, Olivier last_name: Meurette - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Göran full_name: Sandberg, Göran last_name: Sandberg - first_name: Paul full_name: Hooykaas, Paul last_name: Hooykaas - first_name: Remko full_name: Offringa, Remko last_name: Offringa citation: ama: Weijers D, Sauer M, Meurette O, et al. Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis. Plant Cell. 2005;17(9):2517-2526. doi:10.1105/tpc.105.034637 apa: Weijers, D., Sauer, M., Meurette, O., Friml, J., Ljung, K., Sandberg, G., … Offringa, R. (2005). Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.105.034637 chicago: Weijers, Dolf, Michael Sauer, Olivier Meurette, Jiří Friml, Karin Ljung, Göran Sandberg, Paul Hooykaas, and Remko Offringa. “Maintenance of Embryonic Auxin Distribution for Apical Basal Patterning by PIN FORMED Dependent Auxin Transport in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2005. https://doi.org/10.1105/tpc.105.034637. ieee: D. Weijers et al., “Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis,” Plant Cell, vol. 17, no. 9. American Society of Plant Biologists, pp. 2517–2526, 2005. ista: Weijers D, Sauer M, Meurette O, Friml J, Ljung K, Sandberg G, Hooykaas P, Offringa R. 2005. Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis. Plant Cell. 17(9), 2517–2526. mla: Weijers, Dolf, et al. “Maintenance of Embryonic Auxin Distribution for Apical Basal Patterning by PIN FORMED Dependent Auxin Transport in Arabidopsis.” Plant Cell, vol. 17, no. 9, American Society of Plant Biologists, 2005, pp. 2517–26, doi:10.1105/tpc.105.034637. short: D. Weijers, M. Sauer, O. Meurette, J. Friml, K. Ljung, G. Sandberg, P. Hooykaas, R. Offringa, Plant Cell 17 (2005) 2517–2526. date_created: 2018-12-11T12:00:48Z date_published: 2005-07-01T00:00:00Z date_updated: 2021-01-12T07:40:24Z day: '01' doi: 10.1105/tpc.105.034637 extern: 1 intvolume: ' 17' issue: '9' month: '07' page: 2517 - 2526 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '3698' quality_controlled: 0 status: public title: Maintenance of embryonic auxin distribution for apical basal patterning by PIN FORMED dependent auxin transport in Arabidopsis type: journal_article volume: 17 year: '2005' ... --- _id: '3000' abstract: - lang: eng text: 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: - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Jürgen full_name: Kleine Vehn, Jürgen last_name: Kleine Vehn - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Dhonukshe P, Kleine Vehn J, Friml J. Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first? Protoplasma. 2005;226(1-2):67-73. doi:10.1007/s00709-005-0104-8' apa: 'Dhonukshe, P., Kleine Vehn, J., & Friml, J. (2005). Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first? Protoplasma. Springer. https://doi.org/10.1007/s00709-005-0104-8' chicago: 'Dhonukshe, Pankaj, Jürgen Kleine Vehn, and Jiří Friml. “Cell Polarity, Auxin Transport and Cytoskeleton Mediated Division Planes: Who Comes First?” Protoplasma. Springer, 2005. https://doi.org/10.1007/s00709-005-0104-8.' ieee: 'P. Dhonukshe, J. Kleine Vehn, and J. Friml, “Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first?,” Protoplasma, vol. 226, no. 1–2. Springer, pp. 67–73, 2005.' ista: 'Dhonukshe P, Kleine Vehn J, Friml J. 2005. Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first? Protoplasma. 226(1–2), 67–73.' mla: 'Dhonukshe, Pankaj, et al. “Cell Polarity, Auxin Transport and Cytoskeleton Mediated Division Planes: Who Comes First?” Protoplasma, vol. 226, no. 1–2, Springer, 2005, pp. 67–73, doi:10.1007/s00709-005-0104-8.' short: P. Dhonukshe, J. Kleine Vehn, J. Friml, Protoplasma 226 (2005) 67–73. date_created: 2018-12-11T12:00:47Z date_published: 2005-10-01T00:00:00Z date_updated: 2021-01-12T07:40:22Z day: '01' doi: 10.1007/s00709-005-0104-8 extern: '1' intvolume: ' 226' issue: 1-2 language: - iso: eng month: '10' oa_version: None page: 67 - 73 publication: Protoplasma publication_status: published publisher: Springer publist_id: '3701' quality_controlled: '1' status: public title: 'Cell polarity, auxin transport and cytoskeleton mediated division planes: Who comes first?' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 226 year: '2005' ... --- _id: '3001' abstract: - lang: eng text: '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: - first_name: Tomasz full_name: Paciorek, Tomasz last_name: Paciorek - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Nadia full_name: Ruthardt, Nadia last_name: Ruthardt - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: York full_name: Stierhof, York-Dieter last_name: Stierhof - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: David full_name: Morris, David A last_name: Morris - first_name: Neil full_name: Emans, Neil last_name: Emans - first_name: Gerd full_name: Jürgens, Gerd last_name: Jürgens - first_name: Niko full_name: Geldner, Niko last_name: Geldner - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Paciorek T, Zažímalová E, Ruthardt N, et al. Auxin inhibits endocytosis and promotes its own efflux from cells. Nature. 2005;435(7046):1251-1256. doi:10.1038/nature03633 apa: Paciorek, T., Zažímalová, E., Ruthardt, N., Petrášek, J., Stierhof, Y., Kleine Vehn, J., … Friml, J. (2005). Auxin inhibits endocytosis and promotes its own efflux from cells. Nature. Nature Publishing Group. https://doi.org/10.1038/nature03633 chicago: Paciorek, Tomasz, Eva Zažímalová, Nadia Ruthardt, Jan Petrášek, York Stierhof, Jürgen Kleine Vehn, David Morris, et al. “Auxin Inhibits Endocytosis and Promotes Its Own Efflux from Cells.” Nature. Nature Publishing Group, 2005. https://doi.org/10.1038/nature03633. ieee: T. Paciorek et al., “Auxin inhibits endocytosis and promotes its own efflux from cells,” Nature, vol. 435, no. 7046. Nature Publishing Group, pp. 1251–1256, 2005. ista: Paciorek T, Zažímalová E, Ruthardt N, Petrášek J, Stierhof Y, Kleine Vehn J, Morris D, Emans N, Jürgens G, Geldner N, Friml J. 2005. Auxin inhibits endocytosis and promotes its own efflux from cells. Nature. 435(7046), 1251–1256. mla: Paciorek, Tomasz, et al. “Auxin Inhibits Endocytosis and Promotes Its Own Efflux from Cells.” Nature, vol. 435, no. 7046, Nature Publishing Group, 2005, pp. 1251–56, doi:10.1038/nature03633. short: T. Paciorek, E. Zažímalová, N. Ruthardt, J. Petrášek, Y. Stierhof, J. Kleine Vehn, D. Morris, N. Emans, G. Jürgens, N. Geldner, J. Friml, Nature 435 (2005) 1251–1256. date_created: 2018-12-11T12:00:47Z date_published: 2005-06-30T00:00:00Z date_updated: 2021-01-12T07:40:23Z day: '30' doi: 10.1038/nature03633 extern: 1 intvolume: ' 435' issue: '7046' month: '06' page: 1251 - 1256 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3702' quality_controlled: 0 status: public title: Auxin inhibits endocytosis and promotes its own efflux from cells type: journal_article volume: 435 year: '2005' ... --- _id: '3003' abstract: - lang: eng text: '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: - first_name: Anne full_name: Vieten, Anne last_name: Vieten - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Justyna full_name: Wiśniewska, Justyna last_name: Wiśniewska - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: René full_name: Benjamins, René last_name: Benjamins - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Christian full_name: Luschnig, Christian last_name: Luschnig - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Vieten A, Vanneste S, Wiśniewska J, et al. Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression. Development. 2005;132(20):4521-4531. doi:10.1242/dev.02027 apa: Vieten, A., Vanneste, S., Wiśniewska, J., Benková, E., Benjamins, R., Beeckman, T., … Friml, J. (2005). Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression. Development. Company of Biologists. https://doi.org/10.1242/dev.02027 chicago: Vieten, Anne, Steffen Vanneste, Justyna Wiśniewska, Eva Benková, René Benjamins, Tom Beeckman, Christian Luschnig, and Jiří Friml. “Functional Redundancy of PIN Proteins Is Accompanied by Auxin-Dependent Cross-Regulation of PIN Expression.” Development. Company of Biologists, 2005. https://doi.org/10.1242/dev.02027. ieee: A. Vieten et al., “Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression,” Development, vol. 132, no. 20. Company of Biologists, pp. 4521–4531, 2005. ista: Vieten A, Vanneste S, Wiśniewska J, Benková E, Benjamins R, Beeckman T, Luschnig C, Friml J. 2005. Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression. Development. 132(20), 4521–4531. mla: Vieten, Anne, et al. “Functional Redundancy of PIN Proteins Is Accompanied by Auxin-Dependent Cross-Regulation of PIN Expression.” Development, vol. 132, no. 20, Company of Biologists, 2005, pp. 4521–31, doi:10.1242/dev.02027. short: A. Vieten, S. Vanneste, J. Wiśniewska, E. Benková, R. Benjamins, T. Beeckman, C. Luschnig, J. Friml, Development 132 (2005) 4521–4531. date_created: 2018-12-11T12:00:48Z date_published: 2005-10-01T00:00:00Z date_updated: 2021-01-12T07:40:23Z day: '01' doi: 10.1242/dev.02027 extern: 1 intvolume: ' 132' issue: '20' month: '10' page: 4521 - 4531 publication: Development publication_status: published publisher: Company of Biologists publist_id: '3700' quality_controlled: 0 status: public title: Functional redundancy of PIN proteins is accompanied by auxin-dependent cross-regulation of PIN expression type: journal_article volume: 132 year: '2005' ... --- _id: '3212' abstract: - lang: eng text: |- 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. acknowledgement: Supported by NSF CAREER Award CCR-0133806 and TC Grant No.CCR-0311095. Supported by the Swiss National Science Foundation, project No. 200020-103847/1 alternative_title: - LNCS author: - first_name: Yevgeniy full_name: Dodis, Yevgeniy last_name: Dodis - first_name: Roberto full_name: Oliveira, Roberto last_name: Oliveira - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Dodis Y, Oliveira R, Pietrzak KZ. On the generic insecurity of the full domain hash. In: Vol 3621. Springer; 2005:449-466. doi:10.1007/11535218_27' apa: 'Dodis, Y., Oliveira, R., & Pietrzak, K. Z. (2005). On the generic insecurity of the full domain hash (Vol. 3621, pp. 449–466). Presented at the CRYPTO: International Cryptology Conference, Springer. https://doi.org/10.1007/11535218_27' chicago: Dodis, Yevgeniy, Roberto Oliveira, and Krzysztof Z Pietrzak. “On the Generic Insecurity of the Full Domain Hash,” 3621:449–66. Springer, 2005. https://doi.org/10.1007/11535218_27. ieee: 'Y. Dodis, R. Oliveira, and K. Z. Pietrzak, “On the generic insecurity of the full domain hash,” presented at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 449–466.' ista: 'Dodis Y, Oliveira R, Pietrzak KZ. 2005. On the generic insecurity of the full domain hash. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 449–466.' mla: Dodis, Yevgeniy, et al. On the Generic Insecurity of the Full Domain Hash. Vol. 3621, Springer, 2005, pp. 449–66, doi:10.1007/11535218_27. short: Y. Dodis, R. Oliveira, K.Z. Pietrzak, in:, Springer, 2005, pp. 449–466. conference: name: 'CRYPTO: International Cryptology Conference' date_created: 2018-12-11T12:02:03Z date_published: 2005-09-12T00:00:00Z date_updated: 2021-01-12T07:41:50Z day: '12' doi: 10.1007/11535218_27 extern: 1 intvolume: ' 3621' month: '09' page: 449 - 466 publication_status: published publisher: Springer publist_id: '3470' quality_controlled: 0 status: public title: On the generic insecurity of the full domain hash type: conference volume: 3621 year: '2005' ... --- _id: '3213' abstract: - lang: eng text: |- 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. acknowledgement: Supported by the Swiss National Science Foundation, project No. 200020-103847/1. alternative_title: - LNCS author: - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Pietrzak KZ. Composition does not imply adaptive security. In: Vol 3621. Springer; 2005:55-65. doi:10.1007/11535218_4' apa: 'Pietrzak, K. Z. (2005). Composition does not imply adaptive security (Vol. 3621, pp. 55–65). Presented at the CRYPTO: International Cryptology Conference, Springer. https://doi.org/10.1007/11535218_4' chicago: Pietrzak, Krzysztof Z. “Composition Does Not Imply Adaptive Security,” 3621:55–65. Springer, 2005. https://doi.org/10.1007/11535218_4. ieee: 'K. Z. Pietrzak, “Composition does not imply adaptive security,” presented at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 55–65.' ista: 'Pietrzak KZ. 2005. Composition does not imply adaptive security. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 55–65.' mla: Pietrzak, Krzysztof Z. Composition Does Not Imply Adaptive Security. Vol. 3621, Springer, 2005, pp. 55–65, doi:10.1007/11535218_4. short: K.Z. Pietrzak, in:, Springer, 2005, pp. 55–65. conference: name: 'CRYPTO: International Cryptology Conference' date_created: 2018-12-11T12:02:03Z date_published: 2005-09-12T00:00:00Z date_updated: 2021-01-12T07:41:50Z day: '12' doi: 10.1007/11535218_4 extern: 1 intvolume: ' 3621' month: '09' page: 55 - 65 publication_status: published publisher: Springer publist_id: '3468' quality_controlled: 0 status: public title: Composition does not imply adaptive security type: conference volume: 3621 year: '2005' ... --- _id: '3211' abstract: - lang: eng text: 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. acknowledgement: Pietrzak was supported by the Swiss National Science Foundation, project No. 200020-103847/1. alternative_title: - LNCS author: - first_name: Mihir full_name: Bellare, Mihir last_name: Bellare - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Phillip full_name: Rogaway, Phillip last_name: Rogaway citation: ama: 'Bellare M, Pietrzak KZ, Rogaway P. Improved security analyses for CBC MACs. In: Vol 3621. Springer; 2005:527-545. doi:10.1007/11535218_32' apa: 'Bellare, M., Pietrzak, K. Z., & Rogaway, P. (2005). Improved security analyses for CBC MACs (Vol. 3621, pp. 527–545). Presented at the CRYPTO: International Cryptology Conference, Springer. https://doi.org/10.1007/11535218_32' chicago: Bellare, Mihir, Krzysztof Z Pietrzak, and Phillip Rogaway. “Improved Security Analyses for CBC MACs,” 3621:527–45. Springer, 2005. https://doi.org/10.1007/11535218_32. ieee: 'M. Bellare, K. Z. Pietrzak, and P. Rogaway, “Improved security analyses for CBC MACs,” presented at the CRYPTO: International Cryptology Conference, 2005, vol. 3621, pp. 527–545.' ista: 'Bellare M, Pietrzak KZ, Rogaway P. 2005. Improved security analyses for CBC MACs. CRYPTO: International Cryptology Conference, LNCS, vol. 3621, 527–545.' mla: Bellare, Mihir, et al. Improved Security Analyses for CBC MACs. Vol. 3621, Springer, 2005, pp. 527–45, doi:10.1007/11535218_32. short: M. Bellare, K.Z. Pietrzak, P. Rogaway, in:, Springer, 2005, pp. 527–545. conference: name: 'CRYPTO: International Cryptology Conference' date_created: 2018-12-11T12:02:02Z date_published: 2005-09-12T00:00:00Z date_updated: 2021-01-12T07:41:50Z day: '12' doi: 10.1007/11535218_32 extern: 1 intvolume: ' 3621' month: '09' page: 527 - 545 publication_status: published publisher: Springer publist_id: '3469' quality_controlled: 0 status: public title: Improved security analyses for CBC MACs type: conference volume: 3621 year: '2005' ... --- _id: '3426' abstract: - lang: eng text: 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. article_processing_charge: No author: - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Karsten full_name: Kruse, Karsten last_name: Kruse - first_name: Periklis full_name: Pantazis, Periklis last_name: Pantazis - first_name: Marcos full_name: González Gaitán, Marcos last_name: González Gaitán - first_name: Frank full_name: Jülicher, Frank last_name: Jülicher citation: ama: Bollenbach MT, Kruse K, Pantazis P, González Gaitán M, Jülicher F. Robust formation of morphogen gradients. Physical Review Letters. 2005;94(1). doi:10.1103/PhysRevLett.94.018103 apa: Bollenbach, M. T., Kruse, K., Pantazis, P., González Gaitán, M., & Jülicher, F. (2005). Robust formation of morphogen gradients. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.94.018103 chicago: Bollenbach, Mark Tobias, Karsten Kruse, Periklis Pantazis, Marcos González Gaitán, and Frank Jülicher. “Robust Formation of Morphogen Gradients.” Physical Review Letters. American Physical Society, 2005. https://doi.org/10.1103/PhysRevLett.94.018103. ieee: M. T. Bollenbach, K. Kruse, P. Pantazis, M. González Gaitán, and F. Jülicher, “Robust formation of morphogen gradients,” Physical Review Letters, vol. 94, no. 1. American Physical Society, 2005. ista: Bollenbach MT, Kruse K, Pantazis P, González Gaitán M, Jülicher F. 2005. Robust formation of morphogen gradients. Physical Review Letters. 94(1). mla: Bollenbach, Mark Tobias, et al. “Robust Formation of Morphogen Gradients.” Physical Review Letters, vol. 94, no. 1, American Physical Society, 2005, doi:10.1103/PhysRevLett.94.018103. short: M.T. Bollenbach, K. Kruse, P. Pantazis, M. González Gaitán, F. Jülicher, Physical Review Letters 94 (2005). date_created: 2018-12-11T12:03:16Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:43:23Z day: '01' doi: 10.1103/PhysRevLett.94.018103 extern: '1' external_id: arxiv: - q-bio/0412014 intvolume: ' 94' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/q-bio/0412014 month: '01' oa: 1 oa_version: Preprint publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '2975' status: public title: Robust formation of morphogen gradients type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 94 year: '2005' ... --- _id: '3443' abstract: - lang: eng text: 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: - first_name: Thomas full_name: Klausberger,Thomas last_name: Klausberger - first_name: Laszlo full_name: Marton,Laszlo F last_name: Marton - first_name: Joseph full_name: Joseph O'Neill id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Jojanneke full_name: Huck, Jojanneke H last_name: Huck - first_name: Yannis full_name: Dalezios, Yannis last_name: Dalezios - first_name: Pablo full_name: Fuentealba,Pablo last_name: Fuentealba - first_name: Wai full_name: Suen, Wai Yee last_name: Suen - first_name: Edit full_name: Papp, Edit Cs last_name: Papp - first_name: Takeshi full_name: Kaneko, Takeshi last_name: Kaneko - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Péter full_name: Somogyi, Péter last_name: Somogyi citation: ama: Klausberger T, Marton L, O’Neill J, et al. Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations. Journal of Neuroscience. 2005;25(42):9782-9793. doi:10.1523/JNEUROSCI.3269-05.2005 apa: Klausberger, T., Marton, L., O’Neill, J., Huck, J., Dalezios, Y., Fuentealba, P., … Somogyi, P. (2005). Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.3269-05.2005 chicago: Klausberger, Thomas, Laszlo Marton, Joseph O’Neill, Jojanneke Huck, Yannis Dalezios, Pablo Fuentealba, Wai Suen, et al. “Complementary Roles of Cholecystokinin- and Parvalbumin-Expressing GABAergic Neurons in Hippocampal Network Oscillations.” Journal of Neuroscience. Society for Neuroscience, 2005. https://doi.org/10.1523/JNEUROSCI.3269-05.2005. ieee: T. Klausberger et al., “Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations,” Journal of Neuroscience, vol. 25, no. 42. Society for Neuroscience, pp. 9782–9793, 2005. ista: Klausberger T, Marton L, O’Neill J, Huck J, Dalezios Y, Fuentealba P, Suen W, Papp E, Kaneko T, Watanabe M, Csicsvari JL, Somogyi P. 2005. Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations. Journal of Neuroscience. 25(42), 9782–9793. mla: Klausberger, Thomas, et al. “Complementary Roles of Cholecystokinin- and Parvalbumin-Expressing GABAergic Neurons in Hippocampal Network Oscillations.” Journal of Neuroscience, vol. 25, no. 42, Society for Neuroscience, 2005, pp. 9782–93, doi:10.1523/JNEUROSCI.3269-05.2005. short: T. Klausberger, L. Marton, J. O’Neill, J. Huck, Y. Dalezios, P. Fuentealba, W. Suen, E. Papp, T. Kaneko, M. Watanabe, J.L. Csicsvari, P. Somogyi, Journal of Neuroscience 25 (2005) 9782–9793. date_created: 2018-12-11T12:03:21Z date_published: 2005-10-19T00:00:00Z date_updated: 2021-01-12T07:43:30Z day: '19' doi: 10.1523/JNEUROSCI.3269-05.2005 extern: 1 intvolume: ' 25' issue: '42' month: '10' page: 9782 - 9793 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '2944' quality_controlled: 0 status: public title: Complementary roles of cholecystokinin- and parvalbumin-expressing GABAergic neurons in hippocampal network oscillations type: journal_article volume: 25 year: '2005' ... --- _id: '3557' abstract: - lang: eng text: 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: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Edelsbrunner H. Surface tiling with differential topology. In: ACM; 2005:9-11. doi:http://dx.doi.org/10.2312/SGP/SGP05/009-011' apa: 'Edelsbrunner, H. (2005). Surface tiling with differential topology (pp. 9–11). Presented at the SGP: Eurographics Symposium on Geometry processing, ACM. http://dx.doi.org/10.2312/SGP/SGP05/009-011' chicago: Edelsbrunner, Herbert. “Surface Tiling with Differential Topology,” 9–11. ACM, 2005. http://dx.doi.org/10.2312/SGP/SGP05/009-011. ieee: 'H. Edelsbrunner, “Surface tiling with differential topology,” presented at the SGP: Eurographics Symposium on Geometry processing, 2005, pp. 9–11.' ista: 'Edelsbrunner H. 2005. Surface tiling with differential topology. SGP: Eurographics Symposium on Geometry processing, 9–11.' mla: Edelsbrunner, Herbert. Surface Tiling with Differential Topology. ACM, 2005, pp. 9–11, doi:http://dx.doi.org/10.2312/SGP/SGP05/009-011. short: H. Edelsbrunner, in:, ACM, 2005, pp. 9–11. conference: name: 'SGP: Eurographics Symposium on Geometry processing' date_created: 2018-12-11T12:03:57Z date_published: 2005-07-01T00:00:00Z date_updated: 2021-01-12T07:44:17Z day: '01' doi: http://dx.doi.org/10.2312/SGP/SGP05/009-011 extern: 1 main_file_link: - open_access: '0' url: http://www.cs.duke.edu/~edels/Papers/2005-P-03-SurfaceTiling.pdf month: '07' page: 9 - 11 publication_status: published publisher: ACM publist_id: '2828' quality_controlled: 0 status: public title: Surface tiling with differential topology type: conference year: '2005' ... --- _id: '3589' abstract: - lang: eng text: 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. article_processing_charge: No author: - first_name: Mathias full_name: Köppen, Mathias last_name: Köppen - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Köppen M, Heisenberg C-PJ. Cleavage and gastrulation in zebrafish embryos. In: Encyclopedia of Life Sciences. Wiley-Blackwell; 2005. doi:10.1038/npg.els.0001072' apa: Köppen, M., & Heisenberg, C.-P. J. (2005). Cleavage and gastrulation in zebrafish embryos. In Encyclopedia of Life Sciences. Wiley-Blackwell. https://doi.org/10.1038/npg.els.0001072 chicago: Köppen, Mathias, and Carl-Philipp J Heisenberg. “Cleavage and Gastrulation in Zebrafish Embryos.” In Encyclopedia of Life Sciences. Wiley-Blackwell, 2005. https://doi.org/10.1038/npg.els.0001072. ieee: M. Köppen and C.-P. J. Heisenberg, “Cleavage and gastrulation in zebrafish embryos,” in Encyclopedia of Life Sciences, Wiley-Blackwell, 2005. ista: 'Köppen M, Heisenberg C-PJ. 2005.Cleavage and gastrulation in zebrafish embryos. In: Encyclopedia of Life Sciences. .' mla: Köppen, Mathias, and Carl-Philipp J. Heisenberg. “Cleavage and Gastrulation in Zebrafish Embryos.” Encyclopedia of Life Sciences, Wiley-Blackwell, 2005, doi:10.1038/npg.els.0001072. short: M. Köppen, C.-P.J. Heisenberg, in:, Encyclopedia of Life Sciences, Wiley-Blackwell, 2005. date_created: 2018-12-11T12:04:07Z date_published: 2005-09-23T00:00:00Z date_updated: 2021-01-12T07:44:30Z day: '23' doi: 10.1038/npg.els.0001072 extern: '1' language: - iso: eng month: '09' oa_version: None publication: Encyclopedia of Life Sciences publication_status: published publisher: Wiley-Blackwell publist_id: '2794' status: public title: Cleavage and gastrulation in zebrafish embryos type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2005' ... --- _id: '3588' article_processing_charge: No author: - first_name: Irinka full_name: Castanon Ortega, Irinka last_name: Castanon Ortega - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: 'Castanon Ortega I, Heisenberg C-PJ. Cell migration during zebrafish gastrulation. In: Wedlich D, ed. Cell Migration in Development and Disease. Wiley-VCH; 2005:71-105. doi:10.1002/3527604669' apa: Castanon Ortega, I., & Heisenberg, C.-P. J. (2005). Cell migration during zebrafish gastrulation. In D. Wedlich (Ed.), Cell Migration in Development and Disease (pp. 71–105). Wiley-VCH. https://doi.org/10.1002/3527604669 chicago: Castanon Ortega, Irinka, and Carl-Philipp J Heisenberg. “Cell Migration during Zebrafish Gastrulation.” In Cell Migration in Development and Disease, edited by Doris Wedlich, 71–105. Wiley-VCH, 2005. https://doi.org/10.1002/3527604669. ieee: I. Castanon Ortega and C.-P. J. Heisenberg, “Cell migration during zebrafish gastrulation,” in Cell Migration in Development and Disease, D. Wedlich, Ed. Wiley-VCH, 2005, pp. 71–105. ista: 'Castanon Ortega I, Heisenberg C-PJ. 2005.Cell migration during zebrafish gastrulation. In: Cell Migration in Development and Disease. , 71–105.' mla: Castanon Ortega, Irinka, and Carl-Philipp J. Heisenberg. “Cell Migration during Zebrafish Gastrulation.” Cell Migration in Development and Disease, edited by Doris Wedlich, Wiley-VCH, 2005, pp. 71–105, doi:10.1002/3527604669. short: I. Castanon Ortega, C.-P.J. Heisenberg, in:, D. Wedlich (Ed.), Cell Migration in Development and Disease, Wiley-VCH, 2005, pp. 71–105. date_created: 2018-12-11T12:04:07Z date_published: 2005-03-14T00:00:00Z date_updated: 2021-01-12T07:44:29Z day: '14' doi: 10.1002/3527604669 editor: - first_name: Doris full_name: Wedlich, Doris last_name: Wedlich extern: '1' language: - iso: eng month: '03' oa_version: None page: 71 - 105 publication: Cell Migration in Development and Disease publication_status: published publisher: Wiley-VCH publist_id: '2795' status: public title: Cell migration during zebrafish gastrulation type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2005' ... --- _id: '3590' acknowledgement: 'BOOK REVIEWED - Gastrulation: From Cells to Embryo, Edited by Claudio Stern. Published by Cold Spring Harbor Laboratory Press: 2004. ' article_processing_charge: No author: - first_name: Irinka full_name: Castanon Ortega, Irinka last_name: Castanon Ortega - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Castanon Ortega I, Heisenberg C-PJ. A stern view of gastrulation. Nature Cell Biology. 2005;7(1):19-19. doi:10.1038/ncb0105-19 apa: Castanon Ortega, I., & Heisenberg, C.-P. J. (2005). A stern view of gastrulation. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb0105-19 chicago: Castanon Ortega, Irinka, and Carl-Philipp J Heisenberg. “A Stern View of Gastrulation.” Nature Cell Biology. Nature Publishing Group, 2005. https://doi.org/10.1038/ncb0105-19. ieee: I. Castanon Ortega and C.-P. J. Heisenberg, “A stern view of gastrulation,” Nature Cell Biology, vol. 7, no. 1. Nature Publishing Group, pp. 19–19, 2005. ista: Castanon Ortega I, Heisenberg C-PJ. 2005. A stern view of gastrulation. Nature Cell Biology. 7(1), 19–19. mla: Castanon Ortega, Irinka, and Carl-Philipp J. Heisenberg. “A Stern View of Gastrulation.” Nature Cell Biology, vol. 7, no. 1, Nature Publishing Group, 2005, pp. 19–19, doi:10.1038/ncb0105-19. short: I. Castanon Ortega, C.-P.J. Heisenberg, Nature Cell Biology 7 (2005) 19–19. date_created: 2018-12-11T12:04:07Z date_published: 2005-01-01T00:00:00Z date_updated: 2020-10-07T06:26:47Z day: '01' doi: 10.1038/ncb0105-19 extern: '1' intvolume: ' 7' issue: '1' language: - iso: eng month: '01' oa_version: None page: 19 - 19 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '2793' status: public title: A stern view of gastrulation type: review user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2005' ... --- _id: '3689' abstract: - lang: eng text: 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. alternative_title: - Document Analysis and Recognition author: - first_name: Adrian full_name: Ulges, Adrian last_name: Ulges - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Thomas full_name: Breuel,Thomas M last_name: Breuel citation: ama: 'Ulges A, Lampert C, Breuel T. Document image dewarping using robust estimation of curled text lines. In: Vol 2. IEEE; 2005:1001-1005. doi: 10.1109/ICDAR.2005.90' apa: 'Ulges, A., Lampert, C., & Breuel, T. (2005). Document image dewarping using robust estimation of curled text lines (Vol. 2, pp. 1001–1005). Presented at the ICDAR: International Conference on Document Analysis and Recognition, IEEE. https://doi.org/ 10.1109/ICDAR.2005.90' chicago: Ulges, Adrian, Christoph Lampert, and Thomas Breuel. “Document Image Dewarping Using Robust Estimation of Curled Text Lines,” 2:1001–5. IEEE, 2005. https://doi.org/ 10.1109/ICDAR.2005.90. ieee: 'A. Ulges, C. Lampert, and T. Breuel, “Document image dewarping using robust estimation of curled text lines,” presented at the ICDAR: International Conference on Document Analysis and Recognition, 2005, vol. 2, pp. 1001–1005.' ista: 'Ulges A, Lampert C, Breuel T. 2005. Document image dewarping using robust estimation of curled text lines. ICDAR: International Conference on Document Analysis and Recognition, Document Analysis and Recognition, vol. 2, 1001–1005.' mla: Ulges, Adrian, et al. Document Image Dewarping Using Robust Estimation of Curled Text Lines. Vol. 2, IEEE, 2005, pp. 1001–05, doi: 10.1109/ICDAR.2005.90. short: A. Ulges, C. Lampert, T. Breuel, in:, IEEE, 2005, pp. 1001–1005. conference: name: 'ICDAR: International Conference on Document Analysis and Recognition' date_created: 2018-12-11T12:04:38Z date_published: 2005-09-01T00:00:00Z date_updated: 2021-01-12T07:48:58Z day: '01' doi: ' 10.1109/ICDAR.2005.90' extern: 1 intvolume: ' 2' main_file_link: - open_access: '0' url: http:/pub.ist.ac.at/~chl/papers/ulges-icdar2004.pdf month: '09' page: 1001 - 1005 publication_status: published publisher: IEEE publist_id: '2680' quality_controlled: 0 status: public title: Document image dewarping using robust estimation of curled text lines type: conference volume: 2 year: '2005' ... --- _id: '3684' abstract: - lang: eng text: |- 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: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Tim full_name: Braun,Tim last_name: Braun - first_name: Adrian full_name: Ulges, Adrian last_name: Ulges - first_name: Daniel full_name: Keysers,Daniel last_name: Keysers - first_name: Thomas full_name: Breuel,Thomas M last_name: Breuel citation: ama: 'Lampert C, Braun T, Ulges A, Keysers D, Breuel T. Oblivious document capture and real-time retrieval. In: CBDAR; 2005:79-86.' apa: 'Lampert, C., Braun, T., Ulges, A., Keysers, D., & Breuel, T. (2005). Oblivious document capture and real-time retrieval (pp. 79–86). Presented at the CBDAR: Camera Based Document Analysis and Recognition , CBDAR.' chicago: Lampert, Christoph, Tim Braun, Adrian Ulges, Daniel Keysers, and Thomas Breuel. “Oblivious Document Capture and Real-Time Retrieval,” 79–86. CBDAR, 2005. ieee: 'C. Lampert, T. Braun, A. Ulges, D. Keysers, and T. Breuel, “Oblivious document capture and real-time retrieval,” presented at the CBDAR: Camera Based Document Analysis and Recognition , 2005, pp. 79–86.' ista: 'Lampert C, Braun T, Ulges A, Keysers D, Breuel T. 2005. Oblivious document capture and real-time retrieval. CBDAR: Camera Based Document Analysis and Recognition , 79–86.' mla: Lampert, Christoph, et al. Oblivious Document Capture and Real-Time Retrieval. CBDAR, 2005, pp. 79–86. short: C. Lampert, T. Braun, A. Ulges, D. Keysers, T. Breuel, in:, CBDAR, 2005, pp. 79–86. conference: name: 'CBDAR: Camera Based Document Analysis and Recognition ' date_created: 2018-12-11T12:04:36Z date_published: 2005-08-29T00:00:00Z date_updated: 2021-01-12T07:45:07Z day: '29' extern: 1 main_file_link: - open_access: '0' url: http://pub.ist.ac.at/~chl/papers/lampert-cbdar2005.pdf month: '08' page: 79 - 86 publication_status: published publisher: CBDAR publist_id: '2693' quality_controlled: 0 status: public title: Oblivious document capture and real-time retrieval type: conference year: '2005' ... --- _id: '3720' article_processing_charge: No author: - first_name: José full_name: Guzmán, José id: 30CC5506-F248-11E8-B48F-1D18A9856A87 last_name: Guzmán - first_name: Zoltan full_name: Gerevich, Zoltan last_name: Gerevich - first_name: Jan full_name: Hengstler, Jan last_name: Hengstler - first_name: Peter full_name: Illes, Peter last_name: Illes - first_name: Werner full_name: Kleemann, Werner last_name: Kleemann citation: ama: Guzmán J, Gerevich Z, Hengstler J, Illes P, Kleemann W. P2Y1 receptors inhibit both strength and plasticity of glutamatergic synaptic neurotransmission in the rat prefrontal cortex. Synapse. 2005;57(4):235-238. doi:10.1002/syn.20177 apa: Guzmán, J., Gerevich, Z., Hengstler, J., Illes, P., & Kleemann, W. (2005). P2Y1 receptors inhibit both strength and plasticity of glutamatergic synaptic neurotransmission in the rat prefrontal cortex. Synapse. Wiley. https://doi.org/10.1002/syn.20177 chicago: Guzmán, José, Zoltan Gerevich, Jan Hengstler, Peter Illes, and Werner Kleemann. “P2Y1 Receptors Inhibit Both Strength and Plasticity of Glutamatergic Synaptic Neurotransmission in the Rat Prefrontal Cortex.” Synapse. Wiley, 2005. https://doi.org/10.1002/syn.20177. ieee: J. Guzmán, Z. Gerevich, J. Hengstler, P. Illes, and W. Kleemann, “P2Y1 receptors inhibit both strength and plasticity of glutamatergic synaptic neurotransmission in the rat prefrontal cortex.,” Synapse, vol. 57, no. 4. Wiley, pp. 235–238, 2005. ista: Guzmán J, Gerevich Z, Hengstler J, Illes P, Kleemann W. 2005. P2Y1 receptors inhibit both strength and plasticity of glutamatergic synaptic neurotransmission in the rat prefrontal cortex. Synapse. 57(4), 235–238. mla: Guzmán, José, et al. “P2Y1 Receptors Inhibit Both Strength and Plasticity of Glutamatergic Synaptic Neurotransmission in the Rat Prefrontal Cortex.” Synapse, vol. 57, no. 4, Wiley, 2005, pp. 235–38, doi:10.1002/syn.20177. short: J. Guzmán, Z. Gerevich, J. Hengstler, P. Illes, W. Kleemann, Synapse 57 (2005) 235–238. date_created: 2018-12-11T12:04:48Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:51:43Z day: '01' doi: 10.1002/syn.20177 extern: '1' intvolume: ' 57' issue: '4' language: - iso: eng month: '01' oa_version: None page: 235 - 238 publication: Synapse publication_status: published publisher: Wiley publist_id: '2510' status: public title: P2Y1 receptors inhibit both strength and plasticity of glutamatergic synaptic neurotransmission in the rat prefrontal cortex. type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2005' ... --- _id: '3753' abstract: - lang: eng text: 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. acknowledgement: '4237' author: - first_name: Thuc full_name: Le,Thuc T. last_name: Le - first_name: Sébastien full_name: Harlepp, Sébastien last_name: Harlepp - first_name: Calin C full_name: Calin Guet id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Kimberly full_name: Dittmar,Kimberly last_name: Dittmar - first_name: Thierry full_name: Emonet,Thierry last_name: Emonet - first_name: Tao full_name: Pan,Tao last_name: Pan - first_name: Philippe full_name: Cluzel,Philippe last_name: Cluzel citation: ama: Le T, Harlepp S, Guet CC, et al. Real-time RNA profiling within a single bacterium. PNAS. 2005;102(26):9160-9164. doi:10.1073/pnas.0503311102 apa: Le, T., Harlepp, S., Guet, C. C., Dittmar, K., Emonet, T., Pan, T., & Cluzel, P. (2005). Real-time RNA profiling within a single bacterium. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0503311102 chicago: Le, Thuc, Sébastien Harlepp, Calin C Guet, Kimberly Dittmar, Thierry Emonet, Tao Pan, and Philippe Cluzel. “Real-Time RNA Profiling within a Single Bacterium.” PNAS. National Academy of Sciences, 2005. https://doi.org/10.1073/pnas.0503311102. ieee: T. Le et al., “Real-time RNA profiling within a single bacterium,” PNAS, vol. 102, no. 26. National Academy of Sciences, pp. 9160–9164, 2005. ista: Le T, Harlepp S, Guet CC, Dittmar K, Emonet T, Pan T, Cluzel P. 2005. Real-time RNA profiling within a single bacterium. PNAS. 102(26), 9160–9164. mla: Le, Thuc, et al. “Real-Time RNA Profiling within a Single Bacterium.” PNAS, vol. 102, no. 26, National Academy of Sciences, 2005, pp. 9160–64, doi:10.1073/pnas.0503311102. short: T. Le, S. Harlepp, C.C. Guet, K. Dittmar, T. Emonet, T. Pan, P. Cluzel, PNAS 102 (2005) 9160–9164. date_created: 2018-12-11T12:04:59Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:51:57Z day: '01' doi: 10.1073/pnas.0503311102 extern: 1 intvolume: ' 102' issue: '26' month: '01' page: 9160 - 9164 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '2476' quality_controlled: 0 status: public title: Real-time RNA profiling within a single bacterium type: journal_article volume: 102 year: '2005' ... --- _id: '3763' abstract: - lang: eng text: 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. article_processing_charge: No author: - first_name: Lin full_name: Shi, Lin last_name: Shi - first_name: Yizhou full_name: Yu, Yizhou last_name: Yu - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Stephen full_name: Chenney, Stephen last_name: Chenney citation: ama: Shi L, Yu Y, Wojtan C, Chenney S. Controllable motion synthesis in a gaseous medium. The Visual Computer. 2005;21(7):474-487. doi:10.1007/s00371-005-0296-0 apa: Shi, L., Yu, Y., Wojtan, C., & Chenney, S. (2005). Controllable motion synthesis in a gaseous medium. The Visual Computer. Springer. https://doi.org/10.1007/s00371-005-0296-0 chicago: Shi, Lin, Yizhou Yu, Chris Wojtan, and Stephen Chenney. “Controllable Motion Synthesis in a Gaseous Medium.” The Visual Computer. Springer, 2005. https://doi.org/10.1007/s00371-005-0296-0. ieee: L. Shi, Y. Yu, C. Wojtan, and S. Chenney, “Controllable motion synthesis in a gaseous medium,” The Visual Computer, vol. 21, no. 7. Springer, pp. 474–487, 2005. ista: Shi L, Yu Y, Wojtan C, Chenney S. 2005. Controllable motion synthesis in a gaseous medium. The Visual Computer. 21(7), 474–487. mla: Shi, Lin, et al. “Controllable Motion Synthesis in a Gaseous Medium.” The Visual Computer, vol. 21, no. 7, Springer, 2005, pp. 474–87, doi:10.1007/s00371-005-0296-0. short: L. Shi, Y. Yu, C. Wojtan, S. Chenney, The Visual Computer 21 (2005) 474–487. date_created: 2018-12-11T12:05:02Z date_published: 2005-08-01T00:00:00Z date_updated: 2023-02-23T11:41:36Z day: '01' doi: 10.1007/s00371-005-0296-0 extern: '1' intvolume: ' 21' issue: '7' language: - iso: eng month: '08' oa_version: None page: 474 - 487 publication: The Visual Computer publication_status: published publisher: Springer publist_id: '2465' status: public title: Controllable motion synthesis in a gaseous medium type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 21 year: '2005' ... --- _id: '3812' abstract: - lang: eng text: 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: - first_name: Stefan full_name: Hefft, Stefan last_name: Hefft - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Hefft S, Jonas PM. Asynchronous GABA release generates long-lasting inhibition at a hippocampal interneuron-principal neuron synapse (Review). Nature Neuroscience. 2005;8(10):1319-1328. doi:10.1038/nn1542 apa: Hefft, S., & Jonas, P. M. (2005). Asynchronous GABA release generates long-lasting inhibition at a hippocampal interneuron-principal neuron synapse (Review). Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn1542 chicago: Hefft, Stefan, and Peter M Jonas. “Asynchronous GABA Release Generates Long-Lasting Inhibition at a Hippocampal Interneuron-Principal Neuron Synapse (Review).” Nature Neuroscience. Nature Publishing Group, 2005. https://doi.org/10.1038/nn1542. ieee: S. Hefft and P. M. Jonas, “Asynchronous GABA release generates long-lasting inhibition at a hippocampal interneuron-principal neuron synapse (Review),” Nature Neuroscience, vol. 8, no. 10. Nature Publishing Group, pp. 1319–28, 2005. ista: Hefft S, Jonas PM. 2005. Asynchronous GABA release generates long-lasting inhibition at a hippocampal interneuron-principal neuron synapse (Review). Nature Neuroscience. 8(10), 1319–28. mla: Hefft, Stefan, and Peter M. Jonas. “Asynchronous GABA Release Generates Long-Lasting Inhibition at a Hippocampal Interneuron-Principal Neuron Synapse (Review).” Nature Neuroscience, vol. 8, no. 10, Nature Publishing Group, 2005, pp. 1319–28, doi:10.1038/nn1542. short: S. Hefft, P.M. Jonas, Nature Neuroscience 8 (2005) 1319–28. date_created: 2018-12-11T12:05:18Z date_published: 2005-01-01T00:00:00Z date_updated: 2019-04-26T07:22:35Z day: '01' doi: 10.1038/nn1542 extern: 1 intvolume: ' 8' issue: '10' month: '01' page: 1319 - 28 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '2399' quality_controlled: 0 status: public title: Asynchronous GABA release generates long-lasting inhibition at a hippocampal interneuron-principal neuron synapse (Review) type: review volume: 8 year: '2005' ... --- _id: '3896' abstract: - lang: eng text: 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. acknowledgement: Pallab Dasgupta and P.P.Chakrabarti thank the Dept. of Science & Tech., Govt. of India, for partial support of this work alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Pallab full_name: Dasgupta, Pallab last_name: Dasgupta - first_name: Partha full_name: Chakrabarti, Partha P last_name: Chakrabarti citation: ama: 'Chatterjee K, Dasgupta P, Chakrabarti P. Complexity of compositional model checking of computation tree logic on simple structures. In: Vol 3326. Springer; 2005:89-102. doi:10.1007/978-3-540-30536-1_13' apa: 'Chatterjee, K., Dasgupta, P., & Chakrabarti, P. (2005). Complexity of compositional model checking of computation tree logic on simple structures (Vol. 3326, pp. 89–102). Presented at the IWDC: International Workshop on Distributed Computing , Springer. https://doi.org/10.1007/978-3-540-30536-1_13' chicago: Chatterjee, Krishnendu, Pallab Dasgupta, and Partha Chakrabarti. “Complexity of Compositional Model Checking of Computation Tree Logic on Simple Structures,” 3326:89–102. Springer, 2005. https://doi.org/10.1007/978-3-540-30536-1_13. ieee: 'K. Chatterjee, P. Dasgupta, and P. Chakrabarti, “Complexity of compositional model checking of computation tree logic on simple structures,” presented at the IWDC: International Workshop on Distributed Computing , 2005, vol. 3326, pp. 89–102.' ista: 'Chatterjee K, Dasgupta P, Chakrabarti P. 2005. Complexity of compositional model checking of computation tree logic on simple structures. IWDC: International Workshop on Distributed Computing , LNCS, vol. 3326, 89–102.' mla: Chatterjee, Krishnendu, et al. Complexity of Compositional Model Checking of Computation Tree Logic on Simple Structures. Vol. 3326, Springer, 2005, pp. 89–102, doi:10.1007/978-3-540-30536-1_13. short: K. Chatterjee, P. Dasgupta, P. Chakrabarti, in:, Springer, 2005, pp. 89–102. conference: name: 'IWDC: International Workshop on Distributed Computing ' date_created: 2018-12-11T12:05:45Z date_published: 2005-02-14T00:00:00Z date_updated: 2021-01-12T07:53:02Z day: '14' doi: 10.1007/978-3-540-30536-1_13 extern: 1 intvolume: ' 3326' month: '02' page: 89 - 102 publication_status: published publisher: Springer publist_id: '2261' quality_controlled: 0 status: public title: Complexity of compositional model checking of computation tree logic on simple structures type: conference volume: 3326 year: '2005' ... --- _id: '3893' abstract: - lang: eng text: '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.' alternative_title: - 'LNCS ' author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Chatterjee K. Two-player nonzero-sum ω-regular games. In: Vol 3653. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2005:413-427. doi:10.1007/11539452_32' apa: 'Chatterjee, K. (2005). Two-player nonzero-sum ω-regular games (Vol. 3653, pp. 413–427). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/11539452_32' chicago: Chatterjee, Krishnendu. “Two-Player Nonzero-Sum ω-Regular Games,” 3653:413–27. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005. https://doi.org/10.1007/11539452_32. ieee: 'K. Chatterjee, “Two-player nonzero-sum ω-regular games,” presented at the CONCUR: Concurrency Theory, 2005, vol. 3653, pp. 413–427.' ista: 'Chatterjee K. 2005. Two-player nonzero-sum ω-regular games. CONCUR: Concurrency Theory, LNCS , vol. 3653, 413–427.' mla: Chatterjee, Krishnendu. Two-Player Nonzero-Sum ω-Regular Games. Vol. 3653, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005, pp. 413–27, doi:10.1007/11539452_32. short: K. Chatterjee, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2005, pp. 413–427. conference: name: 'CONCUR: Concurrency Theory' date_created: 2018-12-11T12:05:44Z date_published: 2005-09-05T00:00:00Z date_updated: 2021-01-12T07:53:00Z day: '05' doi: 10.1007/11539452_32 extern: 1 intvolume: ' 3653' month: '09' page: 413 - 427 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '2267' quality_controlled: 0 status: public title: Two-player nonzero-sum ω-regular games type: conference volume: 3653 year: '2005' ... --- _id: '3916' abstract: - lang: eng text: 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: - first_name: Alexandra full_name: Schrempf, Alexandra last_name: Schrempf - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Schrempf A, Heinze J, Cremer S. Sexual cooperation: mating increases longevity in ant queens. Current Biology. 2005;15(3):267-270. doi:10.1016/j.cub.2005.01.036' apa: 'Schrempf, A., Heinze, J., & Cremer, S. (2005). Sexual cooperation: mating increases longevity in ant queens. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2005.01.036' chicago: 'Schrempf, Alexandra, Jürgen Heinze, and Sylvia Cremer. “Sexual Cooperation: Mating Increases Longevity in Ant Queens.” Current Biology. Cell Press, 2005. https://doi.org/10.1016/j.cub.2005.01.036.' ieee: 'A. Schrempf, J. Heinze, and S. Cremer, “Sexual cooperation: mating increases longevity in ant queens,” Current Biology, vol. 15, no. 3. Cell Press, pp. 267–270, 2005.' ista: 'Schrempf A, Heinze J, Cremer S. 2005. Sexual cooperation: mating increases longevity in ant queens. Current Biology. 15(3), 267–270.' mla: 'Schrempf, Alexandra, et al. “Sexual Cooperation: Mating Increases Longevity in Ant Queens.” Current Biology, vol. 15, no. 3, Cell Press, 2005, pp. 267–70, doi:10.1016/j.cub.2005.01.036.' short: A. Schrempf, J. Heinze, S. Cremer, Current Biology 15 (2005) 267–270. date_created: 2018-12-11T12:05:52Z date_published: 2005-02-08T00:00:00Z date_updated: 2021-01-12T07:53:10Z day: '08' doi: 10.1016/j.cub.2005.01.036 extern: '1' intvolume: ' 15' issue: '3' language: - iso: eng month: '02' oa_version: None page: 267 - 270 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '2238' status: public title: 'Sexual cooperation: mating increases longevity in ant queens' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2005' ... --- _id: '3915' abstract: - lang: eng text: "In the ant Cardiocondyla obscurior, wingless males compete with nestmate males for access to female mating\r\npartners, leading to local mate competition (LMC). Queen number varies between colonies, resulting in\r\nvariation in the strength of LMC. Cremer & Heinze (2002, Proceedings of the Royal Society of London, Series B,\r\n269, 417–422) showed that colonies responded to increasing queen number by producing a less femalebiased\r\nsex ratio, as predicted by LMC theory. However, the proximate mechanisms responsible for this\r\nvariation in the sex ratio could not be determined because the study was restricted to adult sex ratios.With\r\nLMC, the primary sex ratio (proportion of haploid eggs laid by the queen) is expected to be female biased,\r\nwhich lowers the conflict between queens and workers over sex allocation. We compared the primary sex\r\nratios laid by queens in monogynous and in polygynous experimental colonies of C. obscurior. The\r\nproportion of haploid eggs laid by queens was significantly lower in single-queen than in multiple-queen\r\ncolonies. Furthermore, queens rapidly adjusted their primary sex ratios to changes in colony queen\r\nnumber. This is the first report of an adaptive adjustment of the primary sex ratio in response to LMC by\r\nant queens." author: - first_name: Ludivine full_name: De Menten, Ludivine last_name: De Menten - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze - first_name: Serge full_name: Aron, Serge last_name: Aron citation: ama: De Menten L, Cremer S, Heinze J, Aron S. Primary sex ratio adjustment by ant queens in response to local mate competition. Animal Behaviour. 2005;69(5):1031-1035. doi:10.1016/j.anbehav.2004.09.005 apa: De Menten, L., Cremer, S., Heinze, J., & Aron, S. (2005). Primary sex ratio adjustment by ant queens in response to local mate competition. Animal Behaviour. Elsevier. https://doi.org/10.1016/j.anbehav.2004.09.005 chicago: De Menten, Ludivine, Sylvia Cremer, Jürgen Heinze, and Serge Aron. “Primary Sex Ratio Adjustment by Ant Queens in Response to Local Mate Competition.” Animal Behaviour. Elsevier, 2005. https://doi.org/10.1016/j.anbehav.2004.09.005. ieee: L. De Menten, S. Cremer, J. Heinze, and S. Aron, “Primary sex ratio adjustment by ant queens in response to local mate competition,” Animal Behaviour, vol. 69, no. 5. Elsevier, pp. 1031–1035, 2005. ista: De Menten L, Cremer S, Heinze J, Aron S. 2005. Primary sex ratio adjustment by ant queens in response to local mate competition. Animal Behaviour. 69(5), 1031–1035. mla: De Menten, Ludivine, et al. “Primary Sex Ratio Adjustment by Ant Queens in Response to Local Mate Competition.” Animal Behaviour, vol. 69, no. 5, Elsevier, 2005, pp. 1031–35, doi:10.1016/j.anbehav.2004.09.005. short: L. De Menten, S. Cremer, J. Heinze, S. Aron, Animal Behaviour 69 (2005) 1031–1035. date_created: 2018-12-11T12:05:52Z date_published: 2005-05-01T00:00:00Z date_updated: 2021-01-12T07:53:10Z day: '01' doi: 10.1016/j.anbehav.2004.09.005 extern: '1' intvolume: ' 69' issue: '5' language: - iso: eng month: '05' oa_version: None page: 1031 - 1035 publication: Animal Behaviour publication_status: published publisher: Elsevier publist_id: '2237' status: public title: Primary sex ratio adjustment by ant queens in response to local mate competition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2005' ... --- _id: '4167' abstract: - lang: eng text: 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. article_processing_charge: No author: - first_name: Will full_name: Norton, Will last_name: Norton - first_name: Maryam full_name: Mangoli, Maryam last_name: Mangoli - first_name: Zsolt full_name: Lele, Zsolt last_name: Lele - first_name: Hans full_name: Pogoda, Hans last_name: Pogoda - first_name: Brianne full_name: Diamond, Brianne last_name: Diamond - first_name: Sara full_name: Mercurio, Sara last_name: Mercurio - first_name: Claire full_name: Russell, Claire last_name: Russell - first_name: Hiroki full_name: Teraoka, Hiroki last_name: Teraoka - first_name: Heather full_name: Stickney, Heather last_name: Stickney - first_name: Gerd full_name: Rauch, Gerd last_name: Rauch - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Corinne full_name: Houart, Corinne last_name: Houart - first_name: Thomas full_name: Schilling, Thomas last_name: Schilling - first_name: Hans full_name: Frohnhoefer, Hans last_name: Frohnhoefer - first_name: Sepand full_name: Rastegar, Sepand last_name: Rastegar - first_name: Carl full_name: Neumann, Carl last_name: Neumann - first_name: R Mark full_name: Gardiner, R Mark last_name: Gardiner - first_name: Uwe full_name: Strähle, Uwe last_name: Strähle - first_name: Robert full_name: Geisler, Robert last_name: Geisler - first_name: Michelle full_name: Rees, Michelle last_name: Rees - first_name: William full_name: Talbot, William last_name: Talbot - first_name: Stephen full_name: Wilson, Stephen last_name: Wilson citation: ama: Norton W, Mangoli M, Lele Z, et al. Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones. Development. 2005;132(4):645-658. doi:10.1242/dev.01611 apa: Norton, W., Mangoli, M., Lele, Z., Pogoda, H., Diamond, B., Mercurio, S., … Wilson, S. (2005). Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones. Development. Company of Biologists. https://doi.org/10.1242/dev.01611 chicago: Norton, Will, Maryam Mangoli, Zsolt Lele, Hans Pogoda, Brianne Diamond, Sara Mercurio, Claire Russell, et al. “Monorail/Foxa2 Regulates Floorplate Differentiation and Specification of Oligodendrocytes, Serotonergic Raphe Neurones and Cranial Motoneurones.” Development. Company of Biologists, 2005. https://doi.org/10.1242/dev.01611. ieee: W. Norton et al., “Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones,” Development, vol. 132, no. 4. Company of Biologists, pp. 645–658, 2005. ista: Norton W, Mangoli M, Lele Z, Pogoda H, Diamond B, Mercurio S, Russell C, Teraoka H, Stickney H, Rauch G, Heisenberg C-PJ, Houart C, Schilling T, Frohnhoefer H, Rastegar S, Neumann C, Gardiner RM, Strähle U, Geisler R, Rees M, Talbot W, Wilson S. 2005. Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones. Development. 132(4), 645–658. mla: Norton, Will, et al. “Monorail/Foxa2 Regulates Floorplate Differentiation and Specification of Oligodendrocytes, Serotonergic Raphe Neurones and Cranial Motoneurones.” Development, vol. 132, no. 4, Company of Biologists, 2005, pp. 645–58, doi:10.1242/dev.01611. short: W. Norton, M. Mangoli, Z. Lele, H. Pogoda, B. Diamond, S. Mercurio, C. Russell, H. Teraoka, H. Stickney, G. Rauch, C.-P.J. Heisenberg, C. Houart, T. Schilling, H. Frohnhoefer, S. Rastegar, C. Neumann, R.M. Gardiner, U. Strähle, R. Geisler, M. Rees, W. Talbot, S. Wilson, Development 132 (2005) 645–658. date_created: 2018-12-11T12:07:21Z date_published: 2005-02-15T00:00:00Z date_updated: 2021-01-12T07:55:00Z day: '15' doi: 10.1242/dev.01611 extern: '1' intvolume: ' 132' issue: '4' language: - iso: eng month: '02' oa_version: None page: 645 - 658 publication: Development publication_status: published publisher: Company of Biologists publist_id: '1952' status: public title: Monorail/Foxa2 regulates floorplate differentiation and specification of oligodendrocytes, serotonergic raphe neurones and cranial motoneurones type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 132 year: '2005' ... --- _id: '4183' abstract: - lang: eng text: 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. acknowledgement: Poster Abstract article_processing_charge: No author: - first_name: Mathias full_name: Köppen, Mathias last_name: Köppen - first_name: Beatriz full_name: Fernández, Beatriz last_name: Fernández - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - first_name: António full_name: Jacinto, António last_name: Jacinto - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure. Mechanisms of Development. 2005;122(Supplement 1):S112-S113. doi:10.1016/j.mod.2005.06.010 apa: Köppen, M., Fernández, B., Carvalho, L., Jacinto, A., & Heisenberg, C.-P. J. (2005). Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure. Mechanisms of Development. Elsevier. https://doi.org/10.1016/j.mod.2005.06.010 chicago: Köppen, Mathias, Beatriz Fernández, Lara Carvalho, António Jacinto, and Carl-Philipp J Heisenberg. “Misshapen Mediates Actin-Based Cell Contraction during Zebrafish Epiboly and Drosophila Dorsal Closure.” Mechanisms of Development. Elsevier, 2005. https://doi.org/10.1016/j.mod.2005.06.010. ieee: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, and C.-P. J. Heisenberg, “Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure,” Mechanisms of Development, vol. 122, no. Supplement 1. Elsevier, pp. S112–S113, 2005. ista: Köppen M, Fernández B, Carvalho L, Jacinto A, Heisenberg C-PJ. 2005. Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure. Mechanisms of Development. 122(Supplement 1), S112–S113. mla: Köppen, Mathias, et al. “Misshapen Mediates Actin-Based Cell Contraction during Zebrafish Epiboly and Drosophila Dorsal Closure.” Mechanisms of Development, vol. 122, no. Supplement 1, Elsevier, 2005, pp. S112–13, doi:10.1016/j.mod.2005.06.010. short: M. Köppen, B. Fernández, L. Carvalho, A. Jacinto, C.-P.J. Heisenberg, Mechanisms of Development 122 (2005) S112–S113. date_created: 2018-12-11T12:07:27Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:55:07Z day: '01' doi: 10.1016/j.mod.2005.06.010 extern: '1' intvolume: ' 122' issue: Supplement 1 language: - iso: eng month: '01' oa_version: None page: S112 - S113 publication: Mechanisms of Development publication_status: published publisher: Elsevier publist_id: '1936' status: public title: Misshapen mediates actin-based cell contraction during zebrafish epiboly and Drosophila dorsal closure type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 122 year: '2005' ... --- _id: '4367' alternative_title: - LNCS 3672 author: - first_name: Andreas full_name: Podelski,Andreas last_name: Podelski - first_name: Thomas full_name: Thomas Wies id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies citation: ama: 'Podelski A, Wies T. Boolean Heaps. In: Springer; 2005:267-282. doi:1550' apa: 'Podelski, A., & Wies, T. (2005). Boolean Heaps (pp. 267–282). Presented at the SAS: Static Analysis Symposium, Springer. https://doi.org/1550' chicago: Podelski, Andreas, and Thomas Wies. “Boolean Heaps,” 267–82. Springer, 2005. https://doi.org/1550. ieee: 'A. Podelski and T. Wies, “Boolean Heaps,” presented at the SAS: Static Analysis Symposium, 2005, pp. 267–282.' ista: 'Podelski A, Wies T. 2005. Boolean Heaps. SAS: Static Analysis Symposium, LNCS 3672, , 267–282.' mla: Podelski, Andreas, and Thomas Wies. Boolean Heaps. Springer, 2005, pp. 267–82, doi:1550. short: A. Podelski, T. Wies, in:, Springer, 2005, pp. 267–282. conference: name: 'SAS: Static Analysis Symposium' date_created: 2018-12-11T12:08:29Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:56:27Z day: '01' doi: '1550' extern: 1 month: '01' page: 267 - 282 publication_status: published publisher: Springer publist_id: '1092' quality_controlled: 0 status: public title: Boolean Heaps type: conference year: '2005' ... --- _id: '3143' abstract: - lang: eng text: 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: - first_name: Simon full_name: Simon Hippenmeyer id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Eline full_name: Vrieseling, Eline last_name: Vrieseling - first_name: Markus full_name: Sigrist, Markus last_name: Sigrist - first_name: Thomas full_name: Portmann, Thomas last_name: Portmann - first_name: Celia full_name: Laengle, Celia last_name: Laengle - first_name: David full_name: Ladle, David R last_name: Ladle - first_name: Silvia full_name: Arber, Silvia last_name: Arber citation: ama: Hippenmeyer S, Vrieseling E, Sigrist M, et al. A developmental switch in the response of DRG neurons to ETS transcription factor signaling. PLoS Biology. 2005;3(5):0878-0890. doi:10.1371/journal.pbio.0030159 apa: Hippenmeyer, S., Vrieseling, E., Sigrist, M., Portmann, T., Laengle, C., Ladle, D., & Arber, S. (2005). A developmental switch in the response of DRG neurons to ETS transcription factor signaling. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.0030159 chicago: Hippenmeyer, Simon, Eline Vrieseling, Markus Sigrist, Thomas Portmann, Celia Laengle, David Ladle, and Silvia Arber. “A Developmental Switch in the Response of DRG Neurons to ETS Transcription Factor Signaling.” PLoS Biology. Public Library of Science, 2005. https://doi.org/10.1371/journal.pbio.0030159. ieee: S. Hippenmeyer et al., “A developmental switch in the response of DRG neurons to ETS transcription factor signaling,” PLoS Biology, vol. 3, no. 5. Public Library of Science, pp. 0878–0890, 2005. ista: Hippenmeyer S, Vrieseling E, Sigrist M, Portmann T, Laengle C, Ladle D, Arber S. 2005. A developmental switch in the response of DRG neurons to ETS transcription factor signaling. PLoS Biology. 3(5), 0878–0890. mla: Hippenmeyer, Simon, et al. “A Developmental Switch in the Response of DRG Neurons to ETS Transcription Factor Signaling.” PLoS Biology, vol. 3, no. 5, Public Library of Science, 2005, pp. 0878–90, doi:10.1371/journal.pbio.0030159. short: S. Hippenmeyer, E. Vrieseling, M. Sigrist, T. Portmann, C. Laengle, D. Ladle, S. Arber, PLoS Biology 3 (2005) 0878–0890. date_created: 2018-12-11T12:01:38Z date_published: 2005-05-01T00:00:00Z date_updated: 2021-01-12T07:41:21Z day: '01' doi: 10.1371/journal.pbio.0030159 extern: 1 intvolume: ' 3' issue: '5' license: https://creativecommons.org/licenses/by/4.0/ month: '05' page: 0878 - 0890 publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '3552' quality_controlled: 0 status: public title: A developmental switch in the response of DRG neurons to ETS transcription factor signaling tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 3 year: '2005' ... --- _id: '3141' abstract: - lang: eng text: 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: - first_name: Avital full_name: Rodal, Avital A last_name: Rodal - first_name: Olga full_name: Sokolova, Olga last_name: Sokolova - first_name: Deborah full_name: Robins, Deborah B last_name: Robins - first_name: Karen full_name: Daugherty, Karen M last_name: Daugherty - first_name: Simon full_name: Simon Hippenmeyer id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Howard full_name: Riezman, Howard last_name: Riezman - first_name: Nikolaus full_name: Grigorieff, Nikolaus last_name: Grigorieff - first_name: Bruce full_name: Goode, Bruce L last_name: Goode citation: ama: Rodal A, Sokolova O, Robins D, et al. Conformational changes in the Arp2 3 complex leading to actin nucleation. Nature Structural and Molecular Biology. 2005;12(1):26-31. doi:10.1038/nsmb870 apa: Rodal, A., Sokolova, O., Robins, D., Daugherty, K., Hippenmeyer, S., Riezman, H., … Goode, B. (2005). Conformational changes in the Arp2 3 complex leading to actin nucleation. Nature Structural and Molecular Biology. Nature Publishing Group. https://doi.org/10.1038/nsmb870 chicago: Rodal, Avital, Olga Sokolova, Deborah Robins, Karen Daugherty, Simon Hippenmeyer, Howard Riezman, Nikolaus Grigorieff, and Bruce Goode. “Conformational Changes in the Arp2 3 Complex Leading to Actin Nucleation.” Nature Structural and Molecular Biology. Nature Publishing Group, 2005. https://doi.org/10.1038/nsmb870. ieee: A. Rodal et al., “Conformational changes in the Arp2 3 complex leading to actin nucleation,” Nature Structural and Molecular Biology, vol. 12, no. 1. Nature Publishing Group, pp. 26–31, 2005. ista: Rodal A, Sokolova O, Robins D, Daugherty K, Hippenmeyer S, Riezman H, Grigorieff N, Goode B. 2005. Conformational changes in the Arp2 3 complex leading to actin nucleation. Nature Structural and Molecular Biology. 12(1), 26–31. mla: Rodal, Avital, et al. “Conformational Changes in the Arp2 3 Complex Leading to Actin Nucleation.” Nature Structural and Molecular Biology, vol. 12, no. 1, Nature Publishing Group, 2005, pp. 26–31, doi:10.1038/nsmb870. short: A. Rodal, O. Sokolova, D. Robins, K. Daugherty, S. Hippenmeyer, H. Riezman, N. Grigorieff, B. Goode, Nature Structural and Molecular Biology 12 (2005) 26–31. date_created: 2018-12-11T12:01:38Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:41:21Z day: '01' doi: 10.1038/nsmb870 extern: 1 intvolume: ' 12' issue: '1' month: '01' page: 26 - 31 publication: Nature Structural and Molecular Biology publication_status: published publisher: Nature Publishing Group publist_id: '3554' quality_controlled: 0 status: public title: Conformational changes in the Arp2 3 complex leading to actin nucleation type: journal_article volume: 12 year: '2005' ... --- _id: '3175' abstract: - lang: eng text: 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: - first_name: Carsten full_name: Rother, Carsten last_name: Rother - first_name: Sanjiv full_name: Kumar, Sanjiv last_name: Kumar - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Andrew full_name: Blake, Andrew last_name: Blake citation: ama: 'Rother C, Kumar S, Kolmogorov V, Blake A. Digital tapestry. In: Vol 1. IEEE; 2005:589-596. doi:10.1109/CVPR.2005.130' apa: 'Rother, C., Kumar, S., Kolmogorov, V., & Blake, A. (2005). Digital tapestry (Vol. 1, pp. 589–596). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2005.130' chicago: Rother, Carsten, Sanjiv Kumar, Vladimir Kolmogorov, and Andrew Blake. “Digital Tapestry,” 1:589–96. IEEE, 2005. https://doi.org/10.1109/CVPR.2005.130. ieee: 'C. Rother, S. Kumar, V. Kolmogorov, and A. Blake, “Digital tapestry,” presented at the CVPR: Computer Vision and Pattern Recognition, 2005, vol. 1, pp. 589–596.' ista: 'Rother C, Kumar S, Kolmogorov V, Blake A. 2005. Digital tapestry. CVPR: Computer Vision and Pattern Recognition vol. 1, 589–596.' mla: Rother, Carsten, et al. Digital Tapestry. Vol. 1, IEEE, 2005, pp. 589–96, doi:10.1109/CVPR.2005.130. short: C. Rother, S. Kumar, V. Kolmogorov, A. Blake, in:, IEEE, 2005, pp. 589–596. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:01:50Z date_published: 2005-07-25T00:00:00Z date_updated: 2021-01-12T07:41:35Z day: '25' doi: 10.1109/CVPR.2005.130 extern: 1 intvolume: ' 1' main_file_link: - open_access: '0' url: http://research.microsoft.com/en-us/um/people/ablake/papers/ablake/rother_cvpr05.pdf month: '07' page: 589 - 596 publication_status: published publisher: IEEE publist_id: '3503' quality_controlled: 0 status: public title: Digital tapestry type: conference volume: 1 year: '2005' ... --- _id: '3176' abstract: - lang: eng text: | 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: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Antonio full_name: Criminisi, Antonio last_name: Criminisi - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Geoffrey full_name: Cross, Geoffrey last_name: Cross - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation of binocular stereo video. In: IEEE; 2005:1186-1186. doi:10.1109/CVPR.2005.90' apa: 'Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2005). Bi-layer segmentation of binocular stereo video (pp. 1186–1186). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2005.90' chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 1186–1186. IEEE, 2005. https://doi.org/10.1109/CVPR.2005.90. ieee: 'V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer segmentation of binocular stereo video,” presented at the CVPR: Computer Vision and Pattern Recognition, 2005, pp. 1186–1186.' ista: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation of binocular stereo video. CVPR: Computer Vision and Pattern Recognition, 1186–1186.' mla: Kolmogorov, Vladimir, et al. Bi-Layer Segmentation of Binocular Stereo Video. IEEE, 2005, pp. 1186–1186, doi:10.1109/CVPR.2005.90. short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005, pp. 1186–1186. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:01:50Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:41:35Z day: '01' doi: 10.1109/CVPR.2005.90 extern: 1 month: '01' page: 1186 - 1186 publication_status: published publisher: IEEE publist_id: '3504' quality_controlled: 0 status: public title: Bi-layer segmentation of binocular stereo video type: conference year: '2005' ... --- _id: '3183' abstract: - lang: eng text: 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: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Antonio full_name: Criminisi, Antonio last_name: Criminisi - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Geoffrey full_name: Cross, Geoffrey last_name: Cross - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation of binocular stereo video. In: Vol 2. IEEE; 2005:407-414. doi:10.1109/CVPR.2005.91' apa: 'Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2005). Bi-layer segmentation of binocular stereo video (Vol. 2, pp. 407–414). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2005.91' chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 2:407–14. IEEE, 2005. https://doi.org/10.1109/CVPR.2005.91. ieee: 'V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer segmentation of binocular stereo video,” presented at the CVPR: Computer Vision and Pattern Recognition, 2005, vol. 2, pp. 407–414.' ista: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation of binocular stereo video. CVPR: Computer Vision and Pattern Recognition vol. 2, 407–414.' mla: Kolmogorov, Vladimir, et al. Bi-Layer Segmentation of Binocular Stereo Video. Vol. 2, IEEE, 2005, pp. 407–14, doi:10.1109/CVPR.2005.91. short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005, pp. 407–414. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:01:52Z date_published: 2005-07-25T00:00:00Z date_updated: 2021-01-12T07:41:38Z day: '25' doi: 10.1109/CVPR.2005.91 extern: 1 intvolume: ' 2' main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67281/criminisi_cvpr2005.pdf month: '07' page: 407 - 414 publication_status: published publisher: IEEE publist_id: '3502' quality_controlled: 0 status: public title: Bi-layer segmentation of binocular stereo video type: conference volume: 2 year: '2005' ... --- _id: '3182' abstract: - lang: eng text: 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: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Yuri full_name: Boykov, Yuri last_name: Boykov citation: ama: 'Kolmogorov V, Boykov Y. What metrics can be approximated by geo cuts or global optimization of length area and flux. In: Vol 1. IEEE; 2005:564-571. doi:10.1109/ICCV.2005.252' apa: 'Kolmogorov, V., & Boykov, Y. (2005). What metrics can be approximated by geo cuts or global optimization of length area and flux (Vol. 1, pp. 564–571). Presented at the ICCV: International Conference on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2005.252' chicago: Kolmogorov, Vladimir, and Yuri Boykov. “What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux,” 1:564–71. IEEE, 2005. https://doi.org/10.1109/ICCV.2005.252. ieee: 'V. Kolmogorov and Y. Boykov, “What metrics can be approximated by geo cuts or global optimization of length area and flux,” presented at the ICCV: International Conference on Computer Vision, 2005, vol. 1, pp. 564–571.' ista: 'Kolmogorov V, Boykov Y. 2005. What metrics can be approximated by geo cuts or global optimization of length area and flux. ICCV: International Conference on Computer Vision vol. 1, 564–571.' mla: Kolmogorov, Vladimir, and Yuri Boykov. What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux. Vol. 1, IEEE, 2005, pp. 564–71, doi:10.1109/ICCV.2005.252. short: V. Kolmogorov, Y. Boykov, in:, IEEE, 2005, pp. 564–571. conference: name: 'ICCV: International Conference on Computer Vision' date_created: 2018-12-11T12:01:52Z date_published: 2005-12-05T00:00:00Z date_updated: 2021-01-12T07:41:38Z day: '05' doi: 10.1109/ICCV.2005.252 extern: 1 intvolume: ' 1' month: '12' page: 564 - 571 publication_status: published publisher: IEEE publist_id: '3501' quality_controlled: 0 status: public title: What metrics can be approximated by geo cuts or global optimization of length area and flux type: conference volume: 1 year: '2005' ... --- _id: '3181' abstract: - lang: eng text: 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: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Martin full_name: Wainwright, Martin J last_name: Wainwright citation: ama: 'Kolmogorov V, Wainwright M. On the optimality of tree reweighted max product message passing. In: AUAI Press; 2005:316-323.' apa: 'Kolmogorov, V., & Wainwright, M. (2005). On the optimality of tree reweighted max product message passing (pp. 316–323). Presented at the UAI: Uncertainty in Artificial Intelligence, AUAI Press.' chicago: Kolmogorov, Vladimir, and Martin Wainwright. “On the Optimality of Tree Reweighted Max Product Message Passing,” 316–23. AUAI Press, 2005. ieee: 'V. Kolmogorov and M. Wainwright, “On the optimality of tree reweighted max product message passing,” presented at the UAI: Uncertainty in Artificial Intelligence, 2005, pp. 316–323.' ista: 'Kolmogorov V, Wainwright M. 2005. On the optimality of tree reweighted max product message passing. UAI: Uncertainty in Artificial Intelligence, 316–323.' mla: Kolmogorov, Vladimir, and Martin Wainwright. On the Optimality of Tree Reweighted Max Product Message Passing. AUAI Press, 2005, pp. 316–23. short: V. Kolmogorov, M. Wainwright, in:, AUAI Press, 2005, pp. 316–323. conference: name: 'UAI: Uncertainty in Artificial Intelligence' date_created: 2018-12-11T12:01:51Z date_published: 2005-07-01T00:00:00Z date_updated: 2021-01-12T07:41:38Z day: '01' extern: 1 main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67405/trw_opt_uai05.pdf month: '07' page: 316 - 323 publication_status: published publisher: AUAI Press publist_id: '3500' quality_controlled: 0 status: public title: On the optimality of tree reweighted max product message passing type: conference year: '2005' ... --- _id: '3417' abstract: - lang: eng text: 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: - first_name: Michael full_name: Kuhn, Michael last_name: Kuhn - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Maurice full_name: Hubain, Maurice last_name: Hubain - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Kuhn M, Janovjak HL, Hubain M, Mueller D. Automated alignment and pattern recognition of single-molecule force spectroscopy data. Journal of Microscopy. 2005;218(2):125-132. doi:10.1111/j.1365-2818.2005.01478.x apa: Kuhn, M., Janovjak, H. L., Hubain, M., & Mueller, D. (2005). Automated alignment and pattern recognition of single-molecule force spectroscopy data. Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2818.2005.01478.x chicago: Kuhn, Michael, Harald L Janovjak, Maurice Hubain, and Daniel Mueller. “Automated Alignment and Pattern Recognition of Single-Molecule Force Spectroscopy Data.” Journal of Microscopy. Wiley-Blackwell, 2005. https://doi.org/10.1111/j.1365-2818.2005.01478.x. ieee: M. Kuhn, H. L. Janovjak, M. Hubain, and D. Mueller, “Automated alignment and pattern recognition of single-molecule force spectroscopy data,” Journal of Microscopy, vol. 218, no. 2. Wiley-Blackwell, pp. 125–132, 2005. ista: Kuhn M, Janovjak HL, Hubain M, Mueller D. 2005. Automated alignment and pattern recognition of single-molecule force spectroscopy data. Journal of Microscopy. 218(2), 125–132. mla: Kuhn, Michael, et al. “Automated Alignment and Pattern Recognition of Single-Molecule Force Spectroscopy Data.” Journal of Microscopy, vol. 218, no. 2, Wiley-Blackwell, 2005, pp. 125–32, doi:10.1111/j.1365-2818.2005.01478.x. short: M. Kuhn, H.L. Janovjak, M. Hubain, D. Mueller, Journal of Microscopy 218 (2005) 125–132. date_created: 2018-12-11T12:03:13Z date_published: 2005-05-01T00:00:00Z date_updated: 2021-01-12T07:43:20Z day: '01' doi: 10.1111/j.1365-2818.2005.01478.x extern: 1 intvolume: ' 218' issue: '2' month: '05' page: 125 - 132 publication: Journal of Microscopy publication_status: published publisher: Wiley-Blackwell publist_id: '2984' quality_controlled: 0 status: public title: Automated alignment and pattern recognition of single-molecule force spectroscopy data type: journal_article volume: 218 year: '2005' ... --- _id: '3416' abstract: - lang: eng text: 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: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Tanuj full_name: Sapra, Tanuj K last_name: Sapra - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Janovjak HL, Sapra T, Mueller D. Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. 2005;88(5):37-39. doi:10.1529/biophysj.105.059774 apa: Janovjak, H. L., Sapra, T., & Mueller, D. (2005). Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. Biophysical Society. https://doi.org/10.1529/biophysj.105.059774 chicago: Janovjak, Harald L, Tanuj Sapra, and Daniel Mueller. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” Biophysical Journal. Biophysical Society, 2005. https://doi.org/10.1529/biophysj.105.059774. ieee: H. L. Janovjak, T. Sapra, and D. Mueller, “Complex stability of single proteins explored by forced unfolding experiments,” Biophysical Journal, vol. 88, no. 5. Biophysical Society, pp. 37–39, 2005. ista: Janovjak HL, Sapra T, Mueller D. 2005. Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. 88(5), 37–39. mla: Janovjak, Harald L., et al. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” Biophysical Journal, vol. 88, no. 5, Biophysical Society, 2005, pp. 37–39, doi:10.1529/biophysj.105.059774. short: H.L. Janovjak, T. Sapra, D. Mueller, Biophysical Journal 88 (2005) 37–39. date_created: 2018-12-11T12:03:13Z date_published: 2005-05-01T00:00:00Z date_updated: 2021-01-12T07:43:19Z day: '01' doi: 10.1529/biophysj.105.059774 extern: 1 intvolume: ' 88' issue: '5' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305525/ month: '05' oa: 1 page: 37 - 39 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '2985' quality_controlled: 0 status: public title: Complex stability of single proteins explored by forced unfolding experiments type: journal_article volume: 88 year: '2005' ... --- _id: '3418' abstract: - lang: eng text: 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: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Jens full_name: Struckmeier, Jens last_name: Struckmeier - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Janovjak HL, Struckmeier J, Mueller D. Hydrodynamic effects in fast AFM single molecule force measurements. European Biophysics Journal. 2005;34(1):91-96. doi:10.1007/s00249-004-0430-3 apa: Janovjak, H. L., Struckmeier, J., & Mueller, D. (2005). Hydrodynamic effects in fast AFM single molecule force measurements. European Biophysics Journal. Springer. https://doi.org/10.1007/s00249-004-0430-3 chicago: Janovjak, Harald L, Jens Struckmeier, and Daniel Mueller. “Hydrodynamic Effects in Fast AFM Single Molecule Force Measurements.” European Biophysics Journal. Springer, 2005. https://doi.org/10.1007/s00249-004-0430-3. ieee: H. L. Janovjak, J. Struckmeier, and D. Mueller, “Hydrodynamic effects in fast AFM single molecule force measurements,” European Biophysics Journal, vol. 34, no. 1. Springer, pp. 91–96, 2005. ista: Janovjak HL, Struckmeier J, Mueller D. 2005. Hydrodynamic effects in fast AFM single molecule force measurements. European Biophysics Journal. 34(1), 91–96. mla: Janovjak, Harald L., et al. “Hydrodynamic Effects in Fast AFM Single Molecule Force Measurements.” European Biophysics Journal, vol. 34, no. 1, Springer, 2005, pp. 91–96, doi:10.1007/s00249-004-0430-3. short: H.L. Janovjak, J. Struckmeier, D. Mueller, European Biophysics Journal 34 (2005) 91–96. date_created: 2018-12-11T12:03:14Z date_published: 2005-02-01T00:00:00Z date_updated: 2021-01-12T07:43:20Z day: '01' doi: 10.1007/s00249-004-0430-3 extern: 1 intvolume: ' 34' issue: '1' month: '02' page: 91 - 96 publication: European Biophysics Journal publication_status: published publisher: Springer publist_id: '2983' quality_controlled: 0 status: public title: Hydrodynamic effects in fast AFM single molecule force measurements type: journal_article volume: 34 year: '2005' ... --- _id: '3433' author: - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: 'Bollback JP. Posterior mapping and posterior predictive distributions. In: Nielsen R, ed. Statistical Methods in Molecular Evolution. Springer; 2005:439-462. doi:10.1007/0-387-27733-1' apa: Bollback, J. P. (2005). Posterior mapping and posterior predictive distributions. In R. Nielsen (Ed.), Statistical methods in Molecular Evolution (pp. 439–462). Springer. https://doi.org/10.1007/0-387-27733-1 chicago: Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.” In Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen, 439–62. Springer, 2005. https://doi.org/10.1007/0-387-27733-1. ieee: J. P. Bollback, “Posterior mapping and posterior predictive distributions,” in Statistical methods in Molecular Evolution, R. Nielsen, Ed. Springer, 2005, pp. 439–462. ista: 'Bollback JP. 2005.Posterior mapping and posterior predictive distributions. In: Statistical methods in Molecular Evolution. , 439–462.' mla: Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.” Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen, Springer, 2005, pp. 439–62, doi:10.1007/0-387-27733-1. short: J.P. Bollback, in:, R. Nielsen (Ed.), Statistical Methods in Molecular Evolution, Springer, 2005, pp. 439–462. date_created: 2018-12-11T12:03:18Z date_published: 2005-04-21T00:00:00Z date_updated: 2021-01-12T07:43:26Z day: '21' doi: 10.1007/0-387-27733-1 editor: - first_name: Rasmus full_name: Nielsen, Rasmus last_name: Nielsen extern: 1 month: '04' page: 439 - 462 publication: Statistical methods in Molecular Evolution publication_status: published publisher: Springer publist_id: '2967' quality_controlled: 0 status: public title: Posterior mapping and posterior predictive distributions type: book_chapter year: '2005' ... --- _id: '3509' abstract: - lang: eng text: 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. applicant: - Raindrop Geomagic, Inc. article_processing_charge: No author: - first_name: Steven full_name: Williams, Steven last_name: Williams - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ping full_name: Fu, Ping last_name: Fu citation: ama: Williams S, Edelsbrunner H, Fu P. Methods, apparatus and computer program products for modeling three-dimensional colored objects. 2005. apa: Williams, S., Edelsbrunner, H., & Fu, P. (2005). Methods, apparatus and computer program products for modeling three-dimensional colored objects. chicago: Williams, Steven, Herbert Edelsbrunner, and Ping Fu. “Methods, Apparatus and Computer Program Products for Modeling Three-Dimensional Colored Objects,” 2005. ieee: S. Williams, H. Edelsbrunner, and P. Fu, “Methods, apparatus and computer program products for modeling three-dimensional colored objects.” 2005. ista: Williams S, Edelsbrunner H, Fu P. 2005. Methods, apparatus and computer program products for modeling three-dimensional colored objects. mla: Williams, Steven, et al. Methods, Apparatus and Computer Program Products for Modeling Three-Dimensional Colored Objects. 2005. short: S. Williams, H. Edelsbrunner, P. Fu, (2005). date_created: 2018-12-11T12:03:42Z date_published: 2005-02-08T00:00:00Z date_updated: 2022-01-05T13:59:09Z day: '08' extern: '1' ipc: G06T17/20 ; G06T15/04 ipn: US6853373B2 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US6853373B2/ month: '02' oa: 1 oa_version: Published Version publication_date: 2005-02-08 publist_id: '2878' status: public title: Methods, apparatus and computer program products for modeling three-dimensional colored objects type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2005' ... --- _id: '3558' abstract: - lang: eng text: 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. acknowledgement: 'Partially supported the generated triangulations. Two questions arise: “how do by NSF grant CCR-00-86013 (BioGeometry).' author: - first_name: Dominique full_name: Attali, Dominique last_name: Attali - first_name: David full_name: Cohen-Steiner, David last_name: Cohen Steiner - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Attali D, Cohen Steiner D, Edelsbrunner H. Extraction and simplification of iso-surfaces in tandem. In: ACM; 2005:139-148.' apa: 'Attali, D., Cohen Steiner, D., & Edelsbrunner, H. (2005). Extraction and simplification of iso-surfaces in tandem (pp. 139–148). Presented at the SGP: Eurographics Symposium on Geometry processing, ACM.' chicago: Attali, Dominique, David Cohen Steiner, and Herbert Edelsbrunner. “Extraction and Simplification of Iso-Surfaces in Tandem,” 139–48. ACM, 2005. ieee: 'D. Attali, D. Cohen Steiner, and H. Edelsbrunner, “Extraction and simplification of iso-surfaces in tandem,” presented at the SGP: Eurographics Symposium on Geometry processing, 2005, pp. 139–148.' ista: 'Attali D, Cohen Steiner D, Edelsbrunner H. 2005. Extraction and simplification of iso-surfaces in tandem. SGP: Eurographics Symposium on Geometry processing, 139–148.' mla: Attali, Dominique, et al. Extraction and Simplification of Iso-Surfaces in Tandem. ACM, 2005, pp. 139–48. short: D. Attali, D. Cohen Steiner, H. Edelsbrunner, in:, ACM, 2005, pp. 139–148. conference: name: 'SGP: Eurographics Symposium on Geometry processing' date_created: 2018-12-11T12:03:57Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:44:18Z day: '01' extern: 1 main_file_link: - open_access: '0' url: http://dl.acm.org/citation.cfm?id=1281943 month: '01' page: 139 - 148 publication_status: published publisher: ACM publist_id: '2827' quality_controlled: 0 status: public title: Extraction and simplification of iso-surfaces in tandem type: conference year: '2005' ... --- _id: '3576' abstract: - lang: eng text: |- 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. alternative_title: - Mathematical Sciences Research Institute Publications author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Patrice full_name: Koehl, Patrice last_name: Koehl citation: ama: 'Edelsbrunner H, Koehl P. The geometry of biomolecular solvation. In: Combinatorial and Computational Geometry. Vol 52. Cambridge University Press; 2005:243-275.' apa: Edelsbrunner, H., & Koehl, P. (2005). The geometry of biomolecular solvation. In Combinatorial and Computational Geometry (Vol. 52, pp. 243–275). Cambridge University Press. chicago: Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular Solvation.” In Combinatorial and Computational Geometry, 52:243–75. Cambridge University Press, 2005. ieee: H. Edelsbrunner and P. Koehl, “The geometry of biomolecular solvation,” in Combinatorial and Computational Geometry, vol. 52, Cambridge University Press, 2005, pp. 243–275. ista: 'Edelsbrunner H, Koehl P. 2005.The geometry of biomolecular solvation. In: Combinatorial and Computational Geometry. Mathematical Sciences Research Institute Publications, vol. 52, 243–275.' mla: Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular Solvation.” Combinatorial and Computational Geometry, vol. 52, Cambridge University Press, 2005, pp. 243–75. short: H. Edelsbrunner, P. Koehl, in:, Combinatorial and Computational Geometry, Cambridge University Press, 2005, pp. 243–275. date_created: 2018-12-11T12:04:03Z date_published: 2005-08-08T00:00:00Z date_updated: 2021-01-12T07:44:25Z day: '08' extern: 1 intvolume: ' 52' main_file_link: - open_access: '0' url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.117.3732 month: '08' page: 243 - 275 publication: Combinatorial and Computational Geometry publication_status: published publisher: Cambridge University Press publist_id: '2809' quality_controlled: 0 status: public title: The geometry of biomolecular solvation type: book_chapter volume: 52 year: '2005' ... --- _id: '3612' abstract: - lang: eng text: 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: - first_name: Angus full_name: Davison, Angus last_name: Davison - first_name: Satoshi full_name: Chiba, Satoshi last_name: Chiba - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Bernard full_name: Clarke, Bernard last_name: Clarke citation: ama: Davison A, Chiba S, Barton NH, Clarke B. Speciation and gene flow between snails of opposing chirality. PLoS Biology. 2005;3(9). doi:10.1371/journal.pbio.0030282 apa: Davison, A., Chiba, S., Barton, N. H., & Clarke, B. (2005). Speciation and gene flow between snails of opposing chirality. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.0030282 chicago: Davison, Angus, Satoshi Chiba, Nicholas H Barton, and Bernard Clarke. “Speciation and Gene Flow between Snails of Opposing Chirality.” PLoS Biology. Public Library of Science, 2005. https://doi.org/10.1371/journal.pbio.0030282. ieee: A. Davison, S. Chiba, N. H. Barton, and B. Clarke, “Speciation and gene flow between snails of opposing chirality,” PLoS Biology, vol. 3, no. 9. Public Library of Science, 2005. ista: Davison A, Chiba S, Barton NH, Clarke B. 2005. Speciation and gene flow between snails of opposing chirality. PLoS Biology. 3(9). mla: Davison, Angus, et al. “Speciation and Gene Flow between Snails of Opposing Chirality.” PLoS Biology, vol. 3, no. 9, Public Library of Science, 2005, doi:10.1371/journal.pbio.0030282. short: A. Davison, S. Chiba, N.H. Barton, B. Clarke, PLoS Biology 3 (2005). date_created: 2018-12-11T12:04:14Z date_published: 2005-08-09T00:00:00Z date_updated: 2021-01-12T07:44:39Z day: '09' doi: 10.1371/journal.pbio.0030282 extern: 1 intvolume: ' 3' issue: '9' month: '08' publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '2771' quality_controlled: 0 status: public title: Speciation and gene flow between snails of opposing chirality tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 3 year: '2005' ... --- _id: '3611' abstract: - lang: eng text: '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: - first_name: Beate full_name: Nürnberger, Beate last_name: Nürnberger - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Loeske full_name: Kruuk, Loeske E last_name: Kruuk - first_name: Timothy full_name: Vines, Timothy H last_name: Vines citation: ama: 'Nürnberger B, Barton NH, Kruuk L, Vines T. Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes. Heredity. 2005;94(2):247-257. doi:10.1038/sj.hdy.6800607' apa: 'Nürnberger, B., Barton, N. H., Kruuk, L., & Vines, T. (2005). Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes. Heredity. Nature Publishing Group. https://doi.org/10.1038/sj.hdy.6800607' chicago: 'Nürnberger, Beate, Nicholas H Barton, Loeske Kruuk, and Timothy Vines. “Mating Patterns in a Bombina Hybrid Zone: Inferences from Adult and Full Sib Genotypes.” Heredity. Nature Publishing Group, 2005. https://doi.org/10.1038/sj.hdy.6800607.' ieee: 'B. Nürnberger, N. H. Barton, L. Kruuk, and T. Vines, “Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes,” Heredity, vol. 94, no. 2. Nature Publishing Group, pp. 247–257, 2005.' ista: 'Nürnberger B, Barton NH, Kruuk L, Vines T. 2005. Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes. Heredity. 94(2), 247–257.' mla: 'Nürnberger, Beate, et al. “Mating Patterns in a Bombina Hybrid Zone: Inferences from Adult and Full Sib Genotypes.” Heredity, vol. 94, no. 2, Nature Publishing Group, 2005, pp. 247–57, doi:10.1038/sj.hdy.6800607.' short: B. Nürnberger, N.H. Barton, L. Kruuk, T. Vines, Heredity 94 (2005) 247–257. date_created: 2018-12-11T12:04:14Z date_published: 2005-02-01T00:00:00Z date_updated: 2021-01-12T07:44:39Z day: '01' doi: 10.1038/sj.hdy.6800607 extern: 1 intvolume: ' 94' issue: '2' month: '02' page: 247 - 257 publication: Heredity publication_status: published publisher: Nature Publishing Group publist_id: '2772' quality_controlled: 0 status: public title: 'Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes' type: journal_article volume: 94 year: '2005' ... --- _id: '3613' abstract: - lang: eng text: '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: - first_name: Michael full_name: Gardner, Michael P last_name: Gardner - first_name: Kevin full_name: Fowler, Kevin last_name: Fowler - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Linda full_name: Patridge, Linda last_name: Patridge citation: ama: 'Gardner M, Fowler K, Barton NH, Patridge L. Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns. Genetics. 2005;169(3):1553-1571. doi:10.1534/genetics.104.032367' apa: 'Gardner, M., Fowler, K., Barton, N. H., & Patridge, L. (2005). Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.104.032367' chicago: 'Gardner, Michael, Kevin Fowler, Nicholas H Barton, and Linda Patridge. “Genetic Variation for Total Fitness in Drosophila Melanogaster: Complex yet Replicable Patterns.” Genetics. Genetics Society of America, 2005. https://doi.org/10.1534/genetics.104.032367.' ieee: 'M. Gardner, K. Fowler, N. H. Barton, and L. Patridge, “Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns,” Genetics, vol. 169, no. 3. Genetics Society of America, pp. 1553–1571, 2005.' ista: 'Gardner M, Fowler K, Barton NH, Patridge L. 2005. Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns. Genetics. 169(3), 1553–1571.' mla: 'Gardner, Michael, et al. “Genetic Variation for Total Fitness in Drosophila Melanogaster: Complex yet Replicable Patterns.” Genetics, vol. 169, no. 3, Genetics Society of America, 2005, pp. 1553–71, doi:10.1534/genetics.104.032367.' short: M. Gardner, K. Fowler, N.H. Barton, L. Patridge, Genetics 169 (2005) 1553–1571. date_created: 2018-12-11T12:04:15Z date_published: 2005-03-01T00:00:00Z date_updated: 2021-01-12T07:44:40Z day: '01' doi: 10.1534/genetics.104.032367 extern: 1 intvolume: ' 169' issue: '3' month: '03' page: 1553 - 1571 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '2770' quality_controlled: 0 status: public title: 'Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns' type: journal_article volume: 169 year: '2005' ... --- _id: '3691' abstract: - lang: eng text: 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: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Lampert C. Boundary regularity of admissible operators. Publicacions Matemàtiques. 2005;49(1):179-195. doi:10.5565/PUBLMAT_49105_08 apa: Lampert, C. (2005). Boundary regularity of admissible operators. Publicacions Matemàtiques. Universitat Autònoma de Barcelona, Departament de Matemàtique. https://doi.org/10.5565/PUBLMAT_49105_08 chicago: Lampert, Christoph. “Boundary Regularity of Admissible Operators.” Publicacions Matemàtiques. Universitat Autònoma de Barcelona, Departament de Matemàtique, 2005. https://doi.org/10.5565/PUBLMAT_49105_08. ieee: C. Lampert, “Boundary regularity of admissible operators,” Publicacions Matemàtiques, vol. 49, no. 1. Universitat Autònoma de Barcelona, Departament de Matemàtique, pp. 179–195, 2005. ista: Lampert C. 2005. Boundary regularity of admissible operators. Publicacions Matemàtiques. 49(1), 179–195. mla: Lampert, Christoph. “Boundary Regularity of Admissible Operators.” Publicacions Matemàtiques, vol. 49, no. 1, Universitat Autònoma de Barcelona, Departament de Matemàtique, 2005, pp. 179–95, doi:10.5565/PUBLMAT_49105_08. short: C. Lampert, Publicacions Matemàtiques 49 (2005) 179–195. date_created: 2018-12-11T12:04:38Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:48:59Z day: '01' doi: 10.5565/PUBLMAT_49105_08 extern: 1 intvolume: ' 49' issue: '1' month: '01' page: 179 - 195 publication: Publicacions Matemàtiques publication_status: published publisher: Universitat Autònoma de Barcelona, Departament de Matemàtique publist_id: '2673' quality_controlled: 0 status: public title: Boundary regularity of admissible operators type: journal_article volume: 49 year: '2005' ... --- _id: '3721' abstract: - lang: eng text: 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: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller - first_name: Andrew full_name: Humphris, Andrew D last_name: Humphris citation: ama: Janovjak HL, Mueller D, Humphris A. Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins. Biophysical Journal. 2005;88(2):1423-1431. doi:10.1529/biophysj.104.052746 apa: Janovjak, H. L., Mueller, D., & Humphris, A. (2005). Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins. Biophysical Journal. Biophysical Society. https://doi.org/10.1529/biophysj.104.052746 chicago: Janovjak, Harald L, Daniel Mueller, and Andrew Humphris. “Molecular Force Modulation Spectroscopy Revealing the Dynamic Response of Single Bacteriorhodopsins.” Biophysical Journal. Biophysical Society, 2005. https://doi.org/10.1529/biophysj.104.052746. ieee: H. L. Janovjak, D. Mueller, and A. Humphris, “Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins,” Biophysical Journal, vol. 88, no. 2. Biophysical Society, pp. 1423–1431, 2005. ista: Janovjak HL, Mueller D, Humphris A. 2005. Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins. Biophysical Journal. 88(2), 1423–1431. mla: Janovjak, Harald L., et al. “Molecular Force Modulation Spectroscopy Revealing the Dynamic Response of Single Bacteriorhodopsins.” Biophysical Journal, vol. 88, no. 2, Biophysical Society, 2005, pp. 1423–31, doi:10.1529/biophysj.104.052746. short: H.L. Janovjak, D. Mueller, A. Humphris, Biophysical Journal 88 (2005) 1423–1431. date_created: 2018-12-11T12:04:48Z date_published: 2005-02-01T00:00:00Z date_updated: 2021-01-12T07:51:43Z day: '01' doi: 10.1529/biophysj.104.052746 extern: 1 intvolume: ' 88' issue: '2' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305144/ month: '02' oa: 1 page: 1423 - 1431 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '2509' quality_controlled: 0 status: public title: Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins type: journal_article volume: 88 year: '2005' ... --- _id: '3741' abstract: - lang: eng text: 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: - first_name: N. full_name: Slonim,N. last_name: Slonim - first_name: G. full_name: Atwal,G. last_name: Atwal - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: William full_name: Bialek, William S last_name: Bialek citation: ama: Slonim N, Atwal G, Tkačik G, Bialek W. Information-based clustering. PNAS. 2005;102(51):18297-18302. doi:10.1073/pnas.0507432102 apa: Slonim, N., Atwal, G., Tkačik, G., & Bialek, W. (2005). Information-based clustering. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0507432102 chicago: Slonim, N., G. Atwal, Gašper Tkačik, and William Bialek. “Information-Based Clustering.” PNAS. National Academy of Sciences, 2005. https://doi.org/10.1073/pnas.0507432102. ieee: N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Information-based clustering,” PNAS, vol. 102, no. 51. National Academy of Sciences, pp. 18297–18302, 2005. ista: Slonim N, Atwal G, Tkačik G, Bialek W. 2005. Information-based clustering. PNAS. 102(51), 18297–18302. mla: Slonim, N., et al. “Information-Based Clustering.” PNAS, vol. 102, no. 51, National Academy of Sciences, 2005, pp. 18297–302, doi:10.1073/pnas.0507432102. short: N. Slonim, G. Atwal, G. Tkačik, W. Bialek, PNAS 102 (2005) 18297–18302. date_created: 2018-12-11T12:04:55Z date_published: 2005-12-20T00:00:00Z date_updated: 2021-01-12T07:51:52Z day: '20' doi: 10.1073/pnas.0507432102 extern: 1 intvolume: ' 102' issue: '51' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317937 month: '12' oa: 1 page: 18297 - 18302 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '2490' quality_controlled: 0 status: public title: Information-based clustering type: journal_article volume: 102 year: '2005' ... --- _id: '3746' abstract: - lang: eng text: 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: - first_name: Noam full_name: Slonim,Noam last_name: Slonim - first_name: Gurinder full_name: Atwal,Gurinder S last_name: Atwal - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: William full_name: Bialek, William S last_name: Bialek citation: ama: Slonim N, Atwal G, Tkačik G, Bialek W. Estimating mutual information and multi-information in large networks. ArXiv. 2005:1-11. apa: Slonim, N., Atwal, G., Tkačik, G., & Bialek, W. (2005). Estimating mutual information and multi-information in large networks. ArXiv. ArXiv. chicago: Slonim, Noam, Gurinder Atwal, Gašper Tkačik, and William Bialek. “Estimating Mutual Information and Multi-Information in Large Networks.” ArXiv. ArXiv, 2005. ieee: N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Estimating mutual information and multi-information in large networks,” ArXiv. ArXiv, pp. 1–11, 2005. ista: Slonim N, Atwal G, Tkačik G, Bialek W. 2005. Estimating mutual information and multi-information in large networks. ArXiv, 1–11, . mla: Slonim, Noam, et al. “Estimating Mutual Information and Multi-Information in Large Networks.” ArXiv, ArXiv, 2005, pp. 1–11. short: N. Slonim, G. Atwal, G. Tkačik, W. Bialek, ArXiv (2005) 1–11. date_created: 2018-12-11T12:04:56Z date_published: 2005-02-03T00:00:00Z date_updated: 2021-01-12T07:51:54Z day: '03' extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/cs/0502017v1 month: '02' oa: 1 page: 1 - 11 publication: ArXiv publication_status: published publisher: ArXiv publist_id: '2484' quality_controlled: 0 status: public title: Estimating mutual information and multi-information in large networks type: preprint year: '2005' ... --- _id: '3808' abstract: - lang: eng text: 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: - first_name: Dominique full_name: Engel, Dominique last_name: Engel - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Engel D, Jonas PM. Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons. Neuron. 2005;45(3):405-417. doi:10.1016/j.neuron.2004.12.048 apa: Engel, D., & Jonas, P. M. (2005). Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2004.12.048 chicago: Engel, Dominique, and Peter M Jonas. “Presynaptic Action Potential Amplification by Voltage-Gated Na+ Channels in Hippocampal Mossy Fiber Boutons.” Neuron. Elsevier, 2005. https://doi.org/10.1016/j.neuron.2004.12.048 . ieee: D. Engel and P. M. Jonas, “Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons,” Neuron, vol. 45, no. 3. Elsevier, pp. 405–17, 2005. ista: Engel D, Jonas PM. 2005. Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons. Neuron. 45(3), 405–17. mla: Engel, Dominique, and Peter M. Jonas. “Presynaptic Action Potential Amplification by Voltage-Gated Na+ Channels in Hippocampal Mossy Fiber Boutons.” Neuron, vol. 45, no. 3, Elsevier, 2005, pp. 405–17, doi:10.1016/j.neuron.2004.12.048 . short: D. Engel, P.M. Jonas, Neuron 45 (2005) 405–17. date_created: 2018-12-11T12:05:17Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:52:21Z day: '01' doi: '10.1016/j.neuron.2004.12.048 ' extern: 1 intvolume: ' 45' issue: '3' month: '01' page: 405 - 17 publication: Neuron publication_status: published publisher: Elsevier publist_id: '2400' quality_controlled: 0 status: public title: Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons type: journal_article volume: 45 year: '2005' ... --- _id: '3892' abstract: - lang: eng text: '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.' acknowledgement: |- This research was supported in part by the ONR grant N00014-02-1-0671, the AFOSR MURI grant F49620-00-1-0327, and the NSF grant CCR-0225610. This is an extended version of the paper “Games with Secure Equilibria” that appeared in the proceedings of Logic in Computer Science (LICS), 2004. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Marcin full_name: Jurdziński, Marcin last_name: Jurdziński citation: ama: 'Chatterjee K, Henzinger TA, Jurdziński M. Games with secure equilibria. In: Vol 3657. Springer; 2005:141-161. doi:10.1007/11561163_7' apa: 'Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2005). Games with secure equilibria (Vol. 3657, pp. 141–161). Presented at the FMCO: Formal Methods for Components and Objects, Springer. https://doi.org/10.1007/11561163_7' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Games with Secure Equilibria,” 3657:141–61. Springer, 2005. https://doi.org/10.1007/11561163_7. ieee: 'K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Games with secure equilibria,” presented at the FMCO: Formal Methods for Components and Objects, 2005, vol. 3657, pp. 141–161.' ista: 'Chatterjee K, Henzinger TA, Jurdziński M. 2005. Games with secure equilibria. FMCO: Formal Methods for Components and Objects, LNCS, vol. 3657, 141–161.' mla: Chatterjee, Krishnendu, et al. Games with Secure Equilibria. Vol. 3657, Springer, 2005, pp. 141–61, doi:10.1007/11561163_7. short: K. Chatterjee, T.A. Henzinger, M. Jurdziński, in:, Springer, 2005, pp. 141–161. conference: name: 'FMCO: Formal Methods for Components and Objects' date_created: 2018-12-11T12:05:44Z date_published: 2005-09-19T00:00:00Z date_updated: 2021-01-12T07:53:00Z day: '19' doi: 10.1007/11561163_7 extern: 1 intvolume: ' 3657' month: '09' page: 141 - 161 publication_status: published publisher: Springer publist_id: '2269' quality_controlled: 0 status: public title: Games with secure equilibria type: conference volume: 3657 year: '2005' ... --- _id: '3902' author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jacobus full_name: Boomsma, Jacobus last_name: Boomsma citation: ama: 'Cremer S, Boomsma J. The drawback of mobility: invasive species in a globalised world. In: Elsevier; 2005.' apa: 'Cremer, S., & Boomsma, J. (2005). The drawback of mobility: invasive species in a globalised world. Presented at the Marie Curie Conference, Elsevier.' chicago: 'Cremer, Sylvia, and Jacobus Boomsma. “The Drawback of Mobility: Invasive Species in a Globalised World.” Elsevier, 2005.' ieee: 'S. Cremer and J. Boomsma, “The drawback of mobility: invasive species in a globalised world,” presented at the Marie Curie Conference, 2005.' ista: 'Cremer S, Boomsma J. 2005. The drawback of mobility: invasive species in a globalised world. Marie Curie Conference.' mla: 'Cremer, Sylvia, and Jacobus Boomsma. The Drawback of Mobility: Invasive Species in a Globalised World. Elsevier, 2005.' short: S. Cremer, J. Boomsma, in:, Elsevier, 2005. conference: name: Marie Curie Conference date_created: 2018-12-11T12:05:47Z date_published: 2005-09-01T00:00:00Z date_updated: 2021-01-12T07:53:05Z day: '01' extern: '1' language: - iso: eng main_file_link: - url: http://www.docstoc.com/docs/15327566/1-The-drawback-of-mobility-invasive-species-in-a-globalised-world month: '09' oa_version: None publication_status: published publisher: Elsevier publist_id: '2252' status: public title: 'The drawback of mobility: invasive species in a globalised world' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2005' ...