--- _id: '3215' abstract: - lang: eng text: 'Most cryptographic primitives such as encryption, authentication or secret sharing require randomness. Usually one assumes that perfect randomness is available, but those primitives might also be realized under weaker assumptions. In this work we continue the study of building secure cryptographic primitives from imperfect random sources initiated by Dodis and Spencer (FOCS’02). Their main result shows that there exists a (high-entropy) source of randomness allowing for perfect encryption of a bit, and yet from which one cannot extract even a single weakly random bit, separating encryption from extraction. Our main result separates encryption from 2-out-2 secret sharing (both in the information-theoretic and in the computational settings): any source which can be used to achieve one-bit encryption also can be used for 2-out-2 secret sharing of one bit, but the converse is false, even for high-entropy sources. Therefore, possibility of extraction strictly implies encryption, which in turn strictly implies 2-out-2 secret sharing.' acknowledgement: Supported in part by NSF career award CCR-0133806 and NSF grant 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: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Bartosz full_name: Przydatek, Bartosz last_name: Przydatek citation: ama: 'Dodis Y, Pietrzak KZ, Przydatek B. Separating sources for encryption and secret sharing. In: Vol 3876. Springer; 2006:601-616. doi:10.1007/11681878_31' apa: 'Dodis, Y., Pietrzak, K. Z., & Przydatek, B. (2006). Separating sources for encryption and secret sharing (Vol. 3876, pp. 601–616). Presented at the TCC: Theory of Cryptography Conference, Springer. https://doi.org/10.1007/11681878_31' chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Bartosz Przydatek. “Separating Sources for Encryption and Secret Sharing,” 3876:601–16. Springer, 2006. https://doi.org/10.1007/11681878_31. ieee: 'Y. Dodis, K. Z. Pietrzak, and B. Przydatek, “Separating sources for encryption and secret sharing,” presented at the TCC: Theory of Cryptography Conference, 2006, vol. 3876, pp. 601–616.' ista: 'Dodis Y, Pietrzak KZ, Przydatek B. 2006. Separating sources for encryption and secret sharing. TCC: Theory of Cryptography Conference, LNCS, vol. 3876, 601–616.' mla: Dodis, Yevgeniy, et al. Separating Sources for Encryption and Secret Sharing. Vol. 3876, Springer, 2006, pp. 601–16, doi:10.1007/11681878_31. short: Y. Dodis, K.Z. Pietrzak, B. Przydatek, in:, Springer, 2006, pp. 601–616. conference: name: 'TCC: Theory of Cryptography Conference' date_created: 2018-12-11T12:02:04Z date_published: 2006-04-11T00:00:00Z date_updated: 2021-01-12T07:41:51Z day: '11' doi: 10.1007/11681878_31 extern: 1 intvolume: ' 3876' month: '04' page: 601 - 616 publication_status: published publisher: Springer publist_id: '3466' quality_controlled: 0 status: public title: Separating sources for encryption and secret sharing type: conference volume: 3876 year: '2006' ... --- _id: '3217' abstract: - lang: eng text: |- To prove that a secure key-agreement protocol exists one must at least show P ≠NP. Moreover any proof that the sequential composition of two non-adaptively secure pseudorandom functions is secure against at least two adaptive queries must falsify the decisional Diffie-Hellman assumption, a standard assumption from public-key cryptography. Hence proving any of this two seemingly unrelated statements would require a significant breakthrough. We show that at least one of the two statements is true. To our knowledge this gives the first positive cryptographic result (namely that composition implies some weak adaptive security) which holds in Minicrypt, but not in Cryptomania, i.e. under the assumption that one-way functions exist, but public-key cryptography does not. acknowledgement: Author was supported during the writing of this work by the Swiss National Science Foundation, project No. 200020-103847/1. Part of this work is supported by the Commission of the European Communities through the IST program under contract IST-2002-507932 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 implies adaptive security in minicrypt. In: Vol 4004. Springer; 2006:328-338. doi:10.1007/11761679_20' apa: 'Pietrzak, K. Z. (2006). Composition implies adaptive security in minicrypt (Vol. 4004, pp. 328–338). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/11761679_20' chicago: Pietrzak, Krzysztof Z. “Composition Implies Adaptive Security in Minicrypt,” 4004:328–38. Springer, 2006. https://doi.org/10.1007/11761679_20. ieee: 'K. Z. Pietrzak, “Composition implies adaptive security in minicrypt,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2006, vol. 4004, pp. 328–338.' ista: 'Pietrzak KZ. 2006. Composition implies adaptive security in minicrypt. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4004, 328–338.' mla: Pietrzak, Krzysztof Z. Composition Implies Adaptive Security in Minicrypt. Vol. 4004, Springer, 2006, pp. 328–38, doi:10.1007/11761679_20. short: K.Z. Pietrzak, in:, Springer, 2006, pp. 328–338. conference: name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' date_created: 2018-12-11T12:02:04Z date_published: 2006-07-11T00:00:00Z date_updated: 2021-01-12T07:41:52Z day: '11' doi: 10.1007/11761679_20 extern: 1 intvolume: ' 4004' month: '07' page: 328 - 338 publication_status: published publisher: Springer publist_id: '3464' quality_controlled: 0 status: public title: Composition implies adaptive security in minicrypt type: conference volume: 4004 year: '2006' ... --- _id: '3216' abstract: - lang: eng text: |- We prove a new upper bound on the advantage of any adversary for distinguishing the encrypted CBC-MAC (EMAC) based on random permutations from a random function. Our proof uses techniques recently introduced in [BPR05], which again were inspired by [DGH + 04]. The bound we prove is tight — in the sense that it matches the advantage of known attacks up to a constant factor — for a wide range of the parameters: let n denote the block-size, q the number of queries the adversary is allowed to make and ℓ an upper bound on the length (i.e. number of blocks) of the messages, then for ℓ ≤ 2 n/8 and q≥ł2 the advantage is in the order of q 2/2 n (and in particular independent of ℓ). This improves on the previous bound of q 2ℓΘ(1/ln ln ℓ)/2 n from [BPR05] and matches the trivial attack (which thus is basically optimal) where one simply asks random queries until a collision is found. acknowledgement: Part of this work is supported by the Commission of the European Communities through the IST program under contract IST-2002-507932 ECRYPT. 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. A tight bound for EMAC. In: Vol 4052. Springer; 2006:168-179. doi:10.1007/11787006_15' apa: 'Pietrzak, K. Z. (2006). A tight bound for EMAC (Vol. 4052, pp. 168–179). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/11787006_15' chicago: Pietrzak, Krzysztof Z. “A Tight Bound for EMAC,” 4052:168–79. Springer, 2006. https://doi.org/10.1007/11787006_15. ieee: 'K. Z. Pietrzak, “A tight bound for EMAC,” presented at the ICALP: Automata, Languages and Programming, 2006, vol. 4052, pp. 168–179.' ista: 'Pietrzak KZ. 2006. A tight bound for EMAC. ICALP: Automata, Languages and Programming, LNCS, vol. 4052, 168–179.' mla: Pietrzak, Krzysztof Z. A Tight Bound for EMAC. Vol. 4052, Springer, 2006, pp. 168–79, doi:10.1007/11787006_15. short: K.Z. Pietrzak, in:, Springer, 2006, pp. 168–179. conference: name: 'ICALP: Automata, Languages and Programming' date_created: 2018-12-11T12:02:04Z date_published: 2006-07-28T00:00:00Z date_updated: 2021-01-12T07:41:52Z day: '28' doi: 10.1007/11787006_15 extern: 1 intvolume: ' 4052' month: '07' page: 168 - 179 publication_status: published publisher: Springer publist_id: '3463' quality_controlled: 0 status: public title: A tight bound for EMAC type: conference volume: 4052 year: '2006' ... --- _id: '3522' abstract: - lang: eng text: We observed sharp wave/ripples (SWR) during exploration within brief (< 2.4 s) interruptions of or during theta oscillations. CA1 network responses of SWRs occurring during exploration (eSWR) and SWRs detected in waking immobility or sleep were similar. However, neuronal activity during eSWR was location dependent, and eSWR-related firing was stronger inside the place field than outside. The eSPW-related firing increase was stronger than the baseline increase inside compared to outside, suggesting a “supralinear” summation of eSWR and place-selective inputs. Pairs of cells with similar place fields and/or correlated firing during exploration showed stronger coactivation during eSWRs and subsequent sleep-SWRs. Sequential activation of place cells was not required for the reactivation of waking co-firing patterns; cell pairs with symmetrical cross-correlations still showed reactivated waking co-firing patterns during sleep-SWRs. We suggest that place-selective firing during eSWRs facilitates initial associations between cells with similar place fields that enable place-related ensemble patterns to recur during subsequent sleep-SWRs. author: - first_name: Joseph full_name: Joseph O'Neill id: 426376DC-F248-11E8-B48F-1D18A9856A87 last_name: O'Neill - first_name: Timothy full_name: Senior,Timothy last_name: Senior - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: O’Neill J, Senior T, Csicsvari JL. Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. 2006;49(1):143-155. doi:10.1016/j.neuron.2005.10.037 apa: O’Neill, J., Senior, T., & Csicsvari, J. L. (2006). Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2005.10.037 chicago: O’Neill, Joseph, Timothy Senior, and Jozsef L Csicsvari. “Place-Selective Firing of CA1 Pyramidal Cells during Sharp Wave/Ripple Network Patterns in Exploratory Behavior.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2005.10.037. ieee: J. O’Neill, T. Senior, and J. L. Csicsvari, “Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior,” Neuron, vol. 49, no. 1. Elsevier, pp. 143–155, 2006. ista: O’Neill J, Senior T, Csicsvari JL. 2006. Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior. Neuron. 49(1), 143–155. mla: O’Neill, Joseph, et al. “Place-Selective Firing of CA1 Pyramidal Cells during Sharp Wave/Ripple Network Patterns in Exploratory Behavior.” Neuron, vol. 49, no. 1, Elsevier, 2006, pp. 143–55, doi:10.1016/j.neuron.2005.10.037. short: J. O’Neill, T. Senior, J.L. Csicsvari, Neuron 49 (2006) 143–155. date_created: 2018-12-11T12:03:46Z date_published: 2006-01-05T00:00:00Z date_updated: 2021-01-12T07:44:03Z day: '05' doi: 10.1016/j.neuron.2005.10.037 extern: 1 intvolume: ' 49' issue: '1' month: '01' page: 143 - 155 publication: Neuron publication_status: published publisher: Elsevier publist_id: '2863' quality_controlled: 0 status: public title: Place-selective firing of CA1 pyramidal cells during sharp wave/ripple network patterns in exploratory behavior type: journal_article volume: 49 year: '2006' ... --- _id: '3607' abstract: - lang: eng text: We apply new analytical methods to understand the consequences of population bottlenecks for expected additive genetic variance. We analyze essentially all models for multilocus epistasis that have been numerically simulated to demonstrate increased additive variance. We conclude that for biologically plausible models, large increases in expected additive variance–attributable to epistasis rather than dominance–are unlikely. Naciri-Graven and Goudet (2003) found that as the number of epistatically interacting loci increases, additive variance tends to be inflated more after a bottleneck. We argue that this result reflects biologically unrealistic aspects of their models. Specifically, as the number of loci increases, higher-order epistatic interactions become increasingly important in these models, with an increasing fraction of the genetic variance becoming nonadditive, contrary to empirical observations. As shown by Barton and Turelli (2004), without dominance, conversion of nonadditive to additive variance depends only on the variance components and not on the number of loci per se. Numerical results indicating that more inbreeding is needed to produce maximal release of additive variance with more loci follow directly from our analytical results, which show that high levels of inbreeding (F > 0.5) are needed for significant conversion of higher-order components. We discuss alternative approaches to modeling multilocus epistasis and understanding its consequences. author: - first_name: Michael full_name: Turelli, Michael last_name: Turelli - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Turelli M, Barton NH. Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. 2006;60(9):1763-1776. doi:10.1111/j.0014-3820.2006.tb00521.x apa: Turelli, M., & Barton, N. H. (2006). Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x chicago: Turelli, Michael, and Nicholas H Barton. “Will Population Bottlenecks and Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.0014-3820.2006.tb00521.x. ieee: M. Turelli and N. H. Barton, “Will population bottlenecks and multilocus epistasis increase additive genetic variance?,” Evolution; International Journal of Organic Evolution, vol. 60, no. 9. Wiley-Blackwell, pp. 1763–1776, 2006. ista: Turelli M, Barton NH. 2006. Will population bottlenecks and multilocus epistasis increase additive genetic variance? Evolution; International Journal of Organic Evolution. 60(9), 1763–1776. mla: Turelli, Michael, and Nicholas H. Barton. “Will Population Bottlenecks and Multilocus Epistasis Increase Additive Genetic Variance?” Evolution; International Journal of Organic Evolution, vol. 60, no. 9, Wiley-Blackwell, 2006, pp. 1763–76, doi:10.1111/j.0014-3820.2006.tb00521.x. short: M. Turelli, N.H. Barton, Evolution; International Journal of Organic Evolution 60 (2006) 1763–1776. date_created: 2018-12-11T12:04:13Z date_published: 2006-09-01T00:00:00Z date_updated: 2021-01-12T07:44:37Z day: '01' doi: 10.1111/j.0014-3820.2006.tb00521.x extern: 1 intvolume: ' 60' issue: '9' month: '09' page: 1763 - 1776 publication: Evolution; International Journal of Organic Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '2776' quality_controlled: 0 status: public title: Will population bottlenecks and multilocus epistasis increase additive genetic variance? type: journal_article volume: 60 year: '2006' ... --- _id: '3683' abstract: - lang: eng text: Many algorithms to remove distortion from document images have be proposed in recent years, but so far there is no reliable method for comparing their performance. In this paper we propose a collection of methods to measure the quality of such restoration algorithms for document image which show a non-linear distortion due to perspective or page curl. For the result from these measurement to be meaningful, a common data set of ground truth is required. We therefore started with the buildup of a document image database that is meant to serve as a common data basis for all kinds of restoration from images of 3D-shaped document. The long term goal would be to establish this database and following extensions in the area of document image dewarping as an as fruitful and indispensable tool as e.g. the NIST database is for OCR, or the Caltech database is for object and face recognition. author: - 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: 'Lampert C, Breuel T. Objective quality measurement for geometric document image restoration. In: Springer; 2006.' apa: 'Lampert, C., & Breuel, T. (2006). Objective quality measurement for geometric document image restoration. Presented at the DAS: Document Analysis Systems, Springer.' chicago: Lampert, Christoph, and Thomas Breuel. “Objective Quality Measurement for Geometric Document Image Restoration.” Springer, 2006. ieee: 'C. Lampert and T. Breuel, “Objective quality measurement for geometric document image restoration,” presented at the DAS: Document Analysis Systems, 2006.' ista: 'Lampert C, Breuel T. 2006. Objective quality measurement for geometric document image restoration. DAS: Document Analysis Systems.' mla: Lampert, Christoph, and Thomas Breuel. Objective Quality Measurement for Geometric Document Image Restoration. Springer, 2006. short: C. Lampert, T. Breuel, in:, Springer, 2006. conference: name: 'DAS: Document Analysis Systems' date_created: 2018-12-11T12:04:36Z date_published: 2006-03-16T00:00:00Z date_updated: 2021-01-12T07:45:07Z day: '16' extern: 1 main_file_link: - open_access: '0' url: http://pub.ist.ac.at/~chl/papers/lampert-das2006.pdf month: '03' publication_status: published publisher: Springer publist_id: '2692' quality_controlled: 0 status: public title: Objective quality measurement for geometric document image restoration type: conference year: '2006' ... --- _id: '3685' abstract: - lang: eng text: 'Video compression currently is dominated by engineering and fine-tuned heuristic methods. In this paper, we propose to instead apply the well-developed machinery of machine learning in order to support the optimization of existing video encoders and the creation of new ones. Exemplarily, we show how by machine learning we can improve one encoding step that is crucial for the performance of all current video standards: macroblock mode decision. By formulating the problem in a Bayesian setup, we show that macroblock mode decision can be reduced to a classification problem with a cost function for misclassification that is sample dependent. We demonstrate how to apply different machine learning techniques to obtain suitable classifiers and we show in detailed experiments that all of these perform better than the state-of-the-art heuristic method' 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. Machine learning for video compression: Macroblock mode decision. In: IEEE; 2006:936-940. doi:10.1109/ICPR.2006.778' apa: 'Lampert, C. (2006). Machine learning for video compression: Macroblock mode decision (pp. 936–940). Presented at the ICPR: International Conference on Pattern Recognition, IEEE. https://doi.org/10.1109/ICPR.2006.778' chicago: 'Lampert, Christoph. “Machine Learning for Video Compression: Macroblock Mode Decision,” 936–40. IEEE, 2006. https://doi.org/10.1109/ICPR.2006.778.' ieee: 'C. Lampert, “Machine learning for video compression: Macroblock mode decision,” presented at the ICPR: International Conference on Pattern Recognition, 2006, pp. 936–940.' ista: 'Lampert C. 2006. Machine learning for video compression: Macroblock mode decision. ICPR: International Conference on Pattern Recognition, 936–940.' mla: 'Lampert, Christoph. Machine Learning for Video Compression: Macroblock Mode Decision. IEEE, 2006, pp. 936–40, doi:10.1109/ICPR.2006.778.' short: C. Lampert, in:, IEEE, 2006, pp. 936–940. conference: name: 'ICPR: International Conference on Pattern Recognition' date_created: 2018-12-11T12:04:37Z date_published: 2006-09-18T00:00:00Z date_updated: 2021-01-12T07:45:08Z day: '18' doi: 10.1109/ICPR.2006.778 extern: 1 month: '09' page: 936 - 940 publication_status: published publisher: IEEE publist_id: '2689' quality_controlled: 0 status: public title: 'Machine learning for video compression: Macroblock mode decision' type: conference year: '2006' ... --- _id: '3750' abstract: - lang: eng text: We applied a single-cell assay to characterize how transcription dynamics affects protein expression levels of a tetracycline-inducible gene expression system. Transcriptional activity of the tetracycline promoter in response to a steady level of inducer is steady in ΔacrAB efflux mutant but pulsating in wildtype Escherichia coli cells. We found that the expression level of the green fluorescent protein is several folds higher in ΔacrAB efflux mutant than in wildtype cells. author: - first_name: Thuc full_name: Le,Thuc T. last_name: Le - first_name: Calin C full_name: Calin Guet id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Philippe full_name: Cluzel,Philippe last_name: Cluzel citation: ama: Le T, Guet CC, Cluzel P. Protein expression enhancement in efflux-deleted mutant bacteria. Protein Expression and Purification. 2006;48(1):28-31. apa: Le, T., Guet, C. C., & Cluzel, P. (2006). Protein expression enhancement in efflux-deleted mutant bacteria. Protein Expression and Purification. Elsevier. chicago: Le, Thuc, Calin C Guet, and Philippe Cluzel. “Protein Expression Enhancement in Efflux-Deleted Mutant Bacteria.” Protein Expression and Purification. Elsevier, 2006. ieee: T. Le, C. C. Guet, and P. Cluzel, “Protein expression enhancement in efflux-deleted mutant bacteria,” Protein Expression and Purification, vol. 48, no. 1. Elsevier, pp. 28–31, 2006. ista: Le T, Guet CC, Cluzel P. 2006. Protein expression enhancement in efflux-deleted mutant bacteria. Protein Expression and Purification. 48(1), 28–31. mla: Le, Thuc, et al. “Protein Expression Enhancement in Efflux-Deleted Mutant Bacteria.” Protein Expression and Purification, vol. 48, no. 1, Elsevier, 2006, pp. 28–31. short: T. Le, C.C. Guet, P. Cluzel, Protein Expression and Purification 48 (2006) 28–31. date_created: 2018-12-11T12:04:58Z date_published: 2006-07-01T00:00:00Z date_updated: 2021-01-12T07:51:56Z day: '01' extern: 1 intvolume: ' 48' issue: '1' month: '07' page: 28 - 31 publication: Protein Expression and Purification publication_status: published publisher: Elsevier publist_id: '2478' quality_controlled: 0 status: public title: Protein expression enhancement in efflux-deleted mutant bacteria type: journal_article volume: 48 year: '2006' ... --- _id: '3767' abstract: - lang: eng text: Models of RNA secondary structure folding are widely used to study evolution in theory and simulation. However, systematic studies of the parameters involved are rare. In this paper, we study by simulation how RNA evolution is influenced by three different factors, namely the mutation rate, scaling of the fitness function, and distance measure. We found that for low mutation rates the qualitative evolutionary behavior is robust with respect to the scaling of the fitness function. For efficient mutation rates, which are close to the error threshold, scaling and distance measure have a strong influence on the evolutionary behavior. A global distance measure that takes sequence information additively into account lowers the error threshold. When using a local sequence-structure alignment for the distance, we observed a smoother evolution of the fitness over time. Finally, in addition to the well known error threshold, we identify another threshold of the mutation rate, called divergence threshold, where the qualitative transient behavior changes from a localized to an exploratory search. author: - first_name: Anne full_name: Anne Kupczok id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Peter full_name: Dittrich,Peter last_name: Dittrich citation: ama: Kupczok A, Dittrich P. Determinants of simulated RNA evolution. Journal of Theoretical Biology. 2006;238(3):726-735. doi:10.1016/j.jtbi.2005.06.019 apa: Kupczok, A., & Dittrich, P. (2006). Determinants of simulated RNA evolution. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2005.06.019 chicago: Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.” Journal of Theoretical Biology. Elsevier, 2006. https://doi.org/10.1016/j.jtbi.2005.06.019. ieee: A. Kupczok and P. Dittrich, “Determinants of simulated RNA evolution.,” Journal of Theoretical Biology, vol. 238, no. 3. Elsevier, pp. 726–35, 2006. ista: Kupczok A, Dittrich P. 2006. Determinants of simulated RNA evolution. Journal of Theoretical Biology. 238(3), 726–35. mla: Kupczok, Anne, and Peter Dittrich. “Determinants of Simulated RNA Evolution.” Journal of Theoretical Biology, vol. 238, no. 3, Elsevier, 2006, pp. 726–35, doi:10.1016/j.jtbi.2005.06.019. short: A. Kupczok, P. Dittrich, Journal of Theoretical Biology 238 (2006) 726–35. date_created: 2018-12-11T12:05:03Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:03Z day: '01' doi: 10.1016/j.jtbi.2005.06.019 extern: 1 intvolume: ' 238' issue: '3' month: '01' page: 726 - 35 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '2461' quality_controlled: 0 status: public title: Determinants of simulated RNA evolution. type: journal_article volume: 238 year: '2006' ... --- _id: '3813' abstract: - lang: eng text: Hyperpolarization-activated channels (Ih or HCN channels) are widely expressed in principal neurons in the central nervous system. However, Ih in inhibitory GABAergic interneurons is less well characterized. We examined the functional properties of Ih in fast-spiking basket cells (BCs) of the dentate gyrus, using hippocampal slices from 17- to 21-day-old rats. Bath application of the Ih channel blocker ZD 7288 at a concentration of 30 microm induced a hyperpolarization of 5.7 +/- 1.5 mV, an increase in input resistance and a correlated increase in apparent membrane time constant. ZD 7288 blocked a hyperpolarization-activated current in a concentration-dependent manner (IC50, 1.4 microm). The effects of ZD 7288 were mimicked by external Cs+. The reversal potential of Ih was -27.4 mV, corresponding to a Na+ to K+ permeability ratio (PNa/PK) of 0.36. The midpoint potential of the activation curve of Ih was -83.9 mV, and the activation time constant at -120 mV was 190 ms. Single-cell expression analysis using reverse transcription followed by quantitative polymerase chain reaction revealed that BCs coexpress HCN1 and HCN2 subunit mRNA, suggesting the formation of heteromeric HCN1/2 channels. ZD 7288 increased the current threshold for evoking antidromic action potentials by extracellular stimulation, consistent with the expression of Ih in BC axons. Finally, ZD 7288 decreased the frequency of miniature inhibitory postsynaptic currents (mIPSCs) in hippocampal granule cells, the main target cells of BCs, to 70 +/- 4% of the control value. In contrast, the amplitude of mIPSCs was unchanged, consistent with the presence of Ih in inhibitory terminals. In conclusion, our results suggest that Ih channels are expressed in the somatodendritic region, axon and presynaptic elements of fast-spiking BCs in the hippocampus. author: - first_name: Yexica full_name: Aponte, Yexica last_name: Aponte - first_name: Cheng full_name: Lien, Cheng-Chang last_name: Lien - first_name: Ellen full_name: Reisinger, Ellen last_name: Reisinger - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Aponte Y, Lien C, Reisinger E, Jonas PM. Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. 2006;574(Pt 1):229-243. doi:10.1113/jphysiol.2005.104042 apa: Aponte, Y., Lien, C., Reisinger, E., & Jonas, P. M. (2006). Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2005.104042 chicago: Aponte, Yexica, Cheng Lien, Ellen Reisinger, and Peter M Jonas. “Hyperpolarization-Activated Cation Channels in Fast-Spiking Interneurons of Rat Hippocampus.” Journal of Physiology. Wiley-Blackwell, 2006. https://doi.org/10.1113/jphysiol.2005.104042. ieee: Y. Aponte, C. Lien, E. Reisinger, and P. M. Jonas, “Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus,” Journal of Physiology, vol. 574, no. Pt 1. Wiley-Blackwell, pp. 229–43, 2006. ista: Aponte Y, Lien C, Reisinger E, Jonas PM. 2006. Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus. Journal of Physiology. 574(Pt 1), 229–43. mla: Aponte, Yexica, et al. “Hyperpolarization-Activated Cation Channels in Fast-Spiking Interneurons of Rat Hippocampus.” Journal of Physiology, vol. 574, no. Pt 1, Wiley-Blackwell, 2006, pp. 229–43, doi:10.1113/jphysiol.2005.104042. short: Y. Aponte, C. Lien, E. Reisinger, P.M. Jonas, Journal of Physiology 574 (2006) 229–43. date_created: 2018-12-11T12:05:19Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:23Z day: '01' doi: 10.1113/jphysiol.2005.104042 extern: 1 intvolume: ' 574' issue: Pt 1 main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1817792/ month: '01' oa: 1 page: 229 - 43 publication: Journal of Physiology publication_status: published publisher: Wiley-Blackwell publist_id: '2397' quality_controlled: 0 status: public title: Hyperpolarization-activated cation channels in fast-spiking interneurons of rat hippocampus type: journal_article volume: 574 year: '2006' ... --- _id: '3814' abstract: - lang: eng text: The axon terminals (mossy fibers) of hippocampal dentate granule cells form characteristic synaptic connections with large spines or excrescences of both hilar mossy cells and CA3 pyramidal neurons. Interneurons of the hilar region and area CA3 are also prominent targets of mossy fibers. The tracing of biocytin-filled mossy fibers and immunolabeling of target cells with interneuron markers has revealed that the majority of mossy fiber synapses project to gamma aminobutyric acid (GABA)-ergic inhibitory interneurons rather than to excitatory principal cells, although the functional implications of these quantitative differences are unclear. Following a brief description of the "classical" mossy fiber synapse on excrescences of CA3 pyramidal cells, the present review focuses on the contacts formed between granule cells and GABAergic interneurons, both normally and after synaptic reorganization. In response to deafferentation of mossy cell target cells, which include both granule cells and interneurons, mossy fibers "sprout" new axon collaterals that form a band of supragranular mossy fibers in the inner molecular layer of the dentate gyrus. Although most newly formed recurrent mossy fibers establish synapses with granule cells, there is an apparently convergent input of new mossy fibers onto GABA-immunoreactive interneuron dendrites that traverse the inner molecular layer. These mossy fiber-interneuron synapses in the dentate gyrus are observed in chronically epileptic rats and may be the structural correlate of the granule cell hyperinhibition observed in these animals in vivo. Together, the findings reviewed here establish mossy fiber synapses as an important component of inhibitory circuits in the hippocampus. author: - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Robert full_name: Sloviter, Robert S last_name: Sloviter citation: ama: Frotscher M, Jonas PM, Sloviter R. Synapses formed by normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research. 2006;326(2):361-367. doi:10.1007/s00441-006-0269-2 apa: Frotscher, M., Jonas, P. M., & Sloviter, R. (2006). Synapses formed by normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research. Springer. https://doi.org/10.1007/s00441-006-0269-2 chicago: Frotscher, Michael, Peter M Jonas, and Robert Sloviter. “Synapses Formed by Normal and Abnormal Hippocampal Mossy Fibers (Review).” Cell and Tissue Research. Springer, 2006. https://doi.org/10.1007/s00441-006-0269-2. ieee: M. Frotscher, P. M. Jonas, and R. Sloviter, “Synapses formed by normal and abnormal hippocampal mossy fibers (Review),” Cell and Tissue Research, vol. 326, no. 2. Springer, pp. 361–7, 2006. ista: Frotscher M, Jonas PM, Sloviter R. 2006. Synapses formed by normal and abnormal hippocampal mossy fibers (Review). Cell and Tissue Research. 326(2), 361–7. mla: Frotscher, Michael, et al. “Synapses Formed by Normal and Abnormal Hippocampal Mossy Fibers (Review).” Cell and Tissue Research, vol. 326, no. 2, Springer, 2006, pp. 361–67, doi:10.1007/s00441-006-0269-2. short: M. Frotscher, P.M. Jonas, R. Sloviter, Cell and Tissue Research 326 (2006) 361–7. date_created: 2018-12-11T12:05:19Z date_published: 2006-01-01T00:00:00Z date_updated: 2019-04-26T07:22:35Z day: '01' doi: 10.1007/s00441-006-0269-2 extern: 1 intvolume: ' 326' issue: '2' month: '01' page: 361 - 7 publication: Cell and Tissue Research publication_status: published publisher: Springer publist_id: '2395' quality_controlled: 0 status: public title: Synapses formed by normal and abnormal hippocampal mossy fibers (Review) type: review volume: 326 year: '2006' ... --- _id: '3815' abstract: - lang: eng text: It is widely accepted that the hippocampus plays a major role in learning and memory. The mossy fiber synapse between granule cells in the dentate gyrus and pyramidal neurons in the CA3 region is a key component of the hippocampal trisynaptic circuit. Recent work, partially based on direct presynaptic patch-clamp recordings from hippocampal mossy fiber boutons, sheds light on the mechanisms of synaptic transmission and plasticity at mossy fiber synapses. A high Na(+) channel density in mossy fiber boutons leads to a large amplitude of the presynaptic action potential. Together with the fast gating of presynaptic Ca(2+) channels, this generates a large and brief presynaptic Ca(2+) influx, which can trigger transmitter release with high efficiency and temporal precision. The large number of release sites, the large size of the releasable pool of vesicles, and the huge extent of presynaptic plasticity confer unique strength to this synapse, suggesting a large impact onto the CA3 pyramidal cell network under specific behavioral conditions. The characteristic properties of the hippocampal mossy fiber synapse may be important for pattern separation and information storage in the dentate gyrus-CA3 cell network. author: - first_name: Josef full_name: Bischofberger, Josef last_name: Bischofberger - first_name: Dominique full_name: Engel, Dominique last_name: Engel - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers Archiv : European Journal of Physiology. 2006;453(3):361-372. doi:10.1007/s00424-006-0093-2' apa: 'Bischofberger, J., Engel, D., Frotscher, M., & Jonas, P. M. (2006). Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers Archiv : European Journal of Physiology. Springer. https://doi.org/10.1007/s00424-006-0093-2' chicago: 'Bischofberger, Josef, Dominique Engel, Michael Frotscher, and Peter M Jonas. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network.” Pflugers Archiv : European Journal of Physiology. Springer, 2006. https://doi.org/10.1007/s00424-006-0093-2.' ieee: 'J. Bischofberger, D. Engel, M. Frotscher, and P. M. Jonas, “Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network,” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3. Springer, pp. 361–72, 2006.' ista: 'Bischofberger J, Engel D, Frotscher M, Jonas PM. 2006. Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network. Pflugers Archiv : European Journal of Physiology. 453(3), 361–72.' mla: 'Bischofberger, Josef, et al. “Timing and Efficacy of Transmitter Release at Mossy Fiber Synapses in the Hippocampal Network.” Pflugers Archiv : European Journal of Physiology, vol. 453, no. 3, Springer, 2006, pp. 361–72, doi:10.1007/s00424-006-0093-2.' short: 'J. Bischofberger, D. Engel, M. Frotscher, P.M. Jonas, Pflugers Archiv : European Journal of Physiology 453 (2006) 361–72.' date_created: 2018-12-11T12:05:19Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:24Z day: '01' doi: 10.1007/s00424-006-0093-2 extern: 1 intvolume: ' 453' issue: '3' month: '01' page: 361 - 72 publication: 'Pflugers Archiv : European Journal of Physiology' publication_status: published publisher: Springer publist_id: '2396' quality_controlled: 0 status: public title: Timing and efficacy of transmitter release at mossy fiber synapses in the hippocampal network type: journal_article volume: 453 year: '2006' ... --- _id: '3811' abstract: - lang: eng text: Networks of GABAergic neurons are key elements in the generation of gamma oscillations in the brain. Computational studies suggested that the emergence of coherent oscillations requires hyperpolarizing inhibition. Here, we show that GABA(A) receptor-mediated inhibition in mature interneurons of the hippocampal dentate gyrus is shunting rather than hyperpolarizing. Unexpectedly, when shunting inhibition is incorporated into a structured interneuron network model with fast and strong synapses, coherent oscillations emerge. In comparison to hyperpolarizing inhibition, networks with shunting inhibition show several advantages. First, oscillations are generated with smaller tonic excitatory drive. Second, network frequencies are tuned to the gamma band. Finally, robustness against heterogeneity in the excitatory drive is markedly improved. In single interneurons, shunting inhibition shortens the interspike interval for low levels of drive but prolongs it for high levels, leading to homogenization of neuronal firing rates. Thus, shunting inhibition may confer increased robustness to gamma oscillations in the brain. author: - first_name: Imre full_name: Vida, Imre last_name: Vida - first_name: Marlene full_name: Bartos, Marlene last_name: Bartos - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Vida I, Bartos M, Jonas PM. Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates. Neuron. 2006;49(1):107-117. doi:10.1016/j.neuron.2005.11.036 apa: Vida, I., Bartos, M., & Jonas, P. M. (2006). Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2005.11.036 chicago: Vida, Imre, Marlene Bartos, and Peter M Jonas. “Shunting Inhibition Improves Robustness of Gamma Oscillations in Hippocampal Interneuron Networks by Homogenizing Firing Rates.” Neuron. Elsevier, 2006. https://doi.org/10.1016/j.neuron.2005.11.036. ieee: I. Vida, M. Bartos, and P. M. Jonas, “Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates,” Neuron, vol. 49, no. 1. Elsevier, pp. 107–17, 2006. ista: Vida I, Bartos M, Jonas PM. 2006. Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates. Neuron. 49(1), 107–17. mla: Vida, Imre, et al. “Shunting Inhibition Improves Robustness of Gamma Oscillations in Hippocampal Interneuron Networks by Homogenizing Firing Rates.” Neuron, vol. 49, no. 1, Elsevier, 2006, pp. 107–17, doi:10.1016/j.neuron.2005.11.036. short: I. Vida, M. Bartos, P.M. Jonas, Neuron 49 (2006) 107–17. date_created: 2018-12-11T12:05:18Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:22Z day: '01' doi: 10.1016/j.neuron.2005.11.036 extern: 1 intvolume: ' 49' issue: '1' month: '01' page: 107 - 17 publication: Neuron publication_status: published publisher: Elsevier publist_id: '2398' quality_controlled: 0 status: public title: Shunting inhibition improves robustness of gamma oscillations in hippocampal interneuron networks by homogenizing firing rates type: journal_article volume: 49 year: '2006' ... --- _id: '3817' author: - first_name: Michael full_name: Frotscher, Michael last_name: Frotscher - first_name: Eckart full_name: Gundelfinger, Eckart last_name: Gundelfinger - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Erwin full_name: Neher, Erwin last_name: Neher - first_name: Peter full_name: Seeburg, Peter last_name: Seeburg citation: ama: Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. The most important recent advances in synapse research from my point of view--and what remains to be done. Cell and Tissue Research. 2006;326(2):203-204. doi:10.1007/s00441-006-0325-y apa: Frotscher, M., Gundelfinger, E., Jonas, P. M., Neher, E., & Seeburg, P. (2006). The most important recent advances in synapse research from my point of view--and what remains to be done. Cell and Tissue Research. Springer. https://doi.org/10.1007/s00441-006-0325-y chicago: Frotscher, Michael, Eckart Gundelfinger, Peter M Jonas, Erwin Neher, and Peter Seeburg. “The Most Important Recent Advances in Synapse Research from My Point of View--and What Remains to Be Done.” Cell and Tissue Research. Springer, 2006. https://doi.org/10.1007/s00441-006-0325-y. ieee: M. Frotscher, E. Gundelfinger, P. M. Jonas, E. Neher, and P. Seeburg, “The most important recent advances in synapse research from my point of view--and what remains to be done,” Cell and Tissue Research, vol. 326, no. 2. Springer, pp. 203–4, 2006. ista: Frotscher M, Gundelfinger E, Jonas PM, Neher E, Seeburg P. 2006. The most important recent advances in synapse research from my point of view--and what remains to be done. Cell and Tissue Research. 326(2), 203–4. mla: Frotscher, Michael, et al. “The Most Important Recent Advances in Synapse Research from My Point of View--and What Remains to Be Done.” Cell and Tissue Research, vol. 326, no. 2, Springer, 2006, pp. 203–04, doi:10.1007/s00441-006-0325-y. short: M. Frotscher, E. Gundelfinger, P.M. Jonas, E. Neher, P. Seeburg, Cell and Tissue Research 326 (2006) 203–4. date_created: 2018-12-11T12:05:20Z date_published: 2006-01-01T00:00:00Z date_updated: 2021-01-12T07:52:24Z day: '01' doi: 10.1007/s00441-006-0325-y extern: 1 intvolume: ' 326' issue: '2' month: '01' page: 203 - 4 publication: Cell and Tissue Research publication_status: published publisher: Springer publist_id: '2394' quality_controlled: 0 status: public title: The most important recent advances in synapse research from my point of view--and what remains to be done type: journal_article volume: 326 year: '2006' ... --- _id: '3912' abstract: - lang: eng text: Invasive species often dramatically change native species communities by directly and indirectly out-competing native species. We studied the direct interference abilities of the invasive garden ant, Lasius neglectus VAN LOON, BOOMSMA & ANDRÁSFALVY, 1990, by performing one-to-one aggression tests of L. neglectus workers towards three native Lasius ant species that occur at the edge of a L. neglectus supercolony in Seva, Spain. Our results show that L. neglectus is highly aggressive against all three native Lasius species tested (L. grandis FOREL, 1909, L. emarginatus (OLIVIER, 1792), and L. cinereus SEIFERT, 1992), expressed as a higher attack rate of L. neglectus and behavioural dominance throughout the aggressive encounters. Attacks of L. neglectus were performed fastest and most frequent against L. grandis, and also the highest antennation frequencies were observed in encounters between these two species. This could be due to the largest difference in body size, or due to a greater overlap in ecological niche between L. neglectus and L. grandis compared to the other two native species. There was only weak support for L. neglectus workers from the periphery of the supercolony to be more aggressive relative to workers from the centre, even though the former encounter native ant species on a daily basis at the edge of the supercolony. author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Line V full_name: Ugelvig, Line V id: 3DC97C8E-F248-11E8-B48F-1D18A9856A87 last_name: Ugelvig orcid: 0000-0003-1832-8883 - first_name: Suzanne full_name: Lommen, Suzanne last_name: Lommen - first_name: Klaus full_name: Petersen, Klaus last_name: Petersen - first_name: Jes full_name: Pedersen, Jes last_name: Pedersen citation: ama: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. 2006;9:13-19.' apa: 'Cremer, S., Ugelvig, L. V., Lommen, S., Petersen, K., & Pedersen, J. (2006). Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. Österreichische Gesellschaft für Entomofaunistik.' chicago: 'Cremer, Sylvia, Line V Ugelvig, Suzanne Lommen, Klaus Petersen, and Jes Pedersen. “Attack of the Invasive Garden Ant: Aggression Behaviour of Lasius Neglectus (Hymenoptera: Formicidae) against Native Lasius Species in Spain.” Myrmecological News. Österreichische Gesellschaft für Entomofaunistik, 2006.' ieee: 'S. Cremer, L. V. Ugelvig, S. Lommen, K. Petersen, and J. Pedersen, “Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain,” Myrmecological News, vol. 9. Österreichische Gesellschaft für Entomofaunistik, pp. 13–19, 2006.' ista: 'Cremer S, Ugelvig LV, Lommen S, Petersen K, Pedersen J. 2006. Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain. Myrmecological News. 9, 13–19.' mla: 'Cremer, Sylvia, et al. “Attack of the Invasive Garden Ant: Aggression Behaviour of Lasius Neglectus (Hymenoptera: Formicidae) against Native Lasius Species in Spain.” Myrmecological News, vol. 9, Österreichische Gesellschaft für Entomofaunistik, 2006, pp. 13–19.' short: S. Cremer, L.V. Ugelvig, S. Lommen, K. Petersen, J. Pedersen, Myrmecological News 9 (2006) 13–19. date_created: 2018-12-11T12:05:51Z date_published: 2006-12-01T00:00:00Z date_updated: 2021-01-12T07:53:09Z day: '01' extern: '1' intvolume: ' 9' language: - iso: eng month: '12' oa_version: None page: 13 - 19 publication: Myrmecological News publication_status: published publisher: Österreichische Gesellschaft für Entomofaunistik publist_id: '2239' status: public title: 'Attack of the invasive garden ant: aggression behaviour of Lasius neglectus (Hymenoptera: Formicidae) against native Lasius species in Spain' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2006' ... --- _id: '3914' abstract: - lang: eng text: We compare the performances of established means of character selection for discriminant analysis in species distinction with a combination procedure for finding the optimal character combination (minimum classification error, minimum number of required characters), using morphometric data sets from the ant genera Cardiocondyla, Lasius and Tetramorium. The established methods are empirical character selection as well as forward selection, backward elimination and stepwise selection of discriminant analysis. The combination procedure is clearly superior to the established methods of character selection, and is widely applicable. author: - first_name: Karl full_name: Moder, Karl last_name: Moder - first_name: Birgit full_name: Schlick Steiner, Birgit last_name: Schlick Steiner - first_name: Florian full_name: Steiner, Florian last_name: Steiner - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Erhard full_name: Christian, Erhard last_name: Christian - first_name: Bernhard full_name: Seifert, Bernhard last_name: Seifert citation: ama: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. 2006;45(1):82-87. doi:10.1111/j.1439-0469.2006.00372.x' apa: 'Moder, K., Schlick Steiner, B., Steiner, F., Cremer, S., Christian, E., & Seifert, B. (2006). Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell. https://doi.org/10.1111/j.1439-0469.2006.00372.x' chicago: 'Moder, Karl, Birgit Schlick Steiner, Florian Steiner, Sylvia Cremer, Erhard Christian, and Bernhard Seifert. “Optimal Species Distinction by Discriminant Analysis: Comparing Established Methods of Character Selection with a Combination Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics and Evolutionary Research. Wiley-Blackwell, 2006. https://doi.org/10.1111/j.1439-0469.2006.00372.x.' ieee: 'K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, and B. Seifert, “Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study,” Journal of Zoological Systematics and Evolutionary Research, vol. 45, no. 1. Wiley-Blackwell, pp. 82–87, 2006.' ista: 'Moder K, Schlick Steiner B, Steiner F, Cremer S, Christian E, Seifert B. 2006. Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study. Journal of Zoological Systematics and Evolutionary Research. 45(1), 82–87.' mla: 'Moder, Karl, et al. “Optimal Species Distinction by Discriminant Analysis: Comparing Established Methods of Character Selection with a Combination Procedure Using Ant Morphometrics as a Case Study.” Journal of Zoological Systematics and Evolutionary Research, vol. 45, no. 1, Wiley-Blackwell, 2006, pp. 82–87, doi:10.1111/j.1439-0469.2006.00372.x.' short: K. Moder, B. Schlick Steiner, F. Steiner, S. Cremer, E. Christian, B. Seifert, Journal of Zoological Systematics and Evolutionary Research 45 (2006) 82–87. date_created: 2018-12-11T12:05:52Z date_published: 2006-08-29T00:00:00Z date_updated: 2021-01-12T07:53:10Z day: '29' doi: 10.1111/j.1439-0469.2006.00372.x extern: '1' intvolume: ' 45' issue: '1' language: - iso: eng month: '08' oa_version: None page: 82 - 87 publication: Journal of Zoological Systematics and Evolutionary Research publication_status: published publisher: Wiley-Blackwell publist_id: '2241' status: public title: 'Optimal species distinction by discriminant analysis: comparing established methods of character selection with a combination procedure using ant morphometrics as a case study' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 45 year: '2006' ... --- _id: '3913' abstract: - lang: eng text: Many invasive ant species, such as the Argentine ant or the red imported fire ant, have huge colonies with thousands of mass-foraging workers, which quickly monopolise resources and therefore represent a considerable threat to the native ant fauna. Cardiocondyla obscurior and several other species of this myrmicine genus have similarly been transferred throughout the tropics by human activities. However, because their colonies are tiny and workers forage solitarily, Cardiocondyla are often not recognized as successful invaders. Here, we document that the life history of Cardiocondyla closely resembles that of the more conspicuous tramp species, with polygyny, intranidal mating, budding, worker sterility, low genetic variability, and possibly also unicoloniality. Given that introduced Cardiocondyla may locally reach a very high population density, the effects of these stealthy invaders on the native arthropod fauna should receive more attention. author: - 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 - first_name: Norbert full_name: Eckl, Norbert last_name: Eckl - first_name: Alexandra full_name: Schrempf, Alexandra last_name: Schrempf citation: ama: 'Heinze J, Cremer S, Eckl N, Schrempf A. Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. 2006;53(1):1-7. doi:10.1007/s00040-005-0847-4' apa: 'Heinze, J., Cremer, S., Eckl, N., & Schrempf, A. (2006). Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. Springer. https://doi.org/10.1007/s00040-005-0847-4' chicago: 'Heinze, Jürgen, Sylvia Cremer, Norbert Eckl, and Alexandra Schrempf. “Stealthy Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux. Springer, 2006. https://doi.org/10.1007/s00040-005-0847-4.' ieee: 'J. Heinze, S. Cremer, N. Eckl, and A. Schrempf, “Stealthy invaders: the biology of Cardiocondyla tramp ants,” Insectes Sociaux, vol. 53, no. 1. Springer, pp. 1–7, 2006.' ista: 'Heinze J, Cremer S, Eckl N, Schrempf A. 2006. Stealthy invaders: the biology of Cardiocondyla tramp ants. Insectes Sociaux. 53(1), 1–7.' mla: 'Heinze, Jürgen, et al. “Stealthy Invaders: The Biology of Cardiocondyla Tramp Ants.” Insectes Sociaux, vol. 53, no. 1, Springer, 2006, pp. 1–7, doi:10.1007/s00040-005-0847-4.' short: J. Heinze, S. Cremer, N. Eckl, A. Schrempf, Insectes Sociaux 53 (2006) 1–7. date_created: 2018-12-11T12:05:51Z date_published: 2006-02-01T00:00:00Z date_updated: 2021-01-12T07:53:09Z day: '01' doi: 10.1007/s00040-005-0847-4 extern: '1' intvolume: ' 53' issue: '1' language: - iso: eng month: '02' oa_version: None page: 1 - 7 publication: Insectes Sociaux publication_status: published publisher: Springer publist_id: '2240' status: public title: 'Stealthy invaders: the biology of Cardiocondyla tramp ants' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2006' ... --- _id: '3932' abstract: - lang: eng text: 'OBJECTIVES: The EGFR is expressed in malignant ovarian tumor tissue, and tissue content of EGFR has been directly associated with poor prognosis in patients with ovarian cancer. The uPA system plays a role in pericellular proteolysis, cell migration, invasion, and is over-expressed in ovarian cancer. This study explored the effects of EGF on uPAR expression in the ovarian cancer cell line OVCAR-3. METHODS: We used OVCAR-3 cells and the following methods: cell migration assay, time-lapse video microscopy, real-time PCR, assays for cellular binding of 125I-uPA and cellular degradation of 125I-uPA:PAI-1 complex, biosynthetic labeling using 35S-methionin, Western blot, Northern blot, and ELISAs for uPA, PAI-1, and uPAR. RESULTS: EGF up-regulates both protein and mRNA not only for uPAR, but also for the ligand uPA and its inhibitor PAI-1. Cell surface uPAR, in control as well as EGF-stimulated cells, is present only in the intact, not the cleaved, form. Ligand binding experiments showed an increase of endogenously occupied uPAR, whereas non-occupied receptor sites were not increased. In addition, EGF treatment resulted in decreased degradation of radiolabeled uPA:PAI-1 complex. This suggests decreased internalization of uPAR, since the complex is internalized together with uPAR. Like EGF, colchicine, which inhibits endocytosis, increased cell surface expression of uPAR. In addition, we found an immediate increase of uPAR after exposing the cells to EGF and this was accompanied by a transient increase of cell migration. The increase of cell surface uPAR in response to EGF is accompanied by increased release of the soluble form of uPAR (suPAR) to the medium as well as by increased cell migration. Both uPAR and suPAR increased in cells treated with the endocytosis inhibitor colchicine even though cell migration was inhibited, suggesting that the mechanism of uPAR shedding is not related to cell migration. CONCLUSION: Increased cell surface uPAR in response to EGF stimulation results from mobilization of uPAR from detergent-resistant domains, increased expression of uPAR mRNA, and decreased internalization and degradation of uPAR. Both the anti-uPAR antibody R3, which inhibits binding of uPA, and the EGFR phosphorylation inhibitor Iressa inhibited cell migration in response to uPA as well as to EGF, suggesting that EGFR and uPAR are engaged in the same multiprotein assembly on the cell surface.' author: - first_name: Emir full_name: Henic, Emir last_name: Henic - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Stefan full_name: Hansson, Stefan last_name: Hansson - first_name: Gunilla full_name: Høyer-Hansen, Gunilla last_name: Høyer Hansen - first_name: Bertil full_name: Casslén, Bertil last_name: Casslén citation: ama: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. 2006;101(1):28-39. doi:10.1016/j.ygyno.2005.09.038 apa: Henic, E., Sixt, M. K., Hansson, S., Høyer Hansen, G., & Casslén, B. (2006). EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. Elsevier. https://doi.org/10.1016/j.ygyno.2005.09.038 chicago: Henic, Emir, Michael K Sixt, Stefan Hansson, Gunilla Høyer Hansen, and Bertil Casslén. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated with Decreased Internalization, Increased Surface Expression, and Increased Shedding of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology. Elsevier, 2006. https://doi.org/10.1016/j.ygyno.2005.09.038. ieee: E. Henic, M. K. Sixt, S. Hansson, G. Høyer Hansen, and B. Casslén, “EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor,” Gynecologic Oncology, vol. 101, no. 1. Elsevier, pp. 28–39, 2006. ista: Henic E, Sixt MK, Hansson S, Høyer Hansen G, Casslén B. 2006. EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor. Gynecologic Oncology. 101(1), 28–39. mla: Henic, Emir, et al. “EGF-Stimulated Migration in Ovarian Cancer Cells Is Associated with Decreased Internalization, Increased Surface Expression, and Increased Shedding of the Urokinase Plasminogen Activator Receptor.” Gynecologic Oncology, vol. 101, no. 1, Elsevier, 2006, pp. 28–39, doi:10.1016/j.ygyno.2005.09.038. short: E. Henic, M.K. Sixt, S. Hansson, G. Høyer Hansen, B. Casslén, Gynecologic Oncology 101 (2006) 28–39. date_created: 2018-12-11T12:05:57Z date_published: 2006-04-01T00:00:00Z date_updated: 2021-01-12T07:53:17Z day: '01' doi: 10.1016/j.ygyno.2005.09.038 extern: 1 intvolume: ' 101' issue: '1' month: '04' page: 28 - 39 publication: Gynecologic Oncology publication_status: published publisher: Elsevier publist_id: '2194' quality_controlled: 0 status: public title: EGF-stimulated migration in ovarian cancer cells is associated with decreased internalization, increased surface expression, and increased shedding of the urokinase plasminogen activator receptor type: journal_article volume: 101 year: '2006' ... --- _id: '3978' abstract: - lang: eng text: Evaluating the quality of experimentally determined protein structural models is an essential step toward identifying potential errors and guiding further structural refinement. Herein, we report the use of proton local density as a sensitive measure to assess the quality of nuclear magnetic resonance (NMR) structures. Using 256 high-resolution crystal structures with protons added and optimized, we show that the local density of different proton types display distinct distributions. These distributions can be characterized by statistical moments and are used to establish local density Z-scores for evaluating both global and local packing for individual protons. Analysis of 546 crystal structures at various resolutions shows that the local density Z-scores increase as the structural resolution decreases and correlate well with the ClashScore (Word et al. J Mol Biol 1999;285(4):1711-1733) generated by all atom contact analysis. Local density Z-scores for NMR structures exhibit a significantly wider range of values than for X-ray structures and demonstrate a combination of potentially problematic inflation and compression. Water-refined NMR structures show improved packing quality. Our analysis of a high-quality structural ensemble of ubiquitin refined against order parameters shows proton density distributions that correlate nearly perfectly with our standards derived from crystal structures, further validating our approach. We present an automated analysis and visualization tool for proton packing to evaluate the quality of NMR structures. author: - first_name: Yih full_name: Ban, Yih-En Andrew last_name: Ban - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph - first_name: Pei full_name: Zhou, Pei last_name: Zhou - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. 2006;62(4):852-864. doi:10.1002/prot.20811' apa: 'Ban, Y., Rudolph, J., Zhou, P., & Edelsbrunner, H. (2006). Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.20811' chicago: 'Ban, Yih, Johannes Rudolph, Pei Zhou, and Herbert Edelsbrunner. “Evaluating the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2006. https://doi.org/10.1002/prot.20811.' ieee: 'Y. Ban, J. Rudolph, P. Zhou, and H. Edelsbrunner, “Evaluating the quality of NMR structures by local density of protons,” Proteins: Structure, Function and Bioinformatics, vol. 62, no. 4. Wiley-Blackwell, pp. 852–864, 2006.' ista: 'Ban Y, Rudolph J, Zhou P, Edelsbrunner H. 2006. Evaluating the quality of NMR structures by local density of protons. Proteins: Structure, Function and Bioinformatics. 62(4), 852–864.' mla: 'Ban, Yih, et al. “Evaluating the Quality of NMR Structures by Local Density of Protons.” Proteins: Structure, Function and Bioinformatics, vol. 62, no. 4, Wiley-Blackwell, 2006, pp. 852–64, doi:10.1002/prot.20811.' short: 'Y. Ban, J. Rudolph, P. Zhou, H. Edelsbrunner, Proteins: Structure, Function and Bioinformatics 62 (2006) 852–864.' date_created: 2018-12-11T12:06:14Z date_published: 2006-03-01T00:00:00Z date_updated: 2021-01-12T07:53:36Z day: '01' doi: 10.1002/prot.20811 extern: 1 intvolume: ' 62' issue: '4' month: '03' page: 852 - 864 publication: 'Proteins: Structure, Function and Bioinformatics' publication_status: published publisher: Wiley-Blackwell publist_id: '2146' quality_controlled: 0 status: public title: Evaluating the quality of NMR structures by local density of protons type: journal_article volume: 62 year: '2006' ... --- _id: '3979' abstract: - lang: eng text: Protein-protein interactions, which form the basis for most cellular processes, result in the formation of protein interfaces. Believing that the local shape of proteins is crucial, we take a geometric approach and present a definition of an interface surface formed by two or more proteins as a subset of their Voronoi diagram. The definition deals with the difficult and important problem of specifying interface boundaries by invoking methods used in the alpha shape representation of molecules, the discrete flow on Delaunay simplices to define pockets and reconstruct surfaces, and the assessment of the importance of topological features. We present an algorithm to construct the surface and define a hierarchy that distinguishes core and peripheral regions. This hierarchy is shown to have correlation with hot-spots in protein-protein interactions. Finally, we study the geometric and topological properties of interface surfaces and show their high degree of contortion. author: - first_name: Yih full_name: Ban, Yih-En Andrew last_name: Ban - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Johannes full_name: Rudolph, Johannes last_name: Rudolph citation: ama: Ban Y, Edelsbrunner H, Rudolph J. Interface surfaces for protein-protein complexes. Journal of the ACM. 2006;53(3):361-378. doi:10.1145/1147954.1147957 apa: Ban, Y., Edelsbrunner, H., & Rudolph, J. (2006). Interface surfaces for protein-protein complexes. Journal of the ACM. ACM. https://doi.org/10.1145/1147954.1147957 chicago: Ban, Yih, Herbert Edelsbrunner, and Johannes Rudolph. “Interface Surfaces for Protein-Protein Complexes.” Journal of the ACM. ACM, 2006. https://doi.org/10.1145/1147954.1147957. ieee: Y. Ban, H. Edelsbrunner, and J. Rudolph, “Interface surfaces for protein-protein complexes,” Journal of the ACM, vol. 53, no. 3. ACM, pp. 361–378, 2006. ista: Ban Y, Edelsbrunner H, Rudolph J. 2006. Interface surfaces for protein-protein complexes. Journal of the ACM. 53(3), 361–378. mla: Ban, Yih, et al. “Interface Surfaces for Protein-Protein Complexes.” Journal of the ACM, vol. 53, no. 3, ACM, 2006, pp. 361–78, doi:10.1145/1147954.1147957. short: Y. Ban, H. Edelsbrunner, J. Rudolph, Journal of the ACM 53 (2006) 361–378. date_created: 2018-12-11T12:06:14Z date_published: 2006-05-01T00:00:00Z date_updated: 2021-01-12T07:53:37Z day: '01' doi: 10.1145/1147954.1147957 extern: 1 intvolume: ' 53' issue: '3' month: '05' page: 361 - 378 publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '2147' quality_controlled: 0 status: public title: Interface surfaces for protein-protein complexes type: journal_article volume: 53 year: '2006' ...