--- _id: '3534' author: - first_name: David full_name: Dupret, David last_name: Dupret - first_name: Barty full_name: Pleydell-Bouverie, Barty last_name: Pleydell Bouverie - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: Dupret D, Pleydell Bouverie B, Csicsvari JL. Inhibitory interneurons and network oscillations. PNAS. 2008;105(47):18079-18080. doi:10.1073/pnas.0810064105 apa: Dupret, D., Pleydell Bouverie, B., & Csicsvari, J. L. (2008). Inhibitory interneurons and network oscillations. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0810064105 chicago: Dupret, David, Barty Pleydell Bouverie, and Jozsef L Csicsvari. “Inhibitory Interneurons and Network Oscillations.” PNAS. National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0810064105. ieee: D. Dupret, B. Pleydell Bouverie, and J. L. Csicsvari, “Inhibitory interneurons and network oscillations,” PNAS, vol. 105, no. 47. National Academy of Sciences, pp. 18079–18080, 2008. ista: Dupret D, Pleydell Bouverie B, Csicsvari JL. 2008. Inhibitory interneurons and network oscillations. PNAS. 105(47), 18079–18080. mla: Dupret, David, et al. “Inhibitory Interneurons and Network Oscillations.” PNAS, vol. 105, no. 47, National Academy of Sciences, 2008, pp. 18079–80, doi:10.1073/pnas.0810064105. short: D. Dupret, B. Pleydell Bouverie, J.L. Csicsvari, PNAS 105 (2008) 18079–18080. date_created: 2018-12-11T12:03:50Z date_published: 2008-11-25T00:00:00Z date_updated: 2021-01-12T07:44:08Z day: '25' doi: 10.1073/pnas.0810064105 extern: 1 intvolume: ' 105' issue: '47' month: '11' page: 18079 - 18080 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '2852' quality_controlled: 0 status: public title: Inhibitory interneurons and network oscillations type: journal_article volume: 105 year: '2008' ... --- _id: '3600' abstract: - lang: eng text: Scalability is one of the most important issues for optimization algorithms used in wireless sensor networks (WSNs) since there are often many parameters to be optimized at the same time. In this case it is very hard to ensure that an optimization algorithm can be smoothly scaled up from a low-dimensional optimization problem to the one with a high dimensionality. This paper addresses the scalability issue of a novel optimization algorithm inspired by the Shifting Balance Theory (SBT) of evolution in population genetics. Toward this end, a cluster-based WSN is employed in this paper as a benchmark to perform a comparative study. The total energy consumption is minimized under the required quality of service by jointly optimizing the transmission power and rate for each sensor node. The results obtained by the SBT-based algorithm are compared with the Metropolis algorithm (MA) and currently popular particle swarm optimizer (PSO) to assess the scaling performance of the three algorithms against the same WSN optimization problem. alternative_title: - LNCS author: - first_name: Erfu full_name: Yang, Erfu last_name: Yang - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Tughrul full_name: Arslan, Tughrul last_name: Arslan - first_name: Ahmet full_name: Erdogan, Ahmet T last_name: Erdogan citation: ama: 'Yang E, Barton NH, Arslan T, Erdogan A. Scalability of a novel shifting balance theory-based optimization algorithm: A comparative study on a cluster-based wireless sensor network. In: Vol 5216. Springer; 2008:249-260. doi:10.1007/978-3-540-85857-7_22' apa: 'Yang, E., Barton, N. H., Arslan, T., & Erdogan, A. (2008). Scalability of a novel shifting balance theory-based optimization algorithm: A comparative study on a cluster-based wireless sensor network (Vol. 5216, pp. 249–260). Presented at the IECS: International Conference on Evolvable Systems, Springer. https://doi.org/10.1007/978-3-540-85857-7_22' chicago: 'Yang, Erfu, Nicholas H Barton, Tughrul Arslan, and Ahmet Erdogan. “ Scalability of a Novel Shifting Balance Theory-Based Optimization Algorithm: A Comparative Study on a Cluster-Based Wireless Sensor Network,” 5216:249–60. Springer, 2008. https://doi.org/10.1007/978-3-540-85857-7_22.' ieee: 'E. Yang, N. H. Barton, T. Arslan, and A. Erdogan, “ Scalability of a novel shifting balance theory-based optimization algorithm: A comparative study on a cluster-based wireless sensor network,” presented at the IECS: International Conference on Evolvable Systems, 2008, vol. 5216, pp. 249–260.' ista: 'Yang E, Barton NH, Arslan T, Erdogan A. 2008. Scalability of a novel shifting balance theory-based optimization algorithm: A comparative study on a cluster-based wireless sensor network. IECS: International Conference on Evolvable Systems, LNCS, vol. 5216, 249–260.' mla: 'Yang, Erfu, et al. Scalability of a Novel Shifting Balance Theory-Based Optimization Algorithm: A Comparative Study on a Cluster-Based Wireless Sensor Network. Vol. 5216, Springer, 2008, pp. 249–60, doi:10.1007/978-3-540-85857-7_22.' short: E. Yang, N.H. Barton, T. Arslan, A. Erdogan, in:, Springer, 2008, pp. 249–260. conference: name: 'IECS: International Conference on Evolvable Systems' date_created: 2018-12-11T12:04:10Z date_published: 2008-09-08T00:00:00Z date_updated: 2021-01-12T07:44:35Z day: '08' doi: 10.1007/978-3-540-85857-7_22 extern: 1 intvolume: ' 5216' month: '09' page: 249 - 260 publication_status: published publisher: Springer publist_id: '2783' quality_controlled: 0 status: public title: ' Scalability of a novel shifting balance theory-based optimization algorithm: A comparative study on a cluster-based wireless sensor network' type: conference volume: 5216 year: '2008' ... --- _id: '3606' abstract: - lang: eng text: 'Explicit formulae are given for the effects of a barrier to gene flow on random fluctuations in allele frequency; these formulae can also be seen as generating functions for the distribution of coalescence times. The formulae are derived using a continuous diffusion approximation, which is accurate over all but very small spatial scales. The continuous approximation is confirmed by comparison with the exact solution to the stepping stone model. In both one and two spatial dimensions, the variance of fluctuations in allele frequencies increases near the barrier; when the barrier is very strong, the variance doubles. However, the effect on fluctuations close to the barrier is much greater when the population is spread over two spatial dimensions than when it occupies a linear, one-dimensional habitat: barriers of strength comparable with the dispersal range (B≈σ) can have an appreciable effect in two dimensions, whereas only barriers with strength comparable with the characteristic scale (B\! \approx\! L \equals \sigma \sol \sqrt {2 \mu}\hskip2) are significant in one dimension (μ is the rate of mutation or long-range dispersal). Thus, in a two-dimensional population, barriers to gene flow can be detected through their effect on the spatial pattern of genetic marker alleles.' author: - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Barton NH. The effect of a barrier to gene flow on patterns of geographic variation. Genetical Research. 2008;90(1):139-149. doi:10.1017/S0016672307009081 apa: Barton, N. H. (2008). The effect of a barrier to gene flow on patterns of geographic variation. Genetical Research. Cambridge University Press. https://doi.org/10.1017/S0016672307009081 chicago: Barton, Nicholas H. “The Effect of a Barrier to Gene Flow on Patterns of Geographic Variation.” Genetical Research. Cambridge University Press, 2008. https://doi.org/10.1017/S0016672307009081. ieee: N. H. Barton, “The effect of a barrier to gene flow on patterns of geographic variation,” Genetical Research, vol. 90, no. 1. Cambridge University Press, pp. 139–149, 2008. ista: Barton NH. 2008. The effect of a barrier to gene flow on patterns of geographic variation. Genetical Research. 90(1), 139–149. mla: Barton, Nicholas H. “The Effect of a Barrier to Gene Flow on Patterns of Geographic Variation.” Genetical Research, vol. 90, no. 1, Cambridge University Press, 2008, pp. 139–49, doi:10.1017/S0016672307009081. short: N.H. Barton, Genetical Research 90 (2008) 139–149. date_created: 2018-12-11T12:04:12Z date_published: 2008-02-01T00:00:00Z date_updated: 2021-01-12T07:44:37Z day: '01' doi: 10.1017/S0016672307009081 extern: 1 intvolume: ' 90' issue: '1' month: '02' page: 139 - 149 publication: Genetical Research publication_status: published publisher: Cambridge University Press publist_id: '2777' quality_controlled: 0 status: public title: The effect of a barrier to gene flow on patterns of geographic variation type: journal_article volume: 90 year: '2008' ... --- _id: '3605' abstract: - lang: eng text: Many animals and plants show a correlation between the traits of the individuals in the mating pair, implying assortative mating. Given the ubiquity of assortative mating in nature, why and how it has evolved remain open questions. Here we attempt to answer these questions in those cases where the trait under assortment is the same in males and females. We consider the most favorable scenario for assortment to evolve, where the same trait is under assortment and viability selection. We find conditions for assortment to evolve using a multilocus formalism in a haploid population. Our results show how epistasis in fitness between the loci that control the focal trait is crucial for assortment to evolve. We then assume specific forms of assortment in haploids and diploids and study the limiting cases of selective and nonselective mating. We find that selection for increased assortment is weak and that where increased assortment is costly, it does not invade. author: - first_name: Maria full_name: De Cara, Maria A last_name: De Cara - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Mark full_name: Kirkpatrick, Mark last_name: Kirkpatrick citation: ama: De Cara M, Barton NH, Kirkpatrick M. A model for the evolution of assortative mating. American Naturalist. 2008;171(5):580-596. doi:10.1086/587062 apa: De Cara, M., Barton, N. H., & Kirkpatrick, M. (2008). A model for the evolution of assortative mating. American Naturalist. University of Chicago Press. https://doi.org/10.1086/587062 chicago: De Cara, Maria, Nicholas H Barton, and Mark Kirkpatrick. “A Model for the Evolution of Assortative Mating.” American Naturalist. University of Chicago Press, 2008. https://doi.org/10.1086/587062. ieee: M. De Cara, N. H. Barton, and M. Kirkpatrick, “A model for the evolution of assortative mating,” American Naturalist, vol. 171, no. 5. University of Chicago Press, pp. 580–596, 2008. ista: De Cara M, Barton NH, Kirkpatrick M. 2008. A model for the evolution of assortative mating. American Naturalist. 171(5), 580–596. mla: De Cara, Maria, et al. “A Model for the Evolution of Assortative Mating.” American Naturalist, vol. 171, no. 5, University of Chicago Press, 2008, pp. 580–96, doi:10.1086/587062. short: M. De Cara, N.H. Barton, M. Kirkpatrick, American Naturalist 171 (2008) 580–596. date_created: 2018-12-11T12:04:12Z date_published: 2008-05-01T00:00:00Z date_updated: 2021-01-12T07:44:36Z day: '01' doi: 10.1086/587062 extern: 1 intvolume: ' 171' issue: '5' month: '05' page: 580 - 596 publication: American Naturalist publication_status: published publisher: University of Chicago Press publist_id: '2778' quality_controlled: 0 status: public title: A model for the evolution of assortative mating type: journal_article volume: 171 year: '2008' ... --- _id: '3705' abstract: - lang: eng text: 'Sliding window classifiers are among the most successful and widely applied techniques for object localization. However, training is typically done in a way that is not specific to the localization task. First a binary classifier is trained using a sample of positive and negative examples, and this classifier is subsequently applied to multiple regions within test images. We propose instead to treat object localization in a principled way by posing it as a problem of predicting structured data: we model the problem not as binary classification, but as the prediction of the bounding box of objects located in images. The use of a joint-kernel framework allows us to formulate the training procedure as a generalization of an SVM, which can be solved efficiently. We further improve computational efficiency by using a branch-and-bound strategy for localization during both training and testing. Experimental evaluation on the PASCAL VOC and TU Darmstadt datasets show that the structured training procedure improves pe rformance over binary training as well as the best previously published scores.' alternative_title: - LNCS author: - first_name: Matthew full_name: Blaschko,Matthew B last_name: Blaschko - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Blaschko M, Lampert C. Learning to localize objects with structured output regression. In: Vol 5302. Springer; 2008:2-15. doi:10.1007/978-3-540-88682-2_2' apa: 'Blaschko, M., & Lampert, C. (2008). Learning to localize objects with structured output regression (Vol. 5302, pp. 2–15). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/978-3-540-88682-2_2' chicago: Blaschko, Matthew, and Christoph Lampert. “Learning to Localize Objects with Structured Output Regression,” 5302:2–15. Springer, 2008. https://doi.org/10.1007/978-3-540-88682-2_2. ieee: 'M. Blaschko and C. Lampert, “Learning to localize objects with structured output regression,” presented at the ECCV: European Conference on Computer Vision, 2008, vol. 5302, pp. 2–15.' ista: 'Blaschko M, Lampert C. 2008. Learning to localize objects with structured output regression. ECCV: European Conference on Computer Vision, LNCS, vol. 5302, 2–15.' mla: Blaschko, Matthew, and Christoph Lampert. Learning to Localize Objects with Structured Output Regression. Vol. 5302, Springer, 2008, pp. 2–15, doi:10.1007/978-3-540-88682-2_2. short: M. Blaschko, C. Lampert, in:, Springer, 2008, pp. 2–15. conference: name: 'ECCV: European Conference on Computer Vision' date_created: 2018-12-11T12:04:43Z date_published: 2008-11-17T00:00:00Z date_updated: 2021-01-12T07:51:37Z day: '17' doi: 10.1007/978-3-540-88682-2_2 extern: 1 intvolume: ' 5302' main_file_link: - open_access: '0' url: http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/attachments/ECCV2008-Blaschko_5247%5b0%5d.pdf month: '11' page: 2 - 15 publication_status: published publisher: Springer publist_id: '2653' quality_controlled: 0 status: public title: Learning to localize objects with structured output regression type: conference volume: 5302 year: '2008' ... --- _id: '3700' abstract: - lang: eng text: We propose a new method to partition an unlabeled dataset, called Discriminative Context Partitioning (DCP). It is motivated by the idea of splitting the dataset based only on how well the resulting parts can be separated from a context class of disjoint data points. This is in contrast to typical clustering techniques like K-means that are based on a generative model by implicitly or explicitly searching for modes in the distribution of samples. The discriminative criterion in DCP avoids the problems that density based methods have when the a priori assumption of multimodality is violated, when the number of samples becomes small in relation to the dimensionality of the feature space, or if the cluster sizes are strongly unbalanced. We formulate DCP‘s separation property as a large-margin criterion, and show how the resulting optimization problem can be solved efficiently. Experiments on the MNIST and USPS datasets of handwritten digits and on a subset of the Caltech256 dataset show that, given a suitable context, DCP can achieve good results even in situation where density-based clustering techniques fail. acknowledgement: This work was funded in part by the EC project CLASS, IST 027978. 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. Partitioning of image datasets using discriminative context information. In: IEEE; 2008:1-8. doi:10.1109/CVPR.2008.4587448' apa: 'Lampert, C. (2008). Partitioning of image datasets using discriminative context information (pp. 1–8). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2008.4587448' chicago: Lampert, Christoph. “Partitioning of Image Datasets Using Discriminative Context Information,” 1–8. IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587448. ieee: 'C. Lampert, “Partitioning of image datasets using discriminative context information,” presented at the CVPR: Computer Vision and Pattern Recognition, 2008, pp. 1–8.' ista: 'Lampert C. 2008. Partitioning of image datasets using discriminative context information. CVPR: Computer Vision and Pattern Recognition, 1–8.' mla: Lampert, Christoph. Partitioning of Image Datasets Using Discriminative Context Information. IEEE, 2008, pp. 1–8, doi:10.1109/CVPR.2008.4587448. short: C. Lampert, in:, IEEE, 2008, pp. 1–8. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:04:41Z date_published: 2008-09-18T00:00:00Z date_updated: 2021-01-12T07:51:35Z day: '18' doi: 10.1109/CVPR.2008.4587448 extern: 1 main_file_link: - open_access: '0' url: http://pub.ist.ac.at/~chl/papers/lampert-cvpr2008b.pdf month: '09' page: 1 - 8 publication_status: published publisher: IEEE publist_id: '2657' quality_controlled: 0 status: public title: Partitioning of image datasets using discriminative context information type: conference year: '2008' ... --- _id: '3716' abstract: - lang: eng text: | Most current methods for multi-class object classification and localization work as independent 1-vs-rest classifiers. They decide whether and where an object is visible in an image purely on a per-class basis. Joint learning of more than one object class would generally be preferable, since this would allow the use of contextual information such as co-occurrence between classes. However, this approach is usually not employed because of its computational cost. In this paper we propose a method to combine the efficiency of single class localization with a subsequent decision process that works jointly for all given object classes. By following a multiple kernel learning (MKL) approach, we automatically obtain a sparse dependency graph of relevant object classes on which to base the decision. Experiments on the PASCAL VOC 2006 and 2007 datasets show that the subsequent joint decision step clearly improves the accuracy compared to single class detection. alternative_title: - LNCS author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Matthew full_name: Blaschko,Matthew B last_name: Blaschko citation: ama: 'Lampert C, Blaschko M. A multiple kernel learning approach to joint multi-class object detection. In: Vol 5096. Springer; 2008:31-40. doi:10.1007/978-3-540-69321-5_4' apa: 'Lampert, C., & Blaschko, M. (2008). A multiple kernel learning approach to joint multi-class object detection (Vol. 5096, pp. 31–40). Presented at the DAGM: German Association For Pattern Recognition, Springer. https://doi.org/10.1007/978-3-540-69321-5_4' chicago: Lampert, Christoph, and Matthew Blaschko. “A Multiple Kernel Learning Approach to Joint Multi-Class Object Detection,” 5096:31–40. Springer, 2008. https://doi.org/10.1007/978-3-540-69321-5_4. ieee: 'C. Lampert and M. Blaschko, “A multiple kernel learning approach to joint multi-class object detection,” presented at the DAGM: German Association For Pattern Recognition, 2008, vol. 5096, pp. 31–40.' ista: 'Lampert C, Blaschko M. 2008. A multiple kernel learning approach to joint multi-class object detection. DAGM: German Association For Pattern Recognition, LNCS, vol. 5096, 31–40.' mla: Lampert, Christoph, and Matthew Blaschko. A Multiple Kernel Learning Approach to Joint Multi-Class Object Detection. Vol. 5096, Springer, 2008, pp. 31–40, doi:10.1007/978-3-540-69321-5_4. short: C. Lampert, M. Blaschko, in:, Springer, 2008, pp. 31–40. conference: name: 'DAGM: German Association For Pattern Recognition' date_created: 2018-12-11T12:04:46Z date_published: 2008-07-07T00:00:00Z date_updated: 2021-01-12T07:51:41Z day: '07' doi: 10.1007/978-3-540-69321-5_4 extern: 1 intvolume: ' 5096' main_file_link: - open_access: '0' url: http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/attachments/DAGM2008-Lampert-Blaschko_5072%5b0%5d.pdf month: '07' page: 31 - 40 publication_status: published publisher: Springer publist_id: '2641' quality_controlled: 0 status: public title: A multiple kernel learning approach to joint multi-class object detection type: conference volume: 5096 year: '2008' ... --- _id: '3714' abstract: - lang: eng text: Most successful object recognition systems rely on binary classification, deciding only if an object is present or not, but not providing information on the actual object location. To perform localization, one can take a sliding window approach, but this strongly increases the computational cost, because the classifier function has to be evaluated over a large set of candidate subwindows. In this paper, we propose a simple yet powerful branchand- bound scheme that allows efficient maximization of a large class of classifier functions over all possible subimages. It converges to a globally optimal solution typically in sublinear time. We show how our method is applicable to different object detection and retrieval scenarios. The achieved speedup allows the use of classifiers for localization that formerly were considered too slow for this task, such as SVMs with a spatial pyramid kernel or nearest neighbor classifiers based on the 2-distance. We demonstrate state-of-the-art performance of the resulting systems on the UIUC Cars dataset, the PASCAL VOC 2006 dataset and in the PASCAL VOC 2007 competition. author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Matthew full_name: Blaschko,Matthew B last_name: Blaschko - first_name: Thomas full_name: Hofmann,Thomas last_name: Hofmann citation: ama: 'Lampert C, Blaschko M, Hofmann T. Beyond sliding windows: Object localization by efficient subwindow search. In: IEEE; 2008:1-8. doi:10.1109/CVPR.2008.4587586' apa: 'Lampert, C., Blaschko, M., & Hofmann, T. (2008). Beyond sliding windows: Object localization by efficient subwindow search (pp. 1–8). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2008.4587586' chicago: 'Lampert, Christoph, Matthew Blaschko, and Thomas Hofmann. “Beyond Sliding Windows: Object Localization by Efficient Subwindow Search,” 1–8. IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587586.' ieee: 'C. Lampert, M. Blaschko, and T. Hofmann, “Beyond sliding windows: Object localization by efficient subwindow search,” presented at the CVPR: Computer Vision and Pattern Recognition, 2008, pp. 1–8.' ista: 'Lampert C, Blaschko M, Hofmann T. 2008. Beyond sliding windows: Object localization by efficient subwindow search. CVPR: Computer Vision and Pattern Recognition, 1–8.' mla: 'Lampert, Christoph, et al. Beyond Sliding Windows: Object Localization by Efficient Subwindow Search. IEEE, 2008, pp. 1–8, doi:10.1109/CVPR.2008.4587586.' short: C. Lampert, M. Blaschko, T. Hofmann, in:, IEEE, 2008, pp. 1–8. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:04:46Z date_published: 2008-09-18T00:00:00Z date_updated: 2021-01-12T07:51:40Z day: '18' doi: 10.1109/CVPR.2008.4587586 extern: 1 main_file_link: - open_access: '0' url: http://www.kyb.mpg.de/fileadmin/user_upload/files/publications/pdfs/pdf5070.pdf month: '09' page: 1 - 8 publication_status: published publisher: IEEE publist_id: '2644' quality_controlled: 0 status: public title: 'Beyond sliding windows: Object localization by efficient subwindow search' type: conference year: '2008' ... --- _id: '3734' abstract: - lang: eng text: Gene expression levels fluctuate even under constant external conditions. Much emphasis has usually been placed on the components of this noise that are due to randomness in transcription and translation. Here we focus on the role of noise associated with the inputs to transcriptional regulation; in particular, we analyze the effects of random arrival times and binding of transcription factors to their target sites along the genome. This contribution to the total noise sets a fundamental physical limit to the reliability of genetic control, and has clear signatures, but we show that these are easily obscured by experimental limitations and even by conventional methods for plotting the variance vs. mean expression level. We argue that simple, universal models of noise dominated by transcription and translation are inconsistent with the embedding of gene expression in a network of regulatory interactions. Analysis of recent experiments on transcriptional control in the early Drosophila embryo shows that these results are quantitatively consistent with the predicted signatures of input noise, and we discuss the experiments needed to test the importance of input noise more generally. acknowledgement: NSF Grant PHY-0650617; NIH grants P50 GM071508, R01 GM077599; Burroughs Wellcome Program in Biological Dynamics author: - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor - first_name: William full_name: Bialek, William S last_name: Bialek citation: ama: Tkačik G, Gregor T, Bialek W. The role of input noise in transcriptional regulation. PLoS One. 2008;3(7). doi:10.1371/journal.pone.0002774 apa: Tkačik, G., Gregor, T., & Bialek, W. (2008). The role of input noise in transcriptional regulation. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0002774 chicago: Tkačik, Gašper, Thomas Gregor, and William Bialek. “The Role of Input Noise in Transcriptional Regulation.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002774. ieee: G. Tkačik, T. Gregor, and W. Bialek, “The role of input noise in transcriptional regulation,” PLoS One, vol. 3, no. 7. Public Library of Science, 2008. ista: Tkačik G, Gregor T, Bialek W. 2008. The role of input noise in transcriptional regulation. PLoS One. 3(7). mla: Tkačik, Gašper, et al. “The Role of Input Noise in Transcriptional Regulation.” PLoS One, vol. 3, no. 7, Public Library of Science, 2008, doi:10.1371/journal.pone.0002774. short: G. Tkačik, T. Gregor, W. Bialek, PLoS One 3 (2008). date_created: 2018-12-11T12:04:52Z date_published: 2008-07-23T00:00:00Z date_updated: 2021-01-12T07:51:49Z day: '23' doi: 10.1371/journal.pone.0002774 extern: 1 intvolume: ' 3' issue: '7' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2475664 month: '07' oa: 1 publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '2498' quality_controlled: 0 status: public title: The role of input noise in transcriptional regulation 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: '2008' ... --- _id: '3751' abstract: - lang: eng text: 'Revealing the spectrum of combinatorial regulation of transcription at individual promoters is essential for understanding the complex structure of biological networks. However, the computations represented by the integration of various molecular signals at complex promoters are difficult to decipher in the absence of simple cis regulatory codes. Here we synthetically shuffle the regulatory architecture-operator sequences binding activators and repressors-of a canonical bacterial promoter. The resulting library of complex promoters allows for rapid exploration of promoter encoded logic regulation. Among all possible logic functions, NOR and ANDN promoter encoded logics predominate. A simple transcriptional cis regulatory code determines both logics, establishing a straightforward map between promoter structure and logic phenotype. The regulatory code is determined solely by the type of transcriptional regulation combinations: two repressors generate a NOR: NOT (a OR b) whereas a repressor and an activator generate an ANDN: a AND NOT b. Three-input versions of both logics, having an additional repressor as an input, are also present in the library. The resulting complex promoters cover a wide dynamic range of transcriptional strengths. Synthetic promoter shuffling represents a fast and efficient method for exploring the spectrum of complex regulatory functions that can be encoded by complex promoters. From an engineering point of view, synthetic promoter shuffling enables the experimental testing of the functional properties of complex promoters that cannot necessarily be inferred ab initio from the known properties of the individual genetic components. Synthetic promoter shuffling may provide a useful experimental tool for studying naturally occurring promoter shuffling.' article_number: e2030 author: - first_name: Ali full_name: Kinkhabwala, Ali last_name: Kinkhabwala - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Kinkhabwala A, Guet CC. Uncovering cis regulatory codes using synthetic promoter shuffling. PLoS One. 2008;3(4). doi:10.1371/journal.pone.0002030 apa: Kinkhabwala, A., & Guet, C. C. (2008). Uncovering cis regulatory codes using synthetic promoter shuffling. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0002030 chicago: Kinkhabwala, Ali, and Calin C Guet. “Uncovering Cis Regulatory Codes Using Synthetic Promoter Shuffling.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002030. ieee: A. Kinkhabwala and C. C. Guet, “Uncovering cis regulatory codes using synthetic promoter shuffling,” PLoS One, vol. 3, no. 4. Public Library of Science, 2008. ista: Kinkhabwala A, Guet CC. 2008. Uncovering cis regulatory codes using synthetic promoter shuffling. PLoS One. 3(4), e2030. mla: Kinkhabwala, Ali, and Calin C. Guet. “Uncovering Cis Regulatory Codes Using Synthetic Promoter Shuffling.” PLoS One, vol. 3, no. 4, e2030, Public Library of Science, 2008, doi:10.1371/journal.pone.0002030. short: A. Kinkhabwala, C.C. Guet, PLoS One 3 (2008). date_created: 2018-12-11T12:04:58Z date_published: 2008-04-30T00:00:00Z date_updated: 2021-01-12T07:51:56Z day: '30' ddc: - '570' doi: 10.1371/journal.pone.0002030 extern: '1' external_id: pmid: - '18446205' file: - access_level: open_access checksum: 42c26f8337298a9ecadbe34a16139466 content_type: application/pdf creator: dernst date_created: 2019-05-10T11:00:36Z date_updated: 2020-07-14T12:46:15Z file_id: '6400' file_name: 2008_PLOS1_Kinkhabwala.PDF file_size: 679786 relation: main_file file_date_updated: 2020-07-14T12:46:15Z has_accepted_license: '1' intvolume: ' 3' issue: '4' language: - iso: eng license: https://creativecommons.org/publicdomain/zero/1.0/ month: '04' oa: 1 oa_version: Published Version pmid: 1 publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '2477' quality_controlled: '1' status: public title: Uncovering cis regulatory codes using synthetic promoter shuffling tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2008' ... --- _id: '3754' abstract: - lang: eng text: Fluorescence correlation spectroscopy (FCS) has permitted the characterization of high concentrations of noncoding RNAs in a single living bacterium. Here, we extend the use of FCS to low concentrations of coding RNAs in single living cells. We genetically fuse a red fluorescent protein (RFP) gene and two binding sites for an RNA-binding protein, whose translated product is the RFP protein alone. Using this construct, we determine in single cells both the absolute [mRNA] concentration and the associated [RFP] expressed from an inducible plasmid. We find that the FCS method allows us to reliably monitor in real-time [mRNA] down to similar to 40 nM (i.e. approximately two transcripts per volume of detection). To validate these measurements, we show that [mRNA] is proportional to the associated expression of the RFP protein. This FCS-based technique establishes a framework for minimally invasive measurements of mRNA concentration in individual living bacteria. acknowledgement: 'PMCID: PMC2475643 ' author: - first_name: Calin C full_name: Calin Guet id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Luke full_name: Bruneaux,Luke last_name: Bruneaux - first_name: Taejin full_name: Min,Taejin L last_name: Min - first_name: Dan full_name: Siegal-Gaskins,Dan last_name: Siegal Gaskins - first_name: Israel full_name: Figueroa,Israel last_name: Figueroa - first_name: Thierry full_name: Emonet,Thierry last_name: Emonet - first_name: Philippe full_name: Cluzel,Philippe last_name: Cluzel citation: ama: Guet CC, Bruneaux L, Min T, et al. Minimally invasive determination of mRNA concentration in single living bacteria. Nucleic Acids Research. 2008;36(12). doi:10.1093/nar/gkn329 apa: Guet, C. C., Bruneaux, L., Min, T., Siegal Gaskins, D., Figueroa, I., Emonet, T., & Cluzel, P. (2008). Minimally invasive determination of mRNA concentration in single living bacteria. Nucleic Acids Research. Oxford University Press. https://doi.org/10.1093/nar/gkn329 chicago: Guet, Calin C, Luke Bruneaux, Taejin Min, Dan Siegal Gaskins, Israel Figueroa, Thierry Emonet, and Philippe Cluzel. “Minimally Invasive Determination of MRNA Concentration in Single Living Bacteria.” Nucleic Acids Research. Oxford University Press, 2008. https://doi.org/10.1093/nar/gkn329. ieee: C. C. Guet et al., “Minimally invasive determination of mRNA concentration in single living bacteria,” Nucleic Acids Research, vol. 36, no. 12. Oxford University Press, 2008. ista: Guet CC, Bruneaux L, Min T, Siegal Gaskins D, Figueroa I, Emonet T, Cluzel P. 2008. Minimally invasive determination of mRNA concentration in single living bacteria. Nucleic Acids Research. 36(12). mla: Guet, Calin C., et al. “Minimally Invasive Determination of MRNA Concentration in Single Living Bacteria.” Nucleic Acids Research, vol. 36, no. 12, Oxford University Press, 2008, doi:10.1093/nar/gkn329. short: C.C. Guet, L. Bruneaux, T. Min, D. Siegal Gaskins, I. Figueroa, T. Emonet, P. Cluzel, Nucleic Acids Research 36 (2008). date_created: 2018-12-11T12:04:59Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:51:57Z day: '01' doi: 10.1093/nar/gkn329 extern: 1 intvolume: ' 36' issue: '12' license: https://creativecommons.org/licenses/by-nc/4.0/ month: '01' publication: Nucleic Acids Research publication_status: published publisher: Oxford University Press publist_id: '2474' quality_controlled: 0 status: public title: Minimally invasive determination of mRNA concentration in single living bacteria tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article volume: 36 year: '2008' ... --- _id: '3769' abstract: - lang: eng text: The geometrical representation of the space of phylogenetic trees implies a metric on the space of weighted trees. This metric, the geodesic distance, is the length of the shortest path through that space. We present an exact algorithm to compute this metric. For biologically reasonable trees, the implementation allows fast computations of the geodesic distance, although the running time of the algorithm is worst-case exponential. The algorithm was applied to pairs of 118 gene trees of the metazoa. The results show that a special path in tree space, the cone path, which can be computed in linear time, is a good approximation of the geodesic distance. The program GeoMeTree is a python implementation of the geodesic distance, and it is approximations and is available from www.cibiv.at/software/geometree. acknowledgement: 10.1089/cmb.2008.0068 author: - first_name: Anne full_name: Anne Kupczok id: 2BB22BC2-F248-11E8-B48F-1D18A9856A87 last_name: Kupczok - first_name: Arndt full_name: von Haeseler,Arndt last_name: Von Haeseler - first_name: Steffen full_name: Klaere,Steffen last_name: Klaere citation: ama: Kupczok A, Von Haeseler A, Klaere S. An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. Journal of Computational Biology. 2008;15(6):577-591. doi:4200 apa: Kupczok, A., Von Haeseler, A., & Klaere, S. (2008). An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. Journal of Computational Biology. Mary Ann Liebert. https://doi.org/4200 chicago: Kupczok, Anne, Arndt Von Haeseler, and Steffen Klaere. “An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.” Journal of Computational Biology. Mary Ann Liebert, 2008. https://doi.org/4200. ieee: A. Kupczok, A. Von Haeseler, and S. Klaere, “An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.,” Journal of Computational Biology, vol. 15, no. 6. Mary Ann Liebert, pp. 577–591, 2008. ista: Kupczok A, Von Haeseler A, Klaere S. 2008. An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. Journal of Computational Biology. 15(6), 577–591. mla: Kupczok, Anne, et al. “An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees.” Journal of Computational Biology, vol. 15, no. 6, Mary Ann Liebert, 2008, pp. 577–91, doi:4200. short: A. Kupczok, A. Von Haeseler, S. Klaere, Journal of Computational Biology 15 (2008) 577–591. date_created: 2018-12-11T12:05:04Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:52:04Z day: '01' doi: '4200' extern: 1 intvolume: ' 15' issue: '6' month: '01' page: 577 - 591 publication: Journal of Computational Biology publication_status: published publisher: Mary Ann Liebert publist_id: '2458' quality_controlled: 0 status: public title: An Exact Algorithm for the Geodesic Distance between Phylogenetic Trees. type: journal_article volume: 15 year: '2008' ... --- _id: '3826' abstract: - lang: eng text: Gamma frequency (30-100 Hz) oscillations in the mature cortex underlie higher cognitive functions. Fast signaling in GABAergic interneuron networks plays a key role in the generation of these oscillations. During development of the rodent brain, gamma activity appears at the end of the first postnatal week, but frequency and synchrony reach adult levels only by the fourth week. However, the mechanisms underlying the maturation of gamma activity are unclear. Here we demonstrate that hippocampal basket cells (BCs), the proposed cellular substrate of gamma oscillations, undergo marked changes in their morphological, intrinsic, and synaptic properties between postnatal day 6 (P6) and P25. During maturation, action potential duration, propagation time, duration of the release period, and decay time constant of IPSCs decreases by approximately 30-60%. Thus, postnatal development converts BCs from slow into fast signaling devices. Computational analysis reveals that BC networks with young intrinsic and synaptic properties as well as reduced connectivity generate oscillations with moderate coherence in the lower gamma frequency range. In contrast, BC networks with mature properties and increased connectivity generate highly coherent activity in the upper gamma frequency band. Thus, late postnatal maturation of BCs enhances coherence in neuronal networks and will thereby contribute to the development of cognitive brain functions. author: - first_name: Daniel full_name: Doischer, Daniel last_name: Doischer - first_name: Jonas full_name: Hosp, Jonas Aurel last_name: Hosp - first_name: Yuchio full_name: Yanagawa, Yuchio last_name: Yanagawa - first_name: Kunihiko full_name: Obata, Kunihiko last_name: Obata - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Imre full_name: Vida, Imre last_name: Vida - first_name: Marlene full_name: Bartos, Marlene last_name: Bartos citation: ama: Doischer D, Hosp J, Yanagawa Y, et al. Postnatal differentiation of basket cells from slow to fast signaling devices. Journal of Neuroscience. 2008;28(48):12956-12968. doi:10.1523/JNEUROSCI.2890-08.2008 apa: Doischer, D., Hosp, J., Yanagawa, Y., Obata, K., Jonas, P. M., Vida, I., & Bartos, M. (2008). Postnatal differentiation of basket cells from slow to fast signaling devices. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.2890-08.2008 chicago: Doischer, Daniel, Jonas Hosp, Yuchio Yanagawa, Kunihiko Obata, Peter M Jonas, Imre Vida, and Marlene Bartos. “Postnatal Differentiation of Basket Cells from Slow to Fast Signaling Devices.” Journal of Neuroscience. Society for Neuroscience, 2008. https://doi.org/10.1523/JNEUROSCI.2890-08.2008. ieee: D. Doischer et al., “Postnatal differentiation of basket cells from slow to fast signaling devices,” Journal of Neuroscience, vol. 28, no. 48. Society for Neuroscience, pp. 12956–68, 2008. ista: Doischer D, Hosp J, Yanagawa Y, Obata K, Jonas PM, Vida I, Bartos M. 2008. Postnatal differentiation of basket cells from slow to fast signaling devices. Journal of Neuroscience. 28(48), 12956–68. mla: Doischer, Daniel, et al. “Postnatal Differentiation of Basket Cells from Slow to Fast Signaling Devices.” Journal of Neuroscience, vol. 28, no. 48, Society for Neuroscience, 2008, pp. 12956–68, doi:10.1523/JNEUROSCI.2890-08.2008. short: D. Doischer, J. Hosp, Y. Yanagawa, K. Obata, P.M. Jonas, I. Vida, M. Bartos, Journal of Neuroscience 28 (2008) 12956–68. date_created: 2018-12-11T12:05:23Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:52:28Z day: '01' doi: 10.1523/JNEUROSCI.2890-08.2008 extern: 1 intvolume: ' 28' issue: '48' month: '01' page: 12956 - 68 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '2383' quality_controlled: 0 status: public title: Postnatal differentiation of basket cells from slow to fast signaling devices type: journal_article volume: 28 year: '2008' ... --- _id: '3827' abstract: - lang: eng text: Previous studies revealed that synaptotagmin 1 is the major Ca(2+) sensor for fast synchronous transmitter release at excitatory synapses. However, the molecular identity of the Ca(2+) sensor at hippocampal inhibitory synapses has not been determined. To address the functional role of synaptotagmin 1 at identified inhibitory terminals, we made paired recordings from synaptically connected basket cells (BCs) and granule cells (GCs) in the dentate gyrus in organotypic slice cultures from wild-type and synaptotagmin 1-deficient mice. As expected, genetic elimination of synaptotagmin 1 abolished synchronous transmitter release at excitatory GC-BC synapses. However, synchronous release at inhibitory BC-GC synapses was maintained. Quantitative analysis revealed that elimination of synaptotagmin 1 reduced release probability and depression but maintained the synchrony of transmitter release at BC-GC synapses. Elimination of synaptotagmin 1 also increased the frequency of both miniature excitatory postsynaptic currents (measured in BCs) and miniature inhibitory postsynaptic currents (recorded in GCs), consistent with a clamping function of synaptotagmin 1 at both excitatory and inhibitory terminals. Single-cell reverse-transcription quantitative PCR analysis revealed that single BCs coexpressed multiple synaptotagmin isoforms, including synaptotagmin 1-5, 7, and 11-13. Our results indicate that, in contrast to excitatory synapses, synaptotagmin 1 is not absolutely required for synchronous release at inhibitory BC-GC synapses. Thus, alternative fast Ca(2+) sensors contribute to synchronous release of the inhibitory transmitter GABA in cortical circuits. author: - first_name: Angharad full_name: Kerr, Angharad M last_name: Kerr - 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: Kerr A, Reisinger E, Jonas PM. Differential dependence of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses. PNAS. 2008;105(40):15581-15586. doi:10.1073/pnas.0800621105 apa: Kerr, A., Reisinger, E., & Jonas, P. M. (2008). Differential dependence of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0800621105 chicago: Kerr, Angharad, Ellen Reisinger, and Peter M Jonas. “Differential Dependence of Phasic Transmitter Release on Synaptotagmin 1 at GABAergic and Glutamatergic Hippocampal Synapses.” PNAS. National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0800621105. ieee: A. Kerr, E. Reisinger, and P. M. Jonas, “Differential dependence of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses,” PNAS, vol. 105, no. 40. National Academy of Sciences, pp. 15581–6, 2008. ista: Kerr A, Reisinger E, Jonas PM. 2008. Differential dependence of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses. PNAS. 105(40), 15581–6. mla: Kerr, Angharad, et al. “Differential Dependence of Phasic Transmitter Release on Synaptotagmin 1 at GABAergic and Glutamatergic Hippocampal Synapses.” PNAS, vol. 105, no. 40, National Academy of Sciences, 2008, pp. 15581–86, doi:10.1073/pnas.0800621105. short: A. Kerr, E. Reisinger, P.M. Jonas, PNAS 105 (2008) 15581–6. date_created: 2018-12-11T12:05:23Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:52:29Z day: '01' doi: 10.1073/pnas.0800621105 extern: 1 intvolume: ' 105' issue: '40' month: '01' page: 15581 - 6 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '2384' quality_controlled: 0 status: public title: Differential dependence of phasic transmitter release on synaptotagmin 1 at GABAergic and glutamatergic hippocampal synapses type: journal_article volume: 105 year: '2008' ... --- _id: '3504' abstract: - lang: eng text: "Simulation and bisimulation metrics for stochastic systems provide a quantitative gen- eralization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative μ-calculus and related probabilistic logics.\r\nWe present algorithms for computing the metrics on Markov decision processes (MDPs), turn- based stochastic games, and concurrent games. For turn-based games and MDPs, we provide a polynomial-time algorithm based on linear programming for the computation of the one-step metric distance between states. The algorithm improves on the previously known exponential-time algo- rithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known bound for Markov chains. For the bisimulation kernel of the metric, which corresponds to probabilistic bisimulation, our algorithm works in time O(n4) for both turn-based games and MDPs; improving the previously best known O(n9 · log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance between states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be accomplished via a reduction to the theory of real closed fields, involving a\r\nformula with three quantifier alternations, yielding O(|G|O(|G|5)) time complexity, improving the previously known reduction with O(|G|O(|G|7)) time complexity. These algorithms can be iterated\r\nto approximate the metrics using binary search." acknowledgement: This research was supported in part by the NSF grants CCR-0132780 and CNS-0720884. alternative_title: - LIPIcs author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Luca full_name: De Alfaro, Luca last_name: De Alfaro - first_name: Ritankar full_name: Majumdar, Ritankar last_name: Majumdar - first_name: Vishwanath full_name: Raman, Vishwanath last_name: Raman citation: ama: 'Chatterjee K, De Alfaro L, Majumdar R, Raman V. Algorithms for game metrics. In: Vol 2. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:107-118. doi:10.4230/LIPIcs.FSTTCS.2008.1745' apa: 'Chatterjee, K., De Alfaro, L., Majumdar, R., & Raman, V. (2008). Algorithms for game metrics (Vol. 2, pp. 107–118). Presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745' chicago: Chatterjee, Krishnendu, Luca De Alfaro, Ritankar Majumdar, and Vishwanath Raman. “Algorithms for Game Metrics,” 2:107–18. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.4230/LIPIcs.FSTTCS.2008.1745. ieee: 'K. Chatterjee, L. De Alfaro, R. Majumdar, and V. Raman, “Algorithms for game metrics,” presented at the FSTTCS: Foundations of Software Technology and Theoretical Computer Science, 2008, vol. 2, pp. 107–118.' ista: 'Chatterjee K, De Alfaro L, Majumdar R, Raman V. 2008. Algorithms for game metrics. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 2, 107–118.' mla: Chatterjee, Krishnendu, et al. Algorithms for Game Metrics. Vol. 2, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 107–18, doi:10.4230/LIPIcs.FSTTCS.2008.1745. short: K. Chatterjee, L. De Alfaro, R. Majumdar, V. Raman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 107–118. conference: name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science' date_created: 2018-12-11T12:03:40Z date_published: 2008-12-05T00:00:00Z date_updated: 2023-02-23T11:46:14Z day: '05' ddc: - '000' doi: 10.4230/LIPIcs.FSTTCS.2008.1745 extern: '1' file: - access_level: open_access checksum: 0a447454a24e273f7ddf51dbfe47f877 content_type: application/pdf creator: dernst date_created: 2019-05-10T10:01:21Z date_updated: 2020-07-14T12:46:12Z file_id: '6398' file_name: 2008_LIPIcs_Chatterjee.pdf file_size: 442139 relation: main_file file_date_updated: 2020-07-14T12:46:12Z has_accepted_license: '1' intvolume: ' 2' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '12' oa: 1 oa_version: Published Version page: 107 - 118 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '2883' quality_controlled: '1' related_material: record: - id: '3868' relation: later_version status: public status: public title: Algorithms for game metrics tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2008' ... --- _id: '3875' abstract: - lang: eng text: We study the problem of model checking Interval-valued Discrete-time Markov Chains (IDTMC). IDTMCs are discrete-time finite Markov Chains for which the exact transition probabilities are riot known. Instead in IDTMCs, each transition is associated with an interval in which the actual transition probability must lie. We consider two semantic interpretations for the uncertainty in the transition probabilities of an IDTMC. In the first interpretation, we think of an IDTMC as representing a (possibly uncountable) family of (classical) discrete-time Markov Chains, where each member of the family is a Markov Chain whose transition probabilities lie within the interval range given in the IDTMC. We call this semantic interpretation Uncertain Markov Chains (UMC). In the second semantics for an IDTMC, which we call Interval Markov Decision Process (IMDP), we view the uncertainty as being resolved through non-determinism. In other words, each time a state is visited, we adversarially pick a transition distribution that respects the interval constraints, and take a probabilistic step according to the chosen distribution. We introduce a logic omega-PCTL that can express liveness, strong fairness, and omega-regular properties (such properties cannot be expressed in PCTL). We show that the omega-PCTL model checking problem for Uncertain Markov Chain semantics is decidable in PSPACE (same as the best known upper bound for PCTL) and for Interval Markov Decision Process semantics is decidable in coNP (improving the previous known PSPACE bound for PCTL). We also show that the qualitative fragment of the logic can lie solved in coNP for the UMC interpretation, and can be solved in polynomial time for a sub-class of UMCs. We also prove lower bounds for these model checking problems. We show that the model checking problem of IDTMCs with LTL formulas can be solved for both UMC and IMDP semantics by reduction to the model checking problem of IDTMC with omega-PcTL formulas. 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: Koushik full_name: Sen, Koushik last_name: Sen citation: ama: 'Chatterjee K, Henzinger TA, Sen K. Model-checking omega-regular properties of interval Markov chains. In: Vol 4962. Springer; 2008:302-317. doi:10.1007/978-3-540-78499-9_22' apa: 'Chatterjee, K., Henzinger, T. A., & Sen, K. (2008). Model-checking omega-regular properties of interval Markov chains (Vol. 4962, pp. 302–317). Presented at the FoSSaCS: Foundations of Software Science and Computation Structures, Springer. https://doi.org/10.1007/978-3-540-78499-9_22' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Koushik Sen. “Model-Checking Omega-Regular Properties of Interval Markov Chains,” 4962:302–17. Springer, 2008. https://doi.org/10.1007/978-3-540-78499-9_22. ieee: 'K. Chatterjee, T. A. Henzinger, and K. Sen, “Model-checking omega-regular properties of interval Markov chains,” presented at the FoSSaCS: Foundations of Software Science and Computation Structures, 2008, vol. 4962, pp. 302–317.' ista: 'Chatterjee K, Henzinger TA, Sen K. 2008. Model-checking omega-regular properties of interval Markov chains. FoSSaCS: Foundations of Software Science and Computation Structures, LNCS, vol. 4962, 302–317.' mla: Chatterjee, Krishnendu, et al. Model-Checking Omega-Regular Properties of Interval Markov Chains. Vol. 4962, Springer, 2008, pp. 302–17, doi:10.1007/978-3-540-78499-9_22. short: K. Chatterjee, T.A. Henzinger, K. Sen, in:, Springer, 2008, pp. 302–317. conference: name: 'FoSSaCS: Foundations of Software Science and Computation Structures' date_created: 2018-12-11T12:05:39Z date_published: 2008-03-01T00:00:00Z date_updated: 2021-01-12T07:52:52Z day: '01' doi: 10.1007/978-3-540-78499-9_22 extern: 1 intvolume: ' 4962' month: '03' page: 302 - 317 publication_status: published publisher: Springer publist_id: '2298' quality_controlled: 0 status: public title: Model-checking omega-regular properties of interval Markov chains type: conference volume: 4962 year: '2008' ... --- _id: '3873' abstract: - lang: eng text: We study the controller synthesis problem under budget constraints. In this problem, there is a cost associated with making an observation, and a controller can make only a limited number of observations in each round so that the total cost of the observations does not exceed a given fixed budget. The controller must ensure some omega-regular requirement subject to the budget constraint. Budget constraints arise in designing and implementing controllers for resource-constrained embedded systems, where a controller may not have enough power, time, or bandwidth to obtain data from all sensors in each round. They lead to games of imperfect information, where the unknown information is not fixed a priori, but can vary from round to round, based on the choices made by the controller how to allocate its budget. We show that the budget-constrained synthesis problem for W-regular objectives is complete for exponential time. In addition to studying synthesis under a fixed budget constraint, we study the budget optimization problem, where given a plant, an objective, and observation costs, we have to find a controller that achieves the objective with minimal average accumulated cost (or minimal peak cost). We show that this problem is reducible to a game of imperfect information where the winning objective is a conjunction of an omega-regular condition and a long-run average condition (or a least max-cost condition), and this again leads to an exponential-time algorithm. Finally, we extend our results to games over infinite state spaces, and show that the budget-constrained synthesis problem is decidable for infinite state games with stable quotients of finite index. Consequently, the discrete time budget-constrained synthesis problem is decidable for rectangular hybrid automata. 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: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Majumdar R, Henzinger TA. Controller synthesis with budget constraints. In: Vol 4981. Springer; 2008:72-86. doi:DOI: 10.1007/978-3-540-78929-1_6' apa: 'Chatterjee, K., Majumdar, R., & Henzinger, T. A. (2008). Controller synthesis with budget constraints (Vol. 4981, pp. 72–86). Presented at the HSCC: Hybrid Systems - Computation and Control, Springer. https://doi.org/DOI: 10.1007/978-3-540-78929-1_6' chicago: 'Chatterjee, Krishnendu, Ritankar Majumdar, and Thomas A Henzinger. “Controller Synthesis with Budget Constraints,” 4981:72–86. Springer, 2008. https://doi.org/DOI: 10.1007/978-3-540-78929-1_6.' ieee: 'K. Chatterjee, R. Majumdar, and T. A. Henzinger, “Controller synthesis with budget constraints,” presented at the HSCC: Hybrid Systems - Computation and Control, 2008, vol. 4981, pp. 72–86.' ista: 'Chatterjee K, Majumdar R, Henzinger TA. 2008. Controller synthesis with budget constraints. HSCC: Hybrid Systems - Computation and Control, LNCS, vol. 4981, 72–86.' mla: 'Chatterjee, Krishnendu, et al. Controller Synthesis with Budget Constraints. Vol. 4981, Springer, 2008, pp. 72–86, doi:DOI: 10.1007/978-3-540-78929-1_6.' short: K. Chatterjee, R. Majumdar, T.A. Henzinger, in:, Springer, 2008, pp. 72–86. conference: name: 'HSCC: Hybrid Systems - Computation and Control' date_created: 2018-12-11T12:05:38Z date_published: 2008-04-03T00:00:00Z date_updated: 2021-01-12T07:52:51Z day: '03' doi: 'DOI: 10.1007/978-3-540-78929-1_6' extern: 1 intvolume: ' 4981' month: '04' page: 72 - 86 publication_status: published publisher: Springer publist_id: '2296' quality_controlled: 0 status: public title: Controller synthesis with budget constraints type: conference volume: 4981 year: '2008' ... --- _id: '3876' abstract: - lang: eng text: We consider two-player games played in real time on game structures with clocks and parity objectives. The games are concurrent in that at each turn, both players independently propose a time delay and an action, and the action with the shorter delay is chosen. To prevent a player from winning by blocking time, we restrict each player to strategies that ensure that the player cannot be responsible for causing a zeno run. First, we present an efficient reduction of these games to turn-based (i.e., nonconcurrent) finite-state (i.e., untimed) parity games. The states of the resulting game are pairs of clock regions of the original game. Our reduction improves the best known complexity for solving timed parity games. Moreover, the rich class of algorithms for classical parity games can now be applied to timed parity games. Second, we consider two restricted classes of strategies for the player that represents the controller in a real-time synthesis problem, namely, limit-robust and bounded-robust strategies. Using a limit-robust strategy, the controller cannot choose an exact real-valued time delay but must allow for some nonzero jitter in each of its actions. If there is a given lower bound on the jitter, then the strategy is bounded-robust. We show that exact strategies are more powerful than limit-robust strategies, which are more powerful than bounded-robust strategies for any bound. For both kinds of robust strategies, we present efficient reductions to standard timed automaton games. These reductions provide algorithms for the synthesis of robust real-time controllers. acknowledgement: This research was supported in part by the NSF grants CCR-0132780, CNS-0720884, and CCR-0225610, and by the European COMBEST project. 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: Vinayak full_name: Prabhu, Vinayak S last_name: Prabhu citation: ama: 'Chatterjee K, Henzinger TA, Prabhu V. Timed parity games: complexity and robustness. In: Vol 5215. Springer; 2008:124-140. doi:10.1007/978-3-540-85778-5_10' apa: 'Chatterjee, K., Henzinger, T. A., & Prabhu, V. (2008). Timed parity games: complexity and robustness (Vol. 5215, pp. 124–140). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Springer. https://doi.org/10.1007/978-3-540-85778-5_10' chicago: 'Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Timed Parity Games: Complexity and Robustness,” 5215:124–40. Springer, 2008. https://doi.org/10.1007/978-3-540-85778-5_10.' ieee: 'K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Timed parity games: complexity and robustness,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, 2008, vol. 5215, pp. 124–140.' ista: 'Chatterjee K, Henzinger TA, Prabhu V. 2008. Timed parity games: complexity and robustness. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 5215, 124–140.' mla: 'Chatterjee, Krishnendu, et al. Timed Parity Games: Complexity and Robustness. Vol. 5215, Springer, 2008, pp. 124–40, doi:10.1007/978-3-540-85778-5_10.' short: K. Chatterjee, T.A. Henzinger, V. Prabhu, in:, Springer, 2008, pp. 124–140. conference: name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' date_created: 2018-12-11T12:05:39Z date_published: 2008-10-01T00:00:00Z date_updated: 2023-02-23T11:21:54Z day: '01' doi: 10.1007/978-3-540-85778-5_10 extern: 1 intvolume: ' 5215' month: '10' page: 124 - 140 publication_status: published publisher: Springer publist_id: '2294' quality_controlled: 0 related_material: record: - id: '3315' relation: later_version status: public status: public title: 'Timed parity games: complexity and robustness' type: conference volume: 5215 year: '2008' ... --- _id: '3877' abstract: - lang: eng text: The synthesis problem asks to construct a reactive finite-state system from an omega-regular specification. Initial specifications are often unrealizable, which means that there is no system that implements the specification. A common reason for unrealizability is that assumptions on the environment of the system are incomplete. We study the problem of correcting an unrealizable specification phi by computing an environment assumption psi such that the new specification psi -> phi is realizable. Our aim is to construct an assumption psi that constrains only the environment and is as weak as possible. We present a two-step algorithm for computing assumptions. The algorithm operates on the game graph that is used to answer the realizability question. First, we compute a safety assumption that removes a minimal set of environment edges from the graph. Second, we compute a liveness assumption that puts fairness conditions on some of the remaining environment edges. We show that the problem of finding a minimal set of fair edges is computationally hard, and we use probabilistic games to compute a locally minimal fairness assumption. 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: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann citation: ama: 'Chatterjee K, Henzinger TA, Jobstmann B. Environment assumptions for synthesis. In: Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:147-161. doi:10.1007/978-3-540-85361-9_14' apa: 'Chatterjee, K., Henzinger, T. A., & Jobstmann, B. (2008). Environment assumptions for synthesis (Vol. 5201, pp. 147–161). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-85361-9_14' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Barbara Jobstmann. “Environment Assumptions for Synthesis,” 5201:147–61. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9_14. ieee: 'K. Chatterjee, T. A. Henzinger, and B. Jobstmann, “Environment assumptions for synthesis,” presented at the CONCUR: Concurrency Theory, 2008, vol. 5201, pp. 147–161.' ista: 'Chatterjee K, Henzinger TA, Jobstmann B. 2008. Environment assumptions for synthesis. CONCUR: Concurrency Theory, LNCS, vol. 5201, 147–161.' mla: Chatterjee, Krishnendu, et al. Environment Assumptions for Synthesis. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 147–61, doi:10.1007/978-3-540-85361-9_14. short: K. Chatterjee, T.A. Henzinger, B. Jobstmann, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 147–161. conference: name: 'CONCUR: Concurrency Theory' date_created: 2018-12-11T12:05:39Z date_published: 2008-07-30T00:00:00Z date_updated: 2021-01-12T07:52:53Z day: '30' doi: 10.1007/978-3-540-85361-9_14 extern: 1 intvolume: ' 5201' month: '07' page: 147 - 161 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '2295' quality_controlled: 0 status: public title: Environment assumptions for synthesis type: conference volume: 5201 year: '2008' ... --- _id: '3878' abstract: - lang: eng text: We study the problem of generating a test sequence that achieves maximal coverage for a reactive system under test. We formulate the problem as a repeated game between the tester and the system, where the system state space is partitioned according to some coverage criterion and the objective of the tester is to maximize the set of partitions (or coverage goals) visited during the game. We show the complexity of the maximal coverage problem for non-deterministic systems is PSPACE-complete, but is NP-complete for deterministic systems. For the special case of non-deterministic systems with a re-initializing “reset” action, which represent running a new test input on a re-initialized system, we show that the complexity is coNP-complete. Our proof technique for reset games uses randomized testing strategies that circumvent the exponentially large memory requirement of deterministic testing strategies. acknowledgement: This research was supported in part by the NSF grants CCR-0132780 and CNS-0720884. 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: Luca full_name: de Alfaro, Luca last_name: De Alfaro - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar citation: ama: 'Chatterjee K, De Alfaro L, Majumdar R. The complexity of coverage. In: Vol 5356. Springer; 2008:91-106. doi:10.1007/978-3-540-89330-1_7' apa: 'Chatterjee, K., De Alfaro, L., & Majumdar, R. (2008). The complexity of coverage (Vol. 5356, pp. 91–106). Presented at the APLAS: Asian Symposium on Programming Languages and Systems, Springer. https://doi.org/10.1007/978-3-540-89330-1_7' chicago: Chatterjee, Krishnendu, Luca De Alfaro, and Ritankar Majumdar. “The Complexity of Coverage,” 5356:91–106. Springer, 2008. https://doi.org/10.1007/978-3-540-89330-1_7. ieee: 'K. Chatterjee, L. De Alfaro, and R. Majumdar, “The complexity of coverage,” presented at the APLAS: Asian Symposium on Programming Languages and Systems, 2008, vol. 5356, pp. 91–106.' ista: 'Chatterjee K, De Alfaro L, Majumdar R. 2008. The complexity of coverage. APLAS: Asian Symposium on Programming Languages and Systems, LNCS, vol. 5356, 91–106.' mla: Chatterjee, Krishnendu, et al. The Complexity of Coverage. Vol. 5356, Springer, 2008, pp. 91–106, doi:10.1007/978-3-540-89330-1_7. short: K. Chatterjee, L. De Alfaro, R. Majumdar, in:, Springer, 2008, pp. 91–106. conference: name: 'APLAS: Asian Symposium on Programming Languages and Systems' date_created: 2018-12-11T12:05:40Z date_published: 2008-12-03T00:00:00Z date_updated: 2021-01-12T07:52:53Z day: '03' doi: 10.1007/978-3-540-89330-1_7 extern: 1 intvolume: ' 5356' main_file_link: - open_access: '1' url: http://arxiv.org/abs/0804.4525 month: '12' oa: 1 page: 91 - 106 publication_status: published publisher: Springer publist_id: '2292' quality_controlled: 0 status: public title: The complexity of coverage type: conference volume: 5356 year: '2008' ... --- _id: '3874' abstract: - lang: eng text: We consider concurrent two-player timed automaton games with omega-regular objectives specified as parity conditions. These games offer an appropriate model for the synthesis of real-time controllers. Earlier works on timed games focused on pure strategies for each player. We study, for the first time, the use of randomized strategies in such games. While pure (i.e., nonrandomized) strategies in timed games require infinite memory for winning even with respect to reachability objectives, we show that randomized strategies can win with finite memory with respect to all parity objectives. Also, the synthesized randomized real-time controllers are much simpler in structure than the corresponding pure controllers, and therefore easier to implement. For safety objectives we prove the existence of pure finite-memory winning strategies. Finally, while randomization helps in simplifying the strategies required for winning timed parity games, we prove that randomization does not help in winning at more states. acknowledgement: This research was supported in part by the NSF grants CCR-0208875, CCR-0225610, CCR-0234690, by the Swiss National Science Foundation, and by the Artist2 European Network of Excellence. 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: Vinayak full_name: Prabhu, Vinayak S last_name: Prabhu citation: ama: 'Chatterjee K, Henzinger TA, Prabhu V. Trading infinite memory for uniform randomness in timed games. In: Vol 4981. Springer; 2008:87-100. doi:10.1007/978-3-540-78929-1_7' apa: 'Chatterjee, K., Henzinger, T. A., & Prabhu, V. (2008). Trading infinite memory for uniform randomness in timed games (Vol. 4981, pp. 87–100). Presented at the HSCC: Hybrid Systems - Computation and Control, Springer. https://doi.org/10.1007/978-3-540-78929-1_7' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Trading Infinite Memory for Uniform Randomness in Timed Games,” 4981:87–100. Springer, 2008. https://doi.org/10.1007/978-3-540-78929-1_7. ieee: 'K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Trading infinite memory for uniform randomness in timed games,” presented at the HSCC: Hybrid Systems - Computation and Control, 2008, vol. 4981, pp. 87–100.' ista: 'Chatterjee K, Henzinger TA, Prabhu V. 2008. Trading infinite memory for uniform randomness in timed games. HSCC: Hybrid Systems - Computation and Control, LNCS, vol. 4981, 87–100.' mla: Chatterjee, Krishnendu, et al. Trading Infinite Memory for Uniform Randomness in Timed Games. Vol. 4981, Springer, 2008, pp. 87–100, doi:10.1007/978-3-540-78929-1_7. short: K. Chatterjee, T.A. Henzinger, V. Prabhu, in:, Springer, 2008, pp. 87–100. conference: name: 'HSCC: Hybrid Systems - Computation and Control' date_created: 2018-12-11T12:05:38Z date_published: 2008-04-03T00:00:00Z date_updated: 2021-01-12T07:52:51Z day: '03' doi: 10.1007/978-3-540-78929-1_7 extern: 1 intvolume: ' 4981' month: '04' page: 87 - 100 publication_status: published publisher: Springer publist_id: '2297' quality_controlled: 0 status: public title: Trading infinite memory for uniform randomness in timed games type: conference volume: 4981 year: '2008' ... --- _id: '3879' abstract: - lang: eng text: Quantitative generalizations of classical languages, which assign to each word a real number instead of a boolean value, have applications in modeling resource-constrained computation. We use weighted automata (finite automata with transition weights) to define several natural classes of quantitative languages over finite and infinite words; in particular, the real value of an infinite run is computed as the maximum, limsup, liminf, limit average, or discounted sum of the transition weights. We define the classical decision problems of automata theory (emptiness, universality, language inclusion, and language equivalence) in the quantitative setting and study their computational complexity. As the decidability of language inclusion remains open for some classes of weighted automata, we introduce a notion of quantitative simulation that is decidable and implies language inclusion. We also give a complete characterization of the expressive power of the various classes of weighted automata. In particular, we show that most classes of weighted automata cannot be determinized. acknowledgement: Research supported in part by the NSF grants CCR-0132780, CNS-0720884, and CCR-0225610, by the Swiss National Science Foundation, and by the European COMBEST project. 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: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Chatterjee K, Doyen L, Henzinger TA. Quantitative languages. In: Vol 5213. Springer; 2008:385-400. doi:10.1007/978-3-540-87531-4_28' apa: 'Chatterjee, K., Doyen, L., & Henzinger, T. A. (2008). Quantitative languages (Vol. 5213, pp. 385–400). Presented at the CSL: Computer Science Logic, Springer. https://doi.org/10.1007/978-3-540-87531-4_28' chicago: Chatterjee, Krishnendu, Laurent Doyen, and Thomas A Henzinger. “Quantitative Languages,” 5213:385–400. Springer, 2008. https://doi.org/10.1007/978-3-540-87531-4_28. ieee: 'K. Chatterjee, L. Doyen, and T. A. Henzinger, “Quantitative languages,” presented at the CSL: Computer Science Logic, 2008, vol. 5213, pp. 385–400.' ista: 'Chatterjee K, Doyen L, Henzinger TA. 2008. Quantitative languages. CSL: Computer Science Logic, LNCS, vol. 5213, 385–400.' mla: Chatterjee, Krishnendu, et al. Quantitative Languages. Vol. 5213, Springer, 2008, pp. 385–400, doi:10.1007/978-3-540-87531-4_28. short: K. Chatterjee, L. Doyen, T.A. Henzinger, in:, Springer, 2008, pp. 385–400. conference: name: 'CSL: Computer Science Logic' date_created: 2018-12-11T12:05:40Z date_published: 2008-09-10T00:00:00Z date_updated: 2021-01-12T07:52:54Z day: '10' doi: 10.1007/978-3-540-87531-4_28 extern: 1 intvolume: ' 5213' month: '09' page: 385 - 400 publication_status: published publisher: Springer publist_id: '2293' quality_controlled: 0 status: public title: Quantitative languages type: conference volume: 5213 year: '2008' ... --- _id: '3872' abstract: - lang: eng text: We survey value iteration algorithms on graphs. Such algorithms can be used for determining the existence of certain paths (model checking), the existence of certain strategies (game solving), and the probabilities of certain events (performance analysis). We classify the algorithms according to the value domain (boolean, probabilistic, or quantitative); according to the graph structure (nondeterministic, probabilistic, or multi-player); according to the desired property of paths (Borel level 1, 2, or 3); and according to the alternation depth and convergence rate of fixpoint computations. acknowledgement: This research was supported in part by the Swiss National Science Foundation and by the NSF grants CCR-0225610 and CCR-0234690. 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 citation: ama: 'Chatterjee K, Henzinger TA. Value iteration. In: 25 Years in Model Checking. Vol 5000. Springer; 2008:107-138. doi:10.1007/978-3-540-69850-0_7' apa: Chatterjee, K., & Henzinger, T. A. (2008). Value iteration. In 25 Years in Model Checking (Vol. 5000, pp. 107–138). Springer. https://doi.org/10.1007/978-3-540-69850-0_7 chicago: Chatterjee, Krishnendu, and Thomas A Henzinger. “Value Iteration.” In 25 Years in Model Checking, 5000:107–38. Springer, 2008. https://doi.org/10.1007/978-3-540-69850-0_7. ieee: K. Chatterjee and T. A. Henzinger, “Value iteration,” in 25 Years in Model Checking, vol. 5000, Springer, 2008, pp. 107–138. ista: 'Chatterjee K, Henzinger TA. 2008.Value iteration. In: 25 Years in Model Checking. LNCS, vol. 5000, 107–138.' mla: Chatterjee, Krishnendu, and Thomas A. Henzinger. “Value Iteration.” 25 Years in Model Checking, vol. 5000, Springer, 2008, pp. 107–38, doi:10.1007/978-3-540-69850-0_7. short: K. Chatterjee, T.A. Henzinger, in:, 25 Years in Model Checking, Springer, 2008, pp. 107–138. date_created: 2018-12-11T12:05:38Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:52:51Z day: '01' doi: 10.1007/978-3-540-69850-0_7 extern: 1 intvolume: ' 5000' month: '01' page: 107 - 138 publication: 25 Years in Model Checking publication_status: published publisher: Springer publist_id: '2299' quality_controlled: 0 status: public title: Value iteration type: book_chapter volume: 5000 year: '2008' ... --- _id: '3945' abstract: - lang: eng text: Langerhans cells and dermal dendritic cells migrate to the draining lymph nodes through dermal lymphatic vessels. They do so in the steady-state and under inflammatory conditions. Peripheral T cell tolerance or T cell priming, respectively, are the consequences of migration. The nature of dendritic cell-containing vessels was mostly defined by electron microscopy or by their lack of blood endothelial markers. Selective markers for murine lymph endothelium were hitherto rare or not available. Here, we utilised recently developed antibodies against the murine hyaluronan receptor, LYVE-1, to study the lymph vessel network in mouse skin in more detail. In hairless skin from the ears, lymph vessels were spread out in a horizontal plane. They formed anastomoses, and they possessed frequent blind endings that were occasionally open. Lymph vessels were wider than blood vessels, which were identified by their strong CD31 expression. In body wall skin LYVE-1 reactive vessels did not extend laterally but they dived straight down into the deeper dermis. There, they are connected to each other and formed a network similar to ear skin. The number and width of lymph vessels did not grossly change upon inflammatory stimuli such as skin explant culture or tape stripping. There were also no marked changes in caliber in response to the TLR 7/8 ligand Imiquimod. Double-labelling experiments of cultured skin showed that most of the strongly cell surface MHC II-expressing (i.e. activated) dendritic cells were confined to the lymph vessels. Langerin/CD207(+) cells within this population appeared later than dermal dendritic cells, i.e. langerin-negative cells. Comparable results were obtained after stimulating the skin in vivo with the TLR 7/8 ligand Imiquimod or by tape stripping. In untreated skin (i.e. steady state) a few MHC II(+) and Langerin/CD207(+) cells, presumably migrating skin dendritic cells including epidermal Langerhans cells, were consistently observed within the lymph vessels. The novel antibody reagents may serve as important tools to further study the dendritic cell traffic in the skin under physiological conditions as well as in conditions of adoptive dendritic cell transfer in immunotherapy. author: - first_name: Christoph full_name: Tripp, Christoph H last_name: Tripp - first_name: Bernhard full_name: Haid, Bernhard last_name: Haid - first_name: Vincent full_name: Flacher, Vincent last_name: Flacher - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Hannes full_name: Peter, Hannes last_name: Peter - first_name: Julia full_name: Farkas, Julia last_name: Farkas - first_name: Robert full_name: Gschwentner, Robert last_name: Gschwentner - first_name: Lydia full_name: Sorokin, Lydia last_name: Sorokin - first_name: Nikolaus full_name: Romani, Nikolaus last_name: Romani - first_name: Patrizia full_name: Stoitzner, Patrizia last_name: Stoitzner citation: ama: Tripp C, Haid B, Flacher V, et al. The lymph vessel network in mouse skin visualised with antibodies against the hyaluronan receptor LYVE-1. Immunobiology. 2008;213(9-10):715-728. doi:10.1016/j.imbio.2008.07.025 apa: Tripp, C., Haid, B., Flacher, V., Sixt, M. K., Peter, H., Farkas, J., … Stoitzner, P. (2008). The lymph vessel network in mouse skin visualised with antibodies against the hyaluronan receptor LYVE-1. Immunobiology. Elsevier. https://doi.org/10.1016/j.imbio.2008.07.025 chicago: Tripp, Christoph, Bernhard Haid, Vincent Flacher, Michael K Sixt, Hannes Peter, Julia Farkas, Robert Gschwentner, Lydia Sorokin, Nikolaus Romani, and Patrizia Stoitzner. “The Lymph Vessel Network in Mouse Skin Visualised with Antibodies against the Hyaluronan Receptor LYVE-1.” Immunobiology. Elsevier, 2008. https://doi.org/10.1016/j.imbio.2008.07.025. ieee: C. Tripp et al., “The lymph vessel network in mouse skin visualised with antibodies against the hyaluronan receptor LYVE-1,” Immunobiology, vol. 213, no. 9–10. Elsevier, pp. 715–28, 2008. ista: Tripp C, Haid B, Flacher V, Sixt MK, Peter H, Farkas J, Gschwentner R, Sorokin L, Romani N, Stoitzner P. 2008. The lymph vessel network in mouse skin visualised with antibodies against the hyaluronan receptor LYVE-1. Immunobiology. 213(9–10), 715–28. mla: Tripp, Christoph, et al. “The Lymph Vessel Network in Mouse Skin Visualised with Antibodies against the Hyaluronan Receptor LYVE-1.” Immunobiology, vol. 213, no. 9–10, Elsevier, 2008, pp. 715–28, doi:10.1016/j.imbio.2008.07.025. short: C. Tripp, B. Haid, V. Flacher, M.K. Sixt, H. Peter, J. Farkas, R. Gschwentner, L. Sorokin, N. Romani, P. Stoitzner, Immunobiology 213 (2008) 715–28. date_created: 2018-12-11T12:06:02Z date_published: 2008-08-30T00:00:00Z date_updated: 2021-01-12T07:53:23Z day: '30' doi: 10.1016/j.imbio.2008.07.025 extern: 1 intvolume: ' 213' issue: 9-10 month: '08' page: 715 - 28 publication: Immunobiology publication_status: published publisher: Elsevier publist_id: '2182' quality_controlled: 0 status: public title: The lymph vessel network in mouse skin visualised with antibodies against the hyaluronan receptor LYVE-1 type: journal_article volume: 213 year: '2008' ... --- _id: '3942' abstract: - lang: eng text: Recent in vitro studies have suggested a role for sialylation in chemokine receptor binding to its ligand (Bannert, N., S. Craig, M. Farzan, D. Sogah, N.V. Santo, H. Choe, and J. Sodroski. 2001. J. Exp. Med. 194:1661-1673). This prompted us to investigate chemokine-induced leukocyte adhesion in inflamed cremaster muscle venules of alpha2,3 sialyltransferase (ST3Gal-IV)-deficient mice. We found a marked reduction in leukocyte adhesion to inflamed microvessels upon injection of the CXCR2 ligands CXCL1 (keratinocyte-derived chemokine) or CXCL8 (interleukin 8). In addition, extravasation of ST3Gal-IV(-/-) neutrophils into thioglycollate-pretreated peritoneal cavities was significantly decreased. In vitro assays revealed that CXCL8 binding to isolated ST3Gal-IV(-/-) neutrophils was markedly impaired. Furthermore, CXCL1-mediated adhesion of ST3Gal-IV(-/-) leukocytes at physiological flow conditions, as well as transendothelial migration of ST3Gal-IV(-/-) leukocytes in response to CXCL1, was significantly reduced. In human neutrophils, enzymatic desialylation decreased binding of CXCR2 ligands to the neutrophil surface and diminished neutrophil degranulation in response to these chemokines. In addition, binding of alpha2,3-linked sialic acid-specific Maackia amurensis lectin II to purified CXCR2 from neuraminidase-treated CXCR2-transfected HEK293 cells was markedly impaired. Collectively, we provide substantial evidence that sialylation by ST3Gal-IV significantly contributes to CXCR2-mediated leukocyte adhesion during inflammation in vivo. author: - first_name: David full_name: Frommhold, David last_name: Frommhold - first_name: Andreas full_name: Ludwig, Andreas last_name: Ludwig - first_name: M Gabriele full_name: Bixel, M Gabriele last_name: Bixel - first_name: Alexander full_name: Zarbock, Alexander last_name: Zarbock - first_name: Inna full_name: Babushkina, Inna last_name: Babushkina - first_name: Melitta full_name: Weissinger, Melitta last_name: Weissinger - first_name: Sandra full_name: Cauwenberghs, Sandra last_name: Cauwenberghs - first_name: Lesley full_name: Ellies, Lesley G last_name: Ellies - first_name: Jamey full_name: Marth, Jamey D last_name: Marth - first_name: Annette full_name: Beck-Sickinger, Annette G last_name: Beck Sickinger - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Bärbel full_name: Lange-Sperandio, Bärbel last_name: Lange Sperandio - first_name: Alma full_name: Zernecke, Alma last_name: Zernecke - first_name: Ernst full_name: Brandt, Ernst last_name: Brandt - first_name: Christian full_name: Weber, Christian last_name: Weber - first_name: Dietmar full_name: Vestweber, Dietmar last_name: Vestweber - first_name: Klaus full_name: Ley, Klaus last_name: Ley - first_name: Markus full_name: Sperandio, Markus last_name: Sperandio citation: ama: Frommhold D, Ludwig A, Bixel MG, et al. Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during inflammation. The Journal of Experimental Medicine. 2008;205(6):1435-1446. doi:10.1084/jem.20070846 apa: Frommhold, D., Ludwig, A., Bixel, M. G., Zarbock, A., Babushkina, I., Weissinger, M., … Sperandio, M. (2008). Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during inflammation. The Journal of Experimental Medicine. Rockefeller University Press. https://doi.org/10.1084/jem.20070846 chicago: Frommhold, David, Andreas Ludwig, M Gabriele Bixel, Alexander Zarbock, Inna Babushkina, Melitta Weissinger, Sandra Cauwenberghs, et al. “Sialyltransferase ST3Gal-IV Controls CXCR2-Mediated Firm Leukocyte Arrest during Inflammation.” The Journal of Experimental Medicine. Rockefeller University Press, 2008. https://doi.org/10.1084/jem.20070846. ieee: D. Frommhold et al., “Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during inflammation,” The Journal of Experimental Medicine, vol. 205, no. 6. Rockefeller University Press, pp. 1435–1446, 2008. ista: Frommhold D, Ludwig A, Bixel MG, Zarbock A, Babushkina I, Weissinger M, Cauwenberghs S, Ellies L, Marth J, Beck Sickinger A, Sixt MK, Lange Sperandio B, Zernecke A, Brandt E, Weber C, Vestweber D, Ley K, Sperandio M. 2008. Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during inflammation. The Journal of Experimental Medicine. 205(6), 1435–1446. mla: Frommhold, David, et al. “Sialyltransferase ST3Gal-IV Controls CXCR2-Mediated Firm Leukocyte Arrest during Inflammation.” The Journal of Experimental Medicine, vol. 205, no. 6, Rockefeller University Press, 2008, pp. 1435–46, doi:10.1084/jem.20070846. short: D. Frommhold, A. Ludwig, M.G. Bixel, A. Zarbock, I. Babushkina, M. Weissinger, S. Cauwenberghs, L. Ellies, J. Marth, A. Beck Sickinger, M.K. Sixt, B. Lange Sperandio, A. Zernecke, E. Brandt, C. Weber, D. Vestweber, K. Ley, M. Sperandio, The Journal of Experimental Medicine 205 (2008) 1435–1446. date_created: 2018-12-11T12:06:01Z date_published: 2008-06-02T00:00:00Z date_updated: 2021-01-12T07:53:21Z day: '02' doi: 10.1084/jem.20070846 extern: 1 intvolume: ' 205' issue: '6' month: '06' page: 1435 - 1446 publication: The Journal of Experimental Medicine publication_status: published publisher: Rockefeller University Press publist_id: '2185' quality_controlled: 0 status: public title: Sialyltransferase ST3Gal-IV controls CXCR2-mediated firm leukocyte arrest during inflammation type: journal_article volume: 205 year: '2008' ... --- _id: '3943' abstract: - lang: eng text: Neutrophil granulocytes form the body's first line of antibacterial defense, but they also contribute to tissue injury and noninfectious, chronic inflammation. Proteinase 3 (PR3) and neutrophil elastase (NE) are 2 abundant neutrophil serine proteases implicated in antimicrobial defense with overlapping and potentially redundant substrate specificity. Here, we unraveled a cooperative role for PR3 and NE in neutrophil activation and noninfectious inflammation in vivo, which we believe to be novel. Mice lacking both PR3 and NE demonstrated strongly diminished immune complex-mediated (IC-mediated) neutrophil infiltration in vivo as well as reduced activation of isolated neutrophils by ICs in vitro. In contrast, in mice lacking just NE, neutrophil recruitment to ICs was only marginally impaired. The defects in mice lacking both PR3 and NE were directly linked to the accumulation of antiinflammatory progranulin (PGRN). Both PR3 and NE cleaved PGRN in vitro and during neutrophil activation and inflammation in vivo. Local administration of recombinant PGRN potently inhibited neutrophilic inflammation in vivo, demonstrating that PGRN represents a crucial inflammation-suppressing mediator. We conclude that PR3 and NE enhance neutrophil-dependent inflammation by eliminating the local antiinflammatory activity of PGRN. Our results support the use of serine protease inhibitors as antiinflammatory agents. author: - first_name: Kai full_name: Kessenbrock, Kai last_name: Kessenbrock - first_name: Leopold full_name: Fröhlich, Leopold last_name: Fröhlich - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Heiko full_name: Pfister, Heiko last_name: Pfister - first_name: Andrew full_name: Bateman, Andrew last_name: Bateman - first_name: Azzaq full_name: Belaaouaj, Azzaq last_name: Belaaouaj - first_name: Johannes full_name: Ring, Johannes last_name: Ring - first_name: Markus full_name: Ollert, Markus last_name: Ollert - first_name: Reinhard full_name: Fässler, Reinhard last_name: Fässler - first_name: Dieter full_name: Jenne, Dieter E last_name: Jenne citation: ama: Kessenbrock K, Fröhlich L, Sixt MK, et al. Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin. The Journal of Clinical Investigation. 2008;118(7):2438-2447. doi:10.1172/JCI34694 apa: Kessenbrock, K., Fröhlich, L., Sixt, M. K., Lämmermann, T., Pfister, H., Bateman, A., … Jenne, D. (2008). Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin. The Journal of Clinical Investigation. American Society for Clinical Investigation. https://doi.org/10.1172/JCI34694 chicago: Kessenbrock, Kai, Leopold Fröhlich, Michael K Sixt, Tim Lämmermann, Heiko Pfister, Andrew Bateman, Azzaq Belaaouaj, et al. “Proteinase 3 and Neutrophil Elastase Enhance Inflammation in Mice by Inactivating Antiinflammatory Progranulin.” The Journal of Clinical Investigation. American Society for Clinical Investigation, 2008. https://doi.org/10.1172/JCI34694. ieee: K. Kessenbrock et al., “Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin,” The Journal of Clinical Investigation, vol. 118, no. 7. American Society for Clinical Investigation, pp. 2438–2447, 2008. ista: Kessenbrock K, Fröhlich L, Sixt MK, Lämmermann T, Pfister H, Bateman A, Belaaouaj A, Ring J, Ollert M, Fässler R, Jenne D. 2008. Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin. The Journal of Clinical Investigation. 118(7), 2438–2447. mla: Kessenbrock, Kai, et al. “Proteinase 3 and Neutrophil Elastase Enhance Inflammation in Mice by Inactivating Antiinflammatory Progranulin.” The Journal of Clinical Investigation, vol. 118, no. 7, American Society for Clinical Investigation, 2008, pp. 2438–47, doi:10.1172/JCI34694. short: K. Kessenbrock, L. Fröhlich, M.K. Sixt, T. Lämmermann, H. Pfister, A. Bateman, A. Belaaouaj, J. Ring, M. Ollert, R. Fässler, D. Jenne, The Journal of Clinical Investigation 118 (2008) 2438–2447. date_created: 2018-12-11T12:06:01Z date_published: 2008-07-01T00:00:00Z date_updated: 2021-01-12T07:53:22Z day: '01' doi: 10.1172/JCI34694 extern: 1 intvolume: ' 118' issue: '7' month: '07' page: 2438 - 2447 publication: The Journal of Clinical Investigation publication_status: published publisher: American Society for Clinical Investigation publist_id: '2183' quality_controlled: 0 status: public title: Proteinase 3 and neutrophil elastase enhance inflammation in mice by inactivating antiinflammatory progranulin type: journal_article volume: 118 year: '2008' ... --- _id: '3941' abstract: - lang: eng text: All metazoan cells carry transmembrane receptors of the integrin family, which couple the contractile force of the actomyosin cytoskeleton to the extracellular environment. In agreement with this principle, rapidly migrating leukocytes use integrin-mediated adhesion when moving over two-dimensional surfaces. As migration on two-dimensional substrates naturally overemphasizes the role of adhesion, the contribution of integrins during three-dimensional movement of leukocytes within tissues has remained controversial. We studied the interplay between adhesive, contractile and protrusive forces during interstitial leukocyte chemotaxis in vivo and in vitro. We ablated all integrin heterodimers from murine leukocytes, and show here that functional integrins do not contribute to migration in three-dimensional environments. Instead, these cells migrate by the sole force of actin-network expansion, which promotes protrusive flowing of the leading edge. Myosin II-dependent contraction is only required on passage through narrow gaps, where a squeezing contraction of the trailing edge propels the rigid nucleus. author: - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Bernhard full_name: Bader, Bernhard L last_name: Bader - first_name: Susan full_name: Monkley, Susan J last_name: Monkley - first_name: Tim full_name: Worbs, Tim last_name: Worbs - first_name: Roland full_name: Wedlich-Söldner, Roland last_name: Wedlich Söldner - first_name: Karin full_name: Hirsch, Karin last_name: Hirsch - first_name: Markus full_name: Keller, Markus last_name: Keller - first_name: Reinhold full_name: Förster, Reinhold last_name: Förster - first_name: David full_name: Critchley, David R last_name: Critchley - first_name: Reinhard full_name: Fässler, Reinhard last_name: Fässler - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Lämmermann T, Bader B, Monkley S, et al. Rapid leukocyte migration by integrin-independent flowing and squeezing. Nature. 2008;453(7191):51-55. doi:10.1038/nature06887 apa: Lämmermann, T., Bader, B., Monkley, S., Worbs, T., Wedlich Söldner, R., Hirsch, K., … Sixt, M. K. (2008). Rapid leukocyte migration by integrin-independent flowing and squeezing. Nature. Nature Publishing Group. https://doi.org/10.1038/nature06887 chicago: Lämmermann, Tim, Bernhard Bader, Susan Monkley, Tim Worbs, Roland Wedlich Söldner, Karin Hirsch, Markus Keller, et al. “Rapid Leukocyte Migration by Integrin-Independent Flowing and Squeezing.” Nature. Nature Publishing Group, 2008. https://doi.org/10.1038/nature06887. ieee: T. Lämmermann et al., “Rapid leukocyte migration by integrin-independent flowing and squeezing,” Nature, vol. 453, no. 7191. Nature Publishing Group, pp. 51–55, 2008. ista: Lämmermann T, Bader B, Monkley S, Worbs T, Wedlich Söldner R, Hirsch K, Keller M, Förster R, Critchley D, Fässler R, Sixt MK. 2008. Rapid leukocyte migration by integrin-independent flowing and squeezing. Nature. 453(7191), 51–55. mla: Lämmermann, Tim, et al. “Rapid Leukocyte Migration by Integrin-Independent Flowing and Squeezing.” Nature, vol. 453, no. 7191, Nature Publishing Group, 2008, pp. 51–55, doi:10.1038/nature06887. short: T. Lämmermann, B. Bader, S. Monkley, T. Worbs, R. Wedlich Söldner, K. Hirsch, M. Keller, R. Förster, D. Critchley, R. Fässler, M.K. Sixt, Nature 453 (2008) 51–55. date_created: 2018-12-11T12:06:00Z date_published: 2008-05-01T00:00:00Z date_updated: 2021-01-12T07:53:21Z day: '01' doi: 10.1038/nature06887 extern: 1 intvolume: ' 453' issue: '7191' month: '05' page: 51 - 55 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '2186' quality_controlled: 0 status: public title: Rapid leukocyte migration by integrin-independent flowing and squeezing type: journal_article volume: 453 year: '2008' ... --- _id: '3944' abstract: - lang: eng text: Live imaging of the actin cytoskeleton is crucial for the study of many fundamental biological processes, but current approaches to visualize actin have several limitations. Here we describe Lifeact, a 17-amino-acid peptide, which stained filamentous actin (F-actin) structures in eukaryotic cells and tissues. Lifeact did not interfere with actin dynamics in vitro and in vivo and in its chemically modified peptide form allowed visualization of actin dynamics in nontransfectable cells. author: - first_name: Julia full_name: Riedl, Julia last_name: Riedl - first_name: Alvaro full_name: Crevenna, Alvaro H last_name: Crevenna - first_name: Kai full_name: Kessenbrock, Kai last_name: Kessenbrock - first_name: Jerry full_name: Yu, Jerry Haochen last_name: Yu - first_name: Dorothee full_name: Neukirchen, Dorothee last_name: Neukirchen - first_name: Michal full_name: Bista, Michal last_name: Bista - first_name: Frank full_name: Bradke, Frank last_name: Bradke - first_name: Dieter full_name: Jenne, Dieter last_name: Jenne - first_name: Tad full_name: Holak, Tad A last_name: Holak - first_name: Zena full_name: Werb, Zena last_name: Werb - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Roland full_name: Wedlich-Soldner, Roland last_name: Wedlich Soldner citation: ama: 'Riedl J, Crevenna A, Kessenbrock K, et al. Lifeact: a versatile marker to visualize F-actin. Nature Methods. 2008;5(7):605-607. doi:10.1038/nmeth.1220' apa: 'Riedl, J., Crevenna, A., Kessenbrock, K., Yu, J., Neukirchen, D., Bista, M., … Wedlich Soldner, R. (2008). Lifeact: a versatile marker to visualize F-actin. Nature Methods. Nature Publishing Group. https://doi.org/10.1038/nmeth.1220' chicago: 'Riedl, Julia, Alvaro Crevenna, Kai Kessenbrock, Jerry Yu, Dorothee Neukirchen, Michal Bista, Frank Bradke, et al. “Lifeact: A Versatile Marker to Visualize F-Actin.” Nature Methods. Nature Publishing Group, 2008. https://doi.org/10.1038/nmeth.1220.' ieee: 'J. Riedl et al., “Lifeact: a versatile marker to visualize F-actin,” Nature Methods, vol. 5, no. 7. Nature Publishing Group, pp. 605–607, 2008.' ista: 'Riedl J, Crevenna A, Kessenbrock K, Yu J, Neukirchen D, Bista M, Bradke F, Jenne D, Holak T, Werb Z, Sixt MK, Wedlich Soldner R. 2008. Lifeact: a versatile marker to visualize F-actin. Nature Methods. 5(7), 605–607.' mla: 'Riedl, Julia, et al. “Lifeact: A Versatile Marker to Visualize F-Actin.” Nature Methods, vol. 5, no. 7, Nature Publishing Group, 2008, pp. 605–07, doi:10.1038/nmeth.1220.' short: J. Riedl, A. Crevenna, K. Kessenbrock, J. Yu, D. Neukirchen, M. Bista, F. Bradke, D. Jenne, T. Holak, Z. Werb, M.K. Sixt, R. Wedlich Soldner, Nature Methods 5 (2008) 605–607. date_created: 2018-12-11T12:06:02Z date_published: 2008-06-08T00:00:00Z date_updated: 2021-01-12T07:53:22Z day: '08' doi: 10.1038/nmeth.1220 extern: 1 intvolume: ' 5' issue: '7' month: '06' page: 605 - 607 publication: Nature Methods publication_status: published publisher: Nature Publishing Group publist_id: '2184' quality_controlled: 0 status: public title: 'Lifeact: a versatile marker to visualize F-actin' type: journal_article volume: 5 year: '2008' ... --- _id: '3974' abstract: - lang: eng text: Generalizing the concept of a Reeb graph, the Reeb space of a multivariate continuous mapping identifies points of the domain that belong to a common component of the preimage of a point in the range. We study the local and global structure of this space for generic, piecewise linear mappings on a combinatorial manifold. author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Amit full_name: Amit Patel id: 34A254A0-F248-11E8-B48F-1D18A9856A87 last_name: Patel citation: ama: 'Edelsbrunner H, Harer J, Patel A. Reeb spaces of piecewise linear mappings. In: ACM; 2008:242-250. doi:10.1145/1377676.1377720' apa: 'Edelsbrunner, H., Harer, J., & Patel, A. (2008). Reeb spaces of piecewise linear mappings (pp. 242–250). Presented at the SCG: Symposium on Computational Geometry, ACM. https://doi.org/10.1145/1377676.1377720' chicago: Edelsbrunner, Herbert, John Harer, and Amit Patel. “Reeb Spaces of Piecewise Linear Mappings,” 242–50. ACM, 2008. https://doi.org/10.1145/1377676.1377720. ieee: 'H. Edelsbrunner, J. Harer, and A. Patel, “Reeb spaces of piecewise linear mappings,” presented at the SCG: Symposium on Computational Geometry, 2008, pp. 242–250.' ista: 'Edelsbrunner H, Harer J, Patel A. 2008. Reeb spaces of piecewise linear mappings. SCG: Symposium on Computational Geometry, 242–250.' mla: Edelsbrunner, Herbert, et al. Reeb Spaces of Piecewise Linear Mappings. ACM, 2008, pp. 242–50, doi:10.1145/1377676.1377720. short: H. Edelsbrunner, J. Harer, A. Patel, in:, ACM, 2008, pp. 242–250. conference: name: 'SCG: Symposium on Computational Geometry' date_created: 2018-12-11T12:06:13Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:53:35Z day: '01' doi: 10.1145/1377676.1377720 extern: 1 month: '01' page: 242 - 250 publication_status: published publisher: ACM publist_id: '2155' quality_controlled: 0 status: public title: Reeb spaces of piecewise linear mappings type: conference year: '2008' ... --- _id: '4135' author: - first_name: D. full_name: Storch,D. last_name: Storch - first_name: A. full_name: Šizling,A. L last_name: Šizling - first_name: J. full_name: Reif,J. last_name: Reif - first_name: Jitka full_name: Jitka Polechova id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: E. full_name: Šizlingová,E. last_name: Šizlingová - first_name: K. full_name: Gaston,K. J last_name: Gaston citation: ama: 'Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. The quest for a null model for macroecological patterns: geometry of species distributions at multiple spatial scales. Ecology Letters. 2008;11(8):771-784. doi:3817' apa: 'Storch, D., Šizling, A., Reif, J., Polechova, J., Šizlingová, E., & Gaston, K. (2008). The quest for a null model for macroecological patterns: geometry of species distributions at multiple spatial scales. Ecology Letters. Wiley-Blackwell. https://doi.org/3817' chicago: 'Storch, D., A. Šizling, J. Reif, Jitka Polechova, E. Šizlingová, and K. Gaston. “The Quest for a Null Model for Macroecological Patterns: Geometry of Species Distributions at Multiple Spatial Scales.” Ecology Letters. Wiley-Blackwell, 2008. https://doi.org/3817.' ieee: 'D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, and K. Gaston, “The quest for a null model for macroecological patterns: geometry of species distributions at multiple spatial scales,” Ecology Letters, vol. 11, no. 8. Wiley-Blackwell, pp. 771–784, 2008.' ista: 'Storch D, Šizling A, Reif J, Polechova J, Šizlingová E, Gaston K. 2008. The quest for a null model for macroecological patterns: geometry of species distributions at multiple spatial scales. Ecology Letters. 11(8), 771–784.' mla: 'Storch, D., et al. “The Quest for a Null Model for Macroecological Patterns: Geometry of Species Distributions at Multiple Spatial Scales.” Ecology Letters, vol. 11, no. 8, Wiley-Blackwell, 2008, pp. 771–84, doi:3817.' short: D. Storch, A. Šizling, J. Reif, J. Polechova, E. Šizlingová, K. Gaston, Ecology Letters 11 (2008) 771–784. date_created: 2018-12-11T12:07:09Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:54:46Z day: '01' doi: '3817' extern: 1 intvolume: ' 11' issue: '8' month: '01' page: 771 - 784 publication: Ecology Letters publication_status: published publisher: Wiley-Blackwell publist_id: '1985' quality_controlled: 0 status: public title: 'The quest for a null model for macroecological patterns: geometry of species distributions at multiple spatial scales' type: journal_article volume: 11 year: '2008' ... --- _id: '4137' author: - first_name: Jon full_name: Bridle, Jon R last_name: Bridle - first_name: Jitka full_name: Jitka Polechova id: 3BBFB084-F248-11E8-B48F-1D18A9856A87 last_name: Polechova orcid: 0000-0003-0951-3112 - first_name: Timothy full_name: Vines, Timothy H last_name: Vines citation: ama: 'Bridle J, Polechova J, Vines T. Patterns of biodiversity and limits to adaptation in time and space. In: R. K. Butlin JR, Schluter D, eds. Evolution and Speciation. Cambridge University Press; 2008:77-101. doi:3816' apa: Bridle, J., Polechova, J., & Vines, T. (2008). Patterns of biodiversity and limits to adaptation in time and space. In J. R. R. K. Butlin & D. Schluter (Eds.), Evolution and Speciation (pp. 77–101). Cambridge University Press. https://doi.org/3816 chicago: Bridle, Jon, Jitka Polechova, and Timothy Vines. “Patterns of Biodiversity and Limits to Adaptation in Time and Space.” In Evolution and Speciation, edited by J.R. R. K. Butlin and D. Schluter, 77–101. Cambridge University Press, 2008. https://doi.org/3816. ieee: J. Bridle, J. Polechova, and T. Vines, “Patterns of biodiversity and limits to adaptation in time and space,” in Evolution and Speciation, J. R. R. K. Butlin and D. Schluter, Eds. Cambridge University Press, 2008, pp. 77–101. ista: 'Bridle J, Polechova J, Vines T. 2008.Patterns of biodiversity and limits to adaptation in time and space. In: Evolution and Speciation. , 77–101.' mla: Bridle, Jon, et al. “Patterns of Biodiversity and Limits to Adaptation in Time and Space.” Evolution and Speciation, edited by J.R. R. K. Butlin and D. Schluter, Cambridge University Press, 2008, pp. 77–101, doi:3816. short: J. Bridle, J. Polechova, T. Vines, in:, J.R. R. K. Butlin, D. Schluter (Eds.), Evolution and Speciation, Cambridge University Press, 2008, pp. 77–101. date_created: 2018-12-11T12:07:09Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:54:46Z day: '01' doi: '3816' editor: - first_name: J.R. full_name: R. K. Butlin,J.R. Bridle last_name: R. K. Butlin - first_name: D. full_name: Schluter,D. last_name: Schluter extern: 1 month: '01' page: 77 - 101 publication: Evolution and Speciation publication_status: published publisher: Cambridge University Press publist_id: '1984' quality_controlled: 0 status: public title: Patterns of biodiversity and limits to adaptation in time and space type: book_chapter year: '2008' ... --- _id: '4150' abstract: - lang: eng text: This study provides direct functional evidence that differential adhesion, measurable as quantitative differences in tissue surface tension, influences spatial positioning between zebrafish germ layer tissues. We show that embryonic ectodermal and mesendodermal tissues generated by mRNA-overexpression behave on long-time scales like immiscible fluids. When mixed in hanging drop culture, their cells segregate into discrete phases with ectoderm adopting an internal position relative to the mesendoderm. The position adopted directly correlates with differences in tissue surface tension. We also show that germ layer tissues from untreated embryos, when extirpated and placed in culture, adopt a configuration similar to those of their mRNA-overexpressing counterparts. Down-regulating E-cadherin expression in the ectoderm leads to reduced surface tension and results in phase reversal with E-cadherin-depleted ectoderm cells now adopting an external position relative to the mesendoderm. These results show that in vitro cell sorting of zebrafish mesendoderm and ectoderm tissues is specified by tissue interfacial tensions. We perform a mathematical analysis indicating that tissue interfacial tension between actively motile cells contributes to the spatial organization and dynamics of these zebrafish germ layers in vivo. article_processing_charge: No author: - first_name: Eva full_name: Schötz, Eva last_name: Schötz - first_name: Rebecca full_name: Burdine, Rebecca last_name: Burdine - first_name: Frank full_name: Julicher, Frank last_name: Julicher - first_name: Malcolm full_name: Steinberg, Malcolm last_name: Steinberg - 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: Ramsey full_name: Foty, Ramsey last_name: Foty citation: ama: Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. Quantitative differences in tissue surface tension influence zebrafish germ layer positioning. HFSP Journal. 2008;2(1):42-56. doi:10.2976/1.2834817 apa: Schötz, E., Burdine, R., Julicher, F., Steinberg, M., Heisenberg, C.-P. J., & Foty, R. (2008). Quantitative differences in tissue surface tension influence zebrafish germ layer positioning. HFSP Journal. HFSP Publishing. https://doi.org/10.2976/1.2834817 chicago: Schötz, Eva, Rebecca Burdine, Frank Julicher, Malcolm Steinberg, Carl-Philipp J Heisenberg, and Ramsey Foty. “Quantitative Differences in Tissue Surface Tension Influence Zebrafish Germ Layer Positioning.” HFSP Journal. HFSP Publishing, 2008. https://doi.org/10.2976/1.2834817. ieee: E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P. J. Heisenberg, and R. Foty, “Quantitative differences in tissue surface tension influence zebrafish germ layer positioning,” HFSP Journal, vol. 2, no. 1. HFSP Publishing, pp. 42–56, 2008. ista: Schötz E, Burdine R, Julicher F, Steinberg M, Heisenberg C-PJ, Foty R. 2008. Quantitative differences in tissue surface tension influence zebrafish germ layer positioning. HFSP Journal. 2(1), 42–56. mla: Schötz, Eva, et al. “Quantitative Differences in Tissue Surface Tension Influence Zebrafish Germ Layer Positioning.” HFSP Journal, vol. 2, no. 1, HFSP Publishing, 2008, pp. 42–56, doi:10.2976/1.2834817. short: E. Schötz, R. Burdine, F. Julicher, M. Steinberg, C.-P.J. Heisenberg, R. Foty, HFSP Journal 2 (2008) 42–56. date_created: 2018-12-11T12:07:14Z date_published: 2008-02-01T00:00:00Z date_updated: 2021-01-12T07:54:52Z day: '01' doi: 10.2976/1.2834817 extern: '1' intvolume: ' 2' issue: '1' language: - iso: eng month: '02' oa_version: None page: 42 - 56 publication: HFSP Journal publication_status: published publisher: HFSP Publishing publist_id: '1969' status: public title: Quantitative differences in tissue surface tension influence zebrafish germ layer positioning type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2008' ... --- _id: '4181' abstract: - lang: eng text: Understanding the factors that direct tissue organization during development is one of the most fundamental goals in developmental biology. Various hypotheses explain cell sorting and tissue organization on the basis of the adhesive and mechanical properties of the constituent cells(1). However, validating these hypotheses has been difficult due to the lack of appropriate tools to measure these parameters. Here we use atomic force microscopy ( AFM) to quantify the adhesive and mechanical properties of individual ectoderm, mesoderm and endoderm progenitor cells from gastrulating zebrafish embryos. Combining these data with tissue self-assembly in vitro and the sorting behaviour of progenitors in vivo, we have shown that differential actomyosin-dependent cell-cortex tension, regulated by Nodal/ TGF beta-signalling ( transforming growth factor beta), constitutes a key factor that directs progenitor-cell sorting. These results demonstrate a previously unrecognized role for Nodal-controlled cell-cortex tension in germ-layer organization during gastrulation. article_processing_charge: No author: - first_name: Michael full_name: Krieg, Michael last_name: Krieg - first_name: Yohanna full_name: Arboleda Estudillo, Yohanna last_name: Arboleda Estudillo - first_name: Pierre full_name: Puech, Pierre last_name: Puech - first_name: Jos full_name: Käfer, Jos last_name: Käfer - first_name: François full_name: Graner, François last_name: Graner - first_name: Daniel full_name: Mueller, Daniel last_name: Mueller - 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: Krieg M, Arboleda Estudillo Y, Puech P, et al. Tensile forces govern germ-layer organization in zebrafish. Nature Cell Biology. 2008;10(4):429-436. doi:10.1038/ncb1705 apa: Krieg, M., Arboleda Estudillo, Y., Puech, P., Käfer, J., Graner, F., Mueller, D., & Heisenberg, C.-P. J. (2008). Tensile forces govern germ-layer organization in zebrafish. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1705 chicago: Krieg, Michael, Yohanna Arboleda Estudillo, Pierre Puech, Jos Käfer, François Graner, Daniel Mueller, and Carl-Philipp J Heisenberg. “Tensile Forces Govern Germ-Layer Organization in Zebrafish.” Nature Cell Biology. Nature Publishing Group, 2008. https://doi.org/10.1038/ncb1705. ieee: M. Krieg et al., “Tensile forces govern germ-layer organization in zebrafish,” Nature Cell Biology, vol. 10, no. 4. Nature Publishing Group, pp. 429–436, 2008. ista: Krieg M, Arboleda Estudillo Y, Puech P, Käfer J, Graner F, Mueller D, Heisenberg C-PJ. 2008. Tensile forces govern germ-layer organization in zebrafish. Nature Cell Biology. 10(4), 429–436. mla: Krieg, Michael, et al. “Tensile Forces Govern Germ-Layer Organization in Zebrafish.” Nature Cell Biology, vol. 10, no. 4, Nature Publishing Group, 2008, pp. 429–36, doi:10.1038/ncb1705. short: M. Krieg, Y. Arboleda Estudillo, P. Puech, J. Käfer, F. Graner, D. Mueller, C.-P.J. Heisenberg, Nature Cell Biology 10 (2008) 429–436. date_created: 2018-12-11T12:07:26Z date_published: 2008-03-23T00:00:00Z date_updated: 2021-01-12T07:55:07Z day: '23' doi: 10.1038/ncb1705 extern: '1' intvolume: ' 10' issue: '4' language: - iso: eng month: '03' oa_version: None page: 429 - 436 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '1938' status: public title: Tensile forces govern germ-layer organization in zebrafish type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 10 year: '2008' ... --- _id: '4180' abstract: - lang: eng text: '(Figure Presented) The name''s Bond: Separated cells form membranous nanotubes whose tips are tethered by adhesive bonds (see picture). The lifetime of receptor-ligand interactions can be measured by using membrane nanotubes of living cells as constant force actuators. Because the nanotubes are extruded from living cells at conditions approaching the physiological, cellular processes can be both studied and utilized. ' article_processing_charge: No author: - first_name: Michael full_name: Krieg, Michael last_name: Krieg - first_name: Jonne full_name: Helenius, Jonne last_name: Helenius - 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: Daniel full_name: Mueller, Daniel last_name: Mueller citation: ama: 'Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. Angewandte Chemie - International Edition. 2008;47(50):9775-9777. doi:10.1002/anie.200803552' apa: 'Krieg, M., Helenius, J., Heisenberg, C.-P. J., & Mueller, D. (2008). A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. Angewandte Chemie - International Edition. Wiley-Blackwell. https://doi.org/10.1002/anie.200803552' chicago: 'Krieg, Michael, Jonne Helenius, Carl-Philipp J Heisenberg, and Daniel Mueller. “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics.” Angewandte Chemie - International Edition. Wiley-Blackwell, 2008. https://doi.org/10.1002/anie.200803552.' ieee: 'M. Krieg, J. Helenius, C.-P. J. Heisenberg, and D. Mueller, “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics,” Angewandte Chemie - International Edition, vol. 47, no. 50. Wiley-Blackwell, pp. 9775–9777, 2008.' ista: 'Krieg M, Helenius J, Heisenberg C-PJ, Mueller D. 2008. A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics. Angewandte Chemie - International Edition. 47(50), 9775–9777.' mla: 'Krieg, Michael, et al. “A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics.” Angewandte Chemie - International Edition, vol. 47, no. 50, Wiley-Blackwell, 2008, pp. 9775–77, doi:10.1002/anie.200803552.' short: M. Krieg, J. Helenius, C.-P.J. Heisenberg, D. Mueller, Angewandte Chemie - International Edition 47 (2008) 9775–9777. date_created: 2018-12-11T12:07:26Z date_published: 2008-12-01T00:00:00Z date_updated: 2021-01-12T07:55:06Z day: '01' doi: 10.1002/anie.200803552 extern: '1' intvolume: ' 47' issue: '50' language: - iso: eng month: '12' oa_version: None page: 9775 - 9777 publication: Angewandte Chemie - International Edition publication_status: published publisher: Wiley-Blackwell publist_id: '1939' status: public title: 'A Bond for a Lifetime: Employing Membrane Nanotubes from Living Cells to Determine Receptor-Ligand Kinetics' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2008' ... --- _id: '4193' abstract: - lang: eng text: The controlled adhesion of cells to each other and to the extracellular matrix is crucial for tissue development and maintenance. Numerous assays have been developed to quantify cell adhesion. Among these, the use of atomic force microscopy (AFM) for single-cell force spectroscopy (SCFS) has recently been established. This assay permits the adhesion of living cells to be studied in near-physiological conditions. This implementation of AFM allows unrivaled spatial and temporal control of cells, as well as highly quantitative force actuation and force measurement that is sufficiently sensitive to characterize the interaction of single molecules. Therefore, not only overall cell adhesion but also the properties of single adhesion-receptor-ligand interactions can be studied. Here we describe current implementations and applications of SCFS, as well as potential pitfalls, and outline how developments will provide insight into the forces, energetics and kinetics of cell-adhesion processes. article_processing_charge: No author: - first_name: Jonne full_name: Helenius, Jonne last_name: Helenius - 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: Hermann full_name: Gaub, Hermann last_name: Gaub - first_name: Daniel full_name: Mueller, Daniel last_name: Mueller citation: ama: Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. Single-cell force spectroscopy. Journal of Cell Science. 2008;121(11):1785-1791. doi:10.1242/​jcs.030999 apa: Helenius, J., Heisenberg, C.-P. J., Gaub, H., & Mueller, D. (2008). Single-cell force spectroscopy. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/​jcs.030999 chicago: Helenius, Jonne, Carl-Philipp J Heisenberg, Hermann Gaub, and Daniel Mueller. “Single-Cell Force Spectroscopy.” Journal of Cell Science. Company of Biologists, 2008. https://doi.org/10.1242/​jcs.030999. ieee: J. Helenius, C.-P. J. Heisenberg, H. Gaub, and D. Mueller, “Single-cell force spectroscopy,” Journal of Cell Science, vol. 121, no. 11. Company of Biologists, pp. 1785–1791, 2008. ista: Helenius J, Heisenberg C-PJ, Gaub H, Mueller D. 2008. Single-cell force spectroscopy. Journal of Cell Science. 121(11), 1785–1791. mla: Helenius, Jonne, et al. “Single-Cell Force Spectroscopy.” Journal of Cell Science, vol. 121, no. 11, Company of Biologists, 2008, pp. 1785–91, doi:10.1242/​jcs.030999. short: J. Helenius, C.-P.J. Heisenberg, H. Gaub, D. Mueller, Journal of Cell Science 121 (2008) 1785–1791. date_created: 2018-12-11T12:07:30Z date_published: 2008-06-01T00:00:00Z date_updated: 2021-01-12T07:55:12Z day: '01' doi: 10.1242/​jcs.030999 extern: '1' intvolume: ' 121' issue: '11' language: - iso: eng month: '06' oa_version: None page: 1785 - 1791 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '1924' status: public title: Single-cell force spectroscopy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 121 year: '2008' ... --- _id: '4198' abstract: - lang: eng text: Animal body plan arises during gastrulation and organogenesis by the coordination of inductive events and cell movements. Several signaling pathways, such as BMP, FGF, Hedgehog, Nodal, and Wnt have well-recognized instructive roles in cell fate specification during vertebrate embryogenesis. Growing evidence indicates that BMP, Nodal, and FGF signaling also regulate cell movements, and that they do so through mechanisms distinct from those that specify cell fates. Moreover, pathways controlling cell movements can also indirectly influence cell fate specification by regulating dimensions and relative positions of interacting tissues. The current challenge is to delineate the molecular mechanisms via which the major signaling pathways regulate cell fate specification and movements, and how these two processes are coordinated to ensure normal development. article_processing_charge: No author: - 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: Lilianna full_name: Solnica Krezel, Lilianna last_name: Solnica Krezel citation: ama: Heisenberg C-PJ, Solnica Krezel L. Back and forth between cell fate specification and movement during vertebrate gastrulation. Current Opinion in Genetics & Development. 2008;18(4):311-316. doi:10.1016/j.gde.2008.07.011 apa: Heisenberg, C.-P. J., & Solnica Krezel, L. (2008). Back and forth between cell fate specification and movement during vertebrate gastrulation. Current Opinion in Genetics & Development. Elsevier. https://doi.org/10.1016/j.gde.2008.07.011 chicago: Heisenberg, Carl-Philipp J, and Lilianna Solnica Krezel. “Back and Forth between Cell Fate Specification and Movement during Vertebrate Gastrulation.” Current Opinion in Genetics & Development. Elsevier, 2008. https://doi.org/10.1016/j.gde.2008.07.011. ieee: C.-P. J. Heisenberg and L. Solnica Krezel, “Back and forth between cell fate specification and movement during vertebrate gastrulation,” Current Opinion in Genetics & Development, vol. 18, no. 4. Elsevier, pp. 311–316, 2008. ista: Heisenberg C-PJ, Solnica Krezel L. 2008. Back and forth between cell fate specification and movement during vertebrate gastrulation. Current Opinion in Genetics & Development. 18(4), 311–316. mla: Heisenberg, Carl-Philipp J., and Lilianna Solnica Krezel. “Back and Forth between Cell Fate Specification and Movement during Vertebrate Gastrulation.” Current Opinion in Genetics & Development, vol. 18, no. 4, Elsevier, 2008, pp. 311–16, doi:10.1016/j.gde.2008.07.011. short: C.-P.J. Heisenberg, L. Solnica Krezel, Current Opinion in Genetics & Development 18 (2008) 311–316. date_created: 2018-12-11T12:07:32Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:55:14Z day: '01' doi: 10.1016/j.gde.2008.07.011 extern: '1' intvolume: ' 18' issue: '4' language: - iso: eng month: '01' oa_version: None page: 311 - 316 publication: Current Opinion in Genetics & Development publication_status: published publisher: Elsevier publist_id: '1918' status: public title: Back and forth between cell fate specification and movement during vertebrate gastrulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2008' ... --- _id: '4227' abstract: - lang: eng text: 'Morphogen concentration gradients provide positional information by activating target genes in a concentration-dependent manner. Recent reports show that the gradient of the syncytial morphogen Bicoid seems to provide precise positional information to determine target gene domains. For secreted morphogenetic ligands, the precision of the gradients, the signal transduction and the reliability of target gene expression domains have not been studied. Here we investigate these issues for the TGF-beta-type morphogen Dpp. We first studied theoretically how cell-to-cell variability in the source, the target tissue, or both, contribute to the variations of the gradient. Fluctuations in the source and target generate a local maximum of precision at a finite distance to the source. We then determined experimentally in the wing epithelium: (1) the precision of the Dpp concentration gradient; (2) the precision of the Dpp signaling activity profile; and (3) the precision of activation of the Dpp target gene spalt. As captured by our theoretical description, the Dpp gradient provides positional information with a maximal precision a few cells away from the source. This maximal precision corresponds to a positional uncertainly of about a single cell diameter. The precision of the Dpp gradient accounts for the precision of the spalt expression range, implying that Dpp can act as a morphogen to coarsely determine the expression pattern of target genes.' author: - first_name: Tobias full_name: Bollenbach, Tobias last_name: Bollenbach - first_name: Periklis full_name: Pantazis, Periklis last_name: Pantazis - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Christian full_name: Bokel, Christian last_name: Bokel - first_name: Marcos full_name: González-Gaitán, Marcos last_name: González Gaitán - first_name: Frank full_name: Julicher, Frank last_name: Julicher citation: ama: Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher F. Precision of the Dpp gradient. Development. 2008;135(6):1137-1146. doi:10.1242/dev.012062 apa: Bollenbach, T., Pantazis, P., Kicheva, A., Bokel, C., González Gaitán, M., & Julicher, F. (2008). Precision of the Dpp gradient. Development. Company of Biologists. https://doi.org/10.1242/dev.012062 chicago: Bollenbach, Tobias, Periklis Pantazis, Anna Kicheva, Christian Bokel, Marcos González Gaitán, and Frank Julicher. “Precision of the Dpp Gradient.” Development. Company of Biologists, 2008. https://doi.org/10.1242/dev.012062. ieee: T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, and F. Julicher, “Precision of the Dpp gradient,” Development, vol. 135, no. 6. Company of Biologists, pp. 1137–1146, 2008. ista: Bollenbach T, Pantazis P, Kicheva A, Bokel C, González Gaitán M, Julicher F. 2008. Precision of the Dpp gradient. Development. 135(6), 1137–1146. mla: Bollenbach, Tobias, et al. “Precision of the Dpp Gradient.” Development, vol. 135, no. 6, Company of Biologists, 2008, pp. 1137–46, doi:10.1242/dev.012062. short: T. Bollenbach, P. Pantazis, A. Kicheva, C. Bokel, M. González Gaitán, F. Julicher, Development 135 (2008) 1137–1146. date_created: 2018-12-11T12:07:42Z date_published: 2008-03-15T00:00:00Z date_updated: 2021-01-12T07:55:27Z day: '15' doi: 10.1242/dev.012062 extern: 1 intvolume: ' 135' issue: '6' month: '03' page: 1137 - 1146 publication: Development publication_status: published publisher: Company of Biologists publist_id: '1889' quality_controlled: 0 status: public title: Precision of the Dpp gradient type: journal_article volume: 135 year: '2008' ... --- _id: '4245' abstract: - lang: eng text: Sex allocation theory has proved extremely successful at predicting when individuals should adjust the sex of their offspring in response to environmental conditions. However, we know rather little about the underlying genetics of sex ratio or how genetic architecture might constrain adaptive sex-ratio behavior. We examined how mutation influenced genetic variation in the sex ratios produced by the parasitoid wasp Nasonia vitripennis. In a mutation accumulation experiment, we determined the mutability of sex ratio, and compared this with the amount of genetic variation observed in natural populations. We found that the mutability (h2m) ranges from 0.001 to 0.002, similar to estimates for life-history traits in other organisms. These estimates suggest one mutation every 5–60 generations, which shift the sex ratio by approximately 0.01 (proportion males). In this and other studies, the genetic variation in N. vitripennis sex ratio ranged from 0.02 to 0.17 (broad-sense heritability, H2). If sex ratio is maintained by mutation–selection balance, a higher genetic variance would be expected given our mutational parameters. Instead, the observed genetic variance perhaps suggests additional selection against sex-ratio mutations with deleterious effects on other fitness traits as well as sex ratio (i.e., pleiotropy), as has been argued to be the case more generally. author: - first_name: Bart full_name: Pannebakker, Bart A last_name: Pannebakker - first_name: Daniel full_name: Halligan, Daniel last_name: Halligan - first_name: K Tracy full_name: Reynolds, K Tracy last_name: Reynolds - first_name: Gavin full_name: Ballantyne, Gavin A last_name: Ballantyne - first_name: David full_name: Shuker, David M last_name: Shuker - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Stuart full_name: West, Stuart A last_name: West citation: ama: Pannebakker B, Halligan D, Reynolds KT, et al. Effects of spontaneous mutation accumulation on sex ratio traits. Evolution; International Journal of Organic Evolution. 2008;62(8):1921-1935. doi:10.1111/j.1558-5646.2008.00434.x apa: Pannebakker, B., Halligan, D., Reynolds, K. T., Ballantyne, G., Shuker, D., Barton, N. H., & West, S. (2008). Effects of spontaneous mutation accumulation on sex ratio traits. Evolution; International Journal of Organic Evolution. Wiley-Blackwell. https://doi.org/10.1111/j.1558-5646.2008.00434.x chicago: Pannebakker, Bart, Daniel Halligan, K Tracy Reynolds, Gavin Ballantyne, David Shuker, Nicholas H Barton, and Stuart West. “Effects of Spontaneous Mutation Accumulation on Sex Ratio Traits.” Evolution; International Journal of Organic Evolution. Wiley-Blackwell, 2008. https://doi.org/10.1111/j.1558-5646.2008.00434.x. ieee: B. Pannebakker et al., “Effects of spontaneous mutation accumulation on sex ratio traits,” Evolution; International Journal of Organic Evolution, vol. 62, no. 8. Wiley-Blackwell, pp. 1921–1935, 2008. ista: Pannebakker B, Halligan D, Reynolds KT, Ballantyne G, Shuker D, Barton NH, West S. 2008. Effects of spontaneous mutation accumulation on sex ratio traits. Evolution; International Journal of Organic Evolution. 62(8), 1921–1935. mla: Pannebakker, Bart, et al. “Effects of Spontaneous Mutation Accumulation on Sex Ratio Traits.” Evolution; International Journal of Organic Evolution, vol. 62, no. 8, Wiley-Blackwell, 2008, pp. 1921–35, doi:10.1111/j.1558-5646.2008.00434.x. short: B. Pannebakker, D. Halligan, K.T. Reynolds, G. Ballantyne, D. Shuker, N.H. Barton, S. West, Evolution; International Journal of Organic Evolution 62 (2008) 1921–1935. date_created: 2018-12-11T12:07:49Z date_published: 2008-08-01T00:00:00Z date_updated: 2021-01-12T07:55:34Z day: '01' doi: 10.1111/j.1558-5646.2008.00434.x extern: 1 intvolume: ' 62' issue: '8' month: '08' page: 1921 - 1935 publication: Evolution; International Journal of Organic Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '1860' quality_controlled: 0 status: public title: Effects of spontaneous mutation accumulation on sex ratio traits type: journal_article volume: 62 year: '2008' ... --- _id: '4244' abstract: - lang: eng text: This paper presents a new approach to optimization of an energy-constrained modulation scheme for wireless sensor networks by taking advantage of a novel bio-inspired optimization algorithm. The algorithm is inspired by Wrightpsilas shifting balance theory (SBT) of evolution in population genetics. The total energy consumption of an energy-constrained modulation scheme is minimized by using the new SBT-based optimization algorithm. The results obtained by this new algorithm are compared with other popular optimization algorithms. Numerical experiments are performed to demonstrate that the SBT-based algorithm could be used as an efficient optimizer for solving the optimization problems arising from currently emerging energy-efficient wireless sensor networks. author: - first_name: Erfu full_name: Yang, Erfu last_name: Yang - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Tughrul full_name: Arslan, Tughrul last_name: Arslan - first_name: Ahmet full_name: Erdogan, Ahmet T last_name: Erdogan citation: ama: 'Yang E, Barton NH, Arslan T, Erdogan A. A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks. In: IEEE; 2008:2749-2756. doi:10.1109/CEC.2008.4631167' apa: 'Yang, E., Barton, N. H., Arslan, T., & Erdogan, A. (2008). A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks (pp. 2749–2756). Presented at the WCCI: IEEE World Congress on Computational Intelligence, IEEE. https://doi.org/10.1109/CEC.2008.4631167' chicago: Yang, Erfu, Nicholas H Barton, Tughrul Arslan, and Ahmet Erdogan. “A Novel Shifting Balance Theory-Based Approach to Optimization of an Energy-Constrained Modulation Scheme for Wireless Sensor Networks,” 2749–56. IEEE, 2008. https://doi.org/10.1109/CEC.2008.4631167. ieee: 'E. Yang, N. H. Barton, T. Arslan, and A. Erdogan, “A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks,” presented at the WCCI: IEEE World Congress on Computational Intelligence, 2008, pp. 2749–2756.' ista: 'Yang E, Barton NH, Arslan T, Erdogan A. 2008. A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks. WCCI: IEEE World Congress on Computational Intelligence, 2749–2756.' mla: Yang, Erfu, et al. A Novel Shifting Balance Theory-Based Approach to Optimization of an Energy-Constrained Modulation Scheme for Wireless Sensor Networks. IEEE, 2008, pp. 2749–56, doi:10.1109/CEC.2008.4631167. short: E. Yang, N.H. Barton, T. Arslan, A. Erdogan, in:, IEEE, 2008, pp. 2749–2756. conference: name: 'WCCI: IEEE World Congress on Computational Intelligence' date_created: 2018-12-11T12:07:49Z date_published: 2008-09-23T00:00:00Z date_updated: 2021-01-12T07:55:34Z day: '23' doi: 10.1109/CEC.2008.4631167 extern: 1 month: '09' page: 2749 - 2756 publication_status: published publisher: IEEE publist_id: '1861' quality_controlled: 0 status: public title: A novel shifting balance theory-based approach to optimization of an energy-constrained modulation scheme for wireless sensor networks type: conference year: '2008' ... --- _id: '4371' abstract: - lang: eng text: We survey some of the problems associated with checking whether a given behavior (a sequence, a Boolean signal or a continuous signal) satisfies a property specified in an appropriate temporal logic and describe two such monitoring algorithms for the real-time logic MITL. alternative_title: - LNCS article_processing_charge: No author: - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Nickovic, Dejan id: 41BCEE5C-F248-11E8-B48F-1D18A9856A87 last_name: Nickovic - first_name: Amir full_name: Pnueli, Amir last_name: Pnueli citation: ama: 'Maler O, Nickovic D, Pnueli A. Checking Temporal Properties of Discrete, Timed and Continuous Behaviors. In: Pillars of Computer Science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday. Springer; 2008:475-505. doi:10.1007/978-3-540-78127-1_26' apa: 'Maler, O., Nickovic, D., & Pnueli, A. (2008). Checking Temporal Properties of Discrete, Timed and Continuous Behaviors. In Pillars of Computer science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday (pp. 475–505). Springer. https://doi.org/10.1007/978-3-540-78127-1_26' chicago: 'Maler, Oded, Dejan Nickovic, and Amir Pnueli. “Checking Temporal Properties of Discrete, Timed and Continuous Behaviors.” In Pillars of Computer Science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday, 475–505. Springer, 2008. https://doi.org/10.1007/978-3-540-78127-1_26.' ieee: 'O. Maler, D. Nickovic, and A. Pnueli, “Checking Temporal Properties of Discrete, Timed and Continuous Behaviors,” in Pillars of Computer science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday, Springer, 2008, pp. 475–505.' ista: 'Maler O, Nickovic D, Pnueli A. 2008.Checking Temporal Properties of Discrete, Timed and Continuous Behaviors. In: Pillars of Computer science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday. LNCS, , 475–505.' mla: 'Maler, Oded, et al. “Checking Temporal Properties of Discrete, Timed and Continuous Behaviors.” Pillars of Computer Science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday, Springer, 2008, pp. 475–505, doi:10.1007/978-3-540-78127-1_26.' short: 'O. Maler, D. Nickovic, A. Pnueli, in:, Pillars of Computer Science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday, Springer, 2008, pp. 475–505.' date_created: 2018-12-11T12:08:30Z date_published: 2008-03-11T00:00:00Z date_updated: 2023-02-14T10:42:38Z day: '11' doi: 10.1007/978-3-540-78127-1_26 extern: '1' language: - iso: eng month: '03' oa_version: None page: 475 - 505 publication: 'Pillars of Computer science: Essays Dedicated To Boris (Boaz) Trakhtenbrot on the Occasion of His 85th Birthday' publication_identifier: isbn: - '9783540781264' publication_status: published publisher: Springer publist_id: '1087' quality_controlled: '1' scopus_import: '1' status: public title: Checking Temporal Properties of Discrete, Timed and Continuous Behaviors type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2008' ... --- _id: '4366' abstract: - lang: eng text: Termination of a heap-manipulating program generally depends on preconditions that express heap assumptions (i.e., assertions describing reachability, aliasing, separation and sharing in the heap). We present an algorithm for the inference of such preconditions. The algorithm exploits a unique interplay between counterexample-producing abstract termination checker and shape analysis. The shape analysis produces heap assumptions on demand to eliminate counterexamples, i.e., non-terminating abstract computations. The experiments with our prototype implementation indicate its practical potential. alternative_title: - LNCS author: - first_name: Andreas full_name: Podelski,Andreas last_name: Podelski - first_name: Andrey full_name: Rybalchenko, Andrey last_name: Rybalchenko - first_name: Thomas full_name: Thomas Wies id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies citation: ama: 'Podelski A, Rybalchenko A, Wies T. Heap Assumptions on Demand. In: Vol 5123. Springer; 2008:314-327. doi:10.1007/978-3-540-70545-1_31' apa: 'Podelski, A., Rybalchenko, A., & Wies, T. (2008). Heap Assumptions on Demand (Vol. 5123, pp. 314–327). Presented at the CAV: Computer Aided Verification, Springer. https://doi.org/10.1007/978-3-540-70545-1_31' chicago: Podelski, Andreas, Andrey Rybalchenko, and Thomas Wies. “Heap Assumptions on Demand,” 5123:314–27. Springer, 2008. https://doi.org/10.1007/978-3-540-70545-1_31. ieee: 'A. Podelski, A. Rybalchenko, and T. Wies, “Heap Assumptions on Demand,” presented at the CAV: Computer Aided Verification, 2008, vol. 5123, pp. 314–327.' ista: 'Podelski A, Rybalchenko A, Wies T. 2008. Heap Assumptions on Demand. CAV: Computer Aided Verification, LNCS, vol. 5123, 314–327.' mla: Podelski, Andreas, et al. Heap Assumptions on Demand. Vol. 5123, Springer, 2008, pp. 314–27, doi:10.1007/978-3-540-70545-1_31. short: A. Podelski, A. Rybalchenko, T. Wies, in:, Springer, 2008, pp. 314–327. conference: name: 'CAV: Computer Aided Verification' date_created: 2018-12-11T12:08:29Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:56:26Z day: '01' doi: 10.1007/978-3-540-70545-1_31 extern: 1 intvolume: ' 5123' month: '01' page: 314 - 327 publication_status: published publisher: Springer publist_id: '1091' quality_controlled: 0 status: public title: Heap Assumptions on Demand type: conference volume: 5123 year: '2008' ... --- _id: '3038' abstract: - lang: eng text: Lateral roots originate deep within the parental root from a small number of founder cells at the periphery of vascular tissues and must emerge through intervening layers of tissues. We describe how the hormone auxin, which originates from the developing lateral root, acts as a local inductive signal which re-programmes adjacent cells. Auxin induces the expression of a previously uncharacterized auxin influx carrier LAX3 in cortical and epidermal cells directly overlaying new primordia. Increased LAX3 activity reinforces the auxin-dependent induction of a selection of cell-wall-remodelling enzymes, which are likely to promote cell separation in advance of developing lateral root primordia. author: - first_name: Kamal full_name: Swarup, Kamal last_name: Swarup - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Ranjan full_name: Swarup, Ranjan last_name: Swarup - first_name: Ilda full_name: Casimiro, Ilda last_name: Casimiro - first_name: Benjamin full_name: Péret, Benjamin last_name: Péret - first_name: Yaodong full_name: Yang, Yaodong last_name: Yang - first_name: Geraint full_name: Parry, Geraint last_name: Parry - first_name: Erik full_name: Nielsen, Erik last_name: Nielsen - first_name: Ive full_name: De Smet, Ive last_name: De Smet - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Mitchell full_name: Levesque, Mitchell P last_name: Levesque - first_name: David full_name: Carrier, David last_name: Carrier - first_name: Nicholas full_name: James, Nicholas last_name: James - first_name: Vanessa full_name: Calvo, Vanessa last_name: Calvo - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Eric full_name: Kramer, Eric last_name: Kramer - first_name: Rebecca full_name: Roberts, Rebecca last_name: Roberts - first_name: Neil full_name: Graham, Neil last_name: Graham - first_name: Sylvestre full_name: Marillonnet, Sylvestre last_name: Marillonnet - first_name: Kanu full_name: Patel, Kanu last_name: Patel - first_name: Jonathan full_name: Jones, Jonathan D last_name: Jones - first_name: Christopher full_name: Taylor, Christopher G last_name: Taylor - first_name: Daniel full_name: Schachtman, Daniel P last_name: Schachtman - first_name: Sean full_name: May, Sean last_name: May - first_name: Göran full_name: Sandberg, Göran last_name: Sandberg - first_name: Philip full_name: Benfey, Philip N last_name: Benfey - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Ian full_name: Kerr, Ian last_name: Kerr - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Laurent full_name: Laplaze, Laurent last_name: Laplaze - first_name: Malcolm full_name: Bennett, Malcolm J last_name: Bennett citation: ama: Swarup K, Benková E, Swarup R, et al. The auxin influx carrier LAX3 promotes lateral root emergence. Nature Cell Biology. 2008;10(8):946-954. doi:10.1038/ncb1754 apa: Swarup, K., Benková, E., Swarup, R., Casimiro, I., Péret, B., Yang, Y., … Bennett, M. (2008). The auxin influx carrier LAX3 promotes lateral root emergence. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb1754 chicago: Swarup, Kamal, Eva Benková, Ranjan Swarup, Ilda Casimiro, Benjamin Péret, Yaodong Yang, Geraint Parry, et al. “The Auxin Influx Carrier LAX3 Promotes Lateral Root Emergence.” Nature Cell Biology. Nature Publishing Group, 2008. https://doi.org/10.1038/ncb1754. ieee: K. Swarup et al., “The auxin influx carrier LAX3 promotes lateral root emergence,” Nature Cell Biology, vol. 10, no. 8. Nature Publishing Group, pp. 946–954, 2008. ista: Swarup K, Benková E, Swarup R, Casimiro I, Péret B, Yang Y, Parry G, Nielsen E, De Smet I, Vanneste S, Levesque M, Carrier D, James N, Calvo V, Ljung K, Kramer E, Roberts R, Graham N, Marillonnet S, Patel K, Jones J, Taylor C, Schachtman D, May S, Sandberg G, Benfey P, Friml J, Kerr I, Beeckman T, Laplaze L, Bennett M. 2008. The auxin influx carrier LAX3 promotes lateral root emergence. Nature Cell Biology. 10(8), 946–954. mla: Swarup, Kamal, et al. “The Auxin Influx Carrier LAX3 Promotes Lateral Root Emergence.” Nature Cell Biology, vol. 10, no. 8, Nature Publishing Group, 2008, pp. 946–54, doi:10.1038/ncb1754. short: K. Swarup, E. Benková, R. Swarup, I. Casimiro, B. Péret, Y. Yang, G. Parry, E. Nielsen, I. De Smet, S. Vanneste, M. Levesque, D. Carrier, N. James, V. Calvo, K. Ljung, E. Kramer, R. Roberts, N. Graham, S. Marillonnet, K. Patel, J. Jones, C. Taylor, D. Schachtman, S. May, G. Sandberg, P. Benfey, J. Friml, I. Kerr, T. Beeckman, L. Laplaze, M. Bennett, Nature Cell Biology 10 (2008) 946–954. date_created: 2018-12-11T12:01:00Z date_published: 2008-07-11T00:00:00Z date_updated: 2021-01-12T07:40:37Z day: '11' doi: 10.1038/ncb1754 extern: 1 intvolume: ' 10' issue: '8' month: '07' page: 946 - 954 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '3665' quality_controlled: 0 status: public title: The auxin influx carrier LAX3 promotes lateral root emergence type: journal_article volume: 10 year: '2008' ... --- _id: '3036' abstract: - lang: eng text: Plants exhibit an exceptional adaptability to different environmental conditions. To a large extent, this adaptability depends on their ability to initiate and form new organs throughout their entire postembryonic life. Plant shoot and root systems unceasingly branch and form axillary shoots or lateral roots, respectively. The first event in the formation of a new organ is specification of founder cells. Several plant hormones, prominent among them auxin, have been implicated in the acquisition of founder cell identity by differentiated cells, but the mechanisms underlying this process are largely elusive. Here, we show that auxin and its local accumulation in root pericycle cells is a necessary and sufficient signal to respecify these cells into lateral root founder cells. Analysis of the alf4-1 mutant suggests that specification of founder cells and the subsequent activation of cell division leading to primordium formation represent two genetically separable events. Time-lapse experiments show that the activation of an auxin response is the earliest detectable event in founder cell specification. Accordingly, local activation of auxin response correlates absolutely with the acquisition of founder cell identity and precedes the actual formation of a lateral root primordium through patterned cell division. Local production and subsequent accumulation of auxin in single pericycle cells induced by Cre-Lox-based activation of auxin synthesis converts them into founder cells. Thus, auxin is the local instructive signal that is sufficient for acquisition of founder cell identity and can be considered a morphogenetic trigger in postembryonic plant organogenesis. author: - first_name: Joseph full_name: Dubrovsky, Joseph G last_name: Dubrovsky - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Selene full_name: Napsucialy-Mendivil, Selene last_name: Napsucialy Mendivil - first_name: Maria full_name: Ivanchenko, Maria G last_name: Ivanchenko - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Svetlana full_name: Shishkova, Svetlana last_name: Shishkova - first_name: John full_name: Celenza, John last_name: Celenza - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Dubrovsky J, Sauer M, Napsucialy Mendivil S, et al. Auxin acts as a local morphogenetic trigger to specify lateral root founder cells. PNAS. 2008;105(25):8790-8794. doi:10.1073/pnas.0712307105 apa: Dubrovsky, J., Sauer, M., Napsucialy Mendivil, S., Ivanchenko, M., Friml, J., Shishkova, S., … Benková, E. (2008). Auxin acts as a local morphogenetic trigger to specify lateral root founder cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0712307105 chicago: Dubrovsky, Joseph, Michael Sauer, Selene Napsucialy Mendivil, Maria Ivanchenko, Jiří Friml, Svetlana Shishkova, John Celenza, and Eva Benková. “Auxin Acts as a Local Morphogenetic Trigger to Specify Lateral Root Founder Cells.” PNAS. National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0712307105. ieee: J. Dubrovsky et al., “Auxin acts as a local morphogenetic trigger to specify lateral root founder cells,” PNAS, vol. 105, no. 25. National Academy of Sciences, pp. 8790–8794, 2008. ista: Dubrovsky J, Sauer M, Napsucialy Mendivil S, Ivanchenko M, Friml J, Shishkova S, Celenza J, Benková E. 2008. Auxin acts as a local morphogenetic trigger to specify lateral root founder cells. PNAS. 105(25), 8790–8794. mla: Dubrovsky, Joseph, et al. “Auxin Acts as a Local Morphogenetic Trigger to Specify Lateral Root Founder Cells.” PNAS, vol. 105, no. 25, National Academy of Sciences, 2008, pp. 8790–94, doi:10.1073/pnas.0712307105. short: J. Dubrovsky, M. Sauer, S. Napsucialy Mendivil, M. Ivanchenko, J. Friml, S. Shishkova, J. Celenza, E. Benková, PNAS 105 (2008) 8790–8794. date_created: 2018-12-11T12:00:59Z date_published: 2008-06-24T00:00:00Z date_updated: 2021-01-12T07:40:36Z day: '24' doi: 10.1073/pnas.0712307105 extern: 1 intvolume: ' 105' issue: '25' month: '06' page: 8790 - 8794 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '3666' quality_controlled: 0 status: public title: Auxin acts as a local morphogenetic trigger to specify lateral root founder cells type: journal_article volume: 105 year: '2008' ... --- _id: '3030' abstract: - lang: eng text: Telomeres in many eukaryotes are maintained by telomerase in whose absence telomere shortening occurs. However, telomerase-deficient Arabidopsis thaliana mutants (Attert -/-) show extremely low rates of telomere shortening per plant generation (250-500 bp), which does not correspond to the expected outcome of replicative telomere shortening resulting from ca. 1,000 meristem cell divisions per seed-to-seed generation. To investigate the influence of the number of cell divisions per seed-to-seed generation, Attert -/- mutant plants were propagated from seeds coming either from the lower-most or the upper-most siliques (L- and U-plants) and the length of their telomeres were followed over several generations. The rate of telomere shortening was faster in U-plants, than in L-plants, as would be expected from their higher number of cell divisions per generation. However, this trend was observed only in telomeres whose initial length is relatively high and the differences decreased with progressive general telomere shortening over generations. But in generation 4, the L-plants frequently show a net telomere elongation, while the U-plants fail to do so. We propose that this is due to the activation of alternative telomere lengthening (ALT), a process which is activated in early embryonic development in both U- and L-plants, but is overridden in U-plants due to their higher number of cell divisions per generation. These data demonstrate what so far has only been speculated, that in the absence of telomerase, the number of cell divisions within one generation influences the control of telomere lengths. These results also reveal a fast and efficient activation of ALT mechanism(s) in response to the loss of telomerase activity and imply that ALT is probably involved also in normal plant development. author: - first_name: Eva full_name: Růčková, Eva last_name: Růčková - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Petra full_name: Procházková Schrumpfová, Petra last_name: Procházková Schrumpfová - first_name: Jiří full_name: Fajkus, Jiří last_name: Fajkus citation: ama: Růčková E, Friml J, Procházková Schrumpfová P, Fajkus J. Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants. Plant Molecular Biology. 2008;66(6):637-646. doi:10.1007/s11103-008-9295-7 apa: Růčková, E., Friml, J., Procházková Schrumpfová, P., & Fajkus, J. (2008). Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-008-9295-7 chicago: Růčková, Eva, Jiří Friml, Petra Procházková Schrumpfová, and Jiří Fajkus. “Role of Alternative Telomere Lengthening Unmasked in Telomerase Knock-out Mutant Plants.” Plant Molecular Biology. Springer, 2008. https://doi.org/10.1007/s11103-008-9295-7. ieee: E. Růčková, J. Friml, P. Procházková Schrumpfová, and J. Fajkus, “Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants,” Plant Molecular Biology, vol. 66, no. 6. Springer, pp. 637–646, 2008. ista: Růčková E, Friml J, Procházková Schrumpfová P, Fajkus J. 2008. Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants. Plant Molecular Biology. 66(6), 637–646. mla: Růčková, Eva, et al. “Role of Alternative Telomere Lengthening Unmasked in Telomerase Knock-out Mutant Plants.” Plant Molecular Biology, vol. 66, no. 6, Springer, 2008, pp. 637–46, doi:10.1007/s11103-008-9295-7. short: E. Růčková, J. Friml, P. Procházková Schrumpfová, J. Fajkus, Plant Molecular Biology 66 (2008) 637–646. date_created: 2018-12-11T12:00:57Z date_published: 2008-04-01T00:00:00Z date_updated: 2021-01-12T07:40:34Z day: '01' doi: 10.1007/s11103-008-9295-7 extern: 1 intvolume: ' 66' issue: '6' month: '04' page: 637 - 646 publication: Plant Molecular Biology publication_status: published publisher: Springer publist_id: '3671' quality_controlled: 0 status: public title: Role of alternative telomere lengthening unmasked in telomerase knock-out mutant plants type: journal_article volume: 66 year: '2008' ... --- _id: '3032' abstract: - lang: eng text: |2- Cell polarity manifested by the polar cargo delivery to different plasma-membrane domains is a fundamental feature of multicellular organisms. Pathways for polar delivery have been identified in animals; prominent among them is transcytosis, which involves cargo movement between different sides of the cell [1]. PIN transporters are prominent polar cargoes in plants, whose polar subcellular localization determines the directional flow of the signaling molecule auxin [2, 3]. In this study, we address the cellular mechanisms of PIN polar targeting and dynamic polarity changes. We show that apical and basal PIN targeting pathways are interconnected but molecularly distinct by means of ARF GEF vesicle-trafficking regulators. Pharmacological or genetic interference with the Arabidopsis ARF GEF GNOM leads specifically to apicalization of basal cargoes such as PIN1. We visualize the translocation of PIN proteins between the opposite sides of polarized cells in vivo and show that this PIN transcytosis occurs by endocytic recycling and alternative recruitment of the same cargo molecules by apical and basal targeting machineries. Our data suggest that an ARF GEF-dependent transcytosis-like mechanism is operational in plants and provides a plausible mechanism to trigger changes in PIN polarity and hence auxin fluxes during embryogenesis and organogenesis. author: - first_name: Jürgen full_name: Kleine-Vehn, Jürgen last_name: Kleine Vehn - first_name: Pankaj full_name: Dhonukshe, Pankaj last_name: Dhonukshe - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Philip full_name: Brewer, Philip B last_name: Brewer - first_name: Justyna full_name: Wiśniewska, Justyna last_name: Wiśniewska - first_name: Tomasz full_name: Paciorek, Tomasz last_name: Paciorek - first_name: Eva full_name: Eva Benková id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Kleine Vehn J, Dhonukshe P, Sauer M, et al. ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis. Current Biology. 2008;18(7):526-531. doi:10.1016/j.cub.2008.03.021 apa: Kleine Vehn, J., Dhonukshe, P., Sauer, M., Brewer, P., Wiśniewska, J., Paciorek, T., … Friml, J. (2008). ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2008.03.021 chicago: Kleine Vehn, Jürgen, Pankaj Dhonukshe, Michael Sauer, Philip Brewer, Justyna Wiśniewska, Tomasz Paciorek, Eva Benková, and Jiří Friml. “ARF GEF Dependent Transcytosis and Polar Delivery of PIN Auxin Carriers in Arabidopsis.” Current Biology. Cell Press, 2008. https://doi.org/10.1016/j.cub.2008.03.021. ieee: J. Kleine Vehn et al., “ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis,” Current Biology, vol. 18, no. 7. Cell Press, pp. 526–531, 2008. ista: Kleine Vehn J, Dhonukshe P, Sauer M, Brewer P, Wiśniewska J, Paciorek T, Benková E, Friml J. 2008. ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis. Current Biology. 18(7), 526–531. mla: Kleine Vehn, Jürgen, et al. “ARF GEF Dependent Transcytosis and Polar Delivery of PIN Auxin Carriers in Arabidopsis.” Current Biology, vol. 18, no. 7, Cell Press, 2008, pp. 526–31, doi:10.1016/j.cub.2008.03.021. short: J. Kleine Vehn, P. Dhonukshe, M. Sauer, P. Brewer, J. Wiśniewska, T. Paciorek, E. Benková, J. Friml, Current Biology 18 (2008) 526–531. date_created: 2018-12-11T12:00:58Z date_published: 2008-04-08T00:00:00Z date_updated: 2021-01-12T07:40:34Z day: '08' doi: 10.1016/j.cub.2008.03.021 extern: 1 intvolume: ' 18' issue: '7' month: '04' page: 526 - 531 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '3670' quality_controlled: 0 status: public title: ARF GEF dependent transcytosis and polar delivery of PIN auxin carriers in Arabidopsis type: journal_article volume: 18 year: '2008' ... --- _id: '3035' abstract: - lang: eng text: Embryogenesis of Arabidopsis thaliana follows a nearly invariant cell division pattern and provides an ideal system for studies of early plant development. However, experimental manipulation with embryogenesis is difficult, as the embryo develops deeply inside maternal tissues. Here, we present a method to culture zygotic Arabidopsis embryos in vitro. It enables culturing for prolonged periods of time from the first developmental stages on. The technique omits excision of the embryo by culturing the entire ovule, which facilitates the manual procedure. It allows pharmacological manipulation of embryo development and does not interfere with standard techniques for localizing gene expression and protein localization in the cultivated embryos. alternative_title: - Methods In Molecular Biology author: - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Sauer M, Friml J. In vitro culture of Arabidopsis embryos . In: Suárez M, Bozhkov P, eds. Plant Embryogenesis. Vol 427. Humana Press; 2008:71-76. doi:10.1007/978-1-59745-273-1_5' apa: Sauer, M., & Friml, J. (2008). In vitro culture of Arabidopsis embryos . In M. Suárez & P. Bozhkov (Eds.), Plant Embryogenesis (Vol. 427, pp. 71–76). Humana Press. https://doi.org/10.1007/978-1-59745-273-1_5 chicago: Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos .” In Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, 427:71–76. Humana Press, 2008. https://doi.org/10.1007/978-1-59745-273-1_5. ieee: M. Sauer and J. Friml, “In vitro culture of Arabidopsis embryos ,” in Plant Embryogenesis, vol. 427, M. Suárez and P. Bozhkov, Eds. Humana Press, 2008, pp. 71–76. ista: 'Sauer M, Friml J. 2008.In vitro culture of Arabidopsis embryos . In: Plant Embryogenesis. Methods In Molecular Biology, vol. 427, 71–76.' mla: Sauer, Michael, and Jiří Friml. “In Vitro Culture of Arabidopsis Embryos .” Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, vol. 427, Humana Press, 2008, pp. 71–76, doi:10.1007/978-1-59745-273-1_5. short: M. Sauer, J. Friml, in:, M. Suárez, P. Bozhkov (Eds.), Plant Embryogenesis, Humana Press, 2008, pp. 71–76. date_created: 2018-12-11T12:00:59Z date_published: 2008-03-07T00:00:00Z date_updated: 2021-01-12T07:40:35Z day: '07' doi: 10.1007/978-1-59745-273-1_5 editor: - first_name: María full_name: Suárez, María F last_name: Suárez - first_name: Peter full_name: Bozhkov, Peter V last_name: Bozhkov extern: 1 intvolume: ' 427' month: '03' page: 71 - 76 publication: Plant Embryogenesis publication_status: published publisher: Humana Press publist_id: '3667' quality_controlled: 0 status: public title: 'In vitro culture of Arabidopsis embryos ' type: book_chapter volume: 427 year: '2008' ... --- _id: '3033' abstract: - lang: eng text: |2- Embryogenesis in Arabidopsis thaliana depends on the proper establishment and maintenance of local auxin accumulation. In the course of elucidating the connections between developmental progress and auxin distribution, several techniques have been developed to investigate spatial and temporal distribution of auxin response or accumulation in Arabidopsis embryos. This chapter reviews and describes two independent methods, the detection of the activity of auxin responsive transgenes and immunolocalization of auxin itself. alternative_title: - Methods In Molecular Biology author: - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jirí full_name: Jirí Friml id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Sauer M, Friml J. Visualization of auxin gradients in embryogenesis . In: Suárez M, Bozhkov P, eds. Plant Embryogenesis. Vol 427. Humana Press; 2008:137-144. doi:10.1007/978-1-59745-273-1_11' apa: Sauer, M., & Friml, J. (2008). Visualization of auxin gradients in embryogenesis . In M. Suárez & P. Bozhkov (Eds.), Plant Embryogenesis (Vol. 427, pp. 137–144). Humana Press. https://doi.org/10.1007/978-1-59745-273-1_11 chicago: Sauer, Michael, and Jiří Friml. “Visualization of Auxin Gradients in Embryogenesis .” In Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, 427:137–44. Humana Press, 2008. https://doi.org/10.1007/978-1-59745-273-1_11. ieee: M. Sauer and J. Friml, “Visualization of auxin gradients in embryogenesis ,” in Plant Embryogenesis, vol. 427, M. Suárez and P. Bozhkov, Eds. Humana Press, 2008, pp. 137–144. ista: 'Sauer M, Friml J. 2008.Visualization of auxin gradients in embryogenesis . In: Plant Embryogenesis. Methods In Molecular Biology, vol. 427, 137–144.' mla: Sauer, Michael, and Jiří Friml. “Visualization of Auxin Gradients in Embryogenesis .” Plant Embryogenesis, edited by María Suárez and Peter Bozhkov, vol. 427, Humana Press, 2008, pp. 137–44, doi:10.1007/978-1-59745-273-1_11. short: M. Sauer, J. Friml, in:, M. Suárez, P. Bozhkov (Eds.), Plant Embryogenesis, Humana Press, 2008, pp. 137–144. date_created: 2018-12-11T12:00:58Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:40:35Z day: '01' doi: 10.1007/978-1-59745-273-1_11 editor: - first_name: María full_name: Suárez, María F last_name: Suárez - first_name: Peter full_name: Bozhkov, Peter V last_name: Bozhkov extern: 1 intvolume: ' 427' month: '01' page: 137 - 144 publication: Plant Embryogenesis publication_status: published publisher: Humana Press publist_id: '3668' quality_controlled: 0 status: public title: 'Visualization of auxin gradients in embryogenesis ' type: book_chapter volume: 427 year: '2008' ... --- _id: '3037' author: - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Feraru E, Friml J. PIN polar targeting. Plant Physiology. 2008;147(4):1553-1559. doi:10.1104/pp.108.121756 apa: Feraru, E., & Friml, J. (2008). PIN polar targeting. Plant Physiology. American Society of Plant Biologists. https://doi.org/10.1104/pp.108.121756 chicago: Feraru, Elena, and Jiří Friml. “PIN Polar Targeting.” Plant Physiology. American Society of Plant Biologists, 2008. https://doi.org/10.1104/pp.108.121756. ieee: E. Feraru and J. Friml, “PIN polar targeting,” Plant Physiology, vol. 147, no. 4. American Society of Plant Biologists, pp. 1553–1559, 2008. ista: Feraru E, Friml J. 2008. PIN polar targeting. Plant Physiology. 147(4), 1553–1559. mla: Feraru, Elena, and Jiří Friml. “PIN Polar Targeting.” Plant Physiology, vol. 147, no. 4, American Society of Plant Biologists, 2008, pp. 1553–59, doi:10.1104/pp.108.121756. short: E. Feraru, J. Friml, Plant Physiology 147 (2008) 1553–1559. date_created: 2018-12-11T12:01:00Z date_published: 2008-08-04T00:00:00Z date_updated: 2021-01-12T07:40:36Z day: '04' doi: 10.1104/pp.108.121756 extern: '1' external_id: pmid: - '18678746' intvolume: ' 147' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2492634/ month: '08' oa: 1 oa_version: Published Version page: 1553 - 1559 pmid: 1 publication: Plant Physiology publication_status: published publisher: American Society of Plant Biologists publist_id: '3664' quality_controlled: '1' status: public title: PIN polar targeting type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 147 year: '2008' ... --- _id: '3034' abstract: - lang: eng text: 'They can''t move away from shade, so plants resort to a molecular solution to find a place in the sun. The action they take is quite radical, and involves a reprogramming of their development. ' article_type: letter_note author: - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Michael full_name: Sauer, Michael last_name: Sauer citation: ama: 'Friml J, Sauer M. Plant biology: In their neighbour’s shadow. Nature. 2008;453(7193):298-299. doi:10.1038/453298a' apa: 'Friml, J., & Sauer, M. (2008). Plant biology: In their neighbour’s shadow. Nature. Nature Publishing Group. https://doi.org/10.1038/453298a' chicago: 'Friml, Jiří, and Michael Sauer. “Plant Biology: In Their Neighbour’s Shadow.” Nature. Nature Publishing Group, 2008. https://doi.org/10.1038/453298a.' ieee: 'J. Friml and M. Sauer, “Plant biology: In their neighbour’s shadow,” Nature, vol. 453, no. 7193. Nature Publishing Group, pp. 298–299, 2008.' ista: 'Friml J, Sauer M. 2008. Plant biology: In their neighbour’s shadow. Nature. 453(7193), 298–299.' mla: 'Friml, Jiří, and Michael Sauer. “Plant Biology: In Their Neighbour’s Shadow.” Nature, vol. 453, no. 7193, Nature Publishing Group, 2008, pp. 298–99, doi:10.1038/453298a.' short: J. Friml, M. Sauer, Nature 453 (2008) 298–299. date_created: 2018-12-11T12:00:59Z date_published: 2008-05-15T00:00:00Z date_updated: 2021-01-12T07:40:35Z day: '15' doi: 10.1038/453298a extern: '1' intvolume: ' 453' issue: '7193' language: - iso: eng month: '05' oa_version: None page: 298 - 299 publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '3669' quality_controlled: '1' status: public title: 'Plant biology: In their neighbour''s shadow' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 453 year: '2008' ... --- _id: '3196' abstract: - lang: eng text: 'Among the most exciting advances in early vision has been the development of efficient energy minimization algorithms for pixel-labeling tasks such as depth or texture computation. It has been known for decades that such problems can be elegantly expressed as Markov random fields, yet the resulting energy minimization problems have been widely viewed as intractable. Algorithms such as graph cuts and loopy belief propagation (LBP) have proven to be very powerful: For example, such methods form the basis for almost all the top-performing stereo methods. However, the trade-offs among different energy minimization algorithms are still not well understood. In this paper, we describe a set of energy minimization benchmarks and use them to compare the solution quality and runtime of several common energy minimization algorithms. We investigate three promising methods-graph cuts, LBP, and tree-reweighted message passing-in addition to the well-known older iterated conditional mode (ICM) algorithm. Our benchmark problems are drawn from published energy functions used for stereo, image stitching, interactive segmentation, and denoising. We also provide a general-purpose software interface that allows vision researchers to easily switch between optimization methods. The benchmarks, code, images, and results are available at http://vision.middlebury.edu/MRF/.' author: - first_name: Richard full_name: Szeliski, Richard S last_name: Szeliski - first_name: Ramin full_name: Zabih, Ramin last_name: Zabih - first_name: Daniel full_name: Scharstein, Daniel last_name: Scharstein - first_name: Olga full_name: Veksler, Olga last_name: Veksler - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Aseem full_name: Agarwala, Aseem last_name: Agarwala - first_name: Marshall full_name: Tappen, Marshall F last_name: Tappen - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: Szeliski R, Zabih R, Scharstein D, et al. A comparative study of energy minimization methods for Markov random fields with smoothness-based priors. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2008;30(6):1068-1080. doi:10.1109/TPAMI.2007.70844 apa: Szeliski, R., Zabih, R., Scharstein, D., Veksler, O., Kolmogorov, V., Agarwala, A., … Rother, C. (2008). A comparative study of energy minimization methods for Markov random fields with smoothness-based priors. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2007.70844 chicago: Szeliski, Richard, Ramin Zabih, Daniel Scharstein, Olga Veksler, Vladimir Kolmogorov, Aseem Agarwala, Marshall Tappen, and Carsten Rother. “A Comparative Study of Energy Minimization Methods for Markov Random Fields with Smoothness-Based Priors.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2008. https://doi.org/10.1109/TPAMI.2007.70844. ieee: R. Szeliski et al., “A comparative study of energy minimization methods for Markov random fields with smoothness-based priors,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 30, no. 6. IEEE, pp. 1068–1080, 2008. ista: Szeliski R, Zabih R, Scharstein D, Veksler O, Kolmogorov V, Agarwala A, Tappen M, Rother C. 2008. A comparative study of energy minimization methods for Markov random fields with smoothness-based priors. IEEE Transactions on Pattern Analysis and Machine Intelligence. 30(6), 1068–1080. mla: Szeliski, Richard, et al. “A Comparative Study of Energy Minimization Methods for Markov Random Fields with Smoothness-Based Priors.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 30, no. 6, IEEE, 2008, pp. 1068–80, doi:10.1109/TPAMI.2007.70844. short: R. Szeliski, R. Zabih, D. Scharstein, O. Veksler, V. Kolmogorov, A. Agarwala, M. Tappen, C. Rother, IEEE Transactions on Pattern Analysis and Machine Intelligence 30 (2008) 1068–1080. date_created: 2018-12-11T12:01:57Z date_published: 2008-06-01T00:00:00Z date_updated: 2021-01-12T07:41:43Z day: '01' doi: 10.1109/TPAMI.2007.70844 extern: 1 intvolume: ' 30' issue: '6' month: '06' page: 1068 - 1080 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_status: published publisher: IEEE publist_id: '3488' quality_controlled: 0 status: public title: A comparative study of energy minimization methods for Markov random fields with smoothness-based priors type: journal_article volume: 30 year: '2008' ... --- _id: '3198' abstract: - lang: eng text: 'In this paper we present a new approach for establishing correspondences between sparse image features related by an unknown non-rigid mapping and corrupted by clutter and occlusion, such as points extracted from a pair of images containing a human figure in distinct poses. We formulate this matching task as an energy minimization problem by defining a complex objective function of the appearance and the spatial arrangement of the features. Optimization of this energy is an instance of graph matching, which is in general a NP-hard problem. We describe a novel graph matching optimization technique, which we refer to as dual decomposition (DD), and demonstrate on a variety of examples that this method outperforms existing graph matching algorithms. In the majority of our examples DD is able to find the global minimum within a minute. The ability to globally optimize the objective allows us to accurately learn the parameters of our matching model from training examples. We show on several matching tasks that our learned model yields results superior to those of state-of-the-art methods. ' alternative_title: - LNCS author: - first_name: Lorenzo full_name: Torresani, Lorenzo last_name: Torresani - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Torresani L, Kolmogorov V, Rother C. Feature correspondence via graph matching: Models and global optimization. In: Vol 5303. Springer; 2008:596-609. doi:10.1007/978-3-540-88688-4_44' apa: 'Torresani, L., Kolmogorov, V., & Rother, C. (2008). Feature correspondence via graph matching: Models and global optimization (Vol. 5303, pp. 596–609). Presented at the ECCV: European Conference on Computer Vision, Springer. https://doi.org/10.1007/978-3-540-88688-4_44' chicago: 'Torresani, Lorenzo, Vladimir Kolmogorov, and Carsten Rother. “Feature Correspondence via Graph Matching: Models and Global Optimization,” 5303:596–609. Springer, 2008. https://doi.org/10.1007/978-3-540-88688-4_44.' ieee: 'L. Torresani, V. Kolmogorov, and C. Rother, “Feature correspondence via graph matching: Models and global optimization,” presented at the ECCV: European Conference on Computer Vision, 2008, vol. 5303, pp. 596–609.' ista: 'Torresani L, Kolmogorov V, Rother C. 2008. Feature correspondence via graph matching: Models and global optimization. ECCV: European Conference on Computer Vision, LNCS, vol. 5303, 596–609.' mla: 'Torresani, Lorenzo, et al. Feature Correspondence via Graph Matching: Models and Global Optimization. Vol. 5303, Springer, 2008, pp. 596–609, doi:10.1007/978-3-540-88688-4_44.' short: L. Torresani, V. Kolmogorov, C. Rother, in:, Springer, 2008, pp. 596–609. conference: name: 'ECCV: European Conference on Computer Vision' date_created: 2018-12-11T12:01:58Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:41:44Z day: '01' doi: 10.1007/978-3-540-88688-4_44 extern: 1 intvolume: ' 5303' main_file_link: - open_access: '0' url: http://research-srv.microsoft.com/pubs/70610/eccv08-MatchingMRF.pdf month: '01' page: 596 - 609 publication_status: published publisher: Springer publist_id: '3485' quality_controlled: 0 status: public title: 'Feature correspondence via graph matching: Models and global optimization' type: conference volume: 5303 year: '2008' ... --- _id: '3195' abstract: - lang: eng text: 'Graph cut is a popular technique for interactive image segmentation. However, it has certain shortcomings. In particular, graph cut has problems with segmenting thin elongated objects due to the ldquoshrinking biasrdquo. To overcome this problem, we propose to impose an additional connectivity prior, which is a very natural assumption about objects. We formulate several versions of the connectivity constraint and show that the corresponding optimization problems are all NP-hard. For some of these versions we propose two optimization algorithms: (i) a practical heuristic technique which we call DijkstraGC, and (ii) a slow method based on problem decomposition which provides a lower bound on the problem. We use the second technique to verify that for some practical examples DijkstraGC is able to find the global minimum.' author: - first_name: Sara full_name: Vicente, Sara last_name: Vicente - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Vicente S, Kolmogorov V, Rother C. Graph cut based image segmentation with connectivity priors. In: IEEE; 2008. doi:10.1109/CVPR.2008.4587440' apa: 'Vicente, S., Kolmogorov, V., & Rother, C. (2008). Graph cut based image segmentation with connectivity priors. Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2008.4587440' chicago: Vicente, Sara, Vladimir Kolmogorov, and Carsten Rother. “Graph Cut Based Image Segmentation with Connectivity Priors.” IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587440. ieee: 'S. Vicente, V. Kolmogorov, and C. Rother, “Graph cut based image segmentation with connectivity priors,” presented at the CVPR: Computer Vision and Pattern Recognition, 2008.' ista: 'Vicente S, Kolmogorov V, Rother C. 2008. Graph cut based image segmentation with connectivity priors. CVPR: Computer Vision and Pattern Recognition.' mla: Vicente, Sara, et al. Graph Cut Based Image Segmentation with Connectivity Priors. IEEE, 2008, doi:10.1109/CVPR.2008.4587440. short: S. Vicente, V. Kolmogorov, C. Rother, in:, IEEE, 2008. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:01:57Z date_published: 2008-08-05T00:00:00Z date_updated: 2021-01-12T07:41:43Z day: '05' doi: 10.1109/CVPR.2008.4587440 extern: 1 main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/80485/CVPR08-ConnectedGC.pdf month: '08' publication_status: published publisher: IEEE publist_id: '3487' quality_controlled: 0 status: public title: Graph cut based image segmentation with connectivity priors type: conference year: '2008' ... --- _id: '3224' abstract: - lang: eng text: 'We propose a new mode of operation, enciphered CBC, for domain extension of length-preserving functions (like block ciphers), which is a variation on the popular CBC mode of operation. Our new mode is twice slower than CBC, but has many (property-preserving) properties not enjoyed by CBC and other known modes. Most notably, it yields the first constant-rate Variable Input Length (VIL) MAC from any length preserving Fixed Input Length (FIL) MAC. This answers the question of Dodis and Puniya from Eurocrypt 2007. Further, our mode is a secure domain extender for PRFs (with basically the same security as encrypted CBC). This provides a hedge against the security of the block cipher: if the block cipher is pseudorandom, one gets a VIL-PRF, while if it is "only" unpredictable, one "at least" gets a VIL-MAC. Additionally, our mode yields a VIL random oracle (and, hence, a collision-resistant hash function) when instantiated with length-preserving random functions, or even random permutations (which can be queried from both sides). This means that one does not have to re-key the block cipher during the computation, which was critically used in most previous constructions (analyzed in the ideal cipher model). ' 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: Prashant full_name: Puniya, Prashant last_name: Puniya citation: ama: 'Dodis Y, Pietrzak KZ, Puniya P. A new mode of operation for block ciphers and length preserving MACs. In: Vol 4965. Springer; 2008:198-219. doi:10.1007/978-3-540-78967-3_12' apa: 'Dodis, Y., Pietrzak, K. Z., & Puniya, P. (2008). A new mode of operation for block ciphers and length preserving MACs (Vol. 4965, pp. 198–219). Presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, Springer. https://doi.org/10.1007/978-3-540-78967-3_12' chicago: Dodis, Yevgeniy, Krzysztof Z Pietrzak, and Prashant Puniya. “A New Mode of Operation for Block Ciphers and Length Preserving MACs,” 4965:198–219. Springer, 2008. https://doi.org/10.1007/978-3-540-78967-3_12. ieee: 'Y. Dodis, K. Z. Pietrzak, and P. Puniya, “A new mode of operation for block ciphers and length preserving MACs,” presented at the EUROCRYPT: Theory and Applications of Cryptographic Techniques, 2008, vol. 4965, pp. 198–219.' ista: 'Dodis Y, Pietrzak KZ, Puniya P. 2008. A new mode of operation for block ciphers and length preserving MACs. EUROCRYPT: Theory and Applications of Cryptographic Techniques, LNCS, vol. 4965, 198–219.' mla: Dodis, Yevgeniy, et al. A New Mode of Operation for Block Ciphers and Length Preserving MACs. Vol. 4965, Springer, 2008, pp. 198–219, doi:10.1007/978-3-540-78967-3_12. short: Y. Dodis, K.Z. Pietrzak, P. Puniya, in:, Springer, 2008, pp. 198–219. conference: name: 'EUROCRYPT: Theory and Applications of Cryptographic Techniques' date_created: 2018-12-11T12:02:07Z date_published: 2008-04-28T00:00:00Z date_updated: 2021-01-12T07:41:55Z day: '28' doi: 10.1007/978-3-540-78967-3_12 extern: 1 intvolume: ' 4965' month: '04' page: 198 - 219 publication_status: published publisher: Springer publist_id: '3456' quality_controlled: 0 status: public title: A new mode of operation for block ciphers and length preserving MACs type: conference volume: 4965 year: '2008' ... --- _id: '3225' abstract: - lang: eng text: 'A robust multi-property combiner for a set of security properties merges two hash functions such that the resulting function satisfies each of the properties which at least one of the two starting functions has. Fischlin and Lehmann (TCC 2008) recently constructed a combiner which simultaneously preserves collision-resistance, target collision-resistance, message authentication, pseudorandomness and indifferentiability from a random oracle (IRO). Their combiner produces outputs of 5n bits, where n denotes the output length of the underlying hash functions. In this paper we propose improved combiners with shorter outputs. By sacrificing the indifferentiability from random oracles we obtain a combiner which preserves all of the other aforementioned properties but with output length 2n only. This matches a lower bound for black-box combiners for collision-resistance as the only property, showing that the other properties can be achieved without penalizing the length of the hash values. We then propose a combiner which also preserves the IRO property, slightly increasing the output length to 2n + ω(logn). Finally, we show that a twist on our combiners also makes them robust for one-wayness (but at the price of a fixed input length). ' alternative_title: - LNCS author: - first_name: Marc full_name: Fischlin, Marc last_name: Fischlin - first_name: Anja full_name: Lehmann, Anja last_name: Lehmann - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Fischlin M, Lehmann A, Pietrzak KZ. Robust multi property combiners for hash functions revisited. In: Vol 5126. Springer; 2008:655-666. doi:10.1007/978-3-540-70583-3_53' apa: 'Fischlin, M., Lehmann, A., & Pietrzak, K. Z. (2008). Robust multi property combiners for hash functions revisited (Vol. 5126, pp. 655–666). Presented at the ICALP: Automata, Languages and Programming, Springer. https://doi.org/10.1007/978-3-540-70583-3_53' chicago: Fischlin, Marc, Anja Lehmann, and Krzysztof Z Pietrzak. “Robust Multi Property Combiners for Hash Functions Revisited,” 5126:655–66. Springer, 2008. https://doi.org/10.1007/978-3-540-70583-3_53. ieee: 'M. Fischlin, A. Lehmann, and K. Z. Pietrzak, “Robust multi property combiners for hash functions revisited,” presented at the ICALP: Automata, Languages and Programming, 2008, vol. 5126, no. PART 2, pp. 655–666.' ista: 'Fischlin M, Lehmann A, Pietrzak KZ. 2008. Robust multi property combiners for hash functions revisited. ICALP: Automata, Languages and Programming, LNCS, vol. 5126, 655–666.' mla: Fischlin, Marc, et al. Robust Multi Property Combiners for Hash Functions Revisited. Vol. 5126, no. PART 2, Springer, 2008, pp. 655–66, doi:10.1007/978-3-540-70583-3_53. short: M. Fischlin, A. Lehmann, K.Z. Pietrzak, in:, Springer, 2008, pp. 655–666. conference: name: 'ICALP: Automata, Languages and Programming' date_created: 2018-12-11T12:02:07Z date_published: 2008-08-06T00:00:00Z date_updated: 2023-02-23T11:01:10Z day: '06' doi: 10.1007/978-3-540-70583-3_53 extern: 1 intvolume: ' 5126' issue: PART 2 month: '08' page: 655 - 666 publication_status: published publisher: Springer publist_id: '3454' quality_controlled: 0 related_material: record: - id: '2852' relation: later_version status: public status: public title: Robust multi property combiners for hash functions revisited type: conference volume: 5126 year: '2008' ... --- _id: '3291' abstract: - lang: eng text: 'The filamentous fungus Aspergillus fumigatus is responsible for a lethal disease called Invasive Aspergillosis that affects immunocompromised patients. This disease, like other human fungal diseases, is generally treated by compounds targeting the primary fungal cell membrane sterol. Recently, glucan synthesis inhibitors were added to the limited antifungal arsenal and encouraged the search for novel targets in cell wall biosynthesis. Although galactomannan is a major component of the A. fumigatus cell wall and extracellular matrix, the biosynthesis and role of galactomannan are currently unknown. By a targeted gene deletion approach, we demonstrate that UDP-galactopyranose mutase, a key enzyme of galactofuranose metabolism, controls the biosynthesis of galactomannan and galactofuranose containing glycoconjugates. The glfA deletion mutant generated in this study is devoid of galactofuranose and displays attenuated virulence in a low-dose mouse model of invasive aspergillosis that likely reflects the impaired growth of the mutant at mammalian body temperature. Furthermore, the absence of galactofuranose results in a thinner cell wall that correlates with an increased susceptibility to several antifungal agents. The UDP-galactopyranose mutase thus appears to be an appealing adjunct therapeutic target in combination with other drugs against A. fumigatus. Its absence from mammalian cells indeed offers a considerable advantage to achieve therapeutic selectivity. ' author: - first_name: Philipp S full_name: Philipp Schmalhorst id: 309D50DA-F248-11E8-B48F-1D18A9856A87 last_name: Schmalhorst orcid: 0000-0002-5795-0133 - first_name: Sven full_name: Krappmann, Sven last_name: Krappmann - first_name: Wouter full_name: Vervecken, Wouter last_name: Vervecken - first_name: Manfred full_name: Rohde, Manfred last_name: Rohde - first_name: Meike full_name: Müller, Meike last_name: Müller - first_name: Gerhard full_name: Braus, Gerhard H. last_name: Braus - first_name: Roland full_name: Contreras, Roland last_name: Contreras - first_name: Armin full_name: Braun, Armin last_name: Braun - first_name: Hans full_name: Bakker, Hans last_name: Bakker - first_name: Françoise full_name: Routier, Françoise H last_name: Routier citation: ama: Schmalhorst PS, Krappmann S, Vervecken W, et al. Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell. 2008;7(8):1268-1277. doi:10.1128/EC.00065-08 apa: Schmalhorst, P. S., Krappmann, S., Vervecken, W., Rohde, M., Müller, M., Braus, G., … Routier, F. (2008). Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell. American Society for Microbiology. https://doi.org/10.1128/EC.00065-08 chicago: Schmalhorst, Philipp S, Sven Krappmann, Wouter Vervecken, Manfred Rohde, Meike Müller, Gerhard Braus, Roland Contreras, Armin Braun, Hans Bakker, and Françoise Routier. “Contribution of Galactofuranose to the Virulence of the Opportunistic Pathogen Aspergillus Fumigatus.” Eukaryotic Cell. American Society for Microbiology, 2008. https://doi.org/10.1128/EC.00065-08. ieee: P. S. Schmalhorst et al., “Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus,” Eukaryotic Cell, vol. 7, no. 8. American Society for Microbiology, pp. 1268–1277, 2008. ista: Schmalhorst PS, Krappmann S, Vervecken W, Rohde M, Müller M, Braus G, Contreras R, Braun A, Bakker H, Routier F. 2008. Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus. Eukaryotic Cell. 7(8), 1268–1277. mla: Schmalhorst, Philipp S., et al. “Contribution of Galactofuranose to the Virulence of the Opportunistic Pathogen Aspergillus Fumigatus.” Eukaryotic Cell, vol. 7, no. 8, American Society for Microbiology, 2008, pp. 1268–77, doi:10.1128/EC.00065-08. short: P.S. Schmalhorst, S. Krappmann, W. Vervecken, M. Rohde, M. Müller, G. Braus, R. Contreras, A. Braun, H. Bakker, F. Routier, Eukaryotic Cell 7 (2008) 1268–1277. date_created: 2018-12-11T12:02:29Z date_published: 2008-06-13T00:00:00Z date_updated: 2021-01-12T07:42:26Z day: '13' doi: 10.1128/EC.00065-08 extern: 1 intvolume: ' 7' issue: '8' month: '06' page: 1268 - 1277 publication: Eukaryotic Cell publication_status: published publisher: American Society for Microbiology publist_id: '3354' quality_controlled: 0 status: public title: Contribution of galactofuranose to the virulence of the opportunistic pathogen Aspergillus fumigatus type: journal_article volume: 7 year: '2008' ... --- _id: '3307' abstract: - lang: eng text: A complete mitochondrial (mt) genome sequence was reconstructed from a 38,000 year-old Neandertal individual with 8341 mtDNA sequences identified among 4.8 Gb of DNA generated from ∼0.3 g of bone. Analysis of the assembled sequence unequivocally establishes that the Neandertal mtDNA falls outside the variation of extant human mtDNAs, and allows an estimate of the divergence date between the two mtDNA lineages of 660,000 ± 140,000 years. Of the 13 proteins encoded in the mtDNA, subunit 2 of cytochrome c oxidase of the mitochondrial electron transport chain has experienced the largest number of amino acid substitutions in human ancestors since the separation from Neandertals. There is evidence that purifying selection in the Neandertal mtDNA was reduced compared with other primate lineages, suggesting that the effective population size of Neandertals was small. author: - first_name: Richard full_name: Green, Richard E last_name: Green - first_name: Anna full_name: 'Malaspinas, Anna-Sapfo ' last_name: Malaspinas - first_name: Johannes full_name: Krause, Johannes last_name: Krause - first_name: Adrian full_name: Briggs, Adrian W last_name: Briggs - first_name: Philip full_name: Johnson, Philip L last_name: Johnson - first_name: Caroline full_name: Caroline Uhler id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Matthias full_name: Meyer, Matthias last_name: Meyer - first_name: Jeffrey full_name: Good, Jeffrey M last_name: Good - first_name: Tomislav full_name: Maricic, Tomislav last_name: Maricic - first_name: Udo full_name: Stenzel, Udo last_name: Stenzel - first_name: Kay full_name: Prüfer, Kay last_name: Prüfer - first_name: Michael full_name: Siebauer, Michael F last_name: Siebauer - first_name: Hernän full_name: Burbano, Hernän A last_name: Burbano - first_name: Michael full_name: Ronan, Michael T last_name: Ronan - first_name: Jonathan full_name: Rothberg, Jonathan M last_name: Rothberg - first_name: Michael full_name: Egholm, Michael last_name: Egholm - first_name: Pavao full_name: Rudan, Pavao last_name: Rudan - first_name: Dejana full_name: Brajković, Dejana last_name: Brajković - first_name: Željko full_name: Kućan, Željko last_name: Kućan - first_name: Ivan full_name: Gušić, Ivan last_name: Gušić - first_name: Mårten full_name: Wikström, Mårten K last_name: Wikström - first_name: Liisa full_name: Laakkonen, Liisa J last_name: Laakkonen - first_name: Janet full_name: Kelso, Janet F last_name: Kelso - first_name: Montgomery full_name: Slatkin, Montgomery last_name: Slatkin - first_name: Svante full_name: Pääbo, Svante H last_name: Pääbo citation: ama: Green R, Malaspinas A, Krause J, et al. A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing. Cell. 2008;134:416-426. doi:10.1016/j.cell.2008.06.021 apa: Green, R., Malaspinas, A., Krause, J., Briggs, A., Johnson, P., Uhler, C., … Pääbo, S. (2008). A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing. Cell. Cell Press. https://doi.org/10.1016/j.cell.2008.06.021 chicago: Green, Richard, Anna Malaspinas, Johannes Krause, Adrian Briggs, Philip Johnson, Caroline Uhler, Matthias Meyer, et al. “A Complete Neandertal Mitochondrial Genome Sequence Determined by Highhhroughput Sequencing.” Cell. Cell Press, 2008. https://doi.org/10.1016/j.cell.2008.06.021. ieee: R. Green et al., “A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing,” Cell, vol. 134. Cell Press, pp. 416–426, 2008. ista: Green R, Malaspinas A, Krause J, Briggs A, Johnson P, Uhler C, Meyer M, Good J, Maricic T, Stenzel U, Prüfer K, Siebauer M, Burbano H, Ronan M, Rothberg J, Egholm M, Rudan P, Brajković D, Kućan Ž, Gušić I, Wikström M, Laakkonen L, Kelso J, Slatkin M, Pääbo S. 2008. A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing. Cell. 134, 416–426. mla: Green, Richard, et al. “A Complete Neandertal Mitochondrial Genome Sequence Determined by Highhhroughput Sequencing.” Cell, vol. 134, Cell Press, 2008, pp. 416–26, doi:10.1016/j.cell.2008.06.021. short: R. Green, A. Malaspinas, J. Krause, A. Briggs, P. Johnson, C. Uhler, M. Meyer, J. Good, T. Maricic, U. Stenzel, K. Prüfer, M. Siebauer, H. Burbano, M. Ronan, J. Rothberg, M. Egholm, P. Rudan, D. Brajković, Ž. Kućan, I. Gušić, M. Wikström, L. Laakkonen, J. Kelso, M. Slatkin, S. Pääbo, Cell 134 (2008) 416–426. date_created: 2018-12-11T12:02:35Z date_published: 2008-08-01T00:00:00Z date_updated: 2021-01-12T07:42:32Z day: '01' doi: 10.1016/j.cell.2008.06.021 extern: 1 intvolume: ' 134' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2602844/ month: '08' oa: 1 page: 416 - 426 publication: Cell publication_status: published publisher: Cell Press publist_id: '3333' quality_controlled: 0 status: public title: A complete neandertal mitochondrial genome sequence determined by highhhroughput sequencing type: journal_article volume: 134 year: '2008' ... --- _id: '3435' abstract: - lang: eng text: We develop a new method for estimating effective population sizes, Ne, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is ~0.43. author: - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 - first_name: Thomas full_name: York, Thomas L last_name: York - first_name: Rasmus full_name: Nielsen, Rasmus last_name: Nielsen citation: ama: Bollback JP, York T, Nielsen R. Estimation of 2Nes From Temporal Allele Frequency Data. Genetics. 2008;179(1):497-502. doi:10.1534/genetics.107.085019 apa: Bollback, J. P., York, T., & Nielsen, R. (2008). Estimation of 2Nes From Temporal Allele Frequency Data. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.107.085019 chicago: Bollback, Jonathan P, Thomas York, and Rasmus Nielsen. “Estimation of 2Nes From Temporal Allele Frequency Data.” Genetics. Genetics Society of America, 2008. https://doi.org/10.1534/genetics.107.085019. ieee: J. P. Bollback, T. York, and R. Nielsen, “Estimation of 2Nes From Temporal Allele Frequency Data,” Genetics, vol. 179, no. 1. Genetics Society of America, pp. 497–502, 2008. ista: Bollback JP, York T, Nielsen R. 2008. Estimation of 2Nes From Temporal Allele Frequency Data. Genetics. 179(1), 497–502. mla: Bollback, Jonathan P., et al. “Estimation of 2Nes From Temporal Allele Frequency Data.” Genetics, vol. 179, no. 1, Genetics Society of America, 2008, pp. 497–502, doi:10.1534/genetics.107.085019. short: J.P. Bollback, T. York, R. Nielsen, Genetics 179 (2008) 497–502. date_created: 2018-12-11T12:03:19Z date_published: 2008-05-01T00:00:00Z date_updated: 2021-01-12T07:43:27Z day: '01' doi: 10.1534/genetics.107.085019 extern: 1 intvolume: ' 179' issue: '1' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2390626 month: '05' oa: 1 page: 497 - 502 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '2965' quality_controlled: 0 status: public title: Estimation of 2Nes From Temporal Allele Frequency Data type: journal_article volume: 179 year: '2008' ... --- _id: '3516' abstract: - lang: eng text: Temporal coding is a means of representing information by the time, as opposed to the rate, at which neurons fire. Evidence of temporal coding in the hippocampus comes from place cells, whose spike times relative to theta oscillations reflect a rat's position while running along stereotyped trajectories. This arises from the backwards shift in cell firing relative to local theta oscillations (phase precession). Here we demonstrate phase precession during place-field crossings in an open-field foraging task. This produced spike sequences in each theta cycle that disambiguate the rat's trajectory through two-dimensional space and can be used to predict movement direction. Furthermore, position and movement direction were maximally predicted from firing in the early and late portions of the theta cycle, respectively. This represents the first direct evidence of a combined representation of position, trajectory and heading in the hippocampus, organized on a fine temporal scale by theta oscillations. author: - first_name: John full_name: Huxter,John R last_name: Huxter - first_name: Timothy full_name: Senior,Timothy J last_name: Senior - first_name: Kevin full_name: Allen, Kevin last_name: Allen - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: Huxter J, Senior T, Allen K, Csicsvari JL. Theta phase-specific codes for two-dimensional position, trajectory and heading in the hippocampus. Nature Neuroscience. 2008;11(5):587-594. doi:10.1038/nn.2106 apa: Huxter, J., Senior, T., Allen, K., & Csicsvari, J. L. (2008). Theta phase-specific codes for two-dimensional position, trajectory and heading in the hippocampus. Nature Neuroscience. Nature Publishing Group. https://doi.org/10.1038/nn.2106 chicago: Huxter, John, Timothy Senior, Kevin Allen, and Jozsef L Csicsvari. “Theta Phase-Specific Codes for Two-Dimensional Position, Trajectory and Heading in the Hippocampus.” Nature Neuroscience. Nature Publishing Group, 2008. https://doi.org/10.1038/nn.2106. ieee: J. Huxter, T. Senior, K. Allen, and J. L. Csicsvari, “Theta phase-specific codes for two-dimensional position, trajectory and heading in the hippocampus,” Nature Neuroscience, vol. 11, no. 5. Nature Publishing Group, pp. 587–594, 2008. ista: Huxter J, Senior T, Allen K, Csicsvari JL. 2008. Theta phase-specific codes for two-dimensional position, trajectory and heading in the hippocampus. Nature Neuroscience. 11(5), 587–594. mla: Huxter, John, et al. “Theta Phase-Specific Codes for Two-Dimensional Position, Trajectory and Heading in the Hippocampus.” Nature Neuroscience, vol. 11, no. 5, Nature Publishing Group, 2008, pp. 587–94, doi:10.1038/nn.2106. short: J. Huxter, T. Senior, K. Allen, J.L. Csicsvari, Nature Neuroscience 11 (2008) 587–594. date_created: 2018-12-11T12:03:44Z date_published: 2008-05-29T00:00:00Z date_updated: 2021-01-12T07:44:00Z day: '29' doi: 10.1038/nn.2106 extern: 1 intvolume: ' 11' issue: '5' month: '05' page: 587 - 594 publication: Nature Neuroscience publication_status: published publisher: Nature Publishing Group publist_id: '2869' quality_controlled: 0 status: public title: Theta phase-specific codes for two-dimensional position, trajectory and heading in the hippocampus type: journal_article volume: 11 year: '2008' ... --- _id: '3530' abstract: - lang: eng text: In the cerebral cortex, GABAergic interneurons are often regarded as fast-spiking cells. We have identified a type of slow-spiking interneuron that offers distinct contributions to network activity. “Ivy” cells, named after their dense and fine axons innervating mostly basal and oblique pyramidal cell dendrites, are more numerous than the parvalbumin-expressing basket, bistratified, or axo-axonic cells. Ivy cells express nitric oxide synthase, neuropeptide Y, and high levels of GABA(A) receptor alpha 1 subunit; they discharge at a low frequency with wide spikes in vivo, yet are distinctively phase-locked to behaviorally relevant network rhythms including theta, gamma, and ripple oscillations. Paired recordings in vitro showed that Ivy cells receive depressing EPSPs from pyramidal cells, which in turn receive slowly rising and decaying inhibitory input from Ivy cells. In contrast to fast-spiking interneurons operating with millisecond precision, the highly abundant Ivy cells express presynaptically acting neuromodulators and regulate the excitability of pyramidal cell dendrites through slowly rising and decaying GABAergic inputs. author: - first_name: Pablo full_name: Fuentealba,Pablo last_name: Fuentealba - first_name: Rahima full_name: Begum,Rahima last_name: Begum - first_name: Marco full_name: Capogna,Marco last_name: Capogna - first_name: Shozo full_name: Jinno,Shozo last_name: Jinno - first_name: Laszlo full_name: Marton,Laszlo F last_name: Marton - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: Alex full_name: Thomson,Alex last_name: Thomson - first_name: Péter full_name: Somogyi, Péter last_name: Somogyi - first_name: Thomas full_name: Klausberger,Thomas last_name: Klausberger citation: ama: 'Fuentealba P, Begum R, Capogna M, et al. Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic neurons and their involvement in hippocampal network activity. Neuron. 2008;57(6):917-929. doi:10.1016/j.neuron.2008.01.034' apa: 'Fuentealba, P., Begum, R., Capogna, M., Jinno, S., Marton, L., Csicsvari, J. L., … Klausberger, T. (2008). Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic neurons and their involvement in hippocampal network activity. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2008.01.034' chicago: 'Fuentealba, Pablo, Rahima Begum, Marco Capogna, Shozo Jinno, Laszlo Marton, Jozsef L Csicsvari, Alex Thomson, Péter Somogyi, and Thomas Klausberger. “Ivy Cells: A Population of Nitric-Oxide-Producing, Slow-Spiking GABAergic Neurons and Their Involvement in Hippocampal Network Activity.” Neuron. Elsevier, 2008. https://doi.org/10.1016/j.neuron.2008.01.034.' ieee: 'P. Fuentealba et al., “Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic neurons and their involvement in hippocampal network activity,” Neuron, vol. 57, no. 6. Elsevier, pp. 917–929, 2008.' ista: 'Fuentealba P, Begum R, Capogna M, Jinno S, Marton L, Csicsvari JL, Thomson A, Somogyi P, Klausberger T. 2008. Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic neurons and their involvement in hippocampal network activity. Neuron. 57(6), 917–929.' mla: 'Fuentealba, Pablo, et al. “Ivy Cells: A Population of Nitric-Oxide-Producing, Slow-Spiking GABAergic Neurons and Their Involvement in Hippocampal Network Activity.” Neuron, vol. 57, no. 6, Elsevier, 2008, pp. 917–29, doi:10.1016/j.neuron.2008.01.034.' short: P. Fuentealba, R. Begum, M. Capogna, S. Jinno, L. Marton, J.L. Csicsvari, A. Thomson, P. Somogyi, T. Klausberger, Neuron 57 (2008) 917–929. date_created: 2018-12-11T12:03:49Z date_published: 2008-03-27T00:00:00Z date_updated: 2021-01-12T07:44:06Z day: '27' doi: 10.1016/j.neuron.2008.01.034 extern: 1 intvolume: ' 57' issue: '6' month: '03' page: 917 - 929 publication: Neuron publication_status: published publisher: Elsevier publist_id: '2855' quality_controlled: 0 status: public title: 'Ivy cells: A population of nitric-oxide-producing, slow-spiking GABAergic neurons and their involvement in hippocampal network activity' type: journal_article volume: 57 year: '2008' ... --- _id: '3544' abstract: - lang: eng text: In the subthalamic nucleus (STN) of Parkinson's disease (PD) patients, a pronounced synchronization of oscillatory activity at beta frequencies (15-30 Hz) accompanies movement difficulties. Abnormal beta oscillations and motor symptoms are concomitantly and acutely suppressed by dopaminergic therapies, suggesting that these inappropriate rhythms might also emerge acutely from disrupted dopamine transmission. The neural basis of these abnormal beta oscillations is unclear, and how they might compromise information processing, or how they arise, is unknown. Using a 6-hydroxydopamine-lesioned rodent model of PD, we demonstrate that beta oscillations are inappropriately exaggerated, compared with controls, in a brain-state-dependent manner after chronic dopamine loss. Exaggerated beta oscillations are expressed at the levels of single neurons and small neuronal ensembles, and are focally present and spatially distributed within STN. They are also expressed in synchronous population activities, as evinced by oscillatory local field potentials, in STN and cortex. Excessively synchronized beta oscillations reduce the information coding capacity of STN neuronal ensembles, which may contribute to parkinsonian motor impairment. Acute disruption of dopamine transmission in control animals with antagonists of D-1/D-2 receptors did not exaggerate STN or cortical beta oscillations. Moreover, beta oscillations were not exaggerated until several days after 6-hydroxydopamine injections. Thus, contrary to predictions, abnormally amplified beta oscillations in cortico-STN circuits do not result simply from an acute absence of dopamine receptor stimulation, but are instead delayed sequelae of chronic dopamine depletion. Targeting the plastic processes underlying the delayed emergence of pathological beta oscillations after continuing dopaminergic dysfunction may offer considerable therapeutic promise. author: - first_name: Nicolas full_name: Mallet,Nicolas last_name: Mallet - first_name: Alek full_name: Pogosyan,Alek last_name: Pogosyan - first_name: Andrew full_name: Sharott,Andrew last_name: Sharott - first_name: Jozsef L full_name: Jozsef Csicsvari id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 - first_name: John full_name: Bolam, John Paul last_name: Bolam - first_name: Peter full_name: Brown,Peter last_name: Brown - first_name: Peter full_name: Magill,Peter J last_name: Magill citation: ama: Mallet N, Pogosyan A, Sharott A, et al. Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex. Journal of Neuroscience. 2008;28(18):4795-4806. doi:10.1523/JNEUROSCI.0123-08.2008 apa: Mallet, N., Pogosyan, A., Sharott, A., Csicsvari, J. L., Bolam, J., Brown, P., & Magill, P. (2008). Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex. Journal of Neuroscience. Society for Neuroscience. https://doi.org/10.1523/JNEUROSCI.0123-08.2008 chicago: Mallet, Nicolas, Alek Pogosyan, Andrew Sharott, Jozsef L Csicsvari, John Bolam, Peter Brown, and Peter Magill. “Disrupted Dopamine Transmission and the Emergence of Exaggerated Beta Oscillations in Subthalamic Nucleus and Cerebral Cortex.” Journal of Neuroscience. Society for Neuroscience, 2008. https://doi.org/10.1523/JNEUROSCI.0123-08.2008. ieee: N. Mallet et al., “Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex,” Journal of Neuroscience, vol. 28, no. 18. Society for Neuroscience, pp. 4795–4806, 2008. ista: Mallet N, Pogosyan A, Sharott A, Csicsvari JL, Bolam J, Brown P, Magill P. 2008. Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex. Journal of Neuroscience. 28(18), 4795–4806. mla: Mallet, Nicolas, et al. “Disrupted Dopamine Transmission and the Emergence of Exaggerated Beta Oscillations in Subthalamic Nucleus and Cerebral Cortex.” Journal of Neuroscience, vol. 28, no. 18, Society for Neuroscience, 2008, pp. 4795–806, doi:10.1523/JNEUROSCI.0123-08.2008. short: N. Mallet, A. Pogosyan, A. Sharott, J.L. Csicsvari, J. Bolam, P. Brown, P. Magill, Journal of Neuroscience 28 (2008) 4795–4806. date_created: 2018-12-11T12:03:53Z date_published: 2008-04-30T00:00:00Z date_updated: 2021-01-12T07:44:12Z day: '30' doi: 10.1523/JNEUROSCI.0123-08.2008 extern: 1 intvolume: ' 28' issue: '18' month: '04' page: 4795 - 4806 publication: Journal of Neuroscience publication_status: published publisher: Society for Neuroscience publist_id: '2842' quality_controlled: 0 status: public title: Disrupted dopamine transmission and the emergence of exaggerated beta oscillations in subthalamic nucleus and cerebral cortex type: journal_article volume: 28 year: '2008' ... --- _id: '3577' alternative_title: - Mathematics and Visualization author: - first_name: Silvia full_name: Biasotti, Silvia last_name: Biasotti - first_name: Dominique full_name: Attali, Dominique last_name: Attali - first_name: Jean full_name: Boissonnat, Jean-Daniel last_name: Boissonnat - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Gershon full_name: Elber, Gershon last_name: Elber - first_name: Michela full_name: Mortara, Michela last_name: Mortara - first_name: Gabriella full_name: Sanniti di Baja, Gabriella last_name: Sanniti Di Baja - first_name: Michela full_name: Spagnuolo, Michela last_name: Spagnuolo - first_name: Mirela full_name: Tanase, Mirela last_name: Tanase - first_name: Remco full_name: Veltkam, Remco last_name: Veltkam citation: ama: 'Biasotti S, Attali D, Boissonnat J, et al. Skeletal structures. In: Shape Analysis and Structuring. Springer; 2008:145-183. doi:10.1007/978-3-540-33265-7_5' apa: Biasotti, S., Attali, D., Boissonnat, J., Edelsbrunner, H., Elber, G., Mortara, M., … Veltkam, R. (2008). Skeletal structures. In Shape Analysis and Structuring (pp. 145–183). Springer. https://doi.org/10.1007/978-3-540-33265-7_5 chicago: Biasotti, Silvia, Dominique Attali, Jean Boissonnat, Herbert Edelsbrunner, Gershon Elber, Michela Mortara, Gabriella Sanniti Di Baja, Michela Spagnuolo, Mirela Tanase, and Remco Veltkam. “Skeletal Structures.” In Shape Analysis and Structuring, 145–83. Springer, 2008. https://doi.org/10.1007/978-3-540-33265-7_5. ieee: S. Biasotti et al., “Skeletal structures,” in Shape Analysis and Structuring, Springer, 2008, pp. 145–183. ista: 'Biasotti S, Attali D, Boissonnat J, Edelsbrunner H, Elber G, Mortara M, Sanniti Di Baja G, Spagnuolo M, Tanase M, Veltkam R. 2008.Skeletal structures. In: Shape Analysis and Structuring. Mathematics and Visualization, , 145–183.' mla: Biasotti, Silvia, et al. “Skeletal Structures.” Shape Analysis and Structuring, Springer, 2008, pp. 145–83, doi:10.1007/978-3-540-33265-7_5. short: S. Biasotti, D. Attali, J. Boissonnat, H. Edelsbrunner, G. Elber, M. Mortara, G. Sanniti Di Baja, M. Spagnuolo, M. Tanase, R. Veltkam, in:, Shape Analysis and Structuring, Springer, 2008, pp. 145–183. date_created: 2018-12-11T12:04:03Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:44:25Z day: '01' doi: 10.1007/978-3-540-33265-7_5 extern: 1 month: '01' page: 145 - 183 publication: Shape Analysis and Structuring publication_status: published publisher: Springer publist_id: '2808' quality_controlled: 0 status: public title: Skeletal structures type: book_chapter year: '2008' ... --- _id: '3591' abstract: - lang: eng text: The controlled internalization of membrane receptors and lipids is crucial for cells to control signaling pathways and interact with their environment. During clathrin-mediated endocytosis, membrane constituents are transported via endocytic vesicles into early endosomes, from which they are further distributed within the cell. The small guanosine triphosphatase (GTPase) Rab5 is both required and sufficient for the formation of these early endosomes and can be used to experimentally address endocytic processes. Recent evidence shows that endocytic turnover of E-cadherin regulates the migration of mesendodermal cells during zebrafish gastrulation by modulating their adhesive interactions with neighboring cells. This in turn leads to effective and synchronized movement within the embryo. In this review, we discuss techniques to manipulate E-cadherin endocytosis by morpholino-mediated knockdown of rab5 during zebrafish gastrulation. We describe the use of antibodies specifically directed against zebrafish E-cadherin to detect its intracellular localization and of in situ hybridization and primary cell culture to reveal patterns of cell migration and adhesion, respectively article_processing_charge: No author: - first_name: Florian full_name: Ulrich, Florian last_name: Ulrich - 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: Ulrich F, Heisenberg C-PJ. Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish. Methods in Molecular Biology. 2008;440:371-387. doi:10.1007/978-1-59745-178-9_27 apa: Ulrich, F., & Heisenberg, C.-P. J. (2008). Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish. Methods in Molecular Biology. Springer. https://doi.org/10.1007/978-1-59745-178-9_27 chicago: Ulrich, Florian, and Carl-Philipp J Heisenberg. “Probing E-Cadherin Endocytosis by Morpholino-Mediated Rab5 Knock-down in Zebrafish.” Methods in Molecular Biology. Springer, 2008. https://doi.org/10.1007/978-1-59745-178-9_27. ieee: F. Ulrich and C.-P. J. Heisenberg, “Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish.,” Methods in Molecular Biology, vol. 440. Springer, pp. 371–387, 2008. ista: Ulrich F, Heisenberg C-PJ. 2008. Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish. Methods in Molecular Biology. 440, 371–387. mla: Ulrich, Florian, and Carl-Philipp J. Heisenberg. “Probing E-Cadherin Endocytosis by Morpholino-Mediated Rab5 Knock-down in Zebrafish.” Methods in Molecular Biology, vol. 440, Springer, 2008, pp. 371–87, doi:10.1007/978-1-59745-178-9_27. short: F. Ulrich, C.-P.J. Heisenberg, Methods in Molecular Biology 440 (2008) 371–387. date_created: 2018-12-11T12:04:08Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:44:31Z day: '01' doi: 10.1007/978-1-59745-178-9_27 extern: '1' intvolume: ' 440' language: - iso: eng month: '01' oa_version: None page: 371 - 387 publication: Methods in Molecular Biology publication_status: published publisher: Springer publist_id: '2792' status: public title: Probing E-cadherin endocytosis by morpholino-mediated Rab5 knock-down in zebrafish. type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 440 year: '2008' ... --- _id: '3599' abstract: - lang: eng text: In this paper, adaptive formation control and bio-inspired optimization are jointly addressed for a cluster-based satellite wireless sensor network in which there are multiple satellites flying in formation (MSFF) in the presence of unknown disturbances. The full nonlinear dynamics model describing the relative positioning of the MSFF system is used to develop an adaptive formation controller. First, the original nonlinear system is transformed into a linear controllable system with aperturbation term by invoking the input-output feedback linearization technique. Second, by using the integral feedback design scheme, the adaptive formation controller is presented for improving the steady-state performance of the MSFF system in the presence of unknown disturbances. Third, as a currently popular bio-inspired algorithm, PSO (particle swarm optimizer) is employed to minimize the total energy consumption under the required quality of service by jointly optimizing the transmission power and rate for each satellite. Simulation results are provided to demonstrate the effectiveness of the adaptive formation controller and the PSO-based optimization for saving the total communication energy. author: - first_name: Erfu full_name: Yang, Erfu last_name: Yang - first_name: Ahmet full_name: Erdogan, Ahmet T last_name: Erdogan - first_name: Tughrul full_name: Arslan, Tughrul last_name: Arslan - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: 'Yang E, Erdogan A, Arslan T, Barton NH. Adaptive formation control and bio-inspired optimization of a cluster-based satellite wireless sensor network . In: IEEE; 2008:432-439. doi:10.1109/AHS.2008.60' apa: 'Yang, E., Erdogan, A., Arslan, T., & Barton, N. H. (2008). Adaptive formation control and bio-inspired optimization of a cluster-based satellite wireless sensor network (pp. 432–439). Presented at the AHS: NASA/ESA Conference on Adaptive Hardware and Systems, IEEE. https://doi.org/10.1109/AHS.2008.60' chicago: Yang, Erfu, Ahmet Erdogan, Tughrul Arslan, and Nicholas H Barton. “Adaptive Formation Control and Bio-Inspired Optimization of a Cluster-Based Satellite Wireless Sensor Network ,” 432–39. IEEE, 2008. https://doi.org/10.1109/AHS.2008.60. ieee: 'E. Yang, A. Erdogan, T. Arslan, and N. H. Barton, “Adaptive formation control and bio-inspired optimization of a cluster-based satellite wireless sensor network ,” presented at the AHS: NASA/ESA Conference on Adaptive Hardware and Systems, 2008, pp. 432–439.' ista: 'Yang E, Erdogan A, Arslan T, Barton NH. 2008. Adaptive formation control and bio-inspired optimization of a cluster-based satellite wireless sensor network . AHS: NASA/ESA Conference on Adaptive Hardware and Systems, 432–439.' mla: Yang, Erfu, et al. Adaptive Formation Control and Bio-Inspired Optimization of a Cluster-Based Satellite Wireless Sensor Network . IEEE, 2008, pp. 432–39, doi:10.1109/AHS.2008.60. short: E. Yang, A. Erdogan, T. Arslan, N.H. Barton, in:, IEEE, 2008, pp. 432–439. conference: name: 'AHS: NASA/ESA Conference on Adaptive Hardware and Systems' date_created: 2018-12-11T12:04:10Z date_published: 2008-08-01T00:00:00Z date_updated: 2021-01-12T07:44:34Z day: '01' doi: 10.1109/AHS.2008.60 extern: 1 month: '08' page: 432 - 439 publication_status: published publisher: IEEE publist_id: '2784' quality_controlled: 0 status: public title: 'Adaptive formation control and bio-inspired optimization of a cluster-based satellite wireless sensor network ' type: conference year: '2008' ... --- _id: '3698' abstract: - lang: eng text: Kernel canonical correlation analysis (KCCA) is a dimensionality reduction technique for paired data. By finding directions that maximize correlation, KCCA learns representations that are more closely tied to the underlying semantics of the data rather than noise. However, meaningful directions are not only those that have high correlation to another modality, but also those that capture the manifold structure of the data. We propose a method that is simultaneously able to find highly correlated directions that are also located on high variance directions along the data manifold. This is achieved by the use of semi-supervised Laplacian regularization of KCCA. We show experimentally that Laplacian regularized training improves class separation over KCCA with only Tikhonov regularization, while causing no degradation in the correlation between modalities. We propose a model selection criterion based on the Hilbert-Schmidt norm of the semi-supervised Laplacian regularized cross-covariance operator, which we compute in closed form. alternative_title: - LNCS author: - first_name: Matthew full_name: Blaschko,Matthew B last_name: Blaschko - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Arthur full_name: Gretton,Arthur last_name: Gretton citation: ama: 'Blaschko M, Lampert C, Gretton A. Semi-supervised Laplacian regularization of kernel canonical correlation analysis. In: Vol 5211. Springer; 2008:133-145. doi:10.1007/978-3-540-87479-9_27' apa: 'Blaschko, M., Lampert, C., & Gretton, A. (2008). Semi-supervised Laplacian regularization of kernel canonical correlation analysis (Vol. 5211, pp. 133–145). Presented at the ECML: European Conference on Machine Learning, Springer. https://doi.org/10.1007/978-3-540-87479-9_27' chicago: Blaschko, Matthew, Christoph Lampert, and Arthur Gretton. “Semi-Supervised Laplacian Regularization of Kernel Canonical Correlation Analysis,” 5211:133–45. Springer, 2008. https://doi.org/10.1007/978-3-540-87479-9_27. ieee: 'M. Blaschko, C. Lampert, and A. Gretton, “Semi-supervised Laplacian regularization of kernel canonical correlation analysis,” presented at the ECML: European Conference on Machine Learning, 2008, vol. 5211, no. Part 1, pp. 133–145.' ista: 'Blaschko M, Lampert C, Gretton A. 2008. Semi-supervised Laplacian regularization of kernel canonical correlation analysis. ECML: European Conference on Machine Learning, LNCS, vol. 5211, 133–145.' mla: Blaschko, Matthew, et al. Semi-Supervised Laplacian Regularization of Kernel Canonical Correlation Analysis. Vol. 5211, no. Part 1, Springer, 2008, pp. 133–45, doi:10.1007/978-3-540-87479-9_27. short: M. Blaschko, C. Lampert, A. Gretton, in:, Springer, 2008, pp. 133–145. conference: name: 'ECML: European Conference on Machine Learning' date_created: 2018-12-11T12:04:41Z date_published: 2008-10-21T00:00:00Z date_updated: 2021-01-12T07:49:02Z day: '21' doi: 10.1007/978-3-540-87479-9_27 extern: 1 intvolume: ' 5211' issue: Part 1 month: '10' page: 133 - 145 publication_status: published publisher: Springer publist_id: '2662' quality_controlled: 0 status: public title: Semi-supervised Laplacian regularization of kernel canonical correlation analysis type: conference volume: 5211 year: '2008' ... --- _id: '3694' abstract: - lang: eng text: Distributed Denial of Service (DDoS) attacks are today the most destabilizing factor in the global internet and there is a strong need for sophisticated solutions. We introduce a formal statistical framework and derive a Bayes optimal packet classifier from it. Our proposed practical algorithm "Adaptive History-Based IP Filtering" (AHIF) mitigates DDoS attacks near the victim and outperforms existing methods by at least 32% in terms of collateral damage. Furthermore, it adjusts to the strength of an ongoing attack and ensures availability of the attacked server. In contrast to other adaptive solutions, firewall rulesets used to resist an attack can be precalculated before an attack takes place. This ensures an immediate response in a DDoS emergency. For evaluation, simulated DDoS attacks and two real-world user traffic datasets are used. author: - first_name: Markus full_name: Goldstein,Markus last_name: Goldstein - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Matthias full_name: Reif,Matthias last_name: Reif - first_name: Armin full_name: Stahl,Armin last_name: Stahl - first_name: Thomas full_name: Breuel,Thomas M last_name: Breuel citation: ama: 'Goldstein M, Lampert C, Reif M, Stahl A, Breuel T. Bayes optimal DDoS mitigation by adaptive history-based IP filtering. In: IEEE; 2008:174-179. doi:10.1109/ICN.2008.64' apa: 'Goldstein, M., Lampert, C., Reif, M., Stahl, A., & Breuel, T. (2008). Bayes optimal DDoS mitigation by adaptive history-based IP filtering (pp. 174–179). Presented at the ICN: International Conference on Networking, IEEE. https://doi.org/10.1109/ICN.2008.64' chicago: Goldstein, Markus, Christoph Lampert, Matthias Reif, Armin Stahl, and Thomas Breuel. “Bayes Optimal DDoS Mitigation by Adaptive History-Based IP Filtering,” 174–79. IEEE, 2008. https://doi.org/10.1109/ICN.2008.64. ieee: 'M. Goldstein, C. Lampert, M. Reif, A. Stahl, and T. Breuel, “Bayes optimal DDoS mitigation by adaptive history-based IP filtering,” presented at the ICN: International Conference on Networking, 2008, pp. 174–179.' ista: 'Goldstein M, Lampert C, Reif M, Stahl A, Breuel T. 2008. Bayes optimal DDoS mitigation by adaptive history-based IP filtering. ICN: International Conference on Networking, 174–179.' mla: Goldstein, Markus, et al. Bayes Optimal DDoS Mitigation by Adaptive History-Based IP Filtering. IEEE, 2008, pp. 174–79, doi:10.1109/ICN.2008.64. short: M. Goldstein, C. Lampert, M. Reif, A. Stahl, T. Breuel, in:, IEEE, 2008, pp. 174–179. conference: name: 'ICN: International Conference on Networking' date_created: 2018-12-11T12:04:39Z date_published: 2008-04-13T00:00:00Z date_updated: 2021-01-12T07:49:01Z day: '13' doi: 10.1109/ICN.2008.64 extern: 1 main_file_link: - open_access: '0' url: http://pub.ist.ac.at/~chl/papers/goldstein-icn2008.pdf month: '04' page: 174 - 179 publication_status: published publisher: IEEE publist_id: '2671' quality_controlled: 0 status: public title: Bayes optimal DDoS mitigation by adaptive history-based IP filtering type: conference year: '2008' ... --- _id: '3706' abstract: - lang: eng text: We present a new technique for structured prediction that works in a hybrid generative/discriminative way, using a one-class support vector machine to model the joint probability of (input, output)-pairs in a joint reproducing kernel Hilbert space. Compared to discriminative techniques, like conditional random fields or structured output SVMs?, the proposed method has the advantage that its training time depends only on the number of training examples, not on the size of the label space. Due to its generative aspect, it is also very tolerant against ambiguous, incomplete or incorrect labels. Experiments on realistic data show that our method works efficiently and robustly in situations that discriminative techniques have problems with or that are computationally infeasible for them. author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Matthew full_name: Blaschko,Matthew B last_name: Blaschko citation: ama: 'Lampert C, Blaschko M. Joint kernel support estimation for structured prediction. In: Curran Associates, Inc.; 2008:1-4.' apa: 'Lampert, C., & Blaschko, M. (2008). Joint kernel support estimation for structured prediction (pp. 1–4). Presented at the NIPS SISO: NIPS Workshop on “Structured Input - Structured Output,” Curran Associates, Inc.' chicago: Lampert, Christoph, and Matthew Blaschko. “Joint Kernel Support Estimation for Structured Prediction,” 1–4. Curran Associates, Inc., 2008. ieee: 'C. Lampert and M. Blaschko, “Joint kernel support estimation for structured prediction,” presented at the NIPS SISO: NIPS Workshop on “Structured Input - Structured Output,” 2008, pp. 1–4.' ista: 'Lampert C, Blaschko M. 2008. Joint kernel support estimation for structured prediction. NIPS SISO: NIPS Workshop on ‘Structured Input - Structured Output’, 1–4.' mla: Lampert, Christoph, and Matthew Blaschko. Joint Kernel Support Estimation for Structured Prediction. Curran Associates, Inc., 2008, pp. 1–4. short: C. Lampert, M. Blaschko, in:, Curran Associates, Inc., 2008, pp. 1–4. conference: name: 'NIPS SISO: NIPS Workshop on "Structured Input - Structured Output"' date_created: 2018-12-11T12:04:43Z date_published: 2008-12-12T00:00:00Z date_updated: 2021-01-12T07:51:37Z day: '12' extern: 1 main_file_link: - open_access: '0' url: http://agbs.kyb.tuebingen.mpg.de/wikis/bg/siso2008/Blaschkoetal.pdf month: '12' page: 1 - 4 publication_status: published publisher: Curran Associates, Inc. publist_id: '2650' quality_controlled: 0 status: public title: Joint kernel support estimation for structured prediction type: conference year: '2008' ... --- _id: '3712' abstract: - lang: eng text: We present a new method for spectral clustering with paired data based on kernel canonical correlation analysis, called correlational spectral clustering. Paired data are common in real world data sources, such as images with text captions. Traditional spectral clustering algorithms either assume that data can be represented by a single similarity measure, or by co-occurrence matrices that are then used in biclustering. In contrast, the proposed method uses separate similarity measures for each data representation, and allows for projection of previously unseen data that are only observed in one representation (e.g. images but not text). We show that this algorithm generalizes traditional spectral clustering algorithms and show consistent empirical improvement over spectral clustering on a variety of datasets of images with associated text. author: - first_name: Matthew full_name: Blaschko,Matthew B last_name: Blaschko - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Blaschko M, Lampert C. Correlational spectral clustering. In: IEEE; 2008:1-8. doi:10.1109/CVPR.2008.4587353' apa: 'Blaschko, M., & Lampert, C. (2008). Correlational spectral clustering (pp. 1–8). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2008.4587353' chicago: Blaschko, Matthew, and Christoph Lampert. “Correlational Spectral Clustering,” 1–8. IEEE, 2008. https://doi.org/10.1109/CVPR.2008.4587353. ieee: 'M. Blaschko and C. Lampert, “Correlational spectral clustering,” presented at the CVPR: Computer Vision and Pattern Recognition, 2008, pp. 1–8.' ista: 'Blaschko M, Lampert C. 2008. Correlational spectral clustering. CVPR: Computer Vision and Pattern Recognition, 1–8.' mla: Blaschko, Matthew, and Christoph Lampert. Correlational Spectral Clustering. IEEE, 2008, pp. 1–8, doi:10.1109/CVPR.2008.4587353. short: M. Blaschko, C. Lampert, in:, IEEE, 2008, pp. 1–8. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:04:45Z date_published: 2008-09-18T00:00:00Z date_updated: 2021-01-12T07:51:40Z day: '18' doi: 10.1109/CVPR.2008.4587353 extern: 1 month: '09' page: 1 - 8 publication_status: published publisher: IEEE publist_id: '2646' quality_controlled: 0 status: public title: Correlational spectral clustering type: conference year: '2008' ... --- _id: '3726' abstract: - lang: eng text: Single-molecule atomic force microscopy (AFM) provides novel ways to characterize the structure-function relationship of native membrane proteins. High-resolution AFM topographs allow observing the structure of single proteins at sub-nanometer resolution as well as their conformational changes, oligomeric state, molecular dynamics and assembly. We will review these feasibilities illustrating examples of membrane proteins in native and reconstituted membranes. Classification of individual topographs of single proteins allows understanding the principles of motions of their extrinsic domains, to learn about their local structural flexibilities and to find the entropy minima of certain conformations. Combined with the visualization of functionally related conformational changes these insights allow understanding why certain flexibilities are required for the protein to function and how structurally flexible regions allow certain conformational changes. Complementary to AFM imaging, single-molecule force spectroscopy (SMFS) experiments detect molecular interactions established within and between membrane proteins. The sensitivity of this method makes it possible to measure interactions that stabilize secondary structures such as transmembrane α-helices, polypeptide loops and segments within. Changes in temperature or protein-protein assembly do not change the locations of stable structural segments, but influence their stability established by collective molecular interactions. Such changes alter the probability of proteins to choose a certain unfolding pathway. Recent examples have elucidated unfolding and refolding pathways of membrane proteins as well as their energy landscapes. author: - first_name: Andreas full_name: Engel, Andreas last_name: Engel - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Dimtrios full_name: Fotiadis, Dimtrios last_name: Fotiadis - first_name: Alexej full_name: Kedrov, Alexej last_name: Kedrov - first_name: David full_name: Cisneros, David last_name: Cisneros - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: 'Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. Single-molecule microscopy and force spectroscopy of membrane proteins. In: Single Molecules and Nanotechnology. Vol 12. Springer; 2008:279-311. doi:10.1007/978-3-540-73924-1_11' apa: Engel, A., Janovjak, H. L., Fotiadis, D., Kedrov, A., Cisneros, D., & Mueller, D. (2008). Single-molecule microscopy and force spectroscopy of membrane proteins. In Single Molecules and Nanotechnology (Vol. 12, pp. 279–311). Springer. https://doi.org/10.1007/978-3-540-73924-1_11 chicago: Engel, Andreas, Harald L Janovjak, Dimtrios Fotiadis, Alexej Kedrov, David Cisneros, and Daniel Mueller. “Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins.” In Single Molecules and Nanotechnology, 12:279–311. Springer, 2008. https://doi.org/10.1007/978-3-540-73924-1_11. ieee: A. Engel, H. L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, and D. Mueller, “Single-molecule microscopy and force spectroscopy of membrane proteins,” in Single Molecules and Nanotechnology, vol. 12, Springer, 2008, pp. 279–311. ista: 'Engel A, Janovjak HL, Fotiadis D, Kedrov A, Cisneros D, Mueller D. 2008.Single-molecule microscopy and force spectroscopy of membrane proteins. In: Single Molecules and Nanotechnology. vol. 12, 279–311.' mla: Engel, Andreas, et al. “Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins.” Single Molecules and Nanotechnology, vol. 12, Springer, 2008, pp. 279–311, doi:10.1007/978-3-540-73924-1_11. short: A. Engel, H.L. Janovjak, D. Fotiadis, A. Kedrov, D. Cisneros, D. Mueller, in:, Single Molecules and Nanotechnology, Springer, 2008, pp. 279–311. date_created: 2018-12-11T12:04:50Z date_published: 2008-01-08T00:00:00Z date_updated: 2021-01-12T07:51:45Z day: '08' doi: 10.1007/978-3-540-73924-1_11 extern: 1 intvolume: ' 12' month: '01' page: 279 - 311 publication: Single Molecules and Nanotechnology publication_status: published publisher: Springer publist_id: '2503' quality_controlled: 0 status: public title: Single-molecule microscopy and force spectroscopy of membrane proteins type: book_chapter volume: 12 year: '2008' ... --- _id: '3739' abstract: - lang: eng text: 'Changes in a cell''s external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need to perform nontrivial computations that integrate several inputs and affect multiple genes. At the same time, the activities of the regulated genes would fluctuate even if the inputs were held fixed, as a consequence of the intrinsic noise in the system, and such noise must fundamentally limit the reliability of any genetic computation. Here we use information theory to formalize the notion of information transmission in simple genetic regulatory elements in the presence of physically realistic noise sources. The dependence of this "channel capacity" on noise parameters, cooperativity and cost of making signaling molecules is explored systematically. We find that, in the range of parameters probed by recent in vivo measurements, capacities higher than one bit should be achievable. It is of course generally accepted that gene regulatory elements must, in order to function properly, have a capacity of at least one bit. The central point of our analysis is the demonstration that simple physical models of noisy gene transcription, with realistic parameters, can indeed achieve this capacity: it was not self-evident that this should be so. We also demonstrate that capacities significantly greater than one bit are possible, so that transcriptional regulation need not be limited to simple "on-off" components. The question whether real systems actually exploit this richer possibility is beyond the scope of this investigation.' author: - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Curtis full_name: Callan,Curtis G last_name: Callan - first_name: William full_name: Bialek, William S last_name: Bialek citation: ama: Tkačik G, Callan C, Bialek W. Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2008;78(1). doi:10.1103/PhysRevE.78.011910 apa: Tkačik, G., Callan, C., & Bialek, W. (2008). Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.78.011910 chicago: Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Capacity of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2008. https://doi.org/10.1103/PhysRevE.78.011910. ieee: G. Tkačik, C. Callan, and W. Bialek, “Information capacity of genetic regulatory elements,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1. American Institute of Physics, 2008. ista: Tkačik G, Callan C, Bialek W. 2008. Information capacity of genetic regulatory elements. Physical Review E Statistical Nonlinear and Soft Matter Physics. 78(1). mla: Tkačik, Gašper, et al. “Information Capacity of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1, American Institute of Physics, 2008, doi:10.1103/PhysRevE.78.011910. short: G. Tkačik, C. Callan, W. Bialek, Physical Review E Statistical Nonlinear and Soft Matter Physics 78 (2008). date_created: 2018-12-11T12:04:54Z date_published: 2008-07-21T00:00:00Z date_updated: 2021-01-12T07:51:51Z day: '21' doi: 10.1103/PhysRevE.78.011910 extern: 1 intvolume: ' 78' issue: '1' month: '07' publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '2488' quality_controlled: 0 status: public title: Information capacity of genetic regulatory elements type: journal_article volume: 78 year: '2008' ... --- _id: '3740' abstract: - lang: eng text: In the simplest view of transcriptional regulation, the expression of a gene is turned on or off by changes in the concentration of a transcription factor (TF). We use recent data on noise levels in gene expression to show that it should be possible to transmit much more than just one regulatory bit. Realizing this optimal information capacity would require that the dynamic range of TF concentrations used by the cell, the input/output relation of the regulatory module, and the noise in gene expression satisfy certain matching relations, which we derive. These results provide parameter-free, quantitative predictions connecting independently measurable quantities. Although we have considered only the simplified problem of a single gene responding to a single TF, we find that these predictions are in surprisingly good agreement with recent experiments on the Bicoid/Hunchback system in the early Drosophila embryo and that this system achieves approximately 90% of its theoretical maximum information transmission. acknowledgement: P50 GM071508/GM/NIGMS NIH HHS/United States; R01 GM077599/GM/NIGMS NIH HHS/United States author: - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Curtis full_name: Callan,Curtis G last_name: Callan - first_name: William full_name: Bialek, William S last_name: Bialek citation: ama: Tkačik G, Callan C, Bialek W. Information flow and optimization in transcriptional regulation. PNAS. 2008;105(34):12265-12270. doi:10.1073/pnas.0806077105 apa: Tkačik, G., Callan, C., & Bialek, W. (2008). Information flow and optimization in transcriptional regulation. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0806077105 chicago: Tkačik, Gašper, Curtis Callan, and William Bialek. “Information Flow and Optimization in Transcriptional Regulation.” PNAS. National Academy of Sciences, 2008. https://doi.org/10.1073/pnas.0806077105. ieee: G. Tkačik, C. Callan, and W. Bialek, “Information flow and optimization in transcriptional regulation,” PNAS, vol. 105, no. 34. National Academy of Sciences, pp. 12265–12270, 2008. ista: Tkačik G, Callan C, Bialek W. 2008. Information flow and optimization in transcriptional regulation. PNAS. 105(34), 12265–12270. mla: Tkačik, Gašper, et al. “Information Flow and Optimization in Transcriptional Regulation.” PNAS, vol. 105, no. 34, National Academy of Sciences, 2008, pp. 12265–70, doi:10.1073/pnas.0806077105. short: G. Tkačik, C. Callan, W. Bialek, PNAS 105 (2008) 12265–12270. date_created: 2018-12-11T12:04:54Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:51:52Z day: '01' doi: 10.1073/pnas.0806077105 extern: 1 intvolume: ' 105' issue: '34' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527900 month: '01' oa: 1 page: 12265 - 12270 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '2489' quality_controlled: 0 status: public title: Information flow and optimization in transcriptional regulation type: journal_article volume: 105 year: '2008' ... --- _id: '3744' abstract: - lang: eng text: It is widely acknowledged that detailed timing of action potentials is used to encode information, for example, in auditory pathways; however, the computational tools required to analyze encoding through timing are still in their infancy. We present a simple example of encoding, based on a recent model of time-frequency analysis, in which units fire action potentials when a certain condition is met, but the timing of the action potential depends also on other features of the stimulus. We show that, as a result, spike-triggered averages are smoothed so much that they do not represent the true features of the encoding. Inspired by this example, we present a simple method, differential reverse correlations, that can separate an analysis of what causes a neuron to spike, and what controls its timing. We analyze with this method the leaky integrate-and-fire neuron and show the method accurately reconstructs the model's kernel. author: - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Marcelo full_name: Magnasco, Marcelo O last_name: Magnasco citation: ama: 'Tkačik G, Magnasco M. Decoding spike timing: The differential reverse-correlation method. Biosystems. 2008;93(1-2):90-100. doi:10.1016/j.biosystems.2008.04.011' apa: 'Tkačik, G., & Magnasco, M. (2008). Decoding spike timing: The differential reverse-correlation method. Biosystems. Elsevier. https://doi.org/10.1016/j.biosystems.2008.04.011' chicago: 'Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” Biosystems. Elsevier, 2008. https://doi.org/10.1016/j.biosystems.2008.04.011.' ieee: 'G. Tkačik and M. Magnasco, “Decoding spike timing: The differential reverse-correlation method,” Biosystems, vol. 93, no. 1–2. Elsevier, pp. 90–100, 2008.' ista: 'Tkačik G, Magnasco M. 2008. Decoding spike timing: The differential reverse-correlation method. Biosystems. 93(1–2), 90–100.' mla: 'Tkačik, Gašper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” Biosystems, vol. 93, no. 1–2, Elsevier, 2008, pp. 90–100, doi:10.1016/j.biosystems.2008.04.011.' short: G. Tkačik, M. Magnasco, Biosystems 93 (2008) 90–100. date_created: 2018-12-11T12:04:56Z date_published: 2008-07-01T00:00:00Z date_updated: 2021-01-12T07:51:53Z day: '01' doi: 10.1016/j.biosystems.2008.04.011 extern: 1 intvolume: ' 93' issue: 1-2 main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2792887 month: '07' oa: 1 page: 90 - 100 publication: Biosystems publication_status: published publisher: Elsevier publist_id: '2482' quality_controlled: 0 status: public title: 'Decoding spike timing: The differential reverse-correlation method' type: journal_article volume: 93 year: '2008' ... --- _id: '3760' abstract: - lang: eng text: We introduce a method for efficiently animating a wide range of deformable materials. We combine a high resolution surface mesh with a tetrahedral finite element simulator that makes use of frequent re-meshing. This combination allows for fast and detailed simulations of complex elastic and plastic behavior. We significantly expand the range of physical parameters that can be simulated with a single technique, and the results are free from common artifacts such as volume-loss, smoothing, popping, and the absence of thin features like strands and sheets. Our decision to couple a high resolution surface with low-resolution physics leads to efficient simulation and detailed surface features, and our approach to creating the tetrahedral mesh leads to an order-of-magnitude speedup over previous techniques in the time spent re-meshing. We compute masses, collisions, and surface tension forces on the scale of the fine mesh, which helps avoid visual artifacts due to the differing mesh resolutions. The result is a method that can simulate a large array of different material behaviors with high resolution features in a short amount of time. article_processing_charge: No author: - 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: Greg full_name: Turk, Greg last_name: Turk citation: ama: Wojtan C, Turk G. Fast viscoelastic behavior with thin features. ACM Transactions on Graphics. 2008;27(3). doi:10.1145/1360612.1360646 apa: Wojtan, C., & Turk, G. (2008). Fast viscoelastic behavior with thin features. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/1360612.1360646 chicago: Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.” ACM Transactions on Graphics. ACM, 2008. https://doi.org/10.1145/1360612.1360646. ieee: C. Wojtan and G. Turk, “Fast viscoelastic behavior with thin features,” ACM Transactions on Graphics, vol. 27, no. 3. ACM, 2008. ista: Wojtan C, Turk G. 2008. Fast viscoelastic behavior with thin features. ACM Transactions on Graphics. 27(3). mla: Wojtan, Chris, and Greg Turk. “Fast Viscoelastic Behavior with Thin Features.” ACM Transactions on Graphics, vol. 27, no. 3, ACM, 2008, doi:10.1145/1360612.1360646. short: C. Wojtan, G. Turk, ACM Transactions on Graphics 27 (2008). date_created: 2018-12-11T12:05:01Z date_published: 2008-08-01T00:00:00Z date_updated: 2023-02-23T11:41:29Z day: '01' doi: 10.1145/1360612.1360646 extern: '1' intvolume: ' 27' issue: '3' language: - iso: eng main_file_link: - url: http://www.cc.gatech.edu/~turk/my_papers/fast_goop_2008.pdf month: '08' oa_version: None publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '2467' status: public title: Fast viscoelastic behavior with thin features type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2008' ... --- _id: '3825' abstract: - lang: eng text: Fast-spiking parvalbumin-expressing basket cells (BCs) represent a major type of inhibitory interneuron in the hippocampus. These cells inhibit principal cells in a temporally precise manner and are involved in the generation of network oscillations. Although BCs show a unique expression profile of Ca(2+)-permeable receptors, Ca(2+)-binding proteins and Ca(2+)-dependent signalling molecules, physiological Ca(2+) signalling in these interneurons has not been investigated. To study action potential (AP)-induced dendritic Ca(2+) influx and buffering, we combined whole-cell patch-clamp recordings with ratiometric Ca(2+) imaging from the proximal apical dendrites of rigorously identified BCs in acute slices, using the high-affinity Ca(2+) indicator fura-2 or the low-affinity dye fura-FF. Single APs evoked dendritic Ca(2+) transients with small amplitude. Bursts of APs evoked Ca(2+) transients with amplitudes that increased linearly with AP number. Analysis of Ca(2+) transients under steady-state conditions with different fura-2 concentrations and during loading with 200 microm fura-2 indicated that the endogenous Ca(2+)-binding ratio was approximately 200 (kappa(S) = 202 +/- 26 for the loading experiments). The peak amplitude of the Ca(2+) transients measured directly with 100 microm fura-FF was 39 nm AP(-1). At approximately 23 degrees C, the decay time constant of the Ca(2+) transients was 390 ms, corresponding to an extrusion rate of approximately 600 s(-1). At 34 degrees C, the decay time constant was 203 ms and the corresponding extrusion rate was approximately 1100 s(-1). At both temperatures, continuous theta-burst activity with three to five APs per theta cycle, as occurs in vivo during exploration, led to a moderate increase in the global Ca(2+) concentration that was proportional to AP number, whereas more intense stimulation was required to reach micromolar Ca(2+) concentrations and to shift Ca(2+) signalling into a non-linear regime. In conclusion, dentate gyrus BCs show a high endogenous Ca(2+)-binding ratio, a small AP-induced dendritic Ca(2+) influx, and a relatively slow Ca(2+) extrusion. These specific buffering properties of BCs will sharpen the time course of local Ca(2+) signals, while prolonging the decay of global Ca(2+) signals. author: - first_name: Yexica full_name: Aponte, Yexica last_name: Aponte - first_name: Josef full_name: Bischofberger, Josef last_name: Bischofberger - 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, Bischofberger J, Jonas PM. Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus. Journal of Physiology. 2008;586(8):2061-2075. doi:10.1113/jphysiol.2007.147298 apa: Aponte, Y., Bischofberger, J., & Jonas, P. M. (2008). Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2007.147298 chicago: Aponte, Yexica, Josef Bischofberger, and Peter M Jonas. “Efficient Ca(2+) Buffering in Fast-Spiking Basket Cells of Rat Hippocampus.” Journal of Physiology. Wiley-Blackwell, 2008. https://doi.org/10.1113/jphysiol.2007.147298. ieee: Y. Aponte, J. Bischofberger, and P. M. Jonas, “Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus,” Journal of Physiology, vol. 586, no. 8. Wiley-Blackwell, pp. 2061–75, 2008. ista: Aponte Y, Bischofberger J, Jonas PM. 2008. Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus. Journal of Physiology. 586(8), 2061–75. mla: Aponte, Yexica, et al. “Efficient Ca(2+) Buffering in Fast-Spiking Basket Cells of Rat Hippocampus.” Journal of Physiology, vol. 586, no. 8, Wiley-Blackwell, 2008, pp. 2061–75, doi:10.1113/jphysiol.2007.147298. short: Y. Aponte, J. Bischofberger, P.M. Jonas, Journal of Physiology 586 (2008) 2061–75. date_created: 2018-12-11T12:05:22Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:52:28Z day: '01' doi: 10.1113/jphysiol.2007.147298 extern: 1 intvolume: ' 586' issue: '8' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2465201/ month: '01' oa: 1 page: 2061 - 75 publication: Journal of Physiology publication_status: published publisher: Wiley-Blackwell publist_id: '2386' quality_controlled: 0 status: public title: Efficient Ca(2+) buffering in fast-spiking basket cells of rat hippocampus type: journal_article volume: 586 year: '2008' ... --- _id: '3822' abstract: - lang: eng text: Dentate gyrus granule cells transmit action potentials (APs) along their unmyelinated mossy fibre axons to the CA3 region. Although the initiation and propagation of APs are fundamental steps during neural computation, little is known about the site of AP initiation and the speed of propagation in mossy fibre axons. To address these questions, we performed simultaneous somatic and axonal whole-cell recordings from granule cells in acute hippocampal slices of adult mice at approximately 23 degrees C. Injection of short current pulses or synaptic stimulation evoked axonal and somatic APs with similar amplitudes. By contrast, the time course was significantly different, as axonal APs had a higher maximal rate of rise (464 +/- 30 V s(-1) in the axon versus 297 +/- 12 V s(-1) in the soma, mean +/- s.e.m.). Furthermore, analysis of latencies between the axonal and somatic signals showed that APs were initiated in the proximal axon at approximately 20-30 mum distance from the soma, and propagated orthodromically with a velocity of 0.24 m s(-1). Qualitatively similar results were obtained at a recording temperature of approximately 34 degrees C. Modelling of AP propagation in detailed cable models of granule cells suggested that a approximately 4 times higher Na(+) channel density ( approximately 1000 pS mum(-2)) in the axon might account for both the higher rate of rise of axonal APs and the robust AP initiation in the proximal mossy fibre axon. This may be of critical importance to separate dendritic integration of thousands of synaptic inputs from the generation and transmission of a common AP output. author: - first_name: Christoph full_name: Schmidt-Hieber, Christoph last_name: Schmidt Hieber - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Josef full_name: Bischofberger, Josef last_name: Bischofberger citation: ama: Schmidt Hieber C, Jonas PM, Bischofberger J. Action potential initiation and propagation in hippocampal mossy fibre axons. Journal of Physiology. 2008;586(7):1849-1857. doi:10.1113/jphysiol.2007.150151 apa: Schmidt Hieber, C., Jonas, P. M., & Bischofberger, J. (2008). Action potential initiation and propagation in hippocampal mossy fibre axons. Journal of Physiology. Wiley-Blackwell. https://doi.org/10.1113/jphysiol.2007.150151 chicago: Schmidt Hieber, Christoph, Peter M Jonas, and Josef Bischofberger. “Action Potential Initiation and Propagation in Hippocampal Mossy Fibre Axons.” Journal of Physiology. Wiley-Blackwell, 2008. https://doi.org/10.1113/jphysiol.2007.150151 . ieee: C. Schmidt Hieber, P. M. Jonas, and J. Bischofberger, “Action potential initiation and propagation in hippocampal mossy fibre axons,” Journal of Physiology, vol. 586, no. 7. Wiley-Blackwell, pp. 1849–57, 2008. ista: Schmidt Hieber C, Jonas PM, Bischofberger J. 2008. Action potential initiation and propagation in hippocampal mossy fibre axons. Journal of Physiology. 586(7), 1849–57. mla: Schmidt Hieber, Christoph, et al. “Action Potential Initiation and Propagation in Hippocampal Mossy Fibre Axons.” Journal of Physiology, vol. 586, no. 7, Wiley-Blackwell, 2008, pp. 1849–57, doi:10.1113/jphysiol.2007.150151 . short: C. Schmidt Hieber, P.M. Jonas, J. Bischofberger, Journal of Physiology 586 (2008) 1849–57. date_created: 2018-12-11T12:05:21Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:52:27Z day: '01' doi: '10.1113/jphysiol.2007.150151 ' extern: 1 intvolume: ' 586' issue: '7' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2375716/ month: '01' oa: 1 page: 1849 - 57 publication: Journal of Physiology publication_status: published publisher: Wiley-Blackwell publist_id: '2387' quality_controlled: 0 status: public title: Action potential initiation and propagation in hippocampal mossy fibre axons type: journal_article volume: 586 year: '2008' ... --- _id: '3824' abstract: - lang: eng text: It is generally thought that transmitter release at mammalian central synapses is triggered by Ca2+ microdomains, implying loose coupling between presynaptic Ca2+ channels and Ca2+ sensors of exocytosis. Here we show that Ca2+ channel subunit immunoreactivity is highly concentrated in the active zone of GABAergic presynaptic terminals of putative parvalbumin-containing basket cells in the hippocampus. Paired recording combined with presynaptic patch pipette perfusion revealed that GABA release at basket cell-granule cell synapses is sensitive to millimolar concentrations of the fast Ca2+ chelator BAPTA but insensitive to the slow Ca2+ chelator EGTA. These results show that Ca2+ source and Ca2+ sensor are tightly coupled at this synapse, with distances in the range of 10-20 nm. Models of Ca2+ inflow-exocytosis coupling further reveal that the tightness of coupling increases efficacy, speed, and temporal precision of transmitter release. Thus, tight coupling contributes to fast feedforward and feedback inhibition in the hippocampal network. author: - first_name: Iancu full_name: Bucurenciu, Iancu last_name: Bucurenciu - first_name: Ákos full_name: Kulik, Ákos last_name: Kulik - first_name: Beat full_name: Schwaller, Beat last_name: Schwaller - 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: Bucurenciu I, Kulik Á, Schwaller B, Frotscher M, Jonas PM. Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse. Neuron. 2008;57(4):536-545. doi:10.1016/j.neuron.2007.12.026 apa: Bucurenciu, I., Kulik, Á., Schwaller, B., Frotscher, M., & Jonas, P. M. (2008). Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2007.12.026 chicago: Bucurenciu, Iancu, Ákos Kulik, Beat Schwaller, Michael Frotscher, and Peter M Jonas. “Nanodomain Coupling between Ca(2+) Channels and Ca2+ Sensors Promotes Fast and Efficient Transmitter Release at a Cortical GABAergic Synapse.” Neuron. Elsevier, 2008. https://doi.org/10.1016/j.neuron.2007.12.026. ieee: I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, and P. M. Jonas, “Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse,” Neuron, vol. 57, no. 4. Elsevier, pp. 536–45, 2008. ista: Bucurenciu I, Kulik Á, Schwaller B, Frotscher M, Jonas PM. 2008. Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse. Neuron. 57(4), 536–45. mla: Bucurenciu, Iancu, et al. “Nanodomain Coupling between Ca(2+) Channels and Ca2+ Sensors Promotes Fast and Efficient Transmitter Release at a Cortical GABAergic Synapse.” Neuron, vol. 57, no. 4, Elsevier, 2008, pp. 536–45, doi:10.1016/j.neuron.2007.12.026. short: I. Bucurenciu, Á. Kulik, B. Schwaller, M. Frotscher, P.M. Jonas, Neuron 57 (2008) 536–45. date_created: 2018-12-11T12:05:22Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:52:27Z day: '01' doi: 10.1016/j.neuron.2007.12.026 extern: 1 intvolume: ' 57' issue: '4' month: '01' page: 536 - 45 publication: Neuron publication_status: published publisher: Elsevier publist_id: '2385' quality_controlled: 0 status: public title: Nanodomain coupling between Ca(2+) channels and Ca2+ sensors promotes fast and efficient transmitter release at a cortical GABAergic synapse type: journal_article volume: 57 year: '2008' ... --- _id: '3823' abstract: - lang: eng text: Two studies in this issue of Neuron (Kwon and Castillo and Rebola et al.) show that the mossy fiber-CA3 pyramidal neuron synapse, a hippocampal synapse well known for its presynaptic plasticity, exhibits a novel form of long-term potentiation of NMDAR-mediated currents, which is induced and expressed postsynaptically. author: - first_name: Angharad full_name: Kerr, Angharad M last_name: Kerr - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Kerr A, Jonas PM. The two sides of hippocampal mossy fiber plasticity (Review). Neuron. 2008;57(1):5-7. doi:10.1016/j.neuron.2007.12.015 apa: Kerr, A., & Jonas, P. M. (2008). The two sides of hippocampal mossy fiber plasticity (Review). Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2007.12.015 chicago: Kerr, Angharad, and Peter M Jonas. “The Two Sides of Hippocampal Mossy Fiber Plasticity (Review).” Neuron. Elsevier, 2008. https://doi.org/10.1016/j.neuron.2007.12.015. ieee: A. Kerr and P. M. Jonas, “The two sides of hippocampal mossy fiber plasticity (Review),” Neuron, vol. 57, no. 1. Elsevier, pp. 5–7, 2008. ista: Kerr A, Jonas PM. 2008. The two sides of hippocampal mossy fiber plasticity (Review). Neuron. 57(1), 5–7. mla: Kerr, Angharad, and Peter M. Jonas. “The Two Sides of Hippocampal Mossy Fiber Plasticity (Review).” Neuron, vol. 57, no. 1, Elsevier, 2008, pp. 5–7, doi:10.1016/j.neuron.2007.12.015. short: A. Kerr, P.M. Jonas, Neuron 57 (2008) 5–7. date_created: 2018-12-11T12:05:22Z date_published: 2008-01-10T00:00:00Z date_updated: 2021-01-12T07:52:27Z day: '10' doi: 10.1016/j.neuron.2007.12.015 extern: 1 intvolume: ' 57' issue: '1' month: '01' page: 5 - 7 publication: Neuron publication_status: published publisher: Elsevier publist_id: '2388' quality_controlled: 0 status: public title: The two sides of hippocampal mossy fiber plasticity (Review) type: journal_article volume: 57 year: '2008' ... --- _id: '3880' abstract: - lang: eng text: We consider imperfect-information parity games in which strategies rely on observations that provide imperfect information about the history of a play. To solve such games, i.e., to determine the winning regions of players and corresponding winning strategies, one can use the subset construction to build an equivalent perfect-information game. Recently, an algorithm that avoids the inefficient subset construction has been proposed. The algorithm performs a fixed-point computation in a lattice of antichains, thus maintaining a succinct representation of state sets. However, this representation does not allow to recover winning strategies. In this paper, we build on the antichain approach to develop an algorithm for constructing the winning strategies in parity games of imperfect information. We have implemented this algorithm as a prototype. To our knowledge, this is the first implementation of a procedure for solving imperfect-information parity games on graphs. alternative_title: - LNCS author: - first_name: Dietmar full_name: Berwanger, Dietmar last_name: Berwanger - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Sangram full_name: Raje, Sangram last_name: Raje citation: ama: 'Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. Strategy construction for parity games with imperfect information. In: Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:325-339. doi:10.1007/978-3-540-85361-9' apa: 'Berwanger, D., Chatterjee, K., Doyen, L., Henzinger, T. A., & Raje, S. (2008). Strategy construction for parity games with imperfect information (Vol. 5201, pp. 325–339). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-85361-9' chicago: Berwanger, Dietmar, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger, and Sangram Raje. “Strategy Construction for Parity Games with Imperfect Information,” 5201:325–39. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9. ieee: 'D. Berwanger, K. Chatterjee, L. Doyen, T. A. Henzinger, and S. Raje, “Strategy construction for parity games with imperfect information,” presented at the CONCUR: Concurrency Theory, 2008, vol. 5201, pp. 325–339.' ista: 'Berwanger D, Chatterjee K, Doyen L, Henzinger TA, Raje S. 2008. Strategy construction for parity games with imperfect information. CONCUR: Concurrency Theory, LNCS, vol. 5201, 325–339.' mla: Berwanger, Dietmar, et al. Strategy Construction for Parity Games with Imperfect Information. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 325–39, doi:10.1007/978-3-540-85361-9. short: D. Berwanger, K. Chatterjee, L. Doyen, T.A. Henzinger, S. Raje, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 325–339. conference: name: 'CONCUR: Concurrency Theory' date_created: 2018-12-11T12:05:40Z date_published: 2008-07-30T00:00:00Z date_updated: 2023-02-23T11:46:01Z day: '30' doi: 10.1007/978-3-540-85361-9 extern: 1 intvolume: ' 5201' month: '07' page: 325 - 339 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '2291' quality_controlled: 0 related_material: record: - id: '3863' relation: later_version status: public status: public title: Strategy construction for parity games with imperfect information type: conference volume: 5201 year: '2008' ... --- _id: '3903' abstract: - lang: eng text: "Background\r\n\r\nThe invasive garden ant, Lasius neglectus, is the most recently detected pest ant and the first known invasive ant able to become established and thrive in the temperate regions of Eurasia. In this study, we aim to reconstruct the invasion history of this ant in Europe analysing 14 populations with three complementary approaches: genetic microsatellite analysis, chemical analysis of cuticular hydrocarbon profiles and behavioural observations of aggression behaviour. We evaluate the relative informative power of the three methodological approaches and estimate both the number of independent introduction events from a yet unknown native range somewhere in the Black Sea area, and the invasive potential of the existing introduced populations.\r\n\r\nResults\r\n\r\nThree clusters of genetically similar populations were detected, and all but one population had a similar chemical profile. Aggression between populations could be predicted from their genetic and chemical distance, and two major clusters of non-aggressive groups of populations were found. However, populations of L. neglectus did not separate into clear supercolonial associations, as is typical for other invasive ants.\r\n\r\nConclusion\r\n\r\nThe three methodological approaches gave consistent and complementary results. All joint evidence supports the inference that the 14 introduced populations of L. neglectus in Europe likely arose from only very few independent introductions from the native range, and that new infestations were typically started through introductions from other invasive populations. This indicates that existing introduced populations have a very high invasive potential when the ants are inadvertently spread by human transport. " author: - 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: Falko full_name: Drijfhout, Falko last_name: Drijfhout - first_name: Daniel full_name: Kronauer, Daniel last_name: Kronauer - first_name: Jacobus full_name: Boomsma, Jacobus last_name: Boomsma - first_name: Jes full_name: Pedersen, Jes last_name: Pedersen - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: 'Ugelvig LV, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches. BMC Biology. 2008;6(11). doi:10.1186/1741-7007-6-11' apa: 'Ugelvig, L. V., Drijfhout, F., Kronauer, D., Boomsma, J., Pedersen, J., & Cremer, S. (2008). The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches. BMC Biology. BioMed Central. https://doi.org/10.1186/1741-7007-6-11' chicago: 'Ugelvig, Line V, Falko Drijfhout, Daniel Kronauer, Jacobus Boomsma, Jes Pedersen, and Sylvia Cremer. “The Introduction History of Invasive Garden Ants in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology. BioMed Central, 2008. https://doi.org/10.1186/1741-7007-6-11.' ieee: 'L. V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, and S. Cremer, “The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches,” BMC Biology, vol. 6, no. 11. BioMed Central, 2008.' ista: 'Ugelvig LV, Drijfhout F, Kronauer D, Boomsma J, Pedersen J, Cremer S. 2008. The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches. BMC Biology. 6(11).' mla: 'Ugelvig, Line V., et al. “The Introduction History of Invasive Garden Ants in Europe: Integrating Genetic, Chemical and Behavioural Approaches.” BMC Biology, vol. 6, no. 11, BioMed Central, 2008, doi:10.1186/1741-7007-6-11.' short: L.V. Ugelvig, F. Drijfhout, D. Kronauer, J. Boomsma, J. Pedersen, S. Cremer, BMC Biology 6 (2008). date_created: 2018-12-11T12:05:48Z date_published: 2008-02-26T00:00:00Z date_updated: 2021-01-12T07:53:05Z day: '26' doi: 10.1186/1741-7007-6-11 extern: '1' intvolume: ' 6' issue: '11' language: - iso: eng month: '02' oa_version: None publication: BMC Biology publication_status: published publisher: BioMed Central publist_id: '2249' status: public title: 'The introduction history of invasive garden ants in Europe: integrating genetic, chemical and behavioural approaches' 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 user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2008' ... --- _id: '3905' abstract: - lang: eng text: Winged and wingless males coexist in the ant Cardiocondyla obscurior. Wingless (“ergatoid”) males never leave their maternal colony and fight remorselessly among each other for the access to emerging females. The peaceful winged males disperse after about 10 days, but beforehand also mate in the nest. In the first 5 days of their life, winged males perform a chemical female mimicry that protects them against attack and even makes them sexually attractive to ergatoid males. When older, the chemical profile of winged males no longer matches that of virgin females; nevertheless, they are still tolerated, which so far has been puzzling. Contrasting this general pattern, we have identified a single aberrant colony in which all winged males were attacked and killed by the ergatoid males. A comparative analysis of the morphology and chemical profile of these untypical attacked winged males and the tolerated males from several normal colonies revealed that normal old males are still performing some chemical mimicry to the virgin queens, though less perfect than in their young ages. The anomalous attacked winged males, on the other hand, had a very different odour to the females. Our study thus exemplifies that the analysis of rare malfunctioning can add valuable insight on functioning under normal conditions and allows the conclusion that older winged males from normal colonies of the ant C. obscurior are guarded through an imperfect chemical female mimicry, still close enough to protect against attacks by the wingless fighters yet dissimilar enough not to elicit their sexual interest. author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Patrizia full_name: D'Ettorre, Patrizia last_name: D'Ettorre - first_name: Falko full_name: Drijfhout, Falko last_name: Drijfhout - first_name: Matthew full_name: Sledge, Matthew last_name: Sledge - first_name: Stefano full_name: Turillazzi, Stefano last_name: Turillazzi - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze citation: ama: Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften. 2008;95(11):1101-1105. doi:10.1007/s00114-008-0430-8 apa: Cremer, S., D’Ettorre, P., Drijfhout, F., Sledge, M., Turillazzi, S., & Heinze, J. (2008). Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften. Springer. https://doi.org/10.1007/s00114-008-0430-8 chicago: Cremer, Sylvia, Patrizia D’Ettorre, Falko Drijfhout, Matthew Sledge, Stefano Turillazzi, and Jürgen Heinze. “Imperfect Chemical Female Mimicry in Males of the Ant Cardiocondyla Obscurior.” Naturwissenschaften. Springer, 2008. https://doi.org/10.1007/s00114-008-0430-8. ieee: S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, and J. Heinze, “Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior,” Naturwissenschaften, vol. 95, no. 11. Springer, pp. 1101–1105, 2008. ista: Cremer S, D’Ettorre P, Drijfhout F, Sledge M, Turillazzi S, Heinze J. 2008. Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior. Naturwissenschaften. 95(11), 1101–1105. mla: Cremer, Sylvia, et al. “Imperfect Chemical Female Mimicry in Males of the Ant Cardiocondyla Obscurior.” Naturwissenschaften, vol. 95, no. 11, Springer, 2008, pp. 1101–05, doi:10.1007/s00114-008-0430-8. short: S. Cremer, P. D’Ettorre, F. Drijfhout, M. Sledge, S. Turillazzi, J. Heinze, Naturwissenschaften 95 (2008) 1101–1105. date_created: 2018-12-11T12:05:48Z date_published: 2008-08-05T00:00:00Z date_updated: 2021-01-12T07:53:06Z day: '05' doi: 10.1007/s00114-008-0430-8 extern: '1' intvolume: ' 95' issue: '11' language: - iso: eng month: '08' oa_version: None page: 1101 - 1105 publication: Naturwissenschaften publication_status: published publisher: Springer publist_id: '2246' status: public title: Imperfect chemical female mimicry in males of the ant Cardiocondyla obscurior type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 95 year: '2008' ... --- _id: '3907' abstract: - lang: eng text: 'Wingless males of the ant genus Cardiocondyla engage in fatal fighting for access to female sexual nestmates. Older, heavily sclerotized males are usually capable of eliminating all younger rivals, whose cuticle is still soft. In Cardiocondyla sp. A, this type of local mate competition (LMC) has turned the standard pattern of brood production of social insects upside down, in that mother queens in multi-queen colonies produce extremely long-lived sons very early in the life cycle of the colony. Here, we investigated the emergence pattern of sexuals in two species with LMC, in which males are much less long-lived. Queens of Cardiocondyla obscurior and Cardiocondyla minutior reared their first sons significantly earlier in multi-queen than in single-queen societies. In addition, first female sexuals also emerged earlier in multi-queen colonies, so that early males had mating opportunities. Hence, the timing of sexual production appears to be well predicted by evolutionary theory, in particular by local mate and queen–queen competition. ' author: - first_name: Masaki full_name: Suefuji, Masaki last_name: Suefuji - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jan full_name: Oettler, Jan last_name: Oettler - first_name: Jürgen full_name: Heinze, Jürgen last_name: Heinze citation: ama: Suefuji M, Cremer S, Oettler J, Heinze J. Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters. 2008;4(6):670-673. doi:10.1098/rsbl.2008.0355 apa: Suefuji, M., Cremer, S., Oettler, J., & Heinze, J. (2008). Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters. Royal Society, The. https://doi.org/10.1098/rsbl.2008.0355 chicago: Suefuji, Masaki, Sylvia Cremer, Jan Oettler, and Jürgen Heinze. “Queen Number Influences the Timing of the Sexual Production in Colonies of Cardiocondyla Ants.” Biology Letters. Royal Society, The, 2008. https://doi.org/10.1098/rsbl.2008.0355. ieee: M. Suefuji, S. Cremer, J. Oettler, and J. Heinze, “Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants,” Biology Letters, vol. 4, no. 6. Royal Society, The, pp. 670–673, 2008. ista: Suefuji M, Cremer S, Oettler J, Heinze J. 2008. Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants. Biology Letters. 4(6), 670–673. mla: Suefuji, Masaki, et al. “Queen Number Influences the Timing of the Sexual Production in Colonies of Cardiocondyla Ants.” Biology Letters, vol. 4, no. 6, Royal Society, The, 2008, pp. 670–73, doi:10.1098/rsbl.2008.0355. short: M. Suefuji, S. Cremer, J. Oettler, J. Heinze, Biology Letters 4 (2008) 670–673. date_created: 2018-12-11T12:05:49Z date_published: 2008-12-23T00:00:00Z date_updated: 2021-01-12T07:53:07Z day: '23' doi: 10.1098/rsbl.2008.0355 extern: '1' intvolume: ' 4' issue: '6' language: - iso: eng month: '12' oa_version: None page: 670 - 673 publication: Biology Letters publication_status: published publisher: Royal Society, The publist_id: '2248' status: public title: Queen number influences the timing of the sexual production in colonies of Cardiocondyla ants type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2008' ... --- _id: '3906' acknowledgement: 'Funding was obtained from the European Community: FP5 EU research-training network ‘INSECTS’ (JJB SC PD FPD DPH) and FP6 Individual Marie Curie EIF grant (SC), the Alexander-von-Humboldt Foundation (Feodor-Lynen postdoctoral stipend to SC), the Danish Natural Science Research Council (JSP), the Danish National Research Foundation (JJB DRN JSP), and the Austrian Science Fund (BCS FMS CS HK).' 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: Falko full_name: Drijfhout, Falko last_name: Drijfhout - first_name: Birgit full_name: Schlick Steiner, Birgit last_name: Schlick Steiner - first_name: Florian full_name: Steiner, Florian last_name: Steiner - first_name: Bernhard full_name: Seifert, Bernhard last_name: Seifert - first_name: David full_name: Hughes, David last_name: Hughes - first_name: Andreas full_name: Schulz, Andreas last_name: Schulz - first_name: Klaus full_name: Petersen, Klaus last_name: Petersen - first_name: Heino full_name: Konrad, Heino last_name: Konrad - first_name: Christian full_name: Stauffer, Christian last_name: Stauffer - first_name: Kadri full_name: Kiran, Kadri last_name: Kiran - first_name: Xavier full_name: Espadaler, Xavier last_name: Espadaler - first_name: Patrizia full_name: D'Ettorre, Patrizia last_name: D'Ettorre - first_name: Nihat full_name: Aktaç, Nihat last_name: Aktaç - first_name: Jørgen full_name: Eilenberg, Jørgen last_name: Eilenberg - first_name: Graeme full_name: Jones, Graeme last_name: Jones - first_name: David full_name: Nash, David last_name: Nash - first_name: Jes full_name: Pedersen, Jes last_name: Pedersen - first_name: Jacobus full_name: Boomsma, Jacobus last_name: Boomsma citation: ama: Cremer S, Ugelvig LV, Drijfhout F, et al. The evolution of invasiveness in garden ants. PLoS One. 2008;3(12). doi:10.1371/journal.pone.0003838 apa: Cremer, S., Ugelvig, L. V., Drijfhout, F., Schlick Steiner, B., Steiner, F., Seifert, B., … Boomsma, J. (2008). The evolution of invasiveness in garden ants. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0003838 chicago: Cremer, Sylvia, Line V Ugelvig, Falko Drijfhout, Birgit Schlick Steiner, Florian Steiner, Bernhard Seifert, David Hughes, et al. “The Evolution of Invasiveness in Garden Ants.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0003838. ieee: S. Cremer et al., “The evolution of invasiveness in garden ants,” PLoS One, vol. 3, no. 12. Public Library of Science, 2008. ista: Cremer S, Ugelvig LV, Drijfhout F, Schlick Steiner B, Steiner F, Seifert B, Hughes D, Schulz A, Petersen K, Konrad H, Stauffer C, Kiran K, Espadaler X, D’Ettorre P, Aktaç N, Eilenberg J, Jones G, Nash D, Pedersen J, Boomsma J. 2008. The evolution of invasiveness in garden ants. PLoS One. 3(12). mla: Cremer, Sylvia, et al. “The Evolution of Invasiveness in Garden Ants.” PLoS One, vol. 3, no. 12, Public Library of Science, 2008, doi:10.1371/journal.pone.0003838. short: S. Cremer, L.V. Ugelvig, F. Drijfhout, B. Schlick Steiner, F. Steiner, B. Seifert, D. Hughes, A. Schulz, K. Petersen, H. Konrad, C. Stauffer, K. Kiran, X. Espadaler, P. D’Ettorre, N. Aktaç, J. Eilenberg, G. Jones, D. Nash, J. Pedersen, J. Boomsma, PLoS One 3 (2008). date_created: 2018-12-11T12:05:49Z date_published: 2008-12-03T00:00:00Z date_updated: 2021-01-12T07:53:06Z day: '03' doi: 10.1371/journal.pone.0003838 extern: '1' intvolume: ' 3' issue: '12' language: - iso: eng month: '12' oa_version: None publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '2247' status: public title: The evolution of invasiveness in garden ants 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 user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2008' ... --- _id: '3939' abstract: - lang: eng text: The priming of a T cell results from its physical interaction with a dendritic cell (DC) that presents the cognate antigenic peptide. The success rate of such interactions is extremely low, because the precursor frequency of a naive T cell recognizing a specific antigen is in the range of 1:10(5)-10(6). To make this principle practicable, encounter frequencies between DCs and T cells are maximized within lymph nodes (LNs) that are compact immunological projections of the peripheral tissue they drain. But LNs are more than passive meeting places for DCs that immigrated from the tissue and lymphocytes that recirculated via the blood. The microanatomy of the LN stroma actively organizes the cellular encounters by providing preformed migration tracks that create dynamic but highly ordered movement patterns. LN architecture further acts as a sophisticated filtration system that sieves the incoming interstitial fluid at different levels and guarantees that immunologically relevant antigens are loaded on DCs or B cells while inert substances are channeled back into the blood circulation. This review focuses on the non-hematopoietic infrastructure of the lymph node. We describe the association between fibroblastic reticular cell, conduit, DC, and T cell as the essential functional unit of the T-cell cortex. author: - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Lämmermann T, Sixt MK. The microanatomy of T-cell responses. Immunological Reviews. 2008;221(1):26-43. doi:10.1111/j.1600-065X.2008.00592.x apa: Lämmermann, T., & Sixt, M. K. (2008). The microanatomy of T-cell responses. Immunological Reviews. Wiley-Blackwell. https://doi.org/10.1111/j.1600-065X.2008.00592.x chicago: Lämmermann, Tim, and Michael K Sixt. “The Microanatomy of T-Cell Responses.” Immunological Reviews. Wiley-Blackwell, 2008. https://doi.org/10.1111/j.1600-065X.2008.00592.x. ieee: T. Lämmermann and M. K. Sixt, “The microanatomy of T-cell responses,” Immunological Reviews, vol. 221, no. 1. Wiley-Blackwell, pp. 26–43, 2008. ista: Lämmermann T, Sixt MK. 2008. The microanatomy of T-cell responses. Immunological Reviews. 221(1), 26–43. mla: Lämmermann, Tim, and Michael K. Sixt. “The Microanatomy of T-Cell Responses.” Immunological Reviews, vol. 221, no. 1, Wiley-Blackwell, 2008, pp. 26–43, doi:10.1111/j.1600-065X.2008.00592.x. short: T. Lämmermann, M.K. Sixt, Immunological Reviews 221 (2008) 26–43. date_created: 2018-12-11T12:06:00Z date_published: 2008-02-07T00:00:00Z date_updated: 2021-01-12T07:53:20Z day: '07' doi: 10.1111/j.1600-065X.2008.00592.x extern: '1' intvolume: ' 221' issue: '1' language: - iso: eng month: '02' oa_version: None page: 26 - 43 publication: Immunological Reviews publication_status: published publisher: Wiley-Blackwell publist_id: '2187' status: public title: The microanatomy of T-cell responses type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 221 year: '2008' ... --- _id: '3940' abstract: - lang: eng text: Until recently little information was available on the molecular details of the extracellular matrix (ECM) of secondary lymphoid tissues. There is now growing evidence that these ECMs are unique structures, combining characteristics of basement membranes and interstitial or fibrillar matrices, resulting in scaffolds that are strong and highly flexible and, in certain secondary lymphoid compartments, also forming conduit networks for rapid fluid transport. This review will address the structural characteristics of the ECM of the murine spleen and its potential role as an organizer of immune cell compartments, with reference to the lymph node where relevant. author: - first_name: Zerina full_name: Lokmic, Zerina last_name: Lokmic - first_name: Tim full_name: Lämmermann, Tim last_name: Lämmermann - first_name: Michael K full_name: Michael Sixt id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Susanna full_name: Cardell, Susanna last_name: Cardell - first_name: Rupert full_name: Hallmann, Rupert last_name: Hallmann - first_name: Lydia full_name: Sorokin, Lydia last_name: Sorokin citation: ama: Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. The extracellular matrix of the spleen as a potential organizer of immune cell compartments. Seminars in Immunology. 2008;20(1):4-13. doi:10.1016/j.smim.2007.12.009 apa: Lokmic, Z., Lämmermann, T., Sixt, M. K., Cardell, S., Hallmann, R., & Sorokin, L. (2008). The extracellular matrix of the spleen as a potential organizer of immune cell compartments. Seminars in Immunology. Academic Press. https://doi.org/10.1016/j.smim.2007.12.009 chicago: Lokmic, Zerina, Tim Lämmermann, Michael K Sixt, Susanna Cardell, Rupert Hallmann, and Lydia Sorokin. “The Extracellular Matrix of the Spleen as a Potential Organizer of Immune Cell Compartments.” Seminars in Immunology. Academic Press, 2008. https://doi.org/10.1016/j.smim.2007.12.009. ieee: Z. Lokmic, T. Lämmermann, M. K. Sixt, S. Cardell, R. Hallmann, and L. Sorokin, “The extracellular matrix of the spleen as a potential organizer of immune cell compartments,” Seminars in Immunology, vol. 20, no. 1. Academic Press, pp. 4–13, 2008. ista: Lokmic Z, Lämmermann T, Sixt MK, Cardell S, Hallmann R, Sorokin L. 2008. The extracellular matrix of the spleen as a potential organizer of immune cell compartments. Seminars in Immunology. 20(1), 4–13. mla: Lokmic, Zerina, et al. “The Extracellular Matrix of the Spleen as a Potential Organizer of Immune Cell Compartments.” Seminars in Immunology, vol. 20, no. 1, Academic Press, 2008, pp. 4–13, doi:10.1016/j.smim.2007.12.009. short: Z. Lokmic, T. Lämmermann, M.K. Sixt, S. Cardell, R. Hallmann, L. Sorokin, Seminars in Immunology 20 (2008) 4–13. date_created: 2018-12-11T12:06:00Z date_published: 2008-02-01T00:00:00Z date_updated: 2021-01-12T07:53:20Z day: '01' doi: 10.1016/j.smim.2007.12.009 extern: 1 intvolume: ' 20' issue: '1' month: '02' page: 4 - 13 publication: Seminars in Immunology publication_status: published publisher: Academic Press publist_id: '2188' quality_controlled: 0 status: public title: The extracellular matrix of the spleen as a potential organizer of immune cell compartments type: journal_article volume: 20 year: '2008' ... --- _id: '3970' abstract: - lang: eng text: 'While genome-wide gene expression data are generated at an increasing rate, the repertoire of approaches for pattern discovery in these data is still limited. Identifying subtle patterns of interest in large amounts of data (tens of thousands of profiles) associated with a certain level of noise remains a challenge. A microarray time series was recently generated to study the transcriptional program of the mouse segmentation clock, a biological oscillator associated with the periodic formation of the segments of the body axis. A method related to Fourier analysis, the Lomb-Scargle periodogram, was used to detect periodic profiles in the dataset, leading to the identification of a novel set of cyclic genes associated with the segmentation clock. Here, we applied to the same microarray time series dataset four distinct mathematical methods to identify significant patterns in gene expression profiles. These methods are called: Phase consistency, Address reduction, Cyclohedron test and Stable persistence, and are based on different conceptual frameworks that are either hypothesis- or data-driven. Some of the methods, unlike Fourier transforms, are not dependent on the assumption of periodicity of the pattern of interest. Remarkably, these methods identified blindly the expression profiles of known cyclic genes as the most significant patterns in the dataset. Many candidate genes predicted by more than one approach appeared to be true positive cyclic genes and will be of particular interest for future research. In addition, these methods predicted novel candidate cyclic genes that were consistent with previous biological knowledge and experimental validation in mouse embryos. Our results demonstrate the utility of these novel pattern detection strategies, notably for detection of periodic profiles, and suggest that combining several distinct mathematical approaches to analyze microarray datasets is a valuable strategy for identifying genes that exhibit novel, interesting transcriptional patterns.' acknowledgement: This research was partially supported by DARPA grant HR 0011-05-1-0057. HE and YM mathematical work was supported by DARPA grant HR0011-05-1-0007. AS research was supported by a Lucent Technologies Bell Labs Graduate Research. Fellowship; AK and MR research was supported by NIH grant GM U54 GM74942; and SA research was supported by Association pour la Recherche sur le Cancer (ARC), France. OP, AM, MLD, EG and GH research was supported by the Stowers Institute for Medical Research. OP is a Howard Hughes Medical Institute Investigator. author: - first_name: Mary full_name: Dequéant, Mary-Lee last_name: Dequéant - first_name: Sebastian full_name: Ahnert, Sebastian last_name: Ahnert - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Thomas full_name: Fink, Thomas M last_name: Fink - first_name: Earl full_name: Glynn, Earl F last_name: Glynn - first_name: Gaye full_name: Hattem, Gaye last_name: Hattem - first_name: Andrzej full_name: Kudlicki, Andrzej last_name: Kudlicki - first_name: Yuriy full_name: Mileyko, Yuriy last_name: Mileyko - first_name: Jason full_name: Morton, Jason last_name: Morton - first_name: Arcady full_name: Mushegian, Arcady R last_name: Mushegian - first_name: Lior full_name: Pachter, Lior last_name: Pachter - first_name: Maga full_name: Rowicka, Maga last_name: Rowicka - first_name: Anne full_name: Shiu, Anne last_name: Shiu - first_name: Bernd full_name: Sturmfels, Bernd last_name: Sturmfels - first_name: Olivier full_name: Pourquie, Olivier last_name: Pourquie citation: ama: Dequéant M, Ahnert S, Edelsbrunner H, et al. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. 2008;3(8). doi:10.1371/journal.pone.0002856 apa: Dequéant, M., Ahnert, S., Edelsbrunner, H., Fink, T., Glynn, E., Hattem, G., … Pourquie, O. (2008). Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0002856 chicago: Dequéant, Mary, Sebastian Ahnert, Herbert Edelsbrunner, Thomas Fink, Earl Glynn, Gaye Hattem, Andrzej Kudlicki, et al. “Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock.” PLoS One. Public Library of Science, 2008. https://doi.org/10.1371/journal.pone.0002856. ieee: M. Dequéant et al., “Comparison of pattern detection methods in microarray time series of the segmentation clock,” PLoS One, vol. 3, no. 8. Public Library of Science, 2008. ista: Dequéant M, Ahnert S, Edelsbrunner H, Fink T, Glynn E, Hattem G, Kudlicki A, Mileyko Y, Morton J, Mushegian A, Pachter L, Rowicka M, Shiu A, Sturmfels B, Pourquie O. 2008. Comparison of pattern detection methods in microarray time series of the segmentation clock. PLoS One. 3(8). mla: Dequéant, Mary, et al. “Comparison of Pattern Detection Methods in Microarray Time Series of the Segmentation Clock.” PLoS One, vol. 3, no. 8, Public Library of Science, 2008, doi:10.1371/journal.pone.0002856. short: M. Dequéant, S. Ahnert, H. Edelsbrunner, T. Fink, E. Glynn, G. Hattem, A. Kudlicki, Y. Mileyko, J. Morton, A. Mushegian, L. Pachter, M. Rowicka, A. Shiu, B. Sturmfels, O. Pourquie, PLoS One 3 (2008). date_created: 2018-12-11T12:06:11Z date_published: 2008-08-06T00:00:00Z date_updated: 2021-01-12T07:53:33Z day: '06' doi: 10.1371/journal.pone.0002856 extern: 1 intvolume: ' 3' issue: '8' month: '08' publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '2157' quality_controlled: 0 status: public title: Comparison of pattern detection methods in microarray time series of the segmentation clock 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: '2008' ... --- _id: '3971' abstract: - lang: eng text: The Reeb graph is a useful tool in visualizing real-valued data obtained from computational simulations of physical processes. We characterize the evolution of the Reeb graph of a time-varying continuous function defined in three-dimensional space. We show how to maintain the Reeb graph over time and compress the entire sequence of Reeb graphs into a single, partially persistent data structure, and augment this data structure with Betti numbers to describe the topology of level sets and with path seeds to assist in the fast extraction of level sets for visualization. author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer - first_name: Ajith full_name: Mascarenhas, Ajith last_name: Mascarenhas - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci - first_name: Jack full_name: Snoeyink, Jack last_name: Snoeyink citation: ama: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. 2008;41(3):149-166. doi:10.1016/j.comgeo.2007.11.001' apa: 'Edelsbrunner, H., Harer, J., Mascarenhas, A., Pascucci, V., & Snoeyink, J. (2008). Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2007.11.001' chicago: 'Edelsbrunner, Herbert, John Harer, Ajith Mascarenhas, Valerio Pascucci, and Jack Snoeyink. “Time-Varying Reeb Graphs for Continuous Space-Time Data.” Computational Geometry: Theory and Applications. Elsevier, 2008. https://doi.org/10.1016/j.comgeo.2007.11.001.' ieee: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, and J. Snoeyink, “Time-varying Reeb graphs for continuous space-time data,” Computational Geometry: Theory and Applications, vol. 41, no. 3. Elsevier, pp. 149–166, 2008.' ista: 'Edelsbrunner H, Harer J, Mascarenhas A, Pascucci V, Snoeyink J. 2008. Time-varying Reeb graphs for continuous space-time data. Computational Geometry: Theory and Applications. 41(3), 149–166.' mla: 'Edelsbrunner, Herbert, et al. “Time-Varying Reeb Graphs for Continuous Space-Time Data.” Computational Geometry: Theory and Applications, vol. 41, no. 3, Elsevier, 2008, pp. 149–66, doi:10.1016/j.comgeo.2007.11.001.' short: 'H. Edelsbrunner, J. Harer, A. Mascarenhas, V. Pascucci, J. Snoeyink, Computational Geometry: Theory and Applications 41 (2008) 149–166.' date_created: 2018-12-11T12:06:12Z date_published: 2008-11-01T00:00:00Z date_updated: 2021-01-12T07:53:34Z day: '01' doi: 10.1016/j.comgeo.2007.11.001 extern: 1 intvolume: ' 41' issue: '3' month: '11' page: 149 - 166 publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '2158' quality_controlled: 0 status: public title: Time-varying Reeb graphs for continuous space-time data type: journal_article volume: 41 year: '2008' ... --- _id: '3969' abstract: - lang: eng text: Persistent homology is an algebraic tool for measuring topological features of shapes and functions. It casts the multi-scale organization we frequently observe in nature into a mathematical formalism. Here we give a record of the short history of persistent homology and present its basic concepts. Besides the mathematics we focus on algorithms and mention the various connections to applications, including to biomolecules, biological networks, data analysis, and geometric modeling. acknowledgement: Supported in part by DARPA under grants HR0011-05-1-0007 and HR0011-05-0057 and by the NSF under grant DBI-06-06873. alternative_title: - Contemporary Mathematics author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: John full_name: Harer, John last_name: Harer citation: ama: 'Edelsbrunner H, Harer J. Persistent homology - a survey. In: Surveys on Discrete and Computational Geometry: Twenty Years Later. American Mathematical Society; 2008:257-282.' apa: 'Edelsbrunner, H., & Harer, J. (2008). Persistent homology - a survey. In Surveys on Discrete and Computational Geometry: Twenty Years Later (pp. 257–282). American Mathematical Society.' chicago: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” In Surveys on Discrete and Computational Geometry: Twenty Years Later, 257–82. American Mathematical Society, 2008.' ieee: 'H. Edelsbrunner and J. Harer, “Persistent homology - a survey,” in Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–282.' ista: 'Edelsbrunner H, Harer J. 2008.Persistent homology - a survey. In: Surveys on Discrete and Computational Geometry: Twenty Years Later. Contemporary Mathematics, , 257–282.' mla: 'Edelsbrunner, Herbert, and John Harer. “Persistent Homology - a Survey.” Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–82.' short: 'H. Edelsbrunner, J. Harer, in:, Surveys on Discrete and Computational Geometry: Twenty Years Later, American Mathematical Society, 2008, pp. 257–282.' date_created: 2018-12-11T12:06:11Z date_published: 2008-03-28T00:00:00Z date_updated: 2021-01-12T07:53:33Z day: '28' extern: 1 month: '03' page: 257 - 282 publication: 'Surveys on Discrete and Computational Geometry: Twenty Years Later' publication_status: published publisher: American Mathematical Society publist_id: '2156' quality_controlled: 0 status: public title: Persistent homology - a survey type: book_chapter year: '2008' ... --- _id: '4141' abstract: - lang: eng text: The zyxin-related LPP protein is localized at focal adhesions and cell-cell contacts and is involved in the regulation of smooth muscle cell migration. A known interaction partner of LPP in human is the tumor suppressor protein SCRIB. Knocking down scrib expression c uring zebrafish embryonic development results in defects of convergence and extension (C&E) movements, which occur during gastrulation and mediate elongation of the anterior-posterior body axis. Mediolateral cell polarization underlying C&E is regulated by a noncanonical Writ signaling pathway constituting the vertebrate planar cell polarity (PCP) pathway. Here, we investigated the role of Lpp during early zebrafish development. We show that morpholino knockdown of Ipp results in defects of C&E, phenocopying noncanonical Wnt signaling mutants. Time-lapse analysis associates the defective dorsal convergence movements with a reduced ability to migrate along straight paths. In addition, expression of Lpp is significantly reduced in Wnt11 morphants and in embryos overexpressing Wnt11 or a dominant-negative form of Rho kinase 2, which is a downstream effector of Wnt11, Suggesting that Lpp expression is dependent on noncanonical Wnt signaling. Finally, we demonstrate that Lpp interacts with the PCP protein Scrib in zebrafish, and that Lpp and Scrib cooperate for the mediation of C&E. (C) 2008 Elsevier Inc. All rights reserved. article_processing_charge: No author: - first_name: Hilke full_name: Vervenne, Hilke last_name: Vervenne - first_name: Koen full_name: Crombez, Koen last_name: Crombez - first_name: Kathleen full_name: Lambaerts, Kathleen last_name: Lambaerts - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - 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 - first_name: Wim full_name: Van De Ven, Wim last_name: Van De Ven - first_name: Marleen full_name: Petit, Marleen last_name: Petit citation: ama: Vervenne H, Crombez K, Lambaerts K, et al. Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. 2008;320(1):267-277. doi:10.1016/j.ydbio.2008.05.529 apa: Vervenne, H., Crombez, K., Lambaerts, K., Carvalho, L., Köppen, M., Heisenberg, C.-P. J., … Petit, M. (2008). Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2008.05.529 chicago: Vervenne, Hilke, Koen Crombez, Kathleen Lambaerts, Lara Carvalho, Mathias Köppen, Carl-Philipp J Heisenberg, Wim Van De Ven, and Marleen Petit. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.” Developmental Biology. Elsevier, 2008. https://doi.org/10.1016/j.ydbio.2008.05.529. ieee: H. Vervenne et al., “Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation,” Developmental Biology, vol. 320, no. 1. Elsevier, pp. 267–277, 2008. ista: Vervenne H, Crombez K, Lambaerts K, Carvalho L, Köppen M, Heisenberg C-PJ, Van De Ven W, Petit M. 2008. Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation. Developmental Biology. 320(1), 267–277. mla: Vervenne, Hilke, et al. “Lpp Is Involved in Wnt/PCP Signaling and Acts Together with Scrib to Mediate Convergence and Extension Movements during Zebrafish Gastrulation.” Developmental Biology, vol. 320, no. 1, Elsevier, 2008, pp. 267–77, doi:10.1016/j.ydbio.2008.05.529. short: H. Vervenne, K. Crombez, K. Lambaerts, L. Carvalho, M. Köppen, C.-P.J. Heisenberg, W. Van De Ven, M. Petit, Developmental Biology 320 (2008) 267–277. date_created: 2018-12-11T12:07:11Z date_published: 2008-08-01T00:00:00Z date_updated: 2021-01-12T07:54:48Z day: '01' doi: 10.1016/j.ydbio.2008.05.529 extern: '1' intvolume: ' 320' issue: '1' language: - iso: eng month: '08' oa_version: None page: 267 - 277 publication: Developmental Biology publication_status: published publisher: Elsevier publist_id: '1978' status: public title: Lpp is involved in Wnt/PCP signaling and acts together with Scrib to mediate convergence and extension movements during zebrafish gastrulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 320 year: '2008' ... --- _id: '4161' abstract: - lang: eng text: Handedness of the vertebrate body plan critically depends on transient embryonic structures/ organs that generate cilia-dependent leftward fluid flow within constrained extracellular environments. Although the function of ciliated organs in laterality determination has been extensively studied, how they are formed during embryogenesis is still poorly understood. Here we show that Kupffer's vesicle (KV), the zebrafish organ of laterality, arises from a surface epithelium previously thought to adopt exclusively extra-embryonic fates. Live multi-photon confocal imaging reveals that surface epithelial cells undergo Nodal/TGF beta signalling-dependent ingression at the dorsal germ ring margin prior to gastrulation, to give rise to dorsal forerunner cells (DFCs), the precursors of KV. DFCs then migrate attached to the overlying surface epithelium and rearrange into rosette-like epithelial structures at the end of gastrulation. During early somitogenesis, these epithelial rosettes coalesce into a single rosette that differentiates into the KV with a ciliated lumen at its apical centre. Our results provide novel insights into the morphogenetic transformations that shape the laterality organ in zebrafish and suggest a conserved progenitor role of the surface epithelium during laterality organ formation in vertebrates. article_processing_charge: No author: - first_name: Pablo full_name: Oteíza, Pablo last_name: Oteíza - first_name: Mathias full_name: Köppen, Mathias last_name: Köppen - first_name: Miguel full_name: Concha, Miguel last_name: Concha - 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: Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. Origin and shaping of the laterality organ in zebrafish. Development. 2008;135(16):2807-2813. doi:10.1242/dev.022228 apa: Oteíza, P., Köppen, M., Concha, M., & Heisenberg, C.-P. J. (2008). Origin and shaping of the laterality organ in zebrafish. Development. Company of Biologists. https://doi.org/10.1242/dev.022228 chicago: Oteíza, Pablo, Mathias Köppen, Miguel Concha, and Carl-Philipp J Heisenberg. “Origin and Shaping of the Laterality Organ in Zebrafish.” Development. Company of Biologists, 2008. https://doi.org/10.1242/dev.022228. ieee: P. Oteíza, M. Köppen, M. Concha, and C.-P. J. Heisenberg, “Origin and shaping of the laterality organ in zebrafish,” Development, vol. 135, no. 16. Company of Biologists, pp. 2807–2813, 2008. ista: Oteíza P, Köppen M, Concha M, Heisenberg C-PJ. 2008. Origin and shaping of the laterality organ in zebrafish. Development. 135(16), 2807–2813. mla: Oteíza, Pablo, et al. “Origin and Shaping of the Laterality Organ in Zebrafish.” Development, vol. 135, no. 16, Company of Biologists, 2008, pp. 2807–13, doi:10.1242/dev.022228. short: P. Oteíza, M. Köppen, M. Concha, C.-P.J. Heisenberg, Development 135 (2008) 2807–2813. date_created: 2018-12-11T12:07:19Z date_published: 2008-08-15T00:00:00Z date_updated: 2021-01-12T07:54:57Z day: '15' doi: 10.1242/dev.022228 extern: '1' intvolume: ' 135' issue: '16' language: - iso: eng month: '08' oa_version: None page: 2807 - 2813 publication: Development publication_status: published publisher: Company of Biologists publist_id: '1956' status: public title: Origin and shaping of the laterality organ in zebrafish type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2008' ... --- _id: '4190' abstract: - lang: eng text: During vertebrate gastrulation, cells forming the prechordal plate undergo directed migration as a cohesive cluster. Recent studies revealed that E-cadherin-mediated coherence between these cells plays an important role in effective anterior migration, and that platelet-derived growth factor (Pdgf) appears to act as a guidance cue in this process. However, the mechanisms underlying this process at the individual cell level remain poorly understood. We have identified miles apart (mil) as a suppressor of defective anterior migration of the prospective prechordal plate in silberblick (slb)/wnt11 mutant embryos, in which E-cadherin-mediated coherence of cell movement is reduced. mil encodes Edg5, a sphingosine-1-phosphate (S1P) receptor belonging to a family of five G-protein-coupled receptors (S1PRs). S1P is a lipid signalling molecule that has been implicated in regulating cytoskeletal rearrangements, cell motility and cell adhesion in a variety of cell types. We examined the roles of Mil in anterior migration of prechordal plate progenitor cells and found that, in slb embryos injected with mil-MO, cells migrate with increased motility but decreased directionality, without restoring the coherence of cell migration. This indicates that prechordal plate progenitor cells can migrate effectively as individuals, as well as in a coherent cluster of cells. Moreover, we demonstrate that Mil regulates cell motility and polarisation through Pdgf and its intracellular effecter PI3K, but modulates cell coherence independently of the Pdgf/PI3K pathway, thus co-ordinating cell motility and coherence. These results suggest that the net migration of prechordal plate progenitors is determined by different parameters, including motility, persistence and coherence. article_processing_charge: No author: - first_name: Masatake full_name: Kai, Masatake last_name: Kai - 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: Masazumi full_name: Tada, Masazumi last_name: Tada citation: ama: Kai M, Heisenberg C-PJ, Tada M. Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. 2008;135(18):3043-3051. doi:10.1242/dev.020396 apa: Kai, M., Heisenberg, C.-P. J., & Tada, M. (2008). Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. Company of Biologists. https://doi.org/10.1242/dev.020396 chicago: Kai, Masatake, Carl-Philipp J Heisenberg, and Masazumi Tada. “Sphingosine-1-Phosphate Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” Development. Company of Biologists, 2008. https://doi.org/10.1242/dev.020396. ieee: M. Kai, C.-P. J. Heisenberg, and M. Tada, “Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation,” Development, vol. 135, no. 18. Company of Biologists, pp. 3043–3051, 2008. ista: Kai M, Heisenberg C-PJ, Tada M. 2008. Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation. Development. 135(18), 3043–3051. mla: Kai, Masatake, et al. “Sphingosine-1-Phosphate Receptors Regulate Individual Cell Behaviours Underlying the Directed Migration of Prechordal Plate Progenitor Cells during Zebrafish Gastrulation.” Development, vol. 135, no. 18, Company of Biologists, 2008, pp. 3043–51, doi:10.1242/dev.020396. short: M. Kai, C.-P.J. Heisenberg, M. Tada, Development 135 (2008) 3043–3051. date_created: 2018-12-11T12:07:29Z date_published: 2008-09-15T00:00:00Z date_updated: 2021-01-12T07:55:11Z day: '15' doi: 10.1242/dev.020396 extern: '1' intvolume: ' 135' issue: '18' language: - iso: eng month: '09' oa_version: None page: 3043 - 3051 publication: Development publication_status: published publisher: Company of Biologists publist_id: '1928' status: public title: Sphingosine-1-phosphate receptors regulate individual cell behaviours underlying the directed migration of prechordal plate progenitor cells during zebrafish gastrulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2008' ... --- _id: '4384' abstract: - lang: eng text: |- Model checking software transactional memories (STMs) is difficult because of the unbounded number, length, and delay of concurrent transactions and the unbounded size of the memory. We show that, under certain conditions, the verification problem can be reduced to a finite-state problem, and we illustrate the use of the method by proving the correctness of several STMs, including two-phase locking, DSTM, TL2, and optimistic concurrency control. The safety properties we consider include strict serializability and opacity; the liveness properties include obstruction freedom, livelock freedom, and wait freedom. Our main contribution lies in the structure of the proofs, which are largely automated and not restricted to the STMs mentioned above. In a first step we show that every STM that enjoys certain structural properties either violates a safety or liveness requirement on some program with two threads and two shared variables, or satisfies the requirement on all programs. In the second step we use a model checker to prove the requirement for the STM applied to a most general program with two threads and two variables. In the safety case, the model checker constructs a simulation relation between two carefully constructed finite-state transition systems, one representing the given STM applied to a most general program, and the other representing a most liberal safe STM applied to the same program. In the liveness case, the model checker analyzes fairness conditions on the given STM transition system. author: - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Barbara full_name: Jobstmann, Barbara last_name: Jobstmann - first_name: Vasu full_name: Vasu Singh id: 4DAE2708-F248-11E8-B48F-1D18A9856A87 last_name: Singh citation: ama: 'Guerraoui R, Henzinger TA, Jobstmann B, Singh V. Model checking transactional memories. In: ACM; 2008:372-382. doi:10.1145/1375581.1375626' apa: 'Guerraoui, R., Henzinger, T. A., Jobstmann, B., & Singh, V. (2008). Model checking transactional memories (pp. 372–382). Presented at the PLDI: Programming Languages Design and Implementation, ACM. https://doi.org/10.1145/1375581.1375626' chicago: Guerraoui, Rachid, Thomas A Henzinger, Barbara Jobstmann, and Vasu Singh. “Model Checking Transactional Memories,” 372–82. ACM, 2008. https://doi.org/10.1145/1375581.1375626. ieee: 'R. Guerraoui, T. A. Henzinger, B. Jobstmann, and V. Singh, “Model checking transactional memories,” presented at the PLDI: Programming Languages Design and Implementation, 2008, pp. 372–382.' ista: 'Guerraoui R, Henzinger TA, Jobstmann B, Singh V. 2008. Model checking transactional memories. PLDI: Programming Languages Design and Implementation, 372–382.' mla: Guerraoui, Rachid, et al. Model Checking Transactional Memories. ACM, 2008, pp. 372–82, doi:10.1145/1375581.1375626. short: R. Guerraoui, T.A. Henzinger, B. Jobstmann, V. Singh, in:, ACM, 2008, pp. 372–382. conference: name: 'PLDI: Programming Languages Design and Implementation' date_created: 2018-12-11T12:08:34Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:56:34Z day: '01' doi: 10.1145/1375581.1375626 extern: 1 file: - access_level: open_access checksum: 1238258a27f212fc1a2050a9a246da20 content_type: application/pdf creator: system date_created: 2018-12-12T10:14:05Z date_updated: 2020-07-14T12:46:28Z file_id: '5054' file_name: IST-2012-74-v1+1_Model_checking_transactional_memories.pdf file_size: 201583 relation: main_file file_date_updated: 2020-07-14T12:46:28Z main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/model_checking_transactional_memories.pdf month: '01' oa: 1 page: 372 - 382 publication_status: published publisher: ACM publist_id: '1073' quality_controlled: 0 status: public title: Model checking transactional memories type: conference year: '2008' ... --- _id: '4386' abstract: - lang: eng text: We introduce the notion of permissiveness in transactional memories (TM). Intuitively, a TM is permissive if it never aborts a transaction when it need not. More specifically, a TM is permissive with respect to a safety property p if the TM accepts every history that satisfies p. Permissiveness, like safety and liveness, can be used as a metric to compare TMs. We illustrate that it is impractical to achieve permissiveness deterministically, and then show how randomization can be used to achieve permissiveness efficiently. We introduce Adaptive Validation STM (AVSTM), which is probabilistically permissive with respect to opacity; that is, every opaque history is accepted by AVSTM with positive probability. Moreover, AVSTM guarantees lock freedom. Owing to its permissiveness, AVSTM outperforms other STMs by up to 40% in read dominated workloads in high contention scenarios. But, in low contention scenarios, the book-keeping done by AVSTM to achieve permissiveness makes AVSTM, on average, 20-30% worse than existing STMs. acknowledgement: This research was supported by the Swiss National Science Foundation. alternative_title: - LNCS author: - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Vasu full_name: Vasu Singh id: 4DAE2708-F248-11E8-B48F-1D18A9856A87 last_name: Singh citation: ama: 'Guerraoui R, Henzinger TA, Singh V. Permissiveness in transactional memories. In: Vol 5218. Springer; 2008:305-319. doi:10.1007/978-3-540-87779-0_21' apa: 'Guerraoui, R., Henzinger, T. A., & Singh, V. (2008). Permissiveness in transactional memories (Vol. 5218, pp. 305–319). Presented at the DISC: Distributed Computing, Springer. https://doi.org/10.1007/978-3-540-87779-0_21' chicago: Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Permissiveness in Transactional Memories,” 5218:305–19. Springer, 2008. https://doi.org/10.1007/978-3-540-87779-0_21. ieee: 'R. Guerraoui, T. A. Henzinger, and V. Singh, “Permissiveness in transactional memories,” presented at the DISC: Distributed Computing, 2008, vol. 5218, pp. 305–319.' ista: 'Guerraoui R, Henzinger TA, Singh V. 2008. Permissiveness in transactional memories. DISC: Distributed Computing, LNCS, vol. 5218, 305–319.' mla: Guerraoui, Rachid, et al. Permissiveness in Transactional Memories. Vol. 5218, Springer, 2008, pp. 305–19, doi:10.1007/978-3-540-87779-0_21. short: R. Guerraoui, T.A. Henzinger, V. Singh, in:, Springer, 2008, pp. 305–319. conference: name: 'DISC: Distributed Computing' date_created: 2018-12-11T12:08:35Z date_published: 2008-09-10T00:00:00Z date_updated: 2021-01-12T07:56:35Z day: '10' doi: 10.1007/978-3-540-87779-0_21 extern: 1 intvolume: ' 5218' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/permissiveness_in_transactional_memories.pdf month: '09' page: 305 - 319 publication_status: published publisher: Springer publist_id: '1072' quality_controlled: 0 status: public title: Permissiveness in transactional memories type: conference volume: 5218 year: '2008' ... --- _id: '4387' abstract: - lang: eng text: Software transactional memory (STM) offers a disciplined concurrent programming model for exploiting the parallelism of modern processor architectures. This paper presents the first deterministic specification automata for strict serializability and opacity in STMs. Using an antichain-based tool, we show our deterministic specifications to be equivalent to more intuitive, nondeterministic specification automata (which are too large to be determinized automatically). Using deterministic specification automata, we obtain a complete verification tool for STMs. We also show how to model and verify contention management within STMs. We automatically check the opacity of popular STM algorithms, such as TL2 and DSTM, with a universal contention manager. The universal contention manager is nondeterministic and establishes correctness for all possible contention management schemes. acknowledgement: This research was supported by the Swiss National Science Foundation. alternative_title: - LNCS author: - first_name: Rachid full_name: Guerraoui, Rachid last_name: Guerraoui - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Vasu full_name: Vasu Singh id: 4DAE2708-F248-11E8-B48F-1D18A9856A87 last_name: Singh citation: ama: 'Guerraoui R, Henzinger TA, Singh V. Completeness and nondeterminism in model checking transactional memories. In: Vol 5201. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2008:21-35. doi:10.1007/978-3-540-85361-9_6' apa: 'Guerraoui, R., Henzinger, T. A., & Singh, V. (2008). Completeness and nondeterminism in model checking transactional memories (Vol. 5201, pp. 21–35). Presented at the CONCUR: Concurrency Theory, Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.1007/978-3-540-85361-9_6' chicago: Guerraoui, Rachid, Thomas A Henzinger, and Vasu Singh. “Completeness and Nondeterminism in Model Checking Transactional Memories,” 5201:21–35. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008. https://doi.org/10.1007/978-3-540-85361-9_6. ieee: 'R. Guerraoui, T. A. Henzinger, and V. Singh, “Completeness and nondeterminism in model checking transactional memories,” presented at the CONCUR: Concurrency Theory, 2008, vol. 5201, pp. 21–35.' ista: 'Guerraoui R, Henzinger TA, Singh V. 2008. Completeness and nondeterminism in model checking transactional memories. CONCUR: Concurrency Theory, LNCS, vol. 5201, 21–35.' mla: Guerraoui, Rachid, et al. Completeness and Nondeterminism in Model Checking Transactional Memories. Vol. 5201, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 21–35, doi:10.1007/978-3-540-85361-9_6. short: R. Guerraoui, T.A. Henzinger, V. Singh, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2008, pp. 21–35. conference: name: 'CONCUR: Concurrency Theory' date_created: 2018-12-11T12:08:35Z date_published: 2008-07-30T00:00:00Z date_updated: 2021-01-12T07:56:35Z day: '30' doi: 10.1007/978-3-540-85361-9_6 extern: 1 intvolume: ' 5201' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/completeness_and_nondeterminism_in_model_checking_transactional_memories.pdf month: '07' page: 21 - 35 publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '1071' quality_controlled: 0 status: public title: Completeness and nondeterminism in model checking transactional memories type: conference volume: 5201 year: '2008' ... --- _id: '4397' alternative_title: - LNCS 5123 author: - first_name: Dirk full_name: Beyer, Dirk last_name: Beyer - first_name: Damien full_name: Damien Zufferey id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar citation: ama: 'Beyer D, Zufferey D, Majumdar R. CSIsat: Interpolation for LA+EUF. In: Springer; 2008:304-308.' apa: 'Beyer, D., Zufferey, D., & Majumdar, R. (2008). CSIsat: Interpolation for LA+EUF (pp. 304–308). Presented at the CAV: Computer Aided Verification, Springer.' chicago: 'Beyer, Dirk, Damien Zufferey, and Ritankar Majumdar. “CSIsat: Interpolation for LA+EUF,” 304–8. Springer, 2008.' ieee: 'D. Beyer, D. Zufferey, and R. Majumdar, “CSIsat: Interpolation for LA+EUF,” presented at the CAV: Computer Aided Verification, 2008, pp. 304–308.' ista: 'Beyer D, Zufferey D, Majumdar R. 2008. CSIsat: Interpolation for LA+EUF. CAV: Computer Aided Verification, LNCS 5123, , 304–308.' mla: 'Beyer, Dirk, et al. CSIsat: Interpolation for LA+EUF. Springer, 2008, pp. 304–08.' short: D. Beyer, D. Zufferey, R. Majumdar, in:, Springer, 2008, pp. 304–308. conference: name: 'CAV: Computer Aided Verification' date_created: 2018-12-11T12:08:38Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:56:40Z day: '01' extern: 1 month: '01' page: 304 - 308 publication_status: published publisher: Springer publist_id: '1060' quality_controlled: 0 status: public title: 'CSIsat: Interpolation for LA+EUF' type: conference year: '2008' ... --- _id: '4400' author: - first_name: Adam full_name: Aviv,Adam J. last_name: Aviv - first_name: Pavol full_name: Pavol Cerny id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Sandy full_name: Clark,Sandy last_name: Clark - first_name: Eric full_name: Cronin,Eric last_name: Cronin - first_name: Gaurav full_name: Shah,Gaurav last_name: Shah - first_name: Micah full_name: Sherr,Micah last_name: Sherr - first_name: Matt full_name: Blaze,Matt last_name: Blaze citation: ama: 'Aviv A, Cerny P, Clark S, et al. Security Evaluation of ES&S Voting Machines and Election Management System. In: USENIX; 2008. doi:1545' apa: Aviv, A., Cerny, P., Clark, S., Cronin, E., Shah, G., Sherr, M., & Blaze, M. (2008). Security Evaluation of ES&S Voting Machines and Election Management System. Presented at the Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08, USENIX. https://doi.org/1545 chicago: Aviv, Adam, Pavol Cerny, Sandy Clark, Eric Cronin, Gaurav Shah, Micah Sherr, and Matt Blaze. “Security Evaluation of ES&S Voting Machines and Election Management System.” USENIX, 2008. https://doi.org/1545. ieee: A. Aviv et al., “Security Evaluation of ES&S Voting Machines and Election Management System,” presented at the Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08, 2008. ista: Aviv A, Cerny P, Clark S, Cronin E, Shah G, Sherr M, Blaze M. 2008. Security Evaluation of ES&S Voting Machines and Election Management System. Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08. mla: Aviv, Adam, et al. Security Evaluation of ES&S Voting Machines and Election Management System. USENIX, 2008, doi:1545. short: A. Aviv, P. Cerny, S. Clark, E. Cronin, G. Shah, M. Sherr, M. Blaze, in:, USENIX, 2008. conference: name: Usenix/ Accurate Electronic Voting Technology Workshop (EVT) 08 date_created: 2018-12-11T12:08:39Z date_published: 2008-07-29T00:00:00Z date_updated: 2021-01-12T07:56:42Z day: '29' doi: '1545' extern: 1 main_file_link: - open_access: '0' url: http://www.usenix.org/event/evt08/tech/full_papers/aviv/aviv.pdf month: '07' publication_status: published publisher: USENIX publist_id: '1057' quality_controlled: 0 status: public title: Security Evaluation of ES&S Voting Machines and Election Management System type: conference year: '2008' ... --- _id: '4409' abstract: - lang: eng text: "Models of timed systems must incorporate not only the sequence of system events, but the timings of these events as well to capture the real-time aspects of physical systems. Timed automata are models of real-time systems in which states consist of discrete locations and values for real-time clocks. The presence of real-time clocks leads to an uncountable state space. This thesis studies verification problems on timed automata in a game theoretic framework.\r\n\r\nFor untimed systems, two systems are close if every sequence of events of one system is also observable in the second system. For timed systems, the difference in timings of the two corresponding sequences is also of importance. We propose the notion of bisimulation distance which quantifies timing differences; if the bisimulation distance between two systems is epsilon, then (a) every sequence of events of one system has a corresponding matching sequence in the other, and (b) the timings of matching events in between the two corresponding traces do not differ by more than epsilon. We show that we can compute the bisimulation distance between two timed automata to within any desired degree of accuracy. We also show that the timed verification logic TCTL is robust with respect to our notion of quantitative bisimilarity, in particular, if a system satisfies a formula, then every close system satisfies a close formula.\r\n\r\nTimed games are used for distinguishing between the actions of several agents, typically a controller and an environment. The controller must achieve its objective against all possible choices of the environment. The modeling of the passage of time leads to the presence of zeno executions, and corresponding unrealizable strategies of the controller which may achieve objectives by blocking time. We disallow such unreasonable strategies by restricting all agents to use only receptive strategies --strategies which while not being required to ensure time divergence by any agent, are such that no agent is responsible for blocking time. Time divergence is guaranteed when all players use receptive strategies. We show that timed automaton games with receptive strategies can be solved by a reduction to finite state turn based game graphs. We define the logic timed alternating-time temporal logic for verification of timed automaton games and show that the logic can be model checked in EXPTIME. We also show that the minimum time required by an agent to reach a desired location, and the maximum time an agent can stay safe within a set of locations, against all possible actions of its adversaries are both computable.\r\n\r\nWe next study the memory requirements of winning strategies for timed automaton games. We prove that finite memory strategies suffice for safety objectives, and that winning strategies for reachability objectives may require infinite memory in general. We introduce randomized strategies in which an agent can propose a probabilistic distribution of moves and show that finite memory randomized strategies suffice for all omega-regular objectives. We also show that while randomization helps in simplifying winning strategies, and thus allows the construction of simpler controllers, it does not help a player in winning at more states, and thus does not allow the construction of more powerful controllers.\r\n\r\nFinally we study robust winning strategies in timed games. In a physical system, a controller may propose an action together with a time delay, but the action cannot be assumed to be executed at the exact proposed time delay. We present robust strategies which incorporate such jitters and show that the set of states from which an agent can win robustly is computable." article_processing_charge: No author: - first_name: Vinayak full_name: Prabhu, Vinayak last_name: Prabhu citation: ama: Prabhu V. Games for the verification of timed systems. 2008:1-137. apa: Prabhu, V. (2008). Games for the verification of timed systems. University of California, Berkeley. chicago: Prabhu, Vinayak. “Games for the Verification of Timed Systems.” University of California, Berkeley, 2008. ieee: V. Prabhu, “Games for the verification of timed systems,” University of California, Berkeley, 2008. ista: Prabhu V. 2008. Games for the verification of timed systems. University of California, Berkeley. mla: Prabhu, Vinayak. Games for the Verification of Timed Systems. University of California, Berkeley, 2008, pp. 1–137. short: V. Prabhu, Games for the Verification of Timed Systems, University of California, Berkeley, 2008. date_created: 2018-12-11T12:08:42Z date_published: 2008-09-01T00:00:00Z date_updated: 2022-02-14T14:35:11Z day: '01' degree_awarded: PhD extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www2.eecs.berkeley.edu/Pubs/TechRpts/2008/EECS-2008-97.html month: '09' oa: 1 oa_version: None page: 1 - 137 publication_status: published publisher: University of California, Berkeley publist_id: '319' status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: John full_name: Steel, John last_name: Steel - first_name: Pravin full_name: Varaiya, Pravin last_name: Varaiya title: Games for the verification of timed systems type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2008' ... --- _id: '4415' abstract: - lang: eng text: 'Many computing applications, especially those in safety critical embedded systems, require highly predictable timing properties. However, time is often not present in the prevailing computing and networking abstractions. In fact, most advances in computer architecture, software, and networking favor average-case performance over timing predictability. This thesis studies several methods for the design of concurrent and/or distributed embedded systems with precise timing guarantees. The focus is on flexible and compositional methods for programming and verification of the timing properties. The presented methods together with related formalisms cover two levels of design: (1) Programming language/model level. We propose the distributed variant of Giotto, a coordination programming language with an explicit temporal semantics—the logical execution time (LET) semantics. The LET of a task is an interval of time that specifies the time instants at which task inputs and outputs become available (task release and termination instants). The LET of a task is always non-zero. This allows us to communicate values across the network without changing the timing information of the task, and without introducing nondeterminism. We show how this methodology supports distributed code generation for distributed real-time systems. The method gives up some performance in favor of composability and predictability. We characterize the tradeoff by comparing the LET semantics with the semantics used in Simulink. (2) Abstract task graph level. We study interface-based design and verification of applications represented with task graphs. We consider task sequence graphs with general event models, and cyclic graphs with periodic event models with jitter and phase. Here an interface of a component exposes time and resource constraints of the component. Together with interfaces we formally define interface composition operations and the refinement relation. For efficient and flexible composability checking two properties are important: incremental design and independent refinement. According to the incremental design property the composition of interfaces can be performed in any order, even if interfaces for some components are not known. The refinement relation is defined such that in a design we can always substitute a refined interface for an abstract one. We show that the framework supports independent refinement, i.e., the refinement relation is preserved under composition operations.' acknowledgement: 978-0-549-83480-9 article_processing_charge: No author: - first_name: Slobodan full_name: Matic, Slobodan last_name: Matic citation: ama: Matic S. Compositionality in deterministic real-time embedded systems. 2008:1-148. apa: Matic, S. (2008). Compositionality in deterministic real-time embedded systems. University of California, Berkeley. chicago: Matic, Slobodan. “Compositionality in Deterministic Real-Time Embedded Systems.” University of California, Berkeley, 2008. ieee: S. Matic, “Compositionality in deterministic real-time embedded systems,” University of California, Berkeley, 2008. ista: Matic S. 2008. Compositionality in deterministic real-time embedded systems. University of California, Berkeley. mla: Matic, Slobodan. Compositionality in Deterministic Real-Time Embedded Systems. University of California, Berkeley, 2008, pp. 1–148. short: S. Matic, Compositionality in Deterministic Real-Time Embedded Systems, University of California, Berkeley, 2008. date_created: 2018-12-11T12:08:44Z date_published: 2008-01-01T00:00:00Z date_updated: 2022-02-14T14:08:50Z day: '01' degree_awarded: PhD extern: '1' language: - iso: eng month: '01' oa_version: None page: 1 - 148 publication_status: published publisher: University of California, Berkeley publist_id: '316' status: public supervisor: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Edward full_name: Lee, Edward last_name: Lee - first_name: Raja full_name: Sengupta, Raja last_name: Sengupta title: Compositionality in deterministic real-time embedded systems type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2008' ... --- _id: '4452' abstract: - lang: eng text: We describe Valigator, a software tool for imperative program verification that efficiently combines symbolic computation and automated reasoning in a uniform framework. The system offers support for automatically generating and proving verification conditions and, most importantly, for automatically inferring loop invariants and bound assertions by means of symbolic summation, Gröbner basis computation, and quantifier elimination. We present general principles of the implementation and illustrate them on examples. acknowledgement: This research was supported by the Swiss NSF. alternative_title: - LNCS author: - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Thibaud full_name: Hottelier, Thibaud last_name: Hottelier - first_name: Laura full_name: Kovács, Laura last_name: Kovács citation: ama: 'Henzinger TA, Hottelier T, Kovács L. Valigator: A verification tool with bound and invariant generation. In: Vol 5330. Springer; 2008:333-342. doi:10.1007/978-3-540-89439-1_24' apa: 'Henzinger, T. A., Hottelier, T., & Kovács, L. (2008). Valigator: A verification tool with bound and invariant generation (Vol. 5330, pp. 333–342). Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Springer. https://doi.org/10.1007/978-3-540-89439-1_24' chicago: 'Henzinger, Thomas A, Thibaud Hottelier, and Laura Kovács. “Valigator: A Verification Tool with Bound and Invariant Generation,” 5330:333–42. Springer, 2008. https://doi.org/10.1007/978-3-540-89439-1_24.' ieee: 'T. A. Henzinger, T. Hottelier, and L. Kovács, “Valigator: A verification tool with bound and invariant generation,” presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, 2008, vol. 5330, pp. 333–342.' ista: 'Henzinger TA, Hottelier T, Kovács L. 2008. Valigator: A verification tool with bound and invariant generation. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 5330, 333–342.' mla: 'Henzinger, Thomas A., et al. Valigator: A Verification Tool with Bound and Invariant Generation. Vol. 5330, Springer, 2008, pp. 333–42, doi:10.1007/978-3-540-89439-1_24.' short: T.A. Henzinger, T. Hottelier, L. Kovács, in:, Springer, 2008, pp. 333–342. conference: name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning' date_created: 2018-12-11T12:08:55Z date_published: 2008-11-13T00:00:00Z date_updated: 2021-01-12T07:57:04Z day: '13' doi: 10.1007/978-3-540-89439-1_24 extern: 1 intvolume: ' 5330' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/valigator.pdf month: '11' page: 333 - 342 publication_status: published publisher: Springer publist_id: '277' quality_controlled: 0 status: public title: 'Valigator: A verification tool with bound and invariant generation' type: conference volume: 5330 year: '2008' ... --- _id: '4509' abstract: - lang: eng text: 'I discuss two main challenges in embedded systems design: the challenge to build predictable systems, and that to build robust systems. I suggest how predictability can be formalized as a form of determinism, and robustness as a form of continuity.' author: - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Henzinger TA. Two challenges in embedded systems design: Predictability and robustness. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. 2008;366(1881):3727-3736. doi:10.1098/rsta.2008.0141' apa: 'Henzinger, T. A. (2008). Two challenges in embedded systems design: Predictability and robustness. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rsta.2008.0141' chicago: 'Henzinger, Thomas A. “Two Challenges in Embedded Systems Design: Predictability and Robustness.” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. Royal Society of London, 2008. https://doi.org/10.1098/rsta.2008.0141.' ieee: 'T. A. Henzinger, “Two challenges in embedded systems design: Predictability and robustness,” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, vol. 366, no. 1881. Royal Society of London, pp. 3727–3736, 2008.' ista: 'Henzinger TA. 2008. Two challenges in embedded systems design: Predictability and robustness. Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences. 366(1881), 3727–3736.' mla: 'Henzinger, Thomas A. “Two Challenges in Embedded Systems Design: Predictability and Robustness.” Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences, vol. 366, no. 1881, Royal Society of London, 2008, pp. 3727–36, doi:10.1098/rsta.2008.0141.' short: T.A. Henzinger, Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences 366 (2008) 3727–3736. date_created: 2018-12-11T12:09:13Z date_published: 2008-07-31T00:00:00Z date_updated: 2021-01-12T07:59:19Z day: '31' doi: 10.1098/rsta.2008.0141 extern: 1 intvolume: ' 366' issue: '1881' main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/two_challenges_in_embedded_systems_design.pdf month: '07' page: 3727 - 3736 publication: Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences publication_status: published publisher: Royal Society of London publist_id: '219' quality_controlled: 0 status: public title: 'Two challenges in embedded systems design: Predictability and robustness' type: journal_article volume: 366 year: '2008' ... --- _id: '4524' abstract: - lang: eng text: "Complex requirements, time-to-market pressure and regulatory constraints have made the designing of embedded systems extremely challenging. This is evident by the increase in effort and expenditure for design of safety-driven real-time control-dominated applications like automotive and avionic controllers. Design processes are often challenged by lack of proper programming tools for specifying and verifying critical requirements (e.g. timing and reliability) of such applications. Platform based design, an approach for designing embedded systems, addresses the above concerns by separating requirement from architecture. The requirement specifies the intended behavior of an application while the architecture specifies the guarantees (e.g. execution speed, failure rate etc). An implementation, a mapping of the requirement on the architecture, is then analyzed for correctness. The orthogonalization of concerns makes the specification and analyses simpler. An effective use of such design methodology has been proposed in Logical Execution Time (LET) model of real-time tasks. The model separates the timing requirements (specified by release and termination instances of a task) from the architecture guarantees (specified by worst-case execution time of the task).\r\n\r\nThis dissertation proposes a coordination language, Hierarchical Timing Language (HTL), that captures the timing and reliability requirements of real-time applications. An implementation of the program on an architecture is then analyzed to check whether desired timing and reliability requirements are met or not. The core framework extends the LET model by accounting for reliability and refinement. The reliability model separates the reliability requirements of tasks from the reliability guarantees of the architecture. The requirement expresses the desired long-term reliability while the architecture provides a short-term reliability guarantee (e.g. failure rate for each iteration). The analysis checks if the short-term guarantee ensures the desired long-term reliability. The refinement model allows replacing a task by another task during program execution. Refinement preserves schedulability and reliability, i.e., if a refined task is schedulable and reliable for an implementation, then the refining task is also schedulable and reliable for the implementation. Refinement helps in concise specification without overloading analysis.\r\n\r\nThe work presents the formal model, the analyses (both with and without refinement), and a compiler for HTL programs. The compiler checks composition and refinement constraints, performs schedulability and reliability analyses, and generates code for implementation of an HTL program on a virtual machine. Three real-time controllers, one each from automatic control, automotive control and avionic control, are used to illustrate the steps in modeling and analyzing HTL programs." acknowledgement: 978-0-549-83679-7 article_processing_charge: No author: - first_name: Arkadeb full_name: Ghosal, Arkadeb last_name: Ghosal citation: ama: Ghosal A. A hierarchical coordination language for reliable real-time tasks. 2008:1-210. apa: Ghosal, A. (2008). A hierarchical coordination language for reliable real-time tasks. University of California, Berkeley. chicago: Ghosal, Arkadeb. “A Hierarchical Coordination Language for Reliable Real-Time Tasks.” University of California, Berkeley, 2008. ieee: A. Ghosal, “A hierarchical coordination language for reliable real-time tasks,” University of California, Berkeley, 2008. ista: Ghosal A. 2008. A hierarchical coordination language for reliable real-time tasks. University of California, Berkeley. mla: Ghosal, Arkadeb. A Hierarchical Coordination Language for Reliable Real-Time Tasks. University of California, Berkeley, 2008, pp. 1–210. short: A. Ghosal, A Hierarchical Coordination Language for Reliable Real-Time Tasks, University of California, Berkeley, 2008. date_created: 2018-12-11T12:09:18Z date_published: 2008-01-31T00:00:00Z date_updated: 2021-01-12T07:59:26Z day: '31' extern: '1' language: - iso: eng month: '01' oa_version: None page: 1 - 210 publication_status: published publisher: University of California, Berkeley publist_id: '199' status: public supervisor: - first_name: Alberto full_name: Sangiovanni-Vincentelli, Alberto last_name: Sangiovanni-Vincentelli - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 - first_name: Edward full_name: Lee, Edward last_name: Lee - first_name: Karl full_name: Hedrick, Karl last_name: Hedrick title: A hierarchical coordination language for reliable real-time tasks type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2008' ... --- _id: '4521' abstract: - lang: eng text: The search for proof and the search for counterexamples (bugs) are complementary activities that need to be pursued concurrently in order to maximize the practical success rate of verification tools.While this is well-understood in safety verification, the current focus of liveness verification has been almost exclusively on the search for termination proofs. A counterexample to termination is an infinite programexecution. In this paper, we propose a method to search for such counterexamples. The search proceeds in two phases. We first dynamically enumerate lasso-shaped candidate paths for counterexamples, and then statically prove their feasibility. We illustrate the utility of our nontermination prover, called TNT, on several nontrivial examples, some of which require bit-level reasoning about integer representations. author: - first_name: Ashutosh full_name: Ashutosh Gupta id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Ritankar full_name: Majumdar, Ritankar S last_name: Majumdar - first_name: Andrey full_name: Rybalchenko, Andrey last_name: Rybalchenko - first_name: Ru full_name: Xu, Ru-Gang last_name: Xu citation: ama: 'Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. Proving non-termination. In: ACM; 2008:147-158. doi:10.1145/1328438.1328459' apa: 'Gupta, A., Henzinger, T. A., Majumdar, R., Rybalchenko, A., & Xu, R. (2008). Proving non-termination (pp. 147–158). Presented at the POPL: Principles of Programming Languages, ACM. https://doi.org/10.1145/1328438.1328459' chicago: Gupta, Ashutosh, Thomas A Henzinger, Ritankar Majumdar, Andrey Rybalchenko, and Ru Xu. “Proving Non-Termination,” 147–58. ACM, 2008. https://doi.org/10.1145/1328438.1328459. ieee: 'A. Gupta, T. A. Henzinger, R. Majumdar, A. Rybalchenko, and R. Xu, “Proving non-termination,” presented at the POPL: Principles of Programming Languages, 2008, pp. 147–158.' ista: 'Gupta A, Henzinger TA, Majumdar R, Rybalchenko A, Xu R. 2008. Proving non-termination. POPL: Principles of Programming Languages, 147–158.' mla: Gupta, Ashutosh, et al. Proving Non-Termination. ACM, 2008, pp. 147–58, doi:10.1145/1328438.1328459. short: A. Gupta, T.A. Henzinger, R. Majumdar, A. Rybalchenko, R. Xu, in:, ACM, 2008, pp. 147–158. conference: name: 'POPL: Principles of Programming Languages' date_created: 2018-12-11T12:09:17Z date_published: 2008-01-01T00:00:00Z date_updated: 2021-01-12T07:59:25Z day: '01' doi: 10.1145/1328438.1328459 extern: 1 main_file_link: - open_access: '0' url: http://pub.ist.ac.at/%7Etah/Publications/proving_non-termination.pdf month: '01' page: 147 - 158 publication_status: published publisher: ACM publist_id: '208' quality_controlled: 0 status: public title: Proving non-termination type: conference year: '2008' ...