--- _id: '3183' abstract: - lang: eng text: This paper describes two algorithms capable of real-time segmentation of foreground from background layers in stereo video sequences. Automatic separation of layers from colour/contrast or from stereo alone is known to be error-prone. Here, colour, contrast and stereo matching information are fused to infer layers accurately and efficiently. The first algorithm, Layered Dynamic Programming (LDP), solves stereo in an extended 6-state space that represents both foreground/background layers and occluded regions. The stereo-match likelihood is then fused with a contrast-sensitive colour model that is learned on the fly, and stereo disparities are obtained by dynamic programming. The second algorithm, Layered Graph Cut (LGC), does not directly solve stereo. Instead the stereo match likelihood is marginalised over foreground and background hypotheses, and fused with a contrast-sensitive colour model like the one used in LDP. Segmentation is solved efficiently by ternary graph cut. Both algorithms are evaluated with respect to ground truth data and found to have similar perfomance, substantially better than stereo or colour/contrast alone. However, their characteristics with respect to computational efficiency are rather different. The algorithms are demonstrated in the application of background substitution and shown to give good quality composite video output. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Antonio full_name: Criminisi, Antonio last_name: Criminisi - first_name: Andrew full_name: Blake, Andrew last_name: Blake - first_name: Geoffrey full_name: Cross, Geoffrey last_name: Cross - first_name: Carsten full_name: Rother, Carsten last_name: Rother citation: ama: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. Bi-layer segmentation of binocular stereo video. In: Vol 2. IEEE; 2005:407-414. doi:10.1109/CVPR.2005.91' apa: 'Kolmogorov, V., Criminisi, A., Blake, A., Cross, G., & Rother, C. (2005). Bi-layer segmentation of binocular stereo video (Vol. 2, pp. 407–414). Presented at the CVPR: Computer Vision and Pattern Recognition, IEEE. https://doi.org/10.1109/CVPR.2005.91' chicago: Kolmogorov, Vladimir, Antonio Criminisi, Andrew Blake, Geoffrey Cross, and Carsten Rother. “Bi-Layer Segmentation of Binocular Stereo Video,” 2:407–14. IEEE, 2005. https://doi.org/10.1109/CVPR.2005.91. ieee: 'V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, and C. Rother, “Bi-layer segmentation of binocular stereo video,” presented at the CVPR: Computer Vision and Pattern Recognition, 2005, vol. 2, pp. 407–414.' ista: 'Kolmogorov V, Criminisi A, Blake A, Cross G, Rother C. 2005. Bi-layer segmentation of binocular stereo video. CVPR: Computer Vision and Pattern Recognition vol. 2, 407–414.' mla: Kolmogorov, Vladimir, et al. Bi-Layer Segmentation of Binocular Stereo Video. Vol. 2, IEEE, 2005, pp. 407–14, doi:10.1109/CVPR.2005.91. short: V. Kolmogorov, A. Criminisi, A. Blake, G. Cross, C. Rother, in:, IEEE, 2005, pp. 407–414. conference: name: 'CVPR: Computer Vision and Pattern Recognition' date_created: 2018-12-11T12:01:52Z date_published: 2005-07-25T00:00:00Z date_updated: 2021-01-12T07:41:38Z day: '25' doi: 10.1109/CVPR.2005.91 extern: 1 intvolume: ' 2' main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67281/criminisi_cvpr2005.pdf month: '07' page: 407 - 414 publication_status: published publisher: IEEE publist_id: '3502' quality_controlled: 0 status: public title: Bi-layer segmentation of binocular stereo video type: conference volume: 2 year: '2005' ... --- _id: '3182' abstract: - lang: eng text: In the work of the authors (2003), we showed that graph cuts can find hypersurfaces of globally minimal length (or area) under any Riemannian metric. Here we show that graph cuts on directed regular grids can approximate a significantly more general class of continuous non-symmetric metrics. Using submodularity condition (Boros and Hammer, 2002 and Kolmogorov and Zabih, 2004), we obtain a tight characterization of graph-representable metrics. Such "submodular" metrics have an elegant geometric interpretation via hypersurface functionals combining length/area and flux. Practically speaking, we attend 'geo-cuts' algorithm to a wider class of geometrically motivated hypersurface functionals and show how to globally optimize any combination of length/area and flux of a given vector field. The concept of flux was recently introduced into computer vision by Vasilevskiy and Siddiqi (2002) but it was mainly studied within variational framework so far. We are first to show that flux can be integrated into graph cuts as well. Combining geometric concepts of flux and length/area within the global optimization framework of graph cuts allows principled discrete segmentation models and advances the slate of the art for the graph cuts methods in vision. In particular we address the "shrinking" problem of graph cuts, improve segmentation of long thin objects, and introduce useful shape constraints. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Yuri full_name: Boykov, Yuri last_name: Boykov citation: ama: 'Kolmogorov V, Boykov Y. What metrics can be approximated by geo cuts or global optimization of length area and flux. In: Vol 1. IEEE; 2005:564-571. doi:10.1109/ICCV.2005.252' apa: 'Kolmogorov, V., & Boykov, Y. (2005). What metrics can be approximated by geo cuts or global optimization of length area and flux (Vol. 1, pp. 564–571). Presented at the ICCV: International Conference on Computer Vision, IEEE. https://doi.org/10.1109/ICCV.2005.252' chicago: Kolmogorov, Vladimir, and Yuri Boykov. “What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux,” 1:564–71. IEEE, 2005. https://doi.org/10.1109/ICCV.2005.252. ieee: 'V. Kolmogorov and Y. Boykov, “What metrics can be approximated by geo cuts or global optimization of length area and flux,” presented at the ICCV: International Conference on Computer Vision, 2005, vol. 1, pp. 564–571.' ista: 'Kolmogorov V, Boykov Y. 2005. What metrics can be approximated by geo cuts or global optimization of length area and flux. ICCV: International Conference on Computer Vision vol. 1, 564–571.' mla: Kolmogorov, Vladimir, and Yuri Boykov. What Metrics Can Be Approximated by Geo Cuts or Global Optimization of Length Area and Flux. Vol. 1, IEEE, 2005, pp. 564–71, doi:10.1109/ICCV.2005.252. short: V. Kolmogorov, Y. Boykov, in:, IEEE, 2005, pp. 564–571. conference: name: 'ICCV: International Conference on Computer Vision' date_created: 2018-12-11T12:01:52Z date_published: 2005-12-05T00:00:00Z date_updated: 2021-01-12T07:41:38Z day: '05' doi: 10.1109/ICCV.2005.252 extern: 1 intvolume: ' 1' month: '12' page: 564 - 571 publication_status: published publisher: IEEE publist_id: '3501' quality_controlled: 0 status: public title: What metrics can be approximated by geo cuts or global optimization of length area and flux type: conference volume: 1 year: '2005' ... --- _id: '3181' abstract: - lang: eng text: Tree-reweighted max-product (TRW) message passing [9] is a modified form of the ordinary max-product algorithm for attempting to find minimal energy configurations in Markov random field with cycles. For a TRW fixed point satisfying the strong tree agreement condition, the algorithm outputs a configuration that is provably optimal. In this paper, we focus on the case of binary variables with pairwise couplings, and establish stronger properties of TRW fixed points that satisfy only the milder condition of weak tree agreement (WTA). First, we demonstrate how it is possible to identify part of the optimal solution - i.e., a provably optimal solution for a subset of nodes - without knowing a complete solution. Second, we show that for submodular functions, a WTA fixed point always yields a globally optimal solution. We establish that for binary variables, any WTA fixed point always achieves the global maximum of the linear programming relaxation underlying the TRW method. author: - first_name: Vladimir full_name: Vladimir Kolmogorov id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Martin full_name: Wainwright, Martin J last_name: Wainwright citation: ama: 'Kolmogorov V, Wainwright M. On the optimality of tree reweighted max product message passing. In: AUAI Press; 2005:316-323.' apa: 'Kolmogorov, V., & Wainwright, M. (2005). On the optimality of tree reweighted max product message passing (pp. 316–323). Presented at the UAI: Uncertainty in Artificial Intelligence, AUAI Press.' chicago: Kolmogorov, Vladimir, and Martin Wainwright. “On the Optimality of Tree Reweighted Max Product Message Passing,” 316–23. AUAI Press, 2005. ieee: 'V. Kolmogorov and M. Wainwright, “On the optimality of tree reweighted max product message passing,” presented at the UAI: Uncertainty in Artificial Intelligence, 2005, pp. 316–323.' ista: 'Kolmogorov V, Wainwright M. 2005. On the optimality of tree reweighted max product message passing. UAI: Uncertainty in Artificial Intelligence, 316–323.' mla: Kolmogorov, Vladimir, and Martin Wainwright. On the Optimality of Tree Reweighted Max Product Message Passing. AUAI Press, 2005, pp. 316–23. short: V. Kolmogorov, M. Wainwright, in:, AUAI Press, 2005, pp. 316–323. conference: name: 'UAI: Uncertainty in Artificial Intelligence' date_created: 2018-12-11T12:01:51Z date_published: 2005-07-01T00:00:00Z date_updated: 2021-01-12T07:41:38Z day: '01' extern: 1 main_file_link: - open_access: '0' url: http://research.microsoft.com/pubs/67405/trw_opt_uai05.pdf month: '07' page: 316 - 323 publication_status: published publisher: AUAI Press publist_id: '3500' quality_controlled: 0 status: public title: On the optimality of tree reweighted max product message passing type: conference year: '2005' ... --- _id: '3417' abstract: - lang: eng text: Recently, direct measurements of forces stabilizing single proteins or individual receptor–ligand bonds became possible with ultra-sensitive force probe methods like the atomic force microscope (AFM). In force spectroscopy experiments using AFM, a single molecule or receptor–ligand pair is tethered between the tip of a micromachined cantilever and a supporting surface. While the molecule is stretched, forces are measured by the deflection of the cantilever and plotted against extension, yielding a force spectrum characteristic for each biomolecular system. In order to obtain statistically relevant results, several hundred to thousand single-molecule experiments have to be performed, each resulting in a unique force spectrum. We developed software and algorithms to analyse large numbers of force spectra. Our algorithms include the fitting polymer extension models to force peaks as well as the automatic alignment of spectra. The aligned spectra allowed recognition of patterns of peaks across different spectra. We demonstrate the capabilities of our software by analysing force spectra that were recorded by unfolding single transmembrane proteins such as bacteriorhodopsin and NhaA. Different unfolding pathways were detected by classifying peak patterns. Deviant spectra, e.g. those with no attachment or erratic peaks, can be easily identified. The software is based on the programming language C++, the GNU Scientific Library (GSL), the software WaveMetrics IGOR Pro and available open-source at http://bioinformatics.org/fskit/. author: - first_name: Michael full_name: Kuhn, Michael last_name: Kuhn - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Maurice full_name: Hubain, Maurice last_name: Hubain - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Kuhn M, Janovjak HL, Hubain M, Mueller D. Automated alignment and pattern recognition of single-molecule force spectroscopy data. Journal of Microscopy. 2005;218(2):125-132. doi:10.1111/j.1365-2818.2005.01478.x apa: Kuhn, M., Janovjak, H. L., Hubain, M., & Mueller, D. (2005). Automated alignment and pattern recognition of single-molecule force spectroscopy data. Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/j.1365-2818.2005.01478.x chicago: Kuhn, Michael, Harald L Janovjak, Maurice Hubain, and Daniel Mueller. “Automated Alignment and Pattern Recognition of Single-Molecule Force Spectroscopy Data.” Journal of Microscopy. Wiley-Blackwell, 2005. https://doi.org/10.1111/j.1365-2818.2005.01478.x. ieee: M. Kuhn, H. L. Janovjak, M. Hubain, and D. Mueller, “Automated alignment and pattern recognition of single-molecule force spectroscopy data,” Journal of Microscopy, vol. 218, no. 2. Wiley-Blackwell, pp. 125–132, 2005. ista: Kuhn M, Janovjak HL, Hubain M, Mueller D. 2005. Automated alignment and pattern recognition of single-molecule force spectroscopy data. Journal of Microscopy. 218(2), 125–132. mla: Kuhn, Michael, et al. “Automated Alignment and Pattern Recognition of Single-Molecule Force Spectroscopy Data.” Journal of Microscopy, vol. 218, no. 2, Wiley-Blackwell, 2005, pp. 125–32, doi:10.1111/j.1365-2818.2005.01478.x. short: M. Kuhn, H.L. Janovjak, M. Hubain, D. Mueller, Journal of Microscopy 218 (2005) 125–132. date_created: 2018-12-11T12:03:13Z date_published: 2005-05-01T00:00:00Z date_updated: 2021-01-12T07:43:20Z day: '01' doi: 10.1111/j.1365-2818.2005.01478.x extern: 1 intvolume: ' 218' issue: '2' month: '05' page: 125 - 132 publication: Journal of Microscopy publication_status: published publisher: Wiley-Blackwell publist_id: '2984' quality_controlled: 0 status: public title: Automated alignment and pattern recognition of single-molecule force spectroscopy data type: journal_article volume: 218 year: '2005' ... --- _id: '3416' abstract: - lang: eng text: In the last decade atomic force microscopy has been used to measure the mechanical stability of single proteins. These force spectroscopy experiments have shown that many water-soluble and membrane proteins unfold via one or more intermediates. Recently, Li and co-workers found a linear correlation between the unfolding force of the native state and the intermediate in fibronectin, which they suggested indicated the presence of a molecular memory or multiple unfolding pathways (1). Here, we apply two independent methods in combination with Monte Carlo simulations to analyze the unfolding of α-helices E and D of bacteriorhodopsin (BR). We show that correlation analysis of unfolding forces is very sensitive to errors in force calibration of the instrument. In contrast, a comparison of relative forces provides a robust measure for the stability of unfolding intermediates. The proposed approach detects three energetically different states of α-helices E and D in trimeric BR. These states are not observed for monomeric BR and indicate that substantial information is hidden in forced unfolding experiments of single proteins. author: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Tanuj full_name: Sapra, Tanuj K last_name: Sapra - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Janovjak HL, Sapra T, Mueller D. Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. 2005;88(5):37-39. doi:10.1529/biophysj.105.059774 apa: Janovjak, H. L., Sapra, T., & Mueller, D. (2005). Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. Biophysical Society. https://doi.org/10.1529/biophysj.105.059774 chicago: Janovjak, Harald L, Tanuj Sapra, and Daniel Mueller. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” Biophysical Journal. Biophysical Society, 2005. https://doi.org/10.1529/biophysj.105.059774. ieee: H. L. Janovjak, T. Sapra, and D. Mueller, “Complex stability of single proteins explored by forced unfolding experiments,” Biophysical Journal, vol. 88, no. 5. Biophysical Society, pp. 37–39, 2005. ista: Janovjak HL, Sapra T, Mueller D. 2005. Complex stability of single proteins explored by forced unfolding experiments. Biophysical Journal. 88(5), 37–39. mla: Janovjak, Harald L., et al. “Complex Stability of Single Proteins Explored by Forced Unfolding Experiments.” Biophysical Journal, vol. 88, no. 5, Biophysical Society, 2005, pp. 37–39, doi:10.1529/biophysj.105.059774. short: H.L. Janovjak, T. Sapra, D. Mueller, Biophysical Journal 88 (2005) 37–39. date_created: 2018-12-11T12:03:13Z date_published: 2005-05-01T00:00:00Z date_updated: 2021-01-12T07:43:19Z day: '01' doi: 10.1529/biophysj.105.059774 extern: 1 intvolume: ' 88' issue: '5' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305525/ month: '05' oa: 1 page: 37 - 39 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '2985' quality_controlled: 0 status: public title: Complex stability of single proteins explored by forced unfolding experiments type: journal_article volume: 88 year: '2005' ... --- _id: '3418' abstract: - lang: eng text: Atomic force microscopy (AFM) allows the critical forces that unfold single proteins and rupture individual receptor–ligand bonds to be measured. To derive the shape of the energy landscape, the dynamic strength of the system is probed at different force loading rates. This is usually achieved by varying the pulling speed between a few nm/s and a few mgrm/s, although for a more complete investigation of the kinetic properties higher speeds are desirable. Above 10 mgrm/s, the hydrodynamic drag force acting on the AFM cantilever reaches the same order of magnitude as the molecular forces. This has limited the maximum pulling speed in AFM single-molecule force spectroscopy experiments. Here, we present an approach for considering these hydrodynamic effects, thereby allowing a correct evaluation of AFM force measurements recorded over an extended range of pulling speeds (and thus loading rates). To support and illustrate our theoretical considerations, we experimentally evaluated the mechanical unfolding of a multi-domain protein recorded at 30 mgrm/s pulling speed. author: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Jens full_name: Struckmeier, Jens last_name: Struckmeier - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller citation: ama: Janovjak HL, Struckmeier J, Mueller D. Hydrodynamic effects in fast AFM single molecule force measurements. European Biophysics Journal. 2005;34(1):91-96. doi:10.1007/s00249-004-0430-3 apa: Janovjak, H. L., Struckmeier, J., & Mueller, D. (2005). Hydrodynamic effects in fast AFM single molecule force measurements. European Biophysics Journal. Springer. https://doi.org/10.1007/s00249-004-0430-3 chicago: Janovjak, Harald L, Jens Struckmeier, and Daniel Mueller. “Hydrodynamic Effects in Fast AFM Single Molecule Force Measurements.” European Biophysics Journal. Springer, 2005. https://doi.org/10.1007/s00249-004-0430-3. ieee: H. L. Janovjak, J. Struckmeier, and D. Mueller, “Hydrodynamic effects in fast AFM single molecule force measurements,” European Biophysics Journal, vol. 34, no. 1. Springer, pp. 91–96, 2005. ista: Janovjak HL, Struckmeier J, Mueller D. 2005. Hydrodynamic effects in fast AFM single molecule force measurements. European Biophysics Journal. 34(1), 91–96. mla: Janovjak, Harald L., et al. “Hydrodynamic Effects in Fast AFM Single Molecule Force Measurements.” European Biophysics Journal, vol. 34, no. 1, Springer, 2005, pp. 91–96, doi:10.1007/s00249-004-0430-3. short: H.L. Janovjak, J. Struckmeier, D. Mueller, European Biophysics Journal 34 (2005) 91–96. date_created: 2018-12-11T12:03:14Z date_published: 2005-02-01T00:00:00Z date_updated: 2021-01-12T07:43:20Z day: '01' doi: 10.1007/s00249-004-0430-3 extern: 1 intvolume: ' 34' issue: '1' month: '02' page: 91 - 96 publication: European Biophysics Journal publication_status: published publisher: Springer publist_id: '2983' quality_controlled: 0 status: public title: Hydrodynamic effects in fast AFM single molecule force measurements type: journal_article volume: 34 year: '2005' ... --- _id: '3433' author: - first_name: Jonathan P full_name: Jonathan Bollback id: 2C6FA9CC-F248-11E8-B48F-1D18A9856A87 last_name: Bollback orcid: 0000-0002-4624-4612 citation: ama: 'Bollback JP. Posterior mapping and posterior predictive distributions. In: Nielsen R, ed. Statistical Methods in Molecular Evolution. Springer; 2005:439-462. doi:10.1007/0-387-27733-1' apa: Bollback, J. P. (2005). Posterior mapping and posterior predictive distributions. In R. Nielsen (Ed.), Statistical methods in Molecular Evolution (pp. 439–462). Springer. https://doi.org/10.1007/0-387-27733-1 chicago: Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.” In Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen, 439–62. Springer, 2005. https://doi.org/10.1007/0-387-27733-1. ieee: J. P. Bollback, “Posterior mapping and posterior predictive distributions,” in Statistical methods in Molecular Evolution, R. Nielsen, Ed. Springer, 2005, pp. 439–462. ista: 'Bollback JP. 2005.Posterior mapping and posterior predictive distributions. In: Statistical methods in Molecular Evolution. , 439–462.' mla: Bollback, Jonathan P. “Posterior Mapping and Posterior Predictive Distributions.” Statistical Methods in Molecular Evolution, edited by Rasmus Nielsen, Springer, 2005, pp. 439–62, doi:10.1007/0-387-27733-1. short: J.P. Bollback, in:, R. Nielsen (Ed.), Statistical Methods in Molecular Evolution, Springer, 2005, pp. 439–462. date_created: 2018-12-11T12:03:18Z date_published: 2005-04-21T00:00:00Z date_updated: 2021-01-12T07:43:26Z day: '21' doi: 10.1007/0-387-27733-1 editor: - first_name: Rasmus full_name: Nielsen, Rasmus last_name: Nielsen extern: 1 month: '04' page: 439 - 462 publication: Statistical methods in Molecular Evolution publication_status: published publisher: Springer publist_id: '2967' quality_controlled: 0 status: public title: Posterior mapping and posterior predictive distributions type: book_chapter year: '2005' ... --- _id: '3509' abstract: - lang: eng text: Methods, apparatus and computer program products can generate light weight but highly realistic and accurate colored models of three-dimensional colored objects. The colored model may be generated from a second plurality of points that define a coarse digital representation of the surface and at least one texture map containing information derived from a first plurality of colored points that define a fine digital representation of the surface. This derivation is achieved by mapping points within the texture map to the fine digital representation of the three-dimensional surface. Colored scan data may be used to construct the fine digital representation as a triangulated surface (i.e., triangulation) using a wrapping operation. applicant: - Raindrop Geomagic, Inc. article_processing_charge: No author: - first_name: Steven full_name: Williams, Steven last_name: Williams - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Ping full_name: Fu, Ping last_name: Fu citation: ama: Williams S, Edelsbrunner H, Fu P. Methods, apparatus and computer program products for modeling three-dimensional colored objects. 2005. apa: Williams, S., Edelsbrunner, H., & Fu, P. (2005). Methods, apparatus and computer program products for modeling three-dimensional colored objects. chicago: Williams, Steven, Herbert Edelsbrunner, and Ping Fu. “Methods, Apparatus and Computer Program Products for Modeling Three-Dimensional Colored Objects,” 2005. ieee: S. Williams, H. Edelsbrunner, and P. Fu, “Methods, apparatus and computer program products for modeling three-dimensional colored objects.” 2005. ista: Williams S, Edelsbrunner H, Fu P. 2005. Methods, apparatus and computer program products for modeling three-dimensional colored objects. mla: Williams, Steven, et al. Methods, Apparatus and Computer Program Products for Modeling Three-Dimensional Colored Objects. 2005. short: S. Williams, H. Edelsbrunner, P. Fu, (2005). date_created: 2018-12-11T12:03:42Z date_published: 2005-02-08T00:00:00Z date_updated: 2022-01-05T13:59:09Z day: '08' extern: '1' ipc: G06T17/20 ; G06T15/04 ipn: US6853373B2 main_file_link: - open_access: '1' url: https://patents.google.com/patent/US6853373B2/ month: '02' oa: 1 oa_version: Published Version publication_date: 2005-02-08 publist_id: '2878' status: public title: Methods, apparatus and computer program products for modeling three-dimensional colored objects type: patent user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2005' ... --- _id: '3558' abstract: - lang: eng text: The tandem algorithm combines the marching cube algorithm for surface extraction and the edge contraction algorithm for surface simplification in lock-step to avoid the costly intermediate step of storing the entire extracted surface triangulation. Beyond this basic strategy, we introduce refinements to prevent artifacts in the resulting triangulation, first, by carefully monitoring the amount of simplification during the process and, second, by driving the simplification toward a compromise between shape approximation and mesh quality. We have implemented the algorithm and used extensive computational experiments to document the effects of various design options and to further fine-tune the algorithm. acknowledgement: 'Partially supported the generated triangulations. Two questions arise: “how do by NSF grant CCR-00-86013 (BioGeometry).' author: - first_name: Dominique full_name: Attali, Dominique last_name: Attali - first_name: David full_name: Cohen-Steiner, David last_name: Cohen Steiner - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 citation: ama: 'Attali D, Cohen Steiner D, Edelsbrunner H. Extraction and simplification of iso-surfaces in tandem. In: ACM; 2005:139-148.' apa: 'Attali, D., Cohen Steiner, D., & Edelsbrunner, H. (2005). Extraction and simplification of iso-surfaces in tandem (pp. 139–148). Presented at the SGP: Eurographics Symposium on Geometry processing, ACM.' chicago: Attali, Dominique, David Cohen Steiner, and Herbert Edelsbrunner. “Extraction and Simplification of Iso-Surfaces in Tandem,” 139–48. ACM, 2005. ieee: 'D. Attali, D. Cohen Steiner, and H. Edelsbrunner, “Extraction and simplification of iso-surfaces in tandem,” presented at the SGP: Eurographics Symposium on Geometry processing, 2005, pp. 139–148.' ista: 'Attali D, Cohen Steiner D, Edelsbrunner H. 2005. Extraction and simplification of iso-surfaces in tandem. SGP: Eurographics Symposium on Geometry processing, 139–148.' mla: Attali, Dominique, et al. Extraction and Simplification of Iso-Surfaces in Tandem. ACM, 2005, pp. 139–48. short: D. Attali, D. Cohen Steiner, H. Edelsbrunner, in:, ACM, 2005, pp. 139–148. conference: name: 'SGP: Eurographics Symposium on Geometry processing' date_created: 2018-12-11T12:03:57Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:44:18Z day: '01' extern: 1 main_file_link: - open_access: '0' url: http://dl.acm.org/citation.cfm?id=1281943 month: '01' page: 139 - 148 publication_status: published publisher: ACM publist_id: '2827' quality_controlled: 0 status: public title: Extraction and simplification of iso-surfaces in tandem type: conference year: '2005' ... --- _id: '3576' abstract: - lang: eng text: |- ears of research in biology have established that all cellular functions are deeply connected to the shape and dynamics of their molec- ular actors. As a response, structural molecular biology has emerged as a new line of experimental research focused on revealing the structure of biomolecules. The analysis of these structures has led to the development of computational biology, whose aim is to predict from molecular simulation properties inaccessible to experimental probes. Here we focus on the representation of biomolecules used in these sim- ulations, and in particular on the hard sphere models. We review how the geometry of the union of such spheres is used to model their interactions with their environment, and how it has been included in simulations of molecular dynamics. In parallel, we review our own developments in mathematics and com- puter science on understanding the geometry of unions of balls, and their applications in molecular simulation. alternative_title: - Mathematical Sciences Research Institute Publications author: - first_name: Herbert full_name: Herbert Edelsbrunner id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Patrice full_name: Koehl, Patrice last_name: Koehl citation: ama: 'Edelsbrunner H, Koehl P. The geometry of biomolecular solvation. In: Combinatorial and Computational Geometry. Vol 52. Cambridge University Press; 2005:243-275.' apa: Edelsbrunner, H., & Koehl, P. (2005). The geometry of biomolecular solvation. In Combinatorial and Computational Geometry (Vol. 52, pp. 243–275). Cambridge University Press. chicago: Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular Solvation.” In Combinatorial and Computational Geometry, 52:243–75. Cambridge University Press, 2005. ieee: H. Edelsbrunner and P. Koehl, “The geometry of biomolecular solvation,” in Combinatorial and Computational Geometry, vol. 52, Cambridge University Press, 2005, pp. 243–275. ista: 'Edelsbrunner H, Koehl P. 2005.The geometry of biomolecular solvation. In: Combinatorial and Computational Geometry. Mathematical Sciences Research Institute Publications, vol. 52, 243–275.' mla: Edelsbrunner, Herbert, and Patrice Koehl. “The Geometry of Biomolecular Solvation.” Combinatorial and Computational Geometry, vol. 52, Cambridge University Press, 2005, pp. 243–75. short: H. Edelsbrunner, P. Koehl, in:, Combinatorial and Computational Geometry, Cambridge University Press, 2005, pp. 243–275. date_created: 2018-12-11T12:04:03Z date_published: 2005-08-08T00:00:00Z date_updated: 2021-01-12T07:44:25Z day: '08' extern: 1 intvolume: ' 52' main_file_link: - open_access: '0' url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.117.3732 month: '08' page: 243 - 275 publication: Combinatorial and Computational Geometry publication_status: published publisher: Cambridge University Press publist_id: '2809' quality_controlled: 0 status: public title: The geometry of biomolecular solvation type: book_chapter volume: 52 year: '2005' ... --- _id: '3612' abstract: - lang: eng text: Left-right asymmetry in snails is intriguing because individuals of opposite chirality are either unable to mate or can only mate with difficulty, so could be reproductively isolated from each other. We have therefore investigated chiral evolution in the Japanese land snail genus Euhadra to understand whether changes in chirality have promoted speciation. In particular, we aimed to understand the effect of the maternal inheritance of chirality on reproductive isolation and gene flow. We found that the mitochondrial DNA phylogeny of Euhadra is consistent with a single, relatively ancient evolution of sinistral species and suggests either recent “single-gene speciation” or gene flow between chiral morphs that are unable to mate. To clarify the conditions under which new chiral morphs might evolve and whether single-gene speciation can occur, we developed a mathematical model that is relevant to any maternal-effect gene. The model shows that reproductive character displacement can promote the evolution of new chiral morphs, tending to counteract the positive frequency-dependent selection that would otherwise drive the more common chiral morph to fixation. This therefore suggests a general mechanism as to how chiral variation arises in snails. In populations that contain both chiral morphs, two different situations are then possible. In the first, gene flow is substantial between morphs even without interchiral mating, because of the maternal inheritance of chirality. In the second, reproductive isolation is possible but unstable, and will also lead to gene flow if intrachiral matings occasionally produce offspring with the opposite chirality. Together, the results imply that speciation by chiral reversal is only meaningful in the context of a complex biogeographical process, and so must usually involve other factors. In order to understand the roles of reproductive character displacement and gene flow in the chiral evolution of Euhadra, it will be necessary to investigate populations in which both chiral morphs coexist. author: - first_name: Angus full_name: Davison, Angus last_name: Davison - first_name: Satoshi full_name: Chiba, Satoshi last_name: Chiba - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Bernard full_name: Clarke, Bernard last_name: Clarke citation: ama: Davison A, Chiba S, Barton NH, Clarke B. Speciation and gene flow between snails of opposing chirality. PLoS Biology. 2005;3(9). doi:10.1371/journal.pbio.0030282 apa: Davison, A., Chiba, S., Barton, N. H., & Clarke, B. (2005). Speciation and gene flow between snails of opposing chirality. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.0030282 chicago: Davison, Angus, Satoshi Chiba, Nicholas H Barton, and Bernard Clarke. “Speciation and Gene Flow between Snails of Opposing Chirality.” PLoS Biology. Public Library of Science, 2005. https://doi.org/10.1371/journal.pbio.0030282. ieee: A. Davison, S. Chiba, N. H. Barton, and B. Clarke, “Speciation and gene flow between snails of opposing chirality,” PLoS Biology, vol. 3, no. 9. Public Library of Science, 2005. ista: Davison A, Chiba S, Barton NH, Clarke B. 2005. Speciation and gene flow between snails of opposing chirality. PLoS Biology. 3(9). mla: Davison, Angus, et al. “Speciation and Gene Flow between Snails of Opposing Chirality.” PLoS Biology, vol. 3, no. 9, Public Library of Science, 2005, doi:10.1371/journal.pbio.0030282. short: A. Davison, S. Chiba, N.H. Barton, B. Clarke, PLoS Biology 3 (2005). date_created: 2018-12-11T12:04:14Z date_published: 2005-08-09T00:00:00Z date_updated: 2021-01-12T07:44:39Z day: '09' doi: 10.1371/journal.pbio.0030282 extern: 1 intvolume: ' 3' issue: '9' month: '08' publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '2771' quality_controlled: 0 status: public title: Speciation and gene flow between snails of opposing chirality tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article volume: 3 year: '2005' ... --- _id: '3611' abstract: - lang: eng text: 'We present two novel methods to infer mating patterns from genetic data. They differ from existing statistical methods of parentage inference in that they apply to populations that deviate from Hardy–Weinberg and linkage equilibrium, and so are suited for the study of assortative mating in hybrid zones. The core data set consists of genotypes at several loci for a number of full-sib clutches of unknown parentage. Our inference is based throughout on estimates of allelic associations within and across loci, such as heterozygote deficit and pairwise linkage disequilibrium. In the first method, the most likely parents of a given clutch are determined from the genotypic distribution of the associated adult population, given an explicit model of nonrandom mating. This leads to estimates of the strength of assortment. The second approach is based solely on the offspring genotypes and relies on the fact that a linear relation exists between associations among the offspring and those in the population of breeding pairs. We apply both methods to a sample from the hybrid zone between the fire-bellied toads Bombina bombina and B. variegata (Anura: Disco glossidae) in Croatia. Consistently, both approaches provide no evidence for a departure from random mating, despite adequate statistical power. Instead, B. variegata-like individuals among the adults contributed disproportionately to the offspring cohort, consistent with their preference for the type of breeding habitat in which this study was conducted.' author: - first_name: Beate full_name: Nürnberger, Beate last_name: Nürnberger - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Loeske full_name: Kruuk, Loeske E last_name: Kruuk - first_name: Timothy full_name: Vines, Timothy H last_name: Vines citation: ama: 'Nürnberger B, Barton NH, Kruuk L, Vines T. Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes. Heredity. 2005;94(2):247-257. doi:10.1038/sj.hdy.6800607' apa: 'Nürnberger, B., Barton, N. H., Kruuk, L., & Vines, T. (2005). Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes. Heredity. Nature Publishing Group. https://doi.org/10.1038/sj.hdy.6800607' chicago: 'Nürnberger, Beate, Nicholas H Barton, Loeske Kruuk, and Timothy Vines. “Mating Patterns in a Bombina Hybrid Zone: Inferences from Adult and Full Sib Genotypes.” Heredity. Nature Publishing Group, 2005. https://doi.org/10.1038/sj.hdy.6800607.' ieee: 'B. Nürnberger, N. H. Barton, L. Kruuk, and T. Vines, “Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes,” Heredity, vol. 94, no. 2. Nature Publishing Group, pp. 247–257, 2005.' ista: 'Nürnberger B, Barton NH, Kruuk L, Vines T. 2005. Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes. Heredity. 94(2), 247–257.' mla: 'Nürnberger, Beate, et al. “Mating Patterns in a Bombina Hybrid Zone: Inferences from Adult and Full Sib Genotypes.” Heredity, vol. 94, no. 2, Nature Publishing Group, 2005, pp. 247–57, doi:10.1038/sj.hdy.6800607.' short: B. Nürnberger, N.H. Barton, L. Kruuk, T. Vines, Heredity 94 (2005) 247–257. date_created: 2018-12-11T12:04:14Z date_published: 2005-02-01T00:00:00Z date_updated: 2021-01-12T07:44:39Z day: '01' doi: 10.1038/sj.hdy.6800607 extern: 1 intvolume: ' 94' issue: '2' month: '02' page: 247 - 257 publication: Heredity publication_status: published publisher: Nature Publishing Group publist_id: '2772' quality_controlled: 0 status: public title: 'Mating patterns in a Bombina hybrid zone: Inferences from adult and full sib genotypes' type: journal_article volume: 94 year: '2005' ... --- _id: '3613' abstract: - lang: eng text: 'The extent of genetic variation in fitness is a crucial issue in evolutionary biology and yet remains largely unresolved. In Drosophila melanogaster, we have devised a method that allows the net effects on fitness of heterozygous wild-type chromosomes to be measured, by competing them against two different “balancer” chromosomes. We have applied the method to a large sample of 40 wild-type third chromosomes and have measured fitnesses of nonlethal chromosomes as well as chromosomes bearing recessive lethals. The measurements were made in the environment to which the population was adapted and did not involve inbreeding. The results show an extraordinary similarity in the behavior of replicates of the same chromosome, indicating consistent genetic effects on total fitness. Some invading chromosomes increased rapidly and some slowly, and some rose to appreciable frequency after several months, but then declined again: in every case, the same pattern was seen in each replicate. We estimated relative fitnesses, rates of change of fitness, and relative viabilities, for each chromosome. There were significant fluctuations around the fitted model, which were also highly replicable. Wild-type chromosomes varied substantially in their effects on heterozygous fitness, and these effects vary through time, most likely as a result of genotype × environment interactions.' author: - first_name: Michael full_name: Gardner, Michael P last_name: Gardner - first_name: Kevin full_name: Fowler, Kevin last_name: Fowler - first_name: Nicholas H full_name: Nicholas Barton id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Linda full_name: Patridge, Linda last_name: Patridge citation: ama: 'Gardner M, Fowler K, Barton NH, Patridge L. Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns. Genetics. 2005;169(3):1553-1571. doi:10.1534/genetics.104.032367' apa: 'Gardner, M., Fowler, K., Barton, N. H., & Patridge, L. (2005). Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.104.032367' chicago: 'Gardner, Michael, Kevin Fowler, Nicholas H Barton, and Linda Patridge. “Genetic Variation for Total Fitness in Drosophila Melanogaster: Complex yet Replicable Patterns.” Genetics. Genetics Society of America, 2005. https://doi.org/10.1534/genetics.104.032367.' ieee: 'M. Gardner, K. Fowler, N. H. Barton, and L. Patridge, “Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns,” Genetics, vol. 169, no. 3. Genetics Society of America, pp. 1553–1571, 2005.' ista: 'Gardner M, Fowler K, Barton NH, Patridge L. 2005. Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns. Genetics. 169(3), 1553–1571.' mla: 'Gardner, Michael, et al. “Genetic Variation for Total Fitness in Drosophila Melanogaster: Complex yet Replicable Patterns.” Genetics, vol. 169, no. 3, Genetics Society of America, 2005, pp. 1553–71, doi:10.1534/genetics.104.032367.' short: M. Gardner, K. Fowler, N.H. Barton, L. Patridge, Genetics 169 (2005) 1553–1571. date_created: 2018-12-11T12:04:15Z date_published: 2005-03-01T00:00:00Z date_updated: 2021-01-12T07:44:40Z day: '01' doi: 10.1534/genetics.104.032367 extern: 1 intvolume: ' 169' issue: '3' month: '03' page: 1553 - 1571 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '2770' quality_controlled: 0 status: public title: 'Genetic variation for total fitness in Drosophila melanogaster: Complex yet replicable patterns' type: journal_article volume: 169 year: '2005' ... --- _id: '3691' abstract: - lang: eng text: In strictly pseudoconvex domains with smooth boundary, we prove a commutator relationship between admissible integral operators, as introduced by Lieb and Range, and smooth vector fields which are tangential at boundary points. This makes it possible to gain estimates for admissible operators in function spaces which involve tangential derivatives. Examples are given under with circumstances these can be transformed into genuine Sobolev- and C k-estimates. author: - first_name: Christoph full_name: Christoph Lampert id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Lampert C. Boundary regularity of admissible operators. Publicacions Matemàtiques. 2005;49(1):179-195. doi:10.5565/PUBLMAT_49105_08 apa: Lampert, C. (2005). Boundary regularity of admissible operators. Publicacions Matemàtiques. Universitat Autònoma de Barcelona, Departament de Matemàtique. https://doi.org/10.5565/PUBLMAT_49105_08 chicago: Lampert, Christoph. “Boundary Regularity of Admissible Operators.” Publicacions Matemàtiques. Universitat Autònoma de Barcelona, Departament de Matemàtique, 2005. https://doi.org/10.5565/PUBLMAT_49105_08. ieee: C. Lampert, “Boundary regularity of admissible operators,” Publicacions Matemàtiques, vol. 49, no. 1. Universitat Autònoma de Barcelona, Departament de Matemàtique, pp. 179–195, 2005. ista: Lampert C. 2005. Boundary regularity of admissible operators. Publicacions Matemàtiques. 49(1), 179–195. mla: Lampert, Christoph. “Boundary Regularity of Admissible Operators.” Publicacions Matemàtiques, vol. 49, no. 1, Universitat Autònoma de Barcelona, Departament de Matemàtique, 2005, pp. 179–95, doi:10.5565/PUBLMAT_49105_08. short: C. Lampert, Publicacions Matemàtiques 49 (2005) 179–195. date_created: 2018-12-11T12:04:38Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:48:59Z day: '01' doi: 10.5565/PUBLMAT_49105_08 extern: 1 intvolume: ' 49' issue: '1' month: '01' page: 179 - 195 publication: Publicacions Matemàtiques publication_status: published publisher: Universitat Autònoma de Barcelona, Departament de Matemàtique publist_id: '2673' quality_controlled: 0 status: public title: Boundary regularity of admissible operators type: journal_article volume: 49 year: '2005' ... --- _id: '3721' abstract: - lang: eng text: Recent advances in atomic force microscopy allowed globular and membrane proteins to be mechanically unfolded on a single-molecule level. Presented is an extension to the existing force spectroscopy experiments. While unfolding single bacteriorhodopsins from native purple membranes, small oscillation amplitudes (6–9nm) were supplied to the vertical displacement of the cantilever at a frequency of 3kHz. The phase and amplitude response of the cantilever-protein system was converted to reveal the elastic (conservative) and viscous (dissipative) contributions to the unfolding process. The elastic response (stiffness) of the extended parts of the protein were in the range of a few tens pN/nm and could be well described by the derivative of the wormlike chain model. Discrete events in the viscous response coincided with the unfolding of single secondary structure elements and were in the range of 1μNs/m. In addition, these force modulation spectroscopy experiments revealed novel mechanical unfolding intermediates of bacteriorhodopsin. We found that kinks result in a loss of unfolding cooperativity in transmembrane helices. Reconstructing force-distance spectra by the integration of amplitude-distance spectra verified their position, offering a novel approach to detect intermediates during the forced unfolding of single proteins. author: - first_name: Harald L full_name: Harald Janovjak id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Daniel full_name: Mueller, Daniel J last_name: Mueller - first_name: Andrew full_name: Humphris, Andrew D last_name: Humphris citation: ama: Janovjak HL, Mueller D, Humphris A. Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins. Biophysical Journal. 2005;88(2):1423-1431. doi:10.1529/biophysj.104.052746 apa: Janovjak, H. L., Mueller, D., & Humphris, A. (2005). Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins. Biophysical Journal. Biophysical Society. https://doi.org/10.1529/biophysj.104.052746 chicago: Janovjak, Harald L, Daniel Mueller, and Andrew Humphris. “Molecular Force Modulation Spectroscopy Revealing the Dynamic Response of Single Bacteriorhodopsins.” Biophysical Journal. Biophysical Society, 2005. https://doi.org/10.1529/biophysj.104.052746. ieee: H. L. Janovjak, D. Mueller, and A. Humphris, “Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins,” Biophysical Journal, vol. 88, no. 2. Biophysical Society, pp. 1423–1431, 2005. ista: Janovjak HL, Mueller D, Humphris A. 2005. Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins. Biophysical Journal. 88(2), 1423–1431. mla: Janovjak, Harald L., et al. “Molecular Force Modulation Spectroscopy Revealing the Dynamic Response of Single Bacteriorhodopsins.” Biophysical Journal, vol. 88, no. 2, Biophysical Society, 2005, pp. 1423–31, doi:10.1529/biophysj.104.052746. short: H.L. Janovjak, D. Mueller, A. Humphris, Biophysical Journal 88 (2005) 1423–1431. date_created: 2018-12-11T12:04:48Z date_published: 2005-02-01T00:00:00Z date_updated: 2021-01-12T07:51:43Z day: '01' doi: 10.1529/biophysj.104.052746 extern: 1 intvolume: ' 88' issue: '2' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1305144/ month: '02' oa: 1 page: 1423 - 1431 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '2509' quality_controlled: 0 status: public title: Molecular force modulation spectroscopy revealing the dynamic response of single bacteriorhodopsins type: journal_article volume: 88 year: '2005' ... --- _id: '3741' abstract: - lang: eng text: In an age of increasingly large data sets, investigators in many different disciplines have turned to clustering as a tool for data analysis and exploration. Existing clustering methods, however, typically depend on several nontrivial assumptions about the structure of data. Here, we reformulate the clustering problem from an information theoretic perspective that avoids many of these assumptions. In particular, our formulation obviates the need for defining a cluster "prototype," does not require an a priori similarity metric, is invariant to changes in the representation of the data, and naturally captures nonlinear relations. We apply this approach to different domains and find that it consistently produces clusters that are more coherent than those extracted by existing algorithms. Finally, our approach provides a way of clustering based on collective notions of similarity rather than the traditional pairwise measures. author: - first_name: N. full_name: Slonim,N. last_name: Slonim - first_name: G. full_name: Atwal,G. last_name: Atwal - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: William full_name: Bialek, William S last_name: Bialek citation: ama: Slonim N, Atwal G, Tkačik G, Bialek W. Information-based clustering. PNAS. 2005;102(51):18297-18302. doi:10.1073/pnas.0507432102 apa: Slonim, N., Atwal, G., Tkačik, G., & Bialek, W. (2005). Information-based clustering. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.0507432102 chicago: Slonim, N., G. Atwal, Gašper Tkačik, and William Bialek. “Information-Based Clustering.” PNAS. National Academy of Sciences, 2005. https://doi.org/10.1073/pnas.0507432102. ieee: N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Information-based clustering,” PNAS, vol. 102, no. 51. National Academy of Sciences, pp. 18297–18302, 2005. ista: Slonim N, Atwal G, Tkačik G, Bialek W. 2005. Information-based clustering. PNAS. 102(51), 18297–18302. mla: Slonim, N., et al. “Information-Based Clustering.” PNAS, vol. 102, no. 51, National Academy of Sciences, 2005, pp. 18297–302, doi:10.1073/pnas.0507432102. short: N. Slonim, G. Atwal, G. Tkačik, W. Bialek, PNAS 102 (2005) 18297–18302. date_created: 2018-12-11T12:04:55Z date_published: 2005-12-20T00:00:00Z date_updated: 2021-01-12T07:51:52Z day: '20' doi: 10.1073/pnas.0507432102 extern: 1 intvolume: ' 102' issue: '51' main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1317937 month: '12' oa: 1 page: 18297 - 18302 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '2490' quality_controlled: 0 status: public title: Information-based clustering type: journal_article volume: 102 year: '2005' ... --- _id: '3746' abstract: - lang: eng text: We address the practical problems of estimating the information relations that characterize large networks. Building on methods developed for analysis of the neural code, we show that reliable estimates of mutual information can be obtained with manageable computational effort. The same methods allow estimation of higher order, multi-information terms. These ideas are illustrated by analyses of gene expression, financial markets, and consumer preferences. In each case, information theoretic measures correlate with independent, intuitive measures of the underlying structures in the system. author: - first_name: Noam full_name: Slonim,Noam last_name: Slonim - first_name: Gurinder full_name: Atwal,Gurinder S last_name: Atwal - first_name: Gasper full_name: Gasper Tkacik id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: William full_name: Bialek, William S last_name: Bialek citation: ama: Slonim N, Atwal G, Tkačik G, Bialek W. Estimating mutual information and multi-information in large networks. ArXiv. 2005:1-11. apa: Slonim, N., Atwal, G., Tkačik, G., & Bialek, W. (2005). Estimating mutual information and multi-information in large networks. ArXiv. ArXiv. chicago: Slonim, Noam, Gurinder Atwal, Gašper Tkačik, and William Bialek. “Estimating Mutual Information and Multi-Information in Large Networks.” ArXiv. ArXiv, 2005. ieee: N. Slonim, G. Atwal, G. Tkačik, and W. Bialek, “Estimating mutual information and multi-information in large networks,” ArXiv. ArXiv, pp. 1–11, 2005. ista: Slonim N, Atwal G, Tkačik G, Bialek W. 2005. Estimating mutual information and multi-information in large networks. ArXiv, 1–11, . mla: Slonim, Noam, et al. “Estimating Mutual Information and Multi-Information in Large Networks.” ArXiv, ArXiv, 2005, pp. 1–11. short: N. Slonim, G. Atwal, G. Tkačik, W. Bialek, ArXiv (2005) 1–11. date_created: 2018-12-11T12:04:56Z date_published: 2005-02-03T00:00:00Z date_updated: 2021-01-12T07:51:54Z day: '03' extern: 1 main_file_link: - open_access: '1' url: http://arxiv.org/abs/cs/0502017v1 month: '02' oa: 1 page: 1 - 11 publication: ArXiv publication_status: published publisher: ArXiv publist_id: '2484' quality_controlled: 0 status: public title: Estimating mutual information and multi-information in large networks type: preprint year: '2005' ... --- _id: '3808' abstract: - lang: eng text: Action potentials in central neurons are initiated near the axon initial segment, propagate into the axon, and finally invade the presynaptic terminals, where they trigger transmitter release. Voltage-gated Na(+) channels are key determinants of excitability, but Na(+) channel density and properties in axons and presynaptic terminals of cortical neurons have not been examined yet. In hippocampal mossy fiber boutons, which emerge from parent axons en passant, Na(+) channels are very abundant, with an estimated number of approximately 2000 channels per bouton. Presynaptic Na(+) channels show faster inactivation kinetics than somatic channels, suggesting differences between subcellular compartments of the same cell. Computational analysis of action potential propagation in axon-multibouton structures reveals that Na(+) channels in boutons preferentially amplify the presynaptic action potential and enhance Ca(2+) inflow, whereas Na(+) channels in axons control the reliability and speed of propagation. Thus, presynaptic and axonal Na(+) channels contribute differentially to mossy fiber synaptic transmission. author: - first_name: Dominique full_name: Engel, Dominique last_name: Engel - first_name: Peter M full_name: Peter Jonas id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 citation: ama: Engel D, Jonas PM. Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons. Neuron. 2005;45(3):405-417. doi:10.1016/j.neuron.2004.12.048 apa: Engel, D., & Jonas, P. M. (2005). Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2004.12.048 chicago: Engel, Dominique, and Peter M Jonas. “Presynaptic Action Potential Amplification by Voltage-Gated Na+ Channels in Hippocampal Mossy Fiber Boutons.” Neuron. Elsevier, 2005. https://doi.org/10.1016/j.neuron.2004.12.048 . ieee: D. Engel and P. M. Jonas, “Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons,” Neuron, vol. 45, no. 3. Elsevier, pp. 405–17, 2005. ista: Engel D, Jonas PM. 2005. Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons. Neuron. 45(3), 405–17. mla: Engel, Dominique, and Peter M. Jonas. “Presynaptic Action Potential Amplification by Voltage-Gated Na+ Channels in Hippocampal Mossy Fiber Boutons.” Neuron, vol. 45, no. 3, Elsevier, 2005, pp. 405–17, doi:10.1016/j.neuron.2004.12.048 . short: D. Engel, P.M. Jonas, Neuron 45 (2005) 405–17. date_created: 2018-12-11T12:05:17Z date_published: 2005-01-01T00:00:00Z date_updated: 2021-01-12T07:52:21Z day: '01' doi: '10.1016/j.neuron.2004.12.048 ' extern: 1 intvolume: ' 45' issue: '3' month: '01' page: 405 - 17 publication: Neuron publication_status: published publisher: Elsevier publist_id: '2400' quality_controlled: 0 status: public title: Presynaptic action potential amplification by voltage-gated Na+ channels in hippocampal mossy fiber boutons type: journal_article volume: 45 year: '2005' ... --- _id: '3892' abstract: - lang: eng text: 'In 2-player non-zero-sum games, Nash equilibria capture the options for rational behavior if each player attempts to maximize her payoff. In contrast to classical game theory, we consider lexicographic objectives: first, each player tries to maximize her own payoff, and then, the player tries to minimize the opponent''s payoff. Such objectives arise naturally in the verification of systems with multiple components. There, instead of proving that each component satisfies its specification no matter how the other components behave, it often suffices to prove that each component satisfies its specification provided that the other components satisfy their specifications. We say that a Nash equilibrium is secure if it is an equilibrium with respect to the lexicographic objectives of both players. We prove that in graph games with Borel winning conditions, which include the games that arise in verification, there may be several Nash equilibria, but there is always a unique maximal payoff profile of a secure equilibrium. We show how this equilibrium can be computed in the case of omega-regular winning conditions, and we characterize the memory requirements of strategies that achieve the equilibrium.' acknowledgement: |- This research was supported in part by the ONR grant N00014-02-1-0671, the AFOSR MURI grant F49620-00-1-0327, and the NSF grant CCR-0225610. This is an extended version of the paper “Games with Secure Equilibria” that appeared in the proceedings of Logic in Computer Science (LICS), 2004. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Krishnendu Chatterjee id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Thomas Henzinger id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Marcin full_name: Jurdziński, Marcin last_name: Jurdziński citation: ama: 'Chatterjee K, Henzinger TA, Jurdziński M. Games with secure equilibria. In: Vol 3657. Springer; 2005:141-161. doi:10.1007/11561163_7' apa: 'Chatterjee, K., Henzinger, T. A., & Jurdziński, M. (2005). Games with secure equilibria (Vol. 3657, pp. 141–161). Presented at the FMCO: Formal Methods for Components and Objects, Springer. https://doi.org/10.1007/11561163_7' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Marcin Jurdziński. “Games with Secure Equilibria,” 3657:141–61. Springer, 2005. https://doi.org/10.1007/11561163_7. ieee: 'K. Chatterjee, T. A. Henzinger, and M. Jurdziński, “Games with secure equilibria,” presented at the FMCO: Formal Methods for Components and Objects, 2005, vol. 3657, pp. 141–161.' ista: 'Chatterjee K, Henzinger TA, Jurdziński M. 2005. Games with secure equilibria. FMCO: Formal Methods for Components and Objects, LNCS, vol. 3657, 141–161.' mla: Chatterjee, Krishnendu, et al. Games with Secure Equilibria. Vol. 3657, Springer, 2005, pp. 141–61, doi:10.1007/11561163_7. short: K. Chatterjee, T.A. Henzinger, M. Jurdziński, in:, Springer, 2005, pp. 141–161. conference: name: 'FMCO: Formal Methods for Components and Objects' date_created: 2018-12-11T12:05:44Z date_published: 2005-09-19T00:00:00Z date_updated: 2021-01-12T07:53:00Z day: '19' doi: 10.1007/11561163_7 extern: 1 intvolume: ' 3657' month: '09' page: 141 - 161 publication_status: published publisher: Springer publist_id: '2269' quality_controlled: 0 status: public title: Games with secure equilibria type: conference volume: 3657 year: '2005' ... --- _id: '3902' author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Jacobus full_name: Boomsma, Jacobus last_name: Boomsma citation: ama: 'Cremer S, Boomsma J. The drawback of mobility: invasive species in a globalised world. In: Elsevier; 2005.' apa: 'Cremer, S., & Boomsma, J. (2005). The drawback of mobility: invasive species in a globalised world. Presented at the Marie Curie Conference, Elsevier.' chicago: 'Cremer, Sylvia, and Jacobus Boomsma. “The Drawback of Mobility: Invasive Species in a Globalised World.” Elsevier, 2005.' ieee: 'S. Cremer and J. Boomsma, “The drawback of mobility: invasive species in a globalised world,” presented at the Marie Curie Conference, 2005.' ista: 'Cremer S, Boomsma J. 2005. The drawback of mobility: invasive species in a globalised world. Marie Curie Conference.' mla: 'Cremer, Sylvia, and Jacobus Boomsma. The Drawback of Mobility: Invasive Species in a Globalised World. Elsevier, 2005.' short: S. Cremer, J. Boomsma, in:, Elsevier, 2005. conference: name: Marie Curie Conference date_created: 2018-12-11T12:05:47Z date_published: 2005-09-01T00:00:00Z date_updated: 2021-01-12T07:53:05Z day: '01' extern: '1' language: - iso: eng main_file_link: - url: http://www.docstoc.com/docs/15327566/1-The-drawback-of-mobility-invasive-species-in-a-globalised-world month: '09' oa_version: None publication_status: published publisher: Elsevier publist_id: '2252' status: public title: 'The drawback of mobility: invasive species in a globalised world' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2005' ...