[{"quality_controlled":"1","status":"public","day":"14","_id":"3267","date_created":"2018-12-11T12:02:21Z","scopus_import":1,"abstract":[{"text":"We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We study the problem with different measures: volume, diameter and radius. For volume, that is, the 1-norm of a cycle, two main results are presented. First, we prove that the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). The latter result leads to the inapproximability of the problem of computing the nonbounding cycle with the smallest volume and computing cycles representing a homology basis with the minimal total volume. As for the other two measures defined by pairwise geodesic distance, diameter and radius, we show that the localization problem is NP-hard for diameter but is polynomial for radius. Our work is restricted to homology over the ℤ2 field.","lang":"eng"}],"type":"journal_article","volume":45,"citation":{"apa":"Chen, C., &#38; Freedman, D. (2011). Hardness results for homology localization. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-010-9322-8\">https://doi.org/10.1007/s00454-010-9322-8</a>","mla":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Discrete &#38; Computational Geometry</i>, vol. 45, no. 3, Springer, 2011, pp. 425–48, doi:<a href=\"https://doi.org/10.1007/s00454-010-9322-8\">10.1007/s00454-010-9322-8</a>.","ama":"Chen C, Freedman D. Hardness results for homology localization. <i>Discrete &#38; Computational Geometry</i>. 2011;45(3):425-448. doi:<a href=\"https://doi.org/10.1007/s00454-010-9322-8\">10.1007/s00454-010-9322-8</a>","ista":"Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete &#38; Computational Geometry. 45(3), 425–448.","short":"C. Chen, D. Freedman, Discrete &#38; Computational Geometry 45 (2011) 425–448.","ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” <i>Discrete &#38; Computational Geometry</i>, vol. 45, no. 3. Springer, pp. 425–448, 2011.","chicago":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s00454-010-9322-8\">https://doi.org/10.1007/s00454-010-9322-8</a>."},"oa_version":"None","related_material":{"record":[{"id":"10909","relation":"earlier_version","status":"public"}]},"publication":"Discrete & Computational Geometry","doi":"10.1007/s00454-010-9322-8","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chen, Chao","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen"},{"last_name":"Freedman","first_name":"Daniel","full_name":"Freedman, Daniel"}],"title":"Hardness results for homology localization","issue":"3","date_updated":"2023-02-21T16:07:10Z","publisher":"Springer","date_published":"2011-01-14T00:00:00Z","intvolume":"        45","month":"01","year":"2011","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publist_id":"3379","page":"425 - 448"},{"year":"2011","language":[{"iso":"eng"}],"publist_id":"3378","page":"239 - 268","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Algebraic topology for computer vision","author":[{"last_name":"Freedman","first_name":"Daniel","full_name":"Freedman, Daniel"},{"last_name":"Chen","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao"}],"date_updated":"2021-01-12T07:42:16Z","publisher":"Nova Science Publishers","date_published":"2011-11-30T00:00:00Z","alternative_title":["Computer Science, Technology and Applications"],"month":"11","oa_version":"None","publication":"Computer Vision","main_file_link":[{"url":"http://www.hpl.hp.com/techreports/2009/HPL-2009-375.pdf"}],"publication_status":"published","status":"public","day":"30","quality_controlled":"1","date_created":"2018-12-11T12:02:22Z","_id":"3268","abstract":[{"text":"Algebraic topology is generally considered one of the purest subfield of mathematics. However, over the last decade two interesting new lines of research have emerged, one focusing on algorithms for algebraic topology, and the other on applications of algebraic topology in engineering and science. Amongst the new areas in which the techniques have been applied are computer vision and image processing. In this paper, we survey the results of these endeavours. Because algebraic topology is an area of mathematics with which most computer vision practitioners have no experience, we review the machinery behind the theories of homology and persistent homology; our review emphasizes intuitive explanations. In terms of applications to computer vision, we focus on four illustrative problems: shape signatures, natural image statistics, image denoising, and segmentation. Our hope is that this review will stimulate interest on the part of computer vision researchers to both use and extend the tools of this new field. ","lang":"eng"}],"type":"book_chapter","citation":{"ieee":"D. Freedman and C. Chen, “Algebraic topology for computer vision,” in <i>Computer Vision</i>, Nova Science Publishers, 2011, pp. 239–268.","short":"D. Freedman, C. Chen, in:, Computer Vision, Nova Science Publishers, 2011, pp. 239–268.","ista":"Freedman D, Chen C. 2011.Algebraic topology for computer vision. In: Computer Vision. Computer Science, Technology and Applications, , 239–268.","ama":"Freedman D, Chen C. Algebraic topology for computer vision. In: <i>Computer Vision</i>. Nova Science Publishers; 2011:239-268.","chicago":"Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.” In <i>Computer Vision</i>, 239–68. Nova Science Publishers, 2011.","apa":"Freedman, D., &#38; Chen, C. (2011). Algebraic topology for computer vision. In <i>Computer Vision</i> (pp. 239–268). Nova Science Publishers.","mla":"Freedman, Daniel, and Chao Chen. “Algebraic Topology for Computer Vision.” <i>Computer Vision</i>, Nova Science Publishers, 2011, pp. 239–68."},"extern":"1"},{"page":"1261 - 1268","year":"2011","month":"07","intvolume":"        30","date_published":"2011-07-19T00:00:00Z","date_updated":"2021-01-12T07:42:16Z","issue":"4","oa":1,"main_file_link":[{"open_access":"1","url":"http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf"}],"doi":"10.1111/j.1467-8659.2011.01985.x","publication":"Computer Graphics Forum","oa_version":"Published Version","volume":30,"date_created":"2018-12-11T12:02:22Z","status":"public","day":"19","article_processing_charge":"No","publist_id":"3377","department":[{"_id":"HeEd"}],"language":[{"iso":"eng"}],"article_type":"original","publisher":"Wiley-Blackwell","title":"Perceptual global illumination cancellation in complex projection environments","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Yu","last_name":"Sheng","full_name":"Sheng, Yu"},{"last_name":"Cutler","first_name":"Barbara","full_name":"Cutler, Barbara"},{"last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","full_name":"Chen, Chao"},{"last_name":"Nasman","first_name":"Joshua","full_name":"Nasman, Joshua"}],"publication_status":"published","citation":{"ama":"Sheng Y, Cutler B, Chen C, Nasman J. Perceptual global illumination cancellation in complex projection environments. <i>Computer Graphics Forum</i>. 2011;30(4):1261-1268. doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">10.1111/j.1467-8659.2011.01985.x</a>","ista":"Sheng Y, Cutler B, Chen C, Nasman J. 2011. Perceptual global illumination cancellation in complex projection environments. Computer Graphics Forum. 30(4), 1261–1268.","ieee":"Y. Sheng, B. Cutler, C. Chen, and J. Nasman, “Perceptual global illumination cancellation in complex projection environments,” <i>Computer Graphics Forum</i>, vol. 30, no. 4. Wiley-Blackwell, pp. 1261–1268, 2011.","short":"Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011) 1261–1268.","chicago":"Sheng, Yu, Barbara Cutler, Chao Chen, and Joshua Nasman. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” <i>Computer Graphics Forum</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">https://doi.org/10.1111/j.1467-8659.2011.01985.x</a>.","apa":"Sheng, Y., Cutler, B., Chen, C., &#38; Nasman, J. (2011). Perceptual global illumination cancellation in complex projection environments. <i>Computer Graphics Forum</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">https://doi.org/10.1111/j.1467-8659.2011.01985.x</a>","mla":"Sheng, Yu, et al. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” <i>Computer Graphics Forum</i>, vol. 30, no. 4, Wiley-Blackwell, 2011, pp. 1261–68, doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">10.1111/j.1467-8659.2011.01985.x</a>."},"type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"The unintentional scattering of light between neighboring surfaces in complex projection environments increases the brightness and decreases the contrast, disrupting the appearance of the desired imagery. To achieve satisfactory projection results, the inverse problem of global illumination must be solved to cancel this secondary scattering. In this paper, we propose a global illumination cancellation method that minimizes the perceptual difference between the desired imagery and the actual total illumination in the resulting physical environment. Using Gauss-Newton and active set methods, we design a fast solver for the bound constrained nonlinear least squares problem raised by the perceptual error metrics. Our solver is further accelerated with a CUDA implementation and multi-resolution method to achieve 1–2 fps for problems with approximately 3000 variables. We demonstrate the global illumination cancellation algorithm with our multi-projector system. Results show that our method preserves the color fidelity of the desired imagery significantly better than previous methods."}],"_id":"3269","quality_controlled":"1"},{"title":"Persistent homology computation with a twist","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chen, Chao","last_name":"Chen","first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kerber","orcid":"0000-0002-8030-9299","first_name":"Michael","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","full_name":"Kerber, Michael"}],"date_updated":"2021-01-12T07:42:17Z","publisher":"TU Dortmund","date_published":"2011-01-01T00:00:00Z","month":"01","year":"2011","language":[{"iso":"eng"}],"publist_id":"3376","conference":{"name":"EuroCG: European Workshop on Computational Geometry","end_date":"2011-03-30","start_date":"2011-03-28","location":"Morschach, Switzerland"},"department":[{"_id":"HeEd"}],"page":"197 - 200","day":"01","status":"public","quality_controlled":"1","_id":"3270","date_created":"2018-12-11T12:02:22Z","abstract":[{"lang":"eng","text":"The persistence diagram of a filtered simplicial com- plex is usually computed by reducing the boundary matrix of the complex. We introduce a simple op- timization technique: by processing the simplices of the complex in decreasing dimension, we can “kill” columns (i.e., set them to zero) without reducing them. This technique completely avoids reduction on roughly half of the columns. We demonstrate that this idea significantly improves the running time of the reduction algorithm in practice. We also give an output-sensitive complexity analysis for the new al- gorithm which yields to sub-cubic asymptotic bounds under certain assumptions."}],"type":"conference","citation":{"short":"C. Chen, M. Kerber, in:, TU Dortmund, 2011, pp. 197–200.","ieee":"C. Chen and M. Kerber, “Persistent homology computation with a twist,” presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland, 2011, pp. 197–200.","ista":"Chen C, Kerber M. 2011. Persistent homology computation with a twist. EuroCG: European Workshop on Computational Geometry, 197–200.","ama":"Chen C, Kerber M. Persistent homology computation with a twist. In: TU Dortmund; 2011:197-200.","chicago":"Chen, Chao, and Michael Kerber. “Persistent Homology Computation with a Twist,” 197–200. TU Dortmund, 2011.","apa":"Chen, C., &#38; Kerber, M. (2011). Persistent homology computation with a twist (pp. 197–200). Presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland: TU Dortmund.","mla":"Chen, Chao, and Michael Kerber. <i>Persistent Homology Computation with a Twist</i>. TU Dortmund, 2011, pp. 197–200."},"oa_version":"None","publication_status":"published"},{"day":"14","status":"public","quality_controlled":"1","date_created":"2018-12-11T12:02:23Z","_id":"3271","editor":[{"first_name":"Ronald","last_name":"Peikert","full_name":"Peikert, Ronald"},{"first_name":"Helwig","last_name":"Hauser","full_name":"Hauser, Helwig"},{"full_name":"Carr, Hamish","last_name":"Carr","first_name":"Hamish"},{"full_name":"Fuchs, Raphael","first_name":"Raphael","last_name":"Fuchs"}],"scopus_import":1,"abstract":[{"text":"In this paper we present an efficient framework for computation of persis- tent homology of cubical data in arbitrary dimensions. An existing algorithm using simplicial complexes is adapted to the setting of cubical complexes. The proposed approach enables efficient application of persistent homology in domains where the data is naturally given in a cubical form. By avoiding triangulation of the data, we significantly reduce the size of the complex. We also present a data-structure de- signed to compactly store and quickly manipulate cubical complexes. By means of numerical experiments, we show high speed and memory efficiency of our ap- proach. We compare our framework to other available implementations, showing its superiority. Finally, we report performance on selected 3D and 4D data-sets.","lang":"eng"}],"type":"book_chapter","citation":{"apa":"Wagner, H., Chen, C., &#38; Vuçini, E. (2011). Efficient computation of persistent homology for cubical data. In R. Peikert, H. Hauser, H. Carr, &#38; R. Fuchs (Eds.), <i>Topological Methods in Data Analysis and Visualization II</i> (pp. 91–106). Springer. <a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">https://doi.org/10.1007/978-3-642-23175-9_7</a>","mla":"Wagner, Hubert, et al. “Efficient Computation of Persistent Homology for Cubical Data.” <i>Topological Methods in Data Analysis and Visualization II</i>, edited by Ronald Peikert et al., Springer, 2011, pp. 91–106, doi:<a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">10.1007/978-3-642-23175-9_7</a>.","ama":"Wagner H, Chen C, Vuçini E. Efficient computation of persistent homology for cubical data. In: Peikert R, Hauser H, Carr H, Fuchs R, eds. <i>Topological Methods in Data Analysis and Visualization II</i>. Springer; 2011:91-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">10.1007/978-3-642-23175-9_7</a>","short":"H. Wagner, C. Chen, E. Vuçini, in:, R. Peikert, H. Hauser, H. Carr, R. Fuchs (Eds.), Topological Methods in Data Analysis and Visualization II, Springer, 2011, pp. 91–106.","ieee":"H. Wagner, C. Chen, and E. Vuçini, “Efficient computation of persistent homology for cubical data,” in <i>Topological Methods in Data Analysis and Visualization II</i>, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Springer, 2011, pp. 91–106.","ista":"Wagner H, Chen C, Vuçini E. 2011.Efficient computation of persistent homology for cubical data. In: Topological Methods in Data Analysis and Visualization II. Theory, Algorithms, and Applications, , 91–106.","chicago":"Wagner, Hubert, Chao Chen, and Erald Vuçini. “Efficient Computation of Persistent Homology for Cubical Data.” In <i>Topological Methods in Data Analysis and Visualization II</i>, edited by Ronald Peikert, Helwig Hauser, Hamish Carr, and Raphael Fuchs, 91–106. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">https://doi.org/10.1007/978-3-642-23175-9_7</a>."},"oa_version":"None","publication":"Topological Methods in Data Analysis and Visualization II","doi":"10.1007/978-3-642-23175-9_7","publication_status":"published","title":"Efficient computation of persistent homology for cubical data","author":[{"full_name":"Wagner, Hubert","last_name":"Wagner","first_name":"Hubert"},{"last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","full_name":"Chen, Chao"},{"full_name":"Vuçini, Erald","last_name":"Vuçini","first_name":"Erald"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:18Z","publisher":"Springer","alternative_title":["Theory, Algorithms, and Applications"],"date_published":"2011-11-14T00:00:00Z","month":"11","year":"2011","language":[{"iso":"eng"}],"publist_id":"3375","department":[{"_id":"HeEd"}],"page":"91 - 106"},{"title":"Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Maître, Jean-Léon","last_name":"Maître","orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon"}],"date_updated":"2023-09-07T11:30:16Z","publisher":"Institute of Science and Technology Austria","month":"12","alternative_title":["ISTA Thesis"],"date_published":"2011-12-12T00:00:00Z","year":"2011","language":[{"iso":"eng"}],"department":[{"_id":"CaHe"}],"publist_id":"3373","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-0912-4566","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"status":"public","day":"12","date_created":"2018-12-11T12:02:23Z","_id":"3273","type":"dissertation","publication_identifier":{"issn":["2663-337X"]},"citation":{"short":"J.-L. Maître, Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors, Institute of Science and Technology Austria, 2011.","ista":"Maître J-L. 2011. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. Institute of Science and Technology Austria.","ieee":"J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors,” Institute of Science and Technology Austria, 2011.","ama":"Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. 2011.","chicago":"Maître, Jean-Léon. “Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors.” Institute of Science and Technology Austria, 2011.","apa":"Maître, J.-L. (2011). <i>Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors</i>. Institute of Science and Technology Austria.","mla":"Maître, Jean-Léon. <i>Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors</i>. Institute of Science and Technology Austria, 2011."},"oa_version":"None","publication_status":"published","degree_awarded":"PhD"},{"date_updated":"2023-09-07T11:31:48Z","oa":1,"month":"03","date_published":"2011-03-01T00:00:00Z","alternative_title":["ISTA Thesis"],"acknowledgement":"I would like to express my sincere gratitude to the following people who made with their continuous support and encouragement this thesis possible: First, I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring, especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf. Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz, the Recombinant Protein Production core facility and the animal care takers for providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler, Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy labmates for their help, a lot of discussions and to make the Sixt lab to a convenient place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele Weber and Alexander Eichner All members of the Department of Molecular Medicine for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael Ruppert for their friendship, nice chats and their uncensored point of view. ","year":"2011","page":"141","ddc":["570","579"],"date_created":"2018-12-11T12:02:24Z","supervisor":[{"full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt"}],"day":"01","status":"public","oa_version":"Published Version","degree_awarded":"PhD","file":[{"date_updated":"2020-07-14T12:46:06Z","date_created":"2019-03-26T08:12:21Z","file_name":"2011_Thesis_Kathrin_Schumann.pdf","checksum":"e69eee6252660f0b694a2ea8923ddc72","access_level":"closed","relation":"main_file","content_type":"application/pdf","file_id":"6177","file_size":4487708,"creator":"dernst"},{"checksum":"71727d63f424b5b446f68f4b87ecadc0","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"9175","creator":"dernst","file_size":4313127,"date_updated":"2021-02-22T11:24:30Z","date_created":"2021-02-22T11:24:30Z","success":1,"file_name":"2011_Thesis_Schumann_noS.pdf"}],"title":"The role of chemotactic gradients in dendritic cell migration","author":[{"full_name":"Schumann, Kathrin","last_name":"Schumann","first_name":"Kathrin","id":"F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"pubrep_id":"11","article_processing_charge":"No","department":[{"_id":"MiSi"}],"publist_id":"3371","_id":"3275","publication_identifier":{"issn":["2663-337X"]},"citation":{"chicago":"Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell Migration.” Institute of Science and Technology Austria, 2011.","ama":"Schumann K. The role of chemotactic gradients in dendritic cell migration. 2011.","ieee":"K. Schumann, “The role of chemotactic gradients in dendritic cell migration,” Institute of Science and Technology Austria, 2011.","short":"K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration, Institute of Science and Technology Austria, 2011.","ista":"Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration. Institute of Science and Technology Austria.","mla":"Schumann, Kathrin. <i>The Role of Chemotactic Gradients in Dendritic Cell Migration</i>. Institute of Science and Technology Austria, 2011.","apa":"Schumann, K. (2011). <i>The role of chemotactic gradients in dendritic cell migration</i>. Institute of Science and Technology Austria."},"file_date_updated":"2021-02-22T11:24:30Z","type":"dissertation","abstract":[{"text":"Chemokines organize immune cell trafficking by inducing either directed (tactic) or random (kinetic) migration and by activating integrins in order to support surface adhesion (haptic). Beyond that the same chemokines can establish clearly defined functional areas in secondary lymphoid organs. Until now it is unclear how chemokines can fulfill such diverse functions. One decisive prerequisite to explain these capacities is to know how chemokines are presented in tissue. In theory chemokines could occur either soluble or immobilized, and could be distributed either homogenously or as a concentration gradient. To dissect if and how the presenting mode of chemokines influences immune cells, I tested the response of dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen presenting cells that reside in the periphery and migrate into draining lymph nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs are guided to and within the LN by the chemokine receptor CCR7, which has two ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic reticular cells in the LN, but differ in their ability to bind to heparan sulfate residues. CCL21 has a highly charged C-terminal extension, which mediates binding to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes as a soluble molecule. This study shows that surface-bound CCL21 causes random, haptokinetic DC motility, which is confined to the chemokine coated area by insideout activation of β2 integrins that mediate cell binding to the surface. CCL19 on the other hand forms concentration gradients which trigger directional, chemotactic movement, but no surface adhesion. In addition DCs can actively manipulate this system by recruiting and activating serine proteases on their surfaces, which create - by proteolytically removing the adhesive C-terminus - a solubilized variant of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration gradient DCs establish a positive feedback loop to recruit further DCs from the periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients as well as immobilized haptokinetic fields at the same time and integrate these signals. The result is chemotactically biased haptokinesis - directional migration confined to a chemokine coated track or area - which could explain the dynamic but spatially tightly controlled swarming leukocyte locomotion patterns that have been observed in lymphatic organs by intravital microscopists. The finding that DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces coated with immobilized cues raises the question how these cells transmit intracellular forces to the environment, especially in the non-adherent migration mode. In order to migrate, cells have to generate and transmit force to the extracellular substrate. Force transmission is the prerequisite to procure an expansion of the leading edge and a forward motion of the whole cell body. In the current conceptions actin polymerization at the leading edge is coupled to extracellular ligands via the integrin family of transmembrane receptors, which allows the transmission of intracellular force. Against the paradigm of force transmission during migration, leukocytes, like DCs, are able to migrate in threedimensional environments without using integrin transmembrane receptors (Lämmermann et al., 2008). This reflects the biological function of leukocytes, as they can invade almost all tissues, whereby their migration has to be independent from the extracellular environment. How the cells can achieve this is unclear. For this study I examined DC migration in a defined threedimensional environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result was that chemotactic DCs can switch between integrin-dependent and integrin- independent locomotion and can thereby adapt to the adhesive properties of their environment. If the cells are able to couple their actin cytoskeleton to the substrate, actin polymerization is entirely converted into protrusion. Without coupling the actin cortex undergoes slippage and retrograde actin flow can be observed. But retrograde actin flow can be completely compensated by higher actin polymerization rate keeping the migration velocity and the shape of the cells unaltered. Mesenchymal cells like fibroblast cannot balance the loss of adhesive interaction, cannot protrude into open space and, therefore, strictly depend on integrinmediated force coupling. This leukocyte specific phenomenon of “adaptive force transmission” endows these cells with the unique ability to transit and invade almost every type of tissue. ","lang":"eng"}],"publication_status":"published"},{"month":"07","intvolume":"         6","date_published":"2011-07-20T00:00:00Z","publisher":"Public Library of Science","acknowledgement":"This work was supported by National Science Foundation (NSF) grants IBN-0344678, EF-0928048, National Institutes of Health (NIH) grant RO1 EY08124, NIH training grant T32-07035, and NIH training grant 5T90DA022763-04.\n\nMichael Berry and Olivier Marre have developed an algorithm similar to, but different from, ours (manuscript in preparation). We thank them for discussions of their work, and specifically thank Olivier Marre for suggesting to us that the most complete subtraction of a spike can be obtained by refitting the spike without a prior.\n\n","date_updated":"2021-01-12T07:42:19Z","file":[{"date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:11:38Z","file_name":"IST-2015-381-v1+1_journal.pone.0019884.pdf","relation":"main_file","checksum":"654464e99683b55a699734213d5356f1","access_level":"open_access","file_id":"4894","content_type":"application/pdf","file_size":885464,"creator":"system"}],"issue":"7","oa":1,"author":[{"first_name":"Jason","last_name":"Prentice","full_name":"Prentice, Jason S"},{"first_name":"Jan","last_name":"Homann","full_name":"Homann, Jan"},{"full_name":"Simmons, Kristina D","first_name":"Kristina","last_name":"Simmons"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Gasper Tkacik"},{"first_name":"Vijay","last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay"},{"first_name":"Philip","last_name":"Nelson","full_name":"Nelson, Philip C"}],"title":"Fast, scalable, Bayesian spike identification for multi-electrode arrays","publist_id":"3370","pubrep_id":"381","year":"2011","citation":{"mla":"Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” <i>PLoS One</i>, vol. 6, no. 7, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pone.0019884\">10.1371/journal.pone.0019884</a>.","apa":"Prentice, J., Homann, J., Simmons, K., Tkačik, G., Balasubramanian, V., &#38; Nelson, P. (2011). Fast, scalable, Bayesian spike identification for multi-electrode arrays. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0019884\">https://doi.org/10.1371/journal.pone.0019884</a>","chicago":"Prentice, Jason, Jan Homann, Kristina Simmons, Gašper Tkačik, Vijay Balasubramanian, and Philip Nelson. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” <i>PLoS One</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pone.0019884\">https://doi.org/10.1371/journal.pone.0019884</a>.","ista":"Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. 2011. Fast, scalable, Bayesian spike identification for multi-electrode arrays. PLoS One. 6(7).","ieee":"J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, and P. Nelson, “Fast, scalable, Bayesian spike identification for multi-electrode arrays,” <i>PLoS One</i>, vol. 6, no. 7. Public Library of Science, 2011.","short":"J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, P. Nelson, PLoS One 6 (2011).","ama":"Prentice J, Homann J, Simmons K, Tkačik G, Balasubramanian V, Nelson P. Fast, scalable, Bayesian spike identification for multi-electrode arrays. <i>PLoS One</i>. 2011;6(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0019884\">10.1371/journal.pone.0019884</a>"},"extern":1,"volume":6,"type":"journal_article","file_date_updated":"2020-07-14T12:46:06Z","abstract":[{"lang":"eng","text":"We present an algorithm to identify individual neural spikes observed on high-density multi-electrode arrays (MEAs). Our method can distinguish large numbers of distinct neural units, even when spikes overlap, and accounts for intrinsic variability of spikes from each unit. As MEAs grow larger, it is important to find spike-identification methods that are scalable, that is, the computational cost of spike fitting should scale well with the number of units observed. Our algorithm accomplishes this goal, and is fast, because it exploits the spatial locality of each unit and the basic biophysics of extracellular signal propagation. Human interaction plays a key role in our method; but effort is minimized and streamlined via a graphical interface. We illustrate our method on data from guinea pig retinal ganglion cells and document its performance on simulated data consisting of spikes added to experimentally measured background noise. We present several tests demonstrating that the algorithm is highly accurate: it exhibits low error rates on fits to synthetic data, low refractory violation rates, good receptive field coverage, and consistency across users."}],"date_created":"2018-12-11T12:02:24Z","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)"},"_id":"3276","status":"public","quality_controlled":0,"day":"20","doi":"10.1371/journal.pone.0019884","publication_status":"published","publication":"PLoS One"},{"publist_id":"3368","page":"237 - 243","year":"2011","publisher":"Elsevier","date_published":"2011-10-01T00:00:00Z","intvolume":"        61","month":"10","title":"A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade","author":[{"last_name":"Vila","first_name":"Roger","full_name":"Vila, Roger"},{"last_name":"Pierce","first_name":"Naomi","full_name":"Pierce, Naomi E"},{"first_name":"David","last_name":"Nash","full_name":"Nash, David R"},{"full_name":"Line Ugelvig","orcid":"0000-0003-1832-8883","last_name":"Ugelvig","first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87"}],"issue":"1","date_updated":"2021-01-12T07:42:20Z","publication":"Molecular Phylogenetics and Evolution","publication_status":"published","doi":"10.1016/j.ympev.2011.05.016","abstract":[{"text":"Despite much research on the socially parasitic large blue butterflies (genus Maculinea) in the past 40 years, their relationship to their closest relatives, Phengaris, is controversial and the relationships among the remaining genera in the Glaucopsyche section are largely unresolved. The evolutionary history of this butterfly section is particularly important to understand the evolution of life history diversity con- nected to food-plant and host-ant associations in the larval stage. In the present study, we use a combi- nation of four nuclear and two mitochondrial genes to reconstruct the phylogeny of the Glaucopsyche section, and in particular, to study the relationships among and within the Phengaris–Maculinea species.\nWe find a clear pattern between the clades recovered in the Glaucopsyche section phylogeny and their food-plant associations, with only the Phengaris–Maculinea clade utilising more than one plant family. Maculinea is, for the first time, recovered with strong support as a monophyletic group nested within Phengaris, with the closest relative being the rare genus Caerulea. The genus Glaucopsyche is polyphyletic, including the genera Sinia and Iolana. Interestingly, we find evidence for additional potential cryptic spe- cies within the highly endangered Maculinea, which has long been suspected from morphological, ecolog- ical and molecular studies.","lang":"eng"}],"type":"journal_article","volume":61,"citation":{"chicago":"Vila, Roger, Naomi Pierce, David Nash, and Line V Ugelvig. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” <i>Molecular Phylogenetics and Evolution</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.ympev.2011.05.016\">https://doi.org/10.1016/j.ympev.2011.05.016</a>.","ama":"Vila R, Pierce N, Nash D, Ugelvig LV. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. <i>Molecular Phylogenetics and Evolution</i>. 2011;61(1):237-243. doi:<a href=\"https://doi.org/10.1016/j.ympev.2011.05.016\">10.1016/j.ympev.2011.05.016</a>","ista":"Vila R, Pierce N, Nash D, Ugelvig LV. 2011. A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. Molecular Phylogenetics and Evolution. 61(1), 237–243.","short":"R. Vila, N. Pierce, D. Nash, L.V. Ugelvig, Molecular Phylogenetics and Evolution 61 (2011) 237–243.","ieee":"R. Vila, N. Pierce, D. Nash, and L. V. Ugelvig, “A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade,” <i>Molecular Phylogenetics and Evolution</i>, vol. 61, no. 1. Elsevier, pp. 237–243, 2011.","mla":"Vila, Roger, et al. “A Phylogenetic Revision of the Glaucopsyche Section (Lepidoptera: Lycaenidae), with Special Focus on the Phengaris-Maculinea Clade.” <i>Molecular Phylogenetics and Evolution</i>, vol. 61, no. 1, Elsevier, 2011, pp. 237–43, doi:<a href=\"https://doi.org/10.1016/j.ympev.2011.05.016\">10.1016/j.ympev.2011.05.016</a>.","apa":"Vila, R., Pierce, N., Nash, D., &#38; Ugelvig, L. V. (2011). A phylogenetic revision of the Glaucopsyche section (Lepidoptera: Lycaenidae), with special focus on the Phengaris-Maculinea clade. <i>Molecular Phylogenetics and Evolution</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ympev.2011.05.016\">https://doi.org/10.1016/j.ympev.2011.05.016</a>"},"extern":1,"status":"public","day":"01","quality_controlled":0,"_id":"3278","date_created":"2018-12-11T12:02:25Z"},{"day":"08","status":"public","_id":"3285","date_created":"2018-12-11T12:02:27Z","abstract":[{"lang":"eng","text":"Resolving the dynamical interplay of proteins and lipids in the live-cell plasma membrane represents a central goal in current cell biology. Superresolution concepts have introduced a means of capturing spatial heterogeneity at a nanoscopic length scale. Similar concepts for detecting dynamical transitions (superresolution chronoscopy) are still lacking. Here, we show that recently introduced spot-variation fluorescence correlation spectroscopy allows for sensing transient confinement times of membrane constituents at dramatically improved resolution. Using standard diffraction-limited optics, spot-variation fluorescence correlation spectroscopy captures signatures of single retardation events far below the transit time of the tracer through the focal spot. We provide an analytical description of special cases of transient binding of a tracer to pointlike traps, or association of a tracer with nanodomains. The influence of trap mobility and the underlying binding kinetics are quantified. Experimental approaches are suggested that allow for gaining quantitative mechanistic insights into the interaction processes of membrane constituents."}],"type":"journal_article","volume":100,"citation":{"apa":"Ruprecht, V., Wieser, S., Marguet, D., &#38; Schuetz, G. (2011). Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. <i>Biophysical Journal</i>. Biophysical Society. <a href=\"https://doi.org/10.1016/j.bpj.2011.04.035\">https://doi.org/10.1016/j.bpj.2011.04.035</a>","mla":"Ruprecht, Verena, et al. “Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” <i>Biophysical Journal</i>, vol. 100, no. 11, Biophysical Society, 2011, pp. 2839–45, doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.04.035\">10.1016/j.bpj.2011.04.035</a>.","ama":"Ruprecht V, Wieser S, Marguet D, Schuetz G. Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. <i>Biophysical Journal</i>. 2011;100(11):2839-2845. doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.04.035\">10.1016/j.bpj.2011.04.035</a>","ista":"Ruprecht V, Wieser S, Marguet D, Schuetz G. 2011. Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes. Biophysical Journal. 100(11), 2839–2845.","ieee":"V. Ruprecht, S. Wieser, D. Marguet, and G. Schuetz, “Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes,” <i>Biophysical Journal</i>, vol. 100, no. 11. Biophysical Society, pp. 2839–2845, 2011.","short":"V. Ruprecht, S. Wieser, D. Marguet, G. Schuetz, Biophysical Journal 100 (2011) 2839–2845.","chicago":"Ruprecht, Verena, Stefan Wieser, Didier Marguet, and Gerhard Schuetz. “Spot Variation Fluorescence Correlation Spectroscopy Allows for Superresolution Chronoscopy of Confinement Times in Membranes.” <i>Biophysical Journal</i>. Biophysical Society, 2011. <a href=\"https://doi.org/10.1016/j.bpj.2011.04.035\">https://doi.org/10.1016/j.bpj.2011.04.035</a>."},"extern":"1","oa_version":"None","publication":"Biophysical Journal","doi":"10.1016/j.bpj.2011.04.035","publication_status":"published","author":[{"full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena"},{"full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217","last_name":"Wieser","first_name":"Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marguet, Didier","first_name":"Didier","last_name":"Marguet"},{"full_name":"Schuetz, Gerhard","last_name":"Schuetz","first_name":"Gerhard"}],"title":"Spot variation fluorescence correlation spectroscopy allows for superresolution chronoscopy of confinement times in membranes","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"11","date_updated":"2021-01-12T07:42:23Z","publisher":"Biophysical Society","acknowledgement":"Y 250-B03/Austrian Science Fund FWF/Austria","date_published":"2011-06-08T00:00:00Z","month":"06","intvolume":"       100","year":"2011","language":[{"iso":"eng"}],"publist_id":"3360","page":"2839 - 2845"},{"issue":"10","author":[{"full_name":"Weghuber, Julian","last_name":"Weghuber","first_name":"Julian"},{"first_name":"Michael","last_name":"Aichinger","full_name":"Aichinger, Michael C."},{"last_name":"Brameshuber","first_name":"Mario","full_name":"Brameshuber, Mario"},{"full_name":"Stefan Wieser","first_name":"Stefan","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","last_name":"Wieser","orcid":"0000-0002-2670-2217"},{"first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","last_name":"Ruprecht","orcid":"0000-0003-4088-8633","full_name":"Verena Ruprecht"},{"full_name":"Plochberger, Birgit","last_name":"Plochberger","first_name":"Birgit"},{"full_name":"Madl, Josef","last_name":"Madl","first_name":"Josef"},{"first_name":"Andreas","last_name":"Horner","full_name":"Horner, Andreas"},{"last_name":"Reipert","first_name":"Siegfried","full_name":"Reipert, Siegfried"},{"last_name":"Lohner","first_name":"Karl","full_name":"Lohner, Karl"},{"last_name":"Henics","first_name":"Tamas","full_name":"Henics, Tamas"},{"full_name":"Schuetz, Gerhard J","first_name":"Gerhard","last_name":"Schuetz"}],"title":"Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells","date_updated":"2021-01-12T07:42:24Z","acknowledgement":"This work was funded by the GEN-AU project of the Austrian Research Promotion Agency, the Austrian Science Fund (FWF; project Y250-B03) and Intercell AG.\nWe thank the following colleagues for providing plasmids and cells: Daniel Legler (University of Konstanz, Switzerland), Jennifer Lippincott-Schwartz (NIH, Bethesda, USA), Hannes Stockinger (Medical University Vienna, Austria), Katharina Strub (University of Geneva, Switzerland), Lawrence Rajendran (ETH Zurich, Switzerland), Eileen M. Lafer (UTHSC San Antonio, Texas, USA), Mark McNiven (Mayo Clinic, Minnesota, USA), John Silvius (McGill University, Montreal, Canada), Christoph Romanin (JKU Linz, Austria), Herbert Stangl (Medical University Vienna, Austria) and Anton van der Merwe (Oxford University, Oxford, UK). We thank Harald Kotisch (MFPL, Vienna) for excellent technical assistance in the processing of samples for electron microscopy and Sergio Grinstein (Hospital for Sick Children Research Institute, Toronto) for fruitful discussions. ","publisher":"Elsevier","intvolume":"      1808","month":"10","date_published":"2011-10-01T00:00:00Z","year":"2011","publist_id":"3359","page":"2581 - 2590","day":"01","quality_controlled":0,"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","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)"},"date_created":"2018-12-11T12:02:28Z","_id":"3286","type":"journal_article","abstract":[{"lang":"eng","text":"Cationic antimicrobial peptides (CAMPs) selectively target bacterial membranes by electrostatic interactions with negatively charged lipids. It turned out that for inhibition of microbial growth a high CAMP membrane concentration is required, which can be realized by the incorporation of hydrophobic groups within the peptide. Increasing hydrophobicity, however, reduces the CAMP selectivity for bacterial over eukaryotic host membranes, thereby causing the risk of detrimental side-effects. In this study we addressed how cationic amphipathic peptides—in particular a CAMP with Lysine–Leucine–Lysine repeats (termed KLK)—affect the localization and dynamics of molecules in eukaryotic membranes. We found KLK to selectively inhibit the endocytosis of a subgroup of membrane proteins and lipids by electrostatically interacting with negatively charged sialic acid moieties. Ultrastructural characterization revealed the formation of membrane invaginations representing fission or fusion intermediates, in which the sialylated proteins and lipids were immobilized. Experiments on structurally different cationic amphipathic peptides (KLK, 6-MO-LF11-322 and NK14-2) indicated a cooperation of electrostatic and hydrophobic forces that selectively arrest sialylated membrane constituents."}],"extern":1,"citation":{"mla":"Weghuber, Julian, et al. “Cationic Amphipathic Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” <i>Biochimica et Biophysica Acta (BBA) - Biomembranes</i>, vol. 1808, no. 10, Elsevier, 2011, pp. 2581–90, doi:<a href=\"https://doi.org/10.1016/j.bbamem.2011.06.007\">10.1016/j.bbamem.2011.06.007</a>.","apa":"Weghuber, J., Aichinger, M., Brameshuber, M., Wieser, S., Ruprecht, V., Plochberger, B., … Schuetz, G. (2011). Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. <i>Biochimica et Biophysica Acta (BBA) - Biomembranes</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbamem.2011.06.007\">https://doi.org/10.1016/j.bbamem.2011.06.007</a>","chicago":"Weghuber, Julian, Michael Aichinger, Mario Brameshuber, Stefan Wieser, Verena Ruprecht, Birgit Plochberger, Josef Madl, et al. “Cationic Amphipathic Peptides Accumulate Sialylated Proteins and Lipids in the Plasma Membrane of Eukaryotic Host Cells.” <i>Biochimica et Biophysica Acta (BBA) - Biomembranes</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.bbamem.2011.06.007\">https://doi.org/10.1016/j.bbamem.2011.06.007</a>.","ieee":"J. Weghuber <i>et al.</i>, “Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells,” <i>Biochimica et Biophysica Acta (BBA) - Biomembranes</i>, vol. 1808, no. 10. Elsevier, pp. 2581–2590, 2011.","ista":"Weghuber J, Aichinger M, Brameshuber M, Wieser S, Ruprecht V, Plochberger B, Madl J, Horner A, Reipert S, Lohner K, Henics T, Schuetz G. 2011. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. Biochimica et Biophysica Acta (BBA) - Biomembranes. 1808(10), 2581–2590.","short":"J. Weghuber, M. Aichinger, M. Brameshuber, S. Wieser, V. Ruprecht, B. Plochberger, J. Madl, A. Horner, S. Reipert, K. Lohner, T. Henics, G. Schuetz, Biochimica et Biophysica Acta (BBA) - Biomembranes 1808 (2011) 2581–2590.","ama":"Weghuber J, Aichinger M, Brameshuber M, et al. Cationic amphipathic peptides accumulate sialylated proteins and lipids in the plasma membrane of eukaryotic host cells. <i>Biochimica et Biophysica Acta (BBA) - Biomembranes</i>. 2011;1808(10):2581-2590. doi:<a href=\"https://doi.org/10.1016/j.bbamem.2011.06.007\">10.1016/j.bbamem.2011.06.007</a>"},"volume":1808,"doi":"10.1016/j.bbamem.2011.06.007","publication_status":"published","publication":"Biochimica et Biophysica Acta (BBA) - Biomembranes"},{"publisher":"Bentham Science Publishers","month":"12","intvolume":"        12","date_published":"2011-12-01T00:00:00Z","issue":"8","author":[{"full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","last_name":"Ruprecht","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Axmann, Markus","last_name":"Axmann","first_name":"Markus"},{"last_name":"Wieser","orcid":"0000-0002-2670-2217","id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","first_name":"Stefan","full_name":"Wieser, Stefan"},{"first_name":"Gerhard","last_name":"Schuetz","full_name":"Schuetz, Gerhard"}],"title":"What can we learn from single molecule trajectories?","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T07:42:24Z","publist_id":"3358","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"page":"714 - 724","year":"2011","language":[{"iso":"eng"}],"type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"Diffusing membrane constituents are constantly exposed to a variety of forces that influence their stochastic path. Single molecule experiments allow for resolving trajectories at extremely high spatial and temporal accuracy, thereby offering insights into en route interactions of the tracer. In this review we discuss approaches to derive information about the underlying processes, based on single molecule tracking experiments. In particular, we focus on a new versatile way to analyze single molecule diffusion in the absence of a full analytical treatment. The method is based on comprehensive comparison of an experimental data set against the hypothetical outcome of multiple experiments performed on the computer. Since Monte Carlo simulations can be easily and rapidly performed even on state-of-the-art PCs, our method provides a simple way for testing various - even complicated - diffusion models. We describe the new method in detail, and show the applicability on two specific examples: firstly, kinetic rate constants can be derived for the transient interaction of mobile membrane proteins; secondly, residence time and corral size can be extracted for confined diffusion."}],"citation":{"short":"V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein &#38; Peptide Science 12 (2011) 714–724.","ieee":"V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from single molecule trajectories?,” <i>Current Protein &#38; Peptide Science</i>, vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011.","ista":"Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single molecule trajectories? Current Protein &#38; Peptide Science. 12(8), 714–724.","ama":"Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule trajectories? <i>Current Protein &#38; Peptide Science</i>. 2011;12(8):714-724. doi:<a href=\"https://doi.org/10.2174/138920311798841753\">10.2174/138920311798841753</a>","chicago":"Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What Can We Learn from Single Molecule Trajectories?” <i>Current Protein &#38; Peptide Science</i>. Bentham Science Publishers, 2011. <a href=\"https://doi.org/10.2174/138920311798841753\">https://doi.org/10.2174/138920311798841753</a>.","apa":"Ruprecht, V., Axmann, M., Wieser, S., &#38; Schuetz, G. (2011). What can we learn from single molecule trajectories? <i>Current Protein &#38; Peptide Science</i>. Bentham Science Publishers. <a href=\"https://doi.org/10.2174/138920311798841753\">https://doi.org/10.2174/138920311798841753</a>","mla":"Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?” <i>Current Protein &#38; Peptide Science</i>, vol. 12, no. 8, Bentham Science Publishers, 2011, pp. 714–24, doi:<a href=\"https://doi.org/10.2174/138920311798841753\">10.2174/138920311798841753</a>."},"volume":12,"day":"01","quality_controlled":"1","status":"public","_id":"3287","date_created":"2018-12-11T12:02:28Z","publication_status":"published","doi":"10.2174/138920311798841753","publication":"Current Protein & Peptide Science","oa_version":"None"},{"author":[{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Smutny","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael"},{"full_name":"Wu, Selwin","first_name":"Selwin","last_name":"Wu"},{"full_name":"Gomez, Guillermo","last_name":"Gomez","first_name":"Guillermo"},{"first_name":"Sabine","last_name":"Mangold","full_name":"Mangold, Sabine"},{"first_name":"Alpha","last_name":"Yap","full_name":"Yap, Alpha"},{"full_name":"Hamilton, Nicholas","last_name":"Hamilton","first_name":"Nicholas"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens","file":[{"access_level":"open_access","relation":"main_file","checksum":"57a5eb11dd05241c48c44f492b3ec3ac","file_size":1984567,"creator":"dernst","content_type":"application/pdf","file_id":"6399","date_created":"2019-05-10T10:51:43Z","date_updated":"2020-07-14T12:46:06Z","file_name":"2011_PLOS_Smutny.PDF"}],"publisher":"Public Library of Science","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"3357","department":[{"_id":"CaHe"}],"quality_controlled":"1","_id":"3288","abstract":[{"text":"The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion where cellular forces are exerted and resisted. Increasing evidence indicates that E-cadherin adhesion molecules at the ZA serve to sense force applied on the junctions and coordinate cytoskeletal responses to those forces. Efforts to understand the role that cadherins play in mechanotransduction have been limited by the lack of assays to measure the impact of forces on the ZA. In this study we used 4D imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions in confluent epithelial monolayers displayed prominent movements oriented orthogonal (perpendicular) to the ZA itself. Two components were identified in these movements: a relatively slow unidirectional (translational) component that could be readily fitted by least-squares regression analysis, upon which were superimposed more rapid oscillatory movements. Myosin IIB was a dominant factor responsible for driving the unilateral translational movements. In contrast, frequency spectrum analysis revealed that depletion of Myosin IIA increased the power of the oscillatory movements. This implies that Myosin IIA may serve to dampen oscillatory movements of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate that Myosin IIA and Myosin IIB make distinct contributions to junctional movement at the ZA.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:06Z","type":"journal_article","citation":{"mla":"Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” <i>PLoS One</i>, vol. 6, no. 7, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pone.0022458\">10.1371/journal.pone.0022458</a>.","apa":"Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., &#38; Hamilton, N. (2011). Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0022458\">https://doi.org/10.1371/journal.pone.0022458</a>","chicago":"Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap, and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” <i>PLoS One</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pone.0022458\">https://doi.org/10.1371/journal.pone.0022458</a>.","ama":"Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. <i>PLoS One</i>. 2011;6(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0022458\">10.1371/journal.pone.0022458</a>","ieee":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens,” <i>PLoS One</i>, vol. 6, no. 7. Public Library of Science, 2011.","short":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).","ista":"Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. 6(7)."},"publication_status":"published","oa":1,"issue":"7","date_updated":"2021-01-12T07:42:25Z","acknowledgement":"his work was funded by the National Health and Medical Research Council (NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship. A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the Institute for Molecular Bioscience, established with the generous support of the ACRF.","date_published":"2011-07-22T00:00:00Z","month":"07","intvolume":"         6","year":"2011","status":"public","day":"22","date_created":"2018-12-11T12:02:28Z","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)"},"ddc":["570"],"volume":6,"oa_version":"Published Version","publication":"PLoS One","doi":"10.1371/journal.pone.0022458"},{"citation":{"ama":"Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods under the coalescent process. <i>Genetics</i>. 2011;189(3):977-987. doi:<a href=\"https://doi.org/10.1534/genetics.111.129569\">10.1534/genetics.111.129569</a>","ista":"Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods under the coalescent process. Genetics. 189(3), 977–987.","ieee":"K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating likelihoods under the coalescent process,” <i>Genetics</i>, vol. 189, no. 3. Genetics Society of America, pp. 977–987, 2011.","short":"K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.","chicago":"Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method for Calculating Likelihoods under the Coalescent Process.” <i>Genetics</i>. Genetics Society of America, 2011. <a href=\"https://doi.org/10.1534/genetics.111.129569\">https://doi.org/10.1534/genetics.111.129569</a>.","apa":"Lohse, K., Harrison, R., &#38; Barton, N. H. (2011). A general method for calculating likelihoods under the coalescent process. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.111.129569\">https://doi.org/10.1534/genetics.111.129569</a>","mla":"Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the Coalescent Process.” <i>Genetics</i>, vol. 189, no. 3, Genetics Society of America, 2011, pp. 977–87, doi:<a href=\"https://doi.org/10.1534/genetics.111.129569\">10.1534/genetics.111.129569</a>."},"abstract":[{"lang":"eng","text":"Analysis of genomic data requires an efficient way to calculate likelihoods across very large numbers of loci. We describe a general method for finding the distribution of genealogies: we allow migration between demes, splitting of demes [as in the isolation-with-migration (IM) model], and recombination between linked loci. These processes are described by a set of linear recursions for the generating function of branch lengths. Under the infinite-sites model, the probability of any configuration of mutations can be found by differentiating this generating function. Such calculations are feasible for small numbers of sampled genomes: as an example, we show how the generating function can be derived explicitly for three genes under the two-deme IM model. This derivation is done automatically, using Mathematica. Given data from a large number of unlinked and nonrecombining blocks of sequence, these results can be used to find maximum-likelihood estimates of model parameters by tabulating the probabilities of all relevant mutational configurations and then multiplying across loci. The feasibility of the method is demonstrated by applying it to simulated data and to a data set previously analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila simulans and D. melanogaster. Our results suggest that such likelihood calculations are scalable to genomic data as long as the numbers of sampled individuals and mutations per sequence block are small."}],"scopus_import":1,"type":"journal_article","_id":"3290","quality_controlled":"1","project":[{"call_identifier":"FP7","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation"}],"publication_status":"published","publisher":"Genetics Society of America","title":"A general method for calculating likelihoods under the coalescent process","author":[{"full_name":"Lohse, Konrad","first_name":"Konrad","last_name":"Lohse"},{"first_name":"Richard","last_name":"Harrison","full_name":"Harrison, Richard"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240","last_name":"Barton"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"NiBa"}],"publist_id":"3355","language":[{"iso":"eng"}],"volume":189,"date_created":"2018-12-11T12:02:29Z","day":"01","status":"public","publication":"Genetics","doi":"10.1534/genetics.111.129569","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/","open_access":"1"}],"ec_funded":1,"oa_version":"Submitted Version","date_published":"2011-11-01T00:00:00Z","intvolume":"       189","month":"11","date_updated":"2021-01-12T07:42:26Z","oa":1,"issue":"3","page":"977 - 987","year":"2011"},{"ddc":["000"],"date_created":"2018-12-11T12:02:31Z","status":"public","day":"07","doi":"10.1145/2037636.2037644","oa_version":"Published Version","month":"08","date_published":"2011-08-07T00:00:00Z","article_number":"8","date_updated":"2023-02-23T11:21:02Z","oa":1,"conference":{"location":"Vancouver, BC, Canada","end_date":"2011-08-11","start_date":"2011-08-07","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"year":"2011","citation":{"apa":"Wojtan, C., Müller Fischer, M., &#38; Brochu, T. (2011). Liquid simulation with mesh-based surface tracking. Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada: ACM. <a href=\"https://doi.org/10.1145/2037636.2037644\">https://doi.org/10.1145/2037636.2037644</a>","mla":"Wojtan, Chris, et al. <i>Liquid Simulation with Mesh-Based Surface Tracking</i>. 8, ACM, 2011, doi:<a href=\"https://doi.org/10.1145/2037636.2037644\">10.1145/2037636.2037644</a>.","ieee":"C. Wojtan, M. Müller Fischer, and T. Brochu, “Liquid simulation with mesh-based surface tracking,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Vancouver, BC, Canada, 2011.","ista":"Wojtan C, Müller Fischer M, Brochu T. 2011. Liquid simulation with mesh-based surface tracking. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 8.","short":"C. Wojtan, M. Müller Fischer, T. Brochu, in:, ACM, 2011.","ama":"Wojtan C, Müller Fischer M, Brochu T. Liquid simulation with mesh-based surface tracking. In: ACM; 2011. doi:<a href=\"https://doi.org/10.1145/2037636.2037644\">10.1145/2037636.2037644</a>","chicago":"Wojtan, Chris, Matthias Müller Fischer, and Tyson Brochu. “Liquid Simulation with Mesh-Based Surface Tracking.” ACM, 2011. <a href=\"https://doi.org/10.1145/2037636.2037644\">https://doi.org/10.1145/2037636.2037644</a>."},"file_date_updated":"2020-07-14T12:46:06Z","type":"conference","scopus_import":1,"abstract":[{"lang":"eng","text":"Animating detailed liquid surfaces has always been a challenge for computer graphics researchers and visual effects artists. Over the past few years, researchers in this field have focused on mesh-based surface tracking to synthesize extremely detailed liquid surfaces as efficiently as possible. This course provides a solid understanding of the steps required to create a fluid simulator with a mesh-based liquid surface.\r\n\r\nThe course begins with an overview of several existing liquid-surface-tracking techniques and the pros and cons of each method. Then it explains how to embed a triangle mesh into a finite-difference-based fluid simulator and describes several methods for allowing the liquid surface to merge together or break apart. The final section showcases the benefits and further applications of a mesh-based liquid surface, highlighting state-of-the-art methods for tracking colors and textures, maintaining liquid volume, preserving small surface features, and simulating realistic surface-tension waves."}],"_id":"3297","quality_controlled":"1","publication_status":"published","has_accepted_license":"1","publisher":"ACM","file":[{"file_name":"IST-2016-599-v1+1_meshyFluidsCourseSIGGRAPH2011.pdf","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:13:34Z","file_id":"5018","content_type":"application/pdf","file_size":34672096,"creator":"system","checksum":"8d508ad7c82f50978acbaa4170ee0a75","access_level":"open_access","relation":"main_file"}],"title":"Liquid simulation with mesh-based surface tracking","author":[{"orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"},{"full_name":"Müller Fischer, Matthias","first_name":"Matthias","last_name":"Müller Fischer"},{"full_name":"Brochu, Tyson","first_name":"Tyson","last_name":"Brochu"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChWo"}],"publist_id":"3344","language":[{"iso":"eng"}],"pubrep_id":"599"},{"oa_version":"Submitted Version","doi":"10.1145/2019406.2019411","status":"public","day":"05","ddc":["000"],"date_created":"2018-12-11T12:02:32Z","year":"2011","conference":{"name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","start_date":"2011-08-05","end_date":"2011-08-07","location":"Vancouver, Canada"},"page":"33 - 42","oa":1,"date_updated":"2023-02-23T11:21:05Z","date_published":"2011-08-05T00:00:00Z","month":"08","publication_status":"published","quality_controlled":"1","_id":"3298","editor":[{"full_name":"Spencer, Stephen","last_name":"Spencer","first_name":"Stephen"}],"abstract":[{"text":"We present a new algorithm for enforcing incompressibility for Smoothed Particle Hydrodynamics (SPH) by preserving uniform density across the domain. We propose a hybrid method that uses a Poisson solve on a coarse grid to enforce a divergence free velocity field, followed by a local density correction of the particles. This avoids typical grid artifacts and maintains the Lagrangian nature of SPH by directly transferring pressures onto particles. Our method can be easily integrated with existing SPH techniques such as the incompressible PCISPH method as well as weakly compressible SPH by adding an additional force term. We show that this hybrid method accelerates convergence towards uniform density and permits a significantly larger time step compared to earlier approaches while producing similar results. We demonstrate our approach in a variety of scenarios with significant pressure gradients such as splashing liquids.","lang":"eng"}],"scopus_import":1,"type":"conference","file_date_updated":"2020-07-14T12:46:06Z","citation":{"chicago":"Raveendran, Karthik, Chris Wojtan, and Greg Turk. “Hybrid Smoothed Particle Hydrodynamics.” edited by Stephen Spencer, 33–42. ACM, 2011. <a href=\"https://doi.org/10.1145/2019406.2019411\">https://doi.org/10.1145/2019406.2019411</a>.","short":"K. Raveendran, C. Wojtan, G. Turk, in:, S. Spencer (Ed.), ACM, 2011, pp. 33–42.","ieee":"K. Raveendran, C. Wojtan, and G. Turk, “Hybrid smoothed particle hydrodynamics,” presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Vancouver, Canada, 2011, pp. 33–42.","ista":"Raveendran K, Wojtan C, Turk G. 2011. Hybrid smoothed particle hydrodynamics. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 33–42.","ama":"Raveendran K, Wojtan C, Turk G. Hybrid smoothed particle hydrodynamics. In: Spencer S, ed. ACM; 2011:33-42. doi:<a href=\"https://doi.org/10.1145/2019406.2019411\">10.1145/2019406.2019411</a>","mla":"Raveendran, Karthik, et al. <i>Hybrid Smoothed Particle Hydrodynamics</i>. Edited by Stephen Spencer, ACM, 2011, pp. 33–42, doi:<a href=\"https://doi.org/10.1145/2019406.2019411\">10.1145/2019406.2019411</a>.","apa":"Raveendran, K., Wojtan, C., &#38; Turk, G. (2011). Hybrid smoothed particle hydrodynamics. In S. Spencer (Ed.) (pp. 33–42). Presented at the SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, Vancouver, Canada: ACM. <a href=\"https://doi.org/10.1145/2019406.2019411\">https://doi.org/10.1145/2019406.2019411</a>"},"pubrep_id":"598","language":[{"iso":"eng"}],"publist_id":"3343","department":[{"_id":"ChWo"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Hybrid smoothed particle hydrodynamics","author":[{"last_name":"Raveendran","first_name":"Karthik","full_name":"Raveendran, Karthik"},{"last_name":"Wojtan","orcid":"0000-0001-6646-5546","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J"},{"full_name":"Turk, Greg","first_name":"Greg","last_name":"Turk"}],"file":[{"file_name":"IST-2016-598-v1+1_HybridSPH_Preprint.pdf","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:09:44Z","creator":"system","file_size":2536216,"content_type":"application/pdf","file_id":"4769","access_level":"open_access","checksum":"6579d27709946e0eefbfa60a456b4913","relation":"main_file"}],"publisher":"ACM","has_accepted_license":"1"},{"_id":"3299","quality_controlled":"1","citation":{"apa":"Henzinger, T. A., &#38; Mateescu, M. (2011). Propagation models for computing biochemical reaction networks (pp. 1–3). Presented at the CMSB: Computational Methods in Systems Biology, Paris, France: Springer. <a href=\"https://doi.org/10.1145/2037509.2037510\">https://doi.org/10.1145/2037509.2037510</a>","mla":"Henzinger, Thomas A., and Maria Mateescu. <i>Propagation Models for Computing Biochemical Reaction Networks</i>. Springer, 2011, pp. 1–3, doi:<a href=\"https://doi.org/10.1145/2037509.2037510\">10.1145/2037509.2037510</a>.","ama":"Henzinger TA, Mateescu M. Propagation models for computing biochemical reaction networks. In: Springer; 2011:1-3. doi:<a href=\"https://doi.org/10.1145/2037509.2037510\">10.1145/2037509.2037510</a>","short":"T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 1–3.","ieee":"T. A. Henzinger and M. Mateescu, “Propagation models for computing biochemical reaction networks,” presented at the CMSB: Computational Methods in Systems Biology, Paris, France, 2011, pp. 1–3.","ista":"Henzinger TA, Mateescu M. 2011. Propagation models for computing biochemical reaction networks. CMSB: Computational Methods in Systems Biology, 1–3.","chicago":"Henzinger, Thomas A, and Maria Mateescu. “Propagation Models for Computing Biochemical Reaction Networks,” 1–3. Springer, 2011. <a href=\"https://doi.org/10.1145/2037509.2037510\">https://doi.org/10.1145/2037509.2037510</a>."},"type":"conference","file_date_updated":"2020-07-14T12:46:06Z","scopus_import":1,"abstract":[{"lang":"eng","text":"We introduce propagation models, a formalism designed to support general and efficient data structures for the transient analysis of biochemical reaction networks. We give two use cases for propagation abstract data types: the uniformization method and numerical integration. We also sketch an implementation of a propagation abstract data type, which uses abstraction to approximate states."}],"publication_status":"published","file":[{"checksum":"7f5c65509db1a9fb049abedd9663ed06","access_level":"open_access","relation":"main_file","creator":"system","file_size":255780,"file_id":"4649","content_type":"application/pdf","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:07:50Z","file_name":"IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf"}],"title":"Propagation models for computing biochemical reaction networks","author":[{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"first_name":"Maria","last_name":"Mateescu","full_name":"Mateescu, Maria"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","has_accepted_license":"1","publisher":"Springer","language":[{"iso":"eng"}],"pubrep_id":"92","publist_id":"3341","department":[{"_id":"ToHe"}],"ddc":["000","004"],"date_created":"2018-12-11T12:02:32Z","day":"21","status":"public","oa_version":"Submitted Version","doi":"10.1145/2037509.2037510","date_updated":"2021-01-12T07:42:29Z","oa":1,"month":"09","date_published":"2011-09-21T00:00:00Z","year":"2011","page":"1 - 3","conference":{"name":"CMSB: Computational Methods in Systems Biology","start_date":"2011-09-21","end_date":"2011-09-23","location":"Paris, France"}},{"pubrep_id":"91","year":"2011","language":[{"iso":"eng"}],"publist_id":"3339","conference":{"name":"WCSB: Workshop on Computational Systems Biology (TICSP)"},"department":[{"_id":"ToHe"}],"title":"Tail approximation for the chemical master equation","oa":1,"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Mateescu, Maria","first_name":"Maria","last_name":"Mateescu"}],"file":[{"date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:18:12Z","file_name":"IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf","checksum":"aa4d7a832a5419e6c0090650ebff2b9a","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5331","creator":"system","file_size":240820}],"date_updated":"2021-01-12T07:42:30Z","publisher":"Tampere International Center for Signal Processing","date_published":"2011-01-01T00:00:00Z","month":"01","has_accepted_license":"1","oa_version":"Submitted Version","publication_status":"published","status":"public","day":"01","quality_controlled":"1","date_created":"2018-12-11T12:02:33Z","_id":"3301","ddc":["005","570"],"abstract":[{"text":"The chemical master equation is a differential equation describing the time evolution of the probability distribution over the possible “states” of a biochemical system. The solution of this equation is of interest within the systems biology field ever since the importance of the molec- ular noise has been acknowledged. Unfortunately, most of the systems do not have analytical solutions, and numerical solutions suffer from the course of dimensionality and therefore need to be approximated. Here, we introduce the concept of tail approximation, which retrieves an approximation of the probabilities in the tail of a distribution from the total probability of the tail and its conditional expectation. This approximation method can then be used to numerically compute the solution of the chemical master equation on a subset of the state space, thus fighting the explosion of the state space, for which this problem is renowned.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:06Z","type":"conference","citation":{"chicago":"Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical Master Equation.” Tampere International Center for Signal Processing, 2011.","ama":"Henzinger TA, Mateescu M. Tail approximation for the chemical master equation. In: Tampere International Center for Signal Processing; 2011.","ista":"Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master equation. WCSB: Workshop on Computational Systems Biology (TICSP).","short":"T.A. Henzinger, M. Mateescu, in:, Tampere International Center for Signal Processing, 2011.","ieee":"T. A. Henzinger and M. Mateescu, “Tail approximation for the chemical master equation,” presented at the WCSB: Workshop on Computational Systems Biology (TICSP), 2011.","mla":"Henzinger, Thomas A., and Maria Mateescu. <i>Tail Approximation for the Chemical Master Equation</i>. Tampere International Center for Signal Processing, 2011.","apa":"Henzinger, T. A., &#38; Mateescu, M. (2011). Tail approximation for the chemical master equation. Presented at the WCSB: Workshop on Computational Systems Biology (TICSP), Tampere International Center for Signal Processing."}},{"month":"06","has_accepted_license":"1","date_published":"2011-06-14T00:00:00Z","publisher":"USENIX","date_updated":"2021-01-12T07:42:31Z","file":[{"file_size":232770,"creator":"system","file_id":"5333","content_type":"application/pdf","checksum":"21a461ac004bb535c83320fe79b30375","relation":"main_file","access_level":"open_access","file_name":"IST-2012-90-v1+1_Static_scheduling_in_clouds.pdf","date_created":"2018-12-12T10:18:14Z","date_updated":"2020-07-14T12:46:06Z"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Static scheduling in clouds","author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A"},{"full_name":"Singh, Anmol","last_name":"Singh","first_name":"Anmol","id":"72A86902-E99F-11E9-9F62-915534D1B916"},{"first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","last_name":"Singh","full_name":"Singh, Vasu"},{"full_name":"Wies, Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","last_name":"Wies"},{"full_name":"Zufferey, Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","first_name":"Damien","last_name":"Zufferey","orcid":"0000-0002-3197-8736"}],"oa":1,"page":"1 - 6","conference":{"end_date":"2011-06-15","start_date":"2011-06-14","name":"HotCloud: Workshop on Hot Topics in Cloud Computing"},"department":[{"_id":"ToHe"}],"publist_id":"3338","language":[{"iso":"eng"}],"year":"2011","pubrep_id":"90","citation":{"mla":"Henzinger, Thomas A., et al. <i>Static Scheduling in Clouds</i>. USENIX, 2011, pp. 1–6.","apa":"Henzinger, T. A., Singh, A., Singh, V., Wies, T., &#38; Zufferey, D. (2011). Static scheduling in clouds (pp. 1–6). Presented at the HotCloud: Workshop on Hot Topics in Cloud Computing, USENIX.","chicago":"Henzinger, Thomas A, Anmol Singh, Vasu Singh, Thomas Wies, and Damien Zufferey. “Static Scheduling in Clouds,” 1–6. USENIX, 2011.","ama":"Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. Static scheduling in clouds. In: USENIX; 2011:1-6.","ista":"Henzinger TA, Singh A, Singh V, Wies T, Zufferey D. 2011. Static scheduling in clouds. HotCloud: Workshop on Hot Topics in Cloud Computing, 1–6.","short":"T.A. Henzinger, A. Singh, V. Singh, T. Wies, D. Zufferey, in:, USENIX, 2011, pp. 1–6.","ieee":"T. A. Henzinger, A. Singh, V. Singh, T. Wies, and D. Zufferey, “Static scheduling in clouds,” presented at the HotCloud: Workshop on Hot Topics in Cloud Computing, 2011, pp. 1–6."},"type":"conference","file_date_updated":"2020-07-14T12:46:06Z","abstract":[{"text":"Cloud computing aims to give users virtually unlimited pay-per-use computing resources without the burden of managing the underlying infrastructure. We present a new job execution environment Flextic that exploits scal- able static scheduling techniques to provide the user with a flexible pricing model, such as a tradeoff between dif- ferent degrees of execution speed and execution price, and at the same time, reduce scheduling overhead for the cloud provider. We have evaluated a prototype of Flextic on Amazon EC2 and compared it against Hadoop. For various data parallel jobs from machine learning, im- age processing, and gene sequencing that we considered, Flextic has low scheduling overhead and reduces job du- ration by up to 15% compared to Hadoop, a dynamic cloud scheduler.","lang":"eng"}],"ddc":["000","005"],"_id":"3302","date_created":"2018-12-11T12:02:33Z","status":"public","quality_controlled":"1","day":"14","publication_status":"published","oa_version":"Submitted Version"},{"editor":[{"last_name":"van de Weygaert","first_name":"R","full_name":"van de Weygaert, R"},{"last_name":"Vegter","first_name":"G","full_name":"Vegter, G"},{"last_name":"Ritzerveld","first_name":"J","full_name":"Ritzerveld, J"},{"full_name":"Icke, V","last_name":"Icke","first_name":"V"}],"_id":"3311","ddc":["510"],"date_created":"2018-12-11T12:02:36Z","quality_controlled":"1","status":"public","day":"31","citation":{"apa":"Edelsbrunner, H. (n.d.). Alpha shapes - a survey. In R. van de Weygaert, G. Vegter, J. Ritzerveld, &#38; V. Icke (Eds.), <i>Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings</i>. Springer.","mla":"Edelsbrunner, Herbert. “Alpha Shapes - a Survey.” <i>Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings</i>, edited by R van de Weygaert et al., Springer.","ama":"Edelsbrunner H. Alpha shapes - a survey. In: van de Weygaert R, Vegter G, Ritzerveld J, Icke V, eds. <i>Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings</i>. Springer.","ieee":"H. Edelsbrunner, “Alpha shapes - a survey,” in <i>Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings</i>, R. van de Weygaert, G. Vegter, J. Ritzerveld, and V. Icke, Eds. Springer.","ista":"Edelsbrunner H.Alpha shapes - a survey. In: Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings. .","short":"H. Edelsbrunner, in:, R. van de Weygaert, G. Vegter, J. Ritzerveld, V. Icke (Eds.), Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings, Springer, n.d.","chicago":"Edelsbrunner, Herbert. “Alpha Shapes - a Survey.” In <i>Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings</i>, edited by R van de Weygaert, G Vegter, J Ritzerveld, and V Icke. Springer, n.d."},"type":"book_chapter","file_date_updated":"2022-05-24T07:55:05Z","abstract":[{"text":"Alpha shapes have been conceived in 1981 as an attempt to define the shape of a finite set of point in the plane. Since then, connections to diverse areas in the sciences and engineering have developed, including to pattern recognition, digital shape sampling and processing, and structural molecular biology. This survey begins with a historical account and discusses geometric, algorithmic, topological, and combinatorial aspects of alpha shapes in this sequence.","lang":"eng"}],"oa_version":"Submitted Version","publication_status":"inpress","publication":"Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings","date_updated":"2022-05-24T07:56:30Z","file":[{"date_updated":"2022-05-24T07:55:05Z","date_created":"2022-05-24T07:55:05Z","success":1,"file_name":"2010_AlphaShapes.pdf","relation":"main_file","checksum":"a592ea438351e7280eea993a7713ab8f","access_level":"open_access","content_type":"application/pdf","file_id":"11408","file_size":475254,"creator":"dernst"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Alpha shapes - a survey","oa":1,"author":[{"full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"}],"month":"12","has_accepted_license":"1","date_published":"2011-12-31T00:00:00Z","publisher":"Springer","language":[{"iso":"eng"}],"year":"2011","article_processing_charge":"No","publist_id":"3329","department":[{"_id":"HeEd"}]}]