[{"volume":30,"day":"19","status":"public","main_file_link":[{"url":"http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf","open_access":"1"}],"month":"07","doi":"10.1111/j.1467-8659.2011.01985.x","publication":"Computer Graphics Forum","_id":"3269","year":"2011","title":"Perceptual global illumination cancellation in complex projection environments","date_created":"2018-12-11T12:02:22Z","date_updated":"2021-01-12T07:42:16Z","page":"1261 - 1268","date_published":"2011-07-19T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","publication_status":"published","article_processing_charge":"No","article_type":"original","author":[{"first_name":"Yu","full_name":"Sheng, Yu","last_name":"Sheng"},{"last_name":"Cutler","full_name":"Cutler, Barbara","first_name":"Barbara"},{"first_name":"Chao","full_name":"Chen, Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nasman, Joshua","first_name":"Joshua","last_name":"Nasman"}],"oa_version":"Published Version","publisher":"Wiley-Blackwell","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"issue":"4","department":[{"_id":"HeEd"}],"abstract":[{"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.","lang":"eng"}],"intvolume":"        30","publist_id":"3377","citation":{"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>","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>","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>.","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.","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>.","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."},"scopus_import":1},{"language":[{"iso":"eng"}],"page":"141","date_published":"2011-03-01T00:00:00Z","supervisor":[{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K"}],"date_created":"2018-12-11T12:02:24Z","date_updated":"2023-09-07T11:31:48Z","article_processing_charge":"No","publication_status":"published","pubrep_id":"11","publication_identifier":{"issn":["2663-337X"]},"ddc":["570","579"],"month":"03","status":"public","day":"01","file_date_updated":"2021-02-22T11:24:30Z","degree_awarded":"PhD","title":"The role of chemotactic gradients in dendritic cell migration","year":"2011","_id":"3275","has_accepted_license":"1","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"}],"department":[{"_id":"MiSi"}],"citation":{"ieee":"K. Schumann, “The role of chemotactic gradients in dendritic cell migration,” Institute of Science and Technology Austria, 2011.","mla":"Schumann, Kathrin. <i>The Role of Chemotactic Gradients in Dendritic Cell Migration</i>. 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.","ama":"Schumann K. The role of chemotactic gradients in dendritic cell migration. 2011.","apa":"Schumann, K. (2011). <i>The role of chemotactic gradients in dendritic cell migration</i>. Institute of Science and Technology Austria.","short":"K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration, Institute of Science and Technology Austria, 2011.","chicago":"Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell Migration.” Institute of Science and Technology Austria, 2011."},"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. ","publist_id":"3371","author":[{"full_name":"Schumann, Kathrin","first_name":"Kathrin","last_name":"Schumann","id":"F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F"}],"file":[{"file_id":"6177","file_name":"2011_Thesis_Kathrin_Schumann.pdf","file_size":4487708,"relation":"main_file","access_level":"closed","date_updated":"2020-07-14T12:46:06Z","date_created":"2019-03-26T08:12:21Z","checksum":"e69eee6252660f0b694a2ea8923ddc72","content_type":"application/pdf","creator":"dernst"},{"checksum":"71727d63f424b5b446f68f4b87ecadc0","content_type":"application/pdf","file_size":4313127,"relation":"main_file","access_level":"open_access","date_updated":"2021-02-22T11:24:30Z","date_created":"2021-02-22T11:24:30Z","success":1,"creator":"dernst","file_id":"9175","file_name":"2011_Thesis_Schumann_noS.pdf"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"dissertation","oa":1,"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"oa_version":"Published Version"},{"title":"Fast, scalable, Bayesian spike identification for multi-electrode arrays","issue":"7","oa":1,"type":"journal_article","file_date_updated":"2020-07-14T12:46:06Z","_id":"3276","year":"2011","publication":"PLoS One","publisher":"Public Library of Science","doi":"10.1371/journal.pone.0019884","author":[{"first_name":"Jason","full_name":"Prentice, Jason S","last_name":"Prentice"},{"last_name":"Homann","first_name":"Jan","full_name":"Homann, Jan"},{"full_name":"Simmons, Kristina D","first_name":"Kristina","last_name":"Simmons"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","full_name":"Gasper Tkacik","first_name":"Gasper"},{"full_name":"Balasubramanian, Vijay","first_name":"Vijay","last_name":"Balasubramanian"},{"last_name":"Nelson","first_name":"Philip","full_name":"Nelson, Philip C"}],"month":"07","status":"public","day":"20","file":[{"creator":"system","file_size":885464,"date_updated":"2020-07-14T12:46:06Z","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:11:38Z","checksum":"654464e99683b55a699734213d5356f1","content_type":"application/pdf","file_name":"IST-2015-381-v1+1_journal.pone.0019884.pdf","file_id":"4894"}],"volume":6,"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>.","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.","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).","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>","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>.","short":"J. Prentice, J. Homann, K. Simmons, G. Tkačik, V. Balasubramanian, P. Nelson, PLoS One 6 (2011)."},"extern":1,"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","publication_status":"published","pubrep_id":"381","publist_id":"3370","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"intvolume":"         6","quality_controlled":0,"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_published":"2011-07-20T00:00:00Z","date_created":"2018-12-11T12:02:24Z","date_updated":"2021-01-12T07:42:19Z"},{"ddc":["570"],"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publication_status":"published","date_published":"2011-07-22T00:00:00Z","date_created":"2018-12-11T12:02:28Z","date_updated":"2021-01-12T07:42:25Z","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0022458","title":"Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens","file_date_updated":"2020-07-14T12:46:06Z","_id":"3288","year":"2011","publication":"PLoS One","status":"public","volume":6,"day":"22","month":"07","publist_id":"3357","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.","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>.","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.","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).","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>","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>.","short":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011)."},"department":[{"_id":"CaHe"}],"intvolume":"         6","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"}],"has_accepted_license":"1","oa_version":"Published Version","oa":1,"issue":"7","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Public Library of Science","file":[{"creator":"dernst","content_type":"application/pdf","checksum":"57a5eb11dd05241c48c44f492b3ec3ac","file_size":1984567,"relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:06Z","date_created":"2019-05-10T10:51:43Z","file_name":"2011_PLOS_Smutny.PDF","file_id":"6399"}],"author":[{"full_name":"Smutny, Michael","first_name":"Michael","orcid":"0000-0002-5920-9090","last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wu","full_name":"Wu, Selwin","first_name":"Selwin"},{"last_name":"Gomez","first_name":"Guillermo","full_name":"Gomez, Guillermo"},{"full_name":"Mangold, Sabine","first_name":"Sabine","last_name":"Mangold"},{"last_name":"Yap","first_name":"Alpha","full_name":"Yap, Alpha"},{"first_name":"Nicholas","full_name":"Hamilton, Nicholas","last_name":"Hamilton"}]},{"author":[{"first_name":"Konrad","full_name":"Lohse, Konrad","last_name":"Lohse"},{"first_name":"Richard","full_name":"Harrison, Richard","last_name":"Harrison"},{"first_name":"Nicholas H","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"ec_funded":1,"type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"issue":"3","publisher":"Genetics Society of America","oa_version":"Submitted Version","abstract":[{"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.","lang":"eng"}],"intvolume":"       189","department":[{"_id":"NiBa"}],"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>","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>","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>.","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.","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>.","ista":"Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods under the coalescent process. Genetics. 189(3), 977–987."},"scopus_import":1,"project":[{"_id":"25B07788-B435-11E9-9278-68D0E5697425","name":"Limits to selection in biology and in evolutionary computation","call_identifier":"FP7","grant_number":"250152"}],"publist_id":"3355","month":"11","status":"public","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/","open_access":"1"}],"day":"01","volume":189,"title":"A general method for calculating likelihoods under the coalescent process","publication":"Genetics","_id":"3290","year":"2011","doi":"10.1534/genetics.111.129569","quality_controlled":"1","language":[{"iso":"eng"}],"page":"977 - 987","date_published":"2011-11-01T00:00:00Z","date_created":"2018-12-11T12:02:29Z","date_updated":"2021-01-12T07:42:26Z","publication_status":"published"},{"file":[{"relation":"main_file","date_updated":"2020-07-14T12:46:06Z","access_level":"open_access","date_created":"2018-12-12T10:13:34Z","file_size":34672096,"content_type":"application/pdf","checksum":"8d508ad7c82f50978acbaa4170ee0a75","creator":"system","file_id":"5018","file_name":"IST-2016-599-v1+1_meshyFluidsCourseSIGGRAPH2011.pdf"}],"author":[{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"},{"last_name":"Müller Fischer","first_name":"Matthias","full_name":"Müller Fischer, Matthias"},{"first_name":"Tyson","full_name":"Brochu, Tyson","last_name":"Brochu"}],"oa_version":"Published Version","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","publisher":"ACM","department":[{"_id":"ChWo"}],"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."}],"has_accepted_license":"1","publist_id":"3344","scopus_import":1,"citation":{"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.","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.","short":"C. Wojtan, M. Müller Fischer, T. Brochu, in:, ACM, 2011.","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>.","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>","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>"},"status":"public","day":"07","month":"08","doi":"10.1145/2037636.2037644","conference":{"location":"Vancouver, BC, Canada","start_date":"2011-08-07","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2011-08-11"},"title":"Liquid simulation with mesh-based surface tracking","file_date_updated":"2020-07-14T12:46:06Z","_id":"3297","year":"2011","date_published":"2011-08-07T00:00:00Z","date_updated":"2023-02-23T11:21:02Z","date_created":"2018-12-11T12:02:31Z","quality_controlled":"1","language":[{"iso":"eng"}],"pubrep_id":"599","ddc":["000"],"publication_status":"published","article_number":"8"},{"doi":"10.1145/2019406.2019411","conference":{"start_date":"2011-08-05","end_date":"2011-08-07","name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","location":"Vancouver, Canada"},"file_date_updated":"2020-07-14T12:46:06Z","title":"Hybrid smoothed particle hydrodynamics","year":"2011","_id":"3298","status":"public","day":"05","month":"08","pubrep_id":"598","ddc":["000"],"publication_status":"published","page":"33 - 42","date_published":"2011-08-05T00:00:00Z","date_created":"2018-12-11T12:02:32Z","date_updated":"2023-02-23T11:21:05Z","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Submitted Version","editor":[{"last_name":"Spencer","first_name":"Stephen","full_name":"Spencer, Stephen"}],"type":"conference","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"ACM","file":[{"file_id":"4769","file_name":"IST-2016-598-v1+1_HybridSPH_Preprint.pdf","checksum":"6579d27709946e0eefbfa60a456b4913","content_type":"application/pdf","date_created":"2018-12-12T10:09:44Z","date_updated":"2020-07-14T12:46:06Z","relation":"main_file","access_level":"open_access","file_size":2536216,"creator":"system"}],"author":[{"last_name":"Raveendran","full_name":"Raveendran, Karthik","first_name":"Karthik"},{"full_name":"Wojtan, Christopher J","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546","last_name":"Wojtan"},{"last_name":"Turk","first_name":"Greg","full_name":"Turk, Greg"}],"publist_id":"3343","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.","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>","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>","ista":"Raveendran K, Wojtan C, Turk G. 2011. Hybrid smoothed particle hydrodynamics. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 33–42.","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>.","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."},"scopus_import":1,"department":[{"_id":"ChWo"}],"abstract":[{"lang":"eng","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."}],"has_accepted_license":"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."}],"has_accepted_license":"1","department":[{"_id":"ToHe"}],"scopus_import":1,"citation":{"ista":"Henzinger TA, Mateescu M. 2011. Propagation models for computing biochemical reaction networks. CMSB: Computational Methods in Systems Biology, 1–3.","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>.","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.","short":"T.A. Henzinger, M. Mateescu, in:, Springer, 2011, pp. 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>.","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>","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>"},"publist_id":"3341","author":[{"last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","first_name":"Thomas A"},{"last_name":"Mateescu","full_name":"Mateescu, Maria","first_name":"Maria"}],"file":[{"creator":"system","relation":"main_file","access_level":"open_access","date_updated":"2020-07-14T12:46:06Z","date_created":"2018-12-12T10:07:50Z","file_size":255780,"checksum":"7f5c65509db1a9fb049abedd9663ed06","content_type":"application/pdf","file_name":"IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf","file_id":"4649"}],"oa":1,"type":"conference","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","oa_version":"Submitted Version","quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2011-09-21T00:00:00Z","page":"1 - 3","date_created":"2018-12-11T12:02:32Z","date_updated":"2021-01-12T07:42:29Z","publication_status":"published","pubrep_id":"92","ddc":["000","004"],"month":"09","status":"public","day":"21","title":"Propagation models for computing biochemical reaction networks","file_date_updated":"2020-07-14T12:46:06Z","year":"2011","_id":"3299","doi":"10.1145/2037509.2037510","conference":{"location":"Paris, France","end_date":"2011-09-23","name":"CMSB: Computational Methods in Systems Biology","start_date":"2011-09-21"}},{"oa_version":"Submitted Version","conference":{"name":"WCSB: Workshop on Computational Systems Biology (TICSP)"},"file_date_updated":"2020-07-14T12:46:06Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"conference","title":"Tail approximation for the chemical master equation","oa":1,"publisher":"Tampere International Center for Signal Processing","_id":"3301","year":"2011","status":"public","day":"01","file":[{"creator":"system","relation":"main_file","date_created":"2018-12-12T10:18:12Z","access_level":"open_access","date_updated":"2020-07-14T12:46:06Z","file_size":240820,"content_type":"application/pdf","checksum":"aa4d7a832a5419e6c0090650ebff2b9a","file_name":"IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf","file_id":"5331"}],"month":"01","author":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"full_name":"Mateescu, Maria","first_name":"Maria","last_name":"Mateescu"}],"pubrep_id":"91","ddc":["005","570"],"publist_id":"3339","citation":{"ista":"Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master equation. WCSB: Workshop on Computational Systems Biology (TICSP).","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.","chicago":"Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical Master Equation.” Tampere International Center for Signal Processing, 2011.","short":"T.A. Henzinger, M. Mateescu, in:, 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.","ama":"Henzinger TA, Mateescu M. Tail approximation for the chemical master equation. In: Tampere International Center for Signal Processing; 2011."},"publication_status":"published","date_published":"2011-01-01T00:00:00Z","date_updated":"2021-01-12T07:42:30Z","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T12:02:33Z","has_accepted_license":"1","abstract":[{"lang":"eng","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."}],"quality_controlled":"1","language":[{"iso":"eng"}]},{"ddc":["000","005"],"publist_id":"3338","pubrep_id":"90","publication_status":"published","citation":{"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.","mla":"Henzinger, Thomas A., et al. <i>Static Scheduling in Clouds</i>. 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.","short":"T.A. Henzinger, A. Singh, V. Singh, T. Wies, D. Zufferey, in:, USENIX, 2011, pp. 1–6.","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.","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."},"date_updated":"2021-01-12T07:42:31Z","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T12:02:33Z","page":"1 - 6","date_published":"2011-06-14T00:00:00Z","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","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."}],"has_accepted_license":"1","quality_controlled":"1","conference":{"name":"HotCloud: Workshop on Hot Topics in Cloud Computing","start_date":"2011-06-14","end_date":"2011-06-15"},"oa_version":"Submitted Version","publisher":"USENIX","year":"2011","_id":"3302","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","file_date_updated":"2020-07-14T12:46:06Z","title":"Static scheduling in clouds","oa":1,"file":[{"creator":"system","relation":"main_file","date_created":"2018-12-12T10:18:14Z","date_updated":"2020-07-14T12:46:06Z","access_level":"open_access","file_size":232770,"checksum":"21a461ac004bb535c83320fe79b30375","content_type":"application/pdf","file_name":"IST-2012-90-v1+1_Static_scheduling_in_clouds.pdf","file_id":"5333"}],"day":"14","status":"public","month":"06","author":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724"},{"id":"72A86902-E99F-11E9-9F62-915534D1B916","last_name":"Singh","full_name":"Singh, Anmol","first_name":"Anmol"},{"last_name":"Singh","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","full_name":"Singh, Vasu","first_name":"Vasu"},{"first_name":"Thomas","full_name":"Wies, Thomas","last_name":"Wies","id":"447BFB88-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","last_name":"Zufferey","first_name":"Damien","full_name":"Zufferey, Damien"}]},{"ddc":["510"],"publist_id":"3329","publication_status":"inpress","citation":{"ista":"Edelsbrunner H.Alpha shapes - a survey. In: Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings. .","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.","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.","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.","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.","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."},"article_processing_charge":"No","date_updated":"2022-05-24T07:56:30Z","department":[{"_id":"HeEd"}],"date_created":"2018-12-11T12:02:36Z","date_published":"2011-12-31T00:00:00Z","language":[{"iso":"eng"}],"has_accepted_license":"1","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"}],"quality_controlled":"1","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","full_name":"Ritzerveld, J","first_name":"J"},{"last_name":"Icke","full_name":"Icke, V","first_name":"V"}],"oa_version":"Submitted Version","publication":"Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings","publisher":"Springer","year":"2011","_id":"3311","file_date_updated":"2022-05-24T07:55:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"book_chapter","oa":1,"title":"Alpha shapes - a survey","file":[{"file_name":"2010_AlphaShapes.pdf","file_id":"11408","success":1,"creator":"dernst","content_type":"application/pdf","checksum":"a592ea438351e7280eea993a7713ab8f","access_level":"open_access","date_updated":"2022-05-24T07:55:05Z","relation":"main_file","date_created":"2022-05-24T07:55:05Z","file_size":475254}],"day":"31","status":"public","month":"12","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert"}]},{"ddc":["000"],"pubrep_id":"541","article_number":"6126475","publication_status":"published","article_processing_charge":"No","date_updated":"2020-07-14T23:03:43Z","date_created":"2018-12-11T12:02:36Z","date_published":"2011-12-31T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","conference":{"start_date":"2011-11-06","name":"ICCV: International Conference on Computer Vision","end_date":"2011-11-13","location":"Barcelona, Spain"},"doi":"10.1109/ICCV.2011.6126475","publication":"Proceedings of the IEEE International Conference on Computer Vision","year":"2011","_id":"3312","file_date_updated":"2020-07-14T12:46:07Z","title":"Detailed reconstruction of 3D plant root shape","day":"31","status":"public","month":"12","publist_id":"3328","citation":{"ista":"Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. 2011. Detailed reconstruction of 3D plant root shape, IEEE,p.","mla":"Zheng, Ying, et al. “Detailed Reconstruction of 3D Plant Root Shape.” <i>Proceedings of the IEEE International Conference on Computer Vision</i>, 6126475, IEEE, 2011, doi:<a href=\"https://doi.org/10.1109/ICCV.2011.6126475\">10.1109/ICCV.2011.6126475</a>.","ieee":"Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, and P. Benfey, <i>Detailed reconstruction of 3D plant root shape</i>. IEEE, 2011.","chicago":"Zheng, Ying, Steve Gu, Herbert Edelsbrunner, Carlo Tomasi, and Philip Benfey. <i>Detailed Reconstruction of 3D Plant Root Shape</i>. <i>Proceedings of the IEEE International Conference on Computer Vision</i>. IEEE, 2011. <a href=\"https://doi.org/10.1109/ICCV.2011.6126475\">https://doi.org/10.1109/ICCV.2011.6126475</a>.","short":"Y. Zheng, S. Gu, H. Edelsbrunner, C. Tomasi, P. Benfey, Detailed Reconstruction of 3D Plant Root Shape, IEEE, 2011.","apa":"Zheng, Y., Gu, S., Edelsbrunner, H., Tomasi, C., &#38; Benfey, P. (2011). <i>Detailed reconstruction of 3D plant root shape</i>. <i>Proceedings of the IEEE International Conference on Computer Vision</i>. Barcelona, Spain: IEEE. <a href=\"https://doi.org/10.1109/ICCV.2011.6126475\">https://doi.org/10.1109/ICCV.2011.6126475</a>","ama":"Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. <i>Detailed Reconstruction of 3D Plant Root Shape</i>. IEEE; 2011. doi:<a href=\"https://doi.org/10.1109/ICCV.2011.6126475\">10.1109/ICCV.2011.6126475</a>"},"acknowledgement":"This research is supported by the National Science Foundation (NSF) under grant DBI-0820624.","department":[{"_id":"HeEd"}],"abstract":[{"text":"We study the 3D reconstruction of plant roots from multiple 2D images. To meet the challenge caused by the delicate nature of thin branches, we make three innovations to cope with the sensitivity to image quality and calibration. First, we model the background as a harmonic function to improve the segmentation of the root in each 2D image. Second, we develop the concept of the regularized visual hull which reduces the effect of jittering and refraction by ensuring consistency with one 2D image. Third, we guarantee connectedness through adjustments to the 3D reconstruction that minimize global error. Our software is part of a biological phenotype/genotype study of agricultural root systems. It has been tested on more than 40 plant roots and results are promising in terms of reconstruction quality and efficiency.","lang":"eng"}],"has_accepted_license":"1","oa_version":"Submitted Version","publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference_poster","oa":1,"file":[{"creator":"system","content_type":"application/pdf","checksum":"30a33564b7b45a7ee31610898267fd0e","file_size":5622728,"date_created":"2018-12-12T10:09:04Z","relation":"main_file","date_updated":"2020-07-14T12:46:07Z","access_level":"open_access","file_name":"IST-2016-541-v1+1_2011-P-07-RootReconstruction.pdf","file_id":"4727"}],"author":[{"full_name":"Zheng, Ying","first_name":"Ying","last_name":"Zheng"},{"last_name":"Gu","first_name":"Steve","full_name":"Gu, Steve"},{"first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Carlo","full_name":"Tomasi, Carlo","last_name":"Tomasi"},{"first_name":"Philip","full_name":"Benfey, Philip","last_name":"Benfey"}]},{"scopus_import":1,"citation":{"ieee":"C. Chen and H. Edelsbrunner, “Diffusion runs low on persistence fast,” in <i>Proceedings of the IEEE International Conference on Computer Vision</i>, Barcelona, Spain, 2011.","mla":"Chen, Chao, and Herbert Edelsbrunner. “Diffusion Runs Low on Persistence Fast.” <i>Proceedings of the IEEE International Conference on Computer Vision</i>, 6126271, IEEE, 2011, doi:<a href=\"https://doi.org/10.1109/ICCV.2011.6126271\">10.1109/ICCV.2011.6126271</a>.","ista":"Chen C, Edelsbrunner H. 2011. Diffusion runs low on persistence fast. Proceedings of the IEEE International Conference on Computer Vision. ICCV: International Conference on Computer Vision, 6126271.","ama":"Chen C, Edelsbrunner H. Diffusion runs low on persistence fast. In: <i>Proceedings of the IEEE International Conference on Computer Vision</i>. IEEE; 2011. doi:<a href=\"https://doi.org/10.1109/ICCV.2011.6126271\">10.1109/ICCV.2011.6126271</a>","apa":"Chen, C., &#38; Edelsbrunner, H. (2011). Diffusion runs low on persistence fast. In <i>Proceedings of the IEEE International Conference on Computer Vision</i>. Barcelona, Spain: IEEE. <a href=\"https://doi.org/10.1109/ICCV.2011.6126271\">https://doi.org/10.1109/ICCV.2011.6126271</a>","chicago":"Chen, Chao, and Herbert Edelsbrunner. “Diffusion Runs Low on Persistence Fast.” In <i>Proceedings of the IEEE International Conference on Computer Vision</i>. IEEE, 2011. <a href=\"https://doi.org/10.1109/ICCV.2011.6126271\">https://doi.org/10.1109/ICCV.2011.6126271</a>.","short":"C. Chen, H. Edelsbrunner, in:, Proceedings of the IEEE International Conference on Computer Vision, IEEE, 2011."},"publist_id":"3327","abstract":[{"text":"Interpreting an image as a function on a compact sub- set of the Euclidean plane, we get its scale-space by diffu- sion, spreading the image over the entire plane. This gener- ates a 1-parameter family of functions alternatively defined as convolutions with a progressively wider Gaussian ker- nel. We prove that the corresponding 1-parameter family of persistence diagrams have norms that go rapidly to zero as time goes to infinity. This result rationalizes experimental observations about scale-space. We hope this will lead to targeted improvements of related computer vision methods.","lang":"eng"}],"has_accepted_license":"1","department":[{"_id":"HeEd"}],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"conference","publisher":"IEEE","oa_version":"Submitted Version","author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","first_name":"Chao","full_name":"Chen, Chao"},{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","full_name":"Edelsbrunner, Herbert","first_name":"Herbert"}],"file":[{"file_id":"5282","file_name":"IST-2016-540-v1+1_2011-P-08-RunEmpty.pdf","checksum":"6984684081ba123808b344f9f2e64a8f","content_type":"application/pdf","relation":"main_file","date_created":"2018-12-12T10:17:28Z","date_updated":"2020-07-14T12:46:07Z","access_level":"open_access","file_size":614050,"creator":"system"}],"publication_status":"published","article_number":"6126271","pubrep_id":"540","ddc":["000"],"quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2011-11-06T00:00:00Z","date_created":"2018-12-11T12:02:37Z","date_updated":"2021-01-12T07:42:35Z","title":"Diffusion runs low on persistence fast","file_date_updated":"2020-07-14T12:46:07Z","_id":"3313","year":"2011","publication":"Proceedings of the IEEE International Conference on Computer Vision","doi":"10.1109/ICCV.2011.6126271","conference":{"location":"Barcelona, Spain","name":"ICCV: International Conference on Computer Vision","start_date":"2011-11-06","end_date":"2011-11-13"},"month":"11","status":"public","day":"06"},{"doi":"10.2168/LMCS-7(4:8)2011","title":"Timed parity games: Complexity and robustness","file_date_updated":"2020-07-14T12:46:07Z","year":"2011","license":"https://creativecommons.org/licenses/by-nd/4.0/","_id":"3315","publication":"Logical Methods in Computer Science","status":"public","volume":7,"day":"14","month":"12","pubrep_id":"506","ddc":["000","005"],"tmp":{"image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","short":"CC BY-ND (4.0)","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"publication_status":"published","date_published":"2011-12-14T00:00:00Z","date_updated":"2023-02-23T11:46:35Z","date_created":"2018-12-11T12:02:37Z","quality_controlled":"1","language":[{"iso":"eng"}],"oa_version":"Published Version","issue":"4","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","type":"journal_article","publisher":"International Federation of Computational Logic","file":[{"creator":"system","date_created":"2018-12-12T10:16:42Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:46:07Z","file_size":588863,"checksum":"3480e1594bbef25ff7462fa93a8a814e","content_type":"application/pdf","file_name":"IST-2016-86-v2+1_1011.0688_3_.pdf","file_id":"5231"}],"author":[{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Vinayak","full_name":"Prabhu, Vinayak","last_name":"Prabhu"}],"ec_funded":1,"publist_id":"3324","scopus_import":1,"related_material":{"record":[{"status":"public","id":"3876","relation":"earlier_version"}]},"citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Vinayak Prabhu. “Timed Parity Games: Complexity and Robustness.” <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic, 2011. <a href=\"https://doi.org/10.2168/LMCS-7(4:8)2011\">https://doi.org/10.2168/LMCS-7(4:8)2011</a>.","short":"K. Chatterjee, T.A. Henzinger, V. Prabhu, Logical Methods in Computer Science 7 (2011).","ama":"Chatterjee K, Henzinger TA, Prabhu V. Timed parity games: Complexity and robustness. <i>Logical Methods in Computer Science</i>. 2011;7(4). doi:<a href=\"https://doi.org/10.2168/LMCS-7(4:8)2011\">10.2168/LMCS-7(4:8)2011</a>","apa":"Chatterjee, K., Henzinger, T. A., &#38; Prabhu, V. (2011). Timed parity games: Complexity and robustness. <i>Logical Methods in Computer Science</i>. International Federation of Computational Logic. <a href=\"https://doi.org/10.2168/LMCS-7(4:8)2011\">https://doi.org/10.2168/LMCS-7(4:8)2011</a>","ista":"Chatterjee K, Henzinger TA, Prabhu V. 2011. Timed parity games: Complexity and robustness. Logical Methods in Computer Science. 7(4).","ieee":"K. Chatterjee, T. A. Henzinger, and V. Prabhu, “Timed parity games: Complexity and robustness,” <i>Logical Methods in Computer Science</i>, vol. 7, no. 4. International Federation of Computational Logic, 2011.","mla":"Chatterjee, Krishnendu, et al. “Timed Parity Games: Complexity and Robustness.” <i>Logical Methods in Computer Science</i>, vol. 7, no. 4, International Federation of Computational Logic, 2011, doi:<a href=\"https://doi.org/10.2168/LMCS-7(4:8)2011\">10.2168/LMCS-7(4:8)2011</a>."},"project":[{"call_identifier":"FP7","grant_number":"215543","name":"COMponent-Based Embedded Systems design Techniques","_id":"25EFB36C-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"intvolume":"         7","has_accepted_license":"1","abstract":[{"lang":"eng","text":"We consider two-player games played in real time on game structures with clocks where the objectives of players are described using parity conditions. The games are concurrent in that at each turn, both players independently propose a time delay and an action, and the action with the shorter delay is chosen. To prevent a player from winning by blocking time, we restrict each player to play strategies that ensure that the player cannot be responsible for causing a zeno run. First, we present an efficient reduction of these games to turn-based (i.e., not concurrent) finite-state (i.e., untimed) parity games. Our reduction improves the best known complexity for solving timed parity games. Moreover, the rich class of algorithms for classical parity games can now be applied to timed parity games. The states of the resulting game are based on clock regions of the original game, and the state space of the finite game is linear in the size of the region graph. Second, we consider two restricted classes of strategies for the player that represents the controller in a real-time synthesis problem, namely, limit-robust and bounded-robust winning strategies. Using a limit-robust winning strategy, the controller cannot choose an exact real-valued time delay but must allow for some nonzero jitter in each of its actions. If there is a given lower bound on the jitter, then the strategy is bounded-robust winning. We show that exact strategies are more powerful than limit-robust strategies, which are more powerful than bounded-robust winning strategies for any bound. For both kinds of robust strategies, we present efficient reductions to standard timed automaton games. These reductions provide algorithms for the synthesis of robust real-time controllers."}]},{"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"conference","publisher":"IEEE","oa_version":"Published Version","author":[{"first_name":"Roderick","full_name":"Bloem, Roderick","last_name":"Bloem"},{"first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Greimel","first_name":"Karin","full_name":"Greimel, Karin"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A","full_name":"Henzinger, Thomas A"},{"first_name":"Barbara","full_name":"Jobstmann, Barbara","last_name":"Jobstmann"}],"ec_funded":1,"scopus_import":1,"citation":{"short":"R. Bloem, K. Chatterjee, K. Greimel, T.A. Henzinger, B. Jobstmann, in:, 6th IEEE International Symposium on Industrial and Embedded Systems, IEEE, 2011, pp. 176–185.","chicago":"Bloem, Roderick, Krishnendu Chatterjee, Karin Greimel, Thomas A Henzinger, and Barbara Jobstmann. “Specification-Centered Robustness.” In <i>6th IEEE International Symposium on Industrial and Embedded Systems</i>, 176–85. IEEE, 2011. <a href=\"https://doi.org/10.1109/SIES.2011.5953660\">https://doi.org/10.1109/SIES.2011.5953660</a>.","apa":"Bloem, R., Chatterjee, K., Greimel, K., Henzinger, T. A., &#38; Jobstmann, B. (2011). Specification-centered robustness. In <i>6th IEEE International Symposium on Industrial and Embedded Systems</i> (pp. 176–185). Vasteras, Sweden: IEEE. <a href=\"https://doi.org/10.1109/SIES.2011.5953660\">https://doi.org/10.1109/SIES.2011.5953660</a>","ama":"Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. Specification-centered robustness. In: <i>6th IEEE International Symposium on Industrial and Embedded Systems</i>. IEEE; 2011:176-185. doi:<a href=\"https://doi.org/10.1109/SIES.2011.5953660\">10.1109/SIES.2011.5953660</a>","ista":"Bloem R, Chatterjee K, Greimel K, Henzinger TA, Jobstmann B. 2011. Specification-centered robustness. 6th IEEE International Symposium on Industrial and Embedded Systems.  SIES: International Symposium on Industrial Embedded Systems, 176–185.","ieee":"R. Bloem, K. Chatterjee, K. Greimel, T. A. Henzinger, and B. Jobstmann, “Specification-centered robustness,” in <i>6th IEEE International Symposium on Industrial and Embedded Systems</i>, Vasteras, Sweden, 2011, pp. 176–185.","mla":"Bloem, Roderick, et al. “Specification-Centered Robustness.” <i>6th IEEE International Symposium on Industrial and Embedded Systems</i>, IEEE, 2011, pp. 176–85, doi:<a href=\"https://doi.org/10.1109/SIES.2011.5953660\">10.1109/SIES.2011.5953660</a>."},"project":[{"name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11402-N23","name":"Rigorous Systems Engineering","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425"},{"_id":"25F1337C-B435-11E9-9278-68D0E5697425","grant_number":"214373","call_identifier":"FP7","name":"Design for Embedded Systems"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"publist_id":"3323","abstract":[{"text":"In addition to being correct, a system should be robust, that is, it should behave reasonably even after receiving unexpected inputs. In this paper, we summarize two formal notions of robustness that we have introduced previously for reactive systems. One of the notions is based on assigning costs for failures on a user-provided notion of incorrect transitions in a specification. Here, we define a system to be robust if a finite number of incorrect inputs does not lead to an infinite number of incorrect outputs. We also give a more refined notion of robustness that aims to minimize the ratio of output failures to input failures. The second notion is aimed at liveness. In contrast to the previous notion, it has no concept of recovery from an error. Instead, it compares the ratio of the number of liveness constraints that the system violates to the number of liveness constraints that the environment violates.","lang":"eng"}],"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"title":"Specification-centered robustness","_id":"3316","year":"2011","publication":"6th IEEE International Symposium on Industrial and Embedded Systems","doi":"10.1109/SIES.2011.5953660","conference":{"location":"Vasteras, Sweden","name":" SIES: International Symposium on Industrial Embedded Systems","start_date":"2011-06-15","end_date":"2011-06-17"},"month":"07","main_file_link":[{"open_access":"1","url":"https://openlib.tugraz.at/download.php?id=5cb57c8a49344&location=browse"}],"status":"public","day":"14","article_processing_charge":"No","publication_status":"published","quality_controlled":"1","language":[{"iso":"eng"}],"date_published":"2011-07-14T00:00:00Z","page":"176 - 185","date_created":"2018-12-11T12:02:38Z","date_updated":"2021-01-12T07:42:36Z"},{"publisher":"Nature Publishing Group","publication":"Nature Neuroscience","_id":"3318","year":"2011","type":"journal_article","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses","doi":"10.1038/nn.3002","oa_version":"Submitted Version","month":"12","author":[{"last_name":"Eggermann","full_name":"Eggermann, Emmanuel","first_name":"Emmanuel"},{"first_name":"Peter M","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","last_name":"Jonas"}],"volume":15,"day":"04","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3631701/"}],"status":"public","publication_status":"published","citation":{"chicago":"Eggermann, Emmanuel, and Peter M Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.” <i>Nature Neuroscience</i>. Nature Publishing Group, 2011. <a href=\"https://doi.org/10.1038/nn.3002\">https://doi.org/10.1038/nn.3002</a>.","short":"E. Eggermann, P.M. Jonas, Nature Neuroscience 15 (2011) 20–22.","ama":"Eggermann E, Jonas PM. How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. <i>Nature Neuroscience</i>. 2011;15:20-22. doi:<a href=\"https://doi.org/10.1038/nn.3002\">10.1038/nn.3002</a>","apa":"Eggermann, E., &#38; Jonas, P. M. (2011). How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. <i>Nature Neuroscience</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nn.3002\">https://doi.org/10.1038/nn.3002</a>","ista":"Eggermann E, Jonas PM. 2011. How the “slow” Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses. Nature Neuroscience. 15, 20–22.","ieee":"E. Eggermann and P. M. Jonas, “How the ‘slow’ Ca(2+) buffer parvalbumin affects transmitter release in nanodomain coupling regimes at GABAergic synapses,” <i>Nature Neuroscience</i>, vol. 15. Nature Publishing Group, pp. 20–22, 2011.","mla":"Eggermann, Emmanuel, and Peter M. Jonas. “How the ‘Slow’ Ca(2+) Buffer Parvalbumin Affects Transmitter Release in Nanodomain Coupling Regimes at GABAergic Synapses.” <i>Nature Neuroscience</i>, vol. 15, Nature Publishing Group, 2011, pp. 20–22, doi:<a href=\"https://doi.org/10.1038/nn.3002\">10.1038/nn.3002</a>."},"scopus_import":1,"publist_id":"3321","language":[{"iso":"eng"}],"abstract":[{"text":"Parvalbumin is thought to act in a manner similar to EGTA, but how a slow Ca2+ buffer affects nanodomain-coupling regimes at GABAergic synapses is unclear. Direct measurements of parvalbumin concentration and paired recordings in rodent hippocampus and cerebellum revealed that parvalbumin affects synaptic dynamics only when expressed at high levels. Modeling suggests that, in high concentrations, parvalbumin may exert BAPTA-like effects, modulating nanodomain coupling via competition with local saturation of endogenous fixed buffers.","lang":"eng"}],"quality_controlled":"1","intvolume":"        15","date_updated":"2021-01-12T07:42:37Z","department":[{"_id":"PeJo"}],"date_created":"2018-12-11T12:02:38Z","page":"20 - 22","date_published":"2011-12-04T00:00:00Z"},{"ddc":["000"],"article_processing_charge":"No","publication_status":"published","page":"185 - 365","date_published":"2011-05-23T00:00:00Z","date_created":"2018-12-11T12:02:39Z","date_updated":"2023-10-17T11:52:46Z","quality_controlled":"1","language":[{"iso":"eng"}],"doi":"10.1561/0600000033","file_date_updated":"2020-07-14T12:46:07Z","title":"Structured learning and prediction in computer vision","publication":"Foundations and Trends in Computer Graphics and Vision","_id":"3320","year":"2011","status":"public","volume":6,"day":"23","month":"05","publist_id":"3315","citation":{"ista":"Nowozin S, Lampert C. 2011. Structured learning and prediction in computer vision. Foundations and Trends in Computer Graphics and Vision. 6(3–4), 185–365.","mla":"Nowozin, Sebastian, and Christoph Lampert. “Structured Learning and Prediction in Computer Vision.” <i>Foundations and Trends in Computer Graphics and Vision</i>, vol. 6, no. 3–4, Now Publishers, 2011, pp. 185–365, doi:<a href=\"https://doi.org/10.1561/0600000033\">10.1561/0600000033</a>.","ieee":"S. Nowozin and C. Lampert, “Structured learning and prediction in computer vision,” <i>Foundations and Trends in Computer Graphics and Vision</i>, vol. 6, no. 3–4. Now Publishers, pp. 185–365, 2011.","chicago":"Nowozin, Sebastian, and Christoph Lampert. “Structured Learning and Prediction in Computer Vision.” <i>Foundations and Trends in Computer Graphics and Vision</i>. Now Publishers, 2011. <a href=\"https://doi.org/10.1561/0600000033\">https://doi.org/10.1561/0600000033</a>.","short":"S. Nowozin, C. Lampert, Foundations and Trends in Computer Graphics and Vision 6 (2011) 185–365.","ama":"Nowozin S, Lampert C. Structured learning and prediction in computer vision. <i>Foundations and Trends in Computer Graphics and Vision</i>. 2011;6(3-4):185-365. doi:<a href=\"https://doi.org/10.1561/0600000033\">10.1561/0600000033</a>","apa":"Nowozin, S., &#38; Lampert, C. (2011). Structured learning and prediction in computer vision. <i>Foundations and Trends in Computer Graphics and Vision</i>. Now Publishers. <a href=\"https://doi.org/10.1561/0600000033\">https://doi.org/10.1561/0600000033</a>"},"scopus_import":"1","department":[{"_id":"ChLa"}],"has_accepted_license":"1","abstract":[{"text":"Powerful statistical models that can be learned efficiently from large amounts of data are currently revolutionizing computer vision. These models possess a rich internal structure reflecting task-specific relations and constraints. This monograph introduces the reader to the most popular classes of structured models in computer vision. Our focus is discrete undirected graphical models which we cover in detail together with a description of algorithms for both probabilistic inference and maximum a posteriori inference. We discuss separately recently successful techniques for prediction in general structured models. In the second part of this monograph we describe methods for parameter learning where we distinguish the classic maximum likelihood based methods from the more recent prediction-based parameter learning methods. We highlight developments to enhance current models and discuss kernelized models and latent variable models. To make the monograph more practical and to provide links to further study we provide examples of successful application of many methods in the computer vision literature.","lang":"eng"}],"intvolume":"         6","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"journal_article","issue":"3-4","oa":1,"publisher":"Now Publishers","article_type":"original","file":[{"creator":"dernst","file_size":3745064,"date_created":"2020-05-14T14:34:47Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:46:07Z","checksum":"f1043ef389f1558e2a226bb51568511f","content_type":"application/pdf","file_name":"2011_CompGraphicsVision_Nowozin.pdf","file_id":"7837"}],"author":[{"last_name":"Nowozin","full_name":"Nowozin, Sebastian","first_name":"Sebastian"},{"full_name":"Lampert, Christoph","first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}]},{"author":[{"first_name":"Ruzica","full_name":"Piskac, Ruzica","last_name":"Piskac"},{"id":"447BFB88-F248-11E8-B48F-1D18A9856A87","last_name":"Wies","full_name":"Wies, Thomas","first_name":"Thomas"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","type":"conference","oa":1,"publisher":"Springer","alternative_title":["LNCS"],"oa_version":"Submitted Version","editor":[{"last_name":"Jhala","first_name":"Ranjit","full_name":"Jhala, Ranjit"},{"last_name":"Schmidt","full_name":"Schmidt, David","first_name":"David"}],"abstract":[{"lang":"eng","text":"Automated termination provers often use the following schema to prove that a program terminates: construct a relational abstraction of the program's transition relation and then show that the relational abstraction is well-founded. The focus of current tools has been on developing sophisticated techniques for constructing the abstractions while relying on known decidable logics (such as linear arithmetic) to express them. We believe we can significantly increase the class of programs that are amenable to automated termination proofs by identifying more expressive decidable logics for reasoning about well-founded relations. We therefore present a new decision procedure for reasoning about multiset orderings, which are among the most powerful orderings used to prove termination. We show that, using our decision procedure, one can automatically prove termination of natural abstractions of programs."}],"intvolume":"      6538","department":[{"_id":"ToHe"}],"citation":{"chicago":"Piskac, Ruzica, and Thomas Wies. “Decision Procedures for Automating Termination Proofs.” edited by Ranjit Jhala and David Schmidt, 6538:371–86. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-18275-4_26\">https://doi.org/10.1007/978-3-642-18275-4_26</a>.","short":"R. Piskac, T. Wies, in:, R. Jhala, D. Schmidt (Eds.), Springer, 2011, pp. 371–386.","apa":"Piskac, R., &#38; Wies, T. (2011). Decision procedures for automating termination proofs. In R. Jhala &#38; D. Schmidt (Eds.) (Vol. 6538, pp. 371–386). Presented at the VMCAI: Verification Model Checking and Abstract Interpretation, Texas, USA: Springer. <a href=\"https://doi.org/10.1007/978-3-642-18275-4_26\">https://doi.org/10.1007/978-3-642-18275-4_26</a>","ama":"Piskac R, Wies T. Decision procedures for automating termination proofs. In: Jhala R, Schmidt D, eds. Vol 6538. Springer; 2011:371-386. doi:<a href=\"https://doi.org/10.1007/978-3-642-18275-4_26\">10.1007/978-3-642-18275-4_26</a>","ista":"Piskac R, Wies T. 2011. Decision procedures for automating termination proofs. VMCAI: Verification Model Checking and Abstract Interpretation, LNCS, vol. 6538, 371–386.","ieee":"R. Piskac and T. Wies, “Decision procedures for automating termination proofs,” presented at the VMCAI: Verification Model Checking and Abstract Interpretation, Texas, USA, 2011, vol. 6538, pp. 371–386.","mla":"Piskac, Ruzica, and Thomas Wies. <i>Decision Procedures for Automating Termination Proofs</i>. Edited by Ranjit Jhala and David Schmidt, vol. 6538, Springer, 2011, pp. 371–86, doi:<a href=\"https://doi.org/10.1007/978-3-642-18275-4_26\">10.1007/978-3-642-18275-4_26</a>."},"scopus_import":1,"publist_id":"3311","month":"01","status":"public","main_file_link":[{"open_access":"1","url":"https://infoscience.epfl.ch/record/170697/"}],"volume":6538,"day":"01","title":"Decision procedures for automating termination proofs","_id":"3324","year":"2011","doi":"10.1007/978-3-642-18275-4_26","conference":{"name":"VMCAI: Verification Model Checking and Abstract Interpretation","start_date":"2011-01-23","end_date":"2011-01-25","location":"Texas, USA"},"quality_controlled":"1","language":[{"iso":"eng"}],"page":"371 - 386","date_published":"2011-01-01T00:00:00Z","date_updated":"2021-01-12T07:42:39Z","date_created":"2018-12-11T12:02:40Z","publication_status":"published"},{"publist_id":"3309","citation":{"ieee":"S. Almagor, U. Boker, and O. Kupferman, “What’s decidable about weighted automata ,” presented at the ATVA: Automated Technology for Verification and Analysis, Taipei, Taiwan, 2011, vol. 6996, pp. 482–491.","mla":"Almagor, Shaull, et al. <i>What’s Decidable about Weighted Automata </i>. Vol. 6996, Springer, 2011, pp. 482–91, doi:<a href=\"https://doi.org/10.1007/978-3-642-24372-1_37\">10.1007/978-3-642-24372-1_37</a>.","ista":"Almagor S, Boker U, Kupferman O. 2011. What’s decidable about weighted automata . ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 6996, 482–491.","ama":"Almagor S, Boker U, Kupferman O. What’s decidable about weighted automata . In: Vol 6996. Springer; 2011:482-491. doi:<a href=\"https://doi.org/10.1007/978-3-642-24372-1_37\">10.1007/978-3-642-24372-1_37</a>","apa":"Almagor, S., Boker, U., &#38; Kupferman, O. (2011). What’s decidable about weighted automata  (Vol. 6996, pp. 482–491). Presented at the ATVA: Automated Technology for Verification and Analysis, Taipei, Taiwan: Springer. <a href=\"https://doi.org/10.1007/978-3-642-24372-1_37\">https://doi.org/10.1007/978-3-642-24372-1_37</a>","chicago":"Almagor, Shaull, Udi Boker, and Orna Kupferman. “What’s Decidable about Weighted Automata ,” 6996:482–91. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-24372-1_37\">https://doi.org/10.1007/978-3-642-24372-1_37</a>.","short":"S. Almagor, U. Boker, O. Kupferman, in:, Springer, 2011, pp. 482–491."},"department":[{"_id":"ToHe"}],"abstract":[{"lang":"eng","text":"Weighted automata map input words to numerical values. Ap- plications of weighted automata include formal verification of quantitative properties, as well as text, speech, and image processing. A weighted au- tomaton is defined with respect to a semiring. For the tropical semiring, the weight of a run is the sum of the weights of the transitions taken along the run, and the value of a word is the minimal weight of an accepting run on it. In the 90’s, Krob studied the decidability of problems on rational series defined with respect to the tropical semiring. Rational series are strongly related to weighted automata, and Krob’s results apply to them. In par- ticular, it follows from Krob’s results that the universality problem (that is, deciding whether the values of all words are below some threshold) is decidable for weighted automata defined with respect to the tropical semir- ing with domain ∪ {∞}, and that the equality problem is undecidable when the domain is ∪ {∞}. In this paper we continue the study of the borders of decidability in weighted automata, describe alternative and direct proofs of the above results, and tighten them further. Unlike the proofs of Krob, which are algebraic in their nature, our proofs stay in the terrain of state machines, and the reduction is from the halting problem of a two-counter machine. This enables us to significantly simplify Krob’s reasoning, make the un- decidability result accessible to the automata-theoretic community, and strengthen it to apply already to a very simple class of automata: all the states are accepting, there are no initial nor final weights, and all the weights on the transitions are from the set {−1, 0, 1}. The fact we work directly with the automata enables us to tighten also the decidability re- sults and to show that the universality problem for weighted automata defined with respect to the tropical semiring with domain ∪ {∞}, and in fact even with domain ≥0 ∪ {∞}, is PSPACE-complete. Our results thus draw a sharper picture about the decidability of decision problems for weighted automata, in both the front of containment vs. universality and the front of the ∪ {∞} vs. the ∪ {∞} domains."}],"has_accepted_license":"1","intvolume":"      6996","oa_version":"Submitted Version","publisher":"Springer","alternative_title":["LNCS"],"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"file":[{"creator":"dernst","file_size":182309,"relation":"main_file","date_updated":"2020-07-14T12:46:07Z","access_level":"open_access","date_created":"2020-05-19T16:08:32Z","checksum":"a7ca08a2cb1b6925f4c18a3034ae5659","content_type":"application/pdf","file_name":"2011_LNCS_Almagor.pdf","file_id":"7868"}],"author":[{"full_name":"Almagor, Shaull","first_name":"Shaull","last_name":"Almagor"},{"last_name":"Boker","id":"31E297B6-F248-11E8-B48F-1D18A9856A87","first_name":"Udi","full_name":"Boker, Udi"},{"last_name":"Kupferman","full_name":"Kupferman, Orna","first_name":"Orna"}],"ddc":["000"],"publication_status":"published","article_processing_charge":"No","date_created":"2018-12-11T12:02:41Z","date_updated":"2021-01-12T07:42:40Z","page":"482 - 491","date_published":"2011-10-14T00:00:00Z","language":[{"iso":"eng"}],"quality_controlled":"1","conference":{"name":"ATVA: Automated Technology for Verification and Analysis","start_date":"2011-10-11","end_date":"2011-10-14","location":"Taipei, Taiwan"},"doi":"10.1007/978-3-642-24372-1_37","year":"2011","_id":"3326","file_date_updated":"2020-07-14T12:46:07Z","title":"What’s decidable about weighted automata ","volume":6996,"day":"14","status":"public","month":"10"},{"month":"06","author":[{"last_name":"Berberich","first_name":"Eric","full_name":"Berberich, Eric"},{"last_name":"Hemmer","full_name":"Hemmer, Michael","first_name":"Michael"},{"first_name":"Michael","full_name":"Kerber, Michael","orcid":"0000-0002-8030-9299","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87"}],"day":"13","status":"public","main_file_link":[{"url":"https://hal.inria.fr/inria-00480031/file/RR-7274.pdf","open_access":"1"}],"publisher":"ACM","year":"2011","_id":"3328","type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"A generic algebraic kernel for non linear geometric applications","oa":1,"conference":{"end_date":"2011-06-15","start_date":"2011-06-13","name":"SCG: Symposium on Computational Geometry","location":"Paris, France"},"doi":"10.1145/1998196.1998224","oa_version":"Published Version","language":[{"iso":"eng"}],"abstract":[{"text":"We report on a generic uni- and bivariate algebraic kernel that is publicly available with CGAL 3.7. It comprises complete, correct, though efficient state-of-the-art implementations on polynomials, roots of polynomial systems, and the support to analyze algebraic curves defined by bivariate polynomials. The kernel design is generic, that is, various number types and substeps can be exchanged. It is accompanied with a ready-to-use interface to enable arrangements induced by algebraic curves, that have already been used as basis for various geometric applications, as arrangements on Dupin cyclides or the triangulation of algebraic surfaces. We present two novel applications: arrangements of rotated algebraic curves and Boolean set operations on polygons bounded by segments of algebraic curves. We also provide experiments showing that our general implementation is competitive and even often clearly outperforms existing implementations that are explicitly tailored for specific types of non-linear curves that are available in CGAL.","lang":"eng"}],"quality_controlled":"1","date_updated":"2021-01-12T07:42:41Z","date_created":"2018-12-11T12:02:42Z","department":[{"_id":"HeEd"}],"page":"179 - 186","date_published":"2011-06-13T00:00:00Z","publication_status":"published","citation":{"ista":"Berberich E, Hemmer M, Kerber M. 2011. A generic algebraic kernel for non linear geometric applications. SCG: Symposium on Computational Geometry, 179–186.","mla":"Berberich, Eric, et al. <i>A Generic Algebraic Kernel for Non Linear Geometric Applications</i>. ACM, 2011, pp. 179–86, doi:<a href=\"https://doi.org/10.1145/1998196.1998224\">10.1145/1998196.1998224</a>.","ieee":"E. Berberich, M. Hemmer, and M. Kerber, “A generic algebraic kernel for non linear geometric applications,” presented at the SCG: Symposium on Computational Geometry, Paris, France, 2011, pp. 179–186.","short":"E. Berberich, M. Hemmer, M. Kerber, in:, ACM, 2011, pp. 179–186.","chicago":"Berberich, Eric, Michael Hemmer, and Michael Kerber. “A Generic Algebraic Kernel for Non Linear Geometric Applications,” 179–86. ACM, 2011. <a href=\"https://doi.org/10.1145/1998196.1998224\">https://doi.org/10.1145/1998196.1998224</a>.","ama":"Berberich E, Hemmer M, Kerber M. A generic algebraic kernel for non linear geometric applications. In: ACM; 2011:179-186. doi:<a href=\"https://doi.org/10.1145/1998196.1998224\">10.1145/1998196.1998224</a>","apa":"Berberich, E., Hemmer, M., &#38; Kerber, M. (2011). A generic algebraic kernel for non linear geometric applications (pp. 179–186). Presented at the SCG: Symposium on Computational Geometry, Paris, France: ACM. <a href=\"https://doi.org/10.1145/1998196.1998224\">https://doi.org/10.1145/1998196.1998224</a>"},"article_processing_charge":"No","scopus_import":1,"publist_id":"3307"}]