[{"oa":1,"language":[{"iso":"eng"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","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"}],"author":[{"first_name":"Konrad","last_name":"Lohse","full_name":"Lohse, Konrad"},{"first_name":"Richard","last_name":"Harrison","full_name":"Harrison, Richard"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240"}],"page":"977 - 987","oa_version":"Submitted Version","status":"public","ec_funded":1,"year":"2011","day":"01","date_published":"2011-11-01T00:00:00Z","title":"A general method for calculating likelihoods under the coalescent process","publication":"Genetics","quality_controlled":"1","type":"journal_article","scopus_import":1,"publication_status":"published","publisher":"Genetics Society of America","month":"11","citation":{"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>","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.","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>.","short":"K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987."},"publist_id":"3355","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T12:02:29Z","date_updated":"2021-01-12T07:42:26Z","intvolume":"       189","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/","open_access":"1"}],"volume":189,"doi":"10.1534/genetics.111.129569","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"issue":"3","_id":"3290"},{"_id":"3297","conference":{"start_date":"2011-08-07","location":"Vancouver, BC, Canada","name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques","end_date":"2011-08-11"},"file":[{"file_id":"5018","checksum":"8d508ad7c82f50978acbaa4170ee0a75","date_created":"2018-12-12T10:13:34Z","date_updated":"2020-07-14T12:46:06Z","access_level":"open_access","relation":"main_file","content_type":"application/pdf","creator":"system","file_name":"IST-2016-599-v1+1_meshyFluidsCourseSIGGRAPH2011.pdf","file_size":34672096}],"doi":"10.1145/2037636.2037644","date_created":"2018-12-11T12:02:31Z","date_updated":"2023-02-23T11:21:02Z","publist_id":"3344","department":[{"_id":"ChWo"}],"month":"08","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.","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>","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>","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.","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>.","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>."},"scopus_import":1,"type":"conference","quality_controlled":"1","publication_status":"published","publisher":"ACM","has_accepted_license":"1","date_published":"2011-08-07T00:00:00Z","title":"Liquid simulation with mesh-based surface tracking","day":"07","pubrep_id":"599","year":"2011","oa_version":"Published Version","status":"public","author":[{"orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Müller Fischer","full_name":"Müller Fischer, Matthias","first_name":"Matthias"},{"full_name":"Brochu, Tyson","last_name":"Brochu","first_name":"Tyson"}],"abstract":[{"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.","lang":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"8","file_date_updated":"2020-07-14T12:46:06Z","language":[{"iso":"eng"}],"ddc":["000"],"oa":1},{"pubrep_id":"598","year":"2011","page":"33 - 42","author":[{"first_name":"Karthik","full_name":"Raveendran, Karthik","last_name":"Raveendran"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan","full_name":"Wojtan, Christopher J"},{"full_name":"Turk, Greg","last_name":"Turk","first_name":"Greg"}],"editor":[{"full_name":"Spencer, Stephen","last_name":"Spencer","first_name":"Stephen"}],"oa_version":"Submitted Version","status":"public","file_date_updated":"2020-07-14T12:46:06Z","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"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"oa":1,"language":[{"iso":"eng"}],"file":[{"creator":"system","file_name":"IST-2016-598-v1+1_HybridSPH_Preprint.pdf","file_size":2536216,"date_updated":"2020-07-14T12:46:06Z","access_level":"open_access","date_created":"2018-12-12T10:09:44Z","relation":"main_file","checksum":"6579d27709946e0eefbfa60a456b4913","file_id":"4769","content_type":"application/pdf"}],"doi":"10.1145/2019406.2019411","_id":"3298","conference":{"start_date":"2011-08-05","location":"Vancouver, Canada","name":"SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation","end_date":"2011-08-07"},"month":"08","citation":{"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.","short":"K. Raveendran, C. Wojtan, G. Turk, in:, S. Spencer (Ed.), ACM, 2011, pp. 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>.","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>.","ista":"Raveendran K, Wojtan C, Turk G. 2011. Hybrid smoothed particle hydrodynamics. SCA: ACM SIGGRAPH/Eurographics Symposium on Computer animation, 33–42.","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>","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>"},"date_updated":"2023-02-23T11:21:05Z","date_created":"2018-12-11T12:02:32Z","department":[{"_id":"ChWo"}],"publist_id":"3343","has_accepted_license":"1","quality_controlled":"1","publication_status":"published","scopus_import":1,"type":"conference","publisher":"ACM","date_published":"2011-08-05T00:00:00Z","title":"Hybrid smoothed particle hydrodynamics","day":"05"},{"status":"public","oa_version":"Submitted Version","author":[{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Mateescu","full_name":"Mateescu, Maria","first_name":"Maria"}],"page":"1 - 3","year":"2011","pubrep_id":"92","language":[{"iso":"eng"}],"oa":1,"ddc":["000","004"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:06Z","publist_id":"3341","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T12:02:32Z","date_updated":"2021-01-12T07:42:29Z","citation":{"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.","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>.","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>.","ista":"Henzinger TA, Mateescu M. 2011. Propagation models for computing biochemical reaction networks. CMSB: Computational Methods in Systems Biology, 1–3.","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>"},"month":"09","conference":{"start_date":"2011-09-21","location":"Paris, France","end_date":"2011-09-23","name":"CMSB: Computational Methods in Systems Biology"},"_id":"3299","doi":"10.1145/2037509.2037510","file":[{"date_created":"2018-12-12T10:07:50Z","date_updated":"2020-07-14T12:46:06Z","relation":"main_file","access_level":"open_access","checksum":"7f5c65509db1a9fb049abedd9663ed06","file_id":"4649","content_type":"application/pdf","creator":"system","file_name":"IST-2012-92-v1+1_Propagation_models_for_computing_biochemical_reaction_networks.pdf","file_size":255780}],"day":"21","title":"Propagation models for computing biochemical reaction networks","date_published":"2011-09-21T00:00:00Z","publisher":"Springer","type":"conference","publication_status":"published","scopus_import":1,"quality_controlled":"1","has_accepted_license":"1"},{"year":"2011","_id":"3301","conference":{"name":"WCSB: Workshop on Computational Systems Biology (TICSP)"},"pubrep_id":"91","file":[{"content_type":"application/pdf","checksum":"aa4d7a832a5419e6c0090650ebff2b9a","file_id":"5331","access_level":"open_access","date_created":"2018-12-12T10:18:12Z","relation":"main_file","date_updated":"2020-07-14T12:46:06Z","file_name":"IST-2012-91-v1+1_Tail_approximation_for_the_chemical_master_equation.pdf","file_size":240820,"creator":"system"}],"status":"public","date_updated":"2021-01-12T07:42:30Z","date_created":"2018-12-11T12:02:33Z","oa_version":"Submitted Version","department":[{"_id":"ToHe"}],"publist_id":"3339","citation":{"chicago":"Henzinger, Thomas A, and Maria Mateescu. “Tail Approximation for the Chemical Master Equation.” Tampere International Center for Signal Processing, 2011.","mla":"Henzinger, Thomas A., and Maria Mateescu. <i>Tail Approximation for the Chemical Master Equation</i>. Tampere International Center for Signal Processing, 2011.","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.","ama":"Henzinger TA, Mateescu M. Tail approximation for the chemical master equation. 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.","ista":"Henzinger TA, Mateescu M. 2011. Tail approximation for the chemical master equation. WCSB: Workshop on Computational Systems Biology (TICSP)."},"month":"01","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"first_name":"Maria","full_name":"Mateescu, Maria","last_name":"Mateescu"}],"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"}],"publisher":"Tampere International Center for Signal Processing","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","type":"conference","publication_status":"published","file_date_updated":"2020-07-14T12:46:06Z","has_accepted_license":"1","language":[{"iso":"eng"}],"title":"Tail approximation for the chemical master equation","date_published":"2011-01-01T00:00:00Z","day":"01","oa":1,"ddc":["005","570"]},{"oa":1,"ddc":["000","005"],"language":[{"iso":"eng"}],"date_published":"2011-06-14T00:00:00Z","title":"Static scheduling in clouds","day":"14","file_date_updated":"2020-07-14T12:46:06Z","has_accepted_license":"1","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."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"USENIX","publication_status":"published","quality_controlled":"1","type":"conference","citation":{"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.","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.","chicago":"Henzinger, Thomas A, Anmol Singh, Vasu Singh, Thomas Wies, and Damien Zufferey. “Static Scheduling in Clouds,” 1–6. USENIX, 2011.","mla":"Henzinger, Thomas A., et al. <i>Static Scheduling in Clouds</i>. USENIX, 2011, pp. 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."},"month":"06","page":"1 - 6","author":[{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"id":"72A86902-E99F-11E9-9F62-915534D1B916","first_name":"Anmol","last_name":"Singh","full_name":"Singh, Anmol"},{"first_name":"Vasu","id":"4DAE2708-F248-11E8-B48F-1D18A9856A87","last_name":"Singh","full_name":"Singh, Vasu"},{"first_name":"Thomas","id":"447BFB88-F248-11E8-B48F-1D18A9856A87","full_name":"Wies, Thomas","last_name":"Wies"},{"first_name":"Damien","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3197-8736","last_name":"Zufferey","full_name":"Zufferey, Damien"}],"status":"public","date_updated":"2021-01-12T07:42:31Z","date_created":"2018-12-11T12:02:33Z","publist_id":"3338","department":[{"_id":"ToHe"}],"oa_version":"Submitted Version","file":[{"file_size":232770,"file_name":"IST-2012-90-v1+1_Static_scheduling_in_clouds.pdf","creator":"system","content_type":"application/pdf","date_updated":"2020-07-14T12:46:06Z","relation":"main_file","access_level":"open_access","date_created":"2018-12-12T10:18:14Z","checksum":"21a461ac004bb535c83320fe79b30375","file_id":"5333"}],"_id":"3302","year":"2011","conference":{"name":"HotCloud: Workshop on Hot Topics in Cloud Computing","end_date":"2011-06-15","start_date":"2011-06-14"},"pubrep_id":"90"},{"_id":"3311","year":"2011","file":[{"file_size":475254,"file_name":"2010_AlphaShapes.pdf","creator":"dernst","content_type":"application/pdf","file_id":"11408","checksum":"a592ea438351e7280eea993a7713ab8f","relation":"main_file","date_created":"2022-05-24T07:55:05Z","date_updated":"2022-05-24T07:55:05Z","access_level":"open_access","success":1}],"status":"public","oa_version":"Submitted Version","department":[{"_id":"HeEd"}],"publist_id":"3329","date_created":"2018-12-11T12:02:36Z","date_updated":"2022-05-24T07:56:30Z","citation":{"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.","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.","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.","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.","ista":"Edelsbrunner H.Alpha shapes - a survey. In: Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings. ."},"editor":[{"first_name":"R","full_name":"van de Weygaert, R","last_name":"van de Weygaert"},{"first_name":"G","full_name":"Vegter, G","last_name":"Vegter"},{"last_name":"Ritzerveld","full_name":"Ritzerveld, J","first_name":"J"},{"full_name":"Icke, V","last_name":"Icke","first_name":"V"}],"author":[{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"}],"month":"12","publisher":"Springer","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","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"}],"type":"book_chapter","quality_controlled":"1","publication_status":"inpress","file_date_updated":"2022-05-24T07:55:05Z","has_accepted_license":"1","language":[{"iso":"eng"}],"publication":"Tessellations in the Sciences: Virtues, Techniques and Applications of Geometric Tilings","day":"31","date_published":"2011-12-31T00:00:00Z","title":"Alpha shapes - a survey","oa":1,"ddc":["510"]},{"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:46:07Z","date_created":"2018-12-12T10:09:04Z","access_level":"open_access","relation":"main_file","checksum":"30a33564b7b45a7ee31610898267fd0e","file_id":"4727","file_size":5622728,"file_name":"IST-2016-541-v1+1_2011-P-07-RootReconstruction.pdf","creator":"system"}],"doi":"10.1109/ICCV.2011.6126475","conference":{"name":"ICCV: International Conference on Computer Vision","end_date":"2011-11-13","location":"Barcelona, Spain","start_date":"2011-11-06"},"_id":"3312","month":"12","citation":{"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>","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>","ista":"Zheng Y, Gu S, Edelsbrunner H, Tomasi C, Benfey P. 2011. Detailed reconstruction of 3D plant root shape, IEEE,p.","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.","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."},"acknowledgement":"This research is supported by the National Science Foundation (NSF) under grant DBI-0820624.","publist_id":"3328","department":[{"_id":"HeEd"}],"date_updated":"2020-07-14T23:03:43Z","date_created":"2018-12-11T12:02:36Z","has_accepted_license":"1","quality_controlled":"1","publication_status":"published","type":"conference_poster","publisher":"IEEE","day":"31","date_published":"2011-12-31T00:00:00Z","title":"Detailed reconstruction of 3D plant root shape","publication":"Proceedings of the IEEE International Conference on Computer Vision","pubrep_id":"541","year":"2011","author":[{"last_name":"Zheng","full_name":"Zheng, Ying","first_name":"Ying"},{"first_name":"Steve","full_name":"Gu, Steve","last_name":"Gu"},{"orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Tomasi","full_name":"Tomasi, Carlo","first_name":"Carlo"},{"full_name":"Benfey, Philip","last_name":"Benfey","first_name":"Philip"}],"oa_version":"Submitted Version","status":"public","article_number":"6126475","file_date_updated":"2020-07-14T12:46:07Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","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."}],"article_processing_charge":"No","ddc":["000"],"oa":1,"language":[{"iso":"eng"}]},{"file":[{"creator":"system","file_name":"IST-2016-540-v1+1_2011-P-08-RunEmpty.pdf","file_size":614050,"file_id":"5282","checksum":"6984684081ba123808b344f9f2e64a8f","date_created":"2018-12-12T10:17:28Z","access_level":"open_access","relation":"main_file","date_updated":"2020-07-14T12:46:07Z","content_type":"application/pdf"}],"doi":"10.1109/ICCV.2011.6126271","_id":"3313","conference":{"start_date":"2011-11-06","location":"Barcelona, Spain","end_date":"2011-11-13","name":"ICCV: International Conference on Computer Vision"},"month":"11","citation":{"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>","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>","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.","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>.","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.","short":"C. Chen, H. Edelsbrunner, in:, Proceedings of the IEEE International Conference on Computer Vision, IEEE, 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>."},"date_created":"2018-12-11T12:02:37Z","date_updated":"2021-01-12T07:42:35Z","department":[{"_id":"HeEd"}],"publist_id":"3327","has_accepted_license":"1","publication_status":"published","quality_controlled":"1","type":"conference","scopus_import":1,"publisher":"IEEE","title":"Diffusion runs low on persistence fast","date_published":"2011-11-06T00:00:00Z","day":"06","publication":"Proceedings of the IEEE International Conference on Computer Vision","pubrep_id":"540","year":"2011","author":[{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","first_name":"Chao","full_name":"Chen, Chao","last_name":"Chen"},{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}],"oa_version":"Submitted Version","status":"public","article_number":"6126271","file_date_updated":"2020-07-14T12:46:07Z","abstract":[{"lang":"eng","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."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"oa":1,"language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"ddc":["000","005"],"oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","abstract":[{"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.","lang":"eng"}],"file_date_updated":"2020-07-14T12:46:07Z","oa_version":"Published Version","status":"public","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"full_name":"Prabhu, Vinayak","last_name":"Prabhu","first_name":"Vinayak"}],"related_material":{"record":[{"id":"3876","status":"public","relation":"earlier_version"}]},"pubrep_id":"506","year":"2011","ec_funded":1,"tmp":{"short":"CC BY-ND (4.0)","image":"/image/cc_by_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nd/4.0/legalcode","name":"Creative Commons Attribution-NoDerivatives 4.0 International (CC BY-ND 4.0)"},"license":"https://creativecommons.org/licenses/by-nd/4.0/","day":"14","date_published":"2011-12-14T00:00:00Z","title":"Timed parity games: Complexity and robustness","publication":"Logical Methods in Computer Science","publication_status":"published","type":"journal_article","scopus_import":1,"quality_controlled":"1","publisher":"International Federation of Computational Logic","has_accepted_license":"1","publist_id":"3324","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"date_created":"2018-12-11T12:02:37Z","date_updated":"2023-02-23T11:46:35Z","intvolume":"         7","month":"12","citation":{"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>","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>","ista":"Chatterjee K, Henzinger TA, Prabhu V. 2011. Timed parity games: Complexity and robustness. Logical Methods in Computer Science. 7(4).","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>.","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.","short":"K. Chatterjee, T.A. Henzinger, V. Prabhu, Logical Methods in Computer Science 7 (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>."},"issue":"4","_id":"3315","file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:46:07Z","date_created":"2018-12-12T10:16:42Z","relation":"main_file","file_id":"5231","checksum":"3480e1594bbef25ff7462fa93a8a814e","file_size":588863,"file_name":"IST-2016-86-v2+1_1011.0688_3_.pdf","creator":"system"}],"volume":7,"doi":"10.2168/LMCS-7(4:8)2011","project":[{"_id":"25EFB36C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"COMponent-Based Embedded Systems design Techniques","grant_number":"215543"}]},{"abstract":[{"lang":"eng","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."}],"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"oa":1,"year":"2011","ec_funded":1,"oa_version":"Published Version","status":"public","page":"176 - 185","author":[{"first_name":"Roderick","full_name":"Bloem, Roderick","last_name":"Bloem"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Karin","last_name":"Greimel","full_name":"Greimel, Karin"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"full_name":"Jobstmann, Barbara","last_name":"Jobstmann","first_name":"Barbara"}],"quality_controlled":"1","type":"conference","scopus_import":1,"publication_status":"published","publisher":"IEEE","title":"Specification-centered robustness","date_published":"2011-07-14T00:00:00Z","day":"14","publication":"6th IEEE International Symposium on Industrial and Embedded Systems","_id":"3316","conference":{"start_date":"2011-06-15","location":"Vasteras, Sweden","end_date":"2011-06-17","name":" SIES: International Symposium on Industrial Embedded Systems"},"main_file_link":[{"url":"https://openlib.tugraz.at/download.php?id=5cb57c8a49344&location=browse","open_access":"1"}],"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","grant_number":"267989","call_identifier":"FP7"},{"_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FP7","grant_number":"214373","name":"Design for Embedded Systems","_id":"25F1337C-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"}],"doi":"10.1109/SIES.2011.5953660","date_updated":"2021-01-12T07:42:36Z","date_created":"2018-12-11T12:02:38Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publist_id":"3323","month":"07","citation":{"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>","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>","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.","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>.","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>.","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.","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."}},{"publication":"Journal of Cell Biology","title":"POM121 and Sun1 play a role in early steps of interphase NPC assembly","date_published":"2011-07-04T00:00:00Z","keyword":["Cell Biology"],"day":"04","publisher":"Rockefeller University Press","scopus_import":"1","type":"journal_article","quality_controlled":"1","publication_status":"published","intvolume":"       194","date_created":"2022-04-07T07:52:18Z","date_updated":"2022-07-18T08:53:46Z","citation":{"ieee":"J. A. Talamas and M. Hetzer, “POM121 and Sun1 play a role in early steps of interphase NPC assembly,” <i>Journal of Cell Biology</i>, vol. 194, no. 1. Rockefeller University Press, pp. 27–37, 2011.","mla":"Talamas, Jessica A., and Martin Hetzer. “POM121 and Sun1 Play a Role in Early Steps of Interphase NPC Assembly.” <i>Journal of Cell Biology</i>, vol. 194, no. 1, Rockefeller University Press, 2011, pp. 27–37, doi:<a href=\"https://doi.org/10.1083/jcb.201012154\">10.1083/jcb.201012154</a>.","short":"J.A. Talamas, M. Hetzer, Journal of Cell Biology 194 (2011) 27–37.","chicago":"Talamas, Jessica A., and Martin Hetzer. “POM121 and Sun1 Play a Role in Early Steps of Interphase NPC Assembly.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2011. <a href=\"https://doi.org/10.1083/jcb.201012154\">https://doi.org/10.1083/jcb.201012154</a>.","ista":"Talamas JA, Hetzer M. 2011. POM121 and Sun1 play a role in early steps of interphase NPC assembly. Journal of Cell Biology. 194(1), 27–37.","apa":"Talamas, J. A., &#38; Hetzer, M. (2011). POM121 and Sun1 play a role in early steps of interphase NPC assembly. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201012154\">https://doi.org/10.1083/jcb.201012154</a>","ama":"Talamas JA, Hetzer M. POM121 and Sun1 play a role in early steps of interphase NPC assembly. <i>Journal of Cell Biology</i>. 2011;194(1):27-37. doi:<a href=\"https://doi.org/10.1083/jcb.201012154\">10.1083/jcb.201012154</a>"},"month":"07","article_type":"original","extern":"1","_id":"11094","issue":"1","doi":"10.1083/jcb.201012154","volume":194,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1083/jcb.201012154"}],"language":[{"iso":"eng"}],"pmid":1,"oa":1,"abstract":[{"text":"Nuclear pore complexes (NPCs) assemble at the end of mitosis during nuclear envelope (NE) reformation and into an intact NE as cells progress through interphase. Although recent studies have shown that NPC formation occurs by two different molecular mechanisms at two distinct cell cycle stages, little is known about the molecular players that mediate the fusion of the outer and inner nuclear membranes to form pores. In this paper, we provide evidence that the transmembrane nucleoporin (Nup), POM121, but not the Nup107–160 complex, is present at new pore assembly sites at a time that coincides with inner nuclear membrane (INM) and outer nuclear membrane (ONM) fusion. Overexpression of POM121 resulted in juxtaposition of the INM and ONM. Additionally, Sun1, an INM protein that is known to interact with the cytoskeleton, was specifically required for interphase assembly and localized with POM121 at forming pores. We propose a model in which POM121 and Sun1 interact transiently to promote early steps of interphase NPC assembly.","lang":"eng"}],"article_processing_charge":"No","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","external_id":{"pmid":["21727197"]},"status":"public","oa_version":"Published Version","page":"27-37","author":[{"last_name":"Talamas","full_name":"Talamas, Jessica A.","first_name":"Jessica A."},{"first_name":"Martin W","id":"86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed","last_name":"HETZER","full_name":"HETZER, Martin W","orcid":"0000-0002-2111-992X"}],"year":"2011","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]}},{"year":"2011","status":"public","oa_version":"Preprint","author":[{"full_name":"Waitukaitis, Scott R","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","first_name":"Scott R"},{"last_name":"Grütjen","full_name":"Grütjen, Helge","first_name":"Helge"},{"last_name":"Royer","full_name":"Royer, John","first_name":"John"},{"full_name":"Jaeger, Heinrich","last_name":"Jaeger","first_name":"Heinrich"}],"abstract":[{"lang":"eng","text":"Particle beams are important tools for probing atomic and molecular interactions. Here we demonstrate that particle beams also offer a unique opportunity to investigate interactions in macroscopic systems, such as granular media. Motivated by recent experiments on streams of grains that exhibit liquid-like breakup into droplets, we use molecular dynamics simulations to investigate the evolution of a dense stream of macroscopic spheres accelerating out of an opening at the bottom of a reservoir. We show how nanoscale details associated with energy dissipation during collisions modify the stream\\'s macroscopic behavior. We find that inelastic collisions collimate the stream, while the presence of short-range attractive interactions drives structure formation. Parameterizing the collision dynamics by the coefficient of restitution (i.e., the ratio of relative velocities before and after impact) and the strength of the cohesive interaction, we map out a spectrum of behaviors that ranges from gaslike jets in which all grains drift apart to liquid-like streams that break into large droplets containing hundreds of grains. We also find a new, intermediate regime in which small aggregates form by capture from the gas phase, similar to what can be observed in molecular beams. Our results show that nearly all aspects of stream behavior are closely related to the velocity gradient associated with vertical free fall. Led by this observation, we propose a simple energy balance model to explain the droplet formation process. The qualitative as well as many quantitative features of the simulations and the model compare well with available experimental data and provide a first quantitative measure of the role of attractions in freely cooling granular streams."}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1006.1371"]},"article_number":"051302","language":[{"iso":"eng"}],"oa":1,"_id":"112","extern":"1","issue":"5","doi":"10.1103/PhysRevE.83.051302","volume":83,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1006.1371"}],"intvolume":"        83","date_updated":"2021-01-12T06:48:25Z","date_created":"2018-12-11T11:44:41Z","publist_id":"7942","acknowledgement":"This work was supported by the NSF through CBET-0933242. We acknowledge use of shared facilities provided by the Keck Facility for Ultrafast Imaging at the University of Chicago and by the Chicago MRSEC through NSF DMR-0820054. Software support by Itasca Consulting Group, Inc., under the Itasca Educational Partnership is gratefully acknowledged. H.G. thanks the German-American Fulbright Commission for fellowship support during his stay at the University of Chicago.","citation":{"ista":"Waitukaitis SR, Grütjen H, Royer J, Jaeger H. 2011. Droplet and cluster formation in freely falling granular streams. Physical Review E. 83(5), 051302.","apa":"Waitukaitis, S. R., Grütjen, H., Royer, J., &#38; Jaeger, H. (2011). Droplet and cluster formation in freely falling granular streams. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevE.83.051302\">https://doi.org/10.1103/PhysRevE.83.051302</a>","ama":"Waitukaitis SR, Grütjen H, Royer J, Jaeger H. Droplet and cluster formation in freely falling granular streams. <i>Physical Review E</i>. 2011;83(5). doi:<a href=\"https://doi.org/10.1103/PhysRevE.83.051302\">10.1103/PhysRevE.83.051302</a>","ieee":"S. R. Waitukaitis, H. Grütjen, J. Royer, and H. Jaeger, “Droplet and cluster formation in freely falling granular streams,” <i>Physical Review E</i>, vol. 83, no. 5. American Physical Society, 2011.","short":"S.R. Waitukaitis, H. Grütjen, J. Royer, H. Jaeger, Physical Review E 83 (2011).","mla":"Waitukaitis, Scott R., et al. “Droplet and Cluster Formation in Freely Falling Granular Streams.” <i>Physical Review E</i>, vol. 83, no. 5, 051302, American Physical Society, 2011, doi:<a href=\"https://doi.org/10.1103/PhysRevE.83.051302\">10.1103/PhysRevE.83.051302</a>.","chicago":"Waitukaitis, Scott R, Helge Grütjen, John Royer, and Heinrich Jaeger. “Droplet and Cluster Formation in Freely Falling Granular Streams.” <i>Physical Review E</i>. American Physical Society, 2011. <a href=\"https://doi.org/10.1103/PhysRevE.83.051302\">https://doi.org/10.1103/PhysRevE.83.051302</a>."},"month":"05","publisher":"American Physical Society","type":"journal_article","publication_status":"published","quality_controlled":"1","arxiv":1,"publication":"Physical Review E","title":"Droplet and cluster formation in freely falling granular streams","date_published":"2011-05-12T00:00:00Z","day":"12"},{"day":"28","date_published":"2011-09-28T00:00:00Z","title":"Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube","publication":"Development","has_accepted_license":"1","type":"journal_article","quality_controlled":"1","scopus_import":1,"publication_status":"published","publisher":"Company of Biologists","month":"09","article_type":"original","citation":{"mla":"Stockinger, Petra, et al. “Defective Neuroepithelial Cell Cohesion Affects Tangential Branchiomotor Neuron Migration in the Zebrafish Neural Tube.” <i>Development</i>, vol. 138, no. 21, Company of Biologists, 2011, pp. 4673–83, doi:<a href=\"https://doi.org/10.1242/dev.071233\">10.1242/dev.071233</a>.","short":"P. Stockinger, C.-P.J. Heisenberg, J.-L. Maître, Development 138 (2011) 4673–4683.","ieee":"P. Stockinger, C.-P. J. Heisenberg, and J.-L. Maître, “Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube,” <i>Development</i>, vol. 138, no. 21. Company of Biologists, pp. 4673–4683, 2011.","chicago":"Stockinger, Petra, Carl-Philipp J Heisenberg, and Jean-Léon Maître. “Defective Neuroepithelial Cell Cohesion Affects Tangential Branchiomotor Neuron Migration in the Zebrafish Neural Tube.” <i>Development</i>. Company of Biologists, 2011. <a href=\"https://doi.org/10.1242/dev.071233\">https://doi.org/10.1242/dev.071233</a>.","ista":"Stockinger P, Heisenberg C-PJ, Maître J-L. 2011. Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube. Development. 138(21), 4673–4683.","ama":"Stockinger P, Heisenberg C-PJ, Maître J-L. Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube. <i>Development</i>. 2011;138(21):4673-4683. doi:<a href=\"https://doi.org/10.1242/dev.071233\">10.1242/dev.071233</a>","apa":"Stockinger, P., Heisenberg, C.-P. J., &#38; Maître, J.-L. (2011). Defective neuroepithelial cell cohesion affects tangential branchiomotor neuron migration in the zebrafish neural tube. <i>Development</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/dev.071233\">https://doi.org/10.1242/dev.071233</a>"},"department":[{"_id":"CaHe"}],"publist_id":"3210","date_updated":"2021-01-12T07:43:11Z","date_created":"2018-12-11T12:03:06Z","intvolume":"       138","file":[{"relation":"main_file","access_level":"open_access","date_created":"2019-10-07T14:19:42Z","date_updated":"2020-07-14T12:46:12Z","file_id":"6930","checksum":"ca12b79e01ef36c1ef1aea31cf7e7139","content_type":"application/pdf","creator":"dernst","file_size":4672439,"file_name":"2011_Development_Stockinger.pdf"}],"volume":138,"doi":"10.1242/dev.071233","issue":"21","_id":"3396","ddc":["570"],"oa":1,"language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:46:12Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"abstract":[{"lang":"eng","text":"Facial branchiomotor neurons (FBMNs) in zebrafish and mouse embryonic hindbrain undergo a characteristic tangential migration from rhombomere (r) 4, where they are born, to r6/7. Cohesion among neuroepithelial cells (NCs) has been suggested to function in FBMN migration by inhibiting FBMNs positioned in the basal neuroepithelium such that they move apically between NCs towards the midline of the neuroepithelium instead of tangentially along the basal side of the neuroepithelium towards r6/7. However, direct experimental evaluation of this hypothesis is still lacking. Here, we have used a combination of biophysical cell adhesion measurements and high-resolution time-lapse microscopy to determine the role of NC cohesion in FBMN migration. We show that reducing NC cohesion by interfering with Cadherin 2 (Cdh2) activity results in FBMNs positioned at the basal side of the neuroepithelium moving apically towards the neural tube midline instead of tangentially towards r6/7. In embryos with strongly reduced NC cohesion, ectopic apical FBMN movement frequently results in fusion of the bilateral FBMN clusters over the apical midline of the neural tube. By contrast, reducing cohesion among FBMNs by interfering with Contactin 2 (Cntn2) expression in these cells has little effect on apical FBMN movement, but reduces the fusion of the bilateral FBMN clusters in embryos with strongly diminished NC cohesion. These data provide direct experimental evidence that NC cohesion functions in tangential FBMN migration by restricting their apical movement."}],"author":[{"first_name":"Petra","id":"261CB030-E90D-11E9-B182-F697D44B663C","full_name":"Stockinger, Petra","last_name":"Stockinger"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"},{"last_name":"Maître","full_name":"Maître, Jean-Léon","orcid":"0000-0002-3688-1474","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon"}],"page":"4673 - 4683","oa_version":"Published Version","status":"public","year":"2011"},{"year":"2011","oa_version":"Submitted Version","status":"public","page":"102 - 110","author":[{"last_name":"Row","full_name":"Row, Richard","first_name":"Richard"},{"orcid":"0000-0002-3688-1474","full_name":"Maître, Jean-Léon","last_name":"Maître","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","first_name":"Jean-Léon"},{"full_name":"Martin, Benjamin","last_name":"Martin","first_name":"Benjamin"},{"last_name":"Stockinger","full_name":"Stockinger, Petra","id":"261CB030-E90D-11E9-B182-F697D44B663C","first_name":"Petra"},{"last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"},{"first_name":"David","full_name":"Kimelman, David","last_name":"Kimelman"}],"external_id":{"pmid":["1463614"]},"abstract":[{"text":"The process of gastrulation is highly conserved across vertebrates on both the genetic and morphological levels, despite great variety in embryonic shape and speed of development. This mechanism spatially separates the germ layers and establishes the organizational foundation for future development. Mesodermal identity is specified in a superficial layer of cells, the epiblast, where cells maintain an epithelioid morphology. These cells involute to join the deeper hypoblast layer where they adopt a migratory, mesenchymal morphology. Expression of a cascade of related transcription factors orchestrates the parallel genetic transition from primitive to mature mesoderm. Although the early and late stages of this process are increasingly well understood, the transition between them has remained largely mysterious. We present here the first high resolution in vivo observations of the blebby transitional morphology of involuting mesodermal cells in a vertebrate embryo. We further demonstrate that the zebrafish spadetail mutation creates a reversible block in the maturation program, stalling cells in the transition state. This mutation creates an ideal system for dissecting the specific properties of cells undergoing the morphological transition of maturing mesoderm, as we demonstrate with a direct measurement of cell–cell adhesion.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pmid":1,"language":[{"iso":"eng"}],"oa":1,"issue":"1","_id":"3379","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090540/","open_access":"1"}],"volume":354,"doi":"10.1016/j.ydbio.2011.03.025","date_created":"2018-12-11T12:03:00Z","date_updated":"2021-01-12T07:43:04Z","department":[{"_id":"CaHe"}],"publist_id":"3228","intvolume":"       354","article_type":"original","month":"06","citation":{"ista":"Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. 2011. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. 354(1), 102–110.","ama":"Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. <i>Developmental Biology</i>. 2011;354(1):102-110. doi:<a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">10.1016/j.ydbio.2011.03.025</a>","apa":"Row, R., Maître, J.-L., Martin, B., Stockinger, P., Heisenberg, C.-P. J., &#38; Kimelman, D. (2011). Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. <i>Developmental Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">https://doi.org/10.1016/j.ydbio.2011.03.025</a>","short":"R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P.J. Heisenberg, D. Kimelman, Developmental Biology 354 (2011) 102–110.","mla":"Row, Richard, et al. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” <i>Developmental Biology</i>, vol. 354, no. 1, Elsevier, 2011, pp. 102–10, doi:<a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">10.1016/j.ydbio.2011.03.025</a>.","ieee":"R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P. J. Heisenberg, and D. Kimelman, “Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail,” <i>Developmental Biology</i>, vol. 354, no. 1. Elsevier, pp. 102–110, 2011.","chicago":"Row, Richard, Jean-Léon Maître, Benjamin Martin, Petra Stockinger, Carl-Philipp J Heisenberg, and David Kimelman. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” <i>Developmental Biology</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.ydbio.2011.03.025\">https://doi.org/10.1016/j.ydbio.2011.03.025</a>."},"quality_controlled":"1","publication_status":"published","type":"journal_article","scopus_import":1,"publisher":"Elsevier","title":"Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail","date_published":"2011-06-01T00:00:00Z","day":"01","publication":"Developmental Biology"},{"intvolume":"        46","date_created":"2023-02-20T08:18:27Z","date_updated":"2023-02-20T09:39:29Z","citation":{"ista":"Pellicciotti F, Bauder A, Parola M. 2010. Effect of glaciers on streamflow trends in the Swiss Alps. Water Resources Research. 46(10), W10522.","apa":"Pellicciotti, F., Bauder, A., &#38; Parola, M. (2010). Effect of glaciers on streamflow trends in the Swiss Alps. <i>Water Resources Research</i>. American Geophysical Union. <a href=\"https://doi.org/10.1029/2009wr009039\">https://doi.org/10.1029/2009wr009039</a>","ama":"Pellicciotti F, Bauder A, Parola M. Effect of glaciers on streamflow trends in the Swiss Alps. <i>Water Resources Research</i>. 2010;46(10). doi:<a href=\"https://doi.org/10.1029/2009wr009039\">10.1029/2009wr009039</a>","ieee":"F. Pellicciotti, A. Bauder, and M. Parola, “Effect of glaciers on streamflow trends in the Swiss Alps,” <i>Water Resources Research</i>, vol. 46, no. 10. American Geophysical Union, 2010.","mla":"Pellicciotti, Francesca, et al. “Effect of Glaciers on Streamflow Trends in the Swiss Alps.” <i>Water Resources Research</i>, vol. 46, no. 10, W10522, American Geophysical Union, 2010, doi:<a href=\"https://doi.org/10.1029/2009wr009039\">10.1029/2009wr009039</a>.","short":"F. Pellicciotti, A. Bauder, M. Parola, Water Resources Research 46 (2010).","chicago":"Pellicciotti, Francesca, A. Bauder, and M. Parola. “Effect of Glaciers on Streamflow Trends in the Swiss Alps.” <i>Water Resources Research</i>. American Geophysical Union, 2010. <a href=\"https://doi.org/10.1029/2009wr009039\">https://doi.org/10.1029/2009wr009039</a>."},"article_type":"original","month":"10","_id":"12653","extern":"1","issue":"10","doi":"10.1029/2009wr009039","volume":46,"main_file_link":[{"url":"https://doi.org/10.1029/2009WR009039","open_access":"1"}],"publication":"Water Resources Research","keyword":["Water Science and Technology"],"day":"01","title":"Effect of glaciers on streamflow trends in the Swiss Alps","date_published":"2010-10-01T00:00:00Z","publisher":"American Geophysical Union","publication_status":"published","type":"journal_article","quality_controlled":"1","scopus_import":"1","status":"public","oa_version":"Published Version","author":[{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca"},{"last_name":"Bauder","full_name":"Bauder, A.","first_name":"A."},{"full_name":"Parola, M.","last_name":"Parola","first_name":"M."}],"year":"2010","publication_identifier":{"issn":["0043-1397"],"eissn":["1944-7973"]},"language":[{"iso":"eng"}],"oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Daily streamflow from stations close to five Swiss glaciers is analyzed for trends with the Mann-Kendall test. We consider a common period of record (1974–2004) and longer periods based on data availability. The trend statistical significance is tested on annual and seasonal bases. We also examine changes in precipitation, temperature, and snow cover characteristics. Highly glacierized basins show statistically significant positive trends in annual streamflow caused by increasing streamflow in spring and summer. Trends are more numerous and stronger at lower and mid than at the upper quantiles. The basin characterized by lower glacier coverage, conversely, does not exhibit consistently statistically significant trends. Changes in precipitation are not sufficient to explain the observed streamflow trends. Air temperature sees an increase in mean, minimum, and maximum values at all sites. Variations in the seasonal snow accumulation and ablation process are evident. Solid precipitation is decreasing at all sites and trends may be due to a shift from snowfall into rainfall. Mean snow depth is also decreasing, and its duration is getting shorter because of a decrease in solid precipitation and enhanced melting. Trend magnitude attenuates with longer time series. Contrasting trends are detected for different subperiods in the last 70 years: statistically significant negative trends are observed in the periods 1944–1974 and 1954–1984 for Aletschgletscher, in contrast with the results for the common period. These trends are explained by different rates of ice volume changes, and the sign of trends is clearly related to phases of positive or negative glacier mass balance."}],"article_number":"W10522"},{"publication":"Physical Review Letters","date_published":"2010-04-02T00:00:00Z","title":"Colloidal motility and pattern formation under rectified diffusiophoresis","day":"02","publisher":"American Physical Society","type":"journal_article","quality_controlled":"1","scopus_import":"1","publication_status":"published","arxiv":1,"intvolume":"       104","date_created":"2021-01-19T10:25:04Z","date_updated":"2023-02-23T13:46:40Z","citation":{"chicago":"Palacci, Jérémie A, Benjamin Abécassis, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Colloidal Motility and Pattern Formation under Rectified Diffusiophoresis.” <i>Physical Review Letters</i>. American Physical Society, 2010. <a href=\"https://doi.org/10.1103/physrevlett.104.138302\">https://doi.org/10.1103/physrevlett.104.138302</a>.","mla":"Palacci, Jérémie A., et al. “Colloidal Motility and Pattern Formation under Rectified Diffusiophoresis.” <i>Physical Review Letters</i>, vol. 104, no. 13, 138302, American Physical Society, 2010, doi:<a href=\"https://doi.org/10.1103/physrevlett.104.138302\">10.1103/physrevlett.104.138302</a>.","short":"J.A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters 104 (2010).","ieee":"J. A. Palacci, B. Abécassis, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Colloidal motility and pattern formation under rectified diffusiophoresis,” <i>Physical Review Letters</i>, vol. 104, no. 13. American Physical Society, 2010.","ama":"Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. Colloidal motility and pattern formation under rectified diffusiophoresis. <i>Physical Review Letters</i>. 2010;104(13). doi:<a href=\"https://doi.org/10.1103/physrevlett.104.138302\">10.1103/physrevlett.104.138302</a>","apa":"Palacci, J. A., Abécassis, B., Cottin-Bizonne, C., Ybert, C., &#38; Bocquet, L. (2010). Colloidal motility and pattern formation under rectified diffusiophoresis. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevlett.104.138302\">https://doi.org/10.1103/physrevlett.104.138302</a>","ista":"Palacci JA, Abécassis B, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Colloidal motility and pattern formation under rectified diffusiophoresis. Physical Review Letters. 104(13), 138302."},"month":"04","article_type":"letter_note","extern":"1","_id":"9012","issue":"13","doi":"10.1103/physrevlett.104.138302","volume":104,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1004.1256"}],"language":[{"iso":"eng"}],"pmid":1,"oa":1,"abstract":[{"lang":"eng","text":"In this Letter, we characterize experimentally the diffusiophoretic motion of colloids and λ-DNA toward higher concentration of solutes, using microfluidic technology to build spatially and temporally controlled concentration gradients. We then demonstrate that segregation and spatial patterning of the particles can be achieved from temporal variations of the solute concentration profile. This segregation takes the form of a strong trapping potential, stemming from an osmotically induced rectification mechanism of the solute time-dependent variations. Depending on the spatial and temporal symmetry of the solute signal, localization patterns with various shapes can be achieved. These results highlight the role of solute contrasts in out-of-equilibrium processes occurring in soft matter."}],"article_processing_charge":"No","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","external_id":{"arxiv":["1004.1256 "],"pmid":["20481918"]},"article_number":"138302","status":"public","oa_version":"Preprint","author":[{"first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d","last_name":"Palacci","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465"},{"last_name":"Abécassis","full_name":"Abécassis, Benjamin","first_name":"Benjamin"},{"last_name":"Cottin-Bizonne","full_name":"Cottin-Bizonne, Cécile","first_name":"Cécile"},{"first_name":"Christophe","full_name":"Ybert, Christophe","last_name":"Ybert"},{"first_name":"Lydéric","last_name":"Bocquet","full_name":"Bocquet, Lydéric"}],"year":"2010","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]}},{"arxiv":1,"publisher":"American Physical Society ","scopus_import":"1","type":"journal_article","quality_controlled":"1","publication_status":"published","publication":"Physical Review Letters","title":"Sedimentation and effective temperature of active colloidal suspensions","date_published":"2010-08-20T00:00:00Z","day":"20","doi":"10.1103/physrevlett.105.088304","main_file_link":[{"url":"https://arxiv.org/abs/1004.4340","open_access":"1"}],"volume":105,"extern":"1","_id":"9013","issue":"8","citation":{"chicago":"Palacci, Jérémie A, Cécile Cottin-Bizonne, Christophe Ybert, and Lydéric Bocquet. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.” <i>Physical Review Letters</i>. American Physical Society , 2010. <a href=\"https://doi.org/10.1103/physrevlett.105.088304\">https://doi.org/10.1103/physrevlett.105.088304</a>.","ieee":"J. A. Palacci, C. Cottin-Bizonne, C. Ybert, and L. Bocquet, “Sedimentation and effective temperature of active colloidal suspensions,” <i>Physical Review Letters</i>, vol. 105, no. 8. American Physical Society , 2010.","short":"J.A. Palacci, C. Cottin-Bizonne, C. Ybert, L. Bocquet, Physical Review Letters 105 (2010).","mla":"Palacci, Jérémie A., et al. “Sedimentation and Effective Temperature of Active Colloidal Suspensions.” <i>Physical Review Letters</i>, vol. 105, no. 8, 088304, American Physical Society , 2010, doi:<a href=\"https://doi.org/10.1103/physrevlett.105.088304\">10.1103/physrevlett.105.088304</a>.","apa":"Palacci, J. A., Cottin-Bizonne, C., Ybert, C., &#38; Bocquet, L. (2010). Sedimentation and effective temperature of active colloidal suspensions. <i>Physical Review Letters</i>. American Physical Society . <a href=\"https://doi.org/10.1103/physrevlett.105.088304\">https://doi.org/10.1103/physrevlett.105.088304</a>","ama":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. Sedimentation and effective temperature of active colloidal suspensions. <i>Physical Review Letters</i>. 2010;105(8). doi:<a href=\"https://doi.org/10.1103/physrevlett.105.088304\">10.1103/physrevlett.105.088304</a>","ista":"Palacci JA, Cottin-Bizonne C, Ybert C, Bocquet L. 2010. Sedimentation and effective temperature of active colloidal suspensions. Physical Review Letters. 105(8), 088304."},"article_type":"letter_note","month":"08","intvolume":"       105","date_updated":"2023-02-23T13:46:42Z","date_created":"2021-01-19T10:26:33Z","article_number":"088304","abstract":[{"lang":"eng","text":"In this Letter, we investigate experimentally the nonequilibrium steady state of an active colloidal suspension under gravity field. The active particles are made of chemically powered colloids, showing self propulsion in the presence of an added fuel, here hydrogen peroxide. The active suspension is studied in a dedicated microfluidic device, made of permeable gel microstructures. Both the microdynamics of individual colloids and the global stationary state of the suspension under gravity are measured with optical microscopy. This yields a direct measurement of the effective temperature of the active system as a function of the particle activity, on the basis of the fluctuation-dissipation relationship. Our work is a first step in the experimental exploration of the out-of-equilibrium properties of active colloidal systems."}],"article_processing_charge":"No","user_id":"D865714E-FA4E-11E9-B85B-F5C5E5697425","external_id":{"arxiv":["1004.4340"],"pmid":["20868136"]},"oa":1,"language":[{"iso":"eng"}],"pmid":1,"publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"year":"2010","author":[{"last_name":"Palacci","full_name":"Palacci, Jérémie A","orcid":"0000-0002-7253-9465","first_name":"Jérémie A","id":"8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d"},{"last_name":"Cottin-Bizonne","full_name":"Cottin-Bizonne, Cécile","first_name":"Cécile"},{"first_name":"Christophe","last_name":"Ybert","full_name":"Ybert, Christophe"},{"first_name":"Lydéric","full_name":"Bocquet, Lydéric","last_name":"Bocquet"}],"status":"public","oa_version":"Preprint"},{"extern":"1","_id":"9146","issue":"2","doi":"10.1088/1748-9326/5/2/025207","volume":5,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1088/1748-9326/5/2/025207"}],"intvolume":"         5","date_updated":"2022-01-24T13:51:02Z","date_created":"2021-02-15T14:40:46Z","citation":{"apa":"O’Gorman, P. A., &#38; Muller, C. J. (2010). How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? <i>Environmental Research Letters</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">https://doi.org/10.1088/1748-9326/5/2/025207</a>","ama":"O’Gorman PA, Muller CJ. How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? <i>Environmental Research Letters</i>. 2010;5(2). doi:<a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">10.1088/1748-9326/5/2/025207</a>","ista":"O’Gorman PA, Muller CJ. 2010. How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations? Environmental Research Letters. 5(2), 025207.","chicago":"O’Gorman, P A, and Caroline J Muller. “How Closely Do Changes in Surface and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?” <i>Environmental Research Letters</i>. IOP Publishing, 2010. <a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">https://doi.org/10.1088/1748-9326/5/2/025207</a>.","ieee":"P. A. O’Gorman and C. J. Muller, “How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?,” <i>Environmental Research Letters</i>, vol. 5, no. 2. IOP Publishing, 2010.","short":"P.A. O’Gorman, C.J. Muller, Environmental Research Letters 5 (2010).","mla":"O’Gorman, P. A., and Caroline J. Muller. “How Closely Do Changes in Surface and Column Water Vapor Follow Clausius–Clapeyron Scaling in Climate Change Simulations?” <i>Environmental Research Letters</i>, vol. 5, no. 2, 025207, IOP Publishing, 2010, doi:<a href=\"https://doi.org/10.1088/1748-9326/5/2/025207\">10.1088/1748-9326/5/2/025207</a>."},"article_type":"original","month":"04","publisher":"IOP Publishing","quality_controlled":"1","publication_status":"published","type":"journal_article","publication":"Environmental Research Letters","date_published":"2010-04-09T00:00:00Z","title":"How closely do changes in surface and column water vapor follow Clausius–Clapeyron scaling in climate change simulations?","day":"09","keyword":["Renewable Energy","Sustainability and the Environment","Public Health","Environmental and Occupational Health","General Environmental Science"],"year":"2010","publication_identifier":{"issn":["1748-9326"]},"status":"public","oa_version":"Published Version","author":[{"full_name":"O’Gorman, P A","last_name":"O’Gorman","first_name":"P A"},{"orcid":"0000-0001-5836-5350","last_name":"Muller","full_name":"Muller, Caroline J","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J"}],"abstract":[{"lang":"eng","text":"The factors governing the rate of change in the amount of atmospheric water vapor are analyzed in simulations of climate change. The global-mean amount of water vapor is estimated to increase at a differential rate of 7.3% K − 1 with respect to global-mean surface air temperature in the multi-model mean. Larger rates of change result if the fractional change is evaluated over a finite change in temperature (e.g., 8.2% K − 1 for a 3 K warming), and rates of change of zonal-mean column water vapor range from 6 to 12% K − 1 depending on latitude.\r\nClausius–Clapeyron scaling is directly evaluated using an invariant distribution of monthly-mean relative humidity, giving a rate of 7.4% K − 1 for global-mean water vapor. There are deviations from Clausius–Clapeyron scaling of zonal-mean column water vapor in the tropics and mid-latitudes, but they largely cancel in the global mean. A purely thermodynamic scaling based on a saturated troposphere gives a higher global rate of 7.9% K − 1.\r\nSurface specific humidity increases at a rate of 5.7% K − 1, considerably lower than the rate for global-mean water vapor. Surface specific humidity closely follows Clausius–Clapeyron scaling over ocean. But there are widespread decreases in surface relative humidity over land (by more than 1% K − 1 in many regions), and it is argued that decreases of this magnitude could result from the land/ocean contrast in surface warming."}],"article_processing_charge":"No","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_number":"025207","language":[{"iso":"eng"}],"oa":1},{"extern":"1","_id":"7078","issue":"18","doi":"10.1103/physrevb.82.184112","volume":82,"main_file_link":[{"url":"https://arxiv.org/abs/1011.1445","open_access":"1"}],"intvolume":"        82","date_updated":"2021-01-12T08:11:44Z","date_created":"2019-11-19T13:46:28Z","citation":{"mla":"Salje, E. K. H., et al. “Tin Telluride: A Weakly Co-Elastic Metal.” <i>Physical Review B</i>, vol. 82, no. 18, 184112, APS, 2010, doi:<a href=\"https://doi.org/10.1103/physrevb.82.184112\">10.1103/physrevb.82.184112</a>.","short":"E.K.H. Salje, D.J. Safarik, K.A. Modic, J.E. Gubernatis, J.C. Cooley, R.D. Taylor, B. Mihaila, A. Saxena, T. Lookman, J.L. Smith, R.A. Fisher, M. Pasternak, C.P. Opeil, T. Siegrist, P.B. Littlewood, J.C. Lashley, Physical Review B 82 (2010).","ieee":"E. K. H. Salje <i>et al.</i>, “Tin telluride: A weakly co-elastic metal,” <i>Physical Review B</i>, vol. 82, no. 18. APS, 2010.","chicago":"Salje, E. K. H., D. J. Safarik, Kimberly A Modic, J. E. Gubernatis, J. C. Cooley, R. D. Taylor, B. Mihaila, et al. “Tin Telluride: A Weakly Co-Elastic Metal.” <i>Physical Review B</i>. APS, 2010. <a href=\"https://doi.org/10.1103/physrevb.82.184112\">https://doi.org/10.1103/physrevb.82.184112</a>.","ista":"Salje EKH, Safarik DJ, Modic KA, Gubernatis JE, Cooley JC, Taylor RD, Mihaila B, Saxena A, Lookman T, Smith JL, Fisher RA, Pasternak M, Opeil CP, Siegrist T, Littlewood PB, Lashley JC. 2010. Tin telluride: A weakly co-elastic metal. Physical Review B. 82(18), 184112.","ama":"Salje EKH, Safarik DJ, Modic KA, et al. Tin telluride: A weakly co-elastic metal. <i>Physical Review B</i>. 2010;82(18). doi:<a href=\"https://doi.org/10.1103/physrevb.82.184112\">10.1103/physrevb.82.184112</a>","apa":"Salje, E. K. H., Safarik, D. J., Modic, K. A., Gubernatis, J. E., Cooley, J. C., Taylor, R. D., … Lashley, J. C. (2010). Tin telluride: A weakly co-elastic metal. <i>Physical Review B</i>. APS. <a href=\"https://doi.org/10.1103/physrevb.82.184112\">https://doi.org/10.1103/physrevb.82.184112</a>"},"month":"11","article_type":"original","publisher":"APS","quality_controlled":"1","type":"journal_article","publication_status":"published","arxiv":1,"publication":"Physical Review B","day":"18","date_published":"2010-11-18T00:00:00Z","title":"Tin telluride: A weakly co-elastic metal","year":"2010","publication_identifier":{"issn":["1098-0121","1550-235X"]},"status":"public","oa_version":"Preprint","author":[{"full_name":"Salje, E. K. H.","last_name":"Salje","first_name":"E. K. H."},{"last_name":"Safarik","full_name":"Safarik, D. J.","first_name":"D. J."},{"full_name":"Modic, Kimberly A","last_name":"Modic","orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","first_name":"Kimberly A"},{"full_name":"Gubernatis, J. E.","last_name":"Gubernatis","first_name":"J. E."},{"first_name":"J. C.","full_name":"Cooley, J. C.","last_name":"Cooley"},{"first_name":"R. D.","last_name":"Taylor","full_name":"Taylor, R. D."},{"first_name":"B.","last_name":"Mihaila","full_name":"Mihaila, B."},{"full_name":"Saxena, A.","last_name":"Saxena","first_name":"A."},{"first_name":"T.","last_name":"Lookman","full_name":"Lookman, T."},{"full_name":"Smith, J. L.","last_name":"Smith","first_name":"J. L."},{"first_name":"R. A.","full_name":"Fisher, R. A.","last_name":"Fisher"},{"full_name":"Pasternak, M.","last_name":"Pasternak","first_name":"M."},{"first_name":"C. P.","full_name":"Opeil, C. P.","last_name":"Opeil"},{"full_name":"Siegrist, T.","last_name":"Siegrist","first_name":"T."},{"full_name":"Littlewood, P. B.","last_name":"Littlewood","first_name":"P. B."},{"first_name":"J. C.","full_name":"Lashley, J. C.","last_name":"Lashley"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"We report resonant ultrasound spectroscopy (RUS), dilatometry/magnetostriction, magnetotransport, magnetization, specific-heat, and 119Sn Mössbauer spectroscopy measurements on SnTe and Sn0.995Cr0.005Te. Hall measurements at T=77 K indicate that our Bridgman-grown single crystals have a p-type carrier concentration of 3.4×1019 cm−3 and that our Cr-doped crystals have an n-type concentration of 5.8×1022 cm−3. Although our SnTe crystals are diamagnetic over the temperature range 2≤T≤1100 K, the Cr-doped crystals are room-temperature ferromagnets with a Curie temperature of 294 K. For each sample type, three-terminal capacitive dilatometry measurements detect a subtle 0.5 μm distortion at Tc≈85 K. Whereas our RUS measurements on SnTe show elastic hardening near the structural transition, pointing to co-elastic behavior, similar measurements on Sn0.995Cr0.005Te show a pronounced softening, pointing to ferroelastic behavior. Effective Debye temperature, θD, values of SnTe obtained from 119Sn Mössbauer studies show a hardening of phonons in the range 60–115 K (θD=162 K) as compared with the 100–300 K range (θD=150 K). In addition, a precursor softening extending over approximately 100 K anticipates this collapse at the critical temperature and quantitative analysis over three decades of its reduced modulus finds ΔC44/C44=A|(T−T0)/T0|−κ with κ=0.50±0.02, a value indicating a three-dimensional softening of phonon branches at a temperature T0∼75 K, considerably below Tc. We suggest that the differences in these two types of elastic behaviors lie in the absence of elastic domain-wall motion in the one case and their nucleation in the other."}],"external_id":{"arxiv":["1011.1445"]},"article_number":"184112","language":[{"iso":"eng"}],"oa":1}]