[{"alternative_title":["Methods in Molecular Biology"],"year":"2016","page":"203 - 216","date_updated":"2023-09-05T14:09:01Z","publication":"High-Resolution Imaging of Cellular Proteins","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_created":"2018-12-11T11:50:06Z","date_published":"2016-08-12T00:00:00Z","publist_id":"6281","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"RySh"}],"type":"book_chapter","language":[{"iso":"eng"}],"quality_controlled":"1","intvolume":"      1474","publisher":"Springer","doi":"10.1007/978-1-4939-6352-2_12","abstract":[{"text":"Immunogold labeling of freeze-fracture replicas has recently been used for high-resolution visualization of protein localization in electron microscopy. This method has higher labeling efficiency than conventional immunogold methods for membrane molecules allowing precise quantitative measurements. However, one of the limitations of freeze-fracture replica immunolabeling is difficulty in keeping structural orientation and identifying labeled profiles in complex tissues like brain. The difficulty is partly due to fragmentation of freeze-fracture replica preparations during labeling procedures and limited morphological clues on the replica surface. To overcome these issues, we introduce here a grid-glued replica method combined with SEM observation. This method allows histological staining before dissolving the tissue and easy handling of replicas during immunogold labeling, and keeps the whole replica surface intact without fragmentation. The procedure described here is also useful for matched double-replica analysis allowing further identification of labeled profiles in corresponding P-face and E-face.","lang":"eng"}],"_id":"1094","author":[{"orcid":"0000-0001-7429-7896","first_name":"Harumi","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","last_name":"Harada","full_name":"Harada, Harumi"},{"orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"title":"Immunogold protein localization on grid-glued freeze-fracture replicas","ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"We thank Prof. Elek Molnár for providing us a pan-AMPAR anti-body used in Fig.2 and Dr. Ludek Lovicar for technical assistance in scanning electron microscope imaging. This work was supported by the European Union (HBP—Project Ref. 604102). ","project":[{"grant_number":"604102","_id":"25CD3DD2-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Localization of ion channels and receptors by two and three-dimensional immunoelectron microscopic approaches"}],"publication_identifier":{"eissn":["1611-3349"],"issn":["0302-9743"]},"oa_version":"None","month":"08","day":"12","citation":{"ista":"Harada H, Shigemoto R. 2016.Immunogold protein localization on grid-glued freeze-fracture replicas. In: High-Resolution Imaging of Cellular Proteins. Methods in Molecular Biology, vol. 1474, 203–216.","ama":"Harada H, Shigemoto R. Immunogold protein localization on grid-glued freeze-fracture replicas. In: <i>High-Resolution Imaging of Cellular Proteins</i>. Vol 1474. Springer; 2016:203-216. doi:<a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">10.1007/978-1-4939-6352-2_12</a>","short":"H. Harada, R. Shigemoto, in:, High-Resolution Imaging of Cellular Proteins, Springer, 2016, pp. 203–216.","ieee":"H. Harada and R. Shigemoto, “Immunogold protein localization on grid-glued freeze-fracture replicas,” in <i>High-Resolution Imaging of Cellular Proteins</i>, vol. 1474, Springer, 2016, pp. 203–216.","apa":"Harada, H., &#38; Shigemoto, R. (2016). Immunogold protein localization on grid-glued freeze-fracture replicas. In <i>High-Resolution Imaging of Cellular Proteins</i> (Vol. 1474, pp. 203–216). Springer. <a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">https://doi.org/10.1007/978-1-4939-6352-2_12</a>","mla":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” <i>High-Resolution Imaging of Cellular Proteins</i>, vol. 1474, Springer, 2016, pp. 203–16, doi:<a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">10.1007/978-1-4939-6352-2_12</a>.","chicago":"Harada, Harumi, and Ryuichi Shigemoto. “Immunogold Protein Localization on Grid-Glued Freeze-Fracture Replicas.” In <i>High-Resolution Imaging of Cellular Proteins</i>, 1474:203–16. Springer, 2016. <a href=\"https://doi.org/10.1007/978-1-4939-6352-2_12\">https://doi.org/10.1007/978-1-4939-6352-2_12</a>."},"article_processing_charge":"No","volume":1474},{"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","intvolume":"        59","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6280","department":[{"_id":"ToHe"}],"date_created":"2018-12-11T11:50:07Z","scopus_import":1,"date_published":"2016-08-01T00:00:00Z","date_updated":"2021-01-12T06:48:14Z","publication":"Leibniz International Proceedings in Informatics","article_number":"6","oa":1,"year":"2016","alternative_title":["LIPIcs"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_size":589747,"creator":"system","relation":"main_file","file_name":"IST-2017-793-v1+1_LIPIcs-CONCUR-2016-6.pdf","date_updated":"2018-12-12T10:10:10Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:10:10Z","file_id":"4795"}],"volume":59,"has_accepted_license":"1","month":"08","ddc":["004"],"file_date_updated":"2018-12-12T10:10:10Z","pubrep_id":"793","citation":{"chicago":"Haas, Andreas, Thomas A Henzinger, Andreas Holzer, Christoph Kirsch, Michael Lippautz, Hannes Payer, Ali Sezgin, Ana Sokolova, and Helmut Veith. “Local Linearizability for Concurrent Container-Type Data Structures.” In <i>Leibniz International Proceedings in Informatics</i>, Vol. 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.6</a>.","mla":"Haas, Andreas, et al. “Local Linearizability for Concurrent Container-Type Data Structures.” <i>Leibniz International Proceedings in Informatics</i>, vol. 59, 6, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016, doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">10.4230/LIPIcs.CONCUR.2016.6</a>.","ieee":"A. Haas <i>et al.</i>, “Local linearizability for concurrent container-type data structures,” in <i>Leibniz International Proceedings in Informatics</i>, Quebec City; Canada, 2016, vol. 59.","apa":"Haas, A., Henzinger, T. A., Holzer, A., Kirsch, C., Lippautz, M., Payer, H., … Veith, H. (2016). Local linearizability for concurrent container-type data structures. In <i>Leibniz International Proceedings in Informatics</i> (Vol. 59). Quebec City; Canada: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">https://doi.org/10.4230/LIPIcs.CONCUR.2016.6</a>","ama":"Haas A, Henzinger TA, Holzer A, et al. Local linearizability for concurrent container-type data structures. In: <i>Leibniz International Proceedings in Informatics</i>. Vol 59. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2016. doi:<a href=\"https://doi.org/10.4230/LIPIcs.CONCUR.2016.6\">10.4230/LIPIcs.CONCUR.2016.6</a>","short":"A. Haas, T.A. Henzinger, A. Holzer, C. Kirsch, M. Lippautz, H. Payer, A. Sezgin, A. Sokolova, H. Veith, in:, Leibniz International Proceedings in Informatics, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2016.","ista":"Haas A, Henzinger TA, Holzer A, Kirsch C, Lippautz M, Payer H, Sezgin A, Sokolova A, Veith H. 2016. Local linearizability for concurrent container-type data structures. Leibniz International Proceedings in Informatics. CONCUR: Concurrency Theory, LIPIcs, vol. 59, 6."},"day":"01","oa_version":"Published Version","conference":{"name":"CONCUR: Concurrency Theory","start_date":"2016-08-23","location":"Quebec City; Canada","end_date":"2016-08-26"},"license":"https://creativecommons.org/licenses/by/4.0/","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"}],"ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"This work has been supported by the National Research Network RiSE on Rigorous Systems Engineering\r\n(Austrian Science Fund (FWF): S11402-N23, S11403-N23, S11404-N23, S11411-N23), a Google\r\nPhD Fellowship, an Erwin Schrödinger Fellowship (Austrian Science Fund (FWF): J3696-N26), EPSRC\r\ngrants EP/H005633/1 and EP/K008528/1, the Vienna Science and Technology Fund (WWTF) trough\r\ngrant PROSEED, the European Research Council (ERC) under grant 267989 (QUAREM) and by the\r\nAustrian Science Fund (FWF) under grant Z211-N23 (Wittgenstein Award).","_id":"1095","title":"Local linearizability for concurrent container-type data structures","author":[{"first_name":"Andreas","full_name":"Haas, Andreas","last_name":"Haas"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"first_name":"Andreas","full_name":"Holzer, Andreas","last_name":"Holzer"},{"first_name":"Christoph","full_name":"Kirsch, Christoph","last_name":"Kirsch"},{"full_name":"Lippautz, Michael","last_name":"Lippautz","first_name":"Michael"},{"full_name":"Payer, Hannes","last_name":"Payer","first_name":"Hannes"},{"last_name":"Sezgin","full_name":"Sezgin, Ali","first_name":"Ali","id":"4C7638DA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ana","full_name":"Sokolova, Ana","last_name":"Sokolova"},{"first_name":"Helmut","last_name":"Veith","full_name":"Veith, Helmut"}],"doi":"10.4230/LIPIcs.CONCUR.2016.6","abstract":[{"lang":"eng","text":" The semantics of concurrent data structures is usually given by a sequential specification and a consistency condition. Linearizability is the most popular consistency condition due to its simplicity and general applicability. Nevertheless, for applications that do not require all guarantees offered by linearizability, recent research has focused on improving performance and scalability of concurrent data structures by relaxing their semantics. In this paper, we present local linearizability, a relaxed consistency condition that is applicable to container-type concurrent data structures like pools, queues, and stacks. While linearizability requires that the effect of each operation is observed by all threads at the same time, local linearizability only requires that for each thread T, the effects of its local insertion operations and the effects of those removal operations that remove values inserted by T are observed by all threads at the same time. We investigate theoretical and practical properties of local linearizability and its relationship to many existing consistency conditions. We present a generic implementation method for locally linearizable data structures that uses existing linearizable data structures as building blocks. Our implementations show performance and scalability improvements over the original building blocks and outperform the fastest existing container-type implementations. "}]},{"page":"493 - 506","related_material":{"record":[{"id":"7186","status":"public","relation":"part_of_dissertation"}]},"status":"public","publication_status":"published","date_updated":"2023-09-07T12:56:41Z","publication":"Developmental Cell","doi":"10.1016/j.devcel.2016.05.024","year":"2016","issue":"6","_id":"1096","title":"Actin rings of power","author":[{"orcid":"0000-0001-5130-2226","last_name":"Schwayer","full_name":"Schwayer, Cornelia","first_name":"Cornelia","id":"3436488C-F248-11E8-B48F-1D18A9856A87"},{"id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87","first_name":"Mateusz K","full_name":"Sikora, Mateusz K","last_name":"Sikora"},{"full_name":"Slovakova, Jana","last_name":"Slovakova","id":"30F3F2F0-F248-11E8-B48F-1D18A9856A87","first_name":"Jana"},{"last_name":"Kardos","full_name":"Kardos, Roland","first_name":"Roland","id":"4039350E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"volume":37,"quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","publisher":"Cell Press","intvolume":"        37","date_created":"2018-12-11T11:50:07Z","oa_version":"None","scopus_import":1,"date_published":"2016-06-20T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6279","month":"06","citation":{"mla":"Schwayer, Cornelia, et al. “Actin Rings of Power.” <i>Developmental Cell</i>, vol. 37, no. 6, Cell Press, 2016, pp. 493–506, doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">10.1016/j.devcel.2016.05.024</a>.","chicago":"Schwayer, Cornelia, Mateusz K Sikora, Jana Slovakova, Roland Kardos, and Carl-Philipp J Heisenberg. “Actin Rings of Power.” <i>Developmental Cell</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">https://doi.org/10.1016/j.devcel.2016.05.024</a>.","ista":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. 2016. Actin rings of power. Developmental Cell. 37(6), 493–506.","ama":"Schwayer C, Sikora MK, Slovakova J, Kardos R, Heisenberg C-PJ. Actin rings of power. <i>Developmental Cell</i>. 2016;37(6):493-506. doi:<a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">10.1016/j.devcel.2016.05.024</a>","short":"C. Schwayer, M.K. Sikora, J. Slovakova, R. Kardos, C.-P.J. Heisenberg, Developmental Cell 37 (2016) 493–506.","ieee":"C. Schwayer, M. K. Sikora, J. Slovakova, R. Kardos, and C.-P. J. Heisenberg, “Actin rings of power,” <i>Developmental Cell</i>, vol. 37, no. 6. Cell Press, pp. 493–506, 2016.","apa":"Schwayer, C., Sikora, M. K., Slovakova, J., Kardos, R., &#38; Heisenberg, C.-P. J. (2016). Actin rings of power. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2016.05.024\">https://doi.org/10.1016/j.devcel.2016.05.024</a>"},"department":[{"_id":"CaHe"}],"day":"20"},{"publication_status":"published","status":"public","acknowledgement":"We thank Nobuyuki Umetani for his insightful suggestions in our discussions. We thank Alan Schultz and his colleagues at NRL for building the hexacopter and for the valuable discussions. We thank Randall Davis, Boris Katz, and Howard Shrobe at MIT for their advice. We are grateful to Nick Bandiera for preprocessing mechanical parts and providing 3D printing technical support; Charles Blouin from RCBenchmark for dynamometer hardware support; Brian Saavedra for the composition UI; Yingzhe Yuan for data acquisition and video recording in the experiments; Michael Foshey and David Kim for their comments on the draft of the paper. \r\n\r\n\r\nThis work was partially supported by Air Force Research Laboratory’s sponsorship of Julia: A Fresh Approach to Technical Computing and Data Processing (Sponsor Award ID FA8750-15-2- 0272, MIT Award ID 024831-00003), and NSF Expedition project (Sponsor Award ID CCF-1138967, MIT Award ID 020610-00002). The views expressed herein are not endorsed by the sponsors. This project has also received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No 645599. ","ec_funded":1,"project":[{"name":"Soft-bodied intelligence for Manipulation","call_identifier":"H2020","_id":"25082902-B435-11E9-9278-68D0E5697425","grant_number":"645599"}],"abstract":[{"lang":"eng","text":"We present an interactive system for computational design, optimization, and fabrication of multicopters. Our computational approach allows non-experts to design, explore, and evaluate a wide range of different multicopters. We provide users with an intuitive interface for assembling a multicopter from a collection of components (e.g., propellers, motors, and carbon fiber rods). Our algorithm interactively optimizes shape and controller parameters of the current design to ensure its proper operation. In addition, we allow incorporating a variety of other metrics (such as payload, battery usage, size, and cost) into the design process and exploring tradeoffs between them. We show the efficacy of our method and system by designing, optimizing, fabricating, and operating multicopters with complex geometries and propeller configurations. We also demonstrate the ability of our optimization algorithm to improve the multicopter performance under different metrics."}],"issue":"6","doi":"10.1145/2980179.2982427","title":"Computational multicopter design","author":[{"first_name":"Tao","full_name":"Du, Tao","last_name":"Du"},{"first_name":"Adriana","last_name":"Schulz","full_name":"Schulz, Adriana"},{"first_name":"Bo","full_name":"Zhu, Bo","last_name":"Zhu"},{"full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385"},{"full_name":"Matusik, Wojciech","last_name":"Matusik","first_name":"Wojciech"}],"_id":"1097","has_accepted_license":"1","volume":35,"file":[{"date_updated":"2018-12-12T10:17:42Z","access_level":"open_access","content_type":"application/pdf","file_name":"IST-2017-759-v1+1_copter.pdf","relation":"main_file","creator":"system","file_size":33114420,"file_id":"5298","date_created":"2018-12-12T10:17:42Z"}],"oa_version":"Submitted Version","conference":{"name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia","location":"Macao, China","start_date":"2016-12-05","end_date":"2016-12-08"},"pubrep_id":"759","citation":{"mla":"Du, Tao, et al. <i>Computational Multicopter Design</i>. Vol. 35, no. 6, 227, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2980179.2982427\">10.1145/2980179.2982427</a>.","chicago":"Du, Tao, Adriana Schulz, Bo Zhu, Bernd Bickel, and Wojciech Matusik. “Computational Multicopter Design,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2980179.2982427\">https://doi.org/10.1145/2980179.2982427</a>.","ieee":"T. Du, A. Schulz, B. Zhu, B. Bickel, and W. Matusik, “Computational multicopter design,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6.","apa":"Du, T., Schulz, A., Zhu, B., Bickel, B., &#38; Matusik, W. (2016). Computational multicopter design (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. <a href=\"https://doi.org/10.1145/2980179.2982427\">https://doi.org/10.1145/2980179.2982427</a>","ama":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. Computational multicopter design. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2980179.2982427\">10.1145/2980179.2982427</a>","ista":"Du T, Schulz A, Zhu B, Bickel B, Matusik W. 2016. Computational multicopter design. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 227.","short":"T. Du, A. Schulz, B. Zhu, B. Bickel, W. Matusik, in:, ACM, 2016."},"day":"01","ddc":["006"],"month":"11","file_date_updated":"2018-12-12T10:17:42Z","article_number":"227","date_updated":"2021-01-12T06:48:15Z","year":"2016","alternative_title":["ACM Transactions on Graphics"],"oa":1,"language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","publisher":"ACM","intvolume":"        35","date_published":"2016-11-01T00:00:00Z","date_created":"2018-12-11T11:50:07Z","scopus_import":1,"department":[{"_id":"BeBi"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6278"},{"abstract":[{"text":"Better understanding of the potential benefits of information transfer and representation learning is an important step towards the goal of building intelligent systems that are able to persist in the world and learn over time. In this work, we consider a setting where the learner encounters a stream of tasks but is able to retain only limited information from each encountered task, such as a learned predictor. In contrast to most previous works analyzing this scenario, we do not make any distributional assumptions on the task generating process. Instead, we formulate a complexity measure that captures the diversity of the observed tasks. We provide a lifelong learning algorithm with error guarantees for every observed task (rather than on average). We show sample complexity reductions in comparison to solving every task in isolation in terms of our task complexity measure. Further, our algorithmic framework can naturally be viewed as learning a representation from encountered tasks with a neural network.","lang":"eng"}],"title":"Lifelong learning with weighted majority votes","author":[{"id":"42E87FC6-F248-11E8-B48F-1D18A9856A87","first_name":"Anastasia","full_name":"Pentina, Anastasia","last_name":"Pentina"},{"last_name":"Urner","full_name":"Urner, Ruth","first_name":"Ruth"}],"_id":"1098","status":"public","publication_status":"published","acknowledgement":"This work was in parts funded by the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant agreement no 308036.\r\n\r\n","ec_funded":1,"project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"}],"oa_version":"Published Version","conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2016-12-05","location":"Barcelona, Spain","end_date":"2016-12-10"},"citation":{"chicago":"Pentina, Anastasia, and Ruth Urner. “Lifelong Learning with Weighted Majority Votes,” 29:3619–27. Neural Information Processing Systems, 2016.","mla":"Pentina, Anastasia, and Ruth Urner. <i>Lifelong Learning with Weighted Majority Votes</i>. Vol. 29, Neural Information Processing Systems, 2016, pp. 3619–27.","apa":"Pentina, A., &#38; Urner, R. (2016). Lifelong learning with weighted majority votes (Vol. 29, pp. 3619–3627). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems.","ieee":"A. Pentina and R. Urner, “Lifelong learning with weighted majority votes,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 3619–3627.","ista":"Pentina A, Urner R. 2016. Lifelong learning with weighted majority votes. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3619–3627.","ama":"Pentina A, Urner R. Lifelong learning with weighted majority votes. In: Vol 29. Neural Information Processing Systems; 2016:3619-3627.","short":"A. Pentina, R. Urner, in:, Neural Information Processing Systems, 2016, pp. 3619–3627."},"pubrep_id":"775","day":"01","month":"12","file_date_updated":"2018-12-12T10:12:43Z","ddc":["006"],"has_accepted_license":"1","volume":29,"file":[{"file_id":"4961","date_created":"2018-12-12T10:12:42Z","file_name":"IST-2017-775-v1+1_main.pdf","relation":"main_file","file_size":237111,"creator":"system","date_updated":"2018-12-12T10:12:42Z","access_level":"open_access","content_type":"application/pdf"},{"date_created":"2018-12-12T10:12:43Z","file_id":"4962","date_updated":"2018-12-12T10:12:43Z","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_size":185818,"creator":"system","file_name":"IST-2017-775-v1+2_supplementary.pdf"}],"year":"2016","alternative_title":["Advances in Neural Information Processing Systems"],"oa":1,"page":"3619-3627","date_updated":"2021-01-12T06:48:15Z","date_published":"2016-12-01T00:00:00Z","date_created":"2018-12-11T11:50:08Z","scopus_import":1,"department":[{"_id":"ChLa"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6277","language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","publisher":"Neural Information Processing Systems","intvolume":"        29"},{"oa":1,"alternative_title":["ACM Transactions on Graphics"],"year":"2016","date_updated":"2021-01-12T06:48:16Z","article_number":"223","department":[{"_id":"BeBi"}],"publist_id":"6276","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2016-11-01T00:00:00Z","date_created":"2018-12-11T11:50:08Z","scopus_import":1,"publisher":"ACM","intvolume":"        35","language":[{"iso":"eng"}],"quality_controlled":"1","type":"conference","title":"FlexMolds: Automatic design of flexible shells for molding","author":[{"full_name":"Malomo, Luigi","last_name":"Malomo","first_name":"Luigi"},{"first_name":"Nico","full_name":"Pietroni, Nico","last_name":"Pietroni"},{"full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd","orcid":"0000-0001-6511-9385"},{"full_name":"Cignoni, Paolo","last_name":"Cignoni","first_name":"Paolo"}],"_id":"1099","abstract":[{"lang":"eng","text":"We present FlexMolds, a novel computational approach to automatically design flexible, reusable molds that, once 3D printed, allow us to physically fabricate, by means of liquid casting, multiple copies of complex shapes with rich surface details and complex topology. The approach to design such flexible molds is based on a greedy bottom-up search of possible cuts over an object, evaluating for each possible cut the feasibility of the resulting mold. We use a dynamic simulation approach to evaluate candidate molds, providing a heuristic to generate forces that are able to open, detach, and remove a complex mold from the object it surrounds. We have tested the approach with a number of objects with nontrivial shapes and topologies."}],"issue":"6","doi":"10.1145/2980179.2982397","project":[{"grant_number":"645599","_id":"25082902-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Soft-bodied intelligence for Manipulation"}],"publication_status":"published","acknowledgement":"The armadillo, bunny and dragon models are courtesy of the Stanford  3D  Scanning  Repository.   The  bimba,  fertility  and  elephant models are courtesy of the AIM@SHAPE Shape Repository.  \r\nThis project has received funding from the European Union’s Horizon 2020  research  and  innovation  programme  under  grant  agreement\r\nNo. 645599.","status":"public","ec_funded":1,"pubrep_id":"760","citation":{"chicago":"Malomo, Luigi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “FlexMolds: Automatic Design of Flexible Shells for Molding,” Vol. 35. ACM, 2016. <a href=\"https://doi.org/10.1145/2980179.2982397\">https://doi.org/10.1145/2980179.2982397</a>.","mla":"Malomo, Luigi, et al. <i>FlexMolds: Automatic Design of Flexible Shells for Molding</i>. Vol. 35, no. 6, 223, ACM, 2016, doi:<a href=\"https://doi.org/10.1145/2980179.2982397\">10.1145/2980179.2982397</a>.","ama":"Malomo L, Pietroni N, Bickel B, Cignoni P. FlexMolds: Automatic design of flexible shells for molding. In: Vol 35. ACM; 2016. doi:<a href=\"https://doi.org/10.1145/2980179.2982397\">10.1145/2980179.2982397</a>","ista":"Malomo L, Pietroni N, Bickel B, Cignoni P. 2016. FlexMolds: Automatic design of flexible shells for molding. SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, ACM Transactions on Graphics, vol. 35, 223.","short":"L. Malomo, N. Pietroni, B. Bickel, P. Cignoni, in:, ACM, 2016.","apa":"Malomo, L., Pietroni, N., Bickel, B., &#38; Cignoni, P. (2016). FlexMolds: Automatic design of flexible shells for molding (Vol. 35). Presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China: ACM. <a href=\"https://doi.org/10.1145/2980179.2982397\">https://doi.org/10.1145/2980179.2982397</a>","ieee":"L. Malomo, N. Pietroni, B. Bickel, and P. Cignoni, “FlexMolds: Automatic design of flexible shells for molding,” presented at the SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia, Macao, China, 2016, vol. 35, no. 6."},"day":"01","file_date_updated":"2018-12-12T10:12:01Z","ddc":["000","005"],"month":"11","oa_version":"Submitted Version","conference":{"location":"Macao, China","start_date":"2016-12-05","end_date":"2016-12-08","name":"SIGGRAPH Asia: Conference and Exhibition on Computer Graphics and Interactive Techniques in Asia"},"file":[{"relation":"main_file","file_size":11122029,"creator":"system","file_name":"IST-2017-760-v1+1_flexmolds.pdf","date_updated":"2018-12-12T10:12:01Z","content_type":"application/pdf","access_level":"open_access","date_created":"2018-12-12T10:12:01Z","file_id":"4918"}],"has_accepted_license":"1","volume":35},{"title":"Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation","author":[{"orcid":"0000-0002-6453-8075","last_name":"Sako","full_name":"Sako, Keisuke","first_name":"Keisuke","id":"3BED66BE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pradhan, Saurabh","last_name":"Pradhan","first_name":"Saurabh"},{"orcid":"0000-0003-2676-3367","last_name":"Barone","full_name":"Barone, Vanessa","first_name":"Vanessa","id":"419EECCC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Inglés Prieto","full_name":"Inglés Prieto, Álvaro","first_name":"Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571"},{"first_name":"Patrick","full_name":"Mueller, Patrick","last_name":"Mueller"},{"orcid":"0000-0003-4088-8633","last_name":"Ruprecht","full_name":"Ruprecht, Verena","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Daniel","id":"31C42484-F248-11E8-B48F-1D18A9856A87","last_name":"Capek","full_name":"Capek, Daniel","orcid":"0000-0001-5199-9940"},{"first_name":"Sanjeev","full_name":"Galande, Sanjeev","last_name":"Galande"},{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","full_name":"Janovjak, Harald L","last_name":"Janovjak"},{"orcid":"0000-0002-0912-4566","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","full_name":"Heisenberg, Carl-Philipp J"}],"_id":"1100","abstract":[{"text":"During metazoan development, the temporal pattern of morphogen signaling is critical for organizing cell fates in space and time. Yet, tools for temporally controlling morphogen signaling within the embryo are still scarce. Here, we developed a photoactivatable Nodal receptor to determine how the temporal pattern of Nodal signaling affects cell fate specification during zebrafish gastrulation. By using this receptor to manipulate the duration of Nodal signaling in vivo by light, we show that extended Nodal signaling within the organizer promotes prechordal plate specification and suppresses endoderm differentiation. Endoderm differentiation is suppressed by extended Nodal signaling inducing expression of the transcriptional repressor goosecoid (gsc) in prechordal plate progenitors, which in turn restrains Nodal signaling from upregulating the endoderm differentiation gene sox17 within these cells. Thus, optogenetic manipulation of Nodal signaling identifies a critical role of Nodal signaling duration for organizer cell fate specification during gastrulation.","lang":"eng"}],"issue":"3","doi":"10.1016/j.celrep.2016.06.036","project":[{"name":"Cell- and Tissue Mechanics in Zebrafish Germ Layer Formation","call_identifier":"FWF","_id":"2529486C-B435-11E9-9278-68D0E5697425","grant_number":"T 560-B17"},{"grant_number":"I 812-B12","_id":"2527D5CC-B435-11E9-9278-68D0E5697425","name":"Cell Cortex and Germ Layer Formation in Zebrafish Gastrulation","call_identifier":"FWF"},{"name":"Microbial Ion Channels for Synthetic Neurobiology","call_identifier":"FP7","grant_number":"303564","_id":"25548C20-B435-11E9-9278-68D0E5697425"}],"status":"public","publication_status":"published","acknowledgement":"We are grateful to members of the C.-P.H. and H.J. labs for discussions, R. Hauschild and the different Scientific Service Units at IST Austria for technical help, M. Dravecka for performing initial experiments, A. Schier for reading an earlier version of the manuscript, K.W. Rogers for technical help, and C. Hill, A. Bruce, and L. Solnica-Krezel for sending plasmids. This work was supported by grants from the Austrian Science Foundation (FWF): (T560-B17) and (I 812-B12) to V.R. and C.-P.H., and from the European Union (EU FP7): (6275) to H.J. A.I.-P. is supported by a Ramon Areces fellowship.","ec_funded":1,"pubrep_id":"754","citation":{"mla":"Sako, Keisuke, et al. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>, vol. 16, no. 3, Cell Press, 2016, pp. 866–77, doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>.","chicago":"Sako, Keisuke, Saurabh Pradhan, Vanessa Barone, Álvaro Inglés Prieto, Patrick Mueller, Verena Ruprecht, Daniel Capek, Sanjeev Galande, Harald L Janovjak, and Carl-Philipp J Heisenberg. “Optogenetic Control of Nodal Signaling Reveals a Temporal Pattern of Nodal Signaling Regulating Cell Fate Specification during Gastrulation.” <i>Cell Reports</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>.","apa":"Sako, K., Pradhan, S., Barone, V., Inglés Prieto, Á., Mueller, P., Ruprecht, V., … Heisenberg, C.-P. J. (2016). Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">https://doi.org/10.1016/j.celrep.2016.06.036</a>","ieee":"K. Sako <i>et al.</i>, “Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation,” <i>Cell Reports</i>, vol. 16, no. 3. Cell Press, pp. 866–877, 2016.","ama":"Sako K, Pradhan S, Barone V, et al. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. <i>Cell Reports</i>. 2016;16(3):866-877. doi:<a href=\"https://doi.org/10.1016/j.celrep.2016.06.036\">10.1016/j.celrep.2016.06.036</a>","ista":"Sako K, Pradhan S, Barone V, Inglés Prieto Á, Mueller P, Ruprecht V, Capek D, Galande S, Janovjak HL, Heisenberg C-PJ. 2016. Optogenetic control of nodal signaling reveals a temporal pattern of nodal signaling regulating cell fate specification during gastrulation. Cell Reports. 16(3), 866–877.","short":"K. Sako, S. Pradhan, V. Barone, Á. Inglés Prieto, P. Mueller, V. Ruprecht, D. Capek, S. Galande, H.L. Janovjak, C.-P.J. Heisenberg, Cell Reports 16 (2016) 866–877."},"day":"19","ddc":["570","576"],"file_date_updated":"2018-12-12T10:11:04Z","month":"07","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"file_id":"4857","date_created":"2018-12-12T10:11:04Z","file_name":"IST-2017-754-v1+1_1-s2.0-S2211124716307768-main.pdf","relation":"main_file","creator":"system","file_size":3921947,"date_updated":"2018-12-12T10:11:04Z","access_level":"open_access","content_type":"application/pdf"}],"has_accepted_license":"1","volume":16,"oa":1,"year":"2016","publication":"Cell Reports","date_updated":"2024-03-25T23:30:13Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"961"},{"id":"50","relation":"dissertation_contains","status":"public"}]},"page":"866 - 877","department":[{"_id":"CaHe"},{"_id":"HaJa"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"6275","date_published":"2016-07-19T00:00:00Z","date_created":"2018-12-11T11:50:08Z","scopus_import":1,"acknowledged_ssus":[{"_id":"SSU"}],"publisher":"Cell Press","intvolume":"        16","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}]},{"author":[{"last_name":"Mitchell","full_name":"Mitchell, Joshua","first_name":"Joshua"},{"full_name":"Whitfield, Jason","last_name":"Whitfield","first_name":"Jason"},{"full_name":"Zhang, William","last_name":"Zhang","first_name":"William"},{"first_name":"Christian","last_name":"Henneberger","full_name":"Henneberger, Christian"},{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","full_name":"Janovjak, Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"},{"first_name":"Megan","full_name":"O'Mara, Megan","last_name":"O'Mara"},{"last_name":"Jackson","full_name":"Jackson, Colin","first_name":"Colin"}],"title":"Rangefinder: A semisynthetic FRET sensor design algorithm","_id":"1101","issue":"11","year":"2016","abstract":[{"lang":"eng","text":"Optical sensors based on the phenomenon of Förster resonance energy transfer (FRET) are powerful tools that have advanced the study of small molecules in biological systems. However, sensor construction is not trivial and often requires multiple rounds of engineering or an ability to screen large numbers of variants. A method that would allow the accurate rational design of FRET sensors would expedite the production of biologically useful sensors. Here, we present Rangefinder, a computational algorithm that allows rapid in silico screening of dye attachment sites in a ligand-binding protein for the conjugation of a dye molecule to act as a Förster acceptor for a fused fluorescent protein. We present three ratiometric fluorescent sensors designed with Rangefinder, including a maltose sensor with a dynamic range of &gt;300% and the first sensors for the most abundant sialic acid in human cells, N-acetylneuraminic acid. Provided a ligand-binding protein exists, it is our expectation that this model will facilitate the design of an optical sensor for any small molecule of interest."}],"doi":"10.1021/acssensors.6b00576","publication":"ACS SENSORS","date_updated":"2023-03-30T11:32:33Z","acknowledgement":"J.A.M., J.H.W., and W.H.Z. were supported by Australian\r\nPostgraduate Awards (APA), AS Sargeson Supplementary\r\nscholarships, and RSC supplementary scholarships. C.J.J.\r\nacknowledges support from a Human Frontiers in Science\r\nYoung Investigator Award and a Discovery Project and Future\r\nFellowship from the Australian Research Council. M.L.O. is\r\nsupported by an Australian Research Council Discovery Project\r\n(DP130102153) and the Merit Allocation Scheme of the\r\nNational Computational Infrastructure.","status":"public","publication_status":"published","page":"1286 - 1290","department":[{"_id":"HaJa"}],"day":"10","citation":{"ama":"Mitchell J, Whitfield J, Zhang W, et al. Rangefinder: A semisynthetic FRET sensor design algorithm. <i>ACS SENSORS</i>. 2016;1(11):1286-1290. doi:<a href=\"https://doi.org/10.1021/acssensors.6b00576\">10.1021/acssensors.6b00576</a>","ista":"Mitchell J, Whitfield J, Zhang W, Henneberger C, Janovjak HL, O’Mara M, Jackson C. 2016. Rangefinder: A semisynthetic FRET sensor design algorithm. ACS SENSORS. 1(11), 1286–1290.","short":"J. Mitchell, J. Whitfield, W. Zhang, C. Henneberger, H.L. Janovjak, M. O’Mara, C. Jackson, ACS SENSORS 1 (2016) 1286–1290.","apa":"Mitchell, J., Whitfield, J., Zhang, W., Henneberger, C., Janovjak, H. L., O’Mara, M., &#38; Jackson, C. (2016). Rangefinder: A semisynthetic FRET sensor design algorithm. <i>ACS SENSORS</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssensors.6b00576\">https://doi.org/10.1021/acssensors.6b00576</a>","ieee":"J. Mitchell <i>et al.</i>, “Rangefinder: A semisynthetic FRET sensor design algorithm,” <i>ACS SENSORS</i>, vol. 1, no. 11. American Chemical Society, pp. 1286–1290, 2016.","chicago":"Mitchell, Joshua, Jason Whitfield, William Zhang, Christian Henneberger, Harald L Janovjak, Megan O’Mara, and Colin Jackson. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” <i>ACS SENSORS</i>. American Chemical Society, 2016. <a href=\"https://doi.org/10.1021/acssensors.6b00576\">https://doi.org/10.1021/acssensors.6b00576</a>.","mla":"Mitchell, Joshua, et al. “Rangefinder: A Semisynthetic FRET Sensor Design Algorithm.” <i>ACS SENSORS</i>, vol. 1, no. 11, American Chemical Society, 2016, pp. 1286–90, doi:<a href=\"https://doi.org/10.1021/acssensors.6b00576\">10.1021/acssensors.6b00576</a>."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"11","publist_id":"6274","date_published":"2016-11-10T00:00:00Z","scopus_import":"1","oa_version":"None","date_created":"2018-12-11T11:50:09Z","intvolume":"         1","publisher":"American Chemical Society","quality_controlled":"1","language":[{"iso":"eng"}],"type":"journal_article","article_processing_charge":"No","volume":1},{"year":"2016","oa":1,"page":"92.1-92.12","date_updated":"2021-01-12T06:48:18Z","publication":"Proceedings of the British Machine Vision Conference 2016","scopus_import":1,"date_created":"2018-12-11T11:50:09Z","date_published":"2016-09-01T00:00:00Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6273","department":[{"_id":"ChLa"}],"quality_controlled":"1","type":"conference","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.bmva.org/bmvc/2016/papers/paper092/paper092.pdf"}],"publisher":"BMVA Press","doi":"10.5244/C.30.92","abstract":[{"text":"Weakly-supervised object localization methods tend to fail for object classes that consistently co-occur with the same background elements, e.g. trains on tracks. We propose a method to overcome these failures by adding a very small amount of model-specific additional annotation. The main idea is to cluster a deep network\\'s mid-level representations and assign object or distractor labels to each cluster. Experiments show substantially improved localization results on the challenging ILSVC2014 dataset for bounding box detection and the PASCAL VOC2012 dataset for semantic segmentation.","lang":"eng"}],"_id":"1102","author":[{"last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander","first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-8622-7887","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert"}],"title":"Improving weakly-supervised object localization by micro-annotation","ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"This work was funded in parts by the European Research Council\r\nunder the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC grant\r\nagreement no 308036. We gratefully acknowledge the support of NVIDIA Corporation with\r\nthe donation of the GPUs used for this research.","project":[{"call_identifier":"FP7","name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"conference":{"location":"York, United Kingdom","start_date":"2016-09-19","end_date":"2016-09-22","name":"BMVC: British Machine Vision Conference"},"oa_version":"Published Version","month":"09","day":"01","citation":{"chicago":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” In <i>Proceedings of the British Machine Vision Conference 2016</i>, 2016–September:92.1-92.12. BMVA Press, 2016. <a href=\"https://doi.org/10.5244/C.30.92\">https://doi.org/10.5244/C.30.92</a>.","mla":"Kolesnikov, Alexander, and Christoph Lampert. “Improving Weakly-Supervised Object Localization by Micro-Annotation.” <i>Proceedings of the British Machine Vision Conference 2016</i>, vol. 2016–September, BMVA Press, 2016, p. 92.1-92.12, doi:<a href=\"https://doi.org/10.5244/C.30.92\">10.5244/C.30.92</a>.","ama":"Kolesnikov A, Lampert C. Improving weakly-supervised object localization by micro-annotation. In: <i>Proceedings of the British Machine Vision Conference 2016</i>. Vol 2016-September. BMVA Press; 2016:92.1-92.12. doi:<a href=\"https://doi.org/10.5244/C.30.92\">10.5244/C.30.92</a>","short":"A. Kolesnikov, C. Lampert, in:, Proceedings of the British Machine Vision Conference 2016, BMVA Press, 2016, p. 92.1-92.12.","ista":"Kolesnikov A, Lampert C. 2016. Improving weakly-supervised object localization by micro-annotation. Proceedings of the British Machine Vision Conference 2016. BMVC: British Machine Vision Conference vol. 2016–September, 92.1-92.12.","ieee":"A. Kolesnikov and C. Lampert, “Improving weakly-supervised object localization by micro-annotation,” in <i>Proceedings of the British Machine Vision Conference 2016</i>, York, United Kingdom, 2016, vol. 2016–September, p. 92.1-92.12.","apa":"Kolesnikov, A., &#38; Lampert, C. (2016). Improving weakly-supervised object localization by micro-annotation. In <i>Proceedings of the British Machine Vision Conference 2016</i> (Vol. 2016–September, p. 92.1-92.12). York, United Kingdom: BMVA Press. <a href=\"https://doi.org/10.5244/C.30.92\">https://doi.org/10.5244/C.30.92</a>"},"volume":"2016-September"},{"publisher":"IEEE","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.05473"}],"language":[{"iso":"eng"}],"type":"conference","quality_controlled":"1","month":"12","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"6272","citation":{"chicago":"Gurung, Amit, Arup Deka, Ezio Bartocci, Sergiy Bogomolov, Radu Grosu, and Rajarshi Ray. “Parallel Reachability Analysis for Hybrid Systems.” IEEE, 2016. <a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">https://doi.org/10.1109/MEMCOD.2016.7797741</a>.","mla":"Gurung, Amit, et al. <i>Parallel Reachability Analysis for Hybrid Systems</i>. 7797741, IEEE, 2016, doi:<a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">10.1109/MEMCOD.2016.7797741</a>.","ieee":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, and R. Ray, “Parallel reachability analysis for hybrid systems,” presented at the MEMOCODE: International Conference on Formal Methods and Models for System Design, Kanpur, India , 2016.","apa":"Gurung, A., Deka, A., Bartocci, E., Bogomolov, S., Grosu, R., &#38; Ray, R. (2016). Parallel reachability analysis for hybrid systems. Presented at the MEMOCODE: International Conference on Formal Methods and Models for System Design, Kanpur, India : IEEE. <a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">https://doi.org/10.1109/MEMCOD.2016.7797741</a>","short":"A. Gurung, A. Deka, E. Bartocci, S. Bogomolov, R. Grosu, R. Ray, in:, IEEE, 2016.","ista":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. 2016. Parallel reachability analysis for hybrid systems. MEMOCODE: International Conference on Formal Methods and Models for System Design, 7797741.","ama":"Gurung A, Deka A, Bartocci E, Bogomolov S, Grosu R, Ray R. Parallel reachability analysis for hybrid systems. In: IEEE; 2016. doi:<a href=\"https://doi.org/10.1109/MEMCOD.2016.7797741\">10.1109/MEMCOD.2016.7797741</a>"},"day":"27","department":[{"_id":"ToHe"}],"oa_version":"Preprint","date_created":"2018-12-11T11:50:09Z","conference":{"name":"MEMOCODE: International Conference on Formal Methods and Models for System Design","location":"Kanpur, India ","start_date":"2016-11-18","end_date":"2016-11-20"},"scopus_import":1,"date_published":"2016-12-27T00:00:00Z","date_updated":"2021-01-12T06:48:18Z","project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23"}],"article_number":"7797741","ec_funded":1,"publication_status":"published","status":"public","acknowledgement":"This work was supported in part by DST-SERB, GoI under Project No. YSS/2014/000623 and by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award).","_id":"1103","title":"Parallel reachability analysis for hybrid systems","oa":1,"author":[{"last_name":"Gurung","full_name":"Gurung, Amit","first_name":"Amit"},{"first_name":"Arup","full_name":"Deka, Arup","last_name":"Deka"},{"full_name":"Bartocci, Ezio","last_name":"Bartocci","first_name":"Ezio"},{"orcid":"0000-0002-0686-0365","first_name":"Sergiy","id":"369D9A44-F248-11E8-B48F-1D18A9856A87","last_name":"Bogomolov","full_name":"Bogomolov, Sergiy"},{"last_name":"Grosu","full_name":"Grosu, Radu","first_name":"Radu"},{"full_name":"Ray, Rajarshi","last_name":"Ray","first_name":"Rajarshi"}],"doi":"10.1109/MEMCOD.2016.7797741","abstract":[{"lang":"eng","text":"We propose two parallel state-space-exploration algorithms for hybrid automaton (HA), with the goal of enhancing performance on multi-core shared-memory systems. The first uses the parallel, breadth-first-search algorithm (PBFS) of the SPIN model checker, when traversing the discrete modes of the HA, and enhances it with a parallel exploration of the continuous states within each mode. We show that this simple-minded extension of PBFS does not provide the desired load balancing in many HA benchmarks. The second algorithm is a task-parallel BFS algorithm (TP-BFS), which uses a cheap precomputation of the cost associated with the post operations (both continuous and discrete) in order to improve load balancing. We illustrate the TP-BFS and the cost precomputation of the post operators on a support-function-based algorithm for state-space exploration. The performance comparison of the two algorithms shows that, in general, TP-BFS provides a better utilization/load-balancing of the CPU. Both algorithms are implemented in the model checker XSpeed. Our experiments show a maximum speed-up of more than 2000 χ on a navigation benchmark, with respect to SpaceEx LGG scenario. In order to make the comparison fair, we employed an equal number of post operations in both tools. To the best of our knowledge, this paper represents the first attempt to provide parallel, reachability-analysis algorithms for HA."}],"year":"2016"},{"volume":29,"month":"12","day":"01","citation":{"ista":"Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618.","ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems; 2016:3610-3618.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems, 2016, pp. 3610–3618.","apa":"Savin, C., &#38; Tkačik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems.","ieee":"C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618.","chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems, 2016.","mla":"Savin, Cristina, and Gašper Tkačik. <i>Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods</i>. Vol. 29, Neural Information Processing Systems, 2016, pp. 3610–18."},"conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2016-12-05","location":"Barcelona; Spain","end_date":"2016-12-10"},"oa_version":"None","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"ec_funded":1,"status":"public","acknowledgement":"We  thank  Jozsef  Csicsvari  for  kindly  sharing  the  CA1  data.\r\nThis work was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no. 291734.","publication_status":"published","_id":"1105","author":[{"first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","last_name":"Savin","full_name":"Savin, Cristina"},{"orcid":"0000-0002-6699-1455","full_name":"Tkacik, Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","abstract":[{"lang":"eng","text":"Jointly characterizing neural responses in terms of several external variables promises novel insights into circuit function, but remains computationally prohibitive in practice. Here we use gaussian process (GP) priors and exploit recent advances in fast GP inference and learning based on Kronecker methods, to efficiently estimate multidimensional nonlinear tuning functions. Our estimator require considerably less data than traditional methods and further provides principled uncertainty estimates. We apply these tools to hippocampal recordings during open field exploration and use them to characterize the joint dependence of CA1 responses on the position of the animal and several other variables, including the animal\\'s speed, direction of motion, and network oscillations.Our results provide an unprecedentedly detailed quantification of the tuning of hippocampal neurons. The model\\'s generality suggests that our approach can be used to estimate neural response properties in other brain regions."}],"main_file_link":[{"url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods"}],"intvolume":"        29","publisher":"Neural Information Processing Systems","type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1","publist_id":"6265","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GaTk"}],"scopus_import":1,"date_created":"2018-12-11T11:50:10Z","date_published":"2016-12-01T00:00:00Z","date_updated":"2021-01-12T06:48:19Z","page":"3610-3618","alternative_title":["Advances in Neural Information Processing Systems"],"year":"2016"},{"_id":"1115","title":"Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator","oa":1,"author":[{"first_name":"Alfredo","last_name":"Rueda","full_name":"Rueda, Alfredo"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"last_name":"Collodo","full_name":"Collodo, Michele","first_name":"Michele"},{"first_name":"Ulrich","last_name":"Vogl","full_name":"Vogl, Ulrich"},{"first_name":"Birgit","full_name":"Stiller, Birgit","last_name":"Stiller"},{"first_name":"Georg","full_name":"Schunk, Georg","last_name":"Schunk"},{"last_name":"Strekalov","full_name":"Strekalov, Dimitry","first_name":"Dimitry"},{"last_name":"Marquardt","full_name":"Marquardt, Christoph","first_name":"Christoph"},{"orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Oskar","full_name":"Painter, Oskar","last_name":"Painter"},{"first_name":"Gerd","full_name":"Leuchs, Gerd","last_name":"Leuchs"},{"first_name":"Harald","full_name":"Schwefel, Harald","last_name":"Schwefel"}],"doi":"10.1364/CLEO_SI.2016.SF2G.3","abstract":[{"lang":"eng","text":"We present a coherent microwave to telecom signal converter based on the electro-optical effect using a crystalline WGM-resonator coupled to a 3D microwave cavity, achieving high photon conversion efficiency of 0.1% with MHz bandwidth."}],"year":"2016","date_updated":"2022-09-06T07:23:25Z","article_number":"7788479","related_material":{"link":[{"relation":"other","url":"http://ieeexplore.ieee.org/document/7788479/"}]},"publication_status":"published","status":"public","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"6251","citation":{"mla":"Rueda, Alfredo, et al. <i>Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator</i>. 7788479, IEEE, 2016, doi:<a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">10.1364/CLEO_SI.2016.SF2G.3</a>.","chicago":"Rueda, Alfredo, Florian Sedlmeir, Michele Collodo, Ulrich Vogl, Birgit Stiller, Georg Schunk, Dimitry Strekalov, et al. “Efficient Single Sideband Microwave to Optical Conversion Using a LiNbO₃ WGM-Resonator.” IEEE, 2016. <a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">https://doi.org/10.1364/CLEO_SI.2016.SF2G.3</a>.","ista":"Rueda A, Sedlmeir F, Collodo M, Vogl U, Stiller B, Schunk G, Strekalov D, Marquardt C, Fink JM, Painter O, Leuchs G, Schwefel H. 2016. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. CLEO: Conference on Lasers and Electro Optics, 7788479.","ama":"Rueda A, Sedlmeir F, Collodo M, et al. Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. In: IEEE; 2016. doi:<a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">10.1364/CLEO_SI.2016.SF2G.3</a>","short":"A. Rueda, F. Sedlmeir, M. Collodo, U. Vogl, B. Stiller, G. Schunk, D. Strekalov, C. Marquardt, J.M. Fink, O. Painter, G. Leuchs, H. Schwefel, in:, IEEE, 2016.","apa":"Rueda, A., Sedlmeir, F., Collodo, M., Vogl, U., Stiller, B., Schunk, G., … Schwefel, H. (2016). Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator. Presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA: IEEE. <a href=\"https://doi.org/10.1364/CLEO_SI.2016.SF2G.3\">https://doi.org/10.1364/CLEO_SI.2016.SF2G.3</a>","ieee":"A. Rueda <i>et al.</i>, “Efficient single sideband microwave to optical conversion using a LiNbO₃ WGM-resonator,” presented at the CLEO: Conference on Lasers and Electro Optics, San Jose, CA, USA, 2016."},"department":[{"_id":"JoFi"}],"day":"16","date_created":"2018-12-11T11:50:14Z","oa_version":"Preprint","conference":{"end_date":"2016-06-10","start_date":"2016-06-05","location":"San Jose, CA, USA","name":"CLEO: Conference on Lasers and Electro Optics"},"scopus_import":"1","date_published":"2016-12-16T00:00:00Z","publisher":"IEEE","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1601.07261"}],"article_processing_charge":"No","type":"conference","language":[{"iso":"eng"}],"quality_controlled":"1"},{"publication_status":"published","acknowledgement":"This study was supported by European Research Council ERC CoG 2014 – EVOLHGT,\r\nunder the grant number 648440.\r\n\r\nIt is a pleasure to thank the many people who made this thesis possible.\r\nI would like to first thank my advisor, Jonathan Paul Bollback for providing guidance in\r\nall aspects of my life, encouragement, sound advice, and good teaching over the last six\r\nyears.\r\nI would also like to thank the members of my dissertation committee – Călin C. Guet\r\nand John F. Baines – not only for their time and guidance, but for their intellectual\r\ncontributions to my development as a scientist.\r\nI would like to thank Flavia Gama and Rodrigo Redondo who have taught me all the\r\nskills in the laboratory with their graciousness and friendship. Also special thanks to\r\nBollback group for their support and for providing a stimulating and fun environment:\r\nIsabella Tomanek, Fabienne Jesse, Claudia Igler, and Pavel Payne.\r\nJerneja Beslagic is not only an amazing assistant, she also has a smile brighter and\r\nwarmer than the sunshine, bringing happiness to every moment. Always keep your light\r\nNeja, I will miss our invaluable chatters a lot.","status":"public","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"project":[{"_id":"2578D616-B435-11E9-9278-68D0E5697425","grant_number":"648440","call_identifier":"H2020","name":"Selective Barriers to Horizontal Gene Transfer"}],"abstract":[{"lang":"eng","text":"Horizontal gene transfer (HGT), the lateral acquisition of genes across existing species\r\nboundaries, is a major evolutionary force shaping microbial genomes that facilitates\r\nadaptation to new environments as well as resistance to antimicrobial drugs. As such,\r\nunderstanding the mechanisms and constraints that determine the outcomes of HGT\r\nevents is crucial to understand the dynamics of HGT and to design better strategies to\r\novercome the challenges that originate from it.\r\nFollowing the insertion and expression of a newly transferred gene, the success of an\r\nHGT event will depend on the fitness effect it has on the recipient (host) cell. Therefore,\r\npredicting the impact of HGT on the genetic composition of a population critically\r\ndepends on the distribution of fitness effects (DFE) of horizontally transferred genes.\r\nHowever, to date, we have little knowledge of the DFE of newly transferred genes, and\r\nhence little is known about the shape and scale of this distribution.\r\nIt is particularly important to better understand the selective barriers that determine\r\nthe fitness effects of newly transferred genes. In spite of substantial bioinformatics\r\nefforts to identify horizontally transferred genes and selective barriers, a systematic\r\nexperimental approach to elucidate the roles of different selective barriers in defining\r\nthe fate of a transfer event has largely been absent. Similarly, although the fact that\r\nenvironment might alter the fitness effect of a horizontally transferred gene may seem\r\nobvious, little attention has been given to it in a systematic experimental manner.\r\nIn this study, we developed a systematic experimental approach that consists of\r\ntransferring 44 arbitrarily selected Salmonella typhimurium orthologous genes into an\r\nEscherichia coli host, and estimating the fitness effects of these transferred genes at a\r\nconstant expression level by performing competition assays against the wild type.\r\nIn chapter 2, we performed one-to-one competition assays between a mutant strain\r\ncarrying a transferred gene and the wild type strain. By using flow cytometry we\r\nestimated selection coefficients for the transferred genes with a precision level of 10-3,and obtained the DFE of horizontally transferred genes. We then investigated if these\r\nfitness effects could be predicted by any of the intrinsic properties of the genes, namely,\r\nfunctional category, degree of complexity (protein-protein interactions), GC content,\r\ncodon usage and length. Our analyses revealed that the functional category and length\r\nof the genes act as potential selective barriers. Finally, using the same procedure with\r\nthe endogenous E. coli orthologs of these 44 genes, we demonstrated that gene dosage is\r\nthe most prominent selective barrier to HGT.\r\nIn chapter 3, using the same set of genes we investigated the role of environment on the\r\nsuccess of HGT events. Under six different environments with different levels of stress\r\nwe performed more complex competition assays, where we mixed all 44 mutant strains\r\ncarrying transferred genes with the wild type strain. To estimate the fitness effects of\r\ngenes relative to wild type we used next generation sequencing. We found that the DFEs\r\nof horizontally transferred genes are highly dependent on the environment, with\r\nabundant gene–by-environment interactions. Furthermore, we demonstrated a\r\nrelationship between average fitness effect of a gene across all environments and its\r\nenvironmental variance, and thus its predictability. Finally, in spite of the fitness effects\r\nof genes being highly environment-dependent, we still observed a common shape of\r\nDFEs across all tested environments."}],"supervisor":[{"last_name":"Bollback","full_name":"Bollback, Jonathan P","first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612"}],"title":"Selective barriers to horizontal gene transfer","author":[{"orcid":"0000-0003-1986-9753","last_name":"Acar","full_name":"Acar, Hande","first_name":"Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87"}],"_id":"1121","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"file_id":"6814","date_created":"2019-08-13T11:17:50Z","access_level":"closed","checksum":"94bbbc754c36115bf37f8fc11fad43c4","content_type":"application/pdf","date_updated":"2019-08-13T11:17:50Z","file_name":"PhDThesis_HandeAcar_1230.pdf","file_size":3682711,"relation":"main_file","creator":"dernst"},{"date_created":"2021-02-22T11:51:13Z","file_id":"9184","checksum":"94bbbc754c36115bf37f8fc11fad43c4","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-02-22T11:51:13Z","success":1,"file_size":3682711,"creator":"dernst","relation":"main_file","file_name":"2016_Thesis_HandeAcar.pdf"}],"oa_version":"Published Version","citation":{"ieee":"H. Acar, “Selective barriers to horizontal gene transfer,” Institute of Science and Technology Austria, 2016.","apa":"Acar, H. (2016). <i>Selective barriers to horizontal gene transfer</i>. Institute of Science and Technology Austria.","ama":"Acar H. Selective barriers to horizontal gene transfer. 2016.","ista":"Acar H. 2016. Selective barriers to horizontal gene transfer. Institute of Science and Technology Austria.","short":"H. Acar, Selective Barriers to Horizontal Gene Transfer, Institute of Science and Technology Austria, 2016.","mla":"Acar, Hande. <i>Selective Barriers to Horizontal Gene Transfer</i>. Institute of Science and Technology Austria, 2016.","chicago":"Acar, Hande. “Selective Barriers to Horizontal Gene Transfer.” Institute of Science and Technology Austria, 2016."},"day":"01","ddc":["570"],"file_date_updated":"2021-02-22T11:51:13Z","month":"12","page":"75","date_updated":"2023-09-07T11:42:26Z","year":"2016","alternative_title":["ISTA Thesis"],"oa":1,"type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","date_published":"2016-12-01T00:00:00Z","date_created":"2018-12-11T11:50:16Z","department":[{"_id":"JoBo"}],"publist_id":"6239","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6238","department":[{"_id":"ChWo"}],"date_created":"2018-12-11T11:50:16Z","date_published":"2016-07-15T00:00:00Z","publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"oa":1,"alternative_title":["ISTA Thesis"],"year":"2016","date_updated":"2024-02-21T13:50:48Z","page":"114","related_material":{"record":[{"status":"public","relation":"other","id":"5558"}]},"ddc":["004","005","006","532","621"],"month":"07","file_date_updated":"2018-12-12T10:13:02Z","citation":{"apa":"Bojsen-Hansen, M. (2016). <i>Tracking, correcting and absorbing water surface waves</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">https://doi.org/10.15479/AT:ISTA:th_640</a>","ieee":"M. Bojsen-Hansen, “Tracking, correcting and absorbing water surface waves,” Institute of Science and Technology Austria, 2016.","ista":"Bojsen-Hansen M. 2016. Tracking, correcting and absorbing water surface waves. Institute of Science and Technology Austria.","short":"M. Bojsen-Hansen, Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, 2016.","ama":"Bojsen-Hansen M. Tracking, correcting and absorbing water surface waves. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">10.15479/AT:ISTA:th_640</a>","mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">10.15479/AT:ISTA:th_640</a>.","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:th_640\">https://doi.org/10.15479/AT:ISTA:th_640</a>."},"day":"15","oa_version":"Published Version","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2018-12-12T10:13:02Z","file_name":"IST-2016-640-v1+1_2016_Bojsen-Hansen_TCaAWSW.pdf","file_size":13869345,"relation":"main_file","creator":"system","file_id":"4982","date_created":"2018-12-12T10:13:02Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","_id":"1122","supervisor":[{"last_name":"Wojtan","full_name":"Wojtan, Christopher J","first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6646-5546"}],"title":"Tracking, correcting and absorbing water surface waves","author":[{"id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","first_name":"Morten","full_name":"Bojsen-Hansen, Morten","last_name":"Bojsen-Hansen","orcid":"0000-0002-4417-3224"}],"doi":"10.15479/AT:ISTA:th_640","abstract":[{"text":"Computer graphics is an extremely exciting field for two reasons. On the one hand,\r\nthere is a healthy injection of pragmatism coming from the visual effects industry\r\nthat want robust algorithms that work so they can produce results at an increasingly\r\nfrantic pace. On the other hand, they must always try to push the envelope and\r\nachieve the impossible to wow their audiences in the next blockbuster, which means\r\nthat the industry has not succumb to conservatism, and there is plenty of room to\r\ntry out new and crazy ideas if there is a chance that it will pan into something\r\nuseful.\r\nWater simulation has been in visual effects for decades, however it still remains\r\nextremely challenging because of its high computational cost and difficult artdirectability.\r\nThe work in this thesis tries to address some of these difficulties.\r\nSpecifically, we make the following three novel contributions to the state-of-the-art\r\nin water simulation for visual effects.\r\nFirst, we develop the first algorithm that can convert any sequence of closed\r\nsurfaces in time into a moving triangle mesh. State-of-the-art methods at the time\r\ncould only handle surfaces with fixed connectivity, but we are the first to be able to\r\nhandle surfaces that merge and split apart. This is important for water simulation\r\npractitioners, because it allows them to convert splashy water surfaces extracted\r\nfrom particles or simulated using grid-based level sets into triangle meshes that can\r\nbe either textured and enhanced with extra surface dynamics as a post-process.\r\nWe also apply our algorithm to other phenomena that merge and split apart, such\r\nas morphs and noisy reconstructions of human performances.\r\nSecond, we formulate a surface-based energy that measures the deviation of a\r\nwater surface froma physically valid state. Such discrepancies arise when there is a\r\nmismatch in the degrees of freedom between the water surface and the underlying\r\nphysics solver. This commonly happens when practitioners use a moving triangle\r\nmesh with a grid-based physics solver, or when high-resolution grid-based surfaces\r\nare combined with low-resolution physics. Following the direction of steepest\r\ndescent on our surface-based energy, we can either smooth these artifacts or turn\r\nthem into high-resolution waves by interpreting the energy as a physical potential.\r\nThird, we extend state-of-the-art techniques in non-reflecting boundaries to handle spatially and time-varying background flows. This allows a novel new\r\nworkflow where practitioners can re-simulate part of an existing simulation, such\r\nas removing a solid obstacle, adding a new splash or locally changing the resolution.\r\nSuch changes can easily lead to new waves in the re-simulated region that would\r\nreflect off of the new simulation boundary, effectively ruining the illusion of a\r\nseamless simulation boundary between the existing and new simulations. Our\r\nnon-reflecting boundaries makes sure that such waves are absorbed.","lang":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"status":"public","publication_status":"published","acknowledgement":"First and foremost I would like to thank Chris. I have been incredibly lucky to have\r\nyou as my advisor. Your integrity and aspiration to do the right thing in all walks of\r\nlife is something I admire and aspire to. I also really appreciate the fact that when\r\nworking with you it felt like we were equals. I think we had a very synergetic work\r\nrelationship: I learned immensely from you, but I dare say that you learned a few\r\nthings from me as well. ;)\r\nNext, I would like to thank my amazing committee. Hao, it was a fantastic\r\nexperience working with you. You showed me how to persevere and keep morale\r\nhigh when things were looking the most bleak before the deadline. You are an\r\nincredible motivator and super fun to be around! Vladimir, thanks for the shared\r\nlunches and the poker games. Sorry for not bringing them back when I got busy.\r\nAlso, sorry for embarrassing you by asking about your guitar playing that one\r\ntime. You really are quite awesome! Nils, one of the friendliest and most humble\r\npeople you will meet and a top notch researcher to boot! Thank you for joining\r\nmy committee late!\r\nI would also like to acknowledge the Visual Computing group at IST Austria\r\nfrom whom I have learned so much. The excellent discussions we had in reading\r\ngroups and research meetings really helped me become a better researcher!\r\nNext, I would like to thank all the amazing people that I met during my PhD\r\nstudies, both at IST Austria, in Vienna and elsewhere. "},{"date_published":"2016-08-01T00:00:00Z","date_created":"2018-12-11T11:50:16Z","department":[{"_id":"UlWa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6237","type":"dissertation","language":[{"iso":"eng"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"year":"2016","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"2159"}]},"page":"55","date_updated":"2023-09-07T11:56:28Z","oa_version":"Published Version","day":"01","citation":{"apa":"Mabillard, I. (2016). <i>Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture</i>. Institute of Science and Technology Austria.","ieee":"I. Mabillard, “Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture,” Institute of Science and Technology Austria, 2016.","ista":"Mabillard I. 2016. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. Institute of Science and Technology Austria.","short":"I. Mabillard, Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture, Institute of Science and Technology Austria, 2016.","ama":"Mabillard I. Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture. 2016.","chicago":"Mabillard, Isaac. “Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture.” Institute of Science and Technology Austria, 2016.","mla":"Mabillard, Isaac. <i>Eliminating Higher-Multiplicity Intersections: An r-Fold Whitney Trick for the Topological Tverberg Conjecture</i>. Institute of Science and Technology Austria, 2016."},"month":"08","ddc":["500"],"file_date_updated":"2021-02-22T11:36:34Z","has_accepted_license":"1","article_processing_charge":"No","degree_awarded":"PhD","file":[{"date_created":"2019-08-13T08:45:27Z","file_id":"6809","date_updated":"2019-08-13T08:45:27Z","content_type":"application/pdf","checksum":"2d140cc924cd1b764544906fc22684ef","access_level":"closed","creator":"dernst","relation":"main_file","file_size":2227916,"file_name":"Thesis_final version_Mabillard_w_signature_page.pdf"},{"file_id":"9178","date_created":"2021-02-22T11:36:34Z","file_name":"2016_Mabillard_Thesis.pdf","creator":"dernst","file_size":2227916,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"2d140cc924cd1b764544906fc22684ef","success":1,"date_updated":"2021-02-22T11:36:34Z"}],"abstract":[{"text":"Motivated by topological Tverberg-type problems  in topological combinatorics and by classical\r\nresults about embeddings (maps without double points), we study the question whether a finite\r\nsimplicial complex K  can be mapped into Rd  without triple, quadruple, or, more generally, r-fold points  (image points with at least r  distinct preimages), for a given multiplicity r ≤ 2. In particular, we are interested in maps f : K → Rd  that have no global r -fold intersection points, i.e., no r -fold points with preimages in r pairwise disjoint  simplices of K , and we seek necessary and sufficient conditions for the existence of such maps.\r\n\r\nWe present higher-multiplicity analogues of several classical results for embeddings, in particular of the completeness of the Van Kampen obstruction  for embeddability of k -dimensional\r\ncomplexes into R2k , k ≥ 3. Speciffically, we show that under suitable restrictions on the dimensions(viz., if dimK  = (r ≥ 1)k  and d  = rk \\ for some k ≥ 3), a well-known deleted product criterion (DPC ) is not only necessary but also sufficient for the existence of maps without global r -fold points. Our main technical tool is a higher-multiplicity version of the classical Whitney trick , by which pairs of isolated r -fold points of opposite sign  can be eliminated by local modiffications of the map, assuming codimension d – dimK ≥ 3.\r\n\r\nAn important guiding idea for our work was that suffciency of the DPC, together with an old\r\nresult of Özaydin's on the existence of equivariant maps, might yield an approach to disproving the remaining open cases of the the long-standing topological Tverberg conjecture , i.e., to construct maps from the N -simplex σN  to Rd  without r-Tverberg points when r not a prime power  and\r\nN  = (d  + 1)(r – 1). Unfortunately, our proof of the sufficiency of the DPC requires codimension d – dimK ≥ 3, which is not satisfied for K  = σN .\r\n\r\nIn 2015, Frick [16] found a very elegant way to overcome this \\codimension 3 obstacle&quot; and\r\nto construct the first counterexamples to the topological Tverberg conjecture for all parameters(d; r ) with d ≥ 3r  + 1 and r  not a prime power, by a reduction1  to a suitable lower-dimensional skeleton, for which the codimension 3 restriction is satisfied and maps without r -Tverberg points exist by Özaydin's result and sufficiency of the DPC.\r\n\r\nIn this thesis, we present a different construction (which does not use the constraint method) that yields counterexamples for d ≥ 3r , r  not a prime power.     ","lang":"eng"}],"author":[{"id":"32BF9DAA-F248-11E8-B48F-1D18A9856A87","first_name":"Isaac","full_name":"Mabillard, Isaac","last_name":"Mabillard"}],"supervisor":[{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","full_name":"Wagner, Uli","last_name":"Wagner","orcid":"0000-0002-1494-0568"}],"title":"Eliminating higher-multiplicity intersections: an r-fold Whitney trick for the topological Tverberg conjecture","_id":"1123","status":"public","publication_status":"published","acknowledgement":"Foremost, I would like to thank Uli Wagner for introducing me to the exciting interface between\r\ntopology and combinatorics, and for our subsequent years of fruitful collaboration.\r\nIn our creative endeavors to eliminate intersection points, we had the chance to be joined later\r\nby Sergey Avvakumov and Arkadiy Skopenkov, which led us to new surprises in dimension 12.\r\nMy stay at EPFL and IST Austria was made very agreeable thanks to all these wonderful\r\npeople: Cyril Becker, Marek Filakovsky, Peter Franek, Radoslav Fulek, Peter Gazi, Kristof Huszar,\r\nMarek Krcal, Zuzana Masarova, Arnaud de Mesmay, Filip Moric, Michal Rybar, Martin Tancer,\r\nand Stephan Zhechev.\r\nFinally, I would like to thank my thesis committee Herbert Edelsbrunner and Roman Karasev\r\nfor their careful reading of the present manuscript and for the many improvements they suggested.","publication_identifier":{"issn":["2663-337X"]}},{"_id":"1124","author":[{"id":"4863116E-F248-11E8-B48F-1D18A9856A87","first_name":"Maurizio","full_name":"Morri, Maurizio","last_name":"Morri"}],"supervisor":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","first_name":"Harald L","full_name":"Janovjak, Harald L","last_name":"Janovjak","orcid":"0000-0002-8023-9315"}],"title":"Optical functionalization of human class A orphan G-protein coupled receptors","oa":1,"year":"2016","alternative_title":["ISTA Thesis"],"date_updated":"2023-09-07T11:43:03Z","publication_identifier":{"issn":["2663-337X"]},"page":"129","publication_status":"published","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"03","publist_id":"6236","file_date_updated":"2021-02-22T11:42:06Z","ddc":["570"],"day":"01","department":[{"_id":"HaJa"}],"citation":{"chicago":"Morri, Maurizio. “Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors.” Institute of Science and Technology Austria, 2016.","mla":"Morri, Maurizio. <i>Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors</i>. Institute of Science and Technology Austria, 2016.","ista":"Morri M. 2016. Optical functionalization of human class A orphan G-protein coupled receptors. Institute of Science and Technology Austria.","short":"M. Morri, Optical Functionalization of Human Class A Orphan G-Protein Coupled Receptors, Institute of Science and Technology Austria, 2016.","ama":"Morri M. Optical functionalization of human class A orphan G-protein coupled receptors. 2016.","apa":"Morri, M. (2016). <i>Optical functionalization of human class A orphan G-protein coupled receptors</i>. Institute of Science and Technology Austria.","ieee":"M. Morri, “Optical functionalization of human class A orphan G-protein coupled receptors,” Institute of Science and Technology Austria, 2016."},"date_created":"2018-12-11T11:50:17Z","oa_version":"Published Version","date_published":"2016-03-01T00:00:00Z","file":[{"date_updated":"2019-08-13T10:50:00Z","content_type":"application/pdf","checksum":"b439803ac0827cdddd56562a54e3b53b","access_level":"closed","relation":"main_file","creator":"dernst","file_size":4785167,"file_name":"MORRI_PhD_thesis_FINALPLUSSIGNATURES (2).pdf","date_created":"2019-08-13T10:50:00Z","file_id":"6812"},{"date_updated":"2021-02-22T11:42:06Z","success":1,"content_type":"application/pdf","checksum":"dd4136247fe472e7d47880ec68ac8de0","access_level":"open_access","creator":"dernst","relation":"main_file","file_size":4495669,"file_name":"2016_MORRI_Thesis.pdf","date_created":"2021-02-22T11:42:06Z","file_id":"9180"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","language":[{"iso":"eng"}],"type":"dissertation","article_processing_charge":"No","has_accepted_license":"1"},{"file":[{"date_created":"2019-08-13T09:01:00Z","file_id":"6811","content_type":"application/pdf","checksum":"81dcc838dfcf7aa0b1a27ecf4fe2da4e","access_level":"closed","date_updated":"2019-08-13T09:01:00Z","creator":"dernst","relation":"main_file","file_size":3564901,"file_name":"Novak_thesis.pdf"},{"date_created":"2021-02-22T13:42:47Z","file_id":"9186","date_updated":"2021-02-22T13:42:47Z","success":1,"content_type":"application/pdf","checksum":"30808d2f7ca920e09f63a95cdc49bffd","access_level":"open_access","relation":"main_file","file_size":2814384,"creator":"dernst","file_name":"2016_Novak_Thesis.pdf"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","month":"07","file_date_updated":"2021-02-22T13:42:47Z","ddc":["576"],"day":"01","citation":{"ieee":"S. Novak, “Evolutionary proccesses in variable emvironments,” Institute of Science and Technology Austria, 2016.","apa":"Novak, S. (2016). <i>Evolutionary proccesses in variable emvironments</i>. Institute of Science and Technology Austria.","short":"S. Novak, Evolutionary Proccesses in Variable Emvironments, Institute of Science and Technology Austria, 2016.","ama":"Novak S. Evolutionary proccesses in variable emvironments. 2016.","ista":"Novak S. 2016. Evolutionary proccesses in variable emvironments. Institute of Science and Technology Austria.","chicago":"Novak, Sebastian. “Evolutionary Proccesses in Variable Emvironments.” Institute of Science and Technology Austria, 2016.","mla":"Novak, Sebastian. <i>Evolutionary Proccesses in Variable Emvironments</i>. Institute of Science and Technology Austria, 2016."},"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"status":"public","publication_status":"published","_id":"1125","author":[{"orcid":"0000-0002-2519-824X","last_name":"Novak","full_name":"Novak, Sebastian","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"}],"title":"Evolutionary proccesses in variable emvironments","supervisor":[{"orcid":"0000-0002-8548-5240","last_name":"Barton","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"text":"Natural environments are never constant but subject to spatial and temporal change on\r\nall scales, increasingly so due to human activity. Hence, it is crucial to understand the\r\nimpact of environmental variation on evolutionary processes. In this thesis, I present\r\nthree topics that share the common theme of environmental variation, yet illustrate its\r\neffect from different perspectives.\r\nFirst, I show how a temporally fluctuating environment gives rise to second-order\r\nselection on a modifier for stress-induced mutagenesis. Without fluctuations, when\r\npopulations are adapted to their environment, mutation rates are minimized. I argue\r\nthat a stress-induced mutator mechanism may only be maintained if the population is\r\nrepeatedly subjected to diverse environmental challenges, and I outline implications of\r\nthe presented results to antibiotic treatment strategies.\r\nSecond, I discuss my work on the evolution of dispersal. Besides reproducing\r\nknown results about the effect of heterogeneous habitats on dispersal, it identifies\r\nspatial changes in dispersal type frequencies as a source for selection for increased\r\npropensities to disperse. This concept contains effects of relatedness that are known\r\nto promote dispersal, and I explain how it identifies other forces selecting for dispersal\r\nand puts them on a common scale.\r\nThird, I analyse genetic variances of phenotypic traits under multivariate stabilizing\r\nselection. For the case of constant environments, I generalize known formulae of\r\nequilibrium variances to multiple traits and discuss how the genetic variance of a focal\r\ntrait is influenced by selection on background traits. I conclude by presenting ideas and\r\npreliminary work aiming at including environmental fluctuations in the form of moving\r\ntrait optima into the model.","lang":"eng"}],"publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"publist_id":"6235","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"NiBa"}],"date_created":"2018-12-11T11:50:17Z","date_published":"2016-07-01T00:00:00Z","date_updated":"2025-05-28T11:57:05Z","page":"124","related_material":{"record":[{"id":"2023","relation":"part_of_dissertation","status":"public"}]},"oa":1,"alternative_title":["ISTA Thesis"],"year":"2016"},{"pubrep_id":"776","citation":{"mla":"Pentina, Anastasia. <i>Theoretical Foundations of Multi-Task Lifelong Learning</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">10.15479/AT:ISTA:TH_776</a>.","chicago":"Pentina, Anastasia. “Theoretical Foundations of Multi-Task Lifelong Learning.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">https://doi.org/10.15479/AT:ISTA:TH_776</a>.","short":"A. Pentina, Theoretical Foundations of Multi-Task Lifelong Learning, Institute of Science and Technology Austria, 2016.","ama":"Pentina A. Theoretical foundations of multi-task lifelong learning. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">10.15479/AT:ISTA:TH_776</a>","ista":"Pentina A. 2016. Theoretical foundations of multi-task lifelong learning. Institute of Science and Technology Austria.","apa":"Pentina, A. (2016). <i>Theoretical foundations of multi-task lifelong learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:TH_776\">https://doi.org/10.15479/AT:ISTA:TH_776</a>","ieee":"A. Pentina, “Theoretical foundations of multi-task lifelong learning,” Institute of Science and Technology Austria, 2016."},"day":"01","file_date_updated":"2018-12-12T10:14:07Z","ddc":["006"],"month":"11","oa_version":"Published Version","degree_awarded":"PhD","file":[{"file_id":"5056","date_created":"2018-12-12T10:14:07Z","file_name":"IST-2017-776-v1+1_Pentina_Thesis_2016.pdf","relation":"main_file","creator":"system","file_size":2140062,"access_level":"open_access","content_type":"application/pdf","date_updated":"2018-12-12T10:14:07Z"}],"has_accepted_license":"1","article_processing_charge":"No","title":"Theoretical foundations of multi-task lifelong learning","supervisor":[{"orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Lampert, Christoph","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"author":[{"last_name":"Pentina","full_name":"Pentina, Anastasia","first_name":"Anastasia","id":"42E87FC6-F248-11E8-B48F-1D18A9856A87"}],"_id":"1126","abstract":[{"text":"Traditionally machine learning has been focusing on the problem of solving a single\r\ntask in isolation. While being quite well understood, this approach disregards an\r\nimportant aspect of human learning: when facing a new problem, humans are able to\r\nexploit knowledge acquired from previously learned tasks. Intuitively, access to several\r\nproblems simultaneously or sequentially could also be advantageous for a machine\r\nlearning system, especially if these tasks are closely related. Indeed, results of many\r\nempirical studies have provided justification for this intuition. However, theoretical\r\njustifications of this idea are rather limited.\r\nThe focus of this thesis is to expand the understanding of potential benefits of information\r\ntransfer between several related learning problems. We provide theoretical\r\nanalysis for three scenarios of multi-task learning - multiple kernel learning, sequential\r\nlearning and active task selection. We also provide a PAC-Bayesian perspective on\r\nlifelong learning and investigate how the task generation process influences the generalization\r\nguarantees in this scenario. In addition, we show how some of the obtained\r\ntheoretical results can be used to derive principled multi-task and lifelong learning\r\nalgorithms and illustrate their performance on various synthetic and real-world datasets.","lang":"eng"}],"doi":"10.15479/AT:ISTA:TH_776","publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7"}],"publication_status":"published","acknowledgement":"First and foremost I would like to express my gratitude to my supervisor, Christoph\r\nLampert. Thank you for your patience in teaching me all aspects of doing research\r\n(including English grammar), for your trust in my capabilities and endless support. Thank\r\nyou for granting me freedom in my research and, at the same time, having time and\r\nhelping me cope with the consequences whenever I needed it. Thank you for creating\r\nan excellent atmosphere in the group, it was a great pleasure and honor to be a part of\r\nit. There could not have been a better and more inspiring adviser and mentor.\r\nI thank Shai Ben-David for welcoming me into his group at the University of Waterloo,\r\nfor inspiring discussions and support. It was a great pleasure to work together. I am\r\nalso thankful to Ruth Urner for hosting me at the Max-Planck Institute Tübingen, for the\r\nfruitful collaboration and for taking care of me during that not-so-sunny month of May.\r\nI thank Jan Maas for kindly joining my thesis committee despite the short notice and\r\nproviding me with insightful comments.\r\nI would like to thank my colleagues for their support, entertaining conversations and\r\nendless table soccer games we shared together: Georg, Jan, Amelie and Emilie, Michal\r\nand Alex, Alex K. and Alex Z., Thomas, Sameh, Vlad, Mayu, Nathaniel, Silvester, Neel,\r\nCsaba, Vladimir, Morten. Thank you, Mabel and Ram, for the wonderful time we spent\r\ntogether. I am thankful to Shrinu and Samira for taking care of me during my stay at the\r\nUniversity of Waterloo. Special thanks to Viktoriia for her never-ending optimism and for\r\nbeing so inspiring and supportive, especially at the beginning of my PhD journey.\r\nThanks to IST administration, in particular, Vlad and Elisabeth for shielding me from\r\nmost of the bureaucratic paperwork.\r\n\r\nThis dissertation would not have been possible without funding from the European\r\nResearch Council under the European Union's Seventh Framework Programme\r\n(FP7/2007-2013)/ERC grant agreement no 308036.","status":"public","ec_funded":1,"department":[{"_id":"ChLa"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6234","date_published":"2016-11-01T00:00:00Z","date_created":"2018-12-11T11:50:17Z","publisher":"Institute of Science and Technology Austria","language":[{"iso":"eng"}],"type":"dissertation","oa":1,"year":"2016","alternative_title":["ISTA Thesis"],"date_updated":"2023-09-07T11:52:03Z","page":"127"},{"publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6232","date_published":"2016-08-01T00:00:00Z","date_created":"2018-12-11T11:50:18Z","date_updated":"2023-09-07T11:44:34Z","page":"114","oa":1,"year":"2016","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","file":[{"date_updated":"2019-08-13T11:46:25Z","access_level":"closed","content_type":"application/pdf","checksum":"ec453918c3bf8e6f460fd1156ef7b493","file_name":"Thesis_Georg_Rieckh_w_signature_page.pdf","relation":"main_file","file_size":2614660,"creator":"dernst","file_id":"6815","date_created":"2019-08-13T11:46:25Z"},{"relation":"main_file","creator":"dernst","file_size":6096178,"file_name":"Thesis_Georg_Rieckh.pdf","date_updated":"2020-09-21T11:30:40Z","success":1,"content_type":"application/pdf","checksum":"51ae398166370d18fd22478b6365c4da","access_level":"open_access","date_created":"2020-09-21T11:30:40Z","file_id":"8542"}],"has_accepted_license":"1","article_processing_charge":"No","day":"01","citation":{"ieee":"G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute of Science and Technology Austria, 2016.","apa":"Rieckh, G. (2016). <i>Studying the complexities of transcriptional regulation</i>. Institute of Science and Technology Austria.","short":"G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016.","ista":"Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria.","ama":"Rieckh G. Studying the complexities of transcriptional regulation. 2016.","mla":"Rieckh, Georg. <i>Studying the Complexities of Transcriptional Regulation</i>. Institute of Science and Technology Austria, 2016.","chicago":"Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.” Institute of Science and Technology Austria, 2016."},"file_date_updated":"2020-09-21T11:30:40Z","month":"08","ddc":["570"],"oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"status":"public","publication_status":"published","author":[{"last_name":"Rieckh","full_name":"Rieckh, Georg","first_name":"Georg","id":"34DA8BD6-F248-11E8-B48F-1D18A9856A87"}],"title":"Studying the complexities of transcriptional regulation","supervisor":[{"full_name":"Tkacik, Gasper","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","orcid":"0000-0002-6699-1455"}],"_id":"1128","abstract":[{"lang":"eng","text":"The process of gene expression is central to the modern understanding of how cellular systems\r\nfunction. In this process, a special kind of regulatory proteins, called transcription factors,\r\nare important to determine how much protein is produced from a given gene. As biological\r\ninformation is transmitted from transcription factor concentration to mRNA levels to amounts of\r\nprotein, various sources of noise arise and pose limits to the fidelity of intracellular signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene expression: (i) the mathematical\r\ndescription of complex promoters responsible for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information processing the cell faces due to the interference from multiple\r\nfluctuating signals, (iii) how the presence of gene expression noise influences the evolution\r\nof regulatory sequences, (iv) and tools for the experimental study of origins and consequences\r\nof cell-cell heterogeneity, including an application to bacterial stress response systems."}]},{"date_updated":"2023-09-07T11:54:33Z","page":"178","oa":1,"year":"2016","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","type":"dissertation","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"6231","department":[{"_id":"MiSi"}],"date_created":"2018-12-11T11:50:18Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"}],"date_published":"2016-07-01T00:00:00Z","publication_identifier":{"issn":["2663-337X"]},"acknowledgement":"First, I would like to thank Michael Sixt for being a great supervisor, mentor and\r\nscientist. I highly appreciate his guidance and continued support. Furthermore, I\r\nam very grateful that he gave me the exceptional opportunity to pursue many\r\nideas of which some managed to be included in this thesis.\r\nI owe sincere thanks to the members of my PhD thesis committee, Daria\r\nSiekhaus, Daniel Legler and Harald Janovjak. Especially I would like to thank\r\nDaria for her advice and encouragement during our regular progress meetings.\r\nI also want to thank the team and fellows of the Boehringer Ingelheim Fond\r\n(BIF) PhD Fellowship for amazing and inspiring meetings and the BIF for\r\nfinancial support.\r\nImportant factors for the success of this thesis were the warm, creative\r\nand helpful atmosphere as well as the team spirit of the whole Sixt Lab.\r\nTherefore I would like to thank my current and former colleagues Frank Assen,\r\nMarkus Brown, Ingrid de Vries, Michelle Duggan, Alexander Eichner, Miroslav\r\nHons, Eva Kiermaier, Aglaja Kopf, Alexander Leithner, Christine Moussion, Jan\r\nMüller, Maria Nemethova, Jörg Renkawitz, Anne Reversat, Kari Vaahtomeri,\r\nMichele Weber and Stefan Wieser. We had an amazing time with many\r\nlegendary evenings and events. Along these lines I want to thank the in vitro\r\ncrew of the lab, Jörg, Anne and Alex, for lots of ideas and productive\r\ndiscussions. I am sure, some day we will reveal the secret of the ‘splodge’.\r\nI want to thank the members of the Heisenberg Lab for a great time and\r\nthrilling kicker matches. In this regard I especially want to thank Maurizio\r\n‘Gnocci’ Monti, Gabriel Krens, Alex Eichner, Martin Behrndt, Vanessa Barone,Philipp Schmalhorst, Michael Smutny, Daniel Capek, Anne Reversat, Eva\r\nKiermaier, Frank Assen and Jan Müller for wonderful after-lunch matches.\r\nI would not have been able to analyze the thousands of cell trajectories\r\nand probably hundreds of thousands of mouse clicks without the productive\r\ncollaboration with Veronika Bierbaum and Tobias Bollenbach. Thanks Vroni for\r\ncountless meetings, discussions and graphs and of course for proofreading and\r\nadvice for this thesis. For proofreading I also want to thank Evi, Jörg, Jack and\r\nAnne.\r\nI would like to acknowledge Matthias Mehling for a very productive\r\ncollaboration and for introducing me into the wild world of microfluidics. Jack\r\nMerrin, for countless wafers, PDMS coated coverslips and help with anything\r\nmicro-fabrication related. And Maria Nemethova for establishing the ‘click’\r\npatterning approach with me. Without her it still would be just one of the ideas…\r\nMany thanks to Ekaterina Papusheva, Robert Hauschild, Doreen Milius\r\nand Nasser Darwish from the Bioimaging Facility as well as the Preclinical and\r\nthe Life Science facilities of IST Austria for excellent technical support. At this\r\npoint I especially want to thank Robert for countless image analyses and\r\ntechnical ideas. Always interested and creative he played an essential role in all\r\nof my projects.\r\nAdditionally I want to thank Ingrid and Gabby for welcoming me warmly\r\nwhen I first started at IST, for scientific and especially mental support in all\r\nthose years, countless coffee sessions and Heurigen evenings. #BioimagingFacility #LifeScienceFacility #PreClinicalFacility","status":"public","publication_status":"published","_id":"1129","supervisor":[{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K","last_name":"Sixt"}],"title":"Quantitative analysis of haptotactic cell migration","author":[{"first_name":"Jan","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","full_name":"Schwarz, Jan"}],"abstract":[{"lang":"eng","text":"Directed cell migration is a hallmark feature, present in almost all multi-cellular\r\norganisms. Despite its importance, basic questions regarding force transduction\r\nor directional sensing are still heavily investigated. Directed migration of cells\r\nguided by immobilized guidance cues - haptotaxis - occurs in key-processes,\r\nsuch as embryonic development and immunity (Middleton et al., 1997; Nguyen\r\net al., 2000; Thiery, 1984; Weber et al., 2013). Immobilized guidance cues\r\ncomprise adhesive ligands, such as collagen and fibronectin (Barczyk et al.,\r\n2009), or chemokines - the main guidance cues for migratory leukocytes\r\n(Middleton et al., 1997; Weber et al., 2013). While adhesive ligands serve as\r\nattachment sites guiding cell migration (Carter, 1965), chemokines instruct\r\nhaptotactic migration by inducing adhesion to adhesive ligands and directional\r\nguidance (Rot and Andrian, 2004; Schumann et al., 2010). Quantitative analysis\r\nof the cellular response to immobilized guidance cues requires in vitro assays\r\nthat foster cell migration, offer accurate control of the immobilized cues on a\r\nsubcellular scale and in the ideal case closely reproduce in vivo conditions. The\r\nexploration of haptotactic cell migration through design and employment of such\r\nassays represents the main focus of this work.\r\nDendritic cells (DCs) are leukocytes, which after encountering danger\r\nsignals such as pathogens in peripheral organs instruct naïve T-cells and\r\nconsequently the adaptive immune response in the lymph node (Mellman and\r\nSteinman, 2001). To reach the lymph node from the periphery, DCs follow\r\nhaptotactic gradients of the chemokine CCL21 towards lymphatic vessels\r\n(Weber et al., 2013). Questions about how DCs interpret haptotactic CCL21\r\ngradients have not yet been addressed. The main reason for this is the lack of\r\nan assay that offers diverse haptotactic environments, hence allowing the study\r\nof DC migration as a response to different signals of immobilized guidance cue.\r\nIn this work, we developed an in vitro assay that enables us to\r\nquantitatively assess DC haptotaxis, by combining precisely controllable\r\nchemokine photo-patterning with physically confining migration conditions. With this tool at hand, we studied the influence of CCL21 gradient properties and\r\nconcentration on DC haptotaxis. We found that haptotactic gradient sensing\r\ndepends on the absolute CCL21 concentration in combination with the local\r\nsteepness of the gradient. Our analysis suggests that the directionality of\r\nmigrating DCs is governed by the signal-to-noise ratio of CCL21 binding to its\r\nreceptor CCR7. Moreover, the haptotactic CCL21 gradient formed in vivo\r\nprovides an optimal shape for DCs to recognize haptotactic guidance cue.\r\nBy reconstitution of the CCL21 gradient in vitro we were also able to\r\nstudy the influence of CCR7 signal termination on DC haptotaxis. To this end,\r\nwe used DCs lacking the G-protein coupled receptor kinase GRK6, which is\r\nresponsible for CCL21 induced CCR7 receptor phosphorylation and\r\ndesensitization (Zidar et al., 2009). We found that CCR7 desensitization by\r\nGRK6 is crucial for maintenance of haptotactic CCL21 gradient sensing in vitro\r\nand confirm those observations in vivo.\r\nIn the context of the organism, immobilized haptotactic guidance cues\r\noften coincide and compete with soluble chemotactic guidance cues. During\r\nwound healing, fibroblasts are exposed and influenced by adhesive cues and\r\nsoluble factors at the same time (Wu et al., 2012; Wynn, 2008). Similarly,\r\nmigrating DCs are exposed to both, soluble chemokines (CCL19 and truncated\r\nCCL21) inducing chemotactic behavior as well as the immobilized CCL21. To\r\nquantitatively assess these complex coinciding immobilized and soluble\r\nguidance cues, we implemented our chemokine photo-patterning technique in a\r\nmicrofluidic system allowing for chemotactic gradient generation. To validate\r\nthe assay, we observed DC migration in competing CCL19/CCL21\r\nenvironments.\r\nAdhesiveness guided haptotaxis has been studied intensively over the\r\nlast century. However, quantitative studies leading to conceptual models are\r\nlargely missing, again due to the lack of a precisely controllable in vitro assay. A\r\nrequirement for such an in vitro assay is that it must prevent any uncontrolled\r\ncell adhesion. This can be accomplished by stable passivation of the surface. In\r\naddition, controlled adhesion must be sustainable, quantifiable and dose\r\ndependent in order to create homogenous gradients. Therefore, we developed a novel covalent photo-patterning technique satisfying all these needs. In\r\ncombination with a sustainable poly-vinyl alcohol (PVA) surface coating we\r\nwere able to generate gradients of adhesive cue to direct cell migration. This\r\napproach allowed us to characterize the haptotactic migratory behavior of\r\nzebrafish keratocytes in vitro. Furthermore, defined patterns of adhesive cue\r\nallowed us to control for cell shape and growth on a subcellular scale."}],"file":[{"file_name":"Thesis_JSchwarz_final.pdf","file_size":32044069,"relation":"main_file","creator":"dernst","access_level":"closed","checksum":"e3cd6b28f9c5cccb8891855565a2dade","content_type":"application/pdf","date_updated":"2019-08-13T10:55:35Z","file_id":"6813","date_created":"2019-08-13T10:55:35Z"},{"date_created":"2021-02-22T11:43:14Z","file_id":"9181","content_type":"application/pdf","checksum":"c3dbe219acf87eed2f46d21d5cca00de","access_level":"open_access","date_updated":"2021-02-22T11:43:14Z","success":1,"relation":"main_file","creator":"dernst","file_size":8396717,"file_name":"2016_Thesis_JSchwarz.pdf"}],"degree_awarded":"PhD","article_processing_charge":"No","has_accepted_license":"1","month":"07","file_date_updated":"2021-02-22T11:43:14Z","ddc":["570"],"citation":{"apa":"Schwarz, J. (2016). <i>Quantitative analysis of haptotactic cell migration</i>. Institute of Science and Technology Austria.","ieee":"J. Schwarz, “Quantitative analysis of haptotactic cell migration,” Institute of Science and Technology Austria, 2016.","short":"J. Schwarz, Quantitative Analysis of Haptotactic Cell Migration, Institute of Science and Technology Austria, 2016.","ama":"Schwarz J. Quantitative analysis of haptotactic cell migration. 2016.","ista":"Schwarz J. 2016. Quantitative analysis of haptotactic cell migration. Institute of Science and Technology Austria.","mla":"Schwarz, Jan. <i>Quantitative Analysis of Haptotactic Cell Migration</i>. Institute of Science and Technology Austria, 2016.","chicago":"Schwarz, Jan. “Quantitative Analysis of Haptotactic Cell Migration.” Institute of Science and Technology Austria, 2016."},"day":"01","oa_version":"Published Version"}]