[{"alternative_title":["ISTA Thesis"],"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"5828"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","acknowledgement":"I am very grateful for the opportunity I have had as a graduate student to explore and incredibly interesting branch of neuroscience, and for the people who made it possible. Firstly, I would like to offer my thanks to my supervisor Professor Jozsef Csicsvari for his great support, guidance and patience offered over the years. The door to his office was always open whenever I had questions. I have learned a lot from him about carefully designing experiments, asking interesting questions and how to integrate results into a broader picture. I also express my gratitude to the remarkable post- doc , Dr. Joseph O’Neill. He is a gre at scientific role model who is always willing to teach , and advice and talk through problems with his full attention. Many thanks to my wonderful “office mates” over the years and their support and encouragement, Alice Avernhe, Philipp Schönenberger, Desiree Dickerson, Karel Blahna, Charlotte Boccara, Igor Gridchyn, Peter Baracskay, Krisztián Kovács, Dámaris Rangel, Karola Käfer and Federico Stella. They were the ones in the lab for the many useful discussions about science and for making the laboratory such a nice and friendly place to work in. A special thank goes to Michael LoBianco and Jago Wallenschus for wonderful technical support. I would also like to thank Professor Peter Jonas and Professor David M Bannerman for being my qualifying exam and thesi s committee members despite their busy schedule. I am also very thankful to IST Austria for their support all throughout my PhD. ","oa":1,"page":"93","file_date_updated":"2020-07-14T12:48:12Z","pubrep_id":"858","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"date_created":"2018-12-11T11:48:46Z","_id":"837","month":"08","title":"Reactivation of the hippocampal cognitive map in goal-directed spatial tasks","date_updated":"2023-09-07T12:06:38Z","date_published":"2017-08-23T00:00:00Z","article_processing_charge":"No","type":"dissertation","citation":{"ista":"Xu H. 2017. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. Institute of Science and Technology Austria.","mla":"Xu, Haibing. <i>Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>.","chicago":"Xu, Haibing. “Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>.","ama":"Xu H. Reactivation of the hippocampal cognitive map in goal-directed spatial tasks. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">10.15479/AT:ISTA:th_858</a>","ieee":"H. Xu, “Reactivation of the hippocampal cognitive map in goal-directed spatial tasks,” Institute of Science and Technology Austria, 2017.","apa":"Xu, H. (2017). <i>Reactivation of the hippocampal cognitive map in goal-directed spatial tasks</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_858\">https://doi.org/10.15479/AT:ISTA:th_858</a>","short":"H. Xu, Reactivation of the Hippocampal Cognitive Map in Goal-Directed Spatial Tasks, Institute of Science and Technology Austria, 2017."},"file":[{"checksum":"f11925fbbce31e495124b6bc4f10573c","relation":"source_file","date_updated":"2020-07-14T12:48:12Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":3589490,"file_name":"2017_Xu_Haibing_Thesis_Source.docx","access_level":"closed","file_id":"6213","date_created":"2019-04-05T08:59:51Z","creator":"dernst"},{"creator":"dernst","date_created":"2019-04-05T08:59:51Z","file_id":"6214","access_level":"open_access","file_name":"2017_Xu_Thesis_IST.pdf","date_updated":"2020-07-14T12:48:12Z","content_type":"application/pdf","file_size":11668613,"checksum":"ffb10749a537d615fab1ef0937ccb157","relation":"main_file"}],"ddc":["571"],"language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","publication_status":"published","abstract":[{"text":"The hippocampus is a key brain region for memory and notably for spatial memory, and is needed for both spatial working and reference memories. Hippocampal place cells selectively discharge in specific locations of the environment to form mnemonic represen tations of space. Several behavioral protocols have been designed to test spatial memory which requires the experimental subject to utilize working memory and reference memory. However, less is known about how these memory traces are presented in the hippo campus, especially considering tasks that require both spatial working and long -term reference memory demand. The aim of my thesis was to elucidate how spatial working memory, reference memory, and the combination of both are represented in the hippocampus. In this thesis, using a radial eight -arm maze, I examined how the combined demand on these memories influenced place cell assemblies while reference memories were partially updated by changing some of the reward- arms. This was contrasted with task varian ts requiring working or reference memories only. Reference memory update led to gradual place field shifts towards the rewards on the switched arms. Cells developed enhanced firing in passes between newly -rewarded arms as compared to those containing an unchanged reward. The working memory task did not show such gradual changes. Place assemblies on occasions replayed trajectories of the maze; at decision points the next arm choice was preferentially replayed in tasks needing reference memory while in the pure working memory task the previously visited arm was replayed. Hence trajectory replay only reflected the decision of the animal in tasks needing reference memory update. At the reward locations, in all three tasks outbound trajectories of the current arm were preferentially replayed, showing the animals’ next path to the center. At reward locations trajectories were replayed preferentially in reverse temporal order. Moreover, in the center reverse replay was seen in the working memory task but in the other tasks forward replay was seen. Hence, the direction of reactivation was determined by the goal locations so that part of the trajectory which was closer to the goal was reactivated later in an HSE while places further away from the goal were reactivated earlier. Altogether my work demonstrated that reference memory update triggers several levels of reorganization of the hippocampal cognitive map which are not seen in simpler working memory demand s. Moreover, hippocampus is likely to be involved in spatial decisions through reactivating planned trajectories when reference memory recall is required for such a decision. ","lang":"eng"}],"publist_id":"6811","oa_version":"Published Version","doi":"10.15479/AT:ISTA:th_858","day":"23","publisher":"Institute of Science and Technology Austria","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"JoCs"}],"author":[{"id":"310349D0-F248-11E8-B48F-1D18A9856A87","first_name":"Haibing","full_name":"Xu, Haibing","last_name":"Xu"}],"year":"2017"},{"related_material":{"record":[{"id":"2082","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"6196"}]},"alternative_title":["ISTA Thesis"],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T12:02:28Z","title":"(The exact security of) Message authentication codes","month":"06","article_processing_charge":"No","date_published":"2017-06-26T00:00:00Z","pubrep_id":"828","file_date_updated":"2020-07-14T12:48:12Z","page":"86","_id":"838","date_created":"2018-12-11T11:48:46Z","publist_id":"6810","publication_status":"published","abstract":[{"lang":"eng","text":"In this thesis we discuss the exact security of message authentications codes HMAC , NMAC , and PMAC . NMAC is a mode of operation which turns a fixed input-length keyed hash function f into a variable input-length function. A practical single-key variant of NMAC called HMAC is a very popular and widely deployed message authentication code (MAC). PMAC is a block-cipher based mode of operation, which also happens to be the most famous fully parallel MAC. NMAC was introduced by Bellare, Canetti and Krawczyk Crypto’96, who proved it to be a secure pseudorandom function (PRF), and thus also a MAC, under two assumptions. Unfortunately, for many instantiations of HMAC one of them has been found to be wrong. To restore the provable guarantees for NMAC , Bellare [Crypto’06] showed its security without this assumption. PMAC was introduced by Black and Rogaway at Eurocrypt 2002. If instantiated with a pseudorandom permutation over n -bit strings, PMAC constitutes a provably secure variable input-length PRF. For adversaries making q queries, each of length at most ` (in n -bit blocks), and of total length σ ≤ q` , the original paper proves an upper bound on the distinguishing advantage of O ( σ 2 / 2 n ), while the currently best bound is O ( qσ/ 2 n ). In this work we show that this bound is tight by giving an attack with advantage Ω( q 2 `/ 2 n ). In the PMAC construction one initially XORs a mask to every message block, where the mask for the i th block is computed as τ i := γ i · L , where L is a (secret) random value, and γ i is the i -th codeword of the Gray code. Our attack applies more generally to any sequence of γ i ’s which contains a large coset of a subgroup of GF (2 n ). As for NMAC , our first contribution is a simpler and uniform proof: If f is an ε -secure PRF (against q queries) and a δ - non-adaptively secure PRF (against q queries), then NMAC f is an ( ε + `qδ )-secure PRF against q queries of length at most ` blocks each. We also show that this ε + `qδ bound is basically tight by constructing an f for which an attack with advantage `qδ exists. Moreover, we analyze the PRF-security of a modification of NMAC called NI by An and Bellare that avoids the constant rekeying on multi-block messages in NMAC and allows for an information-theoretic analysis. We carry out such an analysis, obtaining a tight `q 2 / 2 c bound for this step, improving over the trivial bound of ` 2 q 2 / 2 c . Finally, we investigate, if the security of PMAC can be further improved by using τ i ’s that are k -wise independent, for k &gt; 1 (the original has k = 1). We observe that the security of PMAC will not increase in general if k = 2, and then prove that the security increases to O ( q 2 / 2 n ), if the k = 4. Due to simple extension attacks, this is the best bound one can hope for, using any distribution on the masks. Whether k = 3 is already sufficient to get this level of security is left as an open problem. Keywords: Message authentication codes, Pseudorandom functions, HMAC, PMAC. "}],"has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"file":[{"file_id":"4799","creator":"system","date_created":"2018-12-12T10:10:13Z","content_type":"application/pdf","date_updated":"2020-07-14T12:48:12Z","file_size":847400,"checksum":"ff8639ec4bded6186f44c7bd3ee26804","relation":"main_file","access_level":"open_access","file_name":"IST-2017-828-v1+3_2017_Rybar_thesis.pdf"},{"creator":"dernst","date_created":"2019-04-05T08:24:11Z","file_id":"6202","file_name":"2017_Thesis_Rybar_source.zip","access_level":"closed","checksum":"3462101745ce8ad199c2d0f75dae4a7e","relation":"source_file","date_updated":"2020-07-14T12:48:12Z","content_type":"application/zip","file_size":26054879}],"citation":{"mla":"Rybar, Michal. <i>(The Exact Security of) Message Authentication Codes</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>.","ista":"Rybar M. 2017. (The exact security of) Message authentication codes. Institute of Science and Technology Austria.","chicago":"Rybar, Michal. “(The Exact Security of) Message Authentication Codes.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>.","ama":"Rybar M. (The exact security of) Message authentication codes. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">10.15479/AT:ISTA:th_828</a>","ieee":"M. Rybar, “(The exact security of) Message authentication codes,” Institute of Science and Technology Austria, 2017.","apa":"Rybar, M. (2017). <i>(The exact security of) Message authentication codes</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_828\">https://doi.org/10.15479/AT:ISTA:th_828</a>","short":"M. Rybar, (The Exact Security of) Message Authentication Codes, Institute of Science and Technology Austria, 2017."},"type":"dissertation","ddc":["000"],"department":[{"_id":"KrPi"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","year":"2017","author":[{"id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","last_name":"Rybar","full_name":"Rybar, Michal"}],"doi":"10.15479/AT:ISTA:th_828","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","day":"26"},{"title":"Brittle fracture simulation with boundary elements for computer graphics","date_updated":"2024-02-21T13:48:02Z","month":"08","date_published":"2017-08-14T00:00:00Z","article_processing_charge":"No","ec_funded":1,"pubrep_id":"855","file_date_updated":"2020-07-14T12:48:13Z","supervisor":[{"first_name":"Christopher J","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","full_name":"Wojtan, Christopher J","orcid":"0000-0001-6646-5546","last_name":"Wojtan"}],"page":"124","_id":"839","project":[{"name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","grant_number":"638176","call_identifier":"H2020"}],"date_created":"2018-12-11T11:48:47Z","alternative_title":["ISTA Thesis"],"related_material":{"record":[{"id":"1362","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"1633"},{"id":"5568","relation":"popular_science","status":"public"}]},"acknowledgement":"ERC H2020 programme (grant agreement no. 638176)\r\nFirst of all, let me thank my committee members, especially my supervisor, Chris\r\nWojtan, for supporting me throughout my PhD. Obviously, none of this work would\r\nhave been possible without you.\r\nFurthermore, Thank You to all the people who have contributed to this work in various\r\nways, in particular Martin Schanz and his group for providing and supporting the\r\nHyENA boundary element library, as well as Eder Miguel and Morten Bojsen-Hansen\r\nfor (repeatedly) proof reading and providing valuable suggestions during the writing\r\nof this thesis.\r\nI would also like to thank Bernd Bickel, and all the members – past and present – of his\r\nand Chris’ research groups at IST Austria for always providing honest and insightful\r\nfeedback throughout many joint group meetings, as well as Christopher Batty, Eitan\r\nGrinspun, and Fang Da for many insights into boundary element methods during our\r\ncollaboration.\r\nAs only virtual objects have been harmed in the process of creating this work, I would\r\nlike to acknowledge the Stanford scanning repository for providing the “Bunny” and\r\n“Armadillo” models, the AIM@SHAPE repository for “Pierre’s hand, watertight”, and\r\nS. Gainsbourg for the “Column” via Archive3D.net. Sorry for breaking these models\r\nin many different ways.\r\n","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"license":"https://creativecommons.org/licenses/by-sa/4.0/","degree_awarded":"PhD","department":[{"_id":"ChWo"}],"publication_identifier":{"issn":["2663-337X"]},"tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png"},"author":[{"last_name":"Hahn","full_name":"Hahn, David","first_name":"David","id":"357A6A66-F248-11E8-B48F-1D18A9856A87"}],"year":"2017","doi":"10.15479/AT:ISTA:th_855","oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","day":"14","abstract":[{"lang":"eng","text":"This thesis describes a brittle fracture simulation method for visual effects applications. Building upon a symmetric Galerkin boundary element method, we first compute stress intensity factors following the theory of linear elastic fracture mechanics. We then use these stress intensities to simulate the motion of a propagating crack front at a significantly higher resolution than the overall deformation of the breaking object. Allowing for spatial variations of the material's toughness during crack propagation produces visually realistic, highly-detailed fracture surfaces. Furthermore, we introduce approximations for stress intensities and crack opening displacements, resulting in both practical speed-up and theoretically superior runtime complexity compared to previous methods. While we choose a quasi-static approach to fracture mechanics, ignoring dynamic deformations, we also couple our fracture simulation framework to a standard rigid-body dynamics solver, enabling visual effects artists to simulate both large scale motion, as well as fracturing due to collision forces in a combined system. As fractures inside of an object grow, their geometry must be represented both in the coarse boundary element mesh, as well as at the desired fine output resolution. Using a boundary element method, we avoid complicated volumetric meshing operations. Instead we describe a simple set of surface meshing operations that allow us to progressively add cracks to the mesh of an object and still re-use all previously computed entries of the linear boundary element system matrix. On the high resolution level, we opt for an implicit surface representation. We then describe how to capture fracture surfaces during crack propagation, as well as separate the individual fragments resulting from the fracture process, based on this implicit representation. We show results obtained with our method, either solving the full boundary element system in every time step, or alternatively using our fast approximations. These results demonstrate that both of these methods perform well in basic test cases and produce realistic fracture surfaces. Furthermore we show that our fast approximations substantially out-perform the standard approach in more demanding scenarios. Finally, these two methods naturally combine, using the full solution while the problem size is manageably small and switching to the fast approximations later on. The resulting hybrid method gives the user a direct way to choose between speed and accuracy of the simulation. "}],"publication_status":"published","publist_id":"6809","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","file":[{"creator":"system","date_created":"2018-12-12T10:14:46Z","file_id":"5100","access_level":"open_access","file_name":"IST-2017-855-v1+1_thesis_online_pdfA.pdf","file_size":14596191,"date_updated":"2020-07-14T12:48:13Z","content_type":"application/pdf","relation":"main_file","checksum":"6c1ae8c90bfaba5e089417fefbc4a272"},{"file_id":"6207","date_created":"2019-04-05T08:40:30Z","creator":"dernst","date_updated":"2020-07-14T12:48:13Z","content_type":"application/zip","file_size":15060566,"relation":"source_file","checksum":"421672f68d563b029869c5cf1713f919","access_level":"closed","file_name":"2017_thesis_Hahn_source.zip"}],"citation":{"apa":"Hahn, D. (2017). <i>Brittle fracture simulation with boundary elements for computer graphics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>","short":"D. Hahn, Brittle Fracture Simulation with Boundary Elements for Computer Graphics, Institute of Science and Technology Austria, 2017.","ieee":"D. Hahn, “Brittle fracture simulation with boundary elements for computer graphics,” Institute of Science and Technology Austria, 2017.","ama":"Hahn D. Brittle fracture simulation with boundary elements for computer graphics. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>","chicago":"Hahn, David. “Brittle Fracture Simulation with Boundary Elements for Computer Graphics.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">https://doi.org/10.15479/AT:ISTA:th_855</a>.","mla":"Hahn, David. <i>Brittle Fracture Simulation with Boundary Elements for Computer Graphics</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_855\">10.15479/AT:ISTA:th_855</a>.","ista":"Hahn D. 2017. Brittle fracture simulation with boundary elements for computer graphics. Institute of Science and Technology Austria."},"type":"dissertation","ddc":["004","005","006","531","621"]},{"scopus_import":"1","citation":{"ieee":"H. Edelsbrunner and P. Koehl, “Computational topology for structural molecular biology,” in <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, C. Toth, J. O’Rourke, and J. Goodman, Eds. Taylor &#38; Francis, 2017, pp. 1709–1735.","short":"H. Edelsbrunner, P. Koehl, in:, C. Toth, J. O’Rourke, J. Goodman (Eds.), Handbook of Discrete and Computational Geometry, Third Edition, Taylor &#38; Francis, 2017, pp. 1709–1735.","apa":"Edelsbrunner, H., &#38; Koehl, P. (2017). Computational topology for structural molecular biology. In C. Toth, J. O’Rourke, &#38; J. Goodman (Eds.), <i>Handbook of Discrete and Computational Geometry, Third Edition</i> (pp. 1709–1735). Taylor &#38; Francis. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>","ista":"Edelsbrunner H, Koehl P. 2017.Computational topology for structural molecular biology. In: Handbook of Discrete and Computational Geometry, Third Edition. , 1709–1735.","mla":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth et al., Taylor &#38; Francis, 2017, pp. 1709–35, doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>.","chicago":"Edelsbrunner, Herbert, and Patrice Koehl. “Computational Topology for Structural Molecular Biology.” In <i>Handbook of Discrete and Computational Geometry, Third Edition</i>, edited by Csaba Toth, Joseph O’Rourke, and Jacob Goodman, 1709–35. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis, 2017. <a href=\"https://doi.org/10.1201/9781315119601\">https://doi.org/10.1201/9781315119601</a>.","ama":"Edelsbrunner H, Koehl P. Computational topology for structural molecular biology. In: Toth C, O’Rourke J, Goodman J, eds. <i>Handbook of Discrete and Computational Geometry, Third Edition</i>. Handbook of Discrete and Computational Geometry. Taylor &#38; Francis; 2017:1709-1735. doi:<a href=\"https://doi.org/10.1201/9781315119601\">10.1201/9781315119601</a>"},"type":"book_chapter","status":"public","language":[{"iso":"eng"}],"publist_id":"7970","abstract":[{"text":"The advent of high-throughput technologies and the concurrent advances in information sciences have led to a data revolution in biology. This revolution is most significant in molecular biology, with an increase in the number and scale of the “omics” projects over the last decade. Genomics projects, for example, have produced impressive advances in our knowledge of the information concealed into genomes, from the many genes that encode for the proteins that are responsible for most if not all cellular functions, to the noncoding regions that are now known to provide regulatory functions. Proteomics initiatives help to decipher the role of post-translation modifications on the protein structures and provide maps of protein-protein interactions, while functional genomics is the field that attempts to make use of the data produced by these projects to understand protein functions. The biggest challenge today is to assimilate the wealth of information provided by these initiatives into a conceptual framework that will help us decipher life. For example, the current views of the relationship between protein structure and function remain fragmented. We know of their sequences, more and more about their structures, we have information on their biological activities, but we have difficulties connecting this dotted line into an informed whole. We lack the experimental and computational tools for directly studying protein structure, function, and dynamics at the molecular and supra-molecular levels. In this chapter, we review some of the current developments in building the computational tools that are needed, focusing on the role that geometry and topology play in these efforts. One of our goals is to raise the general awareness about the importance of geometric methods in elucidating the mysterious foundations of our very existence. Another goal is the broadening of what we consider a geometric algorithm. There is plenty of valuable no-man’s-land between combinatorial and numerical algorithms, and it seems opportune to explore this land with a computational-geometric frame of mind.","lang":"eng"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","page":"1709 - 1735","oa_version":"None","doi":"10.1201/9781315119601","publication":"Handbook of Discrete and Computational Geometry, Third Edition","day":"09","date_created":"2018-12-11T11:44:32Z","series_title":"Handbook of Discrete and Computational Geometry","_id":"84","publisher":"Taylor & Francis","month":"11","department":[{"_id":"HeEd"}],"publication_identifier":{"eisbn":["9781498711425"]},"title":"Computational topology for structural molecular biology","date_updated":"2023-10-16T11:15:22Z","editor":[{"first_name":"Csaba","full_name":"Toth, Csaba","last_name":"Toth"},{"full_name":"O'Rourke, Joseph","last_name":"O'Rourke","first_name":"Joseph"},{"first_name":"Jacob","full_name":"Goodman, Jacob","last_name":"Goodman"}],"article_processing_charge":"No","year":"2017","date_published":"2017-11-09T00:00:00Z","author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"first_name":"Patrice","full_name":"Koehl, Patrice","last_name":"Koehl"}]},{"pubrep_id":"865","file_date_updated":"2020-07-14T12:48:13Z","publication":"Nano Letters","page":"5706 - 5710","_id":"840","project":[{"name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","_id":"25517E86-B435-11E9-9278-68D0E5697425","grant_number":"335497","call_identifier":"FP7"}],"date_created":"2018-12-11T11:48:47Z","external_id":{"isi":["000411043500078"]},"title":"Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry","date_updated":"2023-09-26T15:50:22Z","month":"08","date_published":"2017-08-10T00:00:00Z","article_processing_charge":"No","ec_funded":1,"scopus_import":"1","volume":17,"related_material":{"record":[{"id":"7977","relation":"popular_science"},{"relation":"dissertation_contains","status":"public","id":"69"},{"id":"7996","status":"public","relation":"dissertation_contains"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"9","intvolume":"        17","oa":1,"doi":"10.1021/acs.nanolett.7b02627","oa_version":"Published Version","publisher":"American Chemical Society","day":"10","publication_identifier":{"issn":["15306984"]},"department":[{"_id":"GeKa"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"orcid":"0000-0003-2424-8636","full_name":"Vukusic, Lada","last_name":"Vukusic","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","last_name":"Watzinger","full_name":"Watzinger, Hannes"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X"}],"isi":1,"year":"2017","file":[{"file_id":"4951","creator":"system","date_created":"2018-12-12T10:12:33Z","content_type":"application/pdf","date_updated":"2020-07-14T12:48:13Z","file_size":2449546,"checksum":"761371a0129b2aa442424b9561450ece","relation":"main_file","access_level":"open_access","file_name":"IST-2017-865-v1+1_acs.nanolett.7b02627.pdf"}],"type":"journal_article","citation":{"ieee":"L. Vukušić, J. Kukucka, H. Watzinger, and G. Katsaros, “Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry,” <i>Nano Letters</i>, vol. 17, no. 9. American Chemical Society, pp. 5706–5710, 2017.","apa":"Vukušić, L., Kukucka, J., Watzinger, H., &#38; Katsaros, G. (2017). Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">https://doi.org/10.1021/acs.nanolett.7b02627</a>","short":"L. Vukušić, J. Kukucka, H. Watzinger, G. Katsaros, Nano Letters 17 (2017) 5706–5710.","mla":"Vukušić, Lada, et al. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” <i>Nano Letters</i>, vol. 17, no. 9, American Chemical Society, 2017, pp. 5706–10, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">10.1021/acs.nanolett.7b02627</a>.","ista":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. 2017. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. Nano Letters. 17(9), 5706–5710.","ama":"Vukušić L, Kukucka J, Watzinger H, Katsaros G. Fast hole tunneling times in germanium hut wires probed by single-shot reflectometry. <i>Nano Letters</i>. 2017;17(9):5706-5710. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">10.1021/acs.nanolett.7b02627</a>","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, and Georgios Katsaros. “Fast Hole Tunneling Times in Germanium Hut Wires Probed by Single-Shot Reflectometry.” <i>Nano Letters</i>. American Chemical Society, 2017. <a href=\"https://doi.org/10.1021/acs.nanolett.7b02627\">https://doi.org/10.1021/acs.nanolett.7b02627</a>."},"ddc":["539"],"acknowledged_ssus":[{"_id":"M-Shop"}],"abstract":[{"text":"Heavy holes confined in quantum dots are predicted to be promising candidates for the realization of spin qubits with long coherence times. Here we focus on such heavy-hole states confined in germanium hut wires. By tuning the growth density of the latter we can realize a T-like structure between two neighboring wires. Such a structure allows the realization of a charge sensor, which is electrostatically and tunnel coupled to a quantum dot, with charge-transfer signals as high as 0.3 e. By integrating the T-like structure into a radiofrequency reflectometry setup, single-shot measurements allowing the extraction of hole tunneling times are performed. The extracted tunneling times of less than 10 μs are attributed to the small effective mass of Ge heavy-hole states and pave the way toward projective spin readout measurements.","lang":"eng"}],"publication_status":"published","publist_id":"6808","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","quality_controlled":"1"},{"ec_funded":1,"date_published":"2017-01-01T00:00:00Z","article_processing_charge":"No","month":"01","title":"On the lengths of curves passing through boundary points of a planar convex shape","date_updated":"2023-10-17T11:24:57Z","date_created":"2018-12-11T11:49:09Z","external_id":{"isi":["000413947300002"],"arxiv":["1605.07997"]},"project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"}],"_id":"909","page":"588 - 596","publication":"The American Mathematical Monthly","issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"       124","oa":1,"volume":124,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.07997"}],"scopus_import":"1","isi":1,"author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"last_name":"Vysotsky","full_name":"Vysotsky, Vladislav","first_name":"Vladislav"}],"year":"2017","department":[{"_id":"HeEd"}],"publication_identifier":{"issn":["00029890"]},"day":"01","publisher":"Mathematical Association of America","arxiv":1,"oa_version":"Submitted Version","doi":"10.4169/amer.math.monthly.124.7.588","quality_controlled":"1","language":[{"iso":"eng"}],"status":"public","abstract":[{"lang":"eng","text":"We study the lengths of curves passing through a fixed number of points on the boundary of a convex shape in the plane. We show that, for any convex shape K, there exist four points on the boundary of K such that the length of any curve passing through these points is at least half of the perimeter of K. It is also shown that the same statement does not remain valid with the additional constraint that the points are extreme points of K. Moreover, the factor &amp;#xbd; cannot be achieved with any fixed number of extreme points. We conclude the paper with a few other inequalities related to the perimeter of a convex shape."}],"publication_status":"published","publist_id":"6534","article_type":"original","citation":{"mla":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” <i>The American Mathematical Monthly</i>, vol. 124, no. 7, Mathematical Association of America, 2017, pp. 588–96, doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">10.4169/amer.math.monthly.124.7.588</a>.","ista":"Akopyan A, Vysotsky V. 2017. On the lengths of curves passing through boundary points of a planar convex shape. The American Mathematical Monthly. 124(7), 588–596.","ama":"Akopyan A, Vysotsky V. On the lengths of curves passing through boundary points of a planar convex shape. <i>The American Mathematical Monthly</i>. 2017;124(7):588-596. doi:<a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">10.4169/amer.math.monthly.124.7.588</a>","chicago":"Akopyan, Arseniy, and Vladislav Vysotsky. “On the Lengths of Curves Passing through Boundary Points of a Planar Convex Shape.” <i>The American Mathematical Monthly</i>. Mathematical Association of America, 2017. <a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">https://doi.org/10.4169/amer.math.monthly.124.7.588</a>.","ieee":"A. Akopyan and V. Vysotsky, “On the lengths of curves passing through boundary points of a planar convex shape,” <i>The American Mathematical Monthly</i>, vol. 124, no. 7. Mathematical Association of America, pp. 588–596, 2017.","apa":"Akopyan, A., &#38; Vysotsky, V. (2017). On the lengths of curves passing through boundary points of a planar convex shape. <i>The American Mathematical Monthly</i>. Mathematical Association of America. <a href=\"https://doi.org/10.4169/amer.math.monthly.124.7.588\">https://doi.org/10.4169/amer.math.monthly.124.7.588</a>","short":"A. Akopyan, V. Vysotsky, The American Mathematical Monthly 124 (2017) 588–596."},"type":"journal_article"},{"year":"2017","isi":1,"author":[{"full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak","id":"461468AE-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"}],"department":[{"_id":"NiBa"}],"publisher":"Genetics Society of America","day":"01","doi":"10.1534/genetics.117.300129","oa_version":"Submitted Version","quality_controlled":"1","publist_id":"6533","abstract":[{"lang":"eng","text":"Frequency-independent selection is generally considered as a force that acts to reduce the genetic variation in evolving populations, yet rigorous arguments for this idea are scarce. When selection fluctuates in time, it is unclear whether frequency-independent selection may maintain genetic polymorphism without invoking additional mechanisms. We show that constant frequency-independent selection with arbitrary epistasis on a well-mixed haploid population eliminates genetic variation if we assume linkage equilibrium between alleles. To this end, we introduce the notion of frequency-independent selection at the level of alleles, which is sufficient to prove our claim and contains the notion of frequency-independent selection on haploids. When selection and recombination are weak but of the same order, there may be strong linkage disequilibrium; numerical calculations show that stable equilibria are highly unlikely. Using the example of a diallelic two-locus model, we then demonstrate that frequency-independent selection that fluctuates in time can maintain stable polymorphism if linkage disequilibrium changes its sign periodically. We put our findings in the context of results from the existing literature and point out those scenarios in which the possible role of frequency-independent selection in maintaining genetic variation remains unclear.\r\n"}],"publication_status":"published","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"ddc":["576"],"file":[{"creator":"system","date_created":"2018-12-12T10:17:12Z","file_id":"5264","access_level":"open_access","file_name":"IST-2018-974-v1+1_manuscript.pdf","file_size":494268,"date_updated":"2020-07-14T12:48:15Z","content_type":"application/pdf","relation":"main_file","checksum":"f7c32dabf52e6d9e709d9203761e39fd"}],"type":"journal_article","citation":{"ieee":"S. Novak and N. H. Barton, “When does frequency-independent selection maintain genetic variation?,” <i>Genetics</i>, vol. 207, no. 2. Genetics Society of America, pp. 653–668, 2017.","short":"S. Novak, N.H. Barton, Genetics 207 (2017) 653–668.","apa":"Novak, S., &#38; Barton, N. H. (2017). When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>","mla":"Novak, Sebastian, and Nicholas H. Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” <i>Genetics</i>, vol. 207, no. 2, Genetics Society of America, 2017, pp. 653–68, doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>.","ista":"Novak S, Barton NH. 2017. When does frequency-independent selection maintain genetic variation? Genetics. 207(2), 653–668.","chicago":"Novak, Sebastian, and Nicholas H Barton. “When Does Frequency-Independent Selection Maintain Genetic Variation?” <i>Genetics</i>. Genetics Society of America, 2017. <a href=\"https://doi.org/10.1534/genetics.117.300129\">https://doi.org/10.1534/genetics.117.300129</a>.","ama":"Novak S, Barton NH. When does frequency-independent selection maintain genetic variation? <i>Genetics</i>. 2017;207(2):653-668. doi:<a href=\"https://doi.org/10.1534/genetics.117.300129\">10.1534/genetics.117.300129</a>"},"article_processing_charge":"No","date_published":"2017-10-01T00:00:00Z","ec_funded":1,"title":"When does frequency-independent selection maintain genetic variation?","date_updated":"2023-09-26T15:49:15Z","month":"10","_id":"910","project":[{"name":"Speed of Adaptation in Population Genetics and Evolutionary Computation","call_identifier":"FP7","grant_number":"618091","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000412232600019"]},"date_created":"2018-12-11T11:49:09Z","publication":"Genetics","file_date_updated":"2020-07-14T12:48:15Z","pubrep_id":"974","page":"653 - 668","oa":1,"intvolume":"       207","issue":"2","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":207,"scopus_import":"1"},{"day":"01","publisher":"BMVA Press","arxiv":1,"oa_version":"Published Version","doi":"10.5244/c.31.85","author":[{"id":"3811D890-F248-11E8-B48F-1D18A9856A87","first_name":"Amélie","last_name":"Royer","orcid":"0000-0002-8407-0705","full_name":"Royer, Amélie"},{"last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander","first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph"}],"year":"2017","conference":{"end_date":"2017-09-07","location":"London, United Kingdom","start_date":"2017-09-04","name":"BMVC: British Machine Vision Conference"},"publication_identifier":{"eisbn":["190172560X"]},"department":[{"_id":"ChLa"}],"ddc":["000"],"citation":{"apa":"Royer, A., Kolesnikov, A., &#38; Lampert, C. (2017). Probabilistic image colorization (p. 85.1-85.12). Presented at the BMVC: British Machine Vision Conference, London, United Kingdom: BMVA Press. <a href=\"https://doi.org/10.5244/c.31.85\">https://doi.org/10.5244/c.31.85</a>","short":"A. Royer, A. Kolesnikov, C. Lampert, in:, BMVA Press, 2017, p. 85.1-85.12.","ieee":"A. Royer, A. Kolesnikov, and C. Lampert, “Probabilistic image colorization,” presented at the BMVC: British Machine Vision Conference, London, United Kingdom, 2017, p. 85.1-85.12.","ama":"Royer A, Kolesnikov A, Lampert C. Probabilistic image colorization. In: BMVA Press; 2017:85.1-85.12. doi:<a href=\"https://doi.org/10.5244/c.31.85\">10.5244/c.31.85</a>","chicago":"Royer, Amélie, Alexander Kolesnikov, and Christoph Lampert. “Probabilistic Image Colorization,” 85.1-85.12. BMVA Press, 2017. <a href=\"https://doi.org/10.5244/c.31.85\">https://doi.org/10.5244/c.31.85</a>.","ista":"Royer A, Kolesnikov A, Lampert C. 2017. Probabilistic image colorization. BMVC: British Machine Vision Conference, 85.1-85.12.","mla":"Royer, Amélie, et al. <i>Probabilistic Image Colorization</i>. BMVA Press, 2017, p. 85.1-85.12, doi:<a href=\"https://doi.org/10.5244/c.31.85\">10.5244/c.31.85</a>."},"type":"conference","file":[{"file_id":"8224","date_created":"2020-08-10T07:14:33Z","creator":"dernst","content_type":"application/pdf","date_updated":"2020-08-10T07:14:33Z","file_size":1625363,"relation":"main_file","success":1,"access_level":"open_access","file_name":"2017_BMVC_Royer.pdf"}],"quality_controlled":"1","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","abstract":[{"lang":"eng","text":"We develop a probabilistic technique for colorizing grayscale natural images. In light of the intrinsic uncertainty of this task, the proposed probabilistic framework has numerous desirable properties. In particular, our model is able to produce multiple plausible and vivid colorizations for a given grayscale image and is one of the first colorization models to provide a proper stochastic sampling scheme. Moreover, our training procedure is supported by a rigorous theoretical framework that does not require any ad hoc heuristics and allows for efficient modeling and learning of the joint pixel color distribution.We demonstrate strong quantitative and qualitative experimental results on the CIFAR-10 dataset and the challenging ILSVRC 2012 dataset."}],"publication_status":"published","publist_id":"6532","date_created":"2018-12-11T11:49:09Z","external_id":{"arxiv":["1705.04258"]},"project":[{"call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"_id":"911","page":"85.1-85.12","file_date_updated":"2020-08-10T07:14:33Z","ec_funded":1,"date_published":"2017-09-01T00:00:00Z","article_processing_charge":"No","month":"09","date_updated":"2023-10-16T10:04:02Z","title":"Probabilistic image colorization","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"8390"}]}},{"publist_id":"6531","abstract":[{"lang":"eng","text":"We consider a many-body system of fermionic atoms interacting via a local pair potential and subject to an external potential within the framework of Bardeen-Cooper-Schrieffer (BCS) theory. We measure the free energy of the whole sample with respect to the free energy of a reference state which allows us to define a BCS functional with boundary conditions at infinity. Our main result is a lower bound for this energy functional in terms of expressions that typically appear in Ginzburg-Landau functionals.\r\n"}],"publication_status":"published","status":"public","language":[{"iso":"eng"}],"quality_controlled":"1","citation":{"ieee":"A. Deuchert, “A lower bound for the BCS functional with boundary conditions at infinity,” <i> Journal of Mathematical Physics</i>, vol. 58, no. 8. AIP Publishing, 2017.","short":"A. Deuchert,  Journal of Mathematical Physics 58 (2017).","apa":"Deuchert, A. (2017). A lower bound for the BCS functional with boundary conditions at infinity. <i> Journal of Mathematical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4996580\">https://doi.org/10.1063/1.4996580</a>","ista":"Deuchert A. 2017. A lower bound for the BCS functional with boundary conditions at infinity.  Journal of Mathematical Physics. 58(8), 081901.","mla":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” <i> Journal of Mathematical Physics</i>, vol. 58, no. 8, 081901, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4996580\">10.1063/1.4996580</a>.","ama":"Deuchert A. A lower bound for the BCS functional with boundary conditions at infinity. <i> Journal of Mathematical Physics</i>. 2017;58(8). doi:<a href=\"https://doi.org/10.1063/1.4996580\">10.1063/1.4996580</a>","chicago":"Deuchert, Andreas. “A Lower Bound for the BCS Functional with Boundary Conditions at Infinity.” <i> Journal of Mathematical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4996580\">https://doi.org/10.1063/1.4996580</a>."},"type":"journal_article","publication_identifier":{"issn":["00222488"]},"department":[{"_id":"RoSe"}],"year":"2017","author":[{"id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","last_name":"Deuchert","full_name":"Deuchert, Andreas","orcid":"0000-0003-3146-6746"}],"isi":1,"doi":"10.1063/1.4996580","oa_version":"Submitted Version","publisher":"AIP Publishing","day":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1703.04616"}],"volume":58,"article_number":"081901","oa":1,"intvolume":"        58","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"8","scopus_import":"1","date_updated":"2024-02-28T13:07:56Z","title":"A lower bound for the BCS functional with boundary conditions at infinity","month":"08","article_processing_charge":"No","date_published":"2017-08-01T00:00:00Z","ec_funded":1,"publication":" Journal of Mathematical Physics","_id":"912","project":[{"call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems"}],"external_id":{"isi":["000409197200015"]},"date_created":"2018-12-11T11:49:10Z"},{"ddc":["576","592"],"file":[{"access_level":"open_access","file_name":"IST-2017-849-v1+1_2017_Grasse_Cremer_AntQueens.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z","file_size":530412,"checksum":"351ae5e7a37e6e7d9295cd41146c4190","relation":"main_file","date_created":"2018-12-12T10:08:24Z","creator":"system","file_id":"4684"}],"citation":{"mla":"Giehr, Julia, et al. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” <i>Royal Society Open Science</i>, vol. 4, no. 7, 170547, Royal Society, The, 2017, doi:<a href=\"https://doi.org/10.1098/rsos.170547\">10.1098/rsos.170547</a>.","ista":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. 2017. Ant queens increase their reproductive efforts after pathogen infection. Royal Society Open Science. 4(7), 170547.","chicago":"Giehr, Julia, Anna V Grasse, Sylvia Cremer, Jürgen Heinze, and Alexandra Schrempf. “Ant Queens Increase Their Reproductive Efforts after Pathogen Infection.” <i>Royal Society Open Science</i>. Royal Society, The, 2017. <a href=\"https://doi.org/10.1098/rsos.170547\">https://doi.org/10.1098/rsos.170547</a>.","ama":"Giehr J, Grasse AV, Cremer S, Heinze J, Schrempf A. Ant queens increase their reproductive efforts after pathogen infection. <i>Royal Society Open Science</i>. 2017;4(7). doi:<a href=\"https://doi.org/10.1098/rsos.170547\">10.1098/rsos.170547</a>","ieee":"J. Giehr, A. V. Grasse, S. Cremer, J. Heinze, and A. Schrempf, “Ant queens increase their reproductive efforts after pathogen infection,” <i>Royal Society Open Science</i>, vol. 4, no. 7. Royal Society, The, 2017.","short":"J. Giehr, A.V. Grasse, S. Cremer, J. Heinze, A. Schrempf, Royal Society Open Science 4 (2017).","apa":"Giehr, J., Grasse, A. V., Cremer, S., Heinze, J., &#38; Schrempf, A. (2017). Ant queens increase their reproductive efforts after pathogen infection. <i>Royal Society Open Science</i>. Royal Society, The. <a href=\"https://doi.org/10.1098/rsos.170547\">https://doi.org/10.1098/rsos.170547</a>"},"type":"journal_article","quality_controlled":"1","abstract":[{"lang":"eng","text":"Infections with potentially lethal pathogens may negatively affect an individual’s lifespan and decrease its reproductive value. The terminal investment hypothesis predicts that individuals faced with a reduced survival should invest more into reproduction instead of maintenance and growth. Several studies suggest that individuals are indeed able to estimate their body condition and to increase their reproductive effort with approaching death, while other studies gave ambiguous results. We investigate whether queens of a perennial social insect (ant) are able to boost their reproduction following infection with an obligate killing pathogen. Social insect queens are special with regard to reproduction and aging, as they outlive conspecific non-reproductive workers. Moreover, in the ant Cardiocondyla obscurior, fecundity increases with queen age. However, it remained unclear whether this reflects negative reproductive senescence or terminal investment in response to approaching death. Here, we test whether queens of C. obscurior react to infection with the entomopathogenic fungus Metarhizium brunneum by an increased egg-laying rate. We show that a fungal infection triggers a reinforced investment in reproduction in queens. This adjustment of the reproductive rate by ant queens is consistent with predictions of the terminal investment hypothesis and is reported for the first time in a social insect."}],"publication_status":"published","publist_id":"6527","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","publisher":"Royal Society, The","day":"05","doi":"10.1098/rsos.170547","oa_version":"Published Version","author":[{"first_name":"Julia","last_name":"Giehr","full_name":"Giehr, Julia"},{"last_name":"Grasse","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"},{"last_name":"Heinze","full_name":"Heinze, Jürgen","first_name":"Jürgen"},{"last_name":"Schrempf","full_name":"Schrempf, Alexandra","first_name":"Alexandra"}],"isi":1,"year":"2017","department":[{"_id":"SyCr"}],"publication_identifier":{"issn":["20545703"]},"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","article_number":"170547","issue":"7","acknowledgement":"We thank two anonymous reviewers for helpful suggestions on the manuscript.","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"         4","oa":1,"volume":4,"related_material":{"record":[{"id":"9853","status":"public","relation":"research_data"}]},"_id":"914","date_created":"2018-12-11T11:49:10Z","external_id":{"isi":["000406670000025"]},"file_date_updated":"2020-07-14T12:48:15Z","pubrep_id":"849","publication":"Royal Society Open Science","date_published":"2017-07-05T00:00:00Z","article_processing_charge":"No","date_updated":"2023-09-26T15:45:47Z","title":"Ant queens increase their reproductive efforts after pathogen infection","month":"07"},{"scopus_import":"1","volume":2017,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"      2017","oa":1,"file_date_updated":"2020-07-14T12:48:15Z","page":"4990-4999","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160"}],"_id":"915","date_created":"2018-12-11T11:49:11Z","external_id":{"isi":["000418371405009"]},"date_updated":"2023-09-26T15:43:27Z","title":"A message passing algorithm for the minimum cost multicut problem","month":"07","date_published":"2017-07-01T00:00:00Z","article_processing_charge":"No","ec_funded":1,"file":[{"file_id":"5849","date_created":"2019-01-18T12:52:46Z","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:48:15Z","file_size":883264,"relation":"main_file","checksum":"7e51dacefa693574581a32da3eff63dc","access_level":"open_access","file_name":"Swoboda_A_Message_Passing_CVPR_2017_paper.pdf"}],"type":"conference","citation":{"ama":"Swoboda P, Andres B. A message passing algorithm for the minimum cost multicut problem. In: Vol 2017. IEEE; 2017:4990-4999. doi:<a href=\"https://doi.org/10.1109/CVPR.2017.530\">10.1109/CVPR.2017.530</a>","chicago":"Swoboda, Paul, and Bjoern Andres. “A Message Passing Algorithm for the Minimum Cost Multicut Problem,” 2017:4990–99. IEEE, 2017. <a href=\"https://doi.org/10.1109/CVPR.2017.530\">https://doi.org/10.1109/CVPR.2017.530</a>.","mla":"Swoboda, Paul, and Bjoern Andres. <i>A Message Passing Algorithm for the Minimum Cost Multicut Problem</i>. Vol. 2017, IEEE, 2017, pp. 4990–99, doi:<a href=\"https://doi.org/10.1109/CVPR.2017.530\">10.1109/CVPR.2017.530</a>.","ista":"Swoboda P, Andres B. 2017. A message passing algorithm for the minimum cost multicut problem. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4990–4999.","apa":"Swoboda, P., &#38; Andres, B. (2017). A message passing algorithm for the minimum cost multicut problem (Vol. 2017, pp. 4990–4999). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2017.530\">https://doi.org/10.1109/CVPR.2017.530</a>","short":"P. Swoboda, B. Andres, in:, IEEE, 2017, pp. 4990–4999.","ieee":"P. Swoboda and B. Andres, “A message passing algorithm for the minimum cost multicut problem,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4990–4999."},"ddc":["000"],"abstract":[{"lang":"eng","text":"We propose a dual decomposition and linear program relaxation of the NP-hard minimum cost multicut problem. Unlike other polyhedral relaxations of the multicut polytope, it is amenable to efficient optimization by message passing. Like other polyhedral relaxations, it can be tightened efficiently by cutting planes.  We define an algorithm that alternates between message passing and efficient separation of cycle- and odd-wheel inequalities. This algorithm is more efficient than state-of-the-art algorithms based on linear programming, including algorithms written in the framework of leading commercial software, as we show in experiments with large instances of the problem from applications in computer vision, biomedical image analysis and data mining."}],"publication_status":"published","publist_id":"6526","language":[{"iso":"eng"}],"has_accepted_license":"1","status":"public","quality_controlled":"1","doi":"10.1109/CVPR.2017.530","oa_version":"Submitted Version","publisher":"IEEE","day":"01","publication_identifier":{"isbn":["978-153860457-1"]},"department":[{"_id":"VlKo"}],"isi":1,"author":[{"first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"first_name":"Bjoern","last_name":"Andres","full_name":"Andres, Bjoern"}],"year":"2017","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","start_date":"2017-07-21","location":"Honolulu, HA, United States","end_date":"2017-07-26"}},{"month":"01","date_updated":"2023-09-26T15:41:40Z","title":"A study of lagrangean decompositions and dual ascent solvers for graph matching","ec_funded":1,"article_processing_charge":"No","date_published":"2017-01-01T00:00:00Z","page":"7062-7071","file_date_updated":"2020-07-14T12:48:15Z","external_id":{"isi":["000418371407018"]},"date_created":"2018-12-11T11:49:11Z","project":[{"call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"_id":"916","volume":2017,"intvolume":"      2017","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","department":[{"_id":"VlKo"}],"publication_identifier":{"isbn":["978-153860457-1"]},"year":"2017","conference":{"end_date":"2017-07-26","location":"Honolulu, HA, United States","start_date":"2017-07-21","name":"CVPR: Computer Vision and Pattern Recognition"},"isi":1,"author":[{"first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"full_name":"Rother, Carsten","last_name":"Rother","first_name":"Carsten"},{"first_name":"Carsten","full_name":"Abu Alhaija, Carsten","last_name":"Abu Alhaija"},{"first_name":"Dagmar","last_name":"Kainmueller","full_name":"Kainmueller, Dagmar"},{"last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan","first_name":"Bogdan"}],"oa_version":"Submitted Version","doi":"10.1109/CVPR.2017.747","day":"01","publisher":"IEEE","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"6525","abstract":[{"lang":"eng","text":"We study the quadratic assignment problem, in computer vision also known as graph matching. Two leading solvers for this problem optimize the Lagrange decomposition duals with sub-gradient and dual ascent (also known as message passing) updates. We explore this direction further and propose several additional Lagrangean relaxations of the graph matching problem along with corresponding algorithms, which are all based on a common dual ascent framework. Our extensive empirical evaluation gives several theoretical insights and suggests a new state-of-the-art anytime solver for the considered problem. Our improvement over state-of-the-art is particularly visible on a new dataset with large-scale sparse problem instances containing more than 500 graph nodes each."}],"publication_status":"published","quality_controlled":"1","type":"conference","citation":{"chicago":"Swoboda, Paul, Carsten Rother, Carsten Abu Alhaija, Dagmar Kainmueller, and Bogdan Savchynskyy. “A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching,” 2017:7062–71. IEEE, 2017. <a href=\"https://doi.org/10.1109/CVPR.2017.747\">https://doi.org/10.1109/CVPR.2017.747</a>.","ama":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. A study of lagrangean decompositions and dual ascent solvers for graph matching. In: Vol 2017. IEEE; 2017:7062-7071. doi:<a href=\"https://doi.org/10.1109/CVPR.2017.747\">10.1109/CVPR.2017.747</a>","mla":"Swoboda, Paul, et al. <i>A Study of Lagrangean Decompositions and Dual Ascent Solvers for Graph Matching</i>. Vol. 2017, IEEE, 2017, pp. 7062–71, doi:<a href=\"https://doi.org/10.1109/CVPR.2017.747\">10.1109/CVPR.2017.747</a>.","ista":"Swoboda P, Rother C, Abu Alhaija C, Kainmueller D, Savchynskyy B. 2017. A study of lagrangean decompositions and dual ascent solvers for graph matching. CVPR: Computer Vision and Pattern Recognition vol. 2017, 7062–7071.","short":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, B. Savchynskyy, in:, IEEE, 2017, pp. 7062–7071.","apa":"Swoboda, P., Rother, C., Abu Alhaija, C., Kainmueller, D., &#38; Savchynskyy, B. (2017). A study of lagrangean decompositions and dual ascent solvers for graph matching (Vol. 2017, pp. 7062–7071). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2017.747\">https://doi.org/10.1109/CVPR.2017.747</a>","ieee":"P. Swoboda, C. Rother, C. Abu Alhaija, D. Kainmueller, and B. Savchynskyy, “A study of lagrangean decompositions and dual ascent solvers for graph matching,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 7062–7071."},"file":[{"file_id":"5848","date_created":"2019-01-18T12:49:38Z","creator":"dernst","checksum":"e38a2740daad1ea178465843b5072906","relation":"main_file","date_updated":"2020-07-14T12:48:15Z","content_type":"application/pdf","file_size":944332,"file_name":"2017_CVPR_Swoboda2.pdf","access_level":"open_access"}],"ddc":["000"]},{"year":"2017","conference":{"name":"CVPR: Computer Vision and Pattern Recognition","end_date":"2017-07-26","location":"Honolulu, HA, United States","start_date":"2017-07-21"},"author":[{"first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","full_name":"Swoboda, Paul","last_name":"Swoboda"},{"full_name":"Kuske, Jan","last_name":"Kuske","first_name":"Jan"},{"first_name":"Bogdan","full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy"}],"isi":1,"publication_identifier":{"isbn":["978-153860457-1"]},"department":[{"_id":"VlKo"}],"publisher":"IEEE","day":"01","doi":"10.1109/CVPR.2017.526","oa_version":"Submitted Version","quality_controlled":"1","publist_id":"6524","publication_status":"published","abstract":[{"text":"We  propose  a  general  dual  ascent  framework  for  Lagrangean decomposition of combinatorial problems.  Although methods of this type have shown their efficiency for a number of problems, so far there was no general algorithm applicable to multiple problem types. In this work, we propose such a general algorithm. It depends on several parameters, which can be used to optimize its performance in each particular setting. We demonstrate efficacy of our method on graph matching and multicut problems, where it outperforms state-of-the-art solvers including those based on subgradient optimization and off-the-shelf linear programming solvers.","lang":"eng"}],"status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"ddc":["000"],"file":[{"access_level":"open_access","file_name":"2017_CVPR_Swoboda.pdf","file_size":898652,"date_updated":"2020-07-14T12:48:15Z","content_type":"application/pdf","relation":"main_file","checksum":"72fd291046bd8e5717961bd68f6b6f03","creator":"dernst","date_created":"2019-01-18T12:45:55Z","file_id":"5847"}],"type":"conference","citation":{"ista":"Swoboda P, Kuske J, Savchynskyy B. 2017. A dual ascent framework for Lagrangean decomposition of combinatorial problems. CVPR: Computer Vision and Pattern Recognition vol. 2017, 4950–4960.","mla":"Swoboda, Paul, et al. <i>A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems</i>. Vol. 2017, IEEE, 2017, pp. 4950–60, doi:<a href=\"https://doi.org/10.1109/CVPR.2017.526\">10.1109/CVPR.2017.526</a>.","ama":"Swoboda P, Kuske J, Savchynskyy B. A dual ascent framework for Lagrangean decomposition of combinatorial problems. In: Vol 2017. IEEE; 2017:4950-4960. doi:<a href=\"https://doi.org/10.1109/CVPR.2017.526\">10.1109/CVPR.2017.526</a>","chicago":"Swoboda, Paul, Jan Kuske, and Bogdan Savchynskyy. “A Dual Ascent Framework for Lagrangean Decomposition of Combinatorial Problems,” 2017:4950–60. IEEE, 2017. <a href=\"https://doi.org/10.1109/CVPR.2017.526\">https://doi.org/10.1109/CVPR.2017.526</a>.","ieee":"P. Swoboda, J. Kuske, and B. Savchynskyy, “A dual ascent framework for Lagrangean decomposition of combinatorial problems,” presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States, 2017, vol. 2017, pp. 4950–4960.","short":"P. Swoboda, J. Kuske, B. Savchynskyy, in:, IEEE, 2017, pp. 4950–4960.","apa":"Swoboda, P., Kuske, J., &#38; Savchynskyy, B. (2017). A dual ascent framework for Lagrangean decomposition of combinatorial problems (Vol. 2017, pp. 4950–4960). Presented at the CVPR: Computer Vision and Pattern Recognition, Honolulu, HA, United States: IEEE. <a href=\"https://doi.org/10.1109/CVPR.2017.526\">https://doi.org/10.1109/CVPR.2017.526</a>"},"article_processing_charge":"No","date_published":"2017-07-01T00:00:00Z","ec_funded":1,"title":"A dual ascent framework for Lagrangean decomposition of combinatorial problems","date_updated":"2023-09-26T15:41:11Z","month":"07","project":[{"name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"_id":"917","external_id":{"isi":["000418371405005"]},"date_created":"2018-12-11T11:49:11Z","file_date_updated":"2020-07-14T12:48:15Z","page":"4950-4960","intvolume":"      2017","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","volume":2017,"scopus_import":"1"},{"month":"06","date_updated":"2023-09-07T12:06:09Z","title":"Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ","article_processing_charge":"No","date_published":"2017-06-02T00:00:00Z","page":"117","supervisor":[{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří"}],"pubrep_id":"842","file_date_updated":"2020-07-14T12:48:15Z","date_created":"2018-12-11T11:49:18Z","_id":"938","related_material":{"record":[{"id":"1591","relation":"part_of_dissertation","status":"public"}]},"alternative_title":["ISTA Thesis"],"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_identifier":{"issn":["2663-337X"]},"department":[{"_id":"JiFr"}],"degree_awarded":"PhD","year":"2017","author":[{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski","first_name":"Maciek","id":"45F536D2-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","doi":"10.15479/AT:ISTA:th_842","day":"02","publisher":"Institute of Science and Technology Austria","status":"public","has_accepted_license":"1","language":[{"iso":"eng"}],"publist_id":"6483","publication_status":"published","abstract":[{"text":"The thesis encompasses several topics of plant cell biology which were studied in the model plant Arabidopsis thaliana. Chapter 1 concerns the plant hormone auxin and its polar transport through cells and tissues. The highly controlled, directional transport of auxin is facilitated by plasma membrane-localized transporters. Transporters from the PIN family direct auxin transport due to their polarized localizations at cell membranes. Substantial effort has been put into research on cellular trafficking of PIN proteins, which is thought to underlie their polar distribution. I participated in a forward genetic screen aimed at identifying novel regulators of PIN polarity. The screen yielded several genes which may be involved in PIN polarity regulation or participate in polar auxin transport by other means. Chapter 2 focuses on the endomembrane system, with particular attention to clathrin-mediated endocytosis. The project started with identification of several proteins that interact with clathrin light chains. Among them, I focused on two putative homologues of auxilin, which in non-plant systems is an endocytotic factor known for uncoating clathrin-coated vesicles in the final step of endocytosis. The body of my work consisted of an in-depth characterization of transgenic A. thaliana lines overexpressing these putative auxilins in an inducible manner. Overexpression of these proteins leads to an inhibition of endocytosis, as documented by imaging of cargoes and clathrin-related endocytic machinery. An extension of this work is an investigation into a concept of homeostatic regulation acting between distinct transport processes in the endomembrane system. With auxilin overexpressing lines, where endocytosis is blocked specifically, I made observations on the mutual relationship between two opposite trafficking processes of secretion and endocytosis. In Chapter 3, I analyze cortical microtubule arrays and their relationship to auxin signaling and polarized growth in elongating cells. In plants, microtubules are organized into arrays just below the plasma membrane, and it is thought that their function is to guide membrane-docked cellulose synthase complexes. These, in turn, influence cell wall structure and cell shape by directed deposition of cellulose fibres. In elongating cells, cortical microtubule arrays are able to reorient in relation to long cell axis, and these reorientations have been linked to cell growth and to signaling of growth-regulating factors such as auxin or light. In this chapter, I am addressing the causal relationship between microtubule array reorientation, growth, and auxin signaling. I arrive at a model where array reorientation is not guided by auxin directly, but instead is only controlled by growth, which, in turn, is regulated by auxin.","lang":"eng"}],"type":"dissertation","citation":{"ieee":"M. Adamowski, “Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana ,” Institute of Science and Technology Austria, 2017.","short":"M. Adamowski, Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana , Institute of Science and Technology Austria, 2017.","apa":"Adamowski, M. (2017). <i>Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">https://doi.org/10.15479/AT:ISTA:th_842</a>","mla":"Adamowski, Maciek. <i>Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana </i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">10.15479/AT:ISTA:th_842</a>.","ista":"Adamowski M. 2017. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . Institute of Science and Technology Austria.","ama":"Adamowski M. Investigations into cell polarity and trafficking in the plant model Arabidopsis thaliana . 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">10.15479/AT:ISTA:th_842</a>","chicago":"Adamowski, Maciek. “Investigations into Cell Polarity and Trafficking in the Plant Model Arabidopsis Thaliana .” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_842\">https://doi.org/10.15479/AT:ISTA:th_842</a>."},"file":[{"file_id":"6215","creator":"dernst","date_created":"2019-04-05T09:03:20Z","checksum":"193425764d9aaaed3ac57062a867b315","relation":"source_file","file_size":46903863,"date_updated":"2020-07-14T12:48:15Z","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_name":"2017_Adamowski-Thesis_Source.docx","access_level":"closed"},{"creator":"dernst","date_created":"2019-04-05T09:03:19Z","file_id":"6216","access_level":"open_access","file_name":"2017_Adamowski-Thesis.pdf","date_updated":"2020-07-14T12:48:15Z","content_type":"application/pdf","file_size":8698888,"relation":"main_file","checksum":"df5ab01be81f821e1b958596a1ec8d21"}],"ddc":["581","583","580"]},{"publisher":"American Physical Society","day":"18","doi":"10.1103/PhysRevLett.119.033905","oa_version":"Submitted Version","isi":1,"author":[{"last_name":"Midya","full_name":"Midya, Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","first_name":"Bikashkali"},{"first_name":"Vladimir","full_name":"Konotop, Vladimir","last_name":"Konotop"}],"year":"2017","publication_identifier":{"issn":["00319007"]},"department":[{"_id":"MiLe"}],"type":"journal_article","citation":{"chicago":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” <i>Physical Review Letters</i>. American Physical Society, 2017. <a href=\"https://doi.org/10.1103/PhysRevLett.119.033905\">https://doi.org/10.1103/PhysRevLett.119.033905</a>.","ama":"Midya B, Konotop V. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. <i>Physical Review Letters</i>. 2017;119(3). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.119.033905\">10.1103/PhysRevLett.119.033905</a>","mla":"Midya, Bikashkali, and Vladimir Konotop. “Waveguides with Absorbing Boundaries: Nonlinearity Controlled by an Exceptional Point and Solitons.” <i>Physical Review Letters</i>, vol. 119, no. 3, 033905, American Physical Society, 2017, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.119.033905\">10.1103/PhysRevLett.119.033905</a>.","ista":"Midya B, Konotop V. 2017. Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. Physical Review Letters. 119(3), 033905.","apa":"Midya, B., &#38; Konotop, V. (2017). Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.119.033905\">https://doi.org/10.1103/PhysRevLett.119.033905</a>","short":"B. Midya, V. Konotop, Physical Review Letters 119 (2017).","ieee":"B. Midya and V. Konotop, “Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons,” <i>Physical Review Letters</i>, vol. 119, no. 3. American Physical Society, 2017."},"quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"We reveal the existence of continuous families of guided single-mode solitons in planar waveguides with weakly nonlinear active core and absorbing boundaries. Stable propagation of TE and TM-polarized solitons is accompanied by attenuation of all other modes, i.e., the waveguide features properties of conservative and dissipative systems. If the linear spectrum of the waveguide possesses exceptional points, which occurs in the case of TM polarization, an originally focusing (defocusing) material nonlinearity may become effectively defocusing (focusing). This occurs due to the geometric phase of the carried eigenmode when the surface impedance encircles the exceptional point. In its turn, the change of the effective nonlinearity ensures the existence of dark (bright) solitons in spite of focusing (defocusing) Kerr nonlinearity of the core. The existence of an exceptional point can also result in anomalous enhancement of the effective nonlinearity. In terms of practical applications, the nonlinearity of the reported waveguide can be manipulated by controlling the properties of the absorbing cladding."}],"publist_id":"6481","language":[{"iso":"eng"}],"status":"public","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"_id":"939","date_created":"2018-12-11T11:49:18Z","external_id":{"isi":["000405718200012"]},"publication":"Physical Review Letters","date_published":"2017-07-18T00:00:00Z","article_processing_charge":"No","ec_funded":1,"title":"Waveguides with absorbing boundaries: Nonlinearity controlled by an exceptional point and solitons","date_updated":"2023-09-26T15:39:46Z","month":"07","scopus_import":"1","article_number":"033905","issue":"3","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"intvolume":"       119","volume":119,"main_file_link":[{"url":"https://arxiv.org/abs/1706.04085 ","open_access":"1"}]},{"month":"06","title":"Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses","date_updated":"2023-02-23T12:54:57Z","article_processing_charge":"Yes (in subscription journal)","date_published":"2017-06-27T00:00:00Z","page":"E5246 - E5255","publication":"PNAS","file_date_updated":"2020-07-14T12:47:44Z","external_id":{"pmid":["28607047"]},"date_created":"2018-12-11T11:47:57Z","_id":"693","volume":114,"intvolume":"       114","oa":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"26","scopus_import":1,"department":[{"_id":"EM-Fac"},{"_id":"RySh"}],"publication_identifier":{"issn":["00278424"]},"year":"2017","author":[{"first_name":"Takafumi","last_name":"Miki","full_name":"Miki, Takafumi"},{"last_name":"Kaufmann","orcid":"0000-0001-9735-5315","full_name":"Kaufmann, Walter","first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gerardo","last_name":"Malagon","full_name":"Malagon, Gerardo"},{"first_name":"Laura","full_name":"Gomez, Laura","last_name":"Gomez"},{"full_name":"Tabuchi, Katsuhiko","last_name":"Tabuchi","first_name":"Katsuhiko"},{"full_name":"Watanabe, Masahiko","last_name":"Watanabe","first_name":"Masahiko"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Marty, Alain","last_name":"Marty","first_name":"Alain"}],"oa_version":"Published Version","doi":"10.1073/pnas.1704470114","day":"27","publisher":"National Academy of Sciences","status":"public","has_accepted_license":"1","pmid":1,"language":[{"iso":"eng"}],"publist_id":"7013","publication_status":"published","abstract":[{"text":"Many central synapses contain a single presynaptic active zone and a single postsynaptic density. Vesicular release statistics at such “simple synapses” indicate that they contain a small complement of docking sites where vesicles repetitively dock and fuse. In this work, we investigate functional and morphological aspects of docking sites at simple synapses made between cerebellar parallel fibers and molecular layer interneurons. Using immunogold labeling of SDS-treated freeze-fracture replicas, we find that Cav2.1 channels form several clusters per active zone with about nine channels per cluster. The mean value and range of intersynaptic variation are similar for Cav2.1 cluster numbers and for functional estimates of docking-site numbers obtained from the maximum numbers of released vesicles per action potential. Both numbers grow in relation with synaptic size and decrease by a similar extent with age between 2 wk and 4 wk postnatal. Thus, the mean docking-site numbers were 3.15 at 2 wk (range: 1–10) and 2.03 at 4 wk (range: 1–4), whereas the mean numbers of Cav2.1 clusters were 2.84 at 2 wk (range: 1–8) and 2.37 at 4 wk (range: 1–5). These changes were accompanied by decreases of miniature current amplitude (from 93 pA to 56 pA), active-zone surface area (from 0.0427 μm2 to 0.0234 μm2), and initial success rate (from 0.609 to 0.353), indicating a tightening of synaptic transmission with development. Altogether, these results suggest a close correspondence between the number of functionally defined vesicular docking sites and that of clusters of voltage-gated calcium channels. ","lang":"eng"}],"quality_controlled":"1","type":"journal_article","citation":{"mla":"Miki, Takafumi, et al. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>, vol. 114, no. 26, National Academy of Sciences, 2017, pp. E5246–55, doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>.","ista":"Miki T, Kaufmann W, Malagon G, Gomez L, Tabuchi K, Watanabe M, Shigemoto R, Marty A. 2017. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. PNAS. 114(26), E5246–E5255.","chicago":"Miki, Takafumi, Walter Kaufmann, Gerardo Malagon, Laura Gomez, Katsuhiko Tabuchi, Masahiko Watanabe, Ryuichi Shigemoto, and Alain Marty. “Numbers of Presynaptic Ca2+ Channel Clusters Match Those of Functionally Defined Vesicular Docking Sites in Single Central Synapses.” <i>PNAS</i>. National Academy of Sciences, 2017. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>.","ama":"Miki T, Kaufmann W, Malagon G, et al. Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. 2017;114(26):E5246-E5255. doi:<a href=\"https://doi.org/10.1073/pnas.1704470114\">10.1073/pnas.1704470114</a>","ieee":"T. Miki <i>et al.</i>, “Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses,” <i>PNAS</i>, vol. 114, no. 26. National Academy of Sciences, pp. E5246–E5255, 2017.","apa":"Miki, T., Kaufmann, W., Malagon, G., Gomez, L., Tabuchi, K., Watanabe, M., … Marty, A. (2017). Numbers of presynaptic Ca2+ channel clusters match those of functionally defined vesicular docking sites in single central synapses. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1704470114\">https://doi.org/10.1073/pnas.1704470114</a>","short":"T. Miki, W. Kaufmann, G. Malagon, L. Gomez, K. Tabuchi, M. Watanabe, R. Shigemoto, A. Marty, PNAS 114 (2017) E5246–E5255."},"file":[{"file_name":"2017_PNAS_Miki.pdf","access_level":"open_access","checksum":"2ab75d554f3df4a34d20fa8040589b7e","relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:47:44Z","file_size":2721544,"date_created":"2020-01-03T13:27:29Z","creator":"kschuh","file_id":"7223"}],"ddc":["570"]},{"scopus_import":1,"volume":130,"intvolume":"       130","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"13","page":"2172 - 2184","publication":"Journal of Cell Science","file_date_updated":"2020-07-14T12:47:45Z","external_id":{"pmid":["28515231"]},"date_created":"2018-12-11T11:47:58Z","_id":"694","month":"07","title":"A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity","date_updated":"2021-01-12T08:09:41Z","date_published":"2017-07-01T00:00:00Z","citation":{"ama":"Veß A, Blache U, Leitner L, et al. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. 2017;130(13):2172-2184. doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>","chicago":"Veß, Astrid, Ulrich Blache, Laura Leitner, Angela Kurz, Anja Ehrenpfordt, Michael K Sixt, and Guido Posern. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>. Company of Biologists, 2017. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>.","mla":"Veß, Astrid, et al. “A Dual Phenotype of MDA MB 468 Cancer Cells Reveals Mutual Regulation of Tensin3 and Adhesion Plasticity.” <i>Journal of Cell Science</i>, vol. 130, no. 13, Company of Biologists, 2017, pp. 2172–84, doi:<a href=\"https://doi.org/10.1242/jcs.200899\">10.1242/jcs.200899</a>.","ista":"Veß A, Blache U, Leitner L, Kurz A, Ehrenpfordt A, Sixt MK, Posern G. 2017. A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. Journal of Cell Science. 130(13), 2172–2184.","short":"A. Veß, U. Blache, L. Leitner, A. Kurz, A. Ehrenpfordt, M.K. Sixt, G. Posern, Journal of Cell Science 130 (2017) 2172–2184.","apa":"Veß, A., Blache, U., Leitner, L., Kurz, A., Ehrenpfordt, A., Sixt, M. K., &#38; Posern, G. (2017). A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity. <i>Journal of Cell Science</i>. Company of Biologists. <a href=\"https://doi.org/10.1242/jcs.200899\">https://doi.org/10.1242/jcs.200899</a>","ieee":"A. Veß <i>et al.</i>, “A dual phenotype of MDA MB 468 cancer cells reveals mutual regulation of tensin3 and adhesion plasticity,” <i>Journal of Cell Science</i>, vol. 130, no. 13. Company of Biologists, pp. 2172–2184, 2017."},"type":"journal_article","file":[{"date_created":"2019-10-24T09:43:56Z","creator":"dernst","file_id":"6966","access_level":"open_access","file_name":"2017_CellScience_Vess.pdf","file_size":10847596,"content_type":"application/pdf","date_updated":"2020-07-14T12:47:45Z","checksum":"42c81a0a4fc3128883b391c3af3f74bc","relation":"main_file"}],"article_type":"original","ddc":["570"],"has_accepted_license":"1","status":"public","pmid":1,"language":[{"iso":"eng"}],"publist_id":"7008","abstract":[{"lang":"eng","text":"A change regarding the extent of adhesion - hereafter referred to as adhesion plasticity - between adhesive and less-adhesive states of mammalian cells is important for their behavior. To investigate adhesion plasticity, we have selected a stable isogenic subpopulation of human MDA-MB-468 breast carcinoma cells growing in suspension. These suspension cells are unable to re-adhere to various matrices or to contract three-dimensional collagen lattices. By using transcriptome analysis, we identified the focal adhesion protein tensin3 (Tns3) as a determinant of adhesion plasticity. Tns3 is strongly reduced at mRNA and protein levels in suspension cells. Furthermore, by transiently challenging breast cancer cells to grow under non-adherent conditions markedly reduces Tns3 protein expression, which is regained upon re-adhesion. Stable knockdown of Tns3 in parental MDA-MB-468 cells results in defective adhesion, spreading and migration. Tns3-knockdown cells display impaired structure and dynamics of focal adhesion complexes as determined by immunostaining. Restoration of Tns3 protein expression in suspension cells partially rescues adhesion and focal contact composition. Our work identifies Tns3 as a crucial focal adhesion component regulated by, and functionally contributing to, the switch between adhesive and non-adhesive states in MDA-MB-468 cancer cells."}],"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","doi":"10.1242/jcs.200899","day":"01","publisher":"Company of Biologists","department":[{"_id":"MiSi"}],"publication_identifier":{"issn":["00219533"]},"year":"2017","author":[{"last_name":"Veß","full_name":"Veß, Astrid","first_name":"Astrid"},{"first_name":"Ulrich","full_name":"Blache, Ulrich","last_name":"Blache"},{"last_name":"Leitner","full_name":"Leitner, Laura","first_name":"Laura"},{"full_name":"Kurz, Angela","last_name":"Kurz","first_name":"Angela"},{"last_name":"Ehrenpfordt","full_name":"Ehrenpfordt, Anja","first_name":"Anja"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"},{"first_name":"Guido","last_name":"Posern","full_name":"Posern, Guido"}]},{"date_updated":"2024-03-25T23:30:14Z","title":"Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes","month":"07","date_published":"2017-07-18T00:00:00Z","ec_funded":1,"file_date_updated":"2020-07-14T12:47:46Z","pubrep_id":"894","publication":"PLoS Computational Biology","project":[{"call_identifier":"FP7","_id":"25B1EC9E-B435-11E9-9278-68D0E5697425","grant_number":"618091","name":"Speed of Adaptation in Population Genetics and Evolutionary Computation"}],"_id":"696","date_created":"2018-12-11T11:47:58Z","volume":13,"related_material":{"record":[{"id":"9849","relation":"research_data","status":"public"},{"relation":"research_data","status":"public","id":"9850"},{"status":"public","relation":"research_data","id":"9851"},{"status":"public","relation":"research_data","id":"9852"},{"relation":"dissertation_contains","status":"public","id":"6263"}]},"article_number":"e1005609","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"7","oa":1,"intvolume":"        13","scopus_import":1,"publication_identifier":{"issn":["1553734X"]},"department":[{"_id":"ToBo"},{"_id":"NiBa"},{"_id":"CaGu"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"last_name":"Lukacisinova","full_name":"Lukacisinova, Marta","orcid":"0000-0002-2519-8004","id":"4342E402-F248-11E8-B48F-1D18A9856A87","first_name":"Marta"},{"full_name":"Novak, Sebastian","orcid":"0000-0002-2519-824X","last_name":"Novak","first_name":"Sebastian","id":"461468AE-F248-11E8-B48F-1D18A9856A87"},{"id":"2C5658E6-F248-11E8-B48F-1D18A9856A87","first_name":"Tiago","last_name":"Paixao","full_name":"Paixao, Tiago","orcid":"0000-0003-2361-3953"}],"year":"2017","doi":"10.1371/journal.pcbi.1005609","oa_version":"Published Version","publisher":"Public Library of Science","day":"18","publication_status":"published","abstract":[{"lang":"eng","text":"Mutator strains are expected to evolve when the availability and effect of beneficial mutations are high enough to counteract the disadvantage from deleterious mutations that will inevitably accumulate. As the population becomes more adapted to its environment, both availability and effect of beneficial mutations necessarily decrease and mutation rates are predicted to decrease. It has been shown that certain molecular mechanisms can lead to increased mutation rates when the organism finds itself in a stressful environment. While this may be a correlated response to other functions, it could also be an adaptive mechanism, raising mutation rates only when it is most advantageous. Here, we use a mathematical model to investigate the plausibility of the adaptive hypothesis. We show that such a mechanism can be mantained if the population is subjected to diverse stresses. By simulating various antibiotic treatment schemes, we find that combination treatments can reduce the effectiveness of second-order selection on stress-induced mutagenesis. We discuss the implications of our results to strategies of antibiotic therapy."}],"publist_id":"7004","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","quality_controlled":"1","file":[{"file_id":"5117","creator":"system","date_created":"2018-12-12T10:15:01Z","relation":"main_file","checksum":"9143c290fa6458ed2563bff4b295554a","content_type":"application/pdf","date_updated":"2020-07-14T12:47:46Z","file_size":3775716,"file_name":"IST-2017-894-v1+1_journal.pcbi.1005609.pdf","access_level":"open_access"}],"type":"journal_article","citation":{"short":"M. Lukacisinova, S. Novak, T. Paixao, PLoS Computational Biology 13 (2017).","apa":"Lukacisinova, M., Novak, S., &#38; Paixao, T. (2017). Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>","ieee":"M. Lukacisinova, S. Novak, and T. Paixao, “Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes,” <i>PLoS Computational Biology</i>, vol. 13, no. 7. Public Library of Science, 2017.","chicago":"Lukacisinova, Marta, Sebastian Novak, and Tiago Paixao. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>. Public Library of Science, 2017. <a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">https://doi.org/10.1371/journal.pcbi.1005609</a>.","ama":"Lukacisinova M, Novak S, Paixao T. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. <i>PLoS Computational Biology</i>. 2017;13(7). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>","mla":"Lukacisinova, Marta, et al. “Stress Induced Mutagenesis: Stress Diversity Facilitates the Persistence of Mutator Genes.” <i>PLoS Computational Biology</i>, vol. 13, no. 7, e1005609, Public Library of Science, 2017, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1005609\">10.1371/journal.pcbi.1005609</a>.","ista":"Lukacisinova M, Novak S, Paixao T. 2017. Stress induced mutagenesis: Stress diversity facilitates the persistence of mutator genes. PLoS Computational Biology. 13(7), e1005609."},"ddc":["576"],"article_type":"original"},{"quality_controlled":"1","has_accepted_license":"1","status":"public","language":[{"iso":"eng"}],"publist_id":"7003","publication_status":"published","abstract":[{"text":"De, Trevisan and Tulsiani [CRYPTO 2010] show that every distribution over n-bit strings which has constant statistical distance to uniform (e.g., the output of a pseudorandom generator mapping n-1 to n bit strings), can be distinguished from the uniform distribution with advantage epsilon by a circuit of size O( 2^n epsilon^2). We generalize this result, showing that a distribution which has less than k bits of min-entropy, can be distinguished from any distribution with k bits of delta-smooth min-entropy with advantage epsilon by a circuit of size O(2^k epsilon^2/delta^2). As a special case, this implies that any distribution with support at most 2^k (e.g., the output of a pseudoentropy generator mapping k to n bit strings) can be distinguished from any given distribution with min-entropy k+1 with advantage epsilon by a circuit of size O(2^k epsilon^2). Our result thus shows that pseudoentropy distributions face basically the same non-uniform attacks as pseudorandom distributions. ","lang":"eng"}],"ddc":["005"],"citation":{"ieee":"K. Z. Pietrzak and M. Skórski, “Non uniform attacks against pseudoentropy,” presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland, 2017, vol. 80.","short":"K.Z. Pietrzak, M. Skórski, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","apa":"Pietrzak, K. Z., &#38; Skórski, M. (2017). Non uniform attacks against pseudoentropy (Vol. 80). Presented at the ICALP: International Colloquium on Automata, Languages, and Programming, Warsaw, Poland: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>","mla":"Pietrzak, Krzysztof Z., and Maciej Skórski. <i>Non Uniform Attacks against Pseudoentropy</i>. Vol. 80, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>.","ista":"Pietrzak KZ, Skórski M. 2017. Non uniform attacks against pseudoentropy. ICALP: International Colloquium on Automata, Languages, and Programming, LIPIcs, vol. 80, 39.","ama":"Pietrzak KZ, Skórski M. Non uniform attacks against pseudoentropy. In: Vol 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">10.4230/LIPIcs.ICALP.2017.39</a>","chicago":"Pietrzak, Krzysztof Z, and Maciej Skórski. “Non Uniform Attacks against Pseudoentropy,” Vol. 80. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.ICALP.2017.39\">https://doi.org/10.4230/LIPIcs.ICALP.2017.39</a>."},"type":"conference","file":[{"file_id":"4701","date_created":"2018-12-12T10:08:40Z","creator":"system","checksum":"e95618a001692f1af2d68f5fde43bc1f","relation":"main_file","date_updated":"2020-07-14T12:47:46Z","content_type":"application/pdf","file_size":601004,"file_name":"IST-2017-893-v1+1_LIPIcs-ICALP-2017-39.pdf","access_level":"open_access"}],"year":"2017","conference":{"end_date":"2017-07-14","location":"Warsaw, Poland","start_date":"2017-07-10","name":"ICALP: International Colloquium on Automata, Languages, and Programming"},"author":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"},{"last_name":"Skórski","full_name":"Skórski, Maciej","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"department":[{"_id":"KrPi"}],"publication_identifier":{"issn":["18688969"]},"day":"01","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa_version":"Published Version","doi":"10.4230/LIPIcs.ICALP.2017.39","oa":1,"intvolume":"        80","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","article_number":"39","alternative_title":["LIPIcs"],"volume":80,"scopus_import":1,"ec_funded":1,"date_published":"2017-07-01T00:00:00Z","month":"07","date_updated":"2021-01-12T08:11:15Z","title":"Non uniform attacks against pseudoentropy","date_created":"2018-12-11T11:47:59Z","project":[{"name":"Teaching Old Crypto New Tricks","call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815"}],"_id":"697","pubrep_id":"893","file_date_updated":"2020-07-14T12:47:46Z"},{"publisher":"American Society for Cell Biology","day":"07","doi":"10.1091/mbc.E16-12-0825","oa_version":"Published Version","author":[{"first_name":"Yejun","last_name":"Wang","full_name":"Wang, Yejun"},{"first_name":"Mallika","full_name":"Nagarajan, Mallika","last_name":"Nagarajan"},{"last_name":"Uhler","orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline"},{"first_name":"Gv","full_name":"Shivashankar, Gv","last_name":"Shivashankar"}],"year":"2017","publication_identifier":{"issn":["10591524"]},"department":[{"_id":"CaUh"}],"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","short":"CC BY-NC-SA (4.0)","image":"/images/cc_by_nc_sa.png"},"ddc":["519"],"file":[{"date_created":"2018-12-12T10:10:53Z","creator":"system","file_id":"4844","access_level":"open_access","file_name":"IST-2017-892-v1+1_Mol._Biol._Cell-2017-Wang-1997-2009.pdf","file_size":1086097,"date_updated":"2020-07-14T12:47:46Z","content_type":"application/pdf","checksum":"de01dac9e30970cfa6ae902480a4e04d","relation":"main_file"}],"type":"journal_article","citation":{"ama":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. 2017;28(14):1997-2009. doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>","chicago":"Wang, Yejun, Mallika Nagarajan, Caroline Uhler, and Gv Shivashankar. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>. American Society for Cell Biology, 2017. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>.","ista":"Wang Y, Nagarajan M, Uhler C, Shivashankar G. 2017. Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. Molecular Biology of the Cell. 28(14), 1997–2009.","mla":"Wang, Yejun, et al. “Orientation and Repositioning of Chromosomes Correlate with Cell Geometry Dependent Gene Expression.” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14, American Society for Cell Biology, 2017, pp. 1997–2009, doi:<a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">10.1091/mbc.E16-12-0825</a>.","apa":"Wang, Y., Nagarajan, M., Uhler, C., &#38; Shivashankar, G. (2017). Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression. <i>Molecular Biology of the Cell</i>. American Society for Cell Biology. <a href=\"https://doi.org/10.1091/mbc.E16-12-0825\">https://doi.org/10.1091/mbc.E16-12-0825</a>","short":"Y. Wang, M. Nagarajan, C. Uhler, G. Shivashankar, Molecular Biology of the Cell 28 (2017) 1997–2009.","ieee":"Y. Wang, M. Nagarajan, C. Uhler, and G. Shivashankar, “Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression,” <i>Molecular Biology of the Cell</i>, vol. 28, no. 14. American Society for Cell Biology, pp. 1997–2009, 2017."},"quality_controlled":"1","publication_status":"published","abstract":[{"lang":"eng","text":"Extracellular matrix signals from the microenvironment regulate gene expression patterns and cell behavior. Using a combination of experiments and geometric models, we demonstrate correlations between cell geometry, three-dimensional (3D) organization of chromosome territories, and gene expression. Fluorescence in situ hybridization experiments showed that micropatterned fibroblasts cultured on anisotropic versus isotropic substrates resulted in repositioning of specific chromosomes, which contained genes that were differentially regulated by cell geometries. Experiments combined with ellipsoid packing models revealed that the mechanosensitivity of chromosomes was correlated with their orientation in the nucleus. Transcription inhibition experiments suggested that the intermingling degree was more sensitive to global changes in transcription than to chromosome radial positioning and its orientations. These results suggested that cell geometry modulated 3D chromosome arrangement, and their neighborhoods correlated with gene expression patterns in a predictable manner. This is central to understanding geometric control of genetic programs involved in cellular homeostasis and the associated diseases. "}],"publist_id":"7001","language":[{"iso":"eng"}],"status":"public","has_accepted_license":"1","project":[{"call_identifier":"FWF","grant_number":"Y 903-N35","_id":"2530CA10-B435-11E9-9278-68D0E5697425","name":"Gaussian Graphical Models: Theory and Applications"}],"_id":"698","date_created":"2018-12-11T11:47:59Z","file_date_updated":"2020-07-14T12:47:46Z","pubrep_id":"892","publication":"Molecular Biology of the Cell","page":"1997 - 2009","date_published":"2017-07-07T00:00:00Z","date_updated":"2021-01-12T08:11:17Z","title":"Orientation and repositioning of chromosomes correlate with cell geometry dependent gene expression","month":"07","scopus_import":1,"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"14","intvolume":"        28","oa":1,"volume":28}]