[{"pubrep_id":"825","abstract":[{"lang":"eng","text":"Cell-cell  contact  formation  constitutes  the  first  step  in  the  emergence  of  multicellularity  in evolution, thereby  allowing  the  differentiation  of  specialized  cell  types.  In  metazoan development, cell-cell contact formation is thought to influence cell fate specification, and cell   fate   specification   has   been   implicated   in   cell-cell  contact formation.   However, remarkably little is yet known about whether and how the interaction and feedback between cell-cell contact formation and cell fate specification affect development. Here we identify a positive  feedback  loop  between  cell-cell  contact  duration,  morphogen  signaling  and mesendoderm  cell  fate  specification  during  zebrafish  gastrulation.  We  show  that  long lasting cell-cell contacts enhance the competence of prechordal plate (ppl) progenitor cells to  respond  to  Nodal  signaling,  required  for  proper  ppl  cell  fate  specification.  We  further show  that  Nodal  signalling  romotes  ppl  cell-cell  contact  duration,  thereby  generating  an effective  positive  feedback  loop  between  ppl  cell-cell  contact  duration  and  cell  fate specification. Finally, by using a combination of theoretical modeling and experimentation, we  show  that  this  feedback  loop  determines  whether  anterior  axial  mesendoderm  cells become  ppl  progenitors  or,  instead,  turn  into  endoderm  progenitors.  Our  findings  reveal that  the  gene  regulatory  networks  leading  to  cell  fate  diversification  within  the  developing embryo  are  controlled  by  the  interdependent  activities  of  cell-cell  signaling  and  contact formation."}],"year":"2017","degree_awarded":"PhD","page":"109","corr_author":"1","supervisor":[{"id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"status":"public","file_date_updated":"2020-07-14T12:48:16Z","article_processing_charge":"No","date_created":"2018-12-11T11:49:25Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2017-03-01T00:00:00Z","ddc":["570","590"],"publisher":"Institute of Science and Technology Austria","file":[{"creator":"dernst","file_name":"2017_Barone_thesis_final.docx","file_size":14497822,"date_created":"2019-04-05T08:36:52Z","date_updated":"2020-07-14T12:48:16Z","checksum":"242f88c87f2cf267bf05049fa26a687b","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_id":"6205","access_level":"closed","relation":"source_file"},{"access_level":"open_access","relation":"main_file","file_id":"6206","content_type":"application/pdf","checksum":"ba5b0613ed8bade73a409acdd880fb8a","date_updated":"2020-07-14T12:48:16Z","date_created":"2019-04-05T08:36:52Z","file_size":14995941,"creator":"dernst","file_name":"2017_Barone_thesis_.pdf"}],"oa":1,"date_updated":"2026-06-18T18:12:40Z","month":"03","has_accepted_license":"1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"735"},{"id":"1100","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"1537"},{"relation":"part_of_dissertation","status":"public","id":"3246"},{"relation":"part_of_dissertation","id":"2926","status":"public"},{"relation":"part_of_dissertation","id":"676","status":"public"},{"relation":"part_of_dissertation","id":"1912","status":"public"}]},"publication_status":"published","_id":"961","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"day":"01","department":[{"_id":"CaHe"}],"type":"dissertation","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa_version":"Published Version","citation":{"chicago":"Barone, Vanessa. “Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation.” Institute of Science and Technology Austria, 2017. <a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">https://doi.org/10.15479/AT:ISTA:th_825</a>.","ama":"Barone V. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. 2017. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">10.15479/AT:ISTA:th_825</a>","apa":"Barone, V. (2017). <i>Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">https://doi.org/10.15479/AT:ISTA:th_825</a>","short":"V. Barone, Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation, Institute of Science and Technology Austria, 2017.","mla":"Barone, Vanessa. <i>Cell Adhesion and Cell Fate: An Effective Feedback Loop during Zebrafish Gastrulation</i>. Institute of Science and Technology Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_825\">10.15479/AT:ISTA:th_825</a>.","ieee":"V. Barone, “Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation,” Institute of Science and Technology Austria, 2017.","ista":"Barone V. 2017. Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation. Institute of Science and Technology Austria."},"title":"Cell adhesion and cell fate: An effective feedback loop during zebrafish gastrulation","publist_id":"6444","OA_place":"publisher","author":[{"orcid":"0000-0003-2676-3367","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","last_name":"Barone","full_name":"Barone, Vanessa","first_name":"Vanessa"}],"doi":"10.15479/AT:ISTA:th_825","alternative_title":["ISTA Thesis"],"license":"https://creativecommons.org/licenses/by/4.0/","acknowledgement":"Many people accompanied me during this trip: I would not have reached my destination nor \r\nenjoyed the travelling without them. First of all, thanks to CP. Thanks for making me part of \r\nyour team, always full of diverse, interesting and incredibly competent people and thanks for \r\nall  the  good  science  I  witnessed  and  participated  in.  It  has  been  a \r\nblast,  an  incredibly \r\nexciting  one!  Thanks  to  JLo,  for  teaching  me  how  to  master  my  pipettes  and  showing  me \r\nthat science is a lot of fun. Many, many thanks to Gabby for teaching me basically everything \r\nabout  zebrafish  and  being  always  there  to  advice,  sugge\r\nst,  support...and  play  fussball! \r\nThank you to Julien, for the critical eye on things, Pedro, for all the invaluable feedback and \r\nthe amazing kicker matches, and Keisuke, for showing me the light, and to the three of them \r\ntogether  for  all  the  good  laughs  we\r\nhad.  My  start  in  Vienna  would  have  been  a  lot  more \r\ndifficult  without  you  guys.  Also  it  would  not  have  been  possible  without  Elena  and  Inês: \r\nthanks  for  helping  setting  up  this  lab  and  for  the  dinners  in  Gugging.  Thanks  to  Martin,  for \r\nhelping  me  understand \r\nthe  physics  behind  biology.  Thanks  to  Philipp,  for  the  interest  and \r\nadvice, and to Michael, for the Viennise take on things. Thanks to Julia, for putting up with \r\nbeing our technician and becoming a friend in the process. And now to the newest members \r\nof th\r\ne lab. Thanks to Daniel for the enthusiasm and the neverending energy and for all your \r\nhelp over the years: thank you! To Jana, for showing me that one doesn’t give up, no matter \r\nwhat.  To  Shayan,  for  being  such  a  motivated  student.  To  Matt,  for  helping  out\r\nwith  coding \r\nand for finding punk solutions to data analysis problems. Thanks to all the members of the \r\nlab, Verena, Hitoshi, Silvia, Conny, Karla, Nicoletta, Zoltan, Peng, Benoit, Roland, Yuuta and \r\nFeyza,  for  the  wonderful  atmosphere  in  the  lab.  Many  than\r\nks  to  Koni  and  Deborah:  doing \r\nexperiments would have been much more difficult without your help. Special thanks to Katjia \r\nfor  setting  up  an  amazing  imaging  facility  and  for  building  the  best  team,  Robert,  Nasser, \r\nAnna and Doreen: thank you for putting up w\r\nith all the late sortings and for helping with all \r\nthe technical problems. Thanks to Eva, Verena and Matthias for keeping the fish happy. Big \r\nthanks to Harald Janovjak for being a present and helpful committee member over the years \r\nand  to  Patrick  Lemaire  f\r\nor  the  helpful  insight  and  extremely  interesting  discussion  we  had \r\nabout  the  project.  Also,  this  journey  would  not  have  been  the  same  without  all  the  friends \r\nthat I met in Dresden and then in Vienna: Daniele, Claire, Kuba, Steffi, Harold, Dejan, Irene, \r\nFab\r\nienne, Hande, Tiago, Marianne, Jon, Srdjan, Branca, Uli, Murat, Alex, Conny, Christoph, \r\nCaro, Simone, Barbara, Felipe, Dama, Jose, Hubert and many others that filled my days with \r\nfun and support. A special thank to my family, always close even if they are \r\nkilometers away. \r\nGrazie  ai  miei  fratelli,  Nunzio  e  William,  e  alla  mia  mamma,  per  essermi  sempre  vicini  pur \r\nvivendo a chilometri di distanza. And, last but not least, thanks to Moritz, for putting up with \r\nthe crazy life of a scientist, the living apart for\r\nso long, never knowing when things are going \r\nto happen. Thanks for being a great partner and my number one fan!"},{"quality_controlled":"1","external_id":{"isi":["000431900900021"]},"publisher":"Springer","article_processing_charge":"No","date_created":"2018-12-11T11:49:26Z","scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2017-01-01T00:00:00Z","intvolume":"     10427","page":"399 - 418","status":"public","project":[{"name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23"},{"call_identifier":"FWF","grant_number":"Z211","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"Formal methods for the design and analysis of complex systems"}],"abstract":[{"lang":"eng","text":"We present a new algorithm for model counting of a class of string constraints. In addition to the classic operation of concatenation, our class includes some recursively defined operations such as Kleene closure, and replacement of substrings. Additionally, our class also includes length constraints on the string expressions, which means, by requiring reasoning about numbers, that we face a multi-sorted logic. In the end, our string constraints are motivated by their use in programming for web applications. Our algorithm comprises two novel features: the ability to use a technique of (1) partial derivatives for constraints that are already in a solved form, i.e. a form where its (string) satisfiability is clearly displayed, and (2) non-progression, where cyclic reasoning in the reduction process may be terminated (thus allowing for the algorithm to look elsewhere). Finally, we experimentally compare our model counter with two recent works on model counting of similar constraints, SMC [18] and ABC [5], to demonstrate its superior performance."}],"year":"2017","author":[{"full_name":"Trinh, Minh","first_name":"Minh","last_name":"Trinh"},{"id":"3598E630-F248-11E8-B48F-1D18A9856A87","full_name":"Chu, Duc Hiep","first_name":"Duc Hiep","last_name":"Chu"},{"last_name":"Jaffar","first_name":"Joxan","full_name":"Jaffar, Joxan"}],"alternative_title":["LNCS"],"doi":"10.1007/978-3-319-63390-9_21","editor":[{"first_name":"Rupak","full_name":"Majumdar, Rupak","last_name":"Majumdar"},{"last_name":"Kunčak","full_name":"Kunčak, Viktor","first_name":"Viktor"}],"type":"conference","oa_version":"None","isi":1,"title":"Model counting for recursively-defined strings","publist_id":"6443","citation":{"ama":"Trinh M, Chu DH, Jaffar J. Model counting for recursively-defined strings. In: Majumdar R, Kunčak V, eds. Vol 10427. Springer; 2017:399-418. doi:<a href=\"https://doi.org/10.1007/978-3-319-63390-9_21\">10.1007/978-3-319-63390-9_21</a>","chicago":"Trinh, Minh, Duc Hiep Chu, and Joxan Jaffar. “Model Counting for Recursively-Defined Strings.” edited by Rupak Majumdar and Viktor Kunčak, 10427:399–418. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-63390-9_21\">https://doi.org/10.1007/978-3-319-63390-9_21</a>.","apa":"Trinh, M., Chu, D. H., &#38; Jaffar, J. (2017). Model counting for recursively-defined strings. In R. Majumdar &#38; V. Kunčak (Eds.) (Vol. 10427, pp. 399–418). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-63390-9_21\">https://doi.org/10.1007/978-3-319-63390-9_21</a>","short":"M. Trinh, D.H. Chu, J. Jaffar, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 399–418.","mla":"Trinh, Minh, et al. <i>Model Counting for Recursively-Defined Strings</i>. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10427, Springer, 2017, pp. 399–418, doi:<a href=\"https://doi.org/10.1007/978-3-319-63390-9_21\">10.1007/978-3-319-63390-9_21</a>.","ieee":"M. Trinh, D. H. Chu, and J. Jaffar, “Model counting for recursively-defined strings,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10427, pp. 399–418.","ista":"Trinh M, Chu DH, Jaffar J. 2017. Model counting for recursively-defined strings. CAV: Computer Aided Verification, LNCS, vol. 10427, 399–418."},"volume":10427,"conference":{"name":"CAV: Computer Aided Verification","end_date":"2017-07-28","location":"Heidelberg, Germany","start_date":"2017-07-24"},"publication_identifier":{"issn":["0302-9743"]},"department":[{"_id":"ToHe"}],"day":"01","_id":"962","publication_status":"published","language":[{"iso":"eng"}],"date_updated":"2026-04-16T09:58:05Z","month":"01"},{"year":"2017","pubrep_id":"829","abstract":[{"text":"Network games are widely used as a model for selfish resource-allocation problems. In the classical model, each player selects a path connecting her source and target vertex. The cost of traversing an edge depends on the number of players that traverse it. Thus, it abstracts the fact that different users may use a resource at different times and for different durations, which plays an important role in defining the costs of the users in reality. For example, when transmitting packets in a communication network, routing traffic in a road network, or processing a task in a production system, the traversal of the network involves an inherent delay, and so sharing and congestion of resources crucially depends on time. We study timed network games , which add a time component to network games. Each vertex v in the network is associated with a cost function, mapping the load on v to the price that a player pays for staying in v for one time unit with this load. In addition, each edge has a guard, describing time intervals in which the edge can be traversed, forcing the players to spend time on vertices. Unlike earlier work that add a time component to network games, the time in our model is continuous and cannot be discretized. In particular, players have uncountably many strategies, and a game may have uncountably many pure Nash equilibria. We study properties of timed network games with cost-sharing or congestion cost functions: their stability, equilibrium inefficiency, and complexity. In particular, we show that the answer to the question whether we can restrict attention to boundary strategies, namely ones in which edges are traversed only at the boundaries of guards, is mixed. ","lang":"eng"}],"project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23"}],"status":"public","intvolume":"        83","ddc":["004"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2017-06-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:49:26Z","file_date_updated":"2020-07-14T12:48:18Z","article_processing_charge":"No","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5059","checksum":"f55eaf7f3c36ea07801112acfedd17d5","date_updated":"2020-07-14T12:48:18Z","date_created":"2018-12-12T10:14:10Z","file_size":369730,"creator":"system","file_name":"IST-2017-829-v1+1_mfcs-cr.pdf"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"quality_controlled":"1","month":"06","date_updated":"2025-07-10T12:01:59Z","language":[{"iso":"eng"}],"_id":"963","publication_status":"published","day":"01","department":[{"_id":"ToHe"}],"publication_identifier":{"issn":["1868-8969"]},"has_accepted_license":"1","related_material":{"record":[{"id":"6005","status":"public","relation":"later_version"}]},"conference":{"name":"MFCS: Mathematical Foundations of Computer Science","location":"Aalborg, Denmark","start_date":"2017-08-21","end_date":"2017-08-25"},"article_number":"37","citation":{"mla":"Avni, Guy, et al. <i>Timed Network Games with Clocks</i>. Vol. 83, 37, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.37\">10.4230/LIPIcs.MFCS.2017.37</a>.","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Aalborg, Denmark, 2017, vol. 83.","ista":"Avni G, Guha S, Kupferman O. 2017. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 83, 37.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.37\">https://doi.org/10.4230/LIPIcs.MFCS.2017.37</a>.","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 83. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.37\">10.4230/LIPIcs.MFCS.2017.37</a>","apa":"Avni, G., Guha, S., &#38; Kupferman, O. (2017). Timed network games with clocks (Vol. 83). Presented at the MFCS: Mathematical Foundations of Computer Science, Aalborg, Denmark: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.MFCS.2017.37\">https://doi.org/10.4230/LIPIcs.MFCS.2017.37</a>","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017."},"volume":83,"publist_id":"6438","title":"Timed network games with clocks","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"conference","oa_version":"Published Version","doi":"10.4230/LIPIcs.MFCS.2017.37","alternative_title":["LIPIcs"],"author":[{"orcid":"0000-0001-5588-8287","last_name":"Avni","first_name":"Guy","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guha","first_name":"Shibashis","full_name":"Guha, Shibashis"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}]},{"publication":"The Journal of Chemical Physics","date_updated":"2023-02-23T14:04:02Z","month":"09","article_type":"original","article_number":"104707","_id":"9660","publication_status":"published","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"day":"14","type":"journal_article","oa_version":"Submitted Version","volume":147,"citation":{"short":"B. Cheng, G.A. Tribello, M. Ceriotti, The Journal of Chemical Physics 147 (2017).","chicago":"Cheng, Bingqing, Gareth A. Tribello, and Michele Ceriotti. “The Gibbs Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4997180\">https://doi.org/10.1063/1.4997180</a>.","ama":"Cheng B, Tribello GA, Ceriotti M. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. <i>The Journal of Chemical Physics</i>. 2017;147(10). doi:<a href=\"https://doi.org/10.1063/1.4997180\">10.1063/1.4997180</a>","apa":"Cheng, B., Tribello, G. A., &#38; Ceriotti, M. (2017). The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4997180\">https://doi.org/10.1063/1.4997180</a>","mla":"Cheng, Bingqing, et al. “The Gibbs Free Energy of Homogeneous Nucleation: From Atomistic Nuclei to the Planar Limit.” <i>The Journal of Chemical Physics</i>, vol. 147, no. 10, 104707, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4997180\">10.1063/1.4997180</a>.","ieee":"B. Cheng, G. A. Tribello, and M. Ceriotti, “The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit,” <i>The Journal of Chemical Physics</i>, vol. 147, no. 10. AIP Publishing, 2017.","ista":"Cheng B, Tribello GA, Ceriotti M. 2017. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit. The Journal of Chemical Physics. 147(10), 104707."},"title":"The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit","author":[{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","last_name":"Cheng","first_name":"Bingqing","full_name":"Cheng, Bingqing","orcid":"0000-0002-3584-9632"},{"last_name":"Tribello","first_name":"Gareth A.","full_name":"Tribello, Gareth A."},{"first_name":"Michele","full_name":"Ceriotti, Michele","last_name":"Ceriotti"}],"doi":"10.1063/1.4997180","main_file_link":[{"url":"https://pure.qub.ac.uk/en/publications/the-gibbs-free-energy-of-homogeneous-nucleation-from-atomistic-nuclei-to-the-planar-limit(4599cdb4-dcc4-4522-8763-7b2a165ebf12).html","open_access":"1"}],"issue":"10","abstract":[{"text":"In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.","lang":"eng"}],"year":"2017","intvolume":"       147","extern":"1","status":"public","article_processing_charge":"No","date_created":"2021-07-15T08:13:29Z","scopus_import":"1","date_published":"2017-09-14T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","pmid":1,"arxiv":1,"publisher":"AIP Publishing","oa":1,"quality_controlled":"1","external_id":{"arxiv":["1703.06062"],"pmid":["28915742"]}},{"year":"2017","issue":"3","abstract":[{"text":"Macroscopic theories of nucleation such as classical nucleation theory envision that clusters of the bulk stable phase form inside the bulk metastable phase. Molecular dynamics simulations are often used to elucidate nucleation mechanisms, by capturing the microscopic configurations of all the atoms. In this paper, we introduce a thermodynamic model that links macroscopic theories and atomic-scale simulations and thus provide a simple and elegant framework for testing the limits of classical nucleation theory.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1610.01322"}],"status":"public","extern":"1","intvolume":"       146","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2017-01-21T00:00:00Z","scopus_import":"1","pmid":1,"article_processing_charge":"No","date_created":"2021-07-15T08:27:31Z","quality_controlled":"1","oa":1,"external_id":{"pmid":["28109231"],"arxiv":["1610.01322"]},"arxiv":1,"publisher":"AIP Publishing","article_type":"original","month":"01","date_updated":"2021-08-09T12:31:57Z","publication":"The Journal of Chemical Physics","publication_identifier":{"eissn":["1089-7690"],"issn":["0021-9606"]},"day":"21","_id":"9661","publication_status":"published","language":[{"iso":"eng"}],"article_number":"034106","title":"Bridging the gap between atomistic and macroscopic models of homogeneous nucleation","citation":{"short":"B. Cheng, M. Ceriotti, The Journal of Chemical Physics 146 (2017).","chicago":"Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2017. <a href=\"https://doi.org/10.1063/1.4973883\">https://doi.org/10.1063/1.4973883</a>.","ama":"Cheng B, Ceriotti M. Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. <i>The Journal of Chemical Physics</i>. 2017;146(3). doi:<a href=\"https://doi.org/10.1063/1.4973883\">10.1063/1.4973883</a>","apa":"Cheng, B., &#38; Ceriotti, M. (2017). Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/1.4973883\">https://doi.org/10.1063/1.4973883</a>","ieee":"B. Cheng and M. Ceriotti, “Bridging the gap between atomistic and macroscopic models of homogeneous nucleation,” <i>The Journal of Chemical Physics</i>, vol. 146, no. 3. AIP Publishing, 2017.","mla":"Cheng, Bingqing, and Michele Ceriotti. “Bridging the Gap between Atomistic and Macroscopic Models of Homogeneous Nucleation.” <i>The Journal of Chemical Physics</i>, vol. 146, no. 3, 034106, AIP Publishing, 2017, doi:<a href=\"https://doi.org/10.1063/1.4973883\">10.1063/1.4973883</a>.","ista":"Cheng B, Ceriotti M. 2017. Bridging the gap between atomistic and macroscopic models of homogeneous nucleation. The Journal of Chemical Physics. 146(3), 034106."},"volume":146,"type":"journal_article","oa_version":"Preprint","doi":"10.1063/1.4973883","author":[{"full_name":"Cheng, Bingqing","first_name":"Bingqing","last_name":"Cheng","id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","orcid":"0000-0002-3584-9632"},{"last_name":"Ceriotti","first_name":"Michele","full_name":"Ceriotti, Michele"}]},{"citation":{"mla":"Riccio, Paul, et al. <i>Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis</i>. Dryad, 2017, doi:<a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>.","ieee":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, and F. Costantini, “Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis.” Dryad, 2017.","ista":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. 2017. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis, Dryad, <a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>.","chicago":"Riccio, Paul, Christina Cebrián, Hui Zong, Simon Hippenmeyer, and Frank Costantini. “Data from: Ret and Etv4 Promote Directed Movements of Progenitor Cells during Renal Branching Morphogenesis.” Dryad, 2017. <a href=\"https://doi.org/10.5061/dryad.pk16b\">https://doi.org/10.5061/dryad.pk16b</a>.","ama":"Riccio P, Cebrián C, Zong H, Hippenmeyer S, Costantini F. Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. 2017. doi:<a href=\"https://doi.org/10.5061/dryad.pk16b\">10.5061/dryad.pk16b</a>","apa":"Riccio, P., Cebrián, C., Zong, H., Hippenmeyer, S., &#38; Costantini, F. (2017). Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis. Dryad. <a href=\"https://doi.org/10.5061/dryad.pk16b\">https://doi.org/10.5061/dryad.pk16b</a>","short":"P. Riccio, C. Cebrián, H. Zong, S. Hippenmeyer, F. Costantini, (2017)."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2017-01-14T00:00:00Z","title":"Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis","type":"research_data_reference","oa_version":"Published Version","date_created":"2021-07-23T09:39:34Z","article_processing_charge":"No","doi":"10.5061/dryad.pk16b","publisher":"Dryad","oa":1,"author":[{"full_name":"Riccio, Paul","first_name":"Paul","last_name":"Riccio"},{"full_name":"Cebrián, Christina","first_name":"Christina","last_name":"Cebrián"},{"last_name":"Zong","first_name":"Hui","full_name":"Zong, Hui"},{"full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061"},{"first_name":"Frank","full_name":"Costantini, Frank","last_name":"Costantini"}],"month":"01","year":"2017","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.pk16b"}],"date_updated":"2022-08-25T13:34:55Z","abstract":[{"lang":"eng","text":"Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive knowledge of the genetic control of these events, it is not understood, at the cellular level, how renal branching morphogenesis is achieved or how Ret signaling influences epithelial cell behaviors to promote this process. Analysis of chimeric embryos previously suggested a role for Ret signaling in promoting cell rearrangements in the nephric duct, but this method was unsuited to study individual cell behaviors during ureteric bud branching. Here, we use Mosaic Analysis with Double Markers (MADM), combined with organ culture and time-lapse imaging, to trace the movements and divisions of individual ureteric bud tip cells. We first examine wild-type clones and then Ret or Etv4 mutant/wild-type clones in which the mutant and wild-type sister cells are differentially and heritably marked by green and red fluorescent proteins. We find that, in normal kidneys, most individual tip cells behave as self-renewing progenitors, some of whose progeny remain at the tips while others populate the growing UB trunks. In Ret or Etv4 MADM clones, the wild-type cells generated at a UB tip are much more likely to remain at, or move to, the new tips during branching and elongation, while their Ret−/− or Etv4−/− sister cells tend to lag behind and contribute only to the trunks. By tracking successive mitoses in a cell lineage, we find that Ret signaling has little effect on proliferation, in contrast to its effects on cell movement. Our results show that Ret/Etv4 signaling promotes directed cell movements in the ureteric bud tips, and suggest a model in which these cell movements mediate branching morphogenesis."}],"_id":"9707","department":[{"_id":"SiHi"}],"status":"public","day":"14","related_material":{"record":[{"relation":"used_in_publication","id":"9702","status":"deleted"}]}},{"month":"10","year":"2017","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.1f1rc"}],"date_updated":"2025-09-22T09:43:12Z","abstract":[{"text":"Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina.","lang":"eng"}],"_id":"9709","status":"public","department":[{"_id":"GaTk"}],"day":"18","related_material":{"record":[{"status":"public","id":"1197","relation":"used_in_publication"}]},"citation":{"chicago":"Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.” Dryad, 2017. <a href=\"https://doi.org/10.5061/dryad.1f1rc\">https://doi.org/10.5061/dryad.1f1rc</a>.","ama":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Data from: Error-robust modes of the retinal population code. 2017. doi:<a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>","apa":"Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., &#38; Berry, M. (2017). Data from: Error-robust modes of the retinal population code. Dryad. <a href=\"https://doi.org/10.5061/dryad.1f1rc\">https://doi.org/10.5061/dryad.1f1rc</a>","short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, (2017).","ieee":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Data from: Error-robust modes of the retinal population code.” Dryad, 2017.","mla":"Prentice, Jason, et al. <i>Data from: Error-Robust Modes of the Retinal Population Code</i>. Dryad, 2017, doi:<a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>.","ista":"Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2017. Data from: Error-robust modes of the retinal population code, Dryad, <a href=\"https://doi.org/10.5061/dryad.1f1rc\">10.5061/dryad.1f1rc</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_published":"2017-10-18T00:00:00Z","title":"Data from: Error-robust modes of the retinal population code","type":"research_data_reference","oa_version":"Published Version","date_created":"2021-07-23T11:34:34Z","article_processing_charge":"No","doi":"10.5061/dryad.1f1rc","publisher":"Dryad","oa":1,"author":[{"full_name":"Prentice, Jason","first_name":"Jason","last_name":"Prentice"},{"first_name":"Olivier","full_name":"Marre, Olivier","last_name":"Marre"},{"first_name":"Mark","full_name":"Ioffe, Mark","last_name":"Ioffe"},{"full_name":"Loback, Adrianna","first_name":"Adrianna","last_name":"Loback"},{"orcid":"0000-0002-6699-1455","last_name":"Tkačik","full_name":"Tkačik, Gašper","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","full_name":"Berry, Michael","last_name":"Berry"}]},{"oa":1,"doi":"10.17632/nw68fxzjpm.1","publisher":"Mendeley Data","author":[{"last_name":"Etheridge","full_name":"Etheridge, Alison","first_name":"Alison"},{"last_name":"Barton","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"}],"title":"Data for: Establishment in a new habitat by polygenic adaptation","citation":{"short":"A. Etheridge, N.H. Barton, (2017).","ama":"Etheridge A, Barton NH. Data for: Establishment in a new habitat by polygenic adaptation. 2017. doi:<a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>","chicago":"Etheridge, Alison, and Nicholas H Barton. “Data for: Establishment in a New Habitat by Polygenic Adaptation.” Mendeley Data, 2017. <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">https://doi.org/10.17632/nw68fxzjpm.1</a>.","apa":"Etheridge, A., &#38; Barton, N. H. (2017). Data for: Establishment in a new habitat by polygenic adaptation. Mendeley Data. <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">https://doi.org/10.17632/nw68fxzjpm.1</a>","ieee":"A. Etheridge and N. H. Barton, “Data for: Establishment in a new habitat by polygenic adaptation.” Mendeley Data, 2017.","mla":"Etheridge, Alison, and Nicholas H. Barton. <i>Data for: Establishment in a New Habitat by Polygenic Adaptation</i>. Mendeley Data, 2017, doi:<a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>.","ista":"Etheridge A, Barton NH. 2017. Data for: Establishment in a new habitat by polygenic adaptation, Mendeley Data, <a href=\"https://doi.org/10.17632/nw68fxzjpm.1\">10.17632/nw68fxzjpm.1</a>."},"date_published":"2017-12-29T00:00:00Z","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","date_created":"2021-08-09T13:18:55Z","article_processing_charge":"No","type":"research_data_reference","oa_version":"Published Version","department":[{"_id":"NiBa"}],"day":"29","status":"public","_id":"9842","related_material":{"record":[{"id":"564","status":"public","relation":"used_in_publication"}]},"year":"2017","month":"12","date_updated":"2025-04-15T07:11:04Z","abstract":[{"lang":"eng","text":"Mathematica notebooks used to generate figures."}],"main_file_link":[{"url":"https://doi.org/10.17632/nw68fxzjpm.1","open_access":"1"}]},{"author":[{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate","first_name":"Mate","last_name":"Gerencser"},{"last_name":"Gyöngy","first_name":"István","full_name":"Gyöngy, István"}],"doi":"10.1090/mcom/3201","oa_version":"Submitted Version","isi":1,"type":"journal_article","publist_id":"7144","title":"Localization errors in solving stochastic partial differential equations in the whole space","volume":86,"citation":{"apa":"Gerencser, M., &#38; Gyöngy, I. (2017). Localization errors in solving stochastic partial differential equations in the whole space. <i>Mathematics of Computation</i>. American Mathematical Society. <a href=\"https://doi.org/10.1090/mcom/3201\">https://doi.org/10.1090/mcom/3201</a>","ama":"Gerencser M, Gyöngy I. Localization errors in solving stochastic partial differential equations in the whole space. <i>Mathematics of Computation</i>. 2017;86(307):2373-2397. doi:<a href=\"https://doi.org/10.1090/mcom/3201\">10.1090/mcom/3201</a>","chicago":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” <i>Mathematics of Computation</i>. American Mathematical Society, 2017. <a href=\"https://doi.org/10.1090/mcom/3201\">https://doi.org/10.1090/mcom/3201</a>.","short":"M. Gerencser, I. Gyöngy, Mathematics of Computation 86 (2017) 2373–2397.","ista":"Gerencser M, Gyöngy I. 2017. Localization errors in solving stochastic partial differential equations in the whole space. Mathematics of Computation. 86(307), 2373–2397.","ieee":"M. Gerencser and I. Gyöngy, “Localization errors in solving stochastic partial differential equations in the whole space,” <i>Mathematics of Computation</i>, vol. 86, no. 307. American Mathematical Society, pp. 2373–2397, 2017.","mla":"Gerencser, Mate, and István Gyöngy. “Localization Errors in Solving Stochastic Partial Differential Equations in the Whole Space.” <i>Mathematics of Computation</i>, vol. 86, no. 307, American Mathematical Society, 2017, pp. 2373–97, doi:<a href=\"https://doi.org/10.1090/mcom/3201\">10.1090/mcom/3201</a>."},"department":[{"_id":"JaMa"}],"day":"01","publication_identifier":{"issn":["0025-5718"]},"language":[{"iso":"eng"}],"_id":"642","publication_status":"published","date_updated":"2025-09-11T07:20:20Z","publication":"Mathematics of Computation","month":"01","external_id":{"isi":["000400929100013"],"arxiv":["1508.05535"]},"quality_controlled":"1","oa":1,"arxiv":1,"publisher":"American Mathematical Society","date_created":"2018-12-11T11:47:40Z","article_processing_charge":"No","date_published":"2017-01-01T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","intvolume":"        86","corr_author":"1","page":"2373 - 2397","status":"public","abstract":[{"text":"Cauchy problems with SPDEs on the whole space are localized to Cauchy problems on a ball of radius R. This localization reduces various kinds of spatial approximation schemes to finite dimensional problems. The error is shown to be exponentially small. As an application, a numerical scheme is presented which combines the localization and the space and time discretization, and thus is fully implementable.","lang":"eng"}],"issue":"307","main_file_link":[{"url":"https://arxiv.org/abs/1508.05535","open_access":"1"}],"year":"2017"},{"language":[{"iso":"eng"}],"_id":"6426","publication_status":"published","day":"04","status":"public","department":[{"_id":"ToHe"}],"publication_identifier":{"issn":["2664-1690"]},"page":"28","has_accepted_license":"1","related_material":{"record":[{"relation":"later_version","id":"133","status":"public"}]},"month":"08","year":"2017","date_updated":"2025-04-15T08:11:53Z","abstract":[{"text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent asynchronous computation threads. We show that specifications and correctness proofs for asynchronous programs can be structured by introducing the fiction, for proof purposes, that intermediate, non-quiescent states of asynchronous operations can be ignored. Then, the task of specification becomes relatively simple and the task of verification can be naturally decomposed into smaller sub-tasks. The sub-tasks iteratively summarize, guided by the structure of an asynchronous program, the atomic effect of non-atomic operations and the synchronous effect of asynchronous operations. This structuring of specifications and proofs corresponds to the introduction of multiple layers of stepwise refinement for asynchronous programs. We present the first proof rule, called synchronization, to reduce asynchronous invocations on a lower layer to synchronous invocations on a higher layer. We implemented our proof method in CIVL and evaluated it on a collection of benchmark programs.","lang":"eng"}],"doi":"10.15479/AT:IST-2018-853-v2-2","file":[{"file_size":971347,"date_updated":"2020-07-14T12:47:30Z","date_created":"2019-05-13T08:14:44Z","creator":"dernst","file_name":"main(1).pdf","relation":"main_file","access_level":"open_access","checksum":"b48d42725182d7ca10107a118815f4cf","content_type":"application/pdf","file_id":"6431"}],"publisher":"IST Austria","alternative_title":["IST Austria Technical Report"],"oa":1,"author":[{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","orcid":"0000−0002−2985−7724"},{"orcid":"0000-0001-7745-9117","first_name":"Bernhard","full_name":"Kragl, Bernhard","last_name":"Kragl","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"}],"citation":{"mla":"Henzinger, Thomas A., et al. <i>Synchronizing the Asynchronous</i>. IST Austria, 2017, doi:<a href=\"https://doi.org/10.15479/AT:IST-2018-853-v2-2\">10.15479/AT:IST-2018-853-v2-2</a>.","ieee":"T. A. Henzinger, B. Kragl, and S. Qadeer, <i>Synchronizing the asynchronous</i>. IST Austria, 2017.","ista":"Henzinger TA, Kragl B, Qadeer S. 2017. Synchronizing the asynchronous, IST Austria, 28p.","short":"T.A. Henzinger, B. Kragl, S. Qadeer, Synchronizing the Asynchronous, IST Austria, 2017.","chicago":"Henzinger, Thomas A, Bernhard Kragl, and Shaz Qadeer. <i>Synchronizing the Asynchronous</i>. IST Austria, 2017. <a href=\"https://doi.org/10.15479/AT:IST-2018-853-v2-2\">https://doi.org/10.15479/AT:IST-2018-853-v2-2</a>.","ama":"Henzinger TA, Kragl B, Qadeer S. <i>Synchronizing the Asynchronous</i>. IST Austria; 2017. doi:<a href=\"https://doi.org/10.15479/AT:IST-2018-853-v2-2\">10.15479/AT:IST-2018-853-v2-2</a>","apa":"Henzinger, T. A., Kragl, B., &#38; Qadeer, S. (2017). <i>Synchronizing the asynchronous</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2018-853-v2-2\">https://doi.org/10.15479/AT:IST-2018-853-v2-2</a>"},"ddc":["000"],"date_published":"2017-08-04T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Synchronizing the asynchronous","type":"technical_report","oa_version":"Published Version","date_created":"2019-05-13T08:15:55Z","file_date_updated":"2020-07-14T12:47:30Z"},{"publication_identifier":{"issn":["0304-4920"]},"department":[{"_id":"RySh"}],"day":"31","publication_status":"published","_id":"643","language":[{"iso":"eng"}],"date_updated":"2025-09-11T07:19:13Z","publication":"Chinese Journal of Physiology","article_type":"original","month":"08","author":[{"first_name":"Wuping","full_name":"Sun, Wuping","last_name":"Sun"},{"id":"34009CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Zhai, Ming-Zhu","first_name":"Ming-Zhu","last_name":"Zhai"},{"first_name":"Qian","full_name":"Zhou, Qian","last_name":"Zhou"},{"last_name":"Qian","full_name":"Qian, Chengrui","first_name":"Chengrui"},{"full_name":"Jiang, Changyu","first_name":"Changyu","last_name":"Jiang"}],"OA_type":"closed access","doi":"10.4077/CJP.2017.BAF469","oa_version":"None","type":"journal_article","isi":1,"title":"Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats","publist_id":"7142","citation":{"mla":"Sun, Wuping, et al. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” <i>Chinese Journal of Physiology</i>, vol. 60, no. 4, Chinese Physiological Society, 2017, pp. 207–14, doi:<a href=\"https://doi.org/10.4077/CJP.2017.BAF469\">10.4077/CJP.2017.BAF469</a>.","ieee":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, and C. Jiang, “Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats,” <i>Chinese Journal of Physiology</i>, vol. 60, no. 4. Chinese Physiological Society, pp. 207–214, 2017.","ista":"Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. 2017. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. Chinese Journal of Physiology. 60(4), 207–214.","short":"W. Sun, M.-Z. Zhai, Q. Zhou, C. Qian, C. Jiang, Chinese Journal of Physiology 60 (2017) 207–214.","ama":"Sun W, Zhai M-Z, Zhou Q, Qian C, Jiang C. Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. <i>Chinese Journal of Physiology</i>. 2017;60(4):207-214. doi:<a href=\"https://doi.org/10.4077/CJP.2017.BAF469\">10.4077/CJP.2017.BAF469</a>","chicago":"Sun, Wuping, Ming-Zhu Zhai, Qian Zhou, Chengrui Qian, and Changyu Jiang. “Effects of B Vitamins Overload on Plasma Insulin Level and Hydrogen Peroxide Generation in Rats.” <i>Chinese Journal of Physiology</i>. Chinese Physiological Society, 2017. <a href=\"https://doi.org/10.4077/CJP.2017.BAF469\">https://doi.org/10.4077/CJP.2017.BAF469</a>.","apa":"Sun, W., Zhai, M.-Z., Zhou, Q., Qian, C., &#38; Jiang, C. (2017). Effects of B vitamins overload on plasma insulin level and hydrogen peroxide generation in rats. <i>Chinese Journal of Physiology</i>. Chinese Physiological Society. <a href=\"https://doi.org/10.4077/CJP.2017.BAF469\">https://doi.org/10.4077/CJP.2017.BAF469</a>"},"volume":60,"intvolume":"        60","page":"207 - 214","status":"public","issue":"4","abstract":[{"text":"It has been reported that nicotinamide-overload induces oxidative stress associated with insulin resistance, the key feature of type 2 diabetes mellitus (T2DM). This study aimed to investigate the effects of B vitamins in T2DM. Glucose tolerance tests (GTT) were carried out in adult Sprague-Dawley rats treated with or without cumulative doses of B vitamins. More specifically, insulin tolerance tests (ITT) were also carried out in adult Sprague-Dawley rats treated with or without cumulative doses of Vitamin B3. We found that cumulative Vitamin B1 and Vitamin B3 administration significantly increased the plasma H2O2 levels associated with high insulin levels. Only Vitamin B3 reduced muscular and hepatic glycogen contents. Cumulative administration of nicotinic acid, another form of Vitamin B3, also significantly increased plasma insulin level and H2O2 generation. Moreover, cumulative administration of nicotinic acid or nicotinamide impaired glucose metabolism. This study suggested that excess Vitamin B1 and Vitamin B3 caused oxidative stress and insulin resistance.","lang":"eng"}],"year":"2017","quality_controlled":"1","external_id":{"pmid":["28847140"],"isi":["000409566300002"]},"publisher":"Chinese Physiological Society","article_processing_charge":"No","date_created":"2018-12-11T11:47:40Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","date_published":"2017-08-31T00:00:00Z","ddc":["570"],"pmid":1},{"doi":"10.1137/16M1091836","author":[{"id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","last_name":"Kolmogorov"},{"first_name":"Andrei","full_name":"Krokhin, Andrei","last_name":"Krokhin"},{"last_name":"Rolinek","full_name":"Rolinek, Michal","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7138","title":"The complexity of general-valued CSPs","citation":{"chicago":"Kolmogorov, Vladimir, Andrei Krokhin, and Michal Rolinek. “The Complexity of General-Valued CSPs.” <i>SIAM Journal on Computing</i>. SIAM, 2017. <a href=\"https://doi.org/10.1137/16M1091836\">https://doi.org/10.1137/16M1091836</a>.","ama":"Kolmogorov V, Krokhin A, Rolinek M. The complexity of general-valued CSPs. <i>SIAM Journal on Computing</i>. 2017;46(3):1087-1110. doi:<a href=\"https://doi.org/10.1137/16M1091836\">10.1137/16M1091836</a>","apa":"Kolmogorov, V., Krokhin, A., &#38; Rolinek, M. (2017). The complexity of general-valued CSPs. <i>SIAM Journal on Computing</i>. SIAM. <a href=\"https://doi.org/10.1137/16M1091836\">https://doi.org/10.1137/16M1091836</a>","short":"V. Kolmogorov, A. Krokhin, M. Rolinek, SIAM Journal on Computing 46 (2017) 1087–1110.","mla":"Kolmogorov, Vladimir, et al. “The Complexity of General-Valued CSPs.” <i>SIAM Journal on Computing</i>, vol. 46, no. 3, SIAM, 2017, pp. 1087–110, doi:<a href=\"https://doi.org/10.1137/16M1091836\">10.1137/16M1091836</a>.","ieee":"V. Kolmogorov, A. Krokhin, and M. Rolinek, “The complexity of general-valued CSPs,” <i>SIAM Journal on Computing</i>, vol. 46, no. 3. SIAM, pp. 1087–1110, 2017.","ista":"Kolmogorov V, Krokhin A, Rolinek M. 2017. The complexity of general-valued CSPs. SIAM Journal on Computing. 46(3), 1087–1110."},"volume":46,"isi":1,"type":"journal_article","oa_version":"Preprint","day":"29","department":[{"_id":"VlKo"}],"language":[{"iso":"eng"}],"_id":"644","publication_status":"published","related_material":{"record":[{"id":"1637","status":"public","relation":"other"}]},"month":"06","date_updated":"2025-09-23T13:45:56Z","publication":"SIAM Journal on Computing","external_id":{"arxiv":["1502.07327"],"isi":["000404774300010"]},"oa":1,"quality_controlled":"1","publisher":"SIAM","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"scopus_import":"1","date_published":"2017-06-29T00:00:00Z","date_created":"2018-12-11T11:47:40Z","article_processing_charge":"No","status":"public","project":[{"grant_number":"616160","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"intvolume":"        46","page":"1087 - 1110","year":"2017","issue":"3","abstract":[{"text":"An instance of the valued constraint satisfaction problem (VCSP) is given by a finite set of variables, a finite domain of labels, and a sum of functions, each function depending on a subset of the variables. Each function can take finite values specifying costs of assignments of labels to its variables or the infinite value, which indicates an infeasible assignment. The goal is to find an assignment of labels to the variables that minimizes the sum. We study, assuming that P 6= NP, how the complexity of this very general problem depends on the set of functions allowed in the instances, the so-called constraint language. The case when all allowed functions take values in f0;1g corresponds to ordinary CSPs, where one deals only with the feasibility issue, and there is no optimization. This case is the subject of the algebraic CSP dichotomy conjecture predicting for which constraint languages CSPs are tractable (i.e., solvable in polynomial time) and for which they are NP-hard. The case when all allowed functions take only finite values corresponds to a finitevalued CSP, where the feasibility aspect is trivial and one deals only with the optimization issue. The complexity of finite-valued CSPs was fully classified by Thapper and Živný. An algebraic necessary condition for tractability of a general-valued CSP with a fixed constraint language was recently given by Kozik and Ochremiak. As our main result, we prove that if a constraint language satisfies this algebraic necessary condition, and the feasibility CSP (i.e., the problem of deciding whether a given instance has a feasible solution) corresponding to the VCSP with this language is tractable, then the VCSP is tractable. The algorithm is a simple combination of the assumed algorithm for the feasibility CSP and the standard LP relaxation. As a corollary, we obtain that a dichotomy for ordinary CSPs would imply a dichotomy for general-valued CSPs.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1502.07327","open_access":"1"}]},{"external_id":{"arxiv":["1705.02326"],"isi":["000432196400010"]},"oa":1,"quality_controlled":"1","arxiv":1,"publisher":"Springer","scopus_import":"1","ec_funded":1,"date_published":"2017-07-13T00:00:00Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:47:41Z","article_processing_charge":"No","status":"public","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"}],"intvolume":"     10426","page":"201 - 221","year":"2017","abstract":[{"text":"Markov decision processes (MDPs) are standard models for probabilistic systems with non-deterministic behaviours. Long-run average rewards provide a mathematically elegant formalism for expressing long term performance. Value iteration (VI) is one of the simplest and most efficient algorithmic approaches to MDPs with other properties, such as reachability objectives. Unfortunately, a naive extension of VI does not work for MDPs with long-run average rewards, as there is no known stopping criterion. In this work our contributions are threefold. (1) We refute a conjecture related to stopping criteria for MDPs with long-run average rewards. (2) We present two practical algorithms for MDPs with long-run average rewards based on VI. First, we show that a combination of applying VI locally for each maximal end-component (MEC) and VI for reachability objectives can provide approximation guarantees. Second, extending the above approach with a simulation-guided on-demand variant of VI, we present an anytime algorithm that is able to deal with very large models. (3) Finally, we present experimental results showing that our methods significantly outperform the standard approaches on several benchmarks.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.02326"}],"alternative_title":["LNCS"],"doi":"10.1007/978-3-319-63387-9_10","author":[{"last_name":"Ashok","full_name":"Ashok, Pranav","first_name":"Pranav"},{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw"},{"orcid":"0000-0002-8122-2881","last_name":"Kretinsky","first_name":"Jan","full_name":"Kretinsky, Jan","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Meggendorfer","full_name":"Meggendorfer, Tobias","first_name":"Tobias"}],"publist_id":"7135","title":"Value iteration for long run average reward in markov decision processes","volume":10426,"citation":{"chicago":"Ashok, Pranav, Krishnendu Chatterjee, Przemyslaw Daca, Jan Kretinsky, and Tobias Meggendorfer. “Value Iteration for Long Run Average Reward in Markov Decision Processes.” edited by Rupak Majumdar and Viktor Kunčak, 10426:201–21. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-63387-9_10\">https://doi.org/10.1007/978-3-319-63387-9_10</a>.","ama":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. Value iteration for long run average reward in markov decision processes. In: Majumdar R, Kunčak V, eds. Vol 10426. Springer; 2017:201-221. doi:<a href=\"https://doi.org/10.1007/978-3-319-63387-9_10\">10.1007/978-3-319-63387-9_10</a>","apa":"Ashok, P., Chatterjee, K., Daca, P., Kretinsky, J., &#38; Meggendorfer, T. (2017). Value iteration for long run average reward in markov decision processes. In R. Majumdar &#38; V. Kunčak (Eds.) (Vol. 10426, pp. 201–221). Presented at the CAV: Computer Aided Verification, Heidelberg, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-63387-9_10\">https://doi.org/10.1007/978-3-319-63387-9_10</a>","short":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, T. Meggendorfer, in:, R. Majumdar, V. Kunčak (Eds.), Springer, 2017, pp. 201–221.","mla":"Ashok, Pranav, et al. <i>Value Iteration for Long Run Average Reward in Markov Decision Processes</i>. Edited by Rupak Majumdar and Viktor Kunčak, vol. 10426, Springer, 2017, pp. 201–21, doi:<a href=\"https://doi.org/10.1007/978-3-319-63387-9_10\">10.1007/978-3-319-63387-9_10</a>.","ieee":"P. Ashok, K. Chatterjee, P. Daca, J. Kretinsky, and T. Meggendorfer, “Value iteration for long run average reward in markov decision processes,” presented at the CAV: Computer Aided Verification, Heidelberg, Germany, 2017, vol. 10426, pp. 201–221.","ista":"Ashok P, Chatterjee K, Daca P, Kretinsky J, Meggendorfer T. 2017. Value iteration for long run average reward in markov decision processes. CAV: Computer Aided Verification, LNCS, vol. 10426, 201–221."},"editor":[{"full_name":"Majumdar, Rupak","first_name":"Rupak","last_name":"Majumdar"},{"first_name":"Viktor","full_name":"Kunčak, Viktor","last_name":"Kunčak"}],"isi":1,"type":"conference","oa_version":"Submitted Version","day":"13","department":[{"_id":"KrCh"}],"publication_identifier":{"isbn":["978-331963386-2"]},"language":[{"iso":"eng"}],"_id":"645","publication_status":"published","conference":{"location":"Heidelberg, Germany","start_date":"2017-07-24","end_date":"2017-07-28","name":"CAV: Computer Aided Verification"},"month":"07","date_updated":"2025-09-11T07:18:04Z"},{"doi":"10.1007/978-3-319-58771-4_19","alternative_title":["LNCS"],"author":[{"full_name":"Kuske, Jan","first_name":"Jan","last_name":"Kuske"},{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","full_name":"Swoboda, Paul","first_name":"Paul","last_name":"Swoboda"},{"last_name":"Petra","first_name":"Stefanie","full_name":"Petra, Stefanie"}],"volume":10302,"citation":{"ista":"Kuske J, Swoboda P, Petra S. 2017. A novel convex relaxation for non binary discrete tomography. SSVM: Scale Space and Variational Methods in Computer Vision, LNCS, vol. 10302, 235–246.","ieee":"J. Kuske, P. Swoboda, and S. Petra, “A novel convex relaxation for non binary discrete tomography,” presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark, 2017, vol. 10302, pp. 235–246.","mla":"Kuske, Jan, et al. <i>A Novel Convex Relaxation for Non Binary Discrete Tomography</i>. Edited by François Lauze et al., vol. 10302, Springer, 2017, pp. 235–46, doi:<a href=\"https://doi.org/10.1007/978-3-319-58771-4_19\">10.1007/978-3-319-58771-4_19</a>.","short":"J. Kuske, P. Swoboda, S. Petra, in:, F. Lauze, Y. Dong, A. Bjorholm Dahl (Eds.), Springer, 2017, pp. 235–246.","apa":"Kuske, J., Swoboda, P., &#38; Petra, S. (2017). A novel convex relaxation for non binary discrete tomography. In F. Lauze, Y. Dong, &#38; A. Bjorholm Dahl (Eds.) (Vol. 10302, pp. 235–246). Presented at the SSVM: Scale Space and Variational Methods in Computer Vision, Kolding, Denmark: Springer. <a href=\"https://doi.org/10.1007/978-3-319-58771-4_19\">https://doi.org/10.1007/978-3-319-58771-4_19</a>","chicago":"Kuske, Jan, Paul Swoboda, and Stefanie Petra. “A Novel Convex Relaxation for Non Binary Discrete Tomography.” edited by François Lauze, Yiqiu Dong, and Anders Bjorholm Dahl, 10302:235–46. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-58771-4_19\">https://doi.org/10.1007/978-3-319-58771-4_19</a>.","ama":"Kuske J, Swoboda P, Petra S. A novel convex relaxation for non binary discrete tomography. In: Lauze F, Dong Y, Bjorholm Dahl A, eds. Vol 10302. Springer; 2017:235-246. doi:<a href=\"https://doi.org/10.1007/978-3-319-58771-4_19\">10.1007/978-3-319-58771-4_19</a>"},"publist_id":"7132","title":"A novel convex relaxation for non binary discrete tomography","type":"conference","oa_version":"Submitted Version","isi":1,"editor":[{"last_name":"Lauze","full_name":"Lauze, François","first_name":"François"},{"last_name":"Dong","full_name":"Dong, Yiqiu","first_name":"Yiqiu"},{"last_name":"Bjorholm Dahl","first_name":"Anders","full_name":"Bjorholm Dahl, Anders"}],"language":[{"iso":"eng"}],"publication_status":"published","_id":"646","department":[{"_id":"VlKo"}],"day":"01","publication_identifier":{"isbn":["978-331958770-7"]},"conference":{"end_date":"2017-06-08","location":"Kolding, Denmark","start_date":"2017-06-04","name":"SSVM: Scale Space and Variational Methods in Computer Vision"},"month":"06","date_updated":"2025-09-11T07:16:00Z","publisher":"Springer","arxiv":1,"external_id":{"arxiv":["1703.03769"],"isi":["000432210900019"]},"oa":1,"quality_controlled":"1","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2017-06-01T00:00:00Z","ec_funded":1,"date_created":"2018-12-11T11:47:41Z","article_processing_charge":"No","project":[{"grant_number":"616160","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"status":"public","page":"235 - 246","intvolume":"     10302","year":"2017","main_file_link":[{"url":"https://arxiv.org/abs/1703.03769","open_access":"1"}],"abstract":[{"lang":"eng","text":"We present a novel convex relaxation and a corresponding inference algorithm for the non-binary discrete tomography problem, that is, reconstructing discrete-valued images from few linear measurements. In contrast to state of the art approaches that split the problem into a continuous reconstruction problem for the linear measurement constraints and a discrete labeling problem to enforce discrete-valued reconstructions, we propose a joint formulation that addresses both problems simultaneously, resulting in a tighter convex relaxation. For this purpose a constrained graphical model is set up and evaluated using a novel relaxation optimized by dual decomposition. We evaluate our approach experimentally and show superior solutions both mathematically (tighter relaxation) and experimentally in comparison to previously proposed relaxations."}]},{"pubrep_id":"831","abstract":[{"text":"Despite researchers’ efforts in the last couple of decades, reachability analysis is still a challenging problem even for linear hybrid systems. Among the existing approaches, the most practical ones are mainly based on bounded-time reachable set over-approximations. For the purpose of unbounded-time analysis, one important strategy is to abstract the original system and find an invariant for the abstraction. In this paper, we propose an approach to constructing a new kind of abstraction called conic abstraction for affine hybrid systems, and to computing reachable sets based on this abstraction. The essential feature of a conic abstraction is that it partitions the state space of a system into a set of convex polyhedral cones which is derived from a uniform conic partition of the derivative space. Such a set of polyhedral cones is able to cut all trajectories of the system into almost straight segments so that every segment of a reach pipe in a polyhedral cone tends to be straight as well, and hence can be over-approximated tightly by polyhedra using similar techniques as HyTech or PHAVer. In particular, for diagonalizable affine systems, our approach can guarantee to find an invariant for unbounded reachable sets, which is beyond the capability of bounded-time reachability analysis tools. We implemented the approach in a tool and experiments on benchmarks show that our approach is more powerful than SpaceEx and PHAVer in dealing with diagonalizable systems.","lang":"eng"}],"year":"2017","page":"116 - 132","corr_author":"1","project":[{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","grant_number":"S11402-N23"},{"name":"Formal methods for the design and analysis of complex systems","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"}],"status":"public","article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:31Z","date_created":"2018-12-11T11:47:41Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","date_published":"2017-09-01T00:00:00Z","ddc":["005"],"publisher":"Springer","file":[{"creator":"system","file_name":"IST-2017-831-v1+1_main.pdf","date_created":"2018-12-12T10:12:38Z","date_updated":"2020-07-14T12:47:31Z","file_size":3806864,"file_id":"4956","content_type":"application/pdf","checksum":"faf546914ba29bcf9974ee36b6b16750","relation":"main_file","access_level":"open_access"}],"oa":1,"quality_controlled":"1","external_id":{"isi":["000611678300007"]},"date_updated":"2026-04-08T07:47:13Z","month":"09","has_accepted_license":"1","conference":{"end_date":"2017-09-07","location":"Berlin, Germany","start_date":"2017-09-05","name":"FORMATS: Formal Modelling and Analysis of Timed Systems"},"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6894"}]},"_id":"647","publication_status":"published","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-331965764-6"]},"day":"01","department":[{"_id":"ToHe"}],"oa_version":"Submitted Version","type":"conference","isi":1,"citation":{"apa":"Bogomolov, S., Giacobbe, M., Henzinger, T. A., &#38; Kong, H. (2017). Conic abstractions for hybrid systems (Vol. 10419, pp. 116–132). Presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-65765-3_7\">https://doi.org/10.1007/978-3-319-65765-3_7</a>","chicago":"Bogomolov, Sergiy, Mirco Giacobbe, Thomas A Henzinger, and Hui Kong. “Conic Abstractions for Hybrid Systems,” 10419:116–32. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-65765-3_7\">https://doi.org/10.1007/978-3-319-65765-3_7</a>.","ama":"Bogomolov S, Giacobbe M, Henzinger TA, Kong H. Conic abstractions for hybrid systems. In: Vol 10419. Springer; 2017:116-132. doi:<a href=\"https://doi.org/10.1007/978-3-319-65765-3_7\">10.1007/978-3-319-65765-3_7</a>","short":"S. Bogomolov, M. Giacobbe, T.A. Henzinger, H. Kong, in:, Springer, 2017, pp. 116–132.","ista":"Bogomolov S, Giacobbe M, Henzinger TA, Kong H. 2017. Conic abstractions for hybrid systems. FORMATS: Formal Modelling and Analysis of Timed Systems, LNCS, vol. 10419, 116–132.","ieee":"S. Bogomolov, M. Giacobbe, T. A. Henzinger, and H. Kong, “Conic abstractions for hybrid systems,” presented at the FORMATS: Formal Modelling and Analysis of Timed Systems, Berlin, Germany, 2017, vol. 10419, pp. 116–132.","mla":"Bogomolov, Sergiy, et al. <i>Conic Abstractions for Hybrid Systems</i>. Vol. 10419, Springer, 2017, pp. 116–32, doi:<a href=\"https://doi.org/10.1007/978-3-319-65765-3_7\">10.1007/978-3-319-65765-3_7</a>."},"volume":"10419 ","title":"Conic abstractions for hybrid systems","publist_id":"7129","author":[{"orcid":"0000-0002-0686-0365","first_name":"Sergiy","full_name":"Bogomolov, Sergiy","last_name":"Bogomolov","id":"369D9A44-F248-11E8-B48F-1D18A9856A87"},{"id":"3444EA5E-F248-11E8-B48F-1D18A9856A87","full_name":"Giacobbe, Mirco","first_name":"Mirco","last_name":"Giacobbe","orcid":"0000-0001-8180-0904"},{"orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"id":"3BDE25AA-F248-11E8-B48F-1D18A9856A87","first_name":"Hui","full_name":"Kong, Hui","last_name":"Kong","orcid":"0000-0002-3066-6941"}],"doi":"10.1007/978-3-319-65765-3_7","alternative_title":["LNCS"]},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2017-04-01T00:00:00Z","scopus_import":"1","date_created":"2018-12-11T11:47:42Z","article_processing_charge":"No","external_id":{"isi":["000425175500043"]},"quality_controlled":"1","oa":1,"publisher":"Springer","year":"2017","abstract":[{"lang":"eng","text":"Pseudoentropy has found a lot of important applications to cryptography and complexity theory. In this paper we focus on the foundational problem that has not been investigated so far, namely by how much pseudoentropy (the amount seen by computationally bounded attackers) differs from its information-theoretic counterpart (seen by unbounded observers), given certain limits on attacker’s computational power? We provide the following answer for HILL pseudoentropy, which exhibits a threshold behavior around the size exponential in the entropy amount:– If the attacker size (s) and advantage () satisfy s (formula presented) where k is the claimed amount of pseudoentropy, then the pseudoentropy boils down to the information-theoretic smooth entropy. – If s (formula presented) then pseudoentropy could be arbitrarily bigger than the information-theoretic smooth entropy. Besides answering the posted question, we show an elegant application of our result to the complexity theory, namely that it implies the clas-sical result on the existence of functions hard to approximate (due to Pippenger). In our approach we utilize non-constructive techniques: the duality of linear programming and the probabilistic method."}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/1186.pdf"}],"status":"public","intvolume":"     10185","page":"600 - 613","corr_author":"1","publist_id":"7125","title":"On the complexity of breaking pseudoentropy","citation":{"apa":"Skórski, M. (2017). On the complexity of breaking pseudoentropy. In G. Jäger &#38; S. Steila (Eds.) (Vol. 10185, pp. 600–613). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. <a href=\"https://doi.org/10.1007/978-3-319-55911-7_43\">https://doi.org/10.1007/978-3-319-55911-7_43</a>","ama":"Skórski M. On the complexity of breaking pseudoentropy. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:600-613. doi:<a href=\"https://doi.org/10.1007/978-3-319-55911-7_43\">10.1007/978-3-319-55911-7_43</a>","chicago":"Skórski, Maciej. “On the Complexity of Breaking Pseudoentropy.” edited by Gerhard Jäger and Silvia Steila, 10185:600–613. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-55911-7_43\">https://doi.org/10.1007/978-3-319-55911-7_43</a>.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 600–613.","ista":"Skórski M. 2017. On the complexity of breaking pseudoentropy. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 600–613.","ieee":"M. Skórski, “On the complexity of breaking pseudoentropy,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 600–613.","mla":"Skórski, Maciej. <i>On the Complexity of Breaking Pseudoentropy</i>. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 600–13, doi:<a href=\"https://doi.org/10.1007/978-3-319-55911-7_43\">10.1007/978-3-319-55911-7_43</a>."},"volume":10185,"editor":[{"first_name":"Gerhard","full_name":"Jäger, Gerhard","last_name":"Jäger"},{"full_name":"Steila, Silvia","first_name":"Silvia","last_name":"Steila"}],"type":"conference","oa_version":"Submitted Version","isi":1,"alternative_title":["LNCS"],"doi":"10.1007/978-3-319-55911-7_43","author":[{"last_name":"Skórski","first_name":"Maciej","full_name":"Skórski, Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"}],"month":"04","date_updated":"2025-09-11T07:14:42Z","day":"01","department":[{"_id":"KrPi"}],"publication_identifier":{"isbn":["978-331955910-0"]},"language":[{"iso":"eng"}],"_id":"648","publication_status":"published","conference":{"end_date":"2017-04-22","location":"Bern, Switzerland","start_date":"2017-04-20","name":"TAMC: Theory and Applications of Models of Computation"}},{"abstract":[{"lang":"eng","text":"We give a short overview on a recently developed notion of Ricci curvature for discrete spaces. This notion relies on geodesic convexity properties of the relative entropy along geodesics in the space of probability densities, for a metric which is similar to (but different from) the 2-Wasserstein metric. The theory can be considered as a discrete counterpart to the theory of Ricci curvature for geodesic measure spaces developed by Lott–Sturm–Villani."}],"year":"2017","intvolume":"      2184","page":"159 - 174","corr_author":"1","status":"public","date_created":"2018-12-11T11:47:42Z","article_processing_charge":"No","date_published":"2017-10-05T00:00:00Z","scopus_import":"1","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","quality_controlled":"1","publisher":"Springer","date_updated":"2026-04-16T08:59:01Z","publication":"Modern Approaches to Discrete Curvature","series_title":"Lecture Notes in Mathematics","month":"10","department":[{"_id":"JaMa"}],"day":"05","publication_identifier":{"isbn":["9783319580012"],"eisbn":["9783319580029"]},"language":[{"iso":"eng"}],"_id":"649","publication_status":"published","editor":[{"first_name":"Laurent","full_name":"Najman, Laurent","last_name":"Najman"},{"last_name":"Romon","full_name":"Romon, Pascal","first_name":"Pascal"}],"type":"book_chapter","oa_version":"None","publist_id":"7123","title":"Entropic Ricci curvature for discrete spaces","volume":2184,"citation":{"mla":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” <i>Modern Approaches to Discrete Curvature</i>, edited by Laurent Najman and Pascal Romon, vol. 2184, Springer, 2017, pp. 159–74, doi:<a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">10.1007/978-3-319-58002-9_5</a>.","ieee":"J. Maas, “Entropic Ricci curvature for discrete spaces,” in <i>Modern Approaches to Discrete Curvature</i>, vol. 2184, L. Najman and P. Romon, Eds. Springer, 2017, pp. 159–174.","ista":"Maas J. 2017.Entropic Ricci curvature for discrete spaces. In: Modern Approaches to Discrete Curvature. vol. 2184, 159–174.","chicago":"Maas, Jan. “Entropic Ricci Curvature for Discrete Spaces.” In <i>Modern Approaches to Discrete Curvature</i>, edited by Laurent Najman and Pascal Romon, 2184:159–74. Lecture Notes in Mathematics. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">https://doi.org/10.1007/978-3-319-58002-9_5</a>.","ama":"Maas J. Entropic Ricci curvature for discrete spaces. In: Najman L, Romon P, eds. <i>Modern Approaches to Discrete Curvature</i>. Vol 2184. Lecture Notes in Mathematics. Springer; 2017:159-174. doi:<a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">10.1007/978-3-319-58002-9_5</a>","apa":"Maas, J. (2017). Entropic Ricci curvature for discrete spaces. In L. Najman &#38; P. Romon (Eds.), <i>Modern Approaches to Discrete Curvature</i> (Vol. 2184, pp. 159–174). Springer. <a href=\"https://doi.org/10.1007/978-3-319-58002-9_5\">https://doi.org/10.1007/978-3-319-58002-9_5</a>","short":"J. Maas, in:, L. Najman, P. Romon (Eds.), Modern Approaches to Discrete Curvature, Springer, 2017, pp. 159–174."},"author":[{"orcid":"0000-0002-0845-1338","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87","full_name":"Maas, Jan","first_name":"Jan","last_name":"Maas"}],"doi":"10.1007/978-3-319-58002-9_5"},{"conference":{"start_date":"2017-04-20","location":"Bern, Switzerland","end_date":"2017-04-22","name":"TAMC: Theory and Applications of Models of Computation"},"department":[{"_id":"KrPi"}],"day":"01","publication_identifier":{"issn":["0302-9743"]},"language":[{"iso":"eng"}],"_id":"650","publication_status":"published","date_updated":"2026-04-16T09:59:38Z","month":"01","author":[{"id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD","first_name":"Maciej","full_name":"Skórski, Maciej","last_name":"Skórski"}],"alternative_title":["LNCS"],"doi":"10.1007/978-3-319-55911-7_42","editor":[{"first_name":"Gerhard","full_name":"Jäger, Gerhard","last_name":"Jäger"},{"full_name":"Steila, Silvia","first_name":"Silvia","last_name":"Steila"}],"type":"conference","oa_version":"Submitted Version","isi":1,"publist_id":"7119","title":"A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds","volume":10185,"citation":{"ista":"Skórski M. 2017. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. TAMC: Theory and Applications of Models of Computation, LNCS, vol. 10185, 586–599.","mla":"Skórski, Maciej. <i>A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds</i>. Edited by Gerhard Jäger and Silvia Steila, vol. 10185, Springer, 2017, pp. 586–99, doi:<a href=\"https://doi.org/10.1007/978-3-319-55911-7_42\">10.1007/978-3-319-55911-7_42</a>.","ieee":"M. Skórski, “A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds,” presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland, 2017, vol. 10185, pp. 586–599.","apa":"Skórski, M. (2017). A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In G. Jäger &#38; S. Steila (Eds.) (Vol. 10185, pp. 586–599). Presented at the TAMC: Theory and Applications of Models of Computation, Bern, Switzerland: Springer. <a href=\"https://doi.org/10.1007/978-3-319-55911-7_42\">https://doi.org/10.1007/978-3-319-55911-7_42</a>","ama":"Skórski M. A cryptographic view of regularity lemmas: Simpler unified proofs and refined bounds. In: Jäger G, Steila S, eds. Vol 10185. Springer; 2017:586-599. doi:<a href=\"https://doi.org/10.1007/978-3-319-55911-7_42\">10.1007/978-3-319-55911-7_42</a>","chicago":"Skórski, Maciej. “A Cryptographic View of Regularity Lemmas: Simpler Unified Proofs and Refined Bounds.” edited by Gerhard Jäger and Silvia Steila, 10185:586–99. Springer, 2017. <a href=\"https://doi.org/10.1007/978-3-319-55911-7_42\">https://doi.org/10.1007/978-3-319-55911-7_42</a>.","short":"M. Skórski, in:, G. Jäger, S. Steila (Eds.), Springer, 2017, pp. 586–599."},"intvolume":"     10185","page":"586 - 599","corr_author":"1","status":"public","abstract":[{"lang":"eng","text":"In this work we present a short and unified proof for the Strong and Weak Regularity Lemma, based on the cryptographic tech-nique called low-complexity approximations. In short, both problems reduce to a task of finding constructively an approximation for a certain target function under a class of distinguishers (test functions), where dis-tinguishers are combinations of simple rectangle-indicators. In our case these approximations can be learned by a simple iterative procedure, which yields a unified and simple proof, achieving for any graph with density d and any approximation parameter the partition size. The novelty in our proof is: (a) a simple approach which yields both strong and weaker variant, and (b) improvements when d = o(1). At an abstract level, our proof can be seen a refinement and simplification of the “analytic” proof given by Lovasz and Szegedy."}],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2016/965.pdf"}],"year":"2017","external_id":{"isi":["000425175500042"]},"oa":1,"quality_controlled":"1","publisher":"Springer","date_created":"2018-12-11T11:47:42Z","article_processing_charge":"No","date_published":"2017-01-01T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","scopus_import":"1"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_published":"2017-01-11T00:00:00Z","scopus_import":"1","article_processing_charge":"No","date_created":"2018-12-11T11:47:43Z","publisher":"Nature Publishing Group","quality_controlled":"1","external_id":{"isi":["000396125500023"]},"year":"2017","issue":"7636","abstract":[{"text":"Superhydrophobic surfaces reduce the frictional drag between water and solid materials, but this effect is often temporary. The realization of sustained drag reduction has applications for water vehicles and pipeline flows.\r\n\r\n","lang":"eng"}],"status":"public","page":"161 - 162","corr_author":"1","intvolume":"       541","volume":541,"citation":{"apa":"Hof, B. (2017). Fluid dynamics: Water flows out of touch. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/541161a\">https://doi.org/10.1038/541161a</a>","ama":"Hof B. Fluid dynamics: Water flows out of touch. <i>Nature</i>. 2017;541(7636):161-162. doi:<a href=\"https://doi.org/10.1038/541161a\">10.1038/541161a</a>","chicago":"Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” <i>Nature</i>. Nature Publishing Group, 2017. <a href=\"https://doi.org/10.1038/541161a\">https://doi.org/10.1038/541161a</a>.","short":"B. Hof, Nature 541 (2017) 161–162.","ista":"Hof B. 2017. Fluid dynamics: Water flows out of touch. Nature. 541(7636), 161–162.","mla":"Hof, Björn. “Fluid Dynamics: Water Flows out of Touch.” <i>Nature</i>, vol. 541, no. 7636, Nature Publishing Group, 2017, pp. 161–62, doi:<a href=\"https://doi.org/10.1038/541161a\">10.1038/541161a</a>.","ieee":"B. Hof, “Fluid dynamics: Water flows out of touch,” <i>Nature</i>, vol. 541, no. 7636. Nature Publishing Group, pp. 161–162, 2017."},"title":"Fluid dynamics: Water flows out of touch","publist_id":"7116","oa_version":"None","isi":1,"type":"journal_article","doi":"10.1038/541161a","author":[{"last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754"}],"month":"01","publication":"Nature","date_updated":"2025-09-11T07:13:33Z","_id":"651","publication_status":"published","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0028-0836"]},"day":"11","department":[{"_id":"BjHo"}]},{"file":[{"creator":"kschuh","file_name":"2017_LIPIcs-Fulek.pdf","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-04T12:20:35Z","file_size":588982,"content_type":"application/pdf","file_id":"6518","checksum":"fc7a643e29621c8bbe49d36b39081f31","access_level":"open_access","relation":"main_file"}],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"date_created":"2019-06-04T12:11:52Z","file_date_updated":"2020-07-14T12:47:33Z","ddc":["510"],"date_published":"2017-12-01T00:00:00Z","ec_funded":1,"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"corr_author":"1","intvolume":"        92","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"call_identifier":"FWF","grant_number":"M02281","name":"Eliminating intersections in drawings of graphs","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"status":"public","abstract":[{"lang":"eng","text":"A (possibly degenerate) drawing of a graph G in the plane is approximable by an embedding if it can be turned into an embedding by an arbitrarily small perturbation. We show that testing, whether a drawing of a planar graph G in the plane is approximable by an embedding, can be carried out in polynomial time, if a desired embedding of G belongs to a fixed isotopy class, i.e., the rotation system (or equivalently the faces) of the embedding of G and the choice of outer face are fixed. In other words, we show that c-planarity with embedded pipes is tractable for graphs with fixed embeddings. To the best of our knowledge an analogous result was previously known essentially only when G is a cycle."}],"year":"2017","author":[{"orcid":"0000-0001-8485-1774","last_name":"Fulek","full_name":"Fulek, Radoslav","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.4230/LIPICS.ISAAC.2017.34","oa_version":"Published Version","tmp":{"image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"type":"conference","citation":{"mla":"Fulek, Radoslav. <i>Embedding Graphs into Embedded Graphs</i>. Vol. 92, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017, doi:<a href=\"https://doi.org/10.4230/LIPICS.ISAAC.2017.34\">10.4230/LIPICS.ISAAC.2017.34</a>.","ieee":"R. Fulek, “Embedding graphs into embedded graphs,” presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand, 2017, vol. 92.","ista":"Fulek R. 2017. Embedding graphs into embedded graphs. ISAAC: International Symposium on Algorithms and Computation vol. 92, 34.","short":"R. Fulek, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017.","chicago":"Fulek, Radoslav. “Embedding Graphs into Embedded Graphs,” Vol. 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2017. <a href=\"https://doi.org/10.4230/LIPICS.ISAAC.2017.34\">https://doi.org/10.4230/LIPICS.ISAAC.2017.34</a>.","ama":"Fulek R. Embedding graphs into embedded graphs. In: Vol 92. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2017. doi:<a href=\"https://doi.org/10.4230/LIPICS.ISAAC.2017.34\">10.4230/LIPICS.ISAAC.2017.34</a>","apa":"Fulek, R. (2017). Embedding graphs into embedded graphs (Vol. 92). Presented at the ISAAC: International Symposium on Algorithms and Computation, Phuket, Thailand: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.ISAAC.2017.34\">https://doi.org/10.4230/LIPICS.ISAAC.2017.34</a>"},"volume":92,"title":"Embedding graphs into embedded graphs","has_accepted_license":"1","conference":{"name":"ISAAC: International Symposium on Algorithms and Computation","start_date":"2017-12-09","end_date":"2017-12-22","location":"Phuket, Thailand"},"article_number":"34","language":[{"iso":"eng"}],"publication_status":"published","_id":"6517","day":"01","department":[{"_id":"UlWa"}],"date_updated":"2024-10-09T20:58:52Z","month":"12"}]