[{"acknowledgement":" Supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No\r\nS11407-N23 (RiSE), ERC Start grant (279307: Graph Games), and Microsoft faculty fellows award.","OA_place":"repository","conference":{"location":"San Diego, CA, United States","start_date":"2014-01-19","end_date":"2014-01-21","name":"VMCAI: Verifcation, Model Checking, and Abstract Interpretation"},"year":"2014","publisher":"Springer Nature","language":[{"iso":"eng"}],"month":"01","date_updated":"2026-04-16T10:00:03Z","_id":"10885","citation":{"ista":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. 2014. Doomsday equilibria for omega-regular games. VMCAI 2014: Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 78–97.","short":"K. Chatterjee, L. Doyen, E. Filiot, J.-F. Raskin, in:, VMCAI 2014: Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 78–97.","apa":"Chatterjee, K., Doyen, L., Filiot, E., &#38; Raskin, J.-F. (2014). Doomsday equilibria for omega-regular games. In <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i> (Vol. 8318, pp. 78–97). San Diego, CA, United States: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">https://doi.org/10.1007/978-3-642-54013-4_5</a>","ieee":"K. Chatterjee, L. Doyen, E. Filiot, and J.-F. Raskin, “Doomsday equilibria for omega-regular games,” in <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>, San Diego, CA, United States, 2014, vol. 8318, pp. 78–97.","mla":"Chatterjee, Krishnendu, et al. “Doomsday Equilibria for Omega-Regular Games.” <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>, vol. 8318, Springer Nature, 2014, pp. 78–97, doi:<a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">10.1007/978-3-642-54013-4_5</a>.","ama":"Chatterjee K, Doyen L, Filiot E, Raskin J-F. Doomsday equilibria for omega-regular games. In: <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>. Vol 8318. Springer Nature; 2014:78-97. doi:<a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">10.1007/978-3-642-54013-4_5</a>","chicago":"Chatterjee, Krishnendu, Laurent Doyen, Emmanuel Filiot, and Jean-François Raskin. “Doomsday Equilibria for Omega-Regular Games.” In <i>VMCAI 2014: Verification, Model Checking, and Abstract Interpretation</i>, 8318:78–97. Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-642-54013-4_5\">https://doi.org/10.1007/978-3-642-54013-4_5</a>."},"page":"78-97","ec_funded":1,"arxiv":1,"title":"Doomsday equilibria for omega-regular games","alternative_title":["LNCS"],"author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Doyen, Laurent","first_name":"Laurent","last_name":"Doyen"},{"full_name":"Filiot, Emmanuel","last_name":"Filiot","first_name":"Emmanuel"},{"last_name":"Raskin","first_name":"Jean-François","full_name":"Raskin, Jean-François"}],"date_published":"2014-01-30T00:00:00Z","type":"conference","publication":"VMCAI 2014: Verification, Model Checking, and Abstract Interpretation","article_processing_charge":"No","publication_identifier":{"isbn":["9783642540127"],"issn":["0302-9743"],"eisbn":["9783642540134"],"eissn":["1611-3349"]},"quality_controlled":"1","oa":1,"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1311.3238","open_access":"1"}],"publication_status":"published","status":"public","doi":"10.1007/978-3-642-54013-4_5","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"day":"30","OA_type":"green","oa_version":"Preprint","date_created":"2022-03-18T13:03:15Z","volume":8318,"related_material":{"record":[{"id":"681","relation":"later_version","status":"public"}]},"abstract":[{"lang":"eng","text":"Two-player games on graphs provide the theoretical framework for many important problems such as reactive synthesis. While the traditional study of two-player zero-sum games has been extended to multi-player games with several notions of equilibria, they are decidable only for perfect-information games, whereas several applications require imperfect-information games.\r\nIn this paper we propose a new notion of equilibria, called doomsday equilibria, which is a strategy profile such that all players satisfy their own objective, and if any coalition of players deviates and violates even one of the players objective, then the objective of every player is violated.\r\nWe present algorithms and complexity results for deciding the existence of doomsday equilibria for various classes of ω-regular objectives, both for imperfect-information games, and for perfect-information games.We provide optimal complexity bounds for imperfect-information games, and in most cases for perfect-information games."}],"scopus_import":"1","external_id":{"arxiv":["1311.3238"]},"intvolume":"      8318"},{"date_published":"2014-01-08T00:00:00Z","has_accepted_license":"1","type":"journal_article","isi":1,"ec_funded":1,"publist_id":"4692","title":"Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations","author":[{"full_name":"Pernia-Andrade, Alejandro","last_name":"Pernia-Andrade","first_name":"Alejandro","id":"36963E98-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"article_processing_charge":"No","publication_identifier":{"issn":["0896-6273"]},"quality_controlled":"1","publication":"Neuron","ddc":["570"],"year":"2014","file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:45:35Z","access_level":"open_access","date_created":"2018-12-12T10:09:48Z","checksum":"438547cfcd9045a22f065f2019f07849","file_size":4373072,"file_name":"IST-2016-422-v1+1_1-s2.0-S0896627313009227-main.pdf","creator":"system","file_id":"4773"}],"publisher":"Elsevier","corr_author":"1","language":[{"iso":"eng"}],"month":"01","page":"140 - 152","_id":"2254","citation":{"ista":"Pernia-Andrade A, Jonas PM. 2014. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. Neuron. 81(1), 140–152.","short":"A. Pernia-Andrade, P.M. Jonas, Neuron 81 (2014) 140–152.","apa":"Pernia-Andrade, A., &#38; Jonas, P. M. (2014). Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">https://doi.org/10.1016/j.neuron.2013.09.046</a>","ieee":"A. Pernia-Andrade and P. M. Jonas, “Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations,” <i>Neuron</i>, vol. 81, no. 1. Elsevier, pp. 140–152, 2014.","mla":"Pernia-Andrade, Alejandro, and Peter M. Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” <i>Neuron</i>, vol. 81, no. 1, Elsevier, 2014, pp. 140–52, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">10.1016/j.neuron.2013.09.046</a>.","ama":"Pernia-Andrade A, Jonas PM. Theta-gamma-modulated synaptic currents in hippocampal granule cells in vivo define a mechanism for network oscillations. <i>Neuron</i>. 2014;81(1):140-152. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">10.1016/j.neuron.2013.09.046</a>","chicago":"Pernia-Andrade, Alejandro, and Peter M Jonas. “Theta-Gamma-Modulated Synaptic Currents in Hippocampal Granule Cells in Vivo Define a Mechanism for Network Oscillations.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2013.09.046\">https://doi.org/10.1016/j.neuron.2013.09.046</a>."},"date_updated":"2026-04-16T10:08:53Z","volume":81,"date_created":"2018-12-11T11:56:35Z","abstract":[{"text":"Theta-gamma network oscillations are thought to represent key reference signals for information processing in neuronal ensembles, but the underlying synaptic mechanisms remain unclear. To address this question, we performed whole-cell (WC) patch-clamp recordings from mature hippocampal granule cells (GCs) in vivo in the dentate gyrus of anesthetized and awake rats. GCs in vivo fired action potentials at low frequency, consistent with sparse coding in the dentate gyrus. GCs were exposed to barrages of fast AMPAR-mediated excitatory postsynaptic currents (EPSCs), primarily relayed from the entorhinal cortex, and inhibitory postsynaptic currents (IPSCs), presumably generated by local interneurons. EPSCs exhibited coherence with the field potential predominantly in the theta frequency band, whereas IPSCs showed coherence primarily in the gamma range. Action potentials in GCs were phase locked to network oscillations. Thus, theta-gamma-modulated synaptic currents may provide a framework for sparse temporal coding of information in the dentate gyrus.","lang":"eng"}],"oa_version":"Published Version","intvolume":"        81","scopus_import":"1","external_id":{"isi":["000329559000015"]},"pubrep_id":"422","file_date_updated":"2020-07-14T12:45:35Z","oa":1,"issue":"1","doi":"10.1016/j.neuron.2013.09.046","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"PeJo"}],"project":[{"name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","call_identifier":"FP7","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425"},{"name":"Mechanisms of transmitter release at GABAergic synapses","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","grant_number":"P24909-B24"}],"day":"08","publication_status":"published","status":"public"},{"publication":"Fluid Dynamics Research","article_processing_charge":"No","quality_controlled":"1","publication_identifier":{"issn":["0169-5983"]},"publist_id":"4740","isi":1,"author":[{"orcid":"0000-0001-5964-0203","id":"2EE67FDC-F248-11E8-B48F-1D18A9856A87","first_name":"Sebastian","last_name":"Altmeyer","full_name":"Altmeyer, Sebastian"}],"title":"On secondary instabilities generating footbridges between spiral vortex flow","date_published":"2014-04-01T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"corr_author":"1","publisher":"IOP Publishing","_id":"2224","date_updated":"2026-04-16T10:07:46Z","citation":{"chicago":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” <i>Fluid Dynamics Research</i>. IOP Publishing, 2014. <a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">https://doi.org/10.1088/0169-5983/46/2/025503</a>.","ista":"Altmeyer S. 2014. On secondary instabilities generating footbridges between spiral vortex flow. Fluid Dynamics Research. 46(2), 025503.","apa":"Altmeyer, S. (2014). On secondary instabilities generating footbridges between spiral vortex flow. <i>Fluid Dynamics Research</i>. IOP Publishing. <a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">https://doi.org/10.1088/0169-5983/46/2/025503</a>","short":"S. Altmeyer, Fluid Dynamics Research 46 (2014).","ieee":"S. Altmeyer, “On secondary instabilities generating footbridges between spiral vortex flow,” <i>Fluid Dynamics Research</i>, vol. 46, no. 2. IOP Publishing, 2014.","ama":"Altmeyer S. On secondary instabilities generating footbridges between spiral vortex flow. <i>Fluid Dynamics Research</i>. 2014;46(2). doi:<a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">10.1088/0169-5983/46/2/025503</a>","mla":"Altmeyer, Sebastian. “On Secondary Instabilities Generating Footbridges between Spiral Vortex Flow.” <i>Fluid Dynamics Research</i>, vol. 46, no. 2, 025503, IOP Publishing, 2014, doi:<a href=\"https://doi.org/10.1088/0169-5983/46/2/025503\">10.1088/0169-5983/46/2/025503</a>."},"month":"04","year":"2014","scopus_import":"1","external_id":{"isi":["000334075800003"]},"intvolume":"        46","oa_version":"None","volume":46,"date_created":"2018-12-11T11:56:25Z","abstract":[{"lang":"eng","text":"This work investigates the transition between different traveling helical waves (spirals, SPIs) in the setup of differentially independent rotating cylinders. We use direct numerical simulations to consider an infinite long and periodic Taylor-Couette apparatus with fixed axial periodicity length. We find so-called mixed-cross-spirals (MCSs), that can be seen as nonlinear superpositions of SPIs, to establish stable footbridges connecting SPI states. While bridging the bifurcation branches of SPIs, the corresponding contributions within the MCS vary continuously with the control parameters. Here discussed MCSs presenting footbridge solutions start and end in different SPI branches. Therefore they differ significantly from the already known MCSs that present bypass solutions (Altmeyer and Hoffmann 2010 New J. Phys. 12 113035). The latter start and end in the same SPI branch, while they always bifurcate out of those SPI branches with the larger mode amplitude. Meanwhile, these only appear within the coexisting region of both SPIs. In contrast, the footbridge solutions can also bifurcate out of the minor SPI contribution. We also find they exist in regions where only one of the SPIs contributions exists. In addition, MCS as footbridge solution can appear either stable or unstable. The latter detected transient solutions offer similar spatio-temporal characteristics to the flow establishing stable footbridges. Such transition processes are interesting for pattern-forming systems in general because they accomplish transitions between traveling waves of different azimuthal wave numbers and have not been described in the literature yet."}],"article_number":"025503","publication_status":"published","status":"public","department":[{"_id":"BjHo"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1088/0169-5983/46/2/025503","day":"01","issue":"2"},{"oa":1,"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3981873/"}],"issue":"1","doi":"10.1111/tpj.12373","department":[{"_id":"JiFr"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"01","publication_status":"published","status":"public","date_created":"2018-12-11T11:56:34Z","volume":77,"abstract":[{"text":"The unfolded protein response (UPR) is a signaling network triggered by overload of protein-folding demand in the endoplasmic reticulum (ER), a condition termed ER stress. The UPR is critical for growth and development; nonetheless, connections between the UPR and other cellular regulatory processes remain largely unknown. Here, we identify a link between the UPR and the phytohormone auxin, a master regulator of plant physiology. We show that ER stress triggers down-regulation of auxin receptors and transporters in Arabidopsis thaliana. We also demonstrate that an Arabidopsis mutant of a conserved ER stress sensor IRE1 exhibits defects in the auxin response and levels. These data not only support that the plant IRE1 is required for auxin homeostasis, they also reveal a species-specific feature of IRE1 in multicellular eukaryotes. Furthermore, by establishing that UPR activation is reduced in mutants of ER-localized auxin transporters, including PIN5, we define a long-neglected biological significance of ER-based auxin regulation. We further examine the functional relationship of IRE1 and PIN5 by showing that an ire1 pin5 triple mutant enhances defects of UPR activation and auxin homeostasis in ire1 or pin5. Our results imply that the plant UPR has evolved a hormone-dependent strategy for coordinating ER function with physiological processes.","lang":"eng"}],"oa_version":"Submitted Version","intvolume":"        77","scopus_import":"1","external_id":{"isi":["000328661300008"]},"year":"2014","publisher":"Wiley-Blackwell","language":[{"iso":"eng"}],"month":"01","citation":{"mla":"Chen, Yani, et al. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” <i>Plant Journal</i>, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 97–107, doi:<a href=\"https://doi.org/10.1111/tpj.12373\">10.1111/tpj.12373</a>.","ama":"Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. Inter-regulation of the unfolded protein response and auxin signaling. <i>Plant Journal</i>. 2014;77(1):97-107. doi:<a href=\"https://doi.org/10.1111/tpj.12373\">10.1111/tpj.12373</a>","ieee":"Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, and F. Brandizzí, “Inter-regulation of the unfolded protein response and auxin signaling,” <i>Plant Journal</i>, vol. 77, no. 1. Wiley-Blackwell, pp. 97–107, 2014.","apa":"Chen, Y., Aung, K., Rolčík, J., Walicki, K., Friml, J., &#38; Brandizzí, F. (2014). Inter-regulation of the unfolded protein response and auxin signaling. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12373\">https://doi.org/10.1111/tpj.12373</a>","short":"Y. Chen, K. Aung, J. Rolčík, K. Walicki, J. Friml, F. Brandizzí, Plant Journal 77 (2014) 97–107.","ista":"Chen Y, Aung K, Rolčík J, Walicki K, Friml J, Brandizzí F. 2014. Inter-regulation of the unfolded protein response and auxin signaling. Plant Journal. 77(1), 97–107.","chicago":"Chen, Yani, Kyaw Aung, Jakub Rolčík, Kathryn Walicki, Jiří Friml, and Federica Brandizzí. “Inter-Regulation of the Unfolded Protein Response and Auxin Signaling.” <i>Plant Journal</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/tpj.12373\">https://doi.org/10.1111/tpj.12373</a>."},"_id":"2249","date_updated":"2026-04-16T10:08:30Z","page":"97 - 107","date_published":"2014-01-01T00:00:00Z","type":"journal_article","isi":1,"publist_id":"4699","title":"Inter-regulation of the unfolded protein response and auxin signaling","author":[{"full_name":"Chen, Yani","last_name":"Chen","first_name":"Yani"},{"first_name":"Kyaw","last_name":"Aung","full_name":"Aung, Kyaw"},{"first_name":"Jakub","last_name":"Rolčík","full_name":"Rolčík, Jakub"},{"full_name":"Walicki, Kathryn","last_name":"Walicki","first_name":"Kathryn"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Brandizzí, Federica","last_name":"Brandizzí","first_name":"Federica"}],"article_processing_charge":"No","publication_identifier":{"issn":["0960-7412"]},"quality_controlled":"1","publication":"Plant Journal"},{"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1303.3777"}],"oa":1,"publication_status":"published","status":"public","doi":"10.1016/j.tcs.2013.11.032","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"KrCh"}],"day":"13","oa_version":"Submitted Version","date_created":"2018-12-11T11:56:33Z","volume":521,"abstract":[{"text":"Muller games are played by two players moving a token along a graph; the winner is determined by the set of vertices that occur infinitely often. The central algorithmic problem is to compute the winning regions for the players. Different classes and representations of Muller games lead to problems of varying computational complexity. One such class are parity games; these are of particular significance in computational complexity, as they remain one of the few combinatorial problems known to be in NP ∩ co-NP but not known to be in P. We show that winning regions for a Muller game can be determined from the alternating structure of its traps. To every Muller game we then associate a natural number that we call its trap depth; this parameter measures how complicated the trap structure is. We present algorithms for parity games that run in polynomial time for graphs of bounded trap depth, and in general run in time exponential in the trap depth. ","lang":"eng"}],"scopus_import":"1","external_id":{"arxiv":["1303.3777"],"isi":["000331433100007"]},"intvolume":"       521","year":"2014","publisher":"Elsevier","corr_author":"1","language":[{"iso":"eng"}],"month":"02","_id":"2246","date_updated":"2026-04-16T10:08:15Z","citation":{"mla":"Grinshpun, Andrey, et al. “Alternating Traps in Muller and Parity Games.” <i>Theoretical Computer Science</i>, vol. 521, Elsevier, 2014, pp. 73–91, doi:<a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">10.1016/j.tcs.2013.11.032</a>.","ama":"Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. Alternating traps in Muller and parity games. <i>Theoretical Computer Science</i>. 2014;521:73-91. doi:<a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">10.1016/j.tcs.2013.11.032</a>","ieee":"A. Grinshpun, P. Phalitnonkiat, S. Rubin, and A. Tarfulea, “Alternating traps in Muller and parity games,” <i>Theoretical Computer Science</i>, vol. 521. Elsevier, pp. 73–91, 2014.","apa":"Grinshpun, A., Phalitnonkiat, P., Rubin, S., &#38; Tarfulea, A. (2014). Alternating traps in Muller and parity games. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">https://doi.org/10.1016/j.tcs.2013.11.032</a>","short":"A. Grinshpun, P. Phalitnonkiat, S. Rubin, A. Tarfulea, Theoretical Computer Science 521 (2014) 73–91.","ista":"Grinshpun A, Phalitnonkiat P, Rubin S, Tarfulea A. 2014. Alternating traps in Muller and parity games. Theoretical Computer Science. 521, 73–91.","chicago":"Grinshpun, Andrey, Pakawat Phalitnonkiat, Sasha Rubin, and Andrei Tarfulea. “Alternating Traps in Muller and Parity Games.” <i>Theoretical Computer Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tcs.2013.11.032\">https://doi.org/10.1016/j.tcs.2013.11.032</a>."},"page":"73 - 91","isi":1,"publist_id":"4703","arxiv":1,"title":"Alternating traps in Muller and parity games","author":[{"first_name":"Andrey","last_name":"Grinshpun","full_name":"Grinshpun, Andrey"},{"full_name":"Phalitnonkiat, Pakawat","first_name":"Pakawat","last_name":"Phalitnonkiat"},{"full_name":"Rubin, Sasha","id":"2EC51194-F248-11E8-B48F-1D18A9856A87","first_name":"Sasha","last_name":"Rubin"},{"full_name":"Tarfulea, Andrei","first_name":"Andrei","last_name":"Tarfulea"}],"date_published":"2014-02-13T00:00:00Z","type":"journal_article","publication":"Theoretical Computer Science","article_processing_charge":"No","publication_identifier":{"issn":["0304-3975"]},"quality_controlled":"1"},{"type":"journal_article","date_published":"2014-01-22T00:00:00Z","author":[{"full_name":"Beppu, Kaoru","first_name":"Kaoru","last_name":"Beppu"},{"last_name":"Sasaki","first_name":"Takuya","full_name":"Sasaki, Takuya"},{"full_name":"Tanaka, Kenji","first_name":"Kenji","last_name":"Tanaka"},{"last_name":"Yamanaka","first_name":"Akihiro","full_name":"Yamanaka, Akihiro"},{"full_name":"Fukazawa, Yugo","last_name":"Fukazawa","first_name":"Yugo"},{"orcid":"0000-0001-8761-9444","full_name":"Shigemoto, Ryuichi","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","first_name":"Ryuichi"},{"full_name":"Matsui, Ko","first_name":"Ko","last_name":"Matsui"}],"title":"Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage","publist_id":"4715","isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0896-6273"]},"article_processing_charge":"No","publication":"Neuron","year":"2014","_id":"2241","citation":{"ista":"Beppu K, Sasaki T, Tanaka K, Yamanaka A, Fukazawa Y, Shigemoto R, Matsui K. 2014. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. Neuron. 81(2), 314–320.","apa":"Beppu, K., Sasaki, T., Tanaka, K., Yamanaka, A., Fukazawa, Y., Shigemoto, R., &#38; Matsui, K. (2014). Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">https://doi.org/10.1016/j.neuron.2013.11.011</a>","short":"K. Beppu, T. Sasaki, K. Tanaka, A. Yamanaka, Y. Fukazawa, R. Shigemoto, K. Matsui, Neuron 81 (2014) 314–320.","ieee":"K. Beppu <i>et al.</i>, “Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage,” <i>Neuron</i>, vol. 81, no. 2. Elsevier, pp. 314–320, 2014.","mla":"Beppu, Kaoru, et al. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” <i>Neuron</i>, vol. 81, no. 2, Elsevier, 2014, pp. 314–20, doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">10.1016/j.neuron.2013.11.011</a>.","ama":"Beppu K, Sasaki T, Tanaka K, et al. Optogenetic countering of glial acidosis suppresses glial glutamate release and ischemic brain damage. <i>Neuron</i>. 2014;81(2):314-320. doi:<a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">10.1016/j.neuron.2013.11.011</a>","chicago":"Beppu, Kaoru, Takuya Sasaki, Kenji Tanaka, Akihiro Yamanaka, Yugo Fukazawa, Ryuichi Shigemoto, and Ko Matsui. “Optogenetic Countering of Glial Acidosis Suppresses Glial Glutamate Release and Ischemic Brain Damage.” <i>Neuron</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.neuron.2013.11.011\">https://doi.org/10.1016/j.neuron.2013.11.011</a>."},"page":"314 - 320","date_updated":"2026-04-16T10:07:56Z","month":"01","language":[{"iso":"eng"}],"publisher":"Elsevier","abstract":[{"lang":"eng","text":"The brain demands high-energy supply and obstruction of blood flow causes rapid deterioration of the healthiness of brain cells. Two major events occur upon ischemia: acidosis and liberation of excess glutamate, which leads to excitotoxicity. However, cellular source of glutamate and its release mechanism upon ischemia remained unknown. Here we show a causal relationship between glial acidosis and neuronal excitotoxicity. As the major cation that flows through channelrhodopsin-2 (ChR2) is proton, this could be regarded as an optogenetic tool for instant intracellular acidification. Optical activation of ChR2 expressed in glial cells led to glial acidification and to release of glutamate. On the other hand, glial alkalization via optogenetic activation of a proton pump, archaerhodopsin (ArchT), led to cessation of glutamate release and to the relief of ischemic brain damage in vivo. Our results suggest that controlling glial pH may be an effective therapeutic strategy for intervention of ischemic brain damage."}],"volume":81,"date_created":"2018-12-11T11:56:31Z","oa_version":"None","intvolume":"        81","external_id":{"isi":["000330420700010"]},"scopus_import":"1","issue":"2","day":"22","department":[{"_id":"RySh"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1016/j.neuron.2013.11.011","status":"public","publication_status":"published"},{"type":"journal_article","has_accepted_license":"1","date_published":"2014-09-01T00:00:00Z","author":[{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833"},{"orcid":"0000-0002-8379-3768","full_name":"Pausinger, Florian","first_name":"Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","last_name":"Pausinger"}],"title":"Stable length estimates of tube-like shapes","ec_funded":1,"publist_id":"4691","isi":1,"quality_controlled":"1","publication_identifier":{"issn":["0924-9907"]},"article_processing_charge":"No","ddc":["000"],"publication":"Journal of Mathematical Imaging and Vision","year":"2014","file":[{"access_level":"open_access","date_updated":"2020-07-14T12:45:35Z","content_type":"application/pdf","relation":"main_file","file_id":"5204","creator":"system","file_name":"IST-2016-549-v1+1_2014-J-06-LengthEstimate.pdf","file_size":3941391,"checksum":"2f93f3e63a38a85cd4404d7953913b14","date_created":"2018-12-12T10:16:18Z"}],"_id":"2255","page":"164 - 177","date_updated":"2026-04-16T10:09:04Z","citation":{"chicago":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” <i>Journal of Mathematical Imaging and Vision</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s10851-013-0468-x\">https://doi.org/10.1007/s10851-013-0468-x</a>.","ieee":"H. Edelsbrunner and F. Pausinger, “Stable length estimates of tube-like shapes,” <i>Journal of Mathematical Imaging and Vision</i>, vol. 50, no. 1. Springer, pp. 164–177, 2014.","ama":"Edelsbrunner H, Pausinger F. Stable length estimates of tube-like shapes. <i>Journal of Mathematical Imaging and Vision</i>. 2014;50(1):164-177. doi:<a href=\"https://doi.org/10.1007/s10851-013-0468-x\">10.1007/s10851-013-0468-x</a>","mla":"Edelsbrunner, Herbert, and Florian Pausinger. “Stable Length Estimates of Tube-like Shapes.” <i>Journal of Mathematical Imaging and Vision</i>, vol. 50, no. 1, Springer, 2014, pp. 164–77, doi:<a href=\"https://doi.org/10.1007/s10851-013-0468-x\">10.1007/s10851-013-0468-x</a>.","ista":"Edelsbrunner H, Pausinger F. 2014. Stable length estimates of tube-like shapes. Journal of Mathematical Imaging and Vision. 50(1), 164–177.","apa":"Edelsbrunner, H., &#38; Pausinger, F. (2014). Stable length estimates of tube-like shapes. <i>Journal of Mathematical Imaging and Vision</i>. Springer. <a href=\"https://doi.org/10.1007/s10851-013-0468-x\">https://doi.org/10.1007/s10851-013-0468-x</a>","short":"H. Edelsbrunner, F. Pausinger, Journal of Mathematical Imaging and Vision 50 (2014) 164–177."},"month":"09","language":[{"iso":"eng"}],"corr_author":"1","publisher":"Springer","abstract":[{"text":"Motivated by applications in biology, we present an algorithm for estimating the length of tube-like shapes in 3-dimensional Euclidean space. In a first step, we combine the tube formula of Weyl with integral geometric methods to obtain an integral representation of the length, which we approximate using a variant of the Koksma-Hlawka Theorem. In a second step, we use tools from computational topology to decrease the dependence on small perturbations of the shape. We present computational experiments that shed light on the stability and the convergence rate of our algorithm.","lang":"eng"}],"related_material":{"record":[{"relation":"earlier_version","id":"2843","status":"public"},{"relation":"dissertation_contains","id":"1399","status":"public"}]},"date_created":"2018-12-11T11:56:36Z","volume":50,"oa_version":"Submitted Version","intvolume":"        50","external_id":{"isi":["000339823000012"]},"scopus_import":"1","oa":1,"file_date_updated":"2020-07-14T12:45:35Z","pubrep_id":"549","issue":"1","project":[{"name":"Topological Complex Systems","grant_number":"318493","_id":"255D761E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"day":"01","department":[{"_id":"HeEd"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","doi":"10.1007/s10851-013-0468-x","status":"public","publication_status":"published"},{"year":"2014","editor":[{"first_name":"Celeste","last_name":"Nelson","full_name":"Nelson, Celeste"}],"publisher":"Springer","corr_author":"1","language":[{"iso":"eng"}],"month":"08","citation":{"ieee":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg, “UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo,” in <i>Tissue Morphogenesis</i>, vol. 1189, C. Nelson, Ed. New York: Springer, 2014, pp. 219–235.","ama":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Nelson C, ed. <i>Tissue Morphogenesis</i>. Vol 1189. MIMB. New York: Springer; 2014:219-235. doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>","mla":"Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>.","ista":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Tissue Morphogenesis. Methods in Molecular Biology, vol. 1189, 219–235.","short":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:, C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, 2014, pp. 219–235.","apa":"Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., &#38; Heisenberg, C.-P. J. (2014). UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), <i>Tissue Morphogenesis</i> (Vol. 1189, pp. 219–235). New York: Springer. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>","chicago":"Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, 1189:219–35. MIMB. New York: Springer, 2014. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>."},"_id":"6178","page":"219-235","date_updated":"2026-04-16T10:31:19Z","date_published":"2014-08-22T00:00:00Z","type":"book_chapter","place":"New York","alternative_title":["Methods in Molecular Biology"],"title":"UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo","series_title":"MIMB","author":[{"last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","full_name":"Smutny, Michael","orcid":"0000-0002-5920-9090"},{"first_name":"Martin","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","last_name":"Behrndt","full_name":"Behrndt, Martin"},{"full_name":"Campinho, Pedro","last_name":"Campinho","id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","first_name":"Pedro","orcid":"0000-0002-8526-5416"},{"id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","first_name":"Verena","last_name":"Ruprecht","full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633"},{"last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J","orcid":"0000-0002-0912-4566"}],"article_processing_charge":"No","publication_identifier":{"eissn":["1940-6029"],"eisbn":["9781493911646"],"issn":["1064-3745"],"isbn":["9781493911639"]},"quality_controlled":"1","publication":"Tissue Morphogenesis","doi":"10.1007/978-1-4939-1164-6_15","department":[{"_id":"CaHe"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","day":"22","publication_status":"published","status":"public","volume":1189,"date_created":"2019-03-26T08:55:59Z","abstract":[{"lang":"eng","text":"Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo."}],"pmid":1,"oa_version":"None","intvolume":"      1189","external_id":{"pmid":["25245697"]}},{"publication":"Pattern Recognition Letters","quality_controlled":"1","article_processing_charge":"No","title":"Domain adaptation of weighted majority votes via perturbed variation-based self-labeling","author":[{"orcid":"0000-0002-8301-7240","last_name":"Morvant","first_name":"Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","full_name":"Morvant, Emilie"}],"isi":1,"publist_id":"4819","ec_funded":1,"arxiv":1,"type":"journal_article","date_published":"2014-10-01T00:00:00Z","month":"10","_id":"2165","date_updated":"2026-04-29T06:03:23Z","citation":{"chicago":"Morvant, Emilie. “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling.” <i>Pattern Recognition Letters</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.patrec.2014.08.013\">https://doi.org/10.1016/j.patrec.2014.08.013</a>.","ista":"Morvant E. 2014. Domain adaptation of weighted majority votes via perturbed variation-based self-labeling. Pattern Recognition Letters. 51, 37–43.","short":"E. Morvant, Pattern Recognition Letters 51 (2014) 37–43.","apa":"Morvant, E. (2014). Domain adaptation of weighted majority votes via perturbed variation-based self-labeling. <i>Pattern Recognition Letters</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.patrec.2014.08.013\">https://doi.org/10.1016/j.patrec.2014.08.013</a>","ieee":"E. Morvant, “Domain adaptation of weighted majority votes via perturbed variation-based self-labeling,” <i>Pattern Recognition Letters</i>, vol. 51. Elsevier, pp. 37–43, 2014.","mla":"Morvant, Emilie. “Domain Adaptation of Weighted Majority Votes via Perturbed Variation-Based Self-Labeling.” <i>Pattern Recognition Letters</i>, vol. 51, Elsevier, 2014, pp. 37–43, doi:<a href=\"https://doi.org/10.1016/j.patrec.2014.08.013\">10.1016/j.patrec.2014.08.013</a>.","ama":"Morvant E. Domain adaptation of weighted majority votes via perturbed variation-based self-labeling. <i>Pattern Recognition Letters</i>. 2014;51:37-43. doi:<a href=\"https://doi.org/10.1016/j.patrec.2014.08.013\">10.1016/j.patrec.2014.08.013</a>"},"page":"37-43","publisher":"Elsevier","language":[{"iso":"eng"}],"acknowledgement":"The work of this paper was carried out while E. Morvant was affiliated with Institute of Science and Technology (IST) Austria, Am Campus 1, Klosterneuburg 3400, Austria.","OA_place":"repository","year":"2014","external_id":{"isi":["000345687500006"],"arxiv":["1410.0334"]},"intvolume":"        51","oa_version":"Preprint","OA_type":"green","abstract":[{"text":"In machine learning, the domain adaptation problem arrives when the test (tar-get) and the train (source) data are generated from different distributions.  A key applied issue is thus the design of algorithms able to generalize on a new distribution,  for which we have no label information.  We focus on learning classification models defined as a weighted majority vote over a set of real-valued functions. In this context, Germain et al. (2013) have shown that a measure of disagreement between these functions is crucial to control. The core of this measure is a theoretical bound—the C-bound (Lacasse et al., 2007)—which involves the disagreement and leads to a well performing majority vote learn-ing algorithm in usual non-adaptative supervised setting: MinCq. In this work,we propose a framework to extend MinCq to a domain adaptation scenario.This procedure takes advantage of the recent perturbed variation divergence between distributions proposed by Harel and Mannor (2012).  Justified by a theoretical bound on the target risk of the vote,  we provide to MinCq a tar-get sample labeled thanks to a perturbed variation-based self-labeling focused on the regions where the source and target marginals appear similar.  We also study the influence of our self-labeling, from which we deduce an original process for tuning the hyperparameters. Finally, our framework called PV-MinCq shows very promising results on a rotation and translation synthetic problem.","lang":"eng"}],"volume":51,"date_created":"2018-12-11T11:56:05Z","article_type":"original","status":"public","publication_status":"published","day":"01","project":[{"name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425","grant_number":"308036"}],"doi":"10.1016/j.patrec.2014.08.013","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"url":"http://arxiv.org/abs/1410.0334","open_access":"1"}],"extern":"1","oa":1},{"title":"Quantitative fair simulation games","alternative_title":["IST Austria Technical Report"],"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Velner","first_name":"Yaron","full_name":"Velner, Yaron"}],"oa_version":"Published Version","date_created":"2018-12-12T11:39:16Z","date_published":"2014-12-05T00:00:00Z","related_material":{"record":[{"status":"public","relation":"later_version","id":"1066"}]},"has_accepted_license":"1","type":"technical_report","abstract":[{"text":"Simulation is an attractive alternative for language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. For non-deterministic automata, while language inclusion is PSPACE-complete, simulation can be computed in polynomial time. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. Again, while fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable for mean-payoff automata and the decidability is open for discounted-sum automata, whereas the (quantitative) simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games. For example, whereas for mean-payoff and discounted-sum games, the players do not need memory to play optimally; we show in contrast that for simulation games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal strategies for both players require infinite memory in general, and (ii) for discounted-sum objectives, optimal strategies need not exist for both players. While the simulation games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory requirements for mean-payoff objectives) as compared to their counterpart without Büchi acceptance conditions, we still present pseudo-polynomial time algorithms to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff and weighted discounted-sum automata.","lang":"eng"}],"ddc":["004"],"publication_identifier":{"issn":["2664-1690"]},"pubrep_id":"315","year":"2014","oa":1,"file_date_updated":"2020-07-14T12:46:52Z","publisher":"IST Austria","language":[{"iso":"eng"}],"publication_status":"published","month":"12","_id":"5428","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. <i>Quantitative Fair Simulation Games</i>. IST Austria, 2014. <a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">https://doi.org/10.15479/AT:IST-2014-315-v1-1</a>.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation games, IST Austria, 26p.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Quantitative Fair Simulation Games, IST Austria, 2014.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Velner, Y. (2014). <i>Quantitative fair simulation games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">https://doi.org/10.15479/AT:IST-2014-315-v1-1</a>","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, <i>Quantitative fair simulation games</i>. IST Austria, 2014.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. <i>Quantitative Fair Simulation Games</i>. IST Austria; 2014. doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">10.15479/AT:IST-2014-315-v1-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Fair Simulation Games</i>. IST Austria, 2014, doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">10.15479/AT:IST-2014-315-v1-1</a>."},"date_updated":"2026-06-18T08:47:00Z","status":"public","page":"26","doi":"10.15479/AT:IST-2014-315-v1-1","file":[{"relation":"main_file","content_type":"application/pdf","date_updated":"2020-07-14T12:46:52Z","access_level":"open_access","file_size":531046,"checksum":"b1d573bc04365625ff9974880c0aa807","date_created":"2018-12-12T11:53:59Z","file_name":"IST-2014-315-v1+1_report.pdf","creator":"system","file_id":"5521"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"05"},{"article_processing_charge":"No","quality_controlled":"1","publication":"Proceedings of the on Future of Software Engineering","ddc":["000"],"date_published":"2014-05-31T00:00:00Z","type":"conference","publist_id":"5816","ec_funded":1,"title":"Probabilistic programming","author":[{"last_name":"Gordon","first_name":"Andrew","full_name":"Gordon, Andrew"},{"orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Nori, Aditya","first_name":"Aditya","last_name":"Nori"},{"first_name":"Sriram","last_name":"Rajamani","full_name":"Rajamani, Sriram"}],"publisher":"ACM","language":[{"iso":"eng"}],"month":"05","date_updated":"2026-06-18T17:31:28Z","_id":"1393","page":"167 - 181","citation":{"chicago":"Gordon, Andrew, Thomas A Henzinger, Aditya Nori, and Sriram Rajamani. “Probabilistic Programming.” In <i>Proceedings of the on Future of Software Engineering</i>, 167–81. ACM, 2014. <a href=\"https://doi.org/10.1145/2593882.2593900\">https://doi.org/10.1145/2593882.2593900</a>.","ista":"Gordon A, Henzinger TA, Nori A, Rajamani S. 2014. Probabilistic programming. Proceedings of the on Future of Software Engineering. FOSE: Future of Software Engineering, 167–181.","apa":"Gordon, A., Henzinger, T. A., Nori, A., &#38; Rajamani, S. (2014). Probabilistic programming. In <i>Proceedings of the on Future of Software Engineering</i> (pp. 167–181). Hyderabad, India: ACM. <a href=\"https://doi.org/10.1145/2593882.2593900\">https://doi.org/10.1145/2593882.2593900</a>","short":"A. Gordon, T.A. Henzinger, A. Nori, S. Rajamani, in:, Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–181.","ieee":"A. Gordon, T. A. Henzinger, A. Nori, and S. Rajamani, “Probabilistic programming,” in <i>Proceedings of the on Future of Software Engineering</i>, Hyderabad, India, 2014, pp. 167–181.","mla":"Gordon, Andrew, et al. “Probabilistic Programming.” <i>Proceedings of the on Future of Software Engineering</i>, ACM, 2014, pp. 167–81, doi:<a href=\"https://doi.org/10.1145/2593882.2593900\">10.1145/2593882.2593900</a>.","ama":"Gordon A, Henzinger TA, Nori A, Rajamani S. Probabilistic programming. In: <i>Proceedings of the on Future of Software Engineering</i>. ACM; 2014:167-181. doi:<a href=\"https://doi.org/10.1145/2593882.2593900\">10.1145/2593882.2593900</a>"},"conference":{"name":"FOSE: Future of Software Engineering","location":"Hyderabad, India","start_date":"2014-05-31","end_date":"2014-06-07"},"year":"2014","scopus_import":"1","date_created":"2018-12-11T11:51:45Z","abstract":[{"text":"Probabilistic programs are usual functional or imperative programs with two added constructs: (1) the ability to draw values at random from distributions, and (2) the ability to condition values of variables in a program via observations. Models from diverse application areas such as computer vision, coding theory, cryptographic protocols, biology and reliability analysis can be written as probabilistic programs. Probabilistic inference is the problem of computing an explicit representation of the probability distribution implicitly specified by a probabilistic program. Depending on the application, the desired output from inference may vary-we may want to estimate the expected value of some function f with respect to the distribution, or the mode of the distribution, or simply a set of samples drawn from the distribution. In this paper, we describe connections this research area called \\Probabilistic Programming&quot; has with programming languages and software engineering, and this includes language design, and the static and dynamic analysis of programs. We survey current state of the art and speculate on promising directions for future research.","lang":"eng"}],"oa_version":"Published Version","doi":"10.1145/2593882.2593900","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ToHe"}],"project":[{"call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"day":"31","publication_status":"published","status":"public","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/2593882.2593900"}]},{"related_material":{"record":[{"status":"public","id":"1433","relation":"later_version"}]},"abstract":[{"text":"PHAT is a C++ library for the computation of persistent homology by matrix reduction. We aim for a simple generic design that decouples algorithms from data structures without sacrificing efficiency or user-friendliness. This makes PHAT a versatile platform for experimenting with algorithmic ideas and comparing them to state of the art implementations.","lang":"eng"}],"date_created":"2022-03-21T07:12:16Z","volume":8592,"oa_version":"None","intvolume":"      8592","scopus_import":"1","day":"01","doi":"10.1007/978-3-662-44199-2_24","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"HeEd"}],"status":"public","publication_status":"published","type":"conference","place":"Berlin, Heidelberg","date_published":"2014-09-01T00:00:00Z","title":"PHAT – Persistent Homology Algorithms Toolbox","series_title":"LNCS","author":[{"orcid":"0000-0002-9683-0724","id":"2ADD483A-F248-11E8-B48F-1D18A9856A87","first_name":"Ulrich","last_name":"Bauer","full_name":"Bauer, Ulrich"},{"full_name":"Kerber, Michael","first_name":"Michael","last_name":"Kerber"},{"full_name":"Reininghaus, Jan","first_name":"Jan","id":"4505473A-F248-11E8-B48F-1D18A9856A87","last_name":"Reininghaus"},{"full_name":"Wagner, Hubert","first_name":"Hubert","last_name":"Wagner"}],"publication_identifier":{"isbn":["9783662441985"],"eisbn":["9783662441992"],"issn":["0302-9743"],"eissn":["1611-3349"]},"quality_controlled":"1","article_processing_charge":"No","publication":"ICMS 2014: International Congress on Mathematical Software","conference":{"name":"ICMS: International Congress on Mathematical Software","start_date":"2014-08-05","location":"Seoul, South Korea","end_date":"2014-08-09"},"year":"2014","month":"09","_id":"10894","date_updated":"2026-06-18T17:35:15Z","page":"137-143","citation":{"apa":"Bauer, U., Kerber, M., Reininghaus, J., &#38; Wagner, H. (2014). PHAT – Persistent Homology Algorithms Toolbox. In <i>ICMS 2014: International Congress on Mathematical Software</i> (Vol. 8592, pp. 137–143). Berlin, Heidelberg: Springer Berlin Heidelberg. <a href=\"https://doi.org/10.1007/978-3-662-44199-2_24\">https://doi.org/10.1007/978-3-662-44199-2_24</a>","short":"U. Bauer, M. Kerber, J. Reininghaus, H. Wagner, in:, ICMS 2014: International Congress on Mathematical Software, Springer Berlin Heidelberg, Berlin, Heidelberg, 2014, pp. 137–143.","ista":"Bauer U, Kerber M, Reininghaus J, Wagner H. 2014. PHAT – Persistent Homology Algorithms Toolbox. ICMS 2014: International Congress on Mathematical Software. ICMS: International Congress on Mathematical SoftwareLNCS vol. 8592, 137–143.","ama":"Bauer U, Kerber M, Reininghaus J, Wagner H. PHAT – Persistent Homology Algorithms Toolbox. In: <i>ICMS 2014: International Congress on Mathematical Software</i>. Vol 8592. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg; 2014:137-143. doi:<a href=\"https://doi.org/10.1007/978-3-662-44199-2_24\">10.1007/978-3-662-44199-2_24</a>","mla":"Bauer, Ulrich, et al. “PHAT – Persistent Homology Algorithms Toolbox.” <i>ICMS 2014: International Congress on Mathematical Software</i>, vol. 8592, Springer Berlin Heidelberg, 2014, pp. 137–43, doi:<a href=\"https://doi.org/10.1007/978-3-662-44199-2_24\">10.1007/978-3-662-44199-2_24</a>.","ieee":"U. Bauer, M. Kerber, J. Reininghaus, and H. Wagner, “PHAT – Persistent Homology Algorithms Toolbox,” in <i>ICMS 2014: International Congress on Mathematical Software</i>, Seoul, South Korea, 2014, vol. 8592, pp. 137–143.","chicago":"Bauer, Ulrich, Michael Kerber, Jan Reininghaus, and Hubert Wagner. “PHAT – Persistent Homology Algorithms Toolbox.” In <i>ICMS 2014: International Congress on Mathematical Software</i>, 8592:137–43. LNCS. Berlin, Heidelberg: Springer Berlin Heidelberg, 2014. <a href=\"https://doi.org/10.1007/978-3-662-44199-2_24\">https://doi.org/10.1007/978-3-662-44199-2_24</a>."},"publisher":"Springer Berlin Heidelberg","language":[{"iso":"eng"}]},{"month":"01","date_updated":"2026-06-18T18:03:30Z","_id":"1902","page":"232 - 238","citation":{"chicago":"Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2014. <a href=\"https://doi.org/10.1093/molbev/mst187\">https://doi.org/10.1093/molbev/mst187</a>.","short":"B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238.","apa":"Hall, B., Acar, H., Nandipati, A., &#38; Barlow, M. (2014). Growth rates made easy. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/mst187\">https://doi.org/10.1093/molbev/mst187</a>","ista":"Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238.","mla":"Hall, Barry, et al. “Growth Rates Made Easy.” <i>Molecular Biology and Evolution</i>, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:<a href=\"https://doi.org/10.1093/molbev/mst187\">10.1093/molbev/mst187</a>.","ama":"Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. <i>Molecular Biology and Evolution</i>. 2014;31(1):232-238. doi:<a href=\"https://doi.org/10.1093/molbev/mst187\">10.1093/molbev/mst187</a>","ieee":"B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” <i>Molecular Biology and Evolution</i>, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014."},"publisher":"Oxford University Press","language":[{"iso":"eng"}],"year":"2014","OA_place":"publisher","publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"quality_controlled":"1","article_processing_charge":"No","ddc":["570"],"publication":"Molecular Biology and Evolution","type":"journal_article","date_published":"2014-01-01T00:00:00Z","title":"Growth rates made easy","author":[{"first_name":"Barry","last_name":"Hall","full_name":"Hall, Barry"},{"full_name":"Acar, Hande","first_name":"Hande","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87","last_name":"Acar","orcid":"0000-0003-1986-9753"},{"first_name":"Anna","last_name":"Nandipati","full_name":"Nandipati, Anna"},{"first_name":"Miriam","last_name":"Barlow","full_name":"Barlow, Miriam"}],"isi":1,"publist_id":"5193","day":"01","doi":"10.1093/molbev/mst187","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JoBo"}],"status":"public","publication_status":"published","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/molbev/mst187"}],"issue":"1","intvolume":"        31","external_id":{"isi":["000329253200022"],"pmid":["24170494"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"In the 1960s-1980s, determination of bacterial growth rates was an important tool in microbial genetics, biochemistry, molecular biology, and microbial physiology. The exciting technical developments of the 1990s and the 2000s eclipsed that tool; as a result, many investigators today lack experience with growth rate measurements. Recently, investigators in a number of areas have started to use measurements of bacterial growth rates for a variety of purposes. Those measurements have been greatly facilitated by the availability of microwell plate readers that permit the simultaneous measurements on up to 384 different cultures. Only the exponential (logarithmic) portions of the resulting growth curves are useful for determining growth rates, and manual determination of that portion and calculation of growth rates can be tedious for high-throughput purposes. Here, we introduce the program GrowthRates that uses plate reader output files to automatically determine the exponential portion of the curve and to automatically calculate the growth rate, the maximum culture density, and the duration of the growth lag phase. GrowthRates is freely available for Macintosh, Windows, and Linux.We discuss the effects of culture volume, the classical bacterial growth curve, and the differences between determinations in rich media and minimal (mineral salts) media. This protocol covers calibration of the plate reader, growth of culture inocula for both rich and minimal media, and experimental setup. As a guide to reliability, we report typical day-to-day variation in growth rates and variation within experiments with respect to position of wells within the plates."}],"volume":31,"date_created":"2018-12-11T11:54:37Z","article_type":"original","pmid":1,"oa_version":"Published Version","OA_type":"free access"},{"volume":38,"date_created":"2018-12-11T11:54:41Z","article_type":"original","abstract":[{"text":"Deposits of phosphorylated tau protein and convergence of pathology in the hippocampus are the hallmarks of neurodegenerative tauopathies. Thus we aimed to evaluate whether regional and cellular vulnerability patterns in the hippocampus distinguish tauopathies or are influenced by their concomitant presence. Methods: We created a heat map of phospho-tau (AT8) immunoreactivity patterns in 24 hippocampal subregions/layers in individuals with Alzheimer's disease (AD)-related neurofibrillary degeneration (n = 40), Pick's disease (n = 8), progressive supranuclear palsy (n = 7), corticobasal degeneration (n = 6), argyrophilic grain disease (AGD, n = 18), globular glial tauopathy (n = 5), and tau-astrogliopathy of the elderly (n = 10). AT8 immunoreactivity patterns were compared by mathematical analysis. Results: Our study reveals disease-specific hot spots and regional selective vulnerability for these disorders. The pattern of hippocampal AD-related tau pathology is strongly influenced by concomitant AGD. Mathematical analysis reveals that hippocampal involvement in primary tauopathies is distinguishable from early-stage AD-related neurofibrillary degeneration. Conclusion: Our data demonstrate disease-specific AT8 immunoreactivity patterns and hot spots in the hippocampus even in tauopathies, which primarily do not affect the hippocampus. These hot spots can be shifted to other regions by the co-occurrence of tauopathies like AGD. Our observations support the notion that globular glial tauopathies and tau-astrogliopathy of the elderly are distinct entities.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","intvolume":"        38","scopus_import":"1","external_id":{"isi":["000344049900011"],"pmid":["25195847"]},"main_file_link":[{"open_access":"1","url":"https://kops.uni-konstanz.de/bitstream/123456789/42127/1/Milenkovic_2-17ivylo2up0798.pdf"}],"oa":1,"issue":"5-6","doi":"10.1159/000365548","department":[{"_id":"CaGu"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"07","publication_status":"published","status":"public","date_published":"2014-11-07T00:00:00Z","type":"journal_article","isi":1,"publist_id":"5181","title":"Patterns of hippocampal tau pathology differentiate neurodegenerative dementias","author":[{"first_name":"Ivan","last_name":"Milenković","full_name":"Milenković, Ivan"},{"full_name":"Petrov, Tatjana","first_name":"Tatjana","id":"3D5811FC-F248-11E8-B48F-1D18A9856A87","last_name":"Petrov","orcid":"0000-0002-9041-0905"},{"full_name":"Kovács, Gábor","first_name":"Gábor","last_name":"Kovács"}],"article_processing_charge":"No","publication_identifier":{"issn":["1420-8008"]},"quality_controlled":"1","publication":"Dementia and Geriatric Cognitive Disorders","ddc":["570"],"year":"2014","acknowledgement":"This study was supported by the European Commission’s 7th Framework Programme under GA No. 278486, ‘DEVELAGE’.","publisher":"Karger Publishers","language":[{"iso":"eng"}],"month":"11","_id":"1913","date_updated":"2026-06-18T18:13:04Z","citation":{"mla":"Milenković, Ivan, et al. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.” <i>Dementia and Geriatric Cognitive Disorders</i>, vol. 38, no. 5–6, Karger Publishers, 2014, pp. 375–88, doi:<a href=\"https://doi.org/10.1159/000365548\">10.1159/000365548</a>.","ama":"Milenković I, Petrov T, Kovács G. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. <i>Dementia and Geriatric Cognitive Disorders</i>. 2014;38(5-6):375-388. doi:<a href=\"https://doi.org/10.1159/000365548\">10.1159/000365548</a>","ieee":"I. Milenković, T. Petrov, and G. Kovács, “Patterns of hippocampal tau pathology differentiate neurodegenerative dementias,” <i>Dementia and Geriatric Cognitive Disorders</i>, vol. 38, no. 5–6. Karger Publishers, pp. 375–388, 2014.","short":"I. Milenković, T. Petrov, G. Kovács, Dementia and Geriatric Cognitive Disorders 38 (2014) 375–388.","apa":"Milenković, I., Petrov, T., &#38; Kovács, G. (2014). Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. <i>Dementia and Geriatric Cognitive Disorders</i>. Karger Publishers. <a href=\"https://doi.org/10.1159/000365548\">https://doi.org/10.1159/000365548</a>","ista":"Milenković I, Petrov T, Kovács G. 2014. Patterns of hippocampal tau pathology differentiate neurodegenerative dementias. Dementia and Geriatric Cognitive Disorders. 38(5–6), 375–388.","chicago":"Milenković, Ivan, Tatjana Petrov, and Gábor Kovács. “Patterns of Hippocampal Tau Pathology Differentiate Neurodegenerative Dementias.” <i>Dementia and Geriatric Cognitive Disorders</i>. Karger Publishers, 2014. <a href=\"https://doi.org/10.1159/000365548\">https://doi.org/10.1159/000365548</a>."},"page":"375 - 388"},{"date_updated":"2026-06-18T18:12:41Z","_id":"1912","page":"774 - 783","citation":{"ista":"Compagnon J, Barone V, Rajshekar S, Kottmeier R, Pranjic-Ferscha K, Behrndt M, Heisenberg C-PJ. 2014. The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. Developmental Cell. 31(6), 774–783.","short":"J. Compagnon, V. Barone, S. Rajshekar, R. Kottmeier, K. Pranjic-Ferscha, M. Behrndt, C.-P.J. Heisenberg, Developmental Cell 31 (2014) 774–783.","apa":"Compagnon, J., Barone, V., Rajshekar, S., Kottmeier, R., Pranjic-Ferscha, K., Behrndt, M., &#38; Heisenberg, C.-P. J. (2014). The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. <i>Developmental Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.devcel.2014.11.003\">https://doi.org/10.1016/j.devcel.2014.11.003</a>","ieee":"J. Compagnon <i>et al.</i>, “The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ,” <i>Developmental Cell</i>, vol. 31, no. 6. Cell Press, pp. 774–783, 2014.","mla":"Compagnon, Julien, et al. “The Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish Laterality Organ.” <i>Developmental Cell</i>, vol. 31, no. 6, Cell Press, 2014, pp. 774–83, doi:<a href=\"https://doi.org/10.1016/j.devcel.2014.11.003\">10.1016/j.devcel.2014.11.003</a>.","ama":"Compagnon J, Barone V, Rajshekar S, et al. The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ. <i>Developmental Cell</i>. 2014;31(6):774-783. doi:<a href=\"https://doi.org/10.1016/j.devcel.2014.11.003\">10.1016/j.devcel.2014.11.003</a>","chicago":"Compagnon, Julien, Vanessa Barone, Srivarsha Rajshekar, Rita Kottmeier, Kornelija Pranjic-Ferscha, Martin Behrndt, and Carl-Philipp J Heisenberg. “The Notochord Breaks Bilateral Symmetry by Controlling Cell Shapes in the Zebrafish Laterality Organ.” <i>Developmental Cell</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.devcel.2014.11.003\">https://doi.org/10.1016/j.devcel.2014.11.003</a>."},"month":"12","language":[{"iso":"eng"}],"corr_author":"1","publisher":"Cell Press","acknowledgement":"We are grateful to members of the C.-P.H. lab, M. Concha, D. Siekhaus, and J. Vermot for comments on the manuscript and to M. Furutani-Seiki for sharing reagents. This work was supported by the Institute of Science and Technology Austria and an Alexander von Humboldt Foundation fellowship to J.C.","year":"2014","ddc":["570"],"publication":"Developmental Cell","quality_controlled":"1","article_processing_charge":"No","author":[{"full_name":"Compagnon, Julien","last_name":"Compagnon","first_name":"Julien","id":"2E3E0988-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Barone","id":"419EECCC-F248-11E8-B48F-1D18A9856A87","first_name":"Vanessa","full_name":"Barone, Vanessa","orcid":"0000-0003-2676-3367"},{"full_name":"Rajshekar, Srivarsha","last_name":"Rajshekar","first_name":"Srivarsha"},{"full_name":"Kottmeier, Rita","last_name":"Kottmeier","first_name":"Rita"},{"full_name":"Pranjic-Ferscha, Kornelija","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija","last_name":"Pranjic-Ferscha"},{"last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Behrndt, Martin"},{"full_name":"Heisenberg, Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","last_name":"Heisenberg","orcid":"0000-0002-0912-4566"}],"title":"The notochord breaks bilateral symmetry by controlling cell shapes in the Zebrafish laterality organ","publist_id":"5182","isi":1,"type":"journal_article","date_published":"2014-12-22T00:00:00Z","status":"public","publication_status":"published","day":"22","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"CaHe"}],"doi":"10.1016/j.devcel.2014.11.003","issue":"6","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/25535919"}],"oa":1,"external_id":{"pmid":["25535919"],"isi":["000346742900012"]},"scopus_import":"1","intvolume":"        31","oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Kupffer's vesicle (KV) is the zebrafish organ of laterality, patterning the embryo along its left-right (LR) axis. Regional differences in cell shape within the lumen-lining KV epithelium are essential for its LR patterning function. However, the processes by which KV cells acquire their characteristic shapes are largely unknown. Here, we show that the notochord induces regional differences in cell shape within KV by triggering extracellular matrix (ECM) accumulation adjacent to anterior-dorsal (AD) regions of KV. This localized ECM deposition restricts apical expansion of lumen-lining epithelial cells in AD regions of KV during lumen growth. Our study provides mechanistic insight into the processes by which KV translates global embryonic patterning into regional cell shape differences required for its LR symmetry-breaking function."}],"related_material":{"record":[{"status":"public","id":"961","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:54:41Z","volume":31},{"day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"SyCr"}],"month":"01","page":"23 - 30","_id":"1887","citation":{"chicago":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” <i>Zoologie</i>. Deutsche Zoologische Gesellschaft, 2014.","ista":"Cremer S. 2014. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie., 23–30.","apa":"Cremer, S. (2014). Gemeinsame Krankheitsabwehr in Ameisengesellschaften. <i>Zoologie</i>. Deutsche Zoologische Gesellschaft.","short":"S. Cremer, Zoologie (2014) 23–30.","ieee":"S. Cremer, “Gemeinsame Krankheitsabwehr in Ameisengesellschaften,” <i>Zoologie</i>. Deutsche Zoologische Gesellschaft, pp. 23–30, 2014.","ama":"Cremer S. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. <i>Zoologie</i>. 2014:23-30.","mla":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” <i>Zoologie</i>, Deutsche Zoologische Gesellschaft, 2014, pp. 23–30."},"date_updated":"2026-06-18T18:02:48Z","status":"public","publisher":"Deutsche Zoologische Gesellschaft","corr_author":"1","publication_status":"published","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"open_access":"1","url":"https://www.dzg-ev.de/wp-content/uploads/2019/05/zoologie2014.pdf"}],"year":"2014","quality_controlled":"1","article_processing_charge":"No","ddc":["570"],"publication":"Zoologie","type":"journal_article","date_created":"2018-12-11T11:54:33Z","date_published":"2014-01-01T00:00:00Z","article_type":"original","title":"Gemeinsame Krankheitsabwehr in Ameisengesellschaften","author":[{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"oa_version":"Published Version","publist_id":"5208"},{"intvolume":"        27","volume":27,"date_created":"2018-12-11T11:55:26Z","abstract":[{"lang":"eng","text":"We show that the usual score function for conditional Markov networks can be written as the expectation over the scores of their spanning trees. We also show that a small random sample of these output trees can attain a significant fraction of the margin obtained by the complete graph and we provide conditions under which we can perform tractable inference. The experimental results confirm that practical learning is scalable to realistic datasets using this approach."}],"OA_type":"gold","oa_version":"Published Version","department":[{"_id":"ChLa"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","publication_status":"published","status":"public","main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01065586","open_access":"1"}],"oa":1,"article_processing_charge":"No","publication_identifier":{"isbn":["9781510800410"]},"publication":"Advances in Neural Information Processing Systems","ddc":["000"],"date_published":"2014-01-01T00:00:00Z","type":"conference","publist_id":"4996","author":[{"first_name":"Mario","last_name":"Marchand","full_name":"Marchand, Mario"},{"first_name":"Su","last_name":"Hongyu","full_name":"Hongyu, Su"},{"full_name":"Morvant, Emilie","last_name":"Morvant","first_name":"Emilie","id":"4BAC2A72-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8301-7240"},{"full_name":"Rousu, Juho","last_name":"Rousu","first_name":"Juho"},{"last_name":"Shawe Taylor","first_name":"John","full_name":"Shawe Taylor, John"}],"title":"Multilabel structured output learning with random spanning trees of max-margin Markov networks","language":[{"iso":"eng"}],"publisher":"Neural Information Processing Systems Foundation","_id":"2051","date_updated":"2026-06-18T18:24:19Z","citation":{"chicago":"Marchand, Mario, Su Hongyu, Emilie Morvant, Juho Rousu, and John Shawe Taylor. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.” In <i>Advances in Neural Information Processing Systems</i>, Vol. 27. Neural Information Processing Systems Foundation, 2014.","short":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, J. Shawe Taylor, in:, Advances in Neural Information Processing Systems, Neural Information Processing Systems Foundation, 2014.","apa":"Marchand, M., Hongyu, S., Morvant, E., Rousu, J., &#38; Shawe Taylor, J. (2014). Multilabel structured output learning with random spanning trees of max-margin Markov networks. In <i>Advances in Neural Information Processing Systems</i> (Vol. 27). Montreal, Canada: Neural Information Processing Systems Foundation.","ista":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. 2014. Multilabel structured output learning with random spanning trees of max-margin Markov networks. Advances in Neural Information Processing Systems. NIPS: Neural Information Processing Systems vol. 27.","mla":"Marchand, Mario, et al. “Multilabel Structured Output Learning with Random Spanning Trees of Max-Margin Markov Networks.” <i>Advances in Neural Information Processing Systems</i>, vol. 27, Neural Information Processing Systems Foundation, 2014.","ama":"Marchand M, Hongyu S, Morvant E, Rousu J, Shawe Taylor J. Multilabel structured output learning with random spanning trees of max-margin Markov networks. In: <i>Advances in Neural Information Processing Systems</i>. Vol 27. Neural Information Processing Systems Foundation; 2014.","ieee":"M. Marchand, S. Hongyu, E. Morvant, J. Rousu, and J. Shawe Taylor, “Multilabel structured output learning with random spanning trees of max-margin Markov networks,” in <i>Advances in Neural Information Processing Systems</i>, Montreal, Canada, 2014, vol. 27."},"month":"01","year":"2014","conference":{"name":"NIPS: Neural Information Processing Systems","end_date":"2014-12-13","location":"Montreal, Canada","start_date":"2014-12-08"},"OA_place":"repository"},{"intvolume":"        77","external_id":{"isi":["000328661300009"]},"scopus_import":"1","abstract":[{"text":"Plant growth is achieved predominantly by cellular elongation, which is thought to be controlled on several levels by apoplastic auxin. Auxin export into the apoplast is achieved by plasma membrane efflux catalysts of the PIN-FORMED (PIN) and ATP-binding cassette protein subfamily B/phosphor- glycoprotein (ABCB/PGP) classes; the latter were shown to depend on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical, biochemical and cell biological analyses we demonstrate the importance of a putative C-terminal in-plane membrane anchor of TWD1 in the regulation of ABCB-mediated auxin transport. In contrast with dwarfed twd1 loss-of-function alleles, TWD1 gain-of-function lines that lack a putative in-plane membrane anchor (HA-TWD1-Ct) show hypermorphic plant architecture, characterized by enhanced stem length and leaf surface but reduced shoot branching. Greater hypocotyl length is the result of enhanced cell elongation that correlates with reduced polar auxin transport capacity for HA-TWD1-Ct. As a consequence, HA-TWD1-Ct displays higher hypocotyl auxin accumulation, which is shown to result in elevated auxin-induced cell elongation rates. Our data highlight the importance of C-terminal membrane anchoring for TWD1 action, which is required for specific regulation of ABCB-mediated auxin transport. These data support a model in which TWD1 controls lateral ABCB1-mediated export into the apoplast, which is required for auxin-mediated cell elongation.","lang":"eng"}],"volume":77,"date_created":"2018-12-11T11:56:35Z","article_type":"original","oa_version":"Published Version","project":[{"name":"Innovationsförderung in der Grenzregion Österreich – Tschechische Republik durch die Schaffung von Synergien im Bereich der Forschungsinfrastruktur","_id":"256BDAB0-B435-11E9-9278-68D0E5697425"}],"day":"01","doi":"10.1111/tpj.12369","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"status":"public","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/tpj.12369"}],"oa":1,"issue":"1","publication_identifier":{"issn":["0960-7412"]},"quality_controlled":"1","article_processing_charge":"No","ddc":["580"],"publication":"Plant Journal","type":"journal_article","date_published":"2014-01-01T00:00:00Z","title":"Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth","author":[{"full_name":"Bailly, Aurélien","first_name":"Aurélien","last_name":"Bailly"},{"last_name":"Wang","first_name":"Bangjun","full_name":"Wang, Bangjun"},{"last_name":"Zwiewka","first_name":"Marta","full_name":"Zwiewka, Marta"},{"first_name":"Stephan","last_name":"Pollmann","full_name":"Pollmann, Stephan"},{"first_name":"Daniel","last_name":"Schenck","full_name":"Schenck, Daniel"},{"full_name":"Lüthen, Hartwig","first_name":"Hartwig","last_name":"Lüthen"},{"first_name":"Alexander","last_name":"Schulz","full_name":"Schulz, Alexander"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"}],"isi":1,"publist_id":"4694","month":"01","page":"108 - 118","_id":"2253","citation":{"apa":"Bailly, A., Wang, B., Zwiewka, M., Pollmann, S., Schenck, D., Lüthen, H., … Geisler, M. (2014). Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. <i>Plant Journal</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/tpj.12369\">https://doi.org/10.1111/tpj.12369</a>","short":"A. Bailly, B. Wang, M. Zwiewka, S. Pollmann, D. Schenck, H. Lüthen, A. Schulz, J. Friml, M. Geisler, Plant Journal 77 (2014) 108–118.","ista":"Bailly A, Wang B, Zwiewka M, Pollmann S, Schenck D, Lüthen H, Schulz A, Friml J, Geisler M. 2014. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. Plant Journal. 77(1), 108–118.","mla":"Bailly, Aurélien, et al. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” <i>Plant Journal</i>, vol. 77, no. 1, Wiley-Blackwell, 2014, pp. 108–18, doi:<a href=\"https://doi.org/10.1111/tpj.12369\">10.1111/tpj.12369</a>.","ama":"Bailly A, Wang B, Zwiewka M, et al. Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth. <i>Plant Journal</i>. 2014;77(1):108-118. doi:<a href=\"https://doi.org/10.1111/tpj.12369\">10.1111/tpj.12369</a>","ieee":"A. Bailly <i>et al.</i>, “Expression of TWISTED DWARF1 lacking its in-plane membrane anchor leads to increased cell elongation and hypermorphic growth,” <i>Plant Journal</i>, vol. 77, no. 1. Wiley-Blackwell, pp. 108–118, 2014.","chicago":"Bailly, Aurélien, Bangjun Wang, Marta Zwiewka, Stephan Pollmann, Daniel Schenck, Hartwig Lüthen, Alexander Schulz, Jiří Friml, and Markus Geisler. “Expression of TWISTED DWARF1 Lacking Its In-Plane Membrane Anchor Leads to Increased Cell Elongation and Hypermorphic Growth.” <i>Plant Journal</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/tpj.12369\">https://doi.org/10.1111/tpj.12369</a>."},"date_updated":"2026-06-18T18:33:25Z","publisher":"Wiley-Blackwell","language":[{"iso":"eng"}],"year":"2014"},{"file":[{"relation":"main_file","content_type":"application/pdf","access_level":"closed","date_updated":"2026-03-09T14:53:14Z","checksum":"67df5501b1b5b313c3bf9a360d713693","file_size":24842978,"date_created":"2026-03-09T14:53:14Z","file_name":"2014 Behrnd final.pdf","creator":"cchlebak","file_id":"21421"}],"month":"08","citation":{"ista":"Behrndt M. 2014. Forces driving epithelial spreading in zebrafish epiboly. IST Austria.","short":"M. Behrndt, Forces Driving Epithelial Spreading in Zebrafish Epiboly, IST Austria, 2014.","apa":"Behrndt, M. (2014). <i>Forces driving epithelial spreading in zebrafish epiboly</i>. IST Austria.","ieee":"M. Behrndt, “Forces driving epithelial spreading in zebrafish epiboly,” IST Austria, 2014.","mla":"Behrndt, Martin. <i>Forces Driving Epithelial Spreading in Zebrafish Epiboly</i>. IST Austria, 2014.","ama":"Behrndt M. Forces driving epithelial spreading in zebrafish epiboly. 2014.","chicago":"Behrndt, Martin. “Forces Driving Epithelial Spreading in Zebrafish Epiboly.” IST Austria, 2014."},"_id":"1403","date_updated":"2026-06-18T18:45:01Z","page":"91","publisher":"IST Austria","corr_author":"1","language":[{"iso":"eng"}],"year":"2014","OA_place":"repository","article_processing_charge":"No","ddc":["590"],"type":"dissertation","has_accepted_license":"1","date_published":"2014-08-01T00:00:00Z","alternative_title":["IST Austria Thesis"],"title":"Forces driving epithelial spreading in zebrafish epiboly","author":[{"full_name":"Behrndt, Martin","last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"}],"publist_id":"5804","day":"01","acknowledged_ssus":[{"_id":"SSU"}],"department":[{"_id":"CaHe"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","status":"public","publication_status":"published","file_date_updated":"2026-03-09T14:53:14Z","degree_awarded":"PhD","related_material":{"record":[{"id":"2282","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"2950"},{"status":"public","id":"3373","relation":"part_of_dissertation"}]},"abstract":[{"text":"A variety of developmental and disease related processes depend on epithelial cell sheet spreading. In order to gain insight into the biophysical mechanism(s) underlying the tissue morphogenesis we studied the spreading of an epithelium during the early development of the zebrafish embryo. In zebrafish epiboly the enveloping cell layer (EVL), a simple squamous epithelium, spreads over the yolk cell to completely engulf it at the end of gastrulation. Previous studies have proposed that an actomyosin ring forming within the yolk syncytial layer (YSL) acts as purse string that through constriction along its circumference pulls on the margin of the EVL. Direct biophysical evidence for this hypothesis has however been missing. The aim of the thesis was to understand how the actomyosin ring may generate pulling forces onto the EVL and what cellular mechanism(s) may facilitate the spreading of the epithelium. Using laser ablation to measure cortical tension within the actomyosin ring we found an anisotropic tension distribution, which was highest along the circumference of the ring. However the low degree of anisotropy was incompatible with the actomyosin ring functioning as a purse string only. Additionally, we observed retrograde cortical flow from vegetal parts of the ring into the EVL margin. Interpreting the experimental data using a theoretical distribution that models  the tissues as active viscous gels led us to proposen that the actomyosin ring has a twofold contribution to EVL epiboly. It not only acts as a purse string through constriction along its circumference, but in addition constriction along the width of the ring generates pulling forces through friction-resisted cortical flow. Moreover, when rendering the purse string mechanism unproductive EVL epiboly proceeded normally indicating that the flow-friction mechanism is sufficient to drive the process. Aiming to understand what cellular mechanism(s) may facilitate the spreading of the epithelium we found that tension-oriented EVL cell divisions limit tissue anisotropy by releasing tension along the division axis and promote epithelial spreading. Notably, EVL cells undergo ectopic cell fusion in conditions in which oriented-cell division is impaired or the epithelium is mechanically challenged. Taken together our study of EVL epiboly suggests a novel mechanism of force generation for actomyosin rings through friction-resisted cortical flow and highlights the importance of tension-oriented cell divisions in epithelial morphogenesis.","lang":"eng"}],"date_created":"2018-12-11T11:51:49Z","supervisor":[{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J"}],"oa_version":"None"},{"scopus_import":"1","intvolume":"         3","oa_version":"Published Version","OA_type":"free access","abstract":[{"text":"Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system.","lang":"eng"}],"volume":3,"date_created":"2020-06-29T07:59:35Z","status":"public","publication_status":"published","day":"01","department":[{"_id":"RoSe"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"http://www.icm2014.org/en/vod/proceedings.html"}],"oa":1,"ddc":["500"],"publication":"Proceeding of the International Congress of Mathematicans","quality_controlled":"1","publication_identifier":{"isbn":["9788961058063"]},"article_processing_charge":"No","author":[{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521"}],"title":"Structure of the excitation spectrum for many-body quantum systems","type":"conference","date_published":"2014-08-01T00:00:00Z","_id":"8044","page":"1175-1194","date_updated":"2026-06-18T19:30:06Z","citation":{"mla":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” <i>Proceeding of the International Congress of Mathematicans</i>, vol. 3, International Congress of Mathematicians, 2014, pp. 1175–94.","ama":"Seiringer R. Structure of the excitation spectrum for many-body quantum systems. In: <i>Proceeding of the International Congress of Mathematicans</i>. Vol 3. International Congress of Mathematicians; 2014:1175-1194.","ieee":"R. Seiringer, “Structure of the excitation spectrum for many-body quantum systems,” in <i>Proceeding of the International Congress of Mathematicans</i>, Seoul, South Korea, 2014, vol. 3, pp. 1175–1194.","short":"R. Seiringer, in:, Proceeding of the International Congress of Mathematicans, International Congress of Mathematicians, 2014, pp. 1175–1194.","apa":"Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum systems. In <i>Proceeding of the International Congress of Mathematicans</i> (Vol. 3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.","ista":"Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum systems. Proceeding of the International Congress of Mathematicans. ICM: International Congress of Mathematicans vol. 3, 1175–1194.","chicago":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” In <i>Proceeding of the International Congress of Mathematicans</i>, 3:1175–94. International Congress of Mathematicians, 2014."},"month":"08","language":[{"iso":"eng"}],"corr_author":"1","publisher":"International Congress of Mathematicians","OA_place":"publisher","year":"2014","conference":{"name":"ICM: International Congress of Mathematicans","end_date":"2014-08-21","location":"Seoul, South Korea","start_date":"2014-08-13"}}]