[{"day":"01","article_processing_charge":"No","scopus_import":"1","date_published":"2014-11-01T00:00:00Z","publication":"ChemSusChem","citation":{"ista":"Moghaddam MM, Pieber B, Glasnov T, Kappe CO. 2014. Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. 7(11), 3122–3131.","ieee":"M. M. Moghaddam, B. Pieber, T. Glasnov, and C. O. Kappe, “Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow,” ChemSusChem, vol. 7, no. 11. Wiley, pp. 3122–3131, 2014.","apa":"Moghaddam, M. M., Pieber, B., Glasnov, T., & Kappe, C. O. (2014). Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.201402455","ama":"Moghaddam MM, Pieber B, Glasnov T, Kappe CO. Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. 2014;7(11):3122-3131. doi:10.1002/cssc.201402455","chicago":"Moghaddam, Mojtaba Mirhosseini, Bartholomäus Pieber, Toma Glasnov, and C. Oliver Kappe. “Immobilized Iron Oxide Nanoparticles as Stable and Reusable Catalysts for Hydrazine-Mediated Nitro Reductions in Continuous Flow.” ChemSusChem. Wiley, 2014. https://doi.org/10.1002/cssc.201402455.","mla":"Moghaddam, Mojtaba Mirhosseini, et al. “Immobilized Iron Oxide Nanoparticles as Stable and Reusable Catalysts for Hydrazine-Mediated Nitro Reductions in Continuous Flow.” ChemSusChem, vol. 7, no. 11, Wiley, 2014, pp. 3122–31, doi:10.1002/cssc.201402455.","short":"M.M. Moghaddam, B. Pieber, T. Glasnov, C.O. Kappe, ChemSusChem 7 (2014) 3122–3131."},"article_type":"original","page":"3122-3131","abstract":[{"text":"An experimentally easy to perform method for the generation of alumina-supported Fe3O4 nanoparticles [(6±1) nm size, 0.67 wt %]and the use of this material in hydrazine-mediated heterogeneously catalyzed reductions of nitroarenes to anilines under batch and continuous-flow conditions is presented. The bench-stable, reusable nano-Fe3O4@Al2O3 catalyst can selectively reduce functionalized nitroarenes at 1 mol % catalyst loading by using a 20 mol % excess of hydrazine hydrate in an elevated temperature regime (150 °C, reaction time 2–6 min in batch). For continuous-flow processing, the catalyst material is packed into dedicated cartridges and used in a commercially available high-temperature/-pressure flow device. In continuous mode, reaction times can be reduced to less than 1 min at 150 °C (30 bar back pressure) in a highly intensified process. The nano-Fe3O4@Al2O3 catalyst demonstrated stable reduction of nitrobenzene (0.5 M in MeOH) for more than 10 h on stream at a productivity of 30 mmol h−1 (0.72 mol per day). Importantly, virtually no leaching of the catalytically active material could be observed by inductively coupled plasma MS monitoring.","lang":"eng"}],"issue":"11","type":"journal_article","oa_version":"None","_id":"11967","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow","status":"public","intvolume":" 7","month":"11","publication_identifier":{"eissn":["1864-564X"],"issn":["1864-5631"]},"doi":"10.1002/cssc.201402455","language":[{"iso":"eng"}],"external_id":{"pmid":["25209099"]},"quality_controlled":"1","extern":"1","author":[{"full_name":"Moghaddam, Mojtaba Mirhosseini","first_name":"Mojtaba Mirhosseini","last_name":"Moghaddam"},{"full_name":"Pieber, Bartholomäus","first_name":"Bartholomäus","last_name":"Pieber","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X"},{"last_name":"Glasnov","first_name":"Toma","full_name":"Glasnov, Toma"},{"first_name":"C. Oliver","last_name":"Kappe","full_name":"Kappe, C. Oliver"}],"date_updated":"2023-02-21T10:09:42Z","date_created":"2022-08-25T08:36:54Z","volume":7,"year":"2014","pmid":1,"publication_status":"published","publisher":"Wiley"},{"type":"journal_article","article_number":"13430","extern":"1","issue":"26","abstract":[{"lang":"eng","text":"A method for the direct lithiation of terminal alkynes and heterocycles with subsequent carboxylation in a continuous flow format was developed. This method provides carboxylic acids at ambient conditions within less than five seconds with only little excess of the organometallic base and CO2."}],"publisher":"Royal Society of Chemistry","intvolume":" 4","status":"public","publication_status":"published","title":"Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"11987","year":"2014","volume":4,"oa_version":"None","date_created":"2022-08-25T11:48:19Z","date_updated":"2023-02-21T10:10:31Z","author":[{"full_name":"Pieber, Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","orcid":"0000-0001-8689-388X","first_name":"Bartholomäus","last_name":"Pieber"},{"first_name":"Toma","last_name":"Glasnov","full_name":"Glasnov, Toma"},{"first_name":"C. O.","last_name":"Kappe","full_name":"Kappe, C. O."}],"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"eissn":["2046-2069"]},"day":"03","month":"03","quality_controlled":"1","article_type":"letter_note","citation":{"short":"B. Pieber, T. Glasnov, C.O. Kappe, RSC Advances 4 (2014).","mla":"Pieber, Bartholomäus, et al. “Flash Carboxylation: Fast Lithiation–Carboxylation Sequence at Room Temperature in Continuous Flow.” RSC Advances, vol. 4, no. 26, 13430, Royal Society of Chemistry, 2014, doi:10.1039/c4ra01442a.","chicago":"Pieber, Bartholomäus, Toma Glasnov, and C. O. Kappe. “Flash Carboxylation: Fast Lithiation–Carboxylation Sequence at Room Temperature in Continuous Flow.” RSC Advances. Royal Society of Chemistry, 2014. https://doi.org/10.1039/c4ra01442a.","ama":"Pieber B, Glasnov T, Kappe CO. Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. 2014;4(26). doi:10.1039/c4ra01442a","apa":"Pieber, B., Glasnov, T., & Kappe, C. O. (2014). Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. Royal Society of Chemistry. https://doi.org/10.1039/c4ra01442a","ieee":"B. Pieber, T. Glasnov, and C. O. Kappe, “Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow,” RSC Advances, vol. 4, no. 26. Royal Society of Chemistry, 2014.","ista":"Pieber B, Glasnov T, Kappe CO. 2014. Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. 4(26), 13430."},"publication":"RSC Advances","language":[{"iso":"eng"}],"date_published":"2014-03-03T00:00:00Z","doi":"10.1039/c4ra01442a"},{"month":"01","day":"01","doi":"10.1007/s00030-013-0235-0","date_published":"2014-01-01T00:00:00Z","citation":{"ama":"Fischer JL. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 2014;21(1):27-50. doi:10.1007/s00030-013-0235-0","ista":"Fischer JL. 2014. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 21(1), 27–50.","ieee":"J. L. Fischer, “Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models,” Nonlinear Differential Equations and Applications, vol. 21, no. 1. Birkhäuser, pp. 27–50, 2014.","apa":"Fischer, J. L. (2014). Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. Birkhäuser. https://doi.org/10.1007/s00030-013-0235-0","mla":"Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications, vol. 21, no. 1, Birkhäuser, 2014, pp. 27–50, doi:10.1007/s00030-013-0235-0.","short":"J.L. Fischer, Nonlinear Differential Equations and Applications 21 (2014) 27–50.","chicago":"Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications. Birkhäuser, 2014. https://doi.org/10.1007/s00030-013-0235-0."},"publication":"Nonlinear Differential Equations and Applications","page":"27 - 50","quality_controlled":0,"issue":"1","publist_id":"5960","abstract":[{"text":"We show that weak solutions of the Derrida-Lebowitz-Speer-Spohn (DLSS) equation display infinite speed of support propagation. We apply our method to the case of the quantum drift-diffusion equation which augments the DLSS equation with a drift term and possibly a second-order diffusion term. The proof is accomplished using weighted entropy estimates, Hardy's inequality and a family of singular weight functions to derive a differential inequality; the differential inequality shows exponential growth of the weighted entropy, with the growth constant blowing up very fast as the singularity of the weight becomes sharper. To the best of our knowledge, this is the first example of a nonnegativity-preserving higher-order parabolic equation displaying infinite speed of support propagation.","lang":"eng"}],"extern":1,"type":"journal_article","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","first_name":"Julian L","last_name":"Fischer","full_name":"Julian Fischer"}],"volume":21,"date_updated":"2021-01-12T06:49:47Z","date_created":"2018-12-11T11:51:17Z","_id":"1309","year":"2014","intvolume":" 21","publisher":"Birkhäuser","publication_status":"published","status":"public","title":"Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models"},{"date_published":"2014-01-01T00:00:00Z","doi":"10.1007/s00205-013-0690-0","citation":{"ieee":"J. L. Fischer, “Upper bounds on waiting times for the Thin-film equation: The case of weak slippage,” Archive for Rational Mechanics and Analysis, vol. 211, no. 3. Springer, pp. 771–818, 2014.","apa":"Fischer, J. L. (2014). Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-013-0690-0","ista":"Fischer JL. 2014. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 211(3), 771–818.","ama":"Fischer JL. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 2014;211(3):771-818. doi:10.1007/s00205-013-0690-0","chicago":"Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis. Springer, 2014. https://doi.org/10.1007/s00205-013-0690-0.","short":"J.L. Fischer, Archive for Rational Mechanics and Analysis 211 (2014) 771–818.","mla":"Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis, vol. 211, no. 3, Springer, 2014, pp. 771–818, doi:10.1007/s00205-013-0690-0."},"publication":"Archive for Rational Mechanics and Analysis","page":"771 - 818","quality_controlled":0,"day":"01","month":"01","author":[{"full_name":"Julian Fischer","first_name":"Julian L","last_name":"Fischer","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X"}],"volume":211,"date_updated":"2021-01-12T06:49:48Z","date_created":"2018-12-11T11:51:18Z","_id":"1312","year":"2014","intvolume":" 211","publisher":"Springer","title":"Upper bounds on waiting times for the Thin-film equation: The case of weak slippage","status":"public","publication_status":"published","publist_id":"5959","issue":"3","abstract":[{"text":"We derive upper bounds on the waiting time of solutions to the thin-film equation in the regime of weak slippage n ∈ [2, 32\\11). In particular, we give sufficient conditions on the initial data for instantaneous forward motion of the free boundary. For n ∈ (2, 32\\11), our estimates are sharp, for n = 2, they are sharp up to a logarithmic correction term. Note that the case n = 2 corresponds-with a grain of salt-to the assumption of the Navier slip condition at the fluid-solid interface. We also obtain results in the regime of strong slippage n ∈ (1,2); however, in this regime we expect them not to be optimal. Our method is based on weighted backward entropy estimates, Hardy's inequality and singular weight functions; we deduce a differential inequality which would enforce blowup of the weighted entropy if the contact line were to remain stationary for too long.","lang":"eng"}],"extern":1,"type":"journal_article"},{"month":"08","doi":"10.1016/j.tcs.2014.06.031","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["1307.4473"]},"main_file_link":[{"url":"http://arxiv.org/abs/1307.4473","open_access":"1"}],"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23"},{"call_identifier":"FWF","name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"_id":"2587B514-B435-11E9-9278-68D0E5697425","name":"Microsoft Research Faculty Fellowship"}],"publist_id":"5836","ec_funded":1,"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"full_name":"Henzinger, Monika H","first_name":"Monika H","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530"},{"full_name":"Krinninger, Sebastian","first_name":"Sebastian","last_name":"Krinninger"},{"first_name":"Veronika","last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika"},{"last_name":"Raskin","first_name":"Michael","full_name":"Raskin, Michael"}],"date_created":"2018-12-11T11:51:40Z","date_updated":"2022-09-09T11:50:58Z","volume":547,"year":"2014","publication_status":"published","publisher":"Elsevier","department":[{"_id":"KrCh"}],"day":"28","article_processing_charge":"No","scopus_import":"1","date_published":"2014-08-28T00:00:00Z","publication":"Theoretical Computer Science","citation":{"ama":"Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. Approximating the minimum cycle mean. Theoretical Computer Science. 2014;547(C):104-116. doi:10.1016/j.tcs.2014.06.031","ista":"Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. 2014. Approximating the minimum cycle mean. Theoretical Computer Science. 547(C), 104–116.","ieee":"K. Chatterjee, M. H. Henzinger, S. Krinninger, V. Loitzenbauer, and M. Raskin, “Approximating the minimum cycle mean,” Theoretical Computer Science, vol. 547, no. C. Elsevier, pp. 104–116, 2014.","apa":"Chatterjee, K., Henzinger, M. H., Krinninger, S., Loitzenbauer, V., & Raskin, M. (2014). Approximating the minimum cycle mean. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2014.06.031","mla":"Chatterjee, Krishnendu, et al. “Approximating the Minimum Cycle Mean.” Theoretical Computer Science, vol. 547, no. C, Elsevier, 2014, pp. 104–16, doi:10.1016/j.tcs.2014.06.031.","short":"K. Chatterjee, M.H. Henzinger, S. Krinninger, V. Loitzenbauer, M. Raskin, Theoretical Computer Science 547 (2014) 104–116.","chicago":"Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, Veronika Loitzenbauer, and Michael Raskin. “Approximating the Minimum Cycle Mean.” Theoretical Computer Science. Elsevier, 2014. https://doi.org/10.1016/j.tcs.2014.06.031."},"article_type":"original","page":"104 - 116","abstract":[{"lang":"eng","text":"We consider directed graphs where each edge is labeled with an integer weight and study the fundamental algorithmic question of computing the value of a cycle with minimum mean weight. Our contributions are twofold: (1) First we show that the algorithmic question is reducible to the problem of a logarithmic number of min-plus matrix multiplications of n×n-matrices, where n is the number of vertices of the graph. (2) Second, when the weights are nonnegative, we present the first (1+ε)-approximation algorithm for the problem and the running time of our algorithm is Õ(nωlog3(nW/ε)/ε),1 where O(nω) is the time required for the classic n×n-matrix multiplication and W is the maximum value of the weights. With an additional O(log(nW/ε)) factor in space a cycle with approximately optimal weight can be computed within the same time bound."}],"issue":"C","type":"journal_article","oa_version":"Preprint","_id":"1375","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Approximating the minimum cycle mean","intvolume":" 547"},{"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"Fault-tolerant distributed algorithms play an important role in ensuring the reliability of many software applications. In this paper we consider distributed algorithms whose computations are organized in rounds. To verify the correctness of such algorithms, we reason about (i) properties (such as invariants) of the state, (ii) the transitions controlled by the algorithm, and (iii) the communication graph. We introduce a logic that addresses these points, and contains set comprehensions with cardinality constraints, function symbols to describe the local states of each process, and a limited form of quantifier alternation to express the verification conditions. We show its use in automating the verification of consensus algorithms. In particular, we give a semi-decision procedure for the unsatisfiability problem of the logic and identify a decidable fragment. We successfully applied our framework to verify the correctness of a variety of consensus algorithms tolerant to both benign faults (message loss, process crashes) and value faults (message corruption).","lang":"eng"}],"_id":"1392","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["000","005"],"title":"A logic-based framework for verifying consensus algorithms","intvolume":" 8318","pubrep_id":"179","file":[{"relation":"main_file","file_id":"4859","date_created":"2018-12-12T10:11:06Z","date_updated":"2020-07-14T12:44:48Z","checksum":"bffa33d39be77df0da39defe97eabf84","file_name":"IST-2014-179-v1+1_vmcai14.pdf","access_level":"open_access","content_type":"application/pdf","file_size":444138,"creator":"system"}],"oa_version":"Submitted Version","scopus_import":1,"day":"01","has_accepted_license":"1","citation":{"mla":"Dragoi, Cezara, et al. A Logic-Based Framework for Verifying Consensus Algorithms. Vol. 8318, Springer, 2014, pp. 161–81, doi:10.1007/978-3-642-54013-4_10.","short":"C. Dragoi, T.A. Henzinger, H. Veith, J. Widder, D. Zufferey, in:, Springer, 2014, pp. 161–181.","chicago":"Dragoi, Cezara, Thomas A Henzinger, Helmut Veith, Josef Widder, and Damien Zufferey. “A Logic-Based Framework for Verifying Consensus Algorithms,” 8318:161–81. Springer, 2014. https://doi.org/10.1007/978-3-642-54013-4_10.","ama":"Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. A logic-based framework for verifying consensus algorithms. In: Vol 8318. Springer; 2014:161-181. doi:10.1007/978-3-642-54013-4_10","ista":"Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. 2014. A logic-based framework for verifying consensus algorithms. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 8318, 161–181.","ieee":"C. Dragoi, T. A. Henzinger, H. Veith, J. Widder, and D. Zufferey, “A logic-based framework for verifying consensus algorithms,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA, 2014, vol. 8318, pp. 161–181.","apa":"Dragoi, C., Henzinger, T. A., Veith, H., Widder, J., & Zufferey, D. (2014). A logic-based framework for verifying consensus algorithms (Vol. 8318, pp. 161–181). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA: Springer. https://doi.org/10.1007/978-3-642-54013-4_10"},"page":"161 - 181","date_published":"2014-01-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:48Z","publist_id":"5817","ec_funded":1,"year":"2014","acknowledgement":"Supported by the Vienna Science and Technology Fund (WWTF) through grant PROSEED.","publication_status":"published","department":[{"_id":"ToHe"}],"publisher":"Springer","author":[{"last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","full_name":"Dragoi, Cezara"},{"last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"full_name":"Veith, Helmut","first_name":"Helmut","last_name":"Veith"},{"first_name":"Josef","last_name":"Widder","full_name":"Widder, Josef"},{"last_name":"Zufferey","first_name":"Damien","orcid":"0000-0002-3197-8736","id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien"}],"date_created":"2018-12-11T11:51:45Z","date_updated":"2021-01-12T06:50:22Z","volume":8318,"month":"01","oa":1,"quality_controlled":"1","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"}],"conference":{"name":"VMCAI: Verification, Model Checking and Abstract Interpretation","end_date":"2014-01-21","start_date":"2014-01-19","location":"San Diego, USA"},"doi":"10.1007/978-3-642-54013-4_10","language":[{"iso":"eng"}]},{"author":[{"first_name":"Andrew","last_name":"Gordon","full_name":"Gordon, Andrew"},{"full_name":"Henzinger, Thomas A","last_name":"Henzinger","first_name":"Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Aditya","last_name":"Nori","full_name":"Nori, Aditya"},{"full_name":"Rajamani, Sriram","first_name":"Sriram","last_name":"Rajamani"}],"date_updated":"2021-01-12T06:50:22Z","date_created":"2018-12-11T11:51:45Z","year":"2014","publisher":"ACM","department":[{"_id":"ToHe"}],"publication_status":"published","publist_id":"5816","ec_funded":1,"doi":"10.1145/2593882.2593900","conference":{"end_date":"2014-06-07","start_date":"2014-05-31","location":"Hyderabad, India","name":"FOSE: Future of Software Engineering"},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1145/2593882.2593900","open_access":"1"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Quantitative Reactive Modeling","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF"}],"quality_controlled":"1","month":"05","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1393","title":"Probabilistic programming","status":"public","abstract":[{"lang":"eng","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" 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."}],"type":"conference","date_published":"2014-05-31T00:00:00Z","citation":{"short":"A. Gordon, T.A. Henzinger, A. Nori, S. Rajamani, in:, Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–181.","mla":"Gordon, Andrew, et al. “Probabilistic Programming.” Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–81, doi:10.1145/2593882.2593900.","chicago":"Gordon, Andrew, Thomas A Henzinger, Aditya Nori, and Sriram Rajamani. “Probabilistic Programming.” In Proceedings of the on Future of Software Engineering, 167–81. ACM, 2014. https://doi.org/10.1145/2593882.2593900.","ama":"Gordon A, Henzinger TA, Nori A, Rajamani S. Probabilistic programming. In: Proceedings of the on Future of Software Engineering. ACM; 2014:167-181. doi:10.1145/2593882.2593900","apa":"Gordon, A., Henzinger, T. A., Nori, A., & Rajamani, S. (2014). Probabilistic programming. In Proceedings of the on Future of Software Engineering (pp. 167–181). Hyderabad, India: ACM. https://doi.org/10.1145/2593882.2593900","ieee":"A. Gordon, T. A. Henzinger, A. Nori, and S. Rajamani, “Probabilistic programming,” in Proceedings of the on Future of Software Engineering, Hyderabad, India, 2014, pp. 167–181.","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."},"publication":"Proceedings of the on Future of Software Engineering","page":"167 - 181","article_processing_charge":"No","day":"31","scopus_import":1},{"citation":{"chicago":"Stock, Miriam. “Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants.” IST Austria, 2014.","mla":"Stock, Miriam. Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants. IST Austria, 2014.","short":"M. Stock, Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants, IST Austria, 2014.","ista":"Stock M. 2014. Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria.","apa":"Stock, M. (2014). Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria.","ieee":"M. Stock, “Evolution of a fungal pathogen towards individual versus social immunity in ants,” IST Austria, 2014.","ama":"Stock M. Evolution of a fungal pathogen towards individual versus social immunity in ants. 2014."},"page":"101","date_published":"2014-04-01T00:00:00Z","language":[{"iso":"eng"}],"supervisor":[{"full_name":"Cremer, Sylvia M","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","first_name":"Sylvia M","last_name":"Cremer"}],"month":"04","day":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1404","year":"2014","acknowledgement":"This work was funded by the DFG and the ERC.","publisher":"IST Austria","department":[{"_id":"SyCr"}],"publication_status":"published","status":"public","title":"Evolution of a fungal pathogen towards individual versus social immunity in ants","author":[{"full_name":"Stock, Miriam","id":"42462816-F248-11E8-B48F-1D18A9856A87","first_name":"Miriam","last_name":"Stock"}],"oa_version":"None","date_created":"2018-12-11T11:51:49Z","date_updated":"2021-01-12T06:50:30Z","type":"dissertation","alternative_title":["IST Austria Thesis"],"publist_id":"5803","abstract":[{"lang":"eng","text":"The co-evolution of hosts and pathogens is characterized by continuous adaptations of both parties. Pathogens of social insects need to adapt towards disease defences at two levels: 1) individual immunity of each colony member consisting of behavioural defence strategies as well as humoral and cellular immune responses and 2) social immunity that is collectively performed by all group members comprising behavioural, physiological and organisational defence strategies.\r\n\r\nTo disentangle the selection pressure on pathogens by the collective versus individual level of disease defence in social insects, we performed an evolution experiment using the Argentine Ant, Linepithema humile, as a host and a mixture of the general insect pathogenic fungus Metarhizium spp. (6 strains) as a pathogen. We allowed pathogen evolution over 10 serial host passages to two different evolution host treatments: (1) only individual host immunity in a single host treatment, and (2) simultaneously acting individual and social immunity in a social host treatment, in which an exposed ant was accompanied by two untreated nestmates.\r\n\r\nBefore starting the pathogen evolution experiment, the 6 Metarhizium spp. strains were characterised concerning conidiospore size killing rates in singly and socially reared ants, their competitiveness under coinfecting conditions and their influence on ant behaviour. We analysed how the ancestral atrain mixture changed in conidiospere size, killing rate and strain composition dependent on host treatment (single or social hosts) during 10 passages and found that killing rate and conidiospere size of the pathogen increased under both evolution regimes, but different depending on host treatment.\r\n\r\nTesting the evolved strain mixtures that evolved under either the single or social host treatment under both single and social current rearing conditions in a full factorial design experiment revealed that the additional collective defences in insect societies add new selection pressure for their coevolving pathogens that compromise their ability to adapt to its host at the group level. To our knowledge, this is the first study directly measuring the influence of social immunity on pathogen evolution."}]},{"month":"01","day":"01","article_processing_charge":"No","conference":{"name":"QMath: Mathematical Results in Quantum Physics","start_date":"2013-09-10","location":"Berlin, Germany","end_date":"2013-09-13"},"date_published":"2014-01-01T00:00:00Z","doi":"10.1142/9789814618144_0007","language":[{"iso":"eng"}],"publication":"Proceedings of the QMath12 Conference","main_file_link":[{"url":"https://arxiv.org/abs/1403.2563","open_access":"1"}],"oa":1,"citation":{"ista":"Bräunlich G, Hainzl C, Seiringer R. 2014. On the BCS gap equation for superfluid fermionic gases. Proceedings of the QMath12 Conference. QMath: Mathematical Results in Quantum Physics, 127–137.","apa":"Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). On the BCS gap equation for superfluid fermionic gases. In Proceedings of the QMath12 Conference (pp. 127–137). Berlin, Germany: World Scientific Publishing. https://doi.org/10.1142/9789814618144_0007","ieee":"G. Bräunlich, C. Hainzl, and R. Seiringer, “On the BCS gap equation for superfluid fermionic gases,” in Proceedings of the QMath12 Conference, Berlin, Germany, 2014, pp. 127–137.","ama":"Bräunlich G, Hainzl C, Seiringer R. On the BCS gap equation for superfluid fermionic gases. In: Proceedings of the QMath12 Conference. World Scientific Publishing; 2014:127-137. doi:10.1142/9789814618144_0007","chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “On the BCS Gap Equation for Superfluid Fermionic Gases.” In Proceedings of the QMath12 Conference, 127–37. World Scientific Publishing, 2014. https://doi.org/10.1142/9789814618144_0007.","mla":"Bräunlich, Gerhard, et al. “On the BCS Gap Equation for Superfluid Fermionic Gases.” Proceedings of the QMath12 Conference, World Scientific Publishing, 2014, pp. 127–37, doi:10.1142/9789814618144_0007.","short":"G. Bräunlich, C. Hainzl, R. Seiringer, in:, Proceedings of the QMath12 Conference, World Scientific Publishing, 2014, pp. 127–137."},"external_id":{"arxiv":["1403.2563"]},"quality_controlled":"1","page":"127 - 137","abstract":[{"lang":"eng","text":"We present a rigorous derivation of the BCS gap equation for superfluid fermionic gases with point interactions. Our starting point is the BCS energy functional, whose minimizer we investigate in the limit when the range of the interaction potential goes to zero.\r\n"}],"publist_id":"5661","type":"conference","author":[{"last_name":"Bräunlich","first_name":"Gerhard","full_name":"Bräunlich, Gerhard"},{"first_name":"Christian","last_name":"Hainzl","full_name":"Hainzl, Christian"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T06:51:19Z","date_created":"2018-12-11T11:52:28Z","oa_version":"Preprint","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","_id":"1516","year":"2014","status":"public","title":"On the BCS gap equation for superfluid fermionic gases","publication_status":"published","department":[{"_id":"RoSe"}],"publisher":"World Scientific Publishing"},{"issue":"2","abstract":[{"lang":"eng","text":"We propose a method for propagating edit operations in 2D vector graphics, based on geometric relationship functions. These functions quantify the geometric relationship of a point to a polygon, such as the distance to the boundary or the direction to the closest corner vertex. The level sets of the relationship functions describe points with the same relationship to a polygon. For a given query point, we first determine a set of relationships to local features, construct all level sets for these relationships, and accumulate them. The maxima of the resulting distribution are points with similar geometric relationships. We show extensions to handle mirror symmetries, and discuss the use of relationship functions as local coordinate systems. Our method can be applied, for example, to interactive floorplan editing, and it is especially useful for large layouts, where individual edits would be cumbersome. We demonstrate populating 2D layouts with tens to hundreds of objects by propagating relatively few edit operations."}],"type":"journal_article","pubrep_id":"577","file":[{"creator":"system","content_type":"application/pdf","file_size":9832561,"file_name":"IST-2016-577-v1+1_2014.TOG.Paul.EditingPropagation.final.pdf","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","date_created":"2018-12-12T10:11:22Z","checksum":"7f91e588a4e888610313b98271e6418e","file_id":"4876","relation":"main_file"}],"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1629","intvolume":" 33","status":"public","ddc":["000"],"title":"Edit propagation using geometric relationship functions","has_accepted_license":"1","day":"01","date_published":"2014-03-01T00:00:00Z","citation":{"short":"P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, ACM Transactions on Graphics 33 (2014).","mla":"Guerrero, Paul, et al. “Edit Propagation Using Geometric Relationship Functions.” ACM Transactions on Graphics, vol. 33, no. 2, 15, ACM, 2014, doi:10.1145/2591010.","chicago":"Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Edit Propagation Using Geometric Relationship Functions.” ACM Transactions on Graphics. ACM, 2014. https://doi.org/10.1145/2591010.","ama":"Guerrero P, Jeschke S, Wimmer M, Wonka P. Edit propagation using geometric relationship functions. ACM Transactions on Graphics. 2014;33(2). doi:10.1145/2591010","apa":"Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2014). Edit propagation using geometric relationship functions. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2591010","ieee":"P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Edit propagation using geometric relationship functions,” ACM Transactions on Graphics, vol. 33, no. 2. ACM, 2014.","ista":"Guerrero P, Jeschke S, Wimmer M, Wonka P. 2014. Edit propagation using geometric relationship functions. ACM Transactions on Graphics. 33(2), 15."},"publication":"ACM Transactions on Graphics","publist_id":"5526","file_date_updated":"2020-07-14T12:45:07Z","article_number":"15","author":[{"full_name":"Guerrero, Paul","first_name":"Paul","last_name":"Guerrero"},{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wimmer, Michael","first_name":"Michael","last_name":"Wimmer"},{"last_name":"Wonka","first_name":"Peter","full_name":"Wonka, Peter"}],"volume":33,"date_created":"2018-12-11T11:53:08Z","date_updated":"2021-01-12T06:52:06Z","year":"2014","publisher":"ACM","department":[{"_id":"ChWo"}],"publication_status":"published","month":"03","doi":"10.1145/2591010","language":[{"iso":"eng"}],"oa":1,"quality_controlled":"1"},{"quality_controlled":"1","external_id":{"arxiv":["1305.4519"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-3-662-45803-7_36","month":"01","publication_identifier":{"issn":["0302-9743"]},"publication_status":"published","department":[{"_id":"UlWa"}],"publisher":"Springer Nature","year":"2014","date_created":"2022-02-25T10:32:14Z","date_updated":"2023-02-23T10:08:04Z","volume":8871,"author":[{"full_name":"Fulek, Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8485-1774","first_name":"Radoslav","last_name":"Fulek"},{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"},{"full_name":"Malinović, Igor","first_name":"Igor","last_name":"Malinović"},{"full_name":"Pálvölgyi, Dömötör","first_name":"Dömötör","last_name":"Pálvölgyi"}],"related_material":{"record":[{"status":"public","relation":"later_version","id":"1642"}]},"place":"Cham","page":"428-436","publication":"International Symposium on Graph Drawing","citation":{"chicago":"Fulek, Radoslav, Jan Kynčl, Igor Malinović, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” In International Symposium on Graph Drawing, 8871:428–36. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-662-45803-7_36.","mla":"Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” International Symposium on Graph Drawing, vol. 8871, Springer Nature, 2014, pp. 428–36, doi:10.1007/978-3-662-45803-7_36.","short":"R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436.","ista":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. 2014. Clustered planarity testing revisited. International Symposium on Graph Drawing. , LNCS, vol. 8871, 428–436.","apa":"Fulek, R., Kynčl, J., Malinović, I., & Pálvölgyi, D. (2014). Clustered planarity testing revisited. In International Symposium on Graph Drawing (Vol. 8871, pp. 428–436). Cham: Springer Nature. https://doi.org/10.1007/978-3-662-45803-7_36","ieee":"R. Fulek, J. Kynčl, I. Malinović, and D. Pálvölgyi, “Clustered planarity testing revisited,” in International Symposium on Graph Drawing, 2014, vol. 8871, pp. 428–436.","ama":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. Clustered planarity testing revisited. In: International Symposium on Graph Drawing. Vol 8871. Cham: Springer Nature; 2014:428-436. doi:10.1007/978-3-662-45803-7_36"},"date_published":"2014-01-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","title":"Clustered planarity testing revisited","status":"public","intvolume":" 8871","_id":"10793","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","alternative_title":["LNCS"],"type":"conference","abstract":[{"lang":"eng","text":"The Hanani–Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this classical result to clustered graphs with two disjoint clusters, and show that a straightforward extension of our result to flat clustered graphs with three or more disjoint clusters is not possible.\r\n\r\nWe also give a new and short proof for a related result by Di Battista and Frati based on the matroid intersection algorithm."}]},{"year":"2014","publication_status":"published","publisher":"Springer","department":[{"_id":"KrPi"}],"editor":[{"full_name":"Abdalla, Michel","last_name":"Abdalla","first_name":"Michel"},{"first_name":"Roberto","last_name":"De Prisco","full_name":"De Prisco, Roberto"}],"author":[{"first_name":"Georg","last_name":"Fuchsbauer","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87","full_name":"Fuchsbauer, Georg"}],"date_created":"2018-12-11T11:53:13Z","date_updated":"2021-01-12T06:52:12Z","volume":8642,"ec_funded":1,"publist_id":"5509","main_file_link":[{"open_access":"1","url":"http://eprint.iacr.org/2014/537"}],"oa":1,"project":[{"grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","name":"Provable Security for Physical Cryptography","call_identifier":"FP7"}],"conference":{"end_date":"2014-09-05","start_date":"2014-09-03","location":"Amalfi, Italy","name":"SCN: Security and Cryptography for Networks"},"doi":"10.1007/978-3-319-10879-7_7","language":[{"iso":"eng"}],"month":"01","_id":"1643","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Constrained Verifiable Random Functions ","status":"public","intvolume":" 8642","oa_version":"Submitted Version","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"We extend the notion of verifiable random functions (VRF) to constrained VRFs, which generalize the concept of constrained pseudorandom functions, put forward by Boneh and Waters (Asiacrypt’13), and independently by Kiayias et al. (CCS’13) and Boyle et al. (PKC’14), who call them delegatable PRFs and functional PRFs, respectively. In a standard VRF the secret key sk allows one to evaluate a pseudorandom function at any point of its domain; in addition, it enables computation of a non-interactive proof that the function value was computed correctly. In a constrained VRF from the key sk one can derive constrained keys skS for subsets S of the domain, which allow computation of function values and proofs only at points in S. After formally defining constrained VRFs, we derive instantiations from the multilinear-maps-based constrained PRFs by Boneh and Waters, yielding a VRF with constrained keys for any set that can be decided by a polynomial-size circuit. Our VRFs have the same function values as the Boneh-Waters PRFs and are proved secure under the same hardness assumption, showing that verifiability comes at no cost. Constrained (functional) VRFs were stated as an open problem by Boyle et al."}],"publication":"SCN 2014","citation":{"ama":"Fuchsbauer G. Constrained Verifiable Random Functions . In: Abdalla M, De Prisco R, eds. SCN 2014. Vol 8642. Springer; 2014:95-114. doi:10.1007/978-3-319-10879-7_7","ista":"Fuchsbauer G. 2014. Constrained Verifiable Random Functions . SCN 2014. SCN: Security and Cryptography for Networks, LNCS, vol. 8642, 95–114.","ieee":"G. Fuchsbauer, “Constrained Verifiable Random Functions ,” in SCN 2014, Amalfi, Italy, 2014, vol. 8642, pp. 95–114.","apa":"Fuchsbauer, G. (2014). Constrained Verifiable Random Functions . In M. Abdalla & R. De Prisco (Eds.), SCN 2014 (Vol. 8642, pp. 95–114). Amalfi, Italy: Springer. https://doi.org/10.1007/978-3-319-10879-7_7","mla":"Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” SCN 2014, edited by Michel Abdalla and Roberto De Prisco, vol. 8642, Springer, 2014, pp. 95–114, doi:10.1007/978-3-319-10879-7_7.","short":"G. Fuchsbauer, in:, M. Abdalla, R. De Prisco (Eds.), SCN 2014, Springer, 2014, pp. 95–114.","chicago":"Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” In SCN 2014, edited by Michel Abdalla and Roberto De Prisco, 8642:95–114. Springer, 2014. https://doi.org/10.1007/978-3-319-10879-7_7."},"page":"95 - 114","date_published":"2014-01-01T00:00:00Z","scopus_import":1,"day":"01"},{"_id":"1702","year":"2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public","publication_status":"published","title":"Generalised interpolation by solving recursion free-horn clauses","department":[{"_id":"ToHe"}],"intvolume":" 169","publisher":"Open Publishing","author":[{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Popeea","first_name":"Corneliu","full_name":"Popeea, Corneliu"},{"full_name":"Rybalchenko, Andrey","last_name":"Rybalchenko","first_name":"Andrey"}],"date_updated":"2021-01-12T06:52:38Z","date_created":"2018-12-11T11:53:33Z","oa_version":"Submitted Version","volume":169,"type":"conference","alternative_title":["EPTCS"],"abstract":[{"lang":"eng","text":"In this paper we present INTERHORN, a solver for recursion-free Horn clauses. The main application domain of INTERHORN lies in solving interpolation problems arising in software verification. We show how a range of interpolation problems, including path, transition, nested, state/transition and well-founded interpolation can be handled directly by INTERHORN. By detailing these interpolation problems and their Horn clause representations, we hope to encourage the emergence of a common back-end interpolation interface useful for diverse verification tools."}],"publist_id":"5435","publication":"Electronic Proceedings in Theoretical Computer Science, EPTCS","main_file_link":[{"url":"http://arxiv.org/abs/1303.7378v2","open_access":"1"}],"oa":1,"citation":{"ama":"Gupta A, Popeea C, Rybalchenko A. Generalised interpolation by solving recursion free-horn clauses. In: Electronic Proceedings in Theoretical Computer Science, EPTCS. Vol 169. Open Publishing; 2014:31-38. doi:10.4204/EPTCS.169.5","apa":"Gupta, A., Popeea, C., & Rybalchenko, A. (2014). Generalised interpolation by solving recursion free-horn clauses. In Electronic Proceedings in Theoretical Computer Science, EPTCS (Vol. 169, pp. 31–38). Vienna, Austria: Open Publishing. https://doi.org/10.4204/EPTCS.169.5","ieee":"A. Gupta, C. Popeea, and A. Rybalchenko, “Generalised interpolation by solving recursion free-horn clauses,” in Electronic Proceedings in Theoretical Computer Science, EPTCS, Vienna, Austria, 2014, vol. 169, pp. 31–38.","ista":"Gupta A, Popeea C, Rybalchenko A. 2014. Generalised interpolation by solving recursion free-horn clauses. Electronic Proceedings in Theoretical Computer Science, EPTCS. HCVS: Horn Clauses for Verification and Synthesis, EPTCS, vol. 169, 31–38.","short":"A. Gupta, C. Popeea, A. Rybalchenko, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, Open Publishing, 2014, pp. 31–38.","mla":"Gupta, Ashutosh, et al. “Generalised Interpolation by Solving Recursion Free-Horn Clauses.” Electronic Proceedings in Theoretical Computer Science, EPTCS, vol. 169, Open Publishing, 2014, pp. 31–38, doi:10.4204/EPTCS.169.5.","chicago":"Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Generalised Interpolation by Solving Recursion Free-Horn Clauses.” In Electronic Proceedings in Theoretical Computer Science, EPTCS, 169:31–38. Open Publishing, 2014. https://doi.org/10.4204/EPTCS.169.5."},"quality_controlled":"1","page":"31 - 38","conference":{"start_date":"2014-07-17","location":"Vienna, Austria","end_date":"2014-07-17","name":"HCVS: Horn Clauses for Verification and Synthesis"},"date_published":"2014-12-02T00:00:00Z","doi":"10.4204/EPTCS.169.5","language":[{"iso":"eng"}],"month":"12","day":"02"},{"month":"01","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"conference":{"name":"NIPS: Neural Information Processing Systems","end_date":"2014-12-13","start_date":"2014-12-08","location":"Montreal, Canada"},"date_published":"2014-01-01T00:00:00Z","quality_controlled":"1","page":"2024 - 2032","citation":{"chicago":"Savin, Cristina, and Sophie Denève. “Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks,” 3:2024–32. Neural Information Processing Systems, 2014.","short":"C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp. 2024–2032.","mla":"Savin, Cristina, and Sophie Denève. Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks. Vol. 3, no. January, Neural Information Processing Systems, 2014, pp. 2024–32.","ieee":"C. Savin and S. Denève, “Spatio-temporal representations of uncertainty in spiking neural networks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2014, vol. 3, no. January, pp. 2024–2032.","apa":"Savin, C., & Denève, S. (2014). Spatio-temporal representations of uncertainty in spiking neural networks (Vol. 3, pp. 2024–2032). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.","ista":"Savin C, Denève S. 2014. Spatio-temporal representations of uncertainty in spiking neural networks. NIPS: Neural Information Processing Systems vol. 3, 2024–2032.","ama":"Savin C, Denève S. Spatio-temporal representations of uncertainty in spiking neural networks. In: Vol 3. Neural Information Processing Systems; 2014:2024-2032."},"main_file_link":[{"url":"http://papers.nips.cc/paper/5343-spatio-temporal-representations-of-uncertainty-in-spiking-neural-networks.pdf"}],"abstract":[{"text":"It has been long argued that, because of inherent ambiguity and noise, the brain needs to represent uncertainty in the form of probability distributions. The neural encoding of such distributions remains however highly controversial. Here we present a novel circuit model for representing multidimensional real-valued distributions using a spike based spatio-temporal code. Our model combines the computational advantages of the currently competing models for probabilistic codes and exhibits realistic neural responses along a variety of classic measures. Furthermore, the model highlights the challenges associated with interpreting neural activity in relation to behavioral uncertainty and points to alternative population-level approaches for the experimental validation of distributed representations.","lang":"eng"}],"issue":"January","publist_id":"5427","type":"conference","date_updated":"2021-01-12T06:52:40Z","date_created":"2018-12-11T11:53:35Z","oa_version":"None","volume":3,"author":[{"id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin","full_name":"Savin, Cristina"},{"first_name":"Sophie","last_name":"Denève","full_name":"Denève, Sophie"}],"title":"Spatio-temporal representations of uncertainty in spiking neural networks","publication_status":"published","status":"public","publisher":"Neural Information Processing Systems","department":[{"_id":"GaTk"}],"intvolume":" 3","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1708","year":"2014"},{"type":"journal_article","extern":1,"publist_id":"5363","issue":"4","abstract":[{"lang":"eng","text":"Metal silicides formed by means of thermal annealing processes are employed as contact materials in microelectronics. Control of the structure of silicide/silicon interfaces becomes a critical issue when the characteristic size of the device is reduced below a few tens of nanometers. Here, we report on silicide clustering occurring within the channel of PtSi/Si/PtSi Schottky-barrier transistors. This phenomenon is investigated through atomistic simulations and low-temperature resonant-tunneling spectroscopy. Our results provide evidence for the segregation of a PtSi cluster with a diameter of a few nanometers from the silicide contact. The cluster acts as a metallic quantum dot giving rise to distinct signatures of quantum transport through its discrete energy states."}],"intvolume":" 3","publisher":"American Physical Society","status":"public","title":"PtSi clustering in silicon probed by transport spectroscopy","publication_status":"published","_id":"1761","acknowledgement":"This work was supported by the Agence Nationale de la Recherche and by the EU through the ERC Starting Grant HybridNano","year":"2014","volume":3,"date_updated":"2021-01-12T06:53:02Z","date_created":"2018-12-11T11:53:52Z","author":[{"full_name":"Mongillo, Massimo","first_name":"Massimo","last_name":"Mongillo"},{"first_name":"Panayotis","last_name":"Spathis","full_name":"Spathis, Panayotis N"},{"full_name":"Georgios Katsaros","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros"},{"first_name":"Silvano","last_name":"De Franceschi","full_name":"De Franceschi, Silvano"},{"full_name":"Gentile, Pascal","last_name":"Gentile","first_name":"Pascal"},{"full_name":"Rurali, Riccardo","last_name":"Rurali","first_name":"Riccardo"},{"last_name":"Cartoixà","first_name":"Xavier","full_name":"Cartoixà, Xavier"}],"month":"01","day":"01","quality_controlled":0,"main_file_link":[{"url":"http://arxiv.org/abs/1407.5413","open_access":"1"}],"oa":1,"citation":{"short":"M. Mongillo, P. Spathis, G. Katsaros, S. De Franceschi, P. Gentile, R. Rurali, X. Cartoixà, Physical Review X 3 (2014).","mla":"Mongillo, Massimo, et al. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X, vol. 3, no. 4, American Physical Society, 2014, doi:10.1103/PhysRevX.3.041025.","chicago":"Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Silvano De Franceschi, Pascal Gentile, Riccardo Rurali, and Xavier Cartoixà. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X. American Physical Society, 2014. https://doi.org/10.1103/PhysRevX.3.041025.","ama":"Mongillo M, Spathis P, Katsaros G, et al. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 2014;3(4). doi:10.1103/PhysRevX.3.041025","ieee":"M. Mongillo et al., “PtSi clustering in silicon probed by transport spectroscopy,” Physical Review X, vol. 3, no. 4. American Physical Society, 2014.","apa":"Mongillo, M., Spathis, P., Katsaros, G., De Franceschi, S., Gentile, P., Rurali, R., & Cartoixà, X. (2014). PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.3.041025","ista":"Mongillo M, Spathis P, Katsaros G, De Franceschi S, Gentile P, Rurali R, Cartoixà X. 2014. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 3(4)."},"publication":"Physical Review X","doi":"10.1103/PhysRevX.3.041025","date_published":"2014-01-01T00:00:00Z"},{"type":"journal_article","extern":1,"abstract":[{"lang":"eng","text":"Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing brain is a powerful technique to study genetic function; however, discrepancies between knockdown and knockout murine phenotypes have left unanswered questions. For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical neuronal migration phenotype. Here we report that in utero electroporation of shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts, as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent but not sequence-specific effect. Profiling RNAs from electroporated cells showed a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated the migration defect. The results suggest that shRNA-mediated knockdown can produce untoward migration effects by altering endogenous miRNA pathways."}],"publist_id":"5322","issue":"6","status":"public","publication_status":"published","title":"Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation","publisher":"Elsevier","intvolume":" 82","_id":"1791","year":"2014","acknowledgement":"This work was supported by the National Institutes of Health R01NS41537. G.K. was supported by an EMBO Long Term Fellowship, S.L.B. by the A.P. Giannini Fellowship, and A.G.F. by the Brain Behavior Research Foundation","date_updated":"2021-01-12T06:53:13Z","date_created":"2018-12-11T11:54:01Z","volume":82,"author":[{"first_name":"Seungtae","last_name":"Baek","full_name":"Baek, SeungTae"},{"full_name":"Kerjan, Géraldine","last_name":"Kerjan","first_name":"Géraldine"},{"full_name":"Bielas, Stephanie L","first_name":"Stephanie","last_name":"Bielas"},{"full_name":"Lee, Jieun","last_name":"Lee","first_name":"Jieun"},{"first_name":"Ali","last_name":"Fenstermaker","full_name":"Fenstermaker, Ali G"},{"full_name":"Gaia Novarino","last_name":"Novarino","first_name":"Gaia","orcid":"0000-0002-7673-7178","id":"3E57A680-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gleeson","first_name":"Joseph","full_name":"Gleeson, Joseph G"}],"month":"06","day":"18","quality_controlled":0,"page":"1255 - 1262","publication":"Neuron","citation":{"ama":"Baek S, Kerjan G, Bielas S, et al. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 2014;82(6):1255-1262. doi:10.1016/j.neuron.2014.04.036","ista":"Baek S, Kerjan G, Bielas S, Lee J, Fenstermaker A, Novarino G, Gleeson J. 2014. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 82(6), 1255–1262.","apa":"Baek, S., Kerjan, G., Bielas, S., Lee, J., Fenstermaker, A., Novarino, G., & Gleeson, J. (2014). Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.036","ieee":"S. Baek et al., “Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation,” Neuron, vol. 82, no. 6. Elsevier, pp. 1255–1262, 2014.","mla":"Baek, Seungtae, et al. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron, vol. 82, no. 6, Elsevier, 2014, pp. 1255–62, doi:10.1016/j.neuron.2014.04.036.","short":"S. Baek, G. Kerjan, S. Bielas, J. Lee, A. Fenstermaker, G. Novarino, J. Gleeson, Neuron 82 (2014) 1255–1262.","chicago":"Baek, Seungtae, Géraldine Kerjan, Stephanie Bielas, Jieun Lee, Ali Fenstermaker, Gaia Novarino, and Joseph Gleeson. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.036."},"date_published":"2014-06-18T00:00:00Z","doi":"10.1016/j.neuron.2014.04.036"},{"month":"04","day":"01","scopus_import":1,"language":[{"iso":"eng"}],"date_published":"2014-04-01T00:00:00Z","doi":"10.1007/978-3-7091-1526-8_8","quality_controlled":"1","page":"143 - 170","publication":"Auxin and Its Role in Plant Development","citation":{"ama":"Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In: Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. Springer; 2014:143-170. doi:10.1007/978-3-7091-1526-8_8","ista":"Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity. In: Auxin and Its Role in Plant Development. , 143–170.","ieee":"P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,” in Auxin and Its Role in Plant Development, E. Zažímalová, J. Petrášek, and E. Benková, Eds. Springer, 2014, pp. 143–170.","apa":"Baster, P., & Friml, J. (2014). Auxin on the road navigated by cellular PIN polarity. In E. Zažímalová, J. Petrášek, & E. Benková (Eds.), Auxin and Its Role in Plant Development (pp. 143–170). Springer. https://doi.org/10.1007/978-3-7091-1526-8_8","mla":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” Auxin and Its Role in Plant Development, edited by Eva Zažímalová et al., Springer, 2014, pp. 143–70, doi:10.1007/978-3-7091-1526-8_8.","short":"P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.), Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170.","chicago":"Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” In Auxin and Its Role in Plant Development, edited by Eva Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. https://doi.org/10.1007/978-3-7091-1526-8_8."},"abstract":[{"lang":"eng","text":"The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants."}],"publist_id":"5304","type":"book_chapter","date_updated":"2021-01-12T06:53:19Z","date_created":"2018-12-11T11:54:07Z","oa_version":"None","author":[{"full_name":"Baster, Pawel","last_name":"Baster","first_name":"Pawel","id":"3028BD74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","title":"Auxin on the road navigated by cellular PIN polarity","status":"public","publisher":"Springer","editor":[{"full_name":"Zažímalová, Eva","last_name":"Zažímalová","first_name":"Eva"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"full_name":"Benková, Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","first_name":"Eva"}],"department":[{"_id":"JiFr"}],"year":"2014","_id":"1806","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87"},{"_id":"1816","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"title":"Topology-preserving watermarking of vector graphics","status":"public","intvolume":" 24","pubrep_id":"443","file":[{"creator":"system","content_type":"application/pdf","file_size":991734,"file_name":"IST-2016-443-v1+1_S0218195914500034.pdf","access_level":"open_access","date_created":"2018-12-12T10:08:43Z","date_updated":"2020-07-14T12:45:17Z","checksum":"be45c133ab4d43351260e21beaa8f4b1","file_id":"4704","relation":"main_file"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques."}],"issue":"1","publication":"International Journal of Computational Geometry and Applications","citation":{"mla":"Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications, vol. 24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:10.1142/S0218195914500034.","short":"S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational Geometry and Applications 24 (2014) 61–86.","chicago":"Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2014. https://doi.org/10.1142/S0218195914500034.","ama":"Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 2014;24(1):61-86. doi:10.1142/S0218195914500034","ista":"Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 24(1), 61–86.","apa":"Huber, S., Held, M., Meerwald, P., & Kwitt, R. (2014). Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195914500034","ieee":"S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking of vector graphics,” International Journal of Computational Geometry and Applications, vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014."},"page":"61 - 86","date_published":"2014-03-16T00:00:00Z","scopus_import":1,"day":"16","has_accepted_license":"1","acknowledgement":"Work by Martin Held and Stefan Huber was supported by Austrian Science Fund (FWF): L367-N15 and P25816-N15.","year":"2014","publication_status":"published","department":[{"_id":"HeEd"}],"publisher":"World Scientific Publishing","author":[{"full_name":"Huber, Stefan","id":"4700A070-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8871-5814","first_name":"Stefan","last_name":"Huber"},{"last_name":"Held","first_name":"Martin","full_name":"Held, Martin"},{"first_name":"Peter","last_name":"Meerwald","full_name":"Meerwald, Peter"},{"first_name":"Roland","last_name":"Kwitt","full_name":"Kwitt, Roland"}],"date_updated":"2021-01-12T06:53:23Z","date_created":"2018-12-11T11:54:10Z","volume":24,"file_date_updated":"2020-07-14T12:45:17Z","publist_id":"5290","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1142/S0218195914500034","language":[{"iso":"eng"}],"month":"03"},{"month":"06","project":[{"name":"NSERC Postdoctoral fellowship","_id":"26450934-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1063/1.4881536","article_number":"1.4881536","publist_id":"5285","file_date_updated":"2020-07-14T12:45:17Z","publisher":"American Institute of Physics","department":[{"_id":"RoSe"}],"publication_status":"published","year":"2014","volume":55,"date_created":"2018-12-11T11:54:11Z","date_updated":"2021-01-12T06:53:25Z","author":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert"}],"scopus_import":1,"has_accepted_license":"1","day":"26","citation":{"chicago":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4881536.","short":"R. Seiringer, Journal of Mathematical Physics 55 (2014).","mla":"Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536, American Institute of Physics, 2014, doi:10.1063/1.4881536.","ieee":"R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014.","apa":"Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4881536","ista":"Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 55(7), 1.4881536.","ama":"Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536"},"publication":"Journal of Mathematical Physics","date_published":"2014-06-26T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"text":"We review recent progress towards a rigorous understanding of the Bogoliubov approximation for bosonic quantum many-body systems. We focus, in particular, on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A list of open problems will be discussed at the end.","lang":"eng"}],"intvolume":" 55","title":"Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation","status":"public","ddc":["510","530"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1821","oa_version":"Submitted Version","file":[{"file_name":"IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf","access_level":"open_access","creator":"system","file_size":269171,"content_type":"application/pdf","file_id":"5172","relation":"main_file","date_updated":"2020-07-14T12:45:17Z","date_created":"2018-12-12T10:15:49Z","checksum":"ed0efc93c10f1341155f0316af617b82"}],"pubrep_id":"532"},{"_id":"1822","year":"2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"RoSe"}],"publisher":"American Institute of Physics","intvolume":" 55","status":"public","title":"Introduction","publication_status":"published","author":[{"first_name":"Vojkan","last_name":"Jakšić","full_name":"Jakšić, Vojkan"},{"full_name":"Pillet, Claude","first_name":"Claude","last_name":"Pillet"},{"full_name":"Seiringer, Robert","last_name":"Seiringer","first_name":"Robert","orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"None","volume":55,"date_updated":"2021-01-12T06:53:25Z","date_created":"2018-12-11T11:54:12Z","type":"journal_article","article_number":"075101","publist_id":"5284","issue":"7","citation":{"short":"V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014).","mla":"Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics, vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:10.1063/1.4884877.","chicago":"Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4884877.","ama":"Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4884877","apa":"Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4884877","ieee":"V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014.","ista":"Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical Physics. 55(7), 075101."},"publication":"Journal of Mathematical Physics","quality_controlled":"1","date_published":"2014-07-01T00:00:00Z","doi":"10.1063/1.4884877","language":[{"iso":"eng"}],"scopus_import":1,"day":"01","month":"07"},{"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1829","year":"2014","publisher":"Springer","intvolume":" 97","editor":[{"last_name":"Kober","first_name":"Jens","full_name":"Kober, Jens"},{"last_name":"Peters","first_name":"Jan","full_name":"Peters, Jan"}],"department":[{"_id":"ChLa"}],"title":"Movement templates for learning of hitting and batting","publication_status":"published","status":"public","author":[{"full_name":"Muelling, Katharina","last_name":"Muelling","first_name":"Katharina"},{"last_name":"Kroemer","first_name":"Oliver","full_name":"Kroemer, Oliver"},{"first_name":"Christoph","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"},{"last_name":"Schölkopf","first_name":"Bernhard","full_name":"Schölkopf, Bernhard"}],"oa_version":"None","volume":97,"date_created":"2018-12-11T11:54:14Z","date_updated":"2021-01-12T06:53:28Z","type":"book_chapter","alternative_title":["Springer Tracts in Advanced Robotics"],"publist_id":"5274","abstract":[{"lang":"eng","text":"Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or baseball batting, depend on predictions where the ball can be intercepted and how it can properly be returned to the opponent. These predictions get more accurate over time, hence the behaviors need to be continuously modified. As a result, movement templates with a learned global shape need to be adapted during the execution so that the racket reaches a target position and velocity that will return the ball over to the other side of the net or court. It requires altering learned movements to hit a varying target with the necessary velocity at a specific instant in time. Such a task cannot be incorporated straightforwardly in most movement representations suitable for learning. For example, the standard formulation of the dynamical system based motor primitives (introduced by Ijspeert et al (2002b)) does not satisfy this property despite their flexibility which has allowed learning tasks ranging from locomotion to kendama. In order to fulfill this requirement, we reformulate the Ijspeert framework to incorporate the possibility of specifying a desired hitting point and a desired hitting velocity while maintaining all advantages of the original formulation.We show that the proposed movement template formulation works well in two scenarios, i.e., for hitting a ball on a string with a table tennis racket at a specified velocity and for returning balls launched by a ball gun successfully over the net using forehand movements."}],"citation":{"ista":"Muelling K, Kroemer O, Lampert C, Schölkopf B. 2014.Movement templates for learning of hitting and batting. In: Learning Motor Skills. Springer Tracts in Advanced Robotics, vol. 97, 69–82.","ieee":"K. Muelling, O. Kroemer, C. Lampert, and B. Schölkopf, “Movement templates for learning of hitting and batting,” in Learning Motor Skills, vol. 97, J. Kober and J. Peters, Eds. Springer, 2014, pp. 69–82.","apa":"Muelling, K., Kroemer, O., Lampert, C., & Schölkopf, B. (2014). Movement templates for learning of hitting and batting. In J. Kober & J. Peters (Eds.), Learning Motor Skills (Vol. 97, pp. 69–82). Springer. https://doi.org/10.1007/978-3-319-03194-1_3","ama":"Muelling K, Kroemer O, Lampert C, Schölkopf B. Movement templates for learning of hitting and batting. In: Kober J, Peters J, eds. Learning Motor Skills. Vol 97. From Algorithms to Robot Experiments. Springer; 2014:69-82. doi:10.1007/978-3-319-03194-1_3","chicago":"Muelling, Katharina, Oliver Kroemer, Christoph Lampert, and Bernhard Schölkopf. “Movement Templates for Learning of Hitting and Batting.” In Learning Motor Skills, edited by Jens Kober and Jan Peters, 97:69–82. From Algorithms to Robot Experiments. Springer, 2014. https://doi.org/10.1007/978-3-319-03194-1_3.","mla":"Muelling, Katharina, et al. “Movement Templates for Learning of Hitting and Batting.” Learning Motor Skills, edited by Jens Kober and Jan Peters, vol. 97, Springer, 2014, pp. 69–82, doi:10.1007/978-3-319-03194-1_3.","short":"K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters (Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82."},"publication":"Learning Motor Skills","page":"69 - 82","quality_controlled":"1","doi":"10.1007/978-3-319-03194-1_3","date_published":"2014-01-01T00:00:00Z","language":[{"iso":"eng"}],"scopus_import":1,"series_title":"From Algorithms to Robot Experiments","day":"01","month":"01"},{"issue":"2","abstract":[{"text":"Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.","lang":"eng"}],"type":"journal_article","pubrep_id":"430","oa_version":"Published Version","file":[{"file_id":"5247","relation":"main_file","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:16:56Z","checksum":"06215318e66be8f3e0c33abb07e9d3da","file_name":"IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf","access_level":"open_access","creator":"system","file_size":1545246,"content_type":"application/pdf"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1844","intvolume":" 32","title":"Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history","ddc":["571"],"status":"public","has_accepted_license":"1","day":"12","scopus_import":1,"date_published":"2014-11-12T00:00:00Z","citation":{"ama":"Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 2014;32(2):440-455. doi:10.1093/molbev/msu312","ista":"Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A, Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 32(2), 440–455.","ieee":"V. Risso et al., “Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 440–455, 2014.","apa":"Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús, A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu312","mla":"Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2014, pp. 440–55, doi:10.1093/molbev/msu312.","short":"V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús, Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez Ruiz, Molecular Biology and Evolution 32 (2014) 440–455.","chicago":"Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu312."},"publication":"Molecular Biology and Evolution","page":"440 - 455","publist_id":"5257","file_date_updated":"2020-07-14T12:45:19Z","license":"https://creativecommons.org/licenses/by-nc/4.0/","author":[{"first_name":"Valeria","last_name":"Risso","full_name":"Risso, Valeria"},{"full_name":"Manssour Triedo, Fadia","last_name":"Manssour Triedo","first_name":"Fadia"},{"full_name":"Delgado Delgado, Asuncion","last_name":"Delgado Delgado","first_name":"Asuncion"},{"last_name":"Arco","first_name":"Rocio","full_name":"Arco, Rocio"},{"first_name":"Alicia","last_name":"Barroso Deljesús","full_name":"Barroso Deljesús, Alicia"},{"first_name":"Álvaro","last_name":"Inglés Prieto","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5409-8571","full_name":"Inglés Prieto, Álvaro"},{"full_name":"Godoy Ruiz, Raquel","first_name":"Raquel","last_name":"Godoy Ruiz"},{"full_name":"Gavira, Josè","first_name":"Josè","last_name":"Gavira"},{"full_name":"Gaucher, Eric","last_name":"Gaucher","first_name":"Eric"},{"full_name":"Ibarra Molero, Beatriz","first_name":"Beatriz","last_name":"Ibarra Molero"},{"full_name":"Sánchez Ruiz, Jose","last_name":"Sánchez Ruiz","first_name":"Jose"}],"volume":32,"date_updated":"2021-01-12T06:53:34Z","date_created":"2018-12-11T11:54:19Z","year":"2014","publisher":"Oxford University Press","department":[{"_id":"HaJa"}],"publication_status":"published","month":"11","doi":"10.1093/molbev/msu312","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"quality_controlled":"1"},{"date_published":"2014-11-14T00:00:00Z","doi":"10.1007/s00454-014-9646-x","language":[{"iso":"eng"}],"publication":"Discrete & Computational Geometry","citation":{"chicago":"Cibulka, Josef, Pu Gao, Marek Krcál, Tomáš Valla, and Pavel Valtr. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9646-x.","short":"J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete & Computational Geometry 53 (2014) 64–79.","mla":"Cibulka, Josef, et al. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry, vol. 53, no. 1, Springer, 2014, pp. 64–79, doi:10.1007/s00454-014-9646-x.","apa":"Cibulka, J., Gao, P., Krcál, M., Valla, T., & Valtr, P. (2014). On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-014-9646-x","ieee":"J. Cibulka, P. Gao, M. Krcál, T. Valla, and P. Valtr, “On the geometric ramsey number of outerplanar graphs,” Discrete & Computational Geometry, vol. 53, no. 1. Springer, pp. 64–79, 2014.","ista":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. 2014. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 53(1), 64–79.","ama":"Cibulka J, Gao P, Krcál M, Valla T, Valtr P. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 2014;53(1):64-79. doi:10.1007/s00454-014-9646-x"},"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1310.7004"}],"oa":1,"page":"64 - 79","month":"11","day":"14","scopus_import":1,"author":[{"last_name":"Cibulka","first_name":"Josef","full_name":"Cibulka, Josef"},{"full_name":"Gao, Pu","last_name":"Gao","first_name":"Pu"},{"first_name":"Marek","last_name":"Krcál","id":"33E21118-F248-11E8-B48F-1D18A9856A87","full_name":"Krcál, Marek"},{"full_name":"Valla, Tomáš","first_name":"Tomáš","last_name":"Valla"},{"full_name":"Valtr, Pavel","last_name":"Valtr","first_name":"Pavel"}],"date_updated":"2021-01-12T06:53:33Z","date_created":"2018-12-11T11:54:18Z","volume":53,"oa_version":"Submitted Version","year":"2014","_id":"1842","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"Marek Krčál was supported by the ERC Advanced Grant No. 267165.","status":"public","publication_status":"published","title":"On the geometric ramsey number of outerplanar graphs","publisher":"Springer","intvolume":" 53","department":[{"_id":"UlWa"},{"_id":"HeEd"}],"abstract":[{"lang":"eng","text":"We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices."}],"issue":"1","publist_id":"5260","type":"journal_article"},{"month":"11","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"doi":"10.1111/cgf.12509","file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5246","publication_status":"published","publisher":"Wiley","department":[{"_id":"ChWo"}],"year":"2014","date_created":"2018-12-11T11:54:22Z","date_updated":"2021-01-12T06:53:38Z","volume":34,"author":[{"first_name":"Paul","last_name":"Guerrero","full_name":"Guerrero, Paul"},{"id":"4718F954-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1546-3265","first_name":"Thomas","last_name":"Auzinger","full_name":"Auzinger, Thomas"},{"first_name":"Michael","last_name":"Wimmer","full_name":"Wimmer, Michael"},{"first_name":"Stefan","last_name":"Jeschke","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan"}],"scopus_import":1,"day":"05","has_accepted_license":"1","page":"239 - 252","publication":"Computer Graphics Forum","citation":{"mla":"Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum, vol. 34, no. 1, Wiley, 2014, pp. 239–52, doi:10.1111/cgf.12509.","short":"P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 34 (2014) 239–252.","chicago":"Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum. Wiley, 2014. https://doi.org/10.1111/cgf.12509.","ama":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 2014;34(1):239-252. doi:10.1111/cgf.12509","ista":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252.","ieee":"P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching using transformation parameter similarity,” Computer Graphics Forum, vol. 34, no. 1. Wiley, pp. 239–252, 2014.","apa":"Guerrero, P., Auzinger, T., Wimmer, M., & Jeschke, S. (2014). Partial shape matching using transformation parameter similarity. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12509"},"date_published":"2014-11-05T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching. In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching."}],"issue":"1","status":"public","title":"Partial shape matching using transformation parameter similarity","ddc":["000"],"intvolume":" 34","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1854","file":[{"access_level":"open_access","file_name":"IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf","content_type":"application/pdf","file_size":24817484,"creator":"system","relation":"main_file","file_id":"5182","checksum":"91946bfc509c77f5fd3151a3ff2b2c8f","date_created":"2018-12-12T10:15:58Z","date_updated":"2020-07-14T12:45:19Z"}],"oa_version":"Submitted Version","pubrep_id":"574"},{"scopus_import":1,"day":"06","citation":{"chicago":"Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.08.036.","mla":"Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology, vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:10.1016/j.cub.2014.08.036.","short":"M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B. Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current Biology 24 (2014) 2335–2342.","ista":"Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B, Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 24(19), 2335–2342.","ieee":"M. Sassi et al., “An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis,” Current Biology, vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014.","apa":"Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas, J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.08.036","ama":"Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 2014;24(19):2335-2342. doi:10.1016/j.cub.2014.08.036"},"publication":"Current Biology","page":"2335 - 2342","date_published":"2014-10-06T00:00:00Z","type":"journal_article","issue":"19","abstract":[{"text":"To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner.","lang":"eng"}],"_id":"1852","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 24","status":"public","title":"An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis","oa_version":"Submitted Version","month":"10","oa":1,"main_file_link":[{"url":"https://hal.archives-ouvertes.fr/hal-01074821","open_access":"1"}],"quality_controlled":"1","doi":"10.1016/j.cub.2014.08.036","language":[{"iso":"eng"}],"publist_id":"5248","acknowledgement":"This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ","year":"2014","department":[{"_id":"JiFr"}],"publisher":"Cell Press","publication_status":"published","author":[{"last_name":"Sassi","first_name":"Massimiliano","full_name":"Sassi, Massimiliano"},{"full_name":"Ali, Olivier","last_name":"Ali","first_name":"Olivier"},{"full_name":"Boudon, Frédéric","last_name":"Boudon","first_name":"Frédéric"},{"first_name":"Gladys","last_name":"Cloarec","full_name":"Cloarec, Gladys"},{"full_name":"Abad, Ursula","last_name":"Abad","first_name":"Ursula"},{"full_name":"Cellier, Coralie","first_name":"Coralie","last_name":"Cellier"},{"full_name":"Chen, Xu","last_name":"Chen","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gilles, Benjamin","first_name":"Benjamin","last_name":"Gilles"},{"full_name":"Milani, Pascale","last_name":"Milani","first_name":"Pascale"},{"full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vernoux, Teva","last_name":"Vernoux","first_name":"Teva"},{"last_name":"Godin","first_name":"Christophe","full_name":"Godin, Christophe"},{"full_name":"Hamant, Olivier","last_name":"Hamant","first_name":"Olivier"},{"first_name":"Jan","last_name":"Traas","full_name":"Traas, Jan"}],"volume":24,"date_updated":"2021-01-12T06:53:37Z","date_created":"2018-12-11T11:54:22Z"},{"author":[{"full_name":"Jha, Susmit","first_name":"Susmit","last_name":"Jha"},{"full_name":"Tripakis, Stavros","last_name":"Tripakis","first_name":"Stavros"},{"full_name":"Seshia, Sanjit","first_name":"Sanjit","last_name":"Seshia"},{"full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2021-01-12T06:53:38Z","date_created":"2018-12-11T11:54:22Z","oa_version":"None","_id":"1853","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2014","title":"Game theoretic secure localization in wireless sensor networks","status":"public","publication_status":"published","department":[{"_id":"KrCh"}],"publisher":"IEEE","abstract":[{"lang":"eng","text":"Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes are expected to form the backbone of future intelligent networks for a broad range of civil, industrial and military applications. These sensor nodes are often deployed through random spreading, and function in dynamic environments. Many applications of WSNs such as pollution tracking, forest fire detection, and military surveillance require knowledge of the location of constituent nodes. But the use of technologies such as GPS on all nodes is prohibitive due to power and cost constraints. So, the sensor nodes need to autonomously determine their locations. Most localization techniques use anchor nodes with known locations to determine the position of remaining nodes. Localization techniques have two conflicting requirements. On one hand, an ideal localization technique should be computationally simple and on the other hand, it must be resistant to attacks that compromise anchor nodes. In this paper, we propose a computationally light-weight game theoretic secure localization technique and demonstrate its effectiveness in comparison to existing techniques."}],"publist_id":"5247","type":"conference","conference":{"end_date":"2014-10-08","start_date":"2014-10-06","location":"Cambridge, USA","name":"IOT: Internet of Things"},"doi":"10.1109/IOT.2014.7030120","date_published":"2014-02-03T00:00:00Z","language":[{"iso":"eng"}],"citation":{"ama":"Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization in wireless sensor networks. In: IEEE; 2014:85-90. doi:10.1109/IOT.2014.7030120","ista":"Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization in wireless sensor networks. IOT: Internet of Things, 85–90.","apa":"Jha, S., Tripakis, S., Seshia, S., & Chatterjee, K. (2014). Game theoretic secure localization in wireless sensor networks (pp. 85–90). Presented at the IOT: Internet of Things, Cambridge, USA: IEEE. https://doi.org/10.1109/IOT.2014.7030120","ieee":"S. Jha, S. Tripakis, S. Seshia, and K. Chatterjee, “Game theoretic secure localization in wireless sensor networks,” presented at the IOT: Internet of Things, Cambridge, USA, 2014, pp. 85–90.","mla":"Jha, Susmit, et al. Game Theoretic Secure Localization in Wireless Sensor Networks. IEEE, 2014, pp. 85–90, doi:10.1109/IOT.2014.7030120.","short":"S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90.","chicago":"Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee. “Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE, 2014. https://doi.org/10.1109/IOT.2014.7030120."},"quality_controlled":"1","page":"85 - 90","day":"03","month":"02"},{"ec_funded":1,"publist_id":"5237","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"EvBe"}],"publisher":"Nature Publishing Group","publication_status":"published","pmid":1,"acknowledgement":"We thank R. Dixit for performing complementary experiments, D. W. Ehrhardt and T. Hashimoto for providing the seeds of TUB6–RFP and EB1b–GFP respectively, E. Zazimalova, J. Petrasek and M. Fendrych for discussing the manuscript and J. Leung for text optimization. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), ANR blanc AuxiWall project (ANR-11-BSV5-0007, to C.P.-R. and L.G.) and the Agency for Innovation by Science and Technology (IWT) (to H.R.). This work benefited from the facilities and expertise of the Imagif Cell Biology platform (http://www.imagif.cnrs.fr), which is supported by the Conseil Général de l’Essonne.","year":"2014","volume":516,"date_created":"2018-12-11T11:54:25Z","date_updated":"2022-05-23T08:26:44Z","author":[{"first_name":"Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Xu"},{"last_name":"Grandont","first_name":"Laurie","full_name":"Grandont, Laurie"},{"last_name":"Li","first_name":"Hongjiang","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","full_name":"Li, Hongjiang"},{"first_name":"Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"first_name":"Sébastien","last_name":"Paque","full_name":"Paque, Sébastien"},{"last_name":"Abuzeineh","first_name":"Anas","full_name":"Abuzeineh, Anas"},{"last_name":"Rakusova","first_name":"Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","full_name":"Rakusova, Hana"},{"full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Perrot Rechenmann","first_name":"Catherine","full_name":"Perrot Rechenmann, Catherine"},{"full_name":"Friml, Jirí","first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596"}],"publication_identifier":{"issn":["0028-0836"],"eissn":["1476-4687"]},"month":"12","project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"quality_controlled":"1","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/"}],"external_id":{"pmid":["25409144"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/nature13889","type":"journal_article","issue":"729","abstract":[{"lang":"eng","text":"The prominent and evolutionarily ancient role of the plant hormone auxin is the regulation of cell expansion. Cell expansion requires ordered arrangement of the cytoskeleton but molecular mechanisms underlying its regulation by signalling molecules including auxin are unknown. Here we show in the model plant Arabidopsis thaliana that in elongating cells exogenous application of auxin or redistribution of endogenous auxin induces very rapid microtubule re-orientation from transverse to longitudinal, coherent with the inhibition of cell expansion. This fast auxin effect requires auxin binding protein 1 (ABP1) and involves a contribution of downstream signalling components such as ROP6 GTPase, ROP-interactive protein RIC1 and the microtubule-severing protein katanin. These components are required for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell elongation in roots and dark-grown hypocotyls as well as asymmetric growth during gravitropic responses."}],"intvolume":" 516","status":"public","title":"Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules","_id":"1862","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":"1","article_processing_charge":"No","day":"04","page":"90 - 93","article_type":"original","citation":{"ama":"Chen X, Grandont L, Li H, et al. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 2014;516(729):90-93. doi:10.1038/nature13889","ista":"Chen X, Grandont L, Li H, Hauschild R, Paque S, Abuzeineh A, Rakusova H, Benková E, Perrot Rechenmann C, Friml J. 2014. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 516(729), 90–93.","ieee":"X. Chen et al., “Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules,” Nature, vol. 516, no. 729. Nature Publishing Group, pp. 90–93, 2014.","apa":"Chen, X., Grandont, L., Li, H., Hauschild, R., Paque, S., Abuzeineh, A., … Friml, J. (2014). Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13889","mla":"Chen, Xu, et al. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” Nature, vol. 516, no. 729, Nature Publishing Group, 2014, pp. 90–93, doi:10.1038/nature13889.","short":"X. Chen, L. Grandont, H. Li, R. Hauschild, S. Paque, A. Abuzeineh, H. Rakusova, E. Benková, C. Perrot Rechenmann, J. Friml, Nature 516 (2014) 90–93.","chicago":"Chen, Xu, Laurie Grandont, Hongjiang Li, Robert Hauschild, Sébastien Paque, Anas Abuzeineh, Hana Rakusova, Eva Benková, Catherine Perrot Rechenmann, and Jiří Friml. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13889."},"publication":"Nature","date_published":"2014-12-04T00:00:00Z"},{"volume":8855,"date_created":"2018-12-11T11:54:27Z","date_updated":"2021-01-12T06:53:44Z","author":[{"full_name":"Hofferek, Georg","last_name":"Hofferek","first_name":"Georg"},{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"}],"editor":[{"full_name":"Yahav, Eran","first_name":"Eran","last_name":"Yahav"}],"department":[{"_id":"ToHe"}],"publisher":"Springer","publication_status":"published","acknowledgement":"The work presented in this paper was supported in part by the European Research Council (ERC) under grant agreement QUAINT (I774-N23)","year":"2014","publist_id":"5228","ec_funded":1,"language":[{"iso":"eng"}],"doi":"10.1007/978-3-319-13338-6_6","conference":{"end_date":"2014-11-20","start_date":"2014-11-18","location":"Haifa, Israel","name":"HVC: Haifa Verification Conference"},"project":[{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989","name":"Quantitative Reactive Modeling","call_identifier":"FP7"},{"call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407"}],"quality_controlled":"1","month":"01","oa_version":"None","intvolume":" 8855","status":"public","title":"Suraq - a controller synthesis tool using uninterpreted functions","_id":"1869","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","abstract":[{"text":"Boolean controllers for systems with complex datapaths are often very difficult to implement correctly, in particular when concurrency is involved. Yet, in many instances it is easy to formally specify correctness. For example, the specification for the controller of a pipelined processor only has to state that the pipelined processor gives the same results as a non-pipelined reference design. This makes such controllers a good target for automated synthesis. However, an efficient abstraction for the complex datapath elements is needed, as a bit-precise description is often infeasible. We present Suraq, the first controller synthesis tool which uses uninterpreted functions for the abstraction. Quantified firstorder formulas (with specific quantifier structure) serve as the specification language from which Suraq synthesizes Boolean controllers. Suraq transforms the specification into an unsatisfiable SMT formula, and uses Craig interpolation to compute its results. Using Suraq, we were able to synthesize a controller (consisting of two Boolean signals) for a five-stage pipelined DLX processor in roughly one hour and 15 minutes.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","date_published":"2014-01-01T00:00:00Z","page":"68 - 74","citation":{"chicago":"Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” In HVC 2014, edited by Eran Yahav, 8855:68–74. Springer, 2014. https://doi.org/10.1007/978-3-319-13338-6_6.","short":"G. Hofferek, A. Gupta, in:, E. Yahav (Ed.), HVC 2014, Springer, 2014, pp. 68–74.","mla":"Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” HVC 2014, edited by Eran Yahav, vol. 8855, Springer, 2014, pp. 68–74, doi:10.1007/978-3-319-13338-6_6.","apa":"Hofferek, G., & Gupta, A. (2014). Suraq - a controller synthesis tool using uninterpreted functions. In E. Yahav (Ed.), HVC 2014 (Vol. 8855, pp. 68–74). Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-13338-6_6","ieee":"G. Hofferek and A. Gupta, “Suraq - a controller synthesis tool using uninterpreted functions,” in HVC 2014, Haifa, Israel, 2014, vol. 8855, pp. 68–74.","ista":"Hofferek G, Gupta A. 2014. Suraq - a controller synthesis tool using uninterpreted functions. HVC 2014. HVC: Haifa Verification Conference, LNCS, vol. 8855, 68–74.","ama":"Hofferek G, Gupta A. Suraq - a controller synthesis tool using uninterpreted functions. In: Yahav E, ed. HVC 2014. Vol 8855. Springer; 2014:68-74. doi:10.1007/978-3-319-13338-6_6"},"publication":"HVC 2014","day":"01"},{"abstract":[{"text":"Extensionality axioms are common when reasoning about data collections, such as arrays and functions in program analysis, or sets in mathematics. An extensionality axiom asserts that two collections are equal if they consist of the same elements at the same indices. Using extensionality is often required to show that two collections are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly, while humans have no problem with proving such set identities using extensionality, they are very hard for superposition theorem provers because of the calculi they use. In this paper we show how addition of a new inference rule, called extensionality resolution, allows first-order theorem provers to easily solve problems no modern first-order theorem prover can solve. We illustrate this by running the VAMPIRE theorem prover with extensionality resolution on a number of set theory and array problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP library of first-order problems that were never solved before by any prover.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"pubrep_id":"641","oa_version":"Submitted Version","file":[{"checksum":"af4bd3fc1f4c93075e4dc5cbf625fe7b","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:10:15Z","file_id":"4801","relation":"main_file","creator":"system","content_type":"application/pdf","file_size":244294,"access_level":"open_access","file_name":"IST-2016-641-v1+1_atva2014.pdf"}],"_id":"1872","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 8837","status":"public","title":"Extensional crisis and proving identity","ddc":["000"],"has_accepted_license":"1","day":"01","scopus_import":1,"date_published":"2014-01-01T00:00:00Z","citation":{"ista":"Gupta A, Kovács L, Kragl B, Voronkov A. 2014. Extensional crisis and proving identity. ATVA 2014. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 185–200.","ieee":"A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving identity,” in ATVA 2014, Sydney, Australia, 2014, vol. 8837, pp. 185–200.","apa":"Gupta, A., Kovács, L., Kragl, B., & Voronkov, A. (2014). Extensional crisis and proving identity. In F. Cassez & J.-F. Raskin (Eds.), ATVA 2014 (Vol. 8837, pp. 185–200). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_14","ama":"Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity. In: Cassez F, Raskin J-F, eds. ATVA 2014. Vol 8837. Springer; 2014:185-200. doi:10.1007/978-3-319-11936-6_14","chicago":"Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional Crisis and Proving Identity.” In ATVA 2014, edited by Franck Cassez and Jean-François Raskin, 8837:185–200. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_14.","mla":"Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” ATVA 2014, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 185–200, doi:10.1007/978-3-319-11936-6_14.","short":"A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, F. Cassez, J.-F. Raskin (Eds.), ATVA 2014, Springer, 2014, pp. 185–200."},"publication":"ATVA 2014","page":"185 - 200","ec_funded":1,"publist_id":"5226","file_date_updated":"2020-07-14T12:45:19Z","author":[{"full_name":"Gupta, Ashutosh","first_name":"Ashutosh","last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kovács, Laura","first_name":"Laura","last_name":"Kovács"},{"full_name":"Kragl, Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7745-9117","first_name":"Bernhard","last_name":"Kragl"},{"full_name":"Voronkov, Andrei","last_name":"Voronkov","first_name":"Andrei"}],"volume":8837,"date_updated":"2021-01-12T06:53:45Z","date_created":"2018-12-11T11:54:28Z","year":"2014","acknowledgement":"This research was supported in part by the Austrian National Research Network RiSE (S11410-N23).","publisher":"Springer","department":[{"_id":"ToHe"}],"editor":[{"first_name":"Franck","last_name":"Cassez","full_name":"Cassez, Franck"},{"first_name":"Jean-François","last_name":"Raskin","full_name":"Raskin, Jean-François"}],"publication_status":"published","month":"01","doi":"10.1007/978-3-319-11936-6_14","conference":{"end_date":"2014-11-07","location":"Sydney, Australia","start_date":"2014-11-03","name":"ATVA: Automated Technology for Verification and Analysis"},"language":[{"iso":"eng"}],"oa":1,"project":[{"name":"Quantitative Reactive Modeling","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","grant_number":"267989"},{"grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","call_identifier":"FWF"}],"quality_controlled":"1"},{"page":"431 - 443","publication":"Leibniz International Proceedings in Informatics, LIPIcs","citation":{"ama":"Henzinger TA, Otop J, Samanta R. Lipschitz robustness of finite-state transducers. In: Leibniz International Proceedings in Informatics, LIPIcs. Vol 29. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:431-443. doi:10.4230/LIPIcs.FSTTCS.2014.431","apa":"Henzinger, T. A., Otop, J., & Samanta, R. (2014). Lipschitz robustness of finite-state transducers. In Leibniz International Proceedings in Informatics, LIPIcs (Vol. 29, pp. 431–443). Delhi, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431","ieee":"T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of finite-state transducers,” in Leibniz International Proceedings in Informatics, LIPIcs, Delhi, India, 2014, vol. 29, pp. 431–443.","ista":"Henzinger TA, Otop J, Samanta R. 2014. Lipschitz robustness of finite-state transducers. Leibniz International Proceedings in Informatics, LIPIcs. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 29, 431–443.","short":"T.A. Henzinger, J. Otop, R. Samanta, in:, Leibniz International Proceedings in Informatics, LIPIcs, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–443.","mla":"Henzinger, Thomas A., et al. “Lipschitz Robustness of Finite-State Transducers.” Leibniz International Proceedings in Informatics, LIPIcs, vol. 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–43, doi:10.4230/LIPIcs.FSTTCS.2014.431.","chicago":"Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Finite-State Transducers.” In Leibniz International Proceedings in Informatics, LIPIcs, 29:431–43. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431."},"date_published":"2014-12-01T00:00:00Z","day":"01","has_accepted_license":"1","ddc":["004"],"status":"public","title":"Lipschitz robustness of finite-state transducers","intvolume":" 29","_id":"1870","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"access_level":"open_access","file_name":"IST-2017-804-v1+1_37.pdf","file_size":562151,"content_type":"application/pdf","creator":"system","relation":"main_file","file_id":"4734","checksum":"7b1aff1710a8bffb7080ec07f62d9a17","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:09:11Z"}],"pubrep_id":"804","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"We investigate the problem of checking if a finite-state transducer is robust to uncertainty in its input. Our notion of robustness is based on the analytic notion of Lipschitz continuity - a transducer is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions. We show that K-robustness is undecidable even for deterministic transducers. We identify a class of functional transducers, which admits a polynomial time automata-theoretic decision procedure for K-robustness. This class includes Mealy machines and functional letter-to-letter transducers. We also study K-robustness of nondeterministic transducers. Since a nondeterministic transducer generates a set of output words for each input word, we quantify output perturbation using setsimilarity functions. We show that K-robustness of nondeterministic transducers is undecidable, even for letter-to-letter transducers. We identify a class of set-similarity functions which admit decidable K-robustness of letter-to-letter transducers.","lang":"eng"}],"quality_controlled":"1","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"language":[{"iso":"eng"}],"conference":{"name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","location":"Delhi, India","start_date":"2014-12-15","end_date":"2014-12-17"},"doi":"10.4230/LIPIcs.FSTTCS.2014.431","month":"12","publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"ToHe"}],"year":"2014","date_created":"2018-12-11T11:54:27Z","date_updated":"2021-01-12T06:53:45Z","volume":29,"author":[{"full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Otop, Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan","last_name":"Otop"},{"id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","last_name":"Samanta","first_name":"Roopsha","full_name":"Samanta, Roopsha"}],"file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5227"},{"day":"01","has_accepted_license":"1","scopus_import":1,"date_published":"2014-09-01T00:00:00Z","page":"268 - 284","citation":{"short":"R. Samanta, O. Olivo, E. Allen, in:, M. Müller-Olm, H. Seidl (Eds.), Springer, 2014, pp. 268–284.","mla":"Samanta, Roopsha, et al. Cost-Aware Automatic Program Repair. Edited by Markus Müller-Olm and Helmut Seidl, vol. 8723, Springer, 2014, pp. 268–84, doi:10.1007/978-3-319-10936-7_17.","chicago":"Samanta, Roopsha, Oswaldo Olivo, and Emerson Allen. “Cost-Aware Automatic Program Repair.” edited by Markus Müller-Olm and Helmut Seidl, 8723:268–84. Springer, 2014. https://doi.org/10.1007/978-3-319-10936-7_17.","ama":"Samanta R, Olivo O, Allen E. Cost-aware automatic program repair. In: Müller-Olm M, Seidl H, eds. Vol 8723. Springer; 2014:268-284. doi:10.1007/978-3-319-10936-7_17","ieee":"R. Samanta, O. Olivo, and E. Allen, “Cost-aware automatic program repair,” presented at the SAS: Static Analysis Symposium, Munich, Germany, 2014, vol. 8723, pp. 268–284.","apa":"Samanta, R., Olivo, O., & Allen, E. (2014). Cost-aware automatic program repair. In M. Müller-Olm & H. Seidl (Eds.) (Vol. 8723, pp. 268–284). Presented at the SAS: Static Analysis Symposium, Munich, Germany: Springer. https://doi.org/10.1007/978-3-319-10936-7_17","ista":"Samanta R, Olivo O, Allen E. 2014. Cost-aware automatic program repair. SAS: Static Analysis Symposium, LNCS, vol. 8723, 268–284."},"abstract":[{"lang":"eng","text":"We present a formal framework for repairing infinite-state, imperative, sequential programs, with (possibly recursive) procedures and multiple assertions; the framework can generate repaired programs by modifying the original erroneous program in multiple program locations, and can ensure the readability of the repaired program using user-defined expression templates; the framework also generates a set of inductive assertions that serve as a proof of correctness of the repaired program. As a step toward integrating programmer intent and intuition in automated program repair, we present a cost-aware formulation - given a cost function associated with permissible statement modifications, the goal is to ensure that the total program modification cost does not exceed a given repair budget. As part of our predicate abstractionbased solution framework, we present a sound and complete algorithm for repair of Boolean programs. We have developed a prototype tool based on SMT solving and used it successfully to repair diverse errors in benchmark C programs."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Submitted Version","file":[{"creator":"system","file_size":409485,"content_type":"application/pdf","file_name":"IST-2014-313-v1+1_SOE.SAS14.pdf","access_level":"open_access","date_created":"2018-12-12T10:07:51Z","date_updated":"2020-07-14T12:45:19Z","checksum":"78ec4ea1bdecc676cd3e8cad35c6182c","file_id":"4650","relation":"main_file"}],"pubrep_id":"313","status":"public","ddc":["000","005"],"title":"Cost-aware automatic program repair","intvolume":" 8723","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1875","month":"09","language":[{"iso":"eng"}],"conference":{"end_date":"2014-09-14","start_date":"2014-09-11","location":"Munich, Germany","name":"SAS: Static Analysis Symposium"},"doi":"10.1007/978-3-319-10936-7_17","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:45:19Z","publist_id":"5221","date_updated":"2021-01-12T06:53:46Z","date_created":"2018-12-11T11:54:29Z","volume":8723,"author":[{"full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","last_name":"Samanta","first_name":"Roopsha"},{"first_name":"Oswaldo","last_name":"Olivo","full_name":"Olivo, Oswaldo"},{"full_name":"Allen, Emerson","last_name":"Allen","first_name":"Emerson"}],"publication_status":"published","publisher":"Springer","editor":[{"full_name":"Müller-Olm, Markus","first_name":"Markus","last_name":"Müller-Olm"},{"full_name":"Seidl, Helmut","first_name":"Helmut","last_name":"Seidl"}],"department":[{"_id":"ToHe"}],"year":"2014"},{"status":"public","title":"Functionals on triangulations of delaunay sets","intvolume":" 14","_id":"1876","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","type":"journal_article","abstract":[{"text":"We study densities of functionals over uniformly bounded triangulations of a Delaunay set of vertices, and prove that the minimum is attained for the Delaunay triangulation if this is the case for finite sets.","lang":"eng"}],"issue":"3","article_type":"original","page":"491 - 504","publication":"Moscow Mathematical Journal","citation":{"ista":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. 2014. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 14(3), 491–504.","ieee":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, and O. Musin, “Functionals on triangulations of delaunay sets,” Moscow Mathematical Journal, vol. 14, no. 3. Independent University of Moscow, pp. 491–504, 2014.","apa":"Dolbilin, N., Edelsbrunner, H., Glazyrin, A., & Musin, O. (2014). Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-3-491-504","ama":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 2014;14(3):491-504. doi:10.17323/1609-4514-2014-14-3-491-504","chicago":"Dolbilin, Nikolai, Herbert Edelsbrunner, Alexey Glazyrin, and Oleg Musin. “Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-3-491-504.","mla":"Dolbilin, Nikolai, et al. “Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal, vol. 14, no. 3, Independent University of Moscow, 2014, pp. 491–504, doi:10.17323/1609-4514-2014-14-3-491-504.","short":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, O. Musin, Moscow Mathematical Journal 14 (2014) 491–504."},"date_published":"2014-07-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","publication_status":"published","publisher":"Independent University of Moscow","department":[{"_id":"HeEd"}],"year":"2014","date_created":"2018-12-11T11:54:29Z","date_updated":"2022-03-03T11:47:09Z","volume":14,"author":[{"first_name":"Nikolai","last_name":"Dolbilin","full_name":"Dolbilin, Nikolai"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Glazyrin","first_name":"Alexey","full_name":"Glazyrin, Alexey"},{"full_name":"Musin, Oleg","first_name":"Oleg","last_name":"Musin"}],"publist_id":"5220","quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1211.7053"}],"external_id":{"arxiv":["1211.7053"]},"language":[{"iso":"eng"}],"doi":"10.17323/1609-4514-2014-14-3-491-504","month":"07","publication_identifier":{"issn":["16093321"]}},{"_id":"1877","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2014","department":[{"_id":"MiSi"}],"publisher":"Springer Nature","intvolume":" 514","publication_status":"published","status":"public","title":"Physiology: Relax and come in","author":[{"first_name":"Michael K","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K"},{"orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","last_name":"Vaahtomeri","first_name":"Kari","full_name":"Vaahtomeri, Kari"}],"volume":514,"oa_version":"None","date_created":"2018-12-11T11:54:30Z","date_updated":"2021-01-12T06:53:47Z","type":"journal_article","publist_id":"5219","issue":"7523","abstract":[{"lang":"eng","text":"During inflammation, lymph nodes swell with an influx of immune cells. New findings identify a signalling pathway that induces relaxation in the contractile cells that give structure to these organs."}],"citation":{"ama":"Sixt MK, Vaahtomeri K. Physiology: Relax and come in. Nature. 2014;514(7523):441-442. doi:10.1038/514441a","ieee":"M. K. Sixt and K. Vaahtomeri, “Physiology: Relax and come in,” Nature, vol. 514, no. 7523. Springer Nature, pp. 441–442, 2014.","apa":"Sixt, M. K., & Vaahtomeri, K. (2014). Physiology: Relax and come in. Nature. Springer Nature. https://doi.org/10.1038/514441a","ista":"Sixt MK, Vaahtomeri K. 2014. Physiology: Relax and come in. Nature. 514(7523), 441–442.","short":"M.K. Sixt, K. Vaahtomeri, Nature 514 (2014) 441–442.","mla":"Sixt, Michael K., and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature, vol. 514, no. 7523, Springer Nature, 2014, pp. 441–42, doi:10.1038/514441a.","chicago":"Sixt, Michael K, and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature. Springer Nature, 2014. https://doi.org/10.1038/514441a."},"publication":"Nature","page":"441 - 442","article_type":"letter_note","quality_controlled":"1","date_published":"2014-10-23T00:00:00Z","doi":"10.1038/514441a","language":[{"iso":"eng"}],"scopus_import":1,"month":"10","day":"23"},{"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","project":[{"call_identifier":"FWF","name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26"}],"doi":"10.7554/eLife.03722","language":[{"iso":"eng"}],"month":"11","year":"2014","publication_status":"published","publisher":"eLife Sciences Publications","department":[{"_id":"GaTk"}],"author":[{"first_name":"Ann","last_name":"Hermundstad","full_name":"Hermundstad, Ann"},{"last_name":"Briguglio","first_name":"John","full_name":"Briguglio, John"},{"full_name":"Conte, Mary","first_name":"Mary","last_name":"Conte"},{"last_name":"Victor","first_name":"Jonathan","full_name":"Victor, Jonathan"},{"first_name":"Vijay","last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik"}],"date_updated":"2021-01-12T06:53:50Z","date_created":"2018-12-11T11:54:32Z","article_number":"e03722","file_date_updated":"2020-07-14T12:45:20Z","publist_id":"5209","publication":"eLife","citation":{"ieee":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” eLife, no. November. eLife Sciences Publications, 2014.","apa":"Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., & Tkačik, G. (2014). Variance predicts salience in central sensory processing. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.03722","ista":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. 2014. Variance predicts salience in central sensory processing. eLife. (November), e03722.","ama":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. Variance predicts salience in central sensory processing. eLife. 2014;(November). doi:10.7554/eLife.03722","chicago":"Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.03722.","short":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014).","mla":"Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722."},"date_published":"2014-11-14T00:00:00Z","scopus_import":1,"day":"14","has_accepted_license":"1","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1886","ddc":["570"],"title":"Variance predicts salience in central sensory processing","status":"public","pubrep_id":"420","file":[{"relation":"main_file","file_id":"4922","date_created":"2018-12-12T10:12:04Z","date_updated":"2020-07-14T12:45:20Z","checksum":"766ac8999ac6e3364f10065a06024b8f","file_name":"IST-2016-420-v1+1_e03722.full.pdf","access_level":"open_access","file_size":5117086,"content_type":"application/pdf","creator":"system"}],"oa_version":"Published Version","type":"journal_article","abstract":[{"lang":"eng","text":"Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime—when sampling limitations constrain performance—efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability."}],"issue":"November"},{"date_published":"2014-02-11T00:00:00Z","page":"385 - 395","publication":"Psychophysiology","citation":{"short":"C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, A. Ischebeck, Psychophysiology 51 (2014) 385–395.","mla":"Körner, Christof, et al. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” Psychophysiology, vol. 51, no. 4, Wiley-Blackwell, 2014, pp. 385–95, doi:10.1111/psyp.12062.","chicago":"Körner, Christof, Verena Braunstein, Matthias Stangl, Alois Schlögl, Christa Neuper, and Anja Ischebeck. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” Psychophysiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/psyp.12062.","ama":"Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. 2014;51(4):385-395. doi:10.1111/psyp.12062","apa":"Körner, C., Braunstein, V., Stangl, M., Schlögl, A., Neuper, C., & Ischebeck, A. (2014). Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. Wiley-Blackwell. https://doi.org/10.1111/psyp.12062","ieee":"C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, and A. Ischebeck, “Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection,” Psychophysiology, vol. 51, no. 4. Wiley-Blackwell, pp. 385–395, 2014.","ista":"Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. 2014. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. 51(4), 385–395."},"day":"11","has_accepted_license":"1","scopus_import":1,"file":[{"date_updated":"2020-07-14T12:45:20Z","date_created":"2018-12-12T10:16:44Z","checksum":"4255b6185e774acce1d99f8e195c564d","relation":"main_file","file_id":"5233","file_size":543243,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-442-v1+1_K-rner_et_al-2014-Psychophysiology.pdf","access_level":"open_access"}],"oa_version":"Published Version","pubrep_id":"442","title":"Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection","status":"public","ddc":["000"],"intvolume":" 51","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1890","abstract":[{"text":"To search for a target in a complex environment is an everyday behavior that ends with finding the target. When we search for two identical targets, however, we must continue the search after finding the first target and memorize its location. We used fixation-related potentials to investigate the neural correlates of different stages of the search, that is, before and after finding the first target. Having found the first target influenced subsequent distractor processing. Compared to distractor fixations before the first target fixation, a negative shift was observed for three subsequent distractor fixations. These results suggest that processing a target in continued search modulates the brain's response, either transiently by reflecting temporary working memory processes or permanently by reflecting working memory retention.","lang":"eng"}],"issue":"4","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1111/psyp.12062","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"02","date_created":"2018-12-11T11:54:34Z","date_updated":"2021-01-12T06:53:52Z","volume":51,"author":[{"full_name":"Körner, Christof","last_name":"Körner","first_name":"Christof"},{"first_name":"Verena","last_name":"Braunstein","full_name":"Braunstein, Verena"},{"full_name":"Stangl, Matthias","last_name":"Stangl","first_name":"Matthias"},{"full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5621-8100","first_name":"Alois","last_name":"Schlögl"},{"first_name":"Christa","last_name":"Neuper","full_name":"Neuper, Christa"},{"full_name":"Ischebeck, Anja","last_name":"Ischebeck","first_name":"Anja"}],"publication_status":"published","publisher":"Wiley-Blackwell","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"acknowledgement":"Funded by Austrian Science Fund (FWF) Grant Number: P 22189-B18; European Union within the 6th Framework Programme Grant Number: 517590; State government of Styria Grant Number: PN 4055","year":"2014","file_date_updated":"2020-07-14T12:45:20Z","publist_id":"5205"},{"publication_status":"published","publisher":"The Royal Society","department":[{"_id":"CampIT"}],"year":"2014","acknowledgement":"This research was supported by grants of the Swiss National Science Foundation to M.T.\r\nWe thank Tetsu Sato for providing field samples, Olivier Goffinet for field assistance, Dolores Schütz for vital help in the field and with the manuscript, David Lank, Barbara Taborsky, Suzanne Alonzo and two anonymous referees for comments on earlier manuscript versions, and the Fisheries Department, Ministry of Agriculture and Livestock of Zambia, for permission and support.","pmid":1,"date_updated":"2022-06-07T09:12:32Z","date_created":"2018-12-11T11:54:34Z","volume":281,"author":[{"full_name":"Ocana, Sabine","first_name":"Sabine","last_name":"Ocana"},{"first_name":"Patrick","last_name":"Meidl","id":"4709BCE6-F248-11E8-B48F-1D18A9856A87","full_name":"Meidl, Patrick"},{"first_name":"Danielle","last_name":"Bonfils","full_name":"Bonfils, Danielle"},{"last_name":"Taborsky","first_name":"Michael","full_name":"Taborsky, Michael"}],"article_number":"20140253","publist_id":"5203","quality_controlled":"1","external_id":{"pmid":["25232141"]},"oa":1,"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211437/","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1098/rspb.2014.0253","month":"11","title":"Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids","status":"public","intvolume":" 281","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1892","oa_version":"Submitted Version","type":"journal_article","abstract":[{"lang":"eng","text":"Behavioural variation among conspecifics is typically contingent on individual state or environmental conditions. Sex-specific genetic polymorphisms are enigmatic because they lack conditionality, and genes causing adaptive trait variation in one sex may reduce Darwinian fitness in the other. One way to avoid such genetic antagonism is to control sex-specific traits by inheritance via sex chromosomes. Here, controlled laboratory crossings suggest that in snail-brooding cichlid fish a single locus, two-allele polymorphism located on a sex-linked chromosome of heterogametic males generates an extreme reproductive dimorphism. Both natural and sexual selection are responsible for exceptionally large body size of bourgeois males, creating a niche for a miniature male phenotype to evolve. This extreme intrasexual dimorphism results from selection on opposite size thresholds caused by a single ecological factor, empty snail shells used as breeding substrate. Paternity analyses reveal that in the field parasitic dwarf males sire the majority of offspring in direct sperm competition with large nest owners exceeding their size more than 40 times. Apparently, use of empty snail shells as breeding substrate and single locus sex-linked inheritance of growth are the major ecological and genetic mechanisms responsible for the extreme intrasexual diversity observed in Lamprologus callipterus."}],"issue":"1794","article_type":"original","publication":"Proceedings of the Royal Society of London Series B Biological Sciences","citation":{"ieee":"S. Ocana, P. Meidl, D. Bonfils, and M. Taborsky, “Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids,” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794. The Royal Society, 2014.","apa":"Ocana, S., Meidl, P., Bonfils, D., & Taborsky, M. (2014). Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society. https://doi.org/10.1098/rspb.2014.0253","ista":"Ocana S, Meidl P, Bonfils D, Taborsky M. 2014. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20140253.","ama":"Ocana S, Meidl P, Bonfils D, Taborsky M. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 2014;281(1794). doi:10.1098/rspb.2014.0253","chicago":"Ocana, Sabine, Patrick Meidl, Danielle Bonfils, and Michael Taborsky. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London Series B Biological Sciences. The Royal Society, 2014. https://doi.org/10.1098/rspb.2014.0253.","short":"S. Ocana, P. Meidl, D. Bonfils, M. Taborsky, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","mla":"Ocana, Sabine, et al. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” Proceedings of the Royal Society of London Series B Biological Sciences, vol. 281, no. 1794, 20140253, The Royal Society, 2014, doi:10.1098/rspb.2014.0253."},"date_published":"2014-11-07T00:00:00Z","scopus_import":"1","day":"07","article_processing_charge":"No"},{"author":[{"last_name":"Chwastyk","first_name":"Mateusz","full_name":"Chwastyk, Mateusz"},{"full_name":"Galera Prat, Albert","first_name":"Albert","last_name":"Galera Prat"},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gómez Sicilia","first_name":"Àngel","full_name":"Gómez Sicilia, Àngel"},{"first_name":"Mariano","last_name":"Carrión Vázquez","full_name":"Carrión Vázquez, Mariano"},{"full_name":"Cieplak, Marek","last_name":"Cieplak","first_name":"Marek"}],"date_created":"2018-12-11T11:54:34Z","date_updated":"2021-01-12T06:53:52Z","oa_version":"None","volume":82,"acknowledgement":"Grant Nr. 2011/01/N/ST3/02475","_id":"1891","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","year":"2014","status":"public","publication_status":"published","title":"Theoretical tests of the mechanical protection strategy in protein nanomechanics","publisher":"Wiley-Blackwell","intvolume":" 82","department":[{"_id":"CaHe"}],"abstract":[{"text":"We provide theoretical tests of a novel experimental technique to determine mechanostability of proteins based on stretching a mechanically protected protein by single-molecule force spectroscopy. This technique involves stretching a homogeneous or heterogeneous chain of reference proteins (single-molecule markers) in which one of them acts as host to the guest protein under study. The guest protein is grafted into the host through genetic engineering. It is expected that unraveling of the host precedes the unraveling of the guest removing ambiguities in the reading of the force-extension patterns of the guest protein. We study examples of such systems within a coarse-grained structure-based model. We consider systems with various ratios of mechanostability for the host and guest molecules and compare them to experimental results involving cohesin I as the guest molecule. For a comparison, we also study the force-displacement patterns in proteins that are linked in a serial fashion. We find that the mechanostability of the guest is similar to that of the isolated or serially linked protein. We also demonstrate that the ideal configuration of this strategy would be one in which the host is much more mechanostable than the single-molecule markers. We finally show that it is troublesome to use the highly stable cystine knot proteins as a host to graft a guest in stretching studies because this would involve a cleaving procedure.","lang":"eng"}],"publist_id":"5204","issue":"5","type":"journal_article","date_published":"2014-05-01T00:00:00Z","doi":"10.1002/prot.24436","language":[{"iso":"eng"}],"publication":"Proteins: Structure, Function and Bioinformatics","citation":{"chicago":"Chwastyk, Mateusz, Albert Galera Prat, Mateusz K Sikora, Àngel Gómez Sicilia, Mariano Carrión Vázquez, and Marek Cieplak. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2014. https://doi.org/10.1002/prot.24436.","mla":"Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:10.1002/prot.24436.","short":"M. Chwastyk, A. Galera Prat, M.K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, M. Cieplak, Proteins: Structure, Function and Bioinformatics 82 (2014) 717–726.","ista":"Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. 2014. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 82(5), 717–726.","ieee":"M. Chwastyk, A. Galera Prat, M. K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, and M. Cieplak, “Theoretical tests of the mechanical protection strategy in protein nanomechanics,” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5. Wiley-Blackwell, pp. 717–726, 2014.","apa":"Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez, M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.24436","ama":"Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 2014;82(5):717-726. doi:10.1002/prot.24436"},"page":"717 - 726","day":"01","month":"05","scopus_import":1},{"publication_status":"published","title":"Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples","status":"public","department":[{"_id":"KrCh"}],"intvolume":" 124","publisher":"American Society of Hematology","year":"2014","_id":"1884","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:54:32Z","date_updated":"2021-01-12T06:53:50Z","oa_version":"None","volume":124,"author":[{"last_name":"Landau","first_name":"Dan","full_name":"Landau, Dan"},{"last_name":"Stewart","first_name":"Chip","full_name":"Stewart, Chip"},{"full_name":"Reiter, Johannes","first_name":"Johannes","last_name":"Reiter","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353"},{"last_name":"Lawrence","first_name":"Michael","full_name":"Lawrence, Michael"},{"full_name":"Sougnez, Carrie","first_name":"Carrie","last_name":"Sougnez"},{"full_name":"Brown, Jennifer","last_name":"Brown","first_name":"Jennifer"},{"full_name":"Lopez Guillermo, Armando","last_name":"Lopez Guillermo","first_name":"Armando"},{"full_name":"Gabriel, Stacey","last_name":"Gabriel","first_name":"Stacey"},{"first_name":"Eric","last_name":"Lander","full_name":"Lander, Eric"},{"full_name":"Neuberg, Donna","last_name":"Neuberg","first_name":"Donna"},{"last_name":"López Otín","first_name":"Carlos","full_name":"López Otín, Carlos"},{"first_name":"Elias","last_name":"Campo","full_name":"Campo, Elias"},{"full_name":"Getz, Gad","last_name":"Getz","first_name":"Gad"},{"last_name":"Wu","first_name":"Catherine","full_name":"Wu, Catherine"}],"type":"journal_article","abstract":[{"text":"Unbiased high-throughput massively parallel sequencing methods have transformed the process of discovery of novel putative driver gene mutations in cancer. In chronic lymphocytic leukemia (CLL), these methods have yielded several unexpected findings, including the driver genes SF3B1, NOTCH1 and POT1. Recent analysis, utilizing down-sampling of existing datasets, has shown that the discovery process of putative drivers is far from complete across cancer. In CLL, while driver gene mutations affecting >10% of patients were efficiently discovered with previously published CLL cohorts of up to 160 samples subjected to whole exome sequencing (WES), this sample size has only 0.78 power to detect drivers affecting 5% of patients, and only 0.12 power for drivers affecting 2% of patients. These calculations emphasize the need to apply unbiased WES to larger patient cohorts.","lang":"eng"}],"publist_id":"5211","issue":"21","page":"1952 - 1952","publication":"Blood","main_file_link":[{"url":"http://www.bloodjournal.org/content/124/21/1952?sso-checked=true"}],"citation":{"chicago":"Landau, Dan, Chip Stewart, Johannes Reiter, Michael Lawrence, Carrie Sougnez, Jennifer Brown, Armando Lopez Guillermo, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” Blood. American Society of Hematology, 2014.","short":"D. Landau, C. Stewart, J. Reiter, M. Lawrence, C. Sougnez, J. Brown, A. Lopez Guillermo, S. Gabriel, E. Lander, D. Neuberg, C. López Otín, E. Campo, G. Getz, C. Wu, Blood 124 (2014) 1952–1952.","mla":"Landau, Dan, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” Blood, vol. 124, no. 21, American Society of Hematology, 2014, pp. 1952–1952.","ieee":"D. Landau et al., “Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples,” Blood, vol. 124, no. 21. American Society of Hematology, pp. 1952–1952, 2014.","apa":"Landau, D., Stewart, C., Reiter, J., Lawrence, M., Sougnez, C., Brown, J., … Wu, C. (2014). Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. American Society of Hematology.","ista":"Landau D, Stewart C, Reiter J, Lawrence M, Sougnez C, Brown J, Lopez Guillermo A, Gabriel S, Lander E, Neuberg D, López Otín C, Campo E, Getz G, Wu C. 2014. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 124(21), 1952–1952.","ama":"Landau D, Stewart C, Reiter J, et al. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 2014;124(21):1952-1952."},"language":[{"iso":"eng"}],"date_published":"2014-12-04T00:00:00Z","month":"12","day":"04"},{"month":"08","main_file_link":[{"url":"http://arxiv.org/abs/1305.5135","open_access":"1"}],"oa":1,"external_id":{"arxiv":["1305.5135"]},"quality_controlled":"1","doi":"10.1142/S0129055X14500123","language":[{"iso":"eng"}],"article_number":"1450012","publist_id":"5206","acknowledgement":"We would like to thank Max Lein and Andreas Deuchert for valuable suggestions and remarks. Partial financial support by the NSERC (R.S.) is gratefully acknowledged.","year":"2014","department":[{"_id":"RoSe"}],"publisher":"World Scientific Publishing","publication_status":"published","author":[{"first_name":"Gerhard","last_name":"Bräunlich","full_name":"Bräunlich, Gerhard"},{"last_name":"Hainzl","first_name":"Christian","full_name":"Hainzl, Christian"},{"full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer"}],"volume":26,"date_updated":"2022-06-07T09:03:09Z","date_created":"2018-12-11T11:54:33Z","scopus_import":"1","article_processing_charge":"No","day":"01","citation":{"chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X14500123.","short":"G. Bräunlich, C. Hainzl, R. Seiringer, Reviews in Mathematical Physics 26 (2014).","mla":"Bräunlich, Gerhard, et al. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics, vol. 26, no. 7, 1450012, World Scientific Publishing, 2014, doi:10.1142/S0129055X14500123.","ieee":"G. Bräunlich, C. Hainzl, and R. Seiringer, “Translation-invariant quasi-free states for fermionic systems and the BCS approximation,” Reviews in Mathematical Physics, vol. 26, no. 7. World Scientific Publishing, 2014.","apa":"Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X14500123","ista":"Bräunlich G, Hainzl C, Seiringer R. 2014. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 26(7), 1450012.","ama":"Bräunlich G, Hainzl C, Seiringer R. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 2014;26(7). doi:10.1142/S0129055X14500123"},"publication":"Reviews in Mathematical Physics","article_type":"original","date_published":"2014-08-01T00:00:00Z","type":"journal_article","issue":"7","abstract":[{"lang":"eng","text":"We study translation-invariant quasi-free states for a system of fermions with two-particle interactions. The associated energy functional is similar to the BCS functional but also includes direct and exchange energies. We show that for suitable short-range interactions, these latter terms only lead to a renormalization of the chemical potential, with the usual properties of the BCS functional left unchanged. Our analysis thus represents a rigorous justification of part of the BCS approximation. We give bounds on the critical temperature below which the system displays superfluidity."}],"_id":"1889","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 26","status":"public","title":"Translation-invariant quasi-free states for fermionic systems and the BCS approximation","oa_version":"Submitted Version"},{"year":"2014","publication_status":"published","department":[{"_id":"CaGu"}],"publisher":"Public Library of Science","author":[{"full_name":"Grabowska, Anna","first_name":"Anna","last_name":"Grabowska"},{"last_name":"Wywiał","first_name":"Ewa","full_name":"Wywiał, Ewa"},{"full_name":"Dunin Horkawicz, Stanislaw","last_name":"Dunin Horkawicz","first_name":"Stanislaw"},{"full_name":"Łasica, Anna","first_name":"Anna","last_name":"Łasica"},{"last_name":"Wösten","first_name":"Marc","full_name":"Wösten, Marc"},{"id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","last_name":"Nagy-Staron","first_name":"Anna A","full_name":"Nagy-Staron, Anna A"},{"last_name":"Godlewska","first_name":"Renata","full_name":"Godlewska, Renata"},{"first_name":"Katarzyna","last_name":"Bocian Ostrzycka","full_name":"Bocian Ostrzycka, Katarzyna"},{"first_name":"Katarzyna","last_name":"Pieńkowska","full_name":"Pieńkowska, Katarzyna"},{"full_name":"Łaniewski, Paweł","last_name":"Łaniewski","first_name":"Paweł"},{"first_name":"Janusz","last_name":"Bujnicki","full_name":"Bujnicki, Janusz"},{"full_name":"Van Putten, Jos","first_name":"Jos","last_name":"Van Putten"},{"first_name":"Elzbieta","last_name":"Jagusztyn Krynicka","full_name":"Jagusztyn Krynicka, Elzbieta"}],"date_updated":"2021-01-12T06:53:54Z","date_created":"2018-12-11T11:54:35Z","volume":9,"article_number":"e106247","file_date_updated":"2020-07-14T12:45:20Z","publist_id":"5201","oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"quality_controlled":"1","doi":"10.1371/journal.pone.0106247","language":[{"iso":"eng"}],"month":"09","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1894","title":"Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA","status":"public","ddc":["570"],"intvolume":" 9","pubrep_id":"438","oa_version":"Published Version","file":[{"file_size":4248801,"content_type":"application/pdf","creator":"system","file_name":"IST-2016-438-v1+1_journal.pone.0106247.pdf","access_level":"open_access","date_created":"2018-12-12T10:16:19Z","date_updated":"2020-07-14T12:45:20Z","checksum":"7d02c3da7f72b82bb5d7932d80c3251f","relation":"main_file","file_id":"5205"}],"type":"journal_article","abstract":[{"text":"Background: Bacterial Dsb enzymes are involved in the oxidative folding of many proteins, through the formation of disulfide bonds between their cysteine residues. The Dsb protein network has been well characterized in cells of the model microorganism Escherichia coli. To gain insight into the functioning of the Dsb system in epsilon-Proteobacteria, where it plays an important role in the colonization process, we studied two homologs of the main Escherichia coli Dsb oxidase (EcDsbA) that are present in the cells of the enteric pathogen Campylobacter jejuni, the most frequently reported bacterial cause of human enteritis in the world. Methods and Results: Phylogenetic analysis suggests the horizontal transfer of the epsilon-Proteobacterial DsbAs from a common ancestor to gamma-Proteobacteria, which then gave rise to the DsbL lineage. Phenotype and enzymatic assays suggest that the two C. jejuni DsbAs play different roles in bacterial cells and have divergent substrate spectra. CjDsbA1 is essential for the motility and autoagglutination phenotypes, while CjDsbA2 has no impact on those processes. CjDsbA1 plays a critical role in the oxidative folding that ensures the activity of alkaline phosphatase CjPhoX, whereas CjDsbA2 is crucial for the activity of arylsulfotransferase CjAstA, encoded within the dsbA2-dsbB-astA operon. Conclusions: Our results show that CjDsbA1 is the primary thiol-oxidoreductase affecting life processes associated with bacterial spread and host colonization, as well as ensuring the oxidative folding of particular protein substrates. In contrast, CjDsbA2 activity does not affect the same processes and so far its oxidative folding activity has been demonstrated for one substrate, arylsulfotransferase CjAstA. The results suggest the cooperation between CjDsbA2 and CjDsbB. In the case of the CjDsbA1, this cooperation is not exclusive and there is probably another protein to be identified in C. jejuni cells that acts to re-oxidize CjDsbA1. Altogether the data presented here constitute the considerable insight to the Epsilonproteobacterial Dsb systems, which have been poorly understood so far.","lang":"eng"}],"issue":"9","publication":"PLoS One","citation":{"chicago":"Grabowska, Anna, Ewa Wywiał, Stanislaw Dunin Horkawicz, Anna Łasica, Marc Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0106247.","short":"A. Grabowska, E. Wywiał, S. Dunin Horkawicz, A. Łasica, M. Wösten, A.A. Nagy-Staron, R. Godlewska, K. Bocian Ostrzycka, K. Pieńkowska, P. Łaniewski, J. Bujnicki, J. Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014).","mla":"Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One, vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:10.1371/journal.pone.0106247.","apa":"Grabowska, A., Wywiał, E., Dunin Horkawicz, S., Łasica, A., Wösten, M., Nagy-Staron, A. A., … Jagusztyn Krynicka, E. (2014). Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0106247","ieee":"A. Grabowska et al., “Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014.","ista":"Grabowska A, Wywiał E, Dunin Horkawicz S, Łasica A, Wösten M, Nagy-Staron AA, Godlewska R, Bocian Ostrzycka K, Pieńkowska K, Łaniewski P, Bujnicki J, Van Putten J, Jagusztyn Krynicka E. 2014. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 9(9), e106247.","ama":"Grabowska A, Wywiał E, Dunin Horkawicz S, et al. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0106247"},"date_published":"2014-09-02T00:00:00Z","scopus_import":1,"day":"02","has_accepted_license":"1"},{"month":"09","doi":"10.1371/journal.pone.0107099","language":[{"iso":"eng"}],"oa":1,"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publist_id":"5200","file_date_updated":"2020-07-14T12:45:20Z","article_number":"e107099","author":[{"full_name":"Edamura, Mitsuhiro","last_name":"Edamura","first_name":"Mitsuhiro"},{"full_name":"Murakami, Gen","last_name":"Murakami","first_name":"Gen"},{"last_name":"Meng","first_name":"Hongrui","full_name":"Meng, Hongrui"},{"first_name":"Makoto","last_name":"Itakura","full_name":"Itakura, Makoto"},{"last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi"},{"full_name":"Fukuda, Atsuo","first_name":"Atsuo","last_name":"Fukuda"},{"full_name":"Nakahara, Daiichiro","first_name":"Daiichiro","last_name":"Nakahara"}],"volume":9,"date_updated":"2021-01-12T06:53:54Z","date_created":"2018-12-11T11:54:35Z","year":"2014","acknowledgement":"This work was supported in part by a Grant-in-Aid for Scientific Research on Innovative Areas (Comprehensive Brain Science Network) and (B) 17330153, from the Ministry of Education, Culture, Sports, Science and Technology of Japan.","department":[{"_id":"RySh"}],"publisher":"Public Library of Science","publication_status":"published","has_accepted_license":"1","day":"30","scopus_import":1,"date_published":"2014-09-30T00:00:00Z","citation":{"short":"M. Edamura, G. Murakami, H. Meng, M. Itakura, R. Shigemoto, A. Fukuda, D. Nakahara, PLoS One 9 (2014).","mla":"Edamura, Mitsuhiro, et al. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One, vol. 9, no. 9, e107099, Public Library of Science, 2014, doi:10.1371/journal.pone.0107099.","chicago":"Edamura, Mitsuhiro, Gen Murakami, Hongrui Meng, Makoto Itakura, Ryuichi Shigemoto, Atsuo Fukuda, and Daiichiro Nakahara. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0107099.","ama":"Edamura M, Murakami G, Meng H, et al. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0107099","ieee":"M. Edamura et al., “Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014.","apa":"Edamura, M., Murakami, G., Meng, H., Itakura, M., Shigemoto, R., Fukuda, A., & Nakahara, D. (2014). Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0107099","ista":"Edamura M, Murakami G, Meng H, Itakura M, Shigemoto R, Fukuda A, Nakahara D. 2014. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 9(9), e107099."},"publication":"PLoS One","issue":"9","abstract":[{"lang":"eng","text":"Major histocompatibility complex class I (MHCI) molecules were recently identified as novel regulators of synaptic plasticity. These molecules are expressed in various brain areas, especially in regions undergoing activity-dependent synaptic plasticity, but their role in the nucleus accumbens (NAc) is unknown. In this study, we investigated the effects of genetic disruption of MHCI function, through deletion of β2-microblobulin, which causes lack of cell surface expression of MHCI. First, we confirmed that MHCI molecules are expressed in the NAc core in wild-type mice. Second, we performed electrophysiological recordings with NAc core slices from wild-type and β2-microglobulin knock-out mice lacking cell surface expression of MHCI. We found that low frequency stimulation induced long-term depression in wild-type but not knock-out mice, whereas high frequency stimulation induced long-term potentiation in both genotypes, with a larger magnitude in knock-out mice. Furthermore, we demonstrated that knock-out mice showed more persistent behavioral sensitization to cocaine, which is a NAc-related behavior. Using this model, we analyzed the density of total AMPA receptors and their subunits GluR1 and GluR2 in the NAc core, by SDS-digested freeze-fracture replica labeling. After repeated cocaine exposure, the density of GluR1 was increased, but there was no change in total AMPA receptors and GluR2 levels in wildtype mice. In contrast, following repeated cocaine exposure, increased densities of total AMPA receptors, GluR1 and GluR2 were observed in knock-out mice. These results indicate that functional deficiency of MHCI enhances synaptic potentiation, induced by electrical and pharmacological stimulation."}],"type":"journal_article","pubrep_id":"439","oa_version":"Published Version","file":[{"date_created":"2018-12-12T10:09:01Z","date_updated":"2020-07-14T12:45:20Z","checksum":"1f3be936be93114596d61ba44cacee69","relation":"main_file","file_id":"4724","content_type":"application/pdf","file_size":6262085,"creator":"system","file_name":"IST-2016-439-v1+1_journal.pone.0107099.pdf","access_level":"open_access"}],"_id":"1895","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","intvolume":" 9","title":"Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice","status":"public","ddc":["570"]},{"doi":"10.1073/pnas.1324264111","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/"}],"oa":1,"project":[{"call_identifier":"FP7","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300"}],"month":"02","author":[{"full_name":"Nováková, Petra","id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","last_name":"Nováková"},{"full_name":"Hirsch, Sibylle","first_name":"Sibylle","last_name":"Hirsch"},{"first_name":"Elena","last_name":"Feraru","full_name":"Feraru, Elena"},{"full_name":"Tejos, Ricardo","last_name":"Tejos","first_name":"Ricardo"},{"first_name":"Ringo","last_name":"Van Wijk","full_name":"Van Wijk, Ringo"},{"full_name":"Viaene, Tom","last_name":"Viaene","first_name":"Tom"},{"last_name":"Heilmann","first_name":"Mareike","full_name":"Heilmann, Mareike"},{"last_name":"Lerche","first_name":"Jennifer","full_name":"Lerche, Jennifer"},{"full_name":"De Rycke, Riet","first_name":"Riet","last_name":"De Rycke"},{"first_name":"Mugurel","last_name":"Feraru","full_name":"Feraru, Mugurel"},{"last_name":"Grones","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","full_name":"Grones, Peter"},{"last_name":"Van Montagu","first_name":"Marc","full_name":"Van Montagu, Marc"},{"full_name":"Heilmann, Ingo","first_name":"Ingo","last_name":"Heilmann"},{"first_name":"Teun","last_name":"Munnik","full_name":"Munnik, Teun"},{"first_name":"Jirí","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí"}],"date_created":"2018-12-11T11:54:34Z","date_updated":"2021-01-12T06:53:53Z","volume":111,"acknowledgement":"This work was supported by grants from the Research Foundation-Flanders (Odysseus).","year":"2014","publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"JiFr"}],"ec_funded":1,"publist_id":"5202","date_published":"2014-02-18T00:00:00Z","publication":"PNAS","citation":{"chicago":"Marhavá, Petra, Sibylle Hirsch, Elena Feraru, Ricardo Tejos, Ringo Van Wijk, Tom Viaene, Mareike Heilmann, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1324264111.","mla":"Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS, vol. 111, no. 7, National Academy of Sciences, 2014, pp. 2818–23, doi:10.1073/pnas.1324264111.","short":"P. Marhavá, S. Hirsch, E. Feraru, R. Tejos, R. Van Wijk, T. Viaene, M. Heilmann, J. Lerche, R. De Rycke, M. Feraru, P. Grones, M. Van Montagu, I. Heilmann, T. Munnik, J. Friml, PNAS 111 (2014) 2818–2823.","ista":"Marhavá P, Hirsch S, Feraru E, Tejos R, Van Wijk R, Viaene T, Heilmann M, Lerche J, De Rycke R, Feraru M, Grones P, Van Montagu M, Heilmann I, Munnik T, Friml J. 2014. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 111(7), 2818–2823.","ieee":"P. Marhavá et al., “SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis,” PNAS, vol. 111, no. 7. National Academy of Sciences, pp. 2818–2823, 2014.","apa":"Marhavá, P., Hirsch, S., Feraru, E., Tejos, R., Van Wijk, R., Viaene, T., … Friml, J. (2014). SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1324264111","ama":"Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 2014;111(7):2818-2823. doi:10.1073/pnas.1324264111"},"page":"2818 - 2823","day":"18","scopus_import":1,"oa_version":"Submitted Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1893","title":"SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis","status":"public","intvolume":" 111","abstract":[{"lang":"eng","text":"Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants."}],"issue":"7","type":"journal_article"},{"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevE.89.032701","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1402.0430"}],"oa":1,"month":"03","volume":89,"date_created":"2018-12-11T11:54:35Z","date_updated":"2022-08-01T10:50:10Z","author":[{"first_name":"Richard","last_name":"Kollár","full_name":"Kollár, Richard"},{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","first_name":"Katarína","last_name":"Bod'ová","full_name":"Bod'ová, Katarína"},{"full_name":"Nosek, Jozef","last_name":"Nosek","first_name":"Jozef"},{"full_name":"Tomáška, Ľubomír","first_name":"Ľubomír","last_name":"Tomáška"}],"publisher":"American Institute of Physics","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"publication_status":"published","year":"2014","acknowledgement":"The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.).","publist_id":"5198","article_number":"032701","date_published":"2014-03-04T00:00:00Z","citation":{"ama":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701","ista":"Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701.","ieee":"R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014.","apa":"Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701","mla":"Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.","short":"R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014).","chicago":"Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.032701."},"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","article_processing_charge":"No","day":"04","scopus_import":"1","oa_version":"Submitted Version","intvolume":" 89","status":"public","title":"Mathematical model of alternative mechanism of telomere length maintenance","_id":"1896","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"lang":"eng","text":"Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings."}],"type":"journal_article"},{"publisher":"American Society of Plant Biologists","department":[{"_id":"JiFr"}],"intvolume":" 26","status":"public","title":"Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis","publication_status":"published","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1897","year":"2014","acknowledgement":"This work was supported by the Odysseus Program of the Research Foundation-Flanders (J.F.).","oa_version":"Submitted Version","volume":26,"date_updated":"2021-01-12T06:53:55Z","date_created":"2018-12-11T11:54:36Z","author":[{"last_name":"Naramoto","first_name":"Satoshi","full_name":"Naramoto, Satoshi"},{"full_name":"Otegui, Marisa","last_name":"Otegui","first_name":"Marisa"},{"full_name":"Kutsuna, Natsumaro","first_name":"Natsumaro","last_name":"Kutsuna"},{"first_name":"Riet","last_name":"De Rycke","full_name":"De Rycke, Riet"},{"first_name":"Tomoko","last_name":"Dainobu","full_name":"Dainobu, Tomoko"},{"first_name":"Michael","last_name":"Karampelias","full_name":"Karampelias, Michael"},{"last_name":"Fujimoto","first_name":"Masaru","full_name":"Fujimoto, Masaru"},{"first_name":"Elena","last_name":"Feraru","full_name":"Feraru, Elena"},{"full_name":"Miki, Daisuke","first_name":"Daisuke","last_name":"Miki"},{"full_name":"Fukuda, Hiroo","last_name":"Fukuda","first_name":"Hiroo"},{"full_name":"Nakano, Akihiko","first_name":"Akihiko","last_name":"Nakano"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jirí","last_name":"Friml","full_name":"Friml, Jirí"}],"type":"journal_article","issue":"7","publist_id":"5199","abstract":[{"text":"GNOM is one of the most characterized membrane trafficking regulators in plants, with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor) class to mediate vesicle budding at endomembranes. The crucial role of GNOM in recycling of PIN auxin transporters and other proteins to the plasma membrane was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM, the most prominent regulator of recycling in plants, has been proposed to act and localize at so far elusive recycling endosomes. Here, we report the GNOM localization in context of its cellular function in Arabidopsis thaliana. State-of-the-art imaging, pharmacological interference, and ultrastructure analysis show that GNOM predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus, whereas prolonged exposures results in GNOM translocation to trans-Golgi network (TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role for GNOM in maintaining TGN/EE function. Our results redefine the subcellular action of GNOM and reevaluate the identity and function of recycling endosomes in plants.","lang":"eng"}],"page":"3062 - 3076","citation":{"ama":"Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 2014;26(7):3062-3076. doi:10.1105/tpc.114.125880","ista":"Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 26(7), 3062–3076.","ieee":"S. Naramoto et al., “Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,” Plant Cell, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076, 2014.","apa":"Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias, M., … Friml, J. (2014). Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.125880","mla":"Naramoto, Satoshi, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell, vol. 26, no. 7, American Society of Plant Biologists, 2014, pp. 3062–76, doi:10.1105/tpc.114.125880.","short":"S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias, M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26 (2014) 3062–3076.","chicago":"Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.125880."},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/"}],"oa":1,"publication":"Plant Cell","language":[{"iso":"eng"}],"date_published":"2014-07-01T00:00:00Z","doi":"10.1105/tpc.114.125880","scopus_import":1,"month":"07","day":"01"},{"article_processing_charge":"No","day":"13","scopus_import":1,"date_published":"2014-07-13T00:00:00Z","citation":{"short":"S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature Cell Biology 16 (2014) 758–769.","mla":"Williams, Scott, et al. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology, vol. 16, no. 8, Nature Publishing Group, 2014, pp. 758–69, doi:10.1038/ncb3001.","chicago":"Williams, Scott, Lyndsay Ratliff, Maria P Postiglione, Juergen Knoblich, and Elaine Fuchs. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb3001.","ama":"Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 2014;16(8):758-769. doi:10.1038/ncb3001","ieee":"S. Williams, L. Ratliff, M. P. Postiglione, J. Knoblich, and E. Fuchs, “Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN,” Nature Cell Biology, vol. 16, no. 8. Nature Publishing Group, pp. 758–769, 2014.","apa":"Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., & Fuchs, E. (2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3001","ista":"Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. 2014. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 16(8), 758–769."},"publication":"Nature Cell Biology","page":"758 - 769","article_type":"original","issue":"8","abstract":[{"text":"Asymmetric cell divisions allow stem cells to balance proliferation and differentiation. During embryogenesis, murine epidermis expands rapidly from a single layer of unspecified basal layer progenitors to a stratified, differentiated epithelium. Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation protein LGN, but little is known about how the apical localization of LGN is regulated. Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas loss of each gene alone leads to randomized division angles, combined loss of Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of LGN. These findings lend experimental support for the hitherto untested model that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular divisions. Finally, we uncover a developmental switch between delamination-driven early stratification and spindle-orientation-dependent differentiation that occurs around E15, revealing a two-step mechanism underlying epidermal maturation.","lang":"eng"}],"type":"journal_article","oa_version":"Submitted Version","_id":"1899","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 16","status":"public","title":"Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN","month":"07","doi":"10.1038/ncb3001","language":[{"iso":"eng"}],"external_id":{"pmid":["25016959"]},"main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/","open_access":"1"}],"oa":1,"quality_controlled":"1","publist_id":"5196","author":[{"last_name":"Williams","first_name":"Scott","full_name":"Williams, Scott"},{"first_name":"Lyndsay","last_name":"Ratliff","full_name":"Ratliff, Lyndsay"},{"full_name":"Postiglione, Maria P","id":"2C67902A-F248-11E8-B48F-1D18A9856A87","first_name":"Maria P","last_name":"Postiglione"},{"first_name":"Juergen","last_name":"Knoblich","full_name":"Knoblich, Juergen"},{"full_name":"Fuchs, Elaine","first_name":"Elaine","last_name":"Fuchs"}],"volume":16,"date_updated":"2021-01-12T06:53:55Z","date_created":"2018-12-11T11:54:36Z","pmid":1,"year":"2014","publisher":"Nature Publishing Group","department":[{"_id":"SiHi"}],"publication_status":"published"},{"abstract":[{"lang":"eng","text":"Fast synaptic transmission is important for rapid information processing. To explore the maximal rate of neuronal signaling and to analyze the presynaptic mechanisms, we focused on the input layer of the cerebellar cortex, where exceptionally high action potential (AP) frequencies have been reported invivo. With paired recordings between presynaptic cerebellar mossy fiber boutons and postsynaptic granule cells, we demonstrate reliable neurotransmission upto ~1 kHz. Presynaptic APs are ultrafast, with ~100μs half-duration. Both Kv1 and Kv3 potassium channels mediate the fast repolarization, rapidly inactivating sodium channels ensure metabolic efficiency, and little AP broadening occurs during bursts of up to 1.5 kHz. Presynaptic Cav2.1 (P/Q-type) calcium channels open efficiently during ultrafast APs. Furthermore, a subset of synaptic vesicles is tightly coupled to Ca2+ channels, and vesicles are rapidly recruited to the release site. These data reveal mechanisms of presynaptic AP generation and transmitter release underlying neuronal kHz signaling."}],"publist_id":"5197","issue":"1","type":"journal_article","author":[{"last_name":"Ritzau Jost","first_name":"Andreas","full_name":"Ritzau Jost, Andreas"},{"first_name":"Igor","last_name":"Delvendahl","full_name":"Delvendahl, Igor"},{"last_name":"Rings","first_name":"Annika","full_name":"Rings, Annika"},{"first_name":"Niklas","last_name":"Byczkowicz","full_name":"Byczkowicz, Niklas"},{"last_name":"Harada","first_name":"Harumi","orcid":"0000-0001-7429-7896","id":"2E55CDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Harada, Harumi"},{"full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi"},{"last_name":"Hirrlinger","first_name":"Johannes","full_name":"Hirrlinger, Johannes"},{"full_name":"Eilers, Jens","last_name":"Eilers","first_name":"Jens"},{"full_name":"Hallermann, Stefan","first_name":"Stefan","last_name":"Hallermann"}],"date_updated":"2021-01-12T06:53:55Z","date_created":"2018-12-11T11:54:36Z","volume":84,"oa_version":"None","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1898","year":"2014","publication_status":"published","status":"public","title":"Ultrafast action potentials mediate kilohertz signaling at a central synapse","publisher":"Elsevier","department":[{"_id":"RySh"}],"intvolume":" 84","month":"10","day":"01","scopus_import":1,"date_published":"2014-10-01T00:00:00Z","doi":"10.1016/j.neuron.2014.08.036","language":[{"iso":"eng"}],"publication":"Neuron","citation":{"ama":"Ritzau Jost A, Delvendahl I, Rings A, et al. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 2014;84(1):152-163. doi:10.1016/j.neuron.2014.08.036","ieee":"A. Ritzau Jost et al., “Ultrafast action potentials mediate kilohertz signaling at a central synapse,” Neuron, vol. 84, no. 1. Elsevier, pp. 152–163, 2014.","apa":"Ritzau Jost, A., Delvendahl, I., Rings, A., Byczkowicz, N., Harada, H., Shigemoto, R., … Hallermann, S. (2014). Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.08.036","ista":"Ritzau Jost A, Delvendahl I, Rings A, Byczkowicz N, Harada H, Shigemoto R, Hirrlinger J, Eilers J, Hallermann S. 2014. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 84(1), 152–163.","short":"A. Ritzau Jost, I. Delvendahl, A. Rings, N. Byczkowicz, H. Harada, R. Shigemoto, J. Hirrlinger, J. Eilers, S. Hallermann, Neuron 84 (2014) 152–163.","mla":"Ritzau Jost, Andreas, et al. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron, vol. 84, no. 1, Elsevier, 2014, pp. 152–63, doi:10.1016/j.neuron.2014.08.036.","chicago":"Ritzau Jost, Andreas, Igor Delvendahl, Annika Rings, Niklas Byczkowicz, Harumi Harada, Ryuichi Shigemoto, Johannes Hirrlinger, Jens Eilers, and Stefan Hallermann. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.08.036."},"quality_controlled":"1","page":"152 - 163"},{"doi":"10.1109/TVCG.2014.2312011","language":[{"iso":"eng"}],"oa":1,"project":[{"_id":"25357BD2-B435-11E9-9278-68D0E5697425","grant_number":"P 24352-N23","call_identifier":"FWF","name":"Deep Pictures: Creating Visual and Haptic Vector Images"}],"month":"09","author":[{"first_name":"Murat","last_name":"Arikan","full_name":"Arikan, Murat"},{"full_name":"Preiner, Reinhold","first_name":"Reinhold","last_name":"Preiner"},{"full_name":"Scheiblauer, Claus","first_name":"Claus","last_name":"Scheiblauer"},{"last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87","full_name":"Jeschke, Stefan"},{"first_name":"Michael","last_name":"Wimmer","full_name":"Wimmer, Michael"}],"date_created":"2018-12-11T11:54:39Z","date_updated":"2021-01-12T06:53:59Z","volume":20,"year":"2014","acknowledgement":"This research was supported by the Austrian Research Promotion Agency (FFG) project REPLICATE (no. 835948), the EU FP7 project HARVEST4D (no. 323567).","publication_status":"published","publisher":"IEEE","department":[{"_id":"ChWo"}],"file_date_updated":"2020-07-14T12:45:20Z","publist_id":"5189","date_published":"2014-09-09T00:00:00Z","publication":"IEEE Transactions on Visualization and Computer Graphics","citation":{"ista":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. 2014. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 20(9), 1280–1292.","apa":"Arikan, M., Preiner, R., Scheiblauer, C., Jeschke, S., & Wimmer, M. (2014). Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2312011","ieee":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, and M. Wimmer, “Large-scale point-cloud visualization through localized textured surface reconstruction,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9. IEEE, pp. 1280–1292, 2014.","ama":"Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 2014;20(9):1280-1292. doi:10.1109/TVCG.2014.2312011","chicago":"Arikan, Murat, Reinhold Preiner, Claus Scheiblauer, Stefan Jeschke, and Michael Wimmer. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2312011.","mla":"Arikan, Murat, et al. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9, IEEE, 2014, pp. 1280–92, doi:10.1109/TVCG.2014.2312011.","short":"M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, M. Wimmer, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 1280–1292."},"page":"1280 - 1292","day":"09","has_accepted_license":"1","scopus_import":1,"pubrep_id":"573","file":[{"checksum":"5bf58942d2eb20adf03c7f9ea2e68124","date_created":"2018-12-12T10:17:41Z","date_updated":"2020-07-14T12:45:20Z","relation":"main_file","file_id":"5297","file_size":13594598,"content_type":"application/pdf","creator":"system","access_level":"open_access","file_name":"IST-2016-573-v1+1_arikan-2014-pcvis-draft.pdf"}],"oa_version":"Submitted Version","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","_id":"1906","title":"Large-scale point-cloud visualization through localized textured surface reconstruction","ddc":["000"],"status":"public","intvolume":" 20","abstract":[{"lang":"eng","text":"In this paper, we introduce a novel scene representation for the visualization of large-scale point clouds accompanied by a set of high-resolution photographs. Many real-world applications deal with very densely sampled point-cloud data, which are augmented with photographs that often reveal lighting variations and inaccuracies in registration. Consequently, the high-quality representation of the captured data, i.e., both point clouds and photographs together, is a challenging and time-consuming task. We propose a two-phase approach, in which the first (preprocessing) phase generates multiple overlapping surface patches and handles the problem of seamless texture generation locally for each patch. The second phase stitches these patches at render-time to produce a high-quality visualization of the data. As a result of the proposed localization of the global texturing problem, our algorithm is more than an order of magnitude faster than equivalent mesh-based texturing techniques. Furthermore, since our preprocessing phase requires only a minor fraction of the whole data set at once, we provide maximum flexibility when dealing with growing data sets."}],"issue":"9","type":"journal_article"},{"external_id":{"pmid":["24725091"]},"quality_controlled":"1","doi":"10.1111/jeb.12370","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"month":"04","pmid":1,"acknowledgement":"This study was funded by grants from the National Science Foundation (NSF) to MT (IOS-1121832) and IS (DEB-0743406) and from the German Science Foundation (DFG; PL 470/1-2) and ‘LOEWE − Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer Exzellenz’ of Hesse's Ministry of Higher Education, Research, and the Arts, to MP.","year":"2014","department":[{"_id":"SyCr"}],"publisher":"Wiley","publication_status":"published","author":[{"full_name":"Tobler, Michael","first_name":"Michael","last_name":"Tobler"},{"full_name":"Plath, Martin","last_name":"Plath","first_name":"Martin"},{"full_name":"Riesch, Rüdiger","last_name":"Riesch","first_name":"Rüdiger"},{"full_name":"Schlupp, Ingo","last_name":"Schlupp","first_name":"Ingo"},{"full_name":"Grasse, Anna V","last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gopi","last_name":"Munimanda","full_name":"Munimanda, Gopi"},{"first_name":"C","last_name":"Setzer","full_name":"Setzer, C"},{"last_name":"Penn","first_name":"Dustin","full_name":"Penn, Dustin"},{"full_name":"Moodley, Yoshan","last_name":"Moodley","first_name":"Yoshan"}],"volume":27,"date_created":"2018-12-11T11:54:38Z","date_updated":"2022-06-07T09:22:20Z","publist_id":"5190","citation":{"mla":"Tobler, Michael, et al. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology, vol. 27, no. 5, Wiley, 2014, pp. 960–74, doi:10.1111/jeb.12370.","short":"M. Tobler, M. Plath, R. Riesch, I. Schlupp, A.V. Grasse, G. Munimanda, C. Setzer, D. Penn, Y. Moodley, Journal of Evolutionary Biology 27 (2014) 960–974.","chicago":"Tobler, Michael, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna V Grasse, Gopi Munimanda, C Setzer, Dustin Penn, and Yoshan Moodley. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology. Wiley, 2014. https://doi.org/10.1111/jeb.12370.","ama":"Tobler M, Plath M, Riesch R, et al. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 2014;27(5):960-974. doi:10.1111/jeb.12370","ista":"Tobler M, Plath M, Riesch R, Schlupp I, Grasse AV, Munimanda G, Setzer C, Penn D, Moodley Y. 2014. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 27(5), 960–974.","apa":"Tobler, M., Plath, M., Riesch, R., Schlupp, I., Grasse, A. V., Munimanda, G., … Moodley, Y. (2014). Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.12370","ieee":"M. Tobler et al., “Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations,” Journal of Evolutionary Biology, vol. 27, no. 5. Wiley, pp. 960–974, 2014."},"publication":"Journal of Evolutionary Biology","page":"960 - 974","article_type":"original","date_published":"2014-04-12T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"12","_id":"1905","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 27","status":"public","title":"Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations","oa_version":"None","type":"journal_article","issue":"5","abstract":[{"lang":"eng","text":"The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution)."}]},{"date_published":"2014-01-01T00:00:00Z","page":"232 - 238","article_type":"original","citation":{"short":"B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238.","mla":"Hall, Barry, et al. “Growth Rates Made Easy.” Molecular Biology and Evolution, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:10.1093/molbev/mst187.","chicago":"Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/mst187.","ama":"Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. Molecular Biology and Evolution. 2014;31(1):232-238. doi:10.1093/molbev/mst187","ieee":"B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” Molecular Biology and Evolution, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014.","apa":"Hall, B., Acar, H., Nandipati, A., & Barlow, M. (2014). Growth rates made easy. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst187","ista":"Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238."},"publication":"Molecular Biology and Evolution","article_processing_charge":"No","day":"01","scopus_import":"1","oa_version":"None","intvolume":" 31","status":"public","title":"Growth rates made easy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"1902","issue":"1","abstract":[{"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.","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1093/molbev/mst187","quality_controlled":"1","external_id":{"pmid":["24170494"]},"publication_identifier":{"eissn":["1537-1719"],"issn":["0737-4038"]},"month":"01","volume":31,"date_created":"2018-12-11T11:54:37Z","date_updated":"2022-06-07T11:08:13Z","author":[{"full_name":"Hall, Barry","last_name":"Hall","first_name":"Barry"},{"full_name":"Acar, Hande","last_name":"Acar","first_name":"Hande","orcid":"0000-0003-1986-9753","id":"2DDF136A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Nandipati, Anna","first_name":"Anna","last_name":"Nandipati"},{"first_name":"Miriam","last_name":"Barlow","full_name":"Barlow, Miriam"}],"department":[{"_id":"JoBo"}],"publisher":"Oxford University Press","publication_status":"published","pmid":1,"year":"2014","publist_id":"5193"},{"publication":"Molecular Plant","citation":{"ista":"Tian H, Wabnik KT, Niu T, Li H, Yu Q, Pollmann S, Vanneste S, Govaerts W, Rolčík J, Geisler M, Friml J, Ding Z. 2014. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 7(2), 277–289.","apa":"Tian, H., Wabnik, K. T., Niu, T., Li, H., Yu, Q., Pollmann, S., … Ding, Z. (2014). WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. Oxford University Press. https://doi.org/10.1093/mp/sst118","ieee":"H. Tian et al., “WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis,” Molecular Plant, vol. 7, no. 2. Oxford University Press, pp. 277–289, 2014.","ama":"Tian H, Wabnik KT, Niu T, et al. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 2014;7(2):277-289. doi:10.1093/mp/sst118","chicago":"Tian, Huiyu, Krzysztof T Wabnik, Tiantian Niu, Hongjiang Li, Qianqian Yu, Stephan Pollmann, Steffen Vanneste, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant. Oxford University Press, 2014. https://doi.org/10.1093/mp/sst118.","mla":"Tian, Huiyu, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant, vol. 7, no. 2, Oxford University Press, 2014, pp. 277–89, doi:10.1093/mp/sst118.","short":"H. Tian, K.T. Wabnik, T. Niu, H. Li, Q. Yu, S. Pollmann, S. Vanneste, W. Govaerts, J. Rolčík, M. Geisler, J. Friml, Z. Ding, Molecular Plant 7 (2014) 277–289."},"page":"277 - 289","date_published":"2014-02-01T00:00:00Z","doi":"10.1093/mp/sst118","language":[{"iso":"eng"}],"scopus_import":1,"month":"02","day":"01","_id":"1901","year":"2014","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by funding from the projects CZ.1.07/2.3.00/20.0043 and CZ.1.05/1.1.00/02.0068 (to CEITEC, Central European Institute of Technology) and the Odysseus program of the Research Foundation-Flanders to J.F\r\n","publication_status":"published","title":"WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis","status":"public","department":[{"_id":"JiFr"}],"publisher":"Oxford University Press","intvolume":" 7","author":[{"full_name":"Tian, Huiyu","first_name":"Huiyu","last_name":"Tian"},{"last_name":"Wabnik","first_name":"Krzysztof T","full_name":"Wabnik, Krzysztof T"},{"full_name":"Niu, Tiantian","first_name":"Tiantian","last_name":"Niu"},{"last_name":"Li","first_name":"Hongjiang","full_name":"Li, Hongjiang"},{"first_name":"Qianqian","last_name":"Yu","full_name":"Yu, Qianqian"},{"first_name":"Stephan","last_name":"Pollmann","full_name":"Pollmann, Stephan"},{"first_name":"Steffen","last_name":"Vanneste","full_name":"Vanneste, Steffen"},{"last_name":"Govaerts","first_name":"Willy","full_name":"Govaerts, Willy"},{"last_name":"Rolčík","first_name":"Jakub","full_name":"Rolčík, Jakub"},{"last_name":"Geisler","first_name":"Markus","full_name":"Geisler, Markus"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jirí","full_name":"Friml, Jirí"},{"last_name":"Ding","first_name":"Zhaojun","full_name":"Ding, Zhaojun"}],"date_updated":"2021-01-12T06:53:57Z","date_created":"2018-12-11T11:54:37Z","volume":7,"oa_version":"None","type":"journal_article","abstract":[{"text":"In plants, the patterning of stem cell-enriched meristems requires a graded auxin response maximum that emerges from the concerted action of polar auxin transport, auxin biosynthesis, auxin metabolism, and cellular auxin response machinery. However, mechanisms underlying this auxin response maximum-mediated root stem cell maintenance are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED HOMEOBOX 5 (WOX5) transcription factor modulates expression of auxin biosynthetic genes in the quiescent center (QC) of the root and thus provides a robust mechanism for the maintenance of auxin response maximum in the root tip. This WOX5 action is balanced through the activity of indole-3-acetic acid 17 (IAA17) auxin response repressor. Our combined genetic, cell biology, and computational modeling studies revealed a previously uncharacterized feedback loop linking WOX5-mediated auxin production to IAA17-dependent repression of auxin responses. This WOX5-IAA17 feedback circuit further assures the maintenance of auxin response maximum in the root tip and thereby contributes to the maintenance of distal stem cell (DSC) populations. Our experimental studies and in silico computer simulations both demonstrate that the WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip and the auxin-mediated root DSC differentiation.","lang":"eng"}],"issue":"2","publist_id":"5194"}]