[{"file":[{"date_updated":"2020-07-14T12:46:52Z","checksum":"9d3b90bf4fff74664f182f2d95ef727a","file_size":405561,"creator":"system","content_type":"application/pdf","relation":"main_file","file_name":"IST-2014-314-v1+1_long.pdf","file_id":"5471","access_level":"open_access","date_created":"2018-12-12T11:53:10Z"}],"date_published":"2014-11-05T00:00:00Z","month":"11","abstract":[{"text":"We consider graphs with n nodes together with their tree-decomposition that has b = O ( n ) bags and width t , on the standard RAM computational model with wordsize W = Θ (log n ) . Our contributions are two-fold: Our first contribution is an algorithm that given a graph and its tree-decomposition as input, computes a binary and balanced tree-decomposition of width at most 4 · t + 3 of the graph in O ( b ) time and space, improving a long-standing (from 1992) bound of O ( n · log n ) time for constant treewidth graphs. Our second contribution is on reachability queries for low treewidth graphs. We build on our tree-balancing algorithm and present a data-structure for graph reachability that requires O ( n · t 2 ) preprocessing time, O ( n · t ) space, and O ( d t/ log n e ) time for pair queries, and O ( n · t · log t/ log n ) time for single-source queries. For constant t our data-structure uses O ( n ) time for preprocessing, O (1) time for pair queries, and O ( n/ log n ) time for single-source queries. This is (asymptotically) optimal and is faster than DFS/BFS when answering more than a constant number of single-source queries.","lang":"eng"}],"ddc":["000"],"oa":1,"date_updated":"2021-01-12T08:02:09Z","publisher":"IST Austria","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"24","alternative_title":["IST Austria Technical Report"],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"day":"05","year":"2014","status":"public","has_accepted_license":"1","title":"Optimal tree-decomposition balancing and reachability on low treewidth graphs","file_date_updated":"2020-07-14T12:46:52Z","type":"technical_report","_id":"5427","oa_version":"Published Version","date_created":"2018-12-12T11:39:16Z","pubrep_id":"314","citation":{"ama":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. <i>Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs</i>. IST Austria; 2014. doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-314-v1-1\">10.15479/AT:IST-2014-314-v1-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs</i>. IST Austria, 2014, doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-314-v1-1\">10.15479/AT:IST-2014-314-v1-1</a>.","ista":"Chatterjee K, Ibsen-Jensen R, Pavlogiannis A. 2014. Optimal tree-decomposition balancing and reachability on low treewidth graphs, IST Austria, 24p.","ieee":"K. Chatterjee, R. Ibsen-Jensen, and A. Pavlogiannis, <i>Optimal tree-decomposition balancing and reachability on low treewidth graphs</i>. IST Austria, 2014.","short":"K. Chatterjee, R. Ibsen-Jensen, A. Pavlogiannis, Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs, IST Austria, 2014.","chicago":"Chatterjee, Krishnendu, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. <i>Optimal Tree-Decomposition Balancing and Reachability on Low Treewidth Graphs</i>. IST Austria, 2014. <a href=\"https://doi.org/10.15479/AT:IST-2014-314-v1-1\">https://doi.org/10.15479/AT:IST-2014-314-v1-1</a>.","apa":"Chatterjee, K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2014). <i>Optimal tree-decomposition balancing and reachability on low treewidth graphs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2014-314-v1-1\">https://doi.org/10.15479/AT:IST-2014-314-v1-1</a>"},"doi":"10.15479/AT:IST-2014-314-v1-1","department":[{"_id":"KrCh"}],"author":[{"last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"last_name":"Ibsen-Jensen","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","orcid":"0000-0003-4783-0389","full_name":"Ibsen-Jensen, Rasmus"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas"}]},{"year":"2014","day":"05","language":[{"iso":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"title":"Quantitative fair simulation games","has_accepted_license":"1","status":"public","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Jan Otop, and Yaron Velner. <i>Quantitative Fair Simulation Games</i>. IST Austria, 2014. <a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">https://doi.org/10.15479/AT:IST-2014-315-v1-1</a>.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, Y. Velner, Quantitative Fair Simulation Games, IST Austria, 2014.","apa":"Chatterjee, K., Henzinger, T. A., Otop, J., &#38; Velner, Y. (2014). <i>Quantitative fair simulation games</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">https://doi.org/10.15479/AT:IST-2014-315-v1-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>Quantitative Fair Simulation Games</i>. IST Austria, 2014, doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">10.15479/AT:IST-2014-315-v1-1</a>.","ieee":"K. Chatterjee, T. A. Henzinger, J. Otop, and Y. Velner, <i>Quantitative fair simulation games</i>. IST Austria, 2014.","ista":"Chatterjee K, Henzinger TA, Otop J, Velner Y. 2014. Quantitative fair simulation games, IST Austria, 26p.","ama":"Chatterjee K, Henzinger TA, Otop J, Velner Y. <i>Quantitative Fair Simulation Games</i>. IST Austria; 2014. doi:<a href=\"https://doi.org/10.15479/AT:IST-2014-315-v1-1\">10.15479/AT:IST-2014-315-v1-1</a>"},"doi":"10.15479/AT:IST-2014-315-v1-1","date_created":"2018-12-12T11:39:16Z","oa_version":"Published Version","pubrep_id":"315","_id":"5428","type":"technical_report","file_date_updated":"2020-07-14T12:46:52Z","related_material":{"record":[{"id":"1066","status":"public","relation":"later_version"}]},"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Otop, Jan","last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Velner, Yaron","first_name":"Yaron","last_name":"Velner"}],"department":[{"_id":"ToHe"},{"_id":"KrCh"}],"ddc":["004"],"oa":1,"abstract":[{"lang":"eng","text":"Simulation is an attractive alternative for language inclusion for automata as it is an under-approximation of language inclusion, but usually has much lower complexity. For non-deterministic automata, while language inclusion is PSPACE-complete, simulation can be computed in polynomial time. Simulation has also been extended in two orthogonal directions, namely, (1) fair simulation, for simulation over specified set of infinite runs; and (2) quantitative simulation, for simulation between weighted automata. Again, while fair trace inclusion is PSPACE-complete, fair simulation can be computed in polynomial time. For weighted automata, the (quantitative) language inclusion problem is undecidable for mean-payoff automata and the decidability is open for discounted-sum automata, whereas the (quantitative) simulation reduce to mean-payoff games and discounted-sum games, which admit pseudo-polynomial time algorithms.\r\n\r\nIn this work, we study (quantitative) simulation for weighted automata with Büchi acceptance conditions, i.e., we generalize fair simulation from non-weighted automata to weighted automata. We show that imposing Büchi acceptance conditions on weighted automata changes many fundamental properties of the simulation games. For example, whereas for mean-payoff and discounted-sum games, the players do not need memory to play optimally; we show in contrast that for simulation games with Büchi acceptance conditions, (i) for mean-payoff objectives, optimal strategies for both players require infinite memory in general, and (ii) for discounted-sum objectives, optimal strategies need not exist for both players. While the simulation games with Büchi acceptance conditions are more complicated (e.g., due to infinite-memory requirements for mean-payoff objectives) as compared to their counterpart without Büchi acceptance conditions, we still present pseudo-polynomial time algorithms to solve simulation games with Büchi acceptance conditions for both weighted mean-payoff and weighted discounted-sum automata."}],"month":"12","date_published":"2014-12-05T00:00:00Z","file":[{"date_updated":"2020-07-14T12:46:52Z","checksum":"b1d573bc04365625ff9974880c0aa807","file_size":531046,"creator":"system","content_type":"application/pdf","file_name":"IST-2014-315-v1+1_report.pdf","relation":"main_file","file_id":"5521","date_created":"2018-12-12T11:53:59Z","access_level":"open_access"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"IST Austria","date_updated":"2023-09-20T12:07:48Z","alternative_title":["IST Austria Technical Report"],"page":"26"},{"title":"On Finding Spherical Geodesic Paths and Circles in ℤ3","volume":8668,"status":"public","intvolume":"      8668","year":"2014","publication_identifier":{"isbn":["9783642387081","9783642387098"],"issn":["0302-9743","1611-3349"]},"language":[{"iso":"eng"}],"author":[{"orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","last_name":"Biswas","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"}],"conference":{"name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","start_date":"2014-09-10","end_date":"2014-09-12","location":"Siena, Italy"},"date_created":"2019-01-08T20:45:32Z","oa_version":"None","quality_controlled":"1","citation":{"apa":"Biswas, R., &#38; Bhowmick, P. (2014). On Finding Spherical Geodesic Paths and Circles in ℤ3. Presented at the DGCI: International Conference on Discrete Geometry for Computer Imagery, Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-319-09955-2_33\">https://doi.org/10.1007/978-3-319-09955-2_33</a>","short":"R. Biswas, P. Bhowmick, 8668 (2014) 396–409.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On Finding Spherical Geodesic Paths and Circles in ℤ3.” Lecture Notes in Computer Science. Berlin, Heidelberg: Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-09955-2_33\">https://doi.org/10.1007/978-3-319-09955-2_33</a>.","ieee":"R. Biswas and P. Bhowmick, “On Finding Spherical Geodesic Paths and Circles in ℤ3,” vol. 8668. Springer, Berlin, Heidelberg, pp. 396–409, 2014.","ista":"Biswas R, Bhowmick P. 2014. On Finding Spherical Geodesic Paths and Circles in ℤ3. 8668, 396–409.","mla":"Biswas, Ranita, and Partha Bhowmick. <i>On Finding Spherical Geodesic Paths and Circles in ℤ3</i>. Vol. 8668, Springer, 2014, pp. 396–409, doi:<a href=\"https://doi.org/10.1007/978-3-319-09955-2_33\">10.1007/978-3-319-09955-2_33</a>.","ama":"Biswas R, Bhowmick P. On Finding Spherical Geodesic Paths and Circles in ℤ3. 2014;8668:396-409. doi:<a href=\"https://doi.org/10.1007/978-3-319-09955-2_33\">10.1007/978-3-319-09955-2_33</a>"},"doi":"10.1007/978-3-319-09955-2_33","extern":"1","_id":"5810","type":"conference","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2019-01-24T13:22:49Z","place":"Berlin, Heidelberg","publisher":"Springer","abstract":[{"text":"A discrete spherical geodesic path between two voxels s and t lying on a discrete sphere is a/the 1-connected shortest path from s to t, comprising voxels of the discrete sphere intersected by the real plane passing through s, t, and the center of the sphere. We show that the set of sphere voxels intersected by the aforesaid real plane always contains a 1-connected cycle passing through s and t, and each voxel in this set lies within an isothetic distance of 32 from the concerned plane. Hence, to compute the path, the algorithm starts from s, and iteratively computes each voxel p of the path from the predecessor of p. A novel number-theoretic property and the 48-symmetry of discrete sphere are used for searching the 1-connected voxels comprising the path. The algorithm is output-sensitive, having its time and space complexities both linear in the length of the path. It can be extended for constructing 1-connected discrete 3D circles of arbitrary orientations, specified by a few appropriate input parameters. Experimental results and related analysis demonstrate its efficiency and versatility.","lang":"eng"}],"date_published":"2014-01-01T00:00:00Z","series_title":"Lecture Notes in Computer Science","page":"396-409"},{"extern":"1","quality_controlled":"1","doi":"10.1007/s00023-013-0302-4","citation":{"ama":"Dereziński J, Napiórkowski MM. Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume limit. <i>Annales Henri Poincaré</i>. 2014;15(12):2409-2439. doi:<a href=\"https://doi.org/10.1007/s00023-013-0302-4\">10.1007/s00023-013-0302-4</a>","ista":"Dereziński J, Napiórkowski MM. 2014. Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume limit. Annales Henri Poincaré. 15(12), 2409–2439.","ieee":"J. Dereziński and M. M. Napiórkowski, “Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume limit,” <i>Annales Henri Poincaré</i>, vol. 15, no. 12. Springer Nature, pp. 2409–2439, 2014.","mla":"Dereziński, Jan, and Marcin M. Napiórkowski. “Excitation Spectrum of Interacting Bosons in the Mean-Field Infinite-Volume Limit.” <i>Annales Henri Poincaré</i>, vol. 15, no. 12, Springer Nature, 2014, pp. 2409–39, doi:<a href=\"https://doi.org/10.1007/s00023-013-0302-4\">10.1007/s00023-013-0302-4</a>.","apa":"Dereziński, J., &#38; Napiórkowski, M. M. (2014). Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume limit. <i>Annales Henri Poincaré</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00023-013-0302-4\">https://doi.org/10.1007/s00023-013-0302-4</a>","short":"J. Dereziński, M.M. Napiórkowski, Annales Henri Poincaré 15 (2014) 2409–2439.","chicago":"Dereziński, Jan, and Marcin M Napiórkowski. “Excitation Spectrum of Interacting Bosons in the Mean-Field Infinite-Volume Limit.” <i>Annales Henri Poincaré</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1007/s00023-013-0302-4\">https://doi.org/10.1007/s00023-013-0302-4</a>."},"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1007/s00023-014-0390-9"}]},"publication_identifier":{"issn":["1424-0637","1424-0661"]},"language":[{"iso":"eng"}],"year":"2014","intvolume":"        15","has_accepted_license":"1","page":"2409-2439","file":[{"relation":"main_file","file_name":"2014_Annales_Derezinski.pdf","content_type":"application/pdf","access_level":"open_access","date_created":"2019-01-10T09:04:45Z","file_id":"5814","date_updated":"2020-07-14T12:47:11Z","creator":"dernst","file_size":865230,"checksum":"1f6c32c5d6ec90cdb0718c7f0103342e"}],"abstract":[{"lang":"eng","text":"We consider homogeneous Bose gas in a large cubic box with periodic boundary conditions, at zero temperature. We analyze its excitation spectrum in a certain kind of a mean-field infinite-volume limit. We prove that under appropriate conditions the excitation spectrum has the form predicted by the Bogoliubov approximation. Our result can be viewed as an extension of the result of Seiringer (Commun. Math. Phys.306:565–578, 2011) to large volumes."}],"ddc":["530"],"oa":1,"publication":"Annales Henri Poincaré","file_date_updated":"2020-07-14T12:47:11Z","_id":"5813","article_processing_charge":"No","issue":"12","type":"journal_article","oa_version":"Published Version","date_created":"2019-01-10T09:02:58Z","author":[{"full_name":"Dereziński, Jan","first_name":"Jan","last_name":"Dereziński"},{"last_name":"Napiórkowski","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","full_name":"Napiórkowski, Marcin M"}],"day":"10","status":"public","title":"Excitation spectrum of interacting bosons in the Mean-Field Infinite-Volume limit","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":15,"date_published":"2014-01-10T00:00:00Z","month":"01","date_updated":"2021-11-16T08:13:24Z","publisher":"Springer Nature","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9"},{"intvolume":"        39","status":"public","title":"Many-atom-cavity QED system with homogeneous atom-cavity coupling","volume":39,"year":"2014","day":"01","author":[{"first_name":"Jongmin","last_name":"Lee","full_name":"Lee, Jongmin"},{"first_name":"Geert","last_name":"Vrijsen","full_name":"Vrijsen, Geert"},{"first_name":"Igor","last_name":"Teper","full_name":"Teper, Igor"},{"id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","first_name":"Onur","last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Onur Hosten"},{"full_name":"Kasevich, Mark A","first_name":"Mark","last_name":"Kasevich"}],"extern":1,"publication":"Optics Letters","type":"journal_article","_id":"589","issue":"13","quality_controlled":0,"date_created":"2018-12-11T11:47:21Z","citation":{"ista":"Lee J, Vrijsen G, Teper I, Hosten O, Kasevich M. 2014. Many-atom-cavity QED system with homogeneous atom-cavity coupling. Optics Letters. 39(13), 4005–4008.","ieee":"J. Lee, G. Vrijsen, I. Teper, O. Hosten, and M. Kasevich, “Many-atom-cavity QED system with homogeneous atom-cavity coupling,” <i>Optics Letters</i>, vol. 39, no. 13. OSA, pp. 4005–4008, 2014.","mla":"Lee, Jongmin, et al. “Many-Atom-Cavity QED System with Homogeneous Atom-Cavity Coupling.” <i>Optics Letters</i>, vol. 39, no. 13, OSA, 2014, pp. 4005–08, doi:<a href=\"https://doi.org/10.1364/OL.39.004005\">10.1364/OL.39.004005</a>.","apa":"Lee, J., Vrijsen, G., Teper, I., Hosten, O., &#38; Kasevich, M. (2014). Many-atom-cavity QED system with homogeneous atom-cavity coupling. <i>Optics Letters</i>. OSA. <a href=\"https://doi.org/10.1364/OL.39.004005\">https://doi.org/10.1364/OL.39.004005</a>","chicago":"Lee, Jongmin, Geert Vrijsen, Igor Teper, Onur Hosten, and Mark Kasevich. “Many-Atom-Cavity QED System with Homogeneous Atom-Cavity Coupling.” <i>Optics Letters</i>. OSA, 2014. <a href=\"https://doi.org/10.1364/OL.39.004005\">https://doi.org/10.1364/OL.39.004005</a>.","short":"J. Lee, G. Vrijsen, I. Teper, O. Hosten, M. Kasevich, Optics Letters 39 (2014) 4005–4008.","ama":"Lee J, Vrijsen G, Teper I, Hosten O, Kasevich M. Many-atom-cavity QED system with homogeneous atom-cavity coupling. <i>Optics Letters</i>. 2014;39(13):4005-4008. doi:<a href=\"https://doi.org/10.1364/OL.39.004005\">10.1364/OL.39.004005</a>"},"doi":"10.1364/OL.39.004005","publist_id":"7216","date_updated":"2021-01-12T08:05:09Z","publisher":"OSA","publication_status":"published","date_published":"2014-07-01T00:00:00Z","month":"07","abstract":[{"text":"We demonstrate a many-atom-cavity system with a high-finesse dual-wavelength standing wave cavity in which all participating rubidium atoms are nearly identically coupled to a 780-nm cavity mode. This homogeneous coupling is enforced by a one-dimensional optical lattice formed by the field of a 1560-nm cavity mode.","lang":"eng"}],"oa":1,"page":"4005 - 4008","main_file_link":[{"url":"https://arxiv.org/abs/1311.1805","open_access":"1"}]},{"external_id":{"pmid":["24439370"]},"page":"69-83","file":[{"date_updated":"2020-07-14T12:47:20Z","file_size":5020084,"checksum":"ad6ef68f37fb711d9abcd97fc06ad316","creator":"kschuh","content_type":"application/pdf","file_name":"2014_Elsevier_Linneweber.pdf","relation":"main_file","file_id":"6123","date_created":"2019-03-19T14:40:38Z","access_level":"open_access"}],"ddc":["570"],"oa":1,"extern":"1","quality_controlled":"1","doi":"10.1016/j.cell.2013.12.008","citation":{"ieee":"G. A. Linneweber <i>et al.</i>, “Neuronal control of metabolism through nutrient-dependent modulation of tracheal branching,” <i>Cell</i>, vol. 156, no. 1–2. Elsevier, pp. 69–83, 2014.","ista":"Linneweber GA, Jacobson J, Busch KE, Hudry B, Christov CP, Dormann D, Yuan M, Otani T, Knust E, de Bono M, Miguel-Aliaga I. 2014. Neuronal control of metabolism through nutrient-dependent modulation of tracheal branching. Cell. 156(1–2), 69–83.","mla":"Linneweber, Gerit A., et al. “Neuronal Control of Metabolism through Nutrient-Dependent Modulation of Tracheal Branching.” <i>Cell</i>, vol. 156, no. 1–2, Elsevier, 2014, pp. 69–83, doi:<a href=\"https://doi.org/10.1016/j.cell.2013.12.008\">10.1016/j.cell.2013.12.008</a>.","apa":"Linneweber, G. A., Jacobson, J., Busch, K. E., Hudry, B., Christov, C. P., Dormann, D., … Miguel-Aliaga, I. (2014). Neuronal control of metabolism through nutrient-dependent modulation of tracheal branching. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2013.12.008\">https://doi.org/10.1016/j.cell.2013.12.008</a>","short":"G.A. Linneweber, J. Jacobson, K.E. Busch, B. Hudry, C.P. Christov, D. Dormann, M. Yuan, T. Otani, E. Knust, M. de Bono, I. Miguel-Aliaga, Cell 156 (2014) 69–83.","chicago":"Linneweber, Gerit A., Jake Jacobson, Karl Emanuel Busch, Bruno Hudry, Christo P. Christov, Dirk Dormann, Michaela Yuan, et al. “Neuronal Control of Metabolism through Nutrient-Dependent Modulation of Tracheal Branching.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2013.12.008\">https://doi.org/10.1016/j.cell.2013.12.008</a>.","ama":"Linneweber GA, Jacobson J, Busch KE, et al. Neuronal control of metabolism through nutrient-dependent modulation of tracheal branching. <i>Cell</i>. 2014;156(1-2):69-83. doi:<a href=\"https://doi.org/10.1016/j.cell.2013.12.008\">10.1016/j.cell.2013.12.008</a>"},"intvolume":"       156","pmid":1,"has_accepted_license":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0092-8674"]},"year":"2014","date_updated":"2021-01-12T08:06:13Z","publisher":"Elsevier","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2014-01-16T00:00:00Z","month":"01","author":[{"first_name":"Gerit A.","last_name":"Linneweber","full_name":"Linneweber, Gerit A."},{"full_name":"Jacobson, Jake","last_name":"Jacobson","first_name":"Jake"},{"full_name":"Busch, Karl Emanuel","first_name":"Karl Emanuel","last_name":"Busch"},{"full_name":"Hudry, Bruno","first_name":"Bruno","last_name":"Hudry"},{"full_name":"Christov, Christo P.","first_name":"Christo P.","last_name":"Christov"},{"last_name":"Dormann","first_name":"Dirk","full_name":"Dormann, Dirk"},{"first_name":"Michaela","last_name":"Yuan","full_name":"Yuan, Michaela"},{"full_name":"Otani, Tomoki","first_name":"Tomoki","last_name":"Otani"},{"first_name":"Elisabeth","last_name":"Knust","full_name":"Knust, Elisabeth"},{"first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","last_name":"de Bono","orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario"},{"first_name":"Irene","last_name":"Miguel-Aliaga","full_name":"Miguel-Aliaga, Irene"}],"publication":"Cell","file_date_updated":"2020-07-14T12:47:20Z","_id":"6122","issue":"1-2","type":"journal_article","date_created":"2019-03-19T14:35:30Z","oa_version":"Published Version","status":"public","title":"Neuronal control of metabolism through nutrient-dependent modulation of tracheal branching","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":156,"day":"16"},{"has_accepted_license":"1","intvolume":"        10","pmid":1,"year":"2014","publication_identifier":{"issn":["1553-7404"]},"language":[{"iso":"eng"}],"quality_controlled":"1","doi":"10.1371/journal.pgen.1004082","citation":{"ama":"Chen C, Itakura E, Weber KP, Hegde RS, de Bono M. An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism. <i>PLoS Genetics</i>. 2014;10(3). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1004082\">10.1371/journal.pgen.1004082</a>","ista":"Chen C, Itakura E, Weber KP, Hegde RS, de Bono M. 2014. An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism. PLoS Genetics. 10(3), e1004082.","ieee":"C. Chen, E. Itakura, K. P. Weber, R. S. Hegde, and M. de Bono, “An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism,” <i>PLoS Genetics</i>, vol. 10, no. 3. Public Library of Science (PLoS), 2014.","mla":"Chen, Changchun, et al. “An ER Complex of ODR-4 and ODR-8/Ufm1 Specific Protease 2 Promotes GPCR Maturation by a Ufm1-Independent Mechanism.” <i>PLoS Genetics</i>, vol. 10, no. 3, e1004082, Public Library of Science (PLoS), 2014, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1004082\">10.1371/journal.pgen.1004082</a>.","apa":"Chen, C., Itakura, E., Weber, K. P., Hegde, R. S., &#38; de Bono, M. (2014). An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism. <i>PLoS Genetics</i>. Public Library of Science (PLoS). <a href=\"https://doi.org/10.1371/journal.pgen.1004082\">https://doi.org/10.1371/journal.pgen.1004082</a>","short":"C. Chen, E. Itakura, K.P. Weber, R.S. Hegde, M. de Bono, PLoS Genetics 10 (2014).","chicago":"Chen, Changchun, Eisuke Itakura, Katherine P. Weber, Ramanujan S. Hegde, and Mario de Bono. “An ER Complex of ODR-4 and ODR-8/Ufm1 Specific Protease 2 Promotes GPCR Maturation by a Ufm1-Independent Mechanism.” <i>PLoS Genetics</i>. Public Library of Science (PLoS), 2014. <a href=\"https://doi.org/10.1371/journal.pgen.1004082\">https://doi.org/10.1371/journal.pgen.1004082</a>."},"extern":"1","abstract":[{"lang":"eng","text":"Despite the importance of G-protein coupled receptors (GPCRs) their biogenesis is poorly understood. Like vertebrates, C. elegans uses a large family of GPCRs as chemoreceptors. A subset of these receptors, such as ODR-10, requires the odr-4 and odr-8 genes to be appropriately localized to sensory cilia. The odr-4 gene encodes a conserved tail-anchored transmembrane protein; the molecular identity of odr-8 is unknown. Here, we show that odr-8 encodes the C. elegans ortholog of Ufm1-specific protease 2 (UfSP2). UfSPs are cysteine proteases identified biochemically by their ability to liberate the ubiquitin-like modifier Ufm1 from its pro-form and protein conjugates. ODR-8/UfSP2 and ODR-4 are expressed in the same set of twelve chemosensory neurons, and physically interact at the ER membrane. ODR-4 also binds ODR-10, suggesting that an ODR-4/ODR-8 complex promotes GPCR folding, maturation, or export from the ER. The physical interaction between human ODR4 and UfSP2 suggests that this complex's role in GPCR biogenesis may be evolutionarily conserved. Unexpectedly, mutant versions of ODR-8/UfSP2 lacking catalytic residues required for protease activity can rescue all odr-8 mutant phenotypes tested. Moreover, deleting C. elegans ufm-1 does not alter chemoreceptor traffic to cilia, either in wild type or in odr-8 mutants. Thus, UfSP2 proteins have protease- and Ufm1-independent functions in GPCR biogenesis."}],"ddc":["570"],"oa":1,"file":[{"date_updated":"2020-07-14T12:47:20Z","checksum":"ac19941089a4262bb5bd74434a08b003","file_size":8286819,"creator":"kschuh","content_type":"application/pdf","file_name":"2014_PLOS_Chen.PDF","relation":"main_file","file_id":"6125","access_level":"open_access","date_created":"2019-03-19T14:50:07Z"}],"external_id":{"pmid":["24603482"]},"title":"An ER complex of ODR-4 and ODR-8/Ufm1 specific protease 2 promotes GPCR maturation by a Ufm1-independent mechanism","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":10,"status":"public","article_number":"e1004082","day":"06","author":[{"last_name":"Chen","first_name":"Changchun","full_name":"Chen, Changchun"},{"full_name":"Itakura, Eisuke","last_name":"Itakura","first_name":"Eisuke"},{"full_name":"Weber, Katherine P.","first_name":"Katherine P.","last_name":"Weber"},{"full_name":"Hegde, Ramanujan S.","last_name":"Hegde","first_name":"Ramanujan S."},{"full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","first_name":"Mario"}],"date_created":"2019-03-19T14:45:56Z","oa_version":"Published Version","file_date_updated":"2020-07-14T12:47:20Z","publication":"PLoS Genetics","_id":"6124","issue":"3","type":"journal_article","publication_status":"published","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:06:14Z","publisher":"Public Library of Science (PLoS)","date_published":"2014-03-06T00:00:00Z","month":"03"},{"file":[{"content_type":"application/pdf","file_name":"2014_SFN_Gross.pdf","relation":"main_file","file_id":"6127","access_level":"open_access","date_created":"2019-03-19T14:55:58Z","date_updated":"2020-07-14T12:47:20Z","file_size":3263422,"checksum":"a3dd71969f94c43909327cd083283d4b","creator":"kschuh"}],"ddc":["570"],"oa":1,"abstract":[{"text":"Aerobic animals constantly monitor and adapt to changes in O2 levels. The molecular mechanisms involved in sensing O2 are, however, incompletely understood. Previous studies showed that a hexacoordinated globin called GLB-5 tunes the dynamic range of O2-sensing neurons in natural C. elegans isolates, but is defective in the N2 lab reference strain (McGrath et al., 2009; Persson et al., 2009). GLB-5 enables a sharp behavioral switch when O2 changes between 21 and 17%. Here, we show that GLB-5 also confers rapid behavioral and cellular recovery from exposure to hypoxia. Hypoxia reconfigures O2-evoked Ca2+ responses in the URX O2 sensors, and GLB-5 enables rapid recovery of these responses upon re-oxygenation. Forward genetic screens indicate that GLB-5's effects on O2 sensing require PDL-1, the C. elegans ortholog of mammalian PrBP/PDE6δ protein. In mammals, PDE6δ regulates the traffic and activity of prenylated proteins (Zhang et al., 2004; Norton et al., 2005). PDL-1 promotes localization of GCY-33 and GCY-35, atypical soluble guanylate cyclases that act as O2 sensors, to the dendritic endings of URX and BAG neurons, where they colocalize with GLB-5. Both GCY-33 and GCY-35 are predicted to be prenylated. Dendritic localization is not essential for GCY-35 to function as an O2 sensor, but disrupting pdl-1 alters the URX neuron's O2 response properties. Functional GLB-5 can restore dendritic localization of GCY-33 in pdl-1 mutants, suggesting GCY-33 and GLB-5 are in a complex. Our data suggest GLB-5 and the soluble guanylate cyclases operate in close proximity to sculpt O2 responses.","lang":"eng"}],"external_id":{"pmid":["25505325"]},"page":"16726-16738","pmid":1,"intvolume":"        34","has_accepted_license":"1","publication_identifier":{"issn":["0270-6474","1529-2401"]},"language":[{"iso":"eng"}],"year":"2014","extern":"1","citation":{"apa":"Gross, E., Soltesz, Z., Oda, S., Zelmanovich, V., Abergel, Z., &#38; de Bono, M. (2014). GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate cyclases to dendritic endings. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/jneurosci.5368-13.2014\">https://doi.org/10.1523/jneurosci.5368-13.2014</a>","chicago":"Gross, E., Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, and Mario de Bono. “GLOBIN-5-Dependent O2 Responses Are Regulated by PDL-1/PrBP That Targets Prenylated Soluble Guanylate Cyclases to Dendritic Endings.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2014. <a href=\"https://doi.org/10.1523/jneurosci.5368-13.2014\">https://doi.org/10.1523/jneurosci.5368-13.2014</a>.","short":"E. Gross, Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, M. de Bono, Journal of Neuroscience 34 (2014) 16726–16738.","ista":"Gross E, Soltesz Z, Oda S, Zelmanovich V, Abergel Z, de Bono M. 2014. GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate cyclases to dendritic endings. Journal of Neuroscience. 34(50), 16726–16738.","ieee":"E. Gross, Z. Soltesz, S. Oda, V. Zelmanovich, Z. Abergel, and M. de Bono, “GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate cyclases to dendritic endings,” <i>Journal of Neuroscience</i>, vol. 34, no. 50. Society for Neuroscience, pp. 16726–16738, 2014.","mla":"Gross, E., et al. “GLOBIN-5-Dependent O2 Responses Are Regulated by PDL-1/PrBP That Targets Prenylated Soluble Guanylate Cyclases to Dendritic Endings.” <i>Journal of Neuroscience</i>, vol. 34, no. 50, Society for Neuroscience, 2014, pp. 16726–38, doi:<a href=\"https://doi.org/10.1523/jneurosci.5368-13.2014\">10.1523/jneurosci.5368-13.2014</a>.","ama":"Gross E, Soltesz Z, Oda S, Zelmanovich V, Abergel Z, de Bono M. GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate cyclases to dendritic endings. <i>Journal of Neuroscience</i>. 2014;34(50):16726-16738. doi:<a href=\"https://doi.org/10.1523/jneurosci.5368-13.2014\">10.1523/jneurosci.5368-13.2014</a>"},"doi":"10.1523/jneurosci.5368-13.2014","quality_controlled":"1","publisher":"Society for Neuroscience","date_updated":"2021-01-12T08:06:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","month":"12","date_published":"2014-12-10T00:00:00Z","status":"public","title":"GLOBIN-5-dependent O2 responses are regulated by PDL-1/PrBP that targets prenylated soluble guanylate cyclases to dendritic endings","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":34,"day":"10","author":[{"full_name":"Gross, E.","last_name":"Gross","first_name":"E."},{"full_name":"Soltesz, Z.","first_name":"Z.","last_name":"Soltesz"},{"full_name":"Oda, S.","last_name":"Oda","first_name":"S."},{"first_name":"V.","last_name":"Zelmanovich","full_name":"Zelmanovich, V."},{"last_name":"Abergel","first_name":"Z.","full_name":"Abergel, Z."},{"orcid":"0000-0001-8347-0443","full_name":"de Bono, Mario","last_name":"de Bono","first_name":"Mario","id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87"}],"_id":"6126","type":"journal_article","issue":"50","file_date_updated":"2020-07-14T12:47:20Z","publication":"Journal of Neuroscience","oa_version":"Published Version","date_created":"2019-03-19T14:52:26Z"},{"abstract":[{"text":"Mechanically coupled cells can generate forces driving cell and tissue morphogenesis during development. Visualization and measuring of these forces is of major importance to better understand the complexity of the biomechanic processes that shape cells and tissues. Here, we describe how UV laser ablation can be utilized to quantitatively assess mechanical tension in different tissues of the developing zebrafish and in cultures of primary germ layer progenitor cells ex vivo.","lang":"eng"}],"place":"New York, NY","editor":[{"full_name":"Nelson, Celeste","last_name":"Nelson","first_name":"Celeste"}],"external_id":{"pmid":["25245697"]},"page":"219-235","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9781493911639","9781493911646"],"eissn":["1940-6029"],"issn":["1064-3745"]},"year":"2014","intvolume":"      1189","pmid":1,"quality_controlled":"1","citation":{"chicago":"Smutny, Michael, Martin Behrndt, Pedro Campinho, Verena Ruprecht, and Carl-Philipp J Heisenberg. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” In <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, 1189:219–35. Methods in Molecular Biology. New York, NY: Springer, 2014. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>.","short":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, C.-P.J. Heisenberg, in:, C. Nelson (Ed.), Tissue Morphogenesis, Springer, New York, NY, 2014, pp. 219–235.","apa":"Smutny, M., Behrndt, M., Campinho, P., Ruprecht, V., &#38; Heisenberg, C.-P. J. (2014). UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In C. Nelson (Ed.), <i>Tissue Morphogenesis</i> (Vol. 1189, pp. 219–235). New York, NY: Springer. <a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">https://doi.org/10.1007/978-1-4939-1164-6_15</a>","mla":"Smutny, Michael, et al. “UV Laser Ablation to Measure Cell and Tissue-Generated Forces in the Zebrafish Embryo in Vivo and Ex Vivo.” <i>Tissue Morphogenesis</i>, edited by Celeste Nelson, vol. 1189, Springer, 2014, pp. 219–35, doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>.","ista":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. 2014.UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Tissue Morphogenesis. vol. 1189, 219–235.","ieee":"M. Smutny, M. Behrndt, P. Campinho, V. Ruprecht, and C.-P. J. Heisenberg, “UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo,” in <i>Tissue Morphogenesis</i>, vol. 1189, C. Nelson, Ed. New York, NY: Springer, 2014, pp. 219–235.","ama":"Smutny M, Behrndt M, Campinho P, Ruprecht V, Heisenberg C-PJ. UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo. In: Nelson C, ed. <i>Tissue Morphogenesis</i>. Vol 1189. Methods in Molecular Biology. New York, NY: Springer; 2014:219-235. doi:<a href=\"https://doi.org/10.1007/978-1-4939-1164-6_15\">10.1007/978-1-4939-1164-6_15</a>"},"doi":"10.1007/978-1-4939-1164-6_15","date_published":"2014-08-22T00:00:00Z","month":"08","date_updated":"2023-09-05T14:12:00Z","publisher":"Springer","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","series_title":"Methods in Molecular Biology","day":"22","status":"public","volume":1189,"title":"UV laser ablation to measure cell and tissue-generated forces in the zebrafish embryo in vivo and ex vivo","publication":"Tissue Morphogenesis","type":"book_chapter","_id":"6178","article_processing_charge":"No","date_created":"2019-03-26T08:55:59Z","oa_version":"None","department":[{"_id":"CaHe"}],"author":[{"id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87","first_name":"Michael","last_name":"Smutny","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael"},{"last_name":"Behrndt","id":"3ECECA3A-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Behrndt, Martin"},{"id":"3AFBBC42-F248-11E8-B48F-1D18A9856A87","first_name":"Pedro","last_name":"Campinho","orcid":"0000-0002-8526-5416","full_name":"Campinho, Pedro"},{"full_name":"Ruprecht, Verena","orcid":"0000-0003-4088-8633","last_name":"Ruprecht","first_name":"Verena","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","first_name":"Carl-Philipp J","id":"39427864-F248-11E8-B48F-1D18A9856A87","last_name":"Heisenberg"}]},{"date_published":"2014-01-01T00:00:00Z","abstract":[{"text":"Nous étudions le comportement asymptotique du nombre de variétés dans une certaine classe ne satisfaisant pas le principe de Hasse. Cette étude repose sur des résultats récemmentobtenus par Colliot-Thélène.","lang":"fre"}],"oa":1,"date_updated":"2021-01-12T08:07:03Z","publisher":"Cellule MathDoc/CEDRAM","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1210.4236"}],"external_id":{"arxiv":["1210.4236"]},"page":"25-44","publication_identifier":{"issn":["1246-7405","2118-8572"]},"language":[{"iso":"eng"}],"year":"2014","status":"public","arxiv":1,"intvolume":"        26","title":"Contre-exemples au principe de Hasse pour certains tores coflasques","volume":26,"extern":"1","publication":"Journal de Théorie des Nombres de Bordeaux","issue":"1","_id":"6319","type":"journal_article","oa_version":"Preprint","date_created":"2019-04-16T13:40:13Z","quality_controlled":"1","citation":{"ama":"Bretèche R de la, Browning TD. Contre-exemples au principe de Hasse pour certains tores coflasques. <i>Journal de Théorie des Nombres de Bordeaux</i>. 2014;26(1):25-44. doi:<a href=\"https://doi.org/10.5802/jtnb.857\">10.5802/jtnb.857</a>","ista":"Bretèche R de la, Browning TD. 2014. Contre-exemples au principe de Hasse pour certains tores coflasques. Journal de Théorie des Nombres de Bordeaux. 26(1), 25–44.","ieee":"R. de la Bretèche and T. D. Browning, “Contre-exemples au principe de Hasse pour certains tores coflasques,” <i>Journal de Théorie des Nombres de Bordeaux</i>, vol. 26, no. 1. Cellule MathDoc/CEDRAM, pp. 25–44, 2014.","mla":"Bretèche, Régis de la, and Timothy D. Browning. “Contre-Exemples Au Principe de Hasse Pour Certains Tores Coflasques.” <i>Journal de Théorie Des Nombres de Bordeaux</i>, vol. 26, no. 1, Cellule MathDoc/CEDRAM, 2014, pp. 25–44, doi:<a href=\"https://doi.org/10.5802/jtnb.857\">10.5802/jtnb.857</a>.","apa":"Bretèche, R. de la, &#38; Browning, T. D. (2014). Contre-exemples au principe de Hasse pour certains tores coflasques. <i>Journal de Théorie Des Nombres de Bordeaux</i>. Cellule MathDoc/CEDRAM. <a href=\"https://doi.org/10.5802/jtnb.857\">https://doi.org/10.5802/jtnb.857</a>","short":"R. de la Bretèche, T.D. Browning, Journal de Théorie Des Nombres de Bordeaux 26 (2014) 25–44.","chicago":"Bretèche, Régis de la, and Timothy D Browning. “Contre-Exemples Au Principe de Hasse Pour Certains Tores Coflasques.” <i>Journal de Théorie Des Nombres de Bordeaux</i>. Cellule MathDoc/CEDRAM, 2014. <a href=\"https://doi.org/10.5802/jtnb.857\">https://doi.org/10.5802/jtnb.857</a>."},"doi":"10.5802/jtnb.857","author":[{"full_name":"Bretèche, Régis de la","first_name":"Régis de la","last_name":"Bretèche"},{"last_name":"Browning","id":"35827D50-F248-11E8-B48F-1D18A9856A87","first_name":"Timothy D","orcid":"0000-0002-8314-0177","full_name":"Browning, Timothy D"}]},{"page":"3084-3091","external_id":{"arxiv":["1401.3127"]},"abstract":[{"text":"We explore the relationship between polar and RM codes and we describe a coding scheme which improves upon the performance of the standard polar code at practical block lengths. Our starting point is the experimental observation that RM codes have a smaller error probability than polar codes under MAP decoding. This motivates us to introduce a family of codes that “interpolates” between RM and polar codes, call this family C inter = {C α : α ∈ [0, 1j}, where C α|α=1 is the original polar code, and C α|α=0 is an RM code. Based on numerical observations, we remark that the error probability under MAP decoding is an increasing function of α. MAP decoding has in general exponential complexity, but empirically the performance of polar codes at finite block lengths is boosted by moving along the family Cinter even under low-complexity decoding schemes such as, for instance, belief propagation or successive cancellation list decoder. We demonstrate the performance gain via numerical simulations for transmission over the erasure channel as well as the Gaussian channel.","lang":"eng"}],"oa":1,"quality_controlled":"1","citation":{"mla":"Mondelli, Marco, et al. “From Polar to Reed-Muller Codes: A Technique to Improve the Finite-Length Performance.” <i>IEEE Transactions on Communications</i>, vol. 62, no. 9, IEEE, 2014, pp. 3084–91, doi:<a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">10.1109/tcomm.2014.2345069</a>.","ieee":"M. Mondelli, H. Hassani, and R. Urbanke, “From polar to Reed-Muller codes: A technique to improve the finite-length performance,” <i>IEEE Transactions on Communications</i>, vol. 62, no. 9. IEEE, pp. 3084–3091, 2014.","ista":"Mondelli M, Hassani H, Urbanke R. 2014. From polar to Reed-Muller codes: A technique to improve the finite-length performance. IEEE Transactions on Communications. 62(9), 3084–3091.","short":"M. Mondelli, H. Hassani, R. Urbanke, IEEE Transactions on Communications 62 (2014) 3084–3091.","chicago":"Mondelli, Marco, Hamed Hassani, and Rudiger Urbanke. “From Polar to Reed-Muller Codes: A Technique to Improve the Finite-Length Performance.” <i>IEEE Transactions on Communications</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">https://doi.org/10.1109/tcomm.2014.2345069</a>.","apa":"Mondelli, M., Hassani, H., &#38; Urbanke, R. (2014). From polar to Reed-Muller codes: A technique to improve the finite-length performance. <i>IEEE Transactions on Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">https://doi.org/10.1109/tcomm.2014.2345069</a>","ama":"Mondelli M, Hassani H, Urbanke R. From polar to Reed-Muller codes: A technique to improve the finite-length performance. <i>IEEE Transactions on Communications</i>. 2014;62(9):3084-3091. doi:<a href=\"https://doi.org/10.1109/tcomm.2014.2345069\">10.1109/tcomm.2014.2345069</a>"},"doi":"10.1109/tcomm.2014.2345069","extern":"1","intvolume":"        62","arxiv":1,"year":"2014","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0090-6778"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1401.3127"}],"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:08:46Z","publisher":"IEEE","date_published":"2014-09-01T00:00:00Z","month":"09","author":[{"last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","full_name":"Mondelli, Marco","orcid":"0000-0002-3242-7020"},{"last_name":"Hassani","first_name":"Hamed","full_name":"Hassani, Hamed"},{"full_name":"Urbanke, Rudiger","first_name":"Rudiger","last_name":"Urbanke"}],"date_created":"2019-07-31T07:20:21Z","oa_version":"Preprint","publication":"IEEE Transactions on Communications","type":"journal_article","issue":"9","_id":"6739","volume":62,"title":"From polar to Reed-Muller codes: A technique to improve the finite-length performance","status":"public","day":"01"},{"month":"10","date_published":"2014-10-01T00:00:00Z","oa":1,"abstract":[{"text":"We describe coding techniques that achieve the capacity of a discrete memoryless asymmetric channel. To do so, we discuss how recent advances in coding for symmetric channels yield more efficient solutions also for the asymmetric case. In more detail, we consider three basic approaches. The first one is Gallager's scheme that concatenates a linear code with a non-linear mapper, in order to bias the input distribution. We explicitly show that both polar codes and spatially coupled codes can be employed in this scenario. Further, we derive a scaling law between the gap to capacity, the cardinality of channel input and output alphabets, and the required size of the mapper. The second one is an integrated approach in which the coding scheme is used both for source coding, in order to create codewords with the capacity-achieving distribution, and for channel coding, in order to provide error protection. Such a technique has been recently introduced by Honda and Yamamoto in the context of polar codes, and we show how to apply it also to the design of sparse graph codes. The third approach is based on an idea due to Böcherer and Mathar and separates completely the two tasks of source coding and channel coding by “chaining” together several codewords. We prove that we can combine any suitable source code with any suitable channel code in order to provide optimal schemes for asymmetric channels. In particular, polar codes and spatially coupled codes fulfill the required conditions.","lang":"eng"}],"publisher":"IEEE","date_updated":"2023-02-23T12:49:36Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","main_file_link":[{"url":"https://arxiv.org/abs/1406.7373","open_access":"1"}],"external_id":{"arxiv":["1406.7373"]},"page":"789-796","language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["978-1-4799-8009-3"]},"day":"01","year":"2014","arxiv":1,"status":"public","title":"How to achieve the capacity of asymmetric channels","_id":"6740","type":"conference","publication":"52nd Annual Allerton Conference on Communication, Control, and Computing","extern":"1","doi":"10.1109/allerton.2014.7028535","citation":{"ieee":"M. Mondelli, R. Urbanke, and H. Hassani, “How to achieve the capacity of asymmetric channels,” in <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>, Monticello, IL, United States, 2014, pp. 789–796.","ista":"Mondelli M, Urbanke R, Hassani H. 2014. How to achieve the capacity of asymmetric channels. 52nd Annual Allerton Conference on Communication, Control, and Computing. Allerton Conference on Communication, Control, and Computing, 789–796.","mla":"Mondelli, Marco, et al. “How to Achieve the Capacity of Asymmetric Channels.” <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>, IEEE, 2014, pp. 789–96, doi:<a href=\"https://doi.org/10.1109/allerton.2014.7028535\">10.1109/allerton.2014.7028535</a>.","apa":"Mondelli, M., Urbanke, R., &#38; Hassani, H. (2014). How to achieve the capacity of asymmetric channels. In <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i> (pp. 789–796). Monticello, IL, United States: IEEE. <a href=\"https://doi.org/10.1109/allerton.2014.7028535\">https://doi.org/10.1109/allerton.2014.7028535</a>","short":"M. Mondelli, R. Urbanke, H. Hassani, in:, 52nd Annual Allerton Conference on Communication, Control, and Computing, IEEE, 2014, pp. 789–796.","chicago":"Mondelli, Marco, Rudiger Urbanke, and Hamed Hassani. “How to Achieve the Capacity of Asymmetric Channels.” In <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>, 789–96. IEEE, 2014. <a href=\"https://doi.org/10.1109/allerton.2014.7028535\">https://doi.org/10.1109/allerton.2014.7028535</a>.","ama":"Mondelli M, Urbanke R, Hassani H. How to achieve the capacity of asymmetric channels. In: <i>52nd Annual Allerton Conference on Communication, Control, and Computing</i>. IEEE; 2014:789-796. doi:<a href=\"https://doi.org/10.1109/allerton.2014.7028535\">10.1109/allerton.2014.7028535</a>"},"quality_controlled":"1","date_created":"2019-07-31T07:24:23Z","oa_version":"Preprint","conference":{"start_date":"2014-09-30","end_date":"2014-10-03","location":"Monticello, IL, United States","name":"Allerton Conference on Communication, Control, and Computing"},"related_material":{"record":[{"status":"public","id":"6678","relation":"later_version"}]},"author":[{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"},{"first_name":"Rudiger","last_name":"Urbanke","full_name":"Urbanke, Rudiger"},{"full_name":"Hassani, Hamed","last_name":"Hassani","first_name":"Hamed"}]},{"page":"1397-1409","abstract":[{"lang":"eng","text":"With the aim of extending the coverage and improving the performance of impulse radio ultra-wideband (UWB) systems, this paper focuses on developing a novel single differential encoded decode and forward (DF) non-cooperative relaying scheme (NCR). To favor simple receiver structures, differential noncoherent detection is employed which enables effective energy capture without any channel estimation. Putting emphasis on the general case of multi-hop relaying, we illustrate an original algorithm for the joint power allocation and path selection (JPAPS), minimizing an approximate expression of the overall bit error rate (BER). In particular, after deriving a closed-form power allocation strategy, the optimal path selection is reduced to a shortest path problem on a connected graph, which can be solved without any topology information with complexity O(N 3 ), N being the number of available relays of the network. An approximate scheme is also presented, which reduces the complexity to O(N 2 ) while showing a negligible performance loss, and for benchmarking purposes, an exhaustive-search based multi-hop DF cooperative strategy is derived. Simulation results for various network setups corroborate the effectiveness of the proposed low-complexity JPAPS algorithm, which favorably compares to existing AF and DF relaying methods."}],"month":"03","date_published":"2014-03-20T00:00:00Z","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:08:48Z","publisher":"IEEE","quality_controlled":"1","oa_version":"None","date_created":"2019-07-31T09:05:07Z","citation":{"chicago":"Mondelli, Marco, Qi Zhou, Vincenzo Lottici, and Xiaoli Ma. “Joint Power Allocation and Path Selection for Multi-Hop Noncoherent Decode and Forward UWB Communications.” <i>IEEE Transactions on Wireless Communications</i>. IEEE, 2014. <a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">https://doi.org/10.1109/twc.2014.020914.130669</a>.","short":"M. Mondelli, Q. Zhou, V. Lottici, X. Ma, IEEE Transactions on Wireless Communications 13 (2014) 1397–1409.","apa":"Mondelli, M., Zhou, Q., Lottici, V., &#38; Ma, X. (2014). Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. <i>IEEE Transactions on Wireless Communications</i>. IEEE. <a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">https://doi.org/10.1109/twc.2014.020914.130669</a>","mla":"Mondelli, Marco, et al. “Joint Power Allocation and Path Selection for Multi-Hop Noncoherent Decode and Forward UWB Communications.” <i>IEEE Transactions on Wireless Communications</i>, vol. 13, no. 3, IEEE, 2014, pp. 1397–409, doi:<a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">10.1109/twc.2014.020914.130669</a>.","ieee":"M. Mondelli, Q. Zhou, V. Lottici, and X. Ma, “Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications,” <i>IEEE Transactions on Wireless Communications</i>, vol. 13, no. 3. IEEE, pp. 1397–1409, 2014.","ista":"Mondelli M, Zhou Q, Lottici V, Ma X. 2014. Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. IEEE Transactions on Wireless Communications. 13(3), 1397–1409.","ama":"Mondelli M, Zhou Q, Lottici V, Ma X. Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications. <i>IEEE Transactions on Wireless Communications</i>. 2014;13(3):1397-1409. doi:<a href=\"https://doi.org/10.1109/twc.2014.020914.130669\">10.1109/twc.2014.020914.130669</a>"},"doi":"10.1109/twc.2014.020914.130669","publication":"IEEE Transactions on Wireless Communications","extern":"1","_id":"6744","issue":"3","type":"journal_article","author":[{"id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco","last_name":"Mondelli","orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco"},{"first_name":"Qi","last_name":"Zhou","full_name":"Zhou, Qi"},{"last_name":"Lottici","first_name":"Vincenzo","full_name":"Lottici, Vincenzo"},{"full_name":"Ma, Xiaoli","first_name":"Xiaoli","last_name":"Ma"}],"day":"20","year":"2014","language":[{"iso":"eng"}],"title":"Joint power allocation and path selection for multi-hop noncoherent decode and forward UWB communications","volume":13,"intvolume":"        13","status":"public"},{"publication_identifier":{"eissn":["2191-5318"],"eisbn":["9-783-3190-5957-0"],"isbn":["9-783-3190-5956-3"],"issn":["2191-530X"]},"language":[{"iso":"eng"}],"day":"01","year":"2014","edition":"1","status":"public","title":"A Short Course in Computational Geometry and Topology","_id":"6853","article_processing_charge":"No","type":"book","date_created":"2019-09-06T09:22:33Z","oa_version":"None","quality_controlled":"1","doi":"10.1007/978-3-319-05957-0","citation":{"ama":"Edelsbrunner H. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. Cham: Springer Nature; 2014. doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>","chicago":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. SpringerBriefs in Applied Sciences and Technology. Cham: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>.","short":"H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st ed., Springer Nature, Cham, 2014.","apa":"Edelsbrunner, H. (2014). <i>A Short Course in Computational Geometry and Topology</i> (1st ed.). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>","mla":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed., Springer Nature, 2014, doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>.","ista":"Edelsbrunner H. 2014. A Short Course in Computational Geometry and Topology 1st ed., Cham: Springer Nature, IX, 110p.","ieee":"H. Edelsbrunner, <i>A Short Course in Computational Geometry and Topology</i>, 1st ed. Cham: Springer Nature, 2014."},"department":[{"_id":"HeEd"}],"author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"relation":"other","description":"available as eBook via catalog IST BookList","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=356106"},{"relation":"other","description":"available via catalog IST BookList","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=373842"}]},"date_published":"2014-01-01T00:00:00Z","month":"01","abstract":[{"text":"This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields.","lang":"eng"}],"date_updated":"2022-03-04T07:47:54Z","place":"Cham","publisher":"Springer Nature","publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["SpringerBriefs in Applied Sciences and Technology"],"page":"IX, 110","series_title":"SpringerBriefs in Applied Sciences and Technology","scopus_import":"1"},{"author":[{"full_name":"Šarić, Anđela","orcid":"0000-0002-7854-2139","first_name":"Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"full_name":"Chebaro, Yassmine C.","first_name":"Yassmine C.","last_name":"Chebaro"},{"first_name":"Tuomas P. J.","last_name":"Knowles","full_name":"Knowles, Tuomas P. J."},{"full_name":"Frenkel, Daan","last_name":"Frenkel","first_name":"Daan"}],"date_created":"2021-11-29T13:09:53Z","oa_version":"Published Version","issue":"50","_id":"10382","type":"journal_article","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","title":"Crucial role of nonspecific interactions in amyloid nucleation","volume":111,"status":"public","day":"01","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.pnas.org/content/111/50/17869"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication_status":"published","publisher":"National Academy of Sciences","date_updated":"2021-11-29T13:29:05Z","month":"12","date_published":"2014-12-01T00:00:00Z","article_type":"original","acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","citation":{"mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>.","ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874.","ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014.","short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874.","chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>.","apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., &#38; Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>","ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(50):17869-17874. doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>"},"doi":"10.1073/pnas.1410159111","quality_controlled":"1","extern":"1","pmid":1,"intvolume":"       111","arxiv":1,"year":"2014","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"page":"17869-17874","external_id":{"pmid":["25453085"],"arxiv":["1412.0897"]},"oa":1,"abstract":[{"text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory.","lang":"eng"}],"keyword":["multidisciplinary"]},{"status":"public","article_number":"052303","title":"Anomalous thermomechanical properties of a self-propelled colloidal fluid","volume":89,"day":"06","author":[{"last_name":"Mallory","first_name":"S. A.","full_name":"Mallory, S. A."},{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","last_name":"Šarić","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela"},{"first_name":"C.","last_name":"Valeriani","full_name":"Valeriani, C."},{"first_name":"A.","last_name":"Cacciuto","full_name":"Cacciuto, A."}],"publication":"Physical Review E","article_processing_charge":"No","_id":"10383","type":"journal_article","issue":"5","oa_version":"Preprint","date_created":"2021-11-29T13:10:33Z","date_updated":"2021-11-29T13:29:01Z","publisher":"American Physical Society","publication_status":"published","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","article_type":"original","month":"05","date_published":"2014-05-06T00:00:00Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.0826"}],"arxiv":1,"intvolume":"        89","pmid":1,"publication_identifier":{"issn":["1539-3755"],"eissn":["1550-2376"]},"language":[{"iso":"eng"}],"year":"2014","extern":"1","quality_controlled":"1","doi":"10.1103/physreve.89.052303","citation":{"mla":"Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” <i>Physical Review E</i>, vol. 89, no. 5, 052303, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.89.052303\">10.1103/physreve.89.052303</a>.","ista":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.","ieee":"S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical properties of a self-propelled colloidal fluid,” <i>Physical Review E</i>, vol. 89, no. 5. American Physical Society, 2014.","chicago":"Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.89.052303\">https://doi.org/10.1103/physreve.89.052303</a>.","short":"S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014).","apa":"Mallory, S. A., Šarić, A., Valeriani, C., &#38; Cacciuto, A. (2014). Anomalous thermomechanical properties of a self-propelled colloidal fluid. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.89.052303\">https://doi.org/10.1103/physreve.89.052303</a>","ama":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. <i>Physical Review E</i>. 2014;89(5). doi:<a href=\"https://doi.org/10.1103/physreve.89.052303\">10.1103/physreve.89.052303</a>"},"abstract":[{"text":"We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles.","lang":"eng"}],"oa":1,"external_id":{"arxiv":["1310.0826"],"pmid":["25353796"]}},{"page":"756 - 762","publisher":"Wiley-Blackwell","publist_id":"6332","date_updated":"2021-01-12T06:47:58Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","date_published":"2014-03-17T00:00:00Z","month":"03","abstract":[{"lang":"eng","text":"Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy) methods typically rely on transiently transferring fluorophores between two states, whereby this transfer is usually laid out as a switch. However, depending on whether this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted) or stochastically on a single-molecule basis, specific requirements on the fluorophores are imposed. Therefore, the fluorophores are usually utilized just for one class of methods only. In this study we demonstrate that the reversibly switchable fluorescent protein Dreiklang enables live-cell recordings in both spatially controlled and stochastic modes. We show that the Dreiklang chromophore entails three different light-induced switching mechanisms, namely a reversible photochemical one, off-switching by stimulated emission, and a reversible transfer to a long-lived dark state from the S1 state, all of which can be utilized to overcome the diffraction barrier. We also find that for the single-molecule- based stochastic GSDIM approach (ground-state depletion followed by individual molecule return), Dreiklang provides a larger number of on-off localization events as compared to its progenitor Citrine. Altogether, Dreiklang is a versatile probe for essentially all popular forms of live-cell fluorescence nanoscopy."}],"author":[{"first_name":"Nickels","last_name":"Jensen","full_name":"Jensen, Nickels"},{"last_name":"Danzl","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"},{"full_name":"Willig, Katrin","first_name":"Katrin","last_name":"Willig"},{"last_name":"Lavoie Cardinal","first_name":"Flavie","full_name":"Lavoie Cardinal, Flavie"},{"last_name":"Brakemann","first_name":"Tanja","full_name":"Brakemann, Tanja"},{"full_name":"Hell, Stefan","last_name":"Hell","first_name":"Stefan"},{"last_name":"Jakobs","first_name":"Stefan","full_name":"Jakobs, Stefan"}],"_id":"1058","type":"journal_article","article_processing_charge":"No","issue":"4","publication":"ChemPhysChem","extern":"1","doi":"10.1002/cphc.201301034","citation":{"mla":"Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” <i>ChemPhysChem</i>, vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:<a href=\"https://doi.org/10.1002/cphc.201301034\">10.1002/cphc.201301034</a>.","ista":"Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4), 756–762.","ieee":"N. Jensen <i>et al.</i>, “Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang,” <i>ChemPhysChem</i>, vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014.","chicago":"Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal, Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” <i>ChemPhysChem</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/cphc.201301034\">https://doi.org/10.1002/cphc.201301034</a>.","short":"N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell, S. Jakobs, ChemPhysChem 15 (2014) 756–762.","apa":"Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell, S., &#38; Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. <i>ChemPhysChem</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cphc.201301034\">https://doi.org/10.1002/cphc.201301034</a>","ama":"Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. <i>ChemPhysChem</i>. 2014;15(4):756-762. doi:<a href=\"https://doi.org/10.1002/cphc.201301034\">10.1002/cphc.201301034</a>"},"oa_version":"None","date_created":"2018-12-11T11:49:55Z","intvolume":"        15","status":"public","volume":15,"title":"Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang","language":[{"iso":"eng"}],"year":"2014","day":"17"},{"month":"01","date_published":"2014-01-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Springer Nature","date_updated":"2023-02-23T10:08:04Z","scopus_import":"1","day":"01","title":"Clustered planarity testing revisited","volume":8871,"status":"public","date_created":"2022-02-25T10:32:14Z","oa_version":"Preprint","type":"conference","_id":"10793","article_processing_charge":"No","publication":"International Symposium on Graph Drawing","author":[{"last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"},{"last_name":"Malinović","first_name":"Igor","full_name":"Malinović, Igor"},{"last_name":"Pálvölgyi","first_name":"Dömötör","full_name":"Pálvölgyi, Dömötör"}],"department":[{"_id":"UlWa"}],"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."}],"place":"Cham","alternative_title":["LNCS"],"page":"428-436","external_id":{"arxiv":["1305.4519"]},"year":"2014","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0302-9743"]},"arxiv":1,"intvolume":"      8871","citation":{"ama":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. Clustered planarity testing revisited. In: <i>International Symposium on Graph Drawing</i>. Vol 8871. Cham: Springer Nature; 2014:428-436. doi:<a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">10.1007/978-3-662-45803-7_36</a>","ieee":"R. Fulek, J. Kynčl, I. Malinović, and D. Pálvölgyi, “Clustered planarity testing revisited,” in <i>International Symposium on Graph Drawing</i>, 2014, vol. 8871, 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.","mla":"Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” <i>International Symposium on Graph Drawing</i>, vol. 8871, Springer Nature, 2014, pp. 428–36, doi:<a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">10.1007/978-3-662-45803-7_36</a>.","apa":"Fulek, R., Kynčl, J., Malinović, I., &#38; Pálvölgyi, D. (2014). Clustered planarity testing revisited. In <i>International Symposium on Graph Drawing</i> (Vol. 8871, pp. 428–436). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">https://doi.org/10.1007/978-3-662-45803-7_36</a>","short":"R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436.","chicago":"Fulek, Radoslav, Jan Kynčl, Igor Malinović, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” In <i>International Symposium on Graph Drawing</i>, 8871:428–36. Cham: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">https://doi.org/10.1007/978-3-662-45803-7_36</a>."},"doi":"10.1007/978-3-662-45803-7_36","quality_controlled":"1","related_material":{"record":[{"status":"public","id":"1642","relation":"later_version"}]}},{"day":"01","year":"2014","edition":"1","publication_identifier":{"isbn":["9783709115251"],"eisbn":["9783709115268"]},"language":[{"iso":"eng"}],"title":"Auxin and Its Role in Plant Development","status":"public","doi":"10.1007/978-3-7091-1526-8","citation":{"apa":"Zažímalová, E., Petrášek, J., &#38; Benková, E. (Eds.). (2014). <i>Auxin and Its Role in Plant Development</i> (1st ed.). Vienna: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">https://doi.org/10.1007/978-3-7091-1526-8</a>","short":"E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant Development, 1st ed., Springer Nature, Vienna, 2014.","chicago":"Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. <i>Auxin and Its Role in Plant Development</i>. 1st ed. Vienna: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">https://doi.org/10.1007/978-3-7091-1526-8</a>.","ista":"Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant Development 1st ed., Vienna: Springer Nature, 444p.","ieee":"E. Zažímalová, J. Petrášek, and E. Benková, Eds., <i>Auxin and Its Role in Plant Development</i>, 1st ed. Vienna: Springer Nature, 2014.","mla":"Zažímalová, Eva, et al., editors. <i>Auxin and Its Role in Plant Development</i>. 1st ed., Springer Nature, 2014, doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">10.1007/978-3-7091-1526-8</a>.","ama":"Zažímalová E, Petrášek J, Benková E, eds. <i>Auxin and Its Role in Plant Development</i>. 1st ed. Vienna: Springer Nature; 2014. doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">10.1007/978-3-7091-1526-8</a>"},"date_created":"2022-03-03T11:52:44Z","quality_controlled":"1","oa_version":"None","type":"book_editor","_id":"10811","article_processing_charge":"No","department":[{"_id":"EvBe"}],"abstract":[{"text":"Auxin is an important signaling compound in plants and vital for plant development and growth. The present book, Auxin and its Role in Plant Development, provides the reader with detailed and comprehensive insight into the functioning of the molecule on the whole and specifically in plant development. In the first part, the functioning, metabolism and signaling pathways of auxin in plants are explained, the second part depicts the specific role of auxin in plant development and the third part describes the interaction and functioning of the signaling compound  upon stimuli of the environment. Each chapter is written by international experts in the respective field and designed for scientists and researchers in plant biology, plant development and cell biology to summarize the recent progress in understanding the role of auxin and suggest future perspectives for auxin research.","lang":"eng"}],"month":"04","date_published":"2014-04-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","publisher":"Springer Nature","place":"Vienna","date_updated":"2022-03-04T07:38:15Z","editor":[{"last_name":"Zažímalová","first_name":"Eva","full_name":"Zažímalová, Eva"},{"last_name":"Petrášek","first_name":"Jan","full_name":"Petrášek, Jan"},{"first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","last_name":"Benková","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"page":"444","scopus_import":"1"},{"page":"21-41","scopus_import":"1","keyword":["General Medicine"],"abstract":[{"text":"We review recent progress towards a rigorous understanding of the excitation spectrum of bosonic quantum many-body systems. In particular, we explain how one can rigorously establish the predictions resulting from the Bogoliubov approximation in the mean field limit. The latter predicts that the spectrum is made up of elementary excitations, whose energy behaves linearly in the momentum for small momentum. This property is crucial for the superfluid behavior of the system. We also discuss a list of open problems in this field.","lang":"eng"}],"date_published":"2014-03-01T00:00:00Z","month":"03","article_type":"original","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publication_status":"published","publisher":"Springer Nature","date_updated":"2023-09-05T14:19:47Z","citation":{"apa":"Seiringer, R. (2014). The excitation spectrum for Bose fluids with weak interactions. <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>. Springer Nature. <a href=\"https://doi.org/10.1365/s13291-014-0083-9\">https://doi.org/10.1365/s13291-014-0083-9</a>","chicago":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1365/s13291-014-0083-9\">https://doi.org/10.1365/s13291-014-0083-9</a>.","short":"R. Seiringer, Jahresbericht Der Deutschen Mathematiker-Vereinigung 116 (2014) 21–41.","ieee":"R. Seiringer, “The excitation spectrum for Bose fluids with weak interactions,” <i>Jahresbericht der Deutschen Mathematiker-Vereinigung</i>, vol. 116. Springer Nature, pp. 21–41, 2014.","ista":"Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41.","mla":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>, vol. 116, Springer Nature, 2014, pp. 21–41, doi:<a href=\"https://doi.org/10.1365/s13291-014-0083-9\">10.1365/s13291-014-0083-9</a>.","ama":"Seiringer R. The excitation spectrum for Bose fluids with weak interactions. <i>Jahresbericht der Deutschen Mathematiker-Vereinigung</i>. 2014;116:21-41. doi:<a href=\"https://doi.org/10.1365/s13291-014-0083-9\">10.1365/s13291-014-0083-9</a>"},"doi":"10.1365/s13291-014-0083-9","date_created":"2022-03-04T07:54:39Z","oa_version":"None","quality_controlled":"1","_id":"10814","type":"journal_article","article_processing_charge":"No","publication":"Jahresbericht der Deutschen Mathematiker-Vereinigung","author":[{"first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"department":[{"_id":"RoSe"}],"year":"2014","day":"01","language":[{"iso":"eng"}],"publication_identifier":{"issn":["0012-0456"],"eissn":["1869-7135"]},"volume":116,"title":"The excitation spectrum for Bose fluids with weak interactions","intvolume":"       116","status":"public"}]