[{"publication":"32nd International Symposium on Theoretical Aspects of Computer Science","author":[{"last_name":"Bhattacharya","full_name":"Bhattacharya, Sayan","first_name":"Sayan"},{"last_name":"Dvorák","full_name":"Dvorák, Wolfgang","first_name":"Wolfgang"},{"first_name":"Monika H","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","orcid":"0000-0002-5008-6530"},{"last_name":"Starnberger","first_name":" Martin","full_name":"Starnberger,  Martin"}],"oa":1,"date_published":"2015-02-26T00:00:00Z","alternative_title":["LIPIcs"],"abstract":[{"lang":"eng","text":"Online social networks allow the collection of large amounts of data about the influence between users connected by a friendship-like relationship. When distributing items among agents forming a social network, this information allows us to exploit network externalities that each agent receives from his neighbors that get the same item. In this paper we consider Friends-of-Friends (2-hop) network externalities, i.e., externalities that not only depend on the neighbors that get the same item but also on neighbors of neighbors. For these externalities we study a setting where multiple different items are assigned to unit-demand agents. Specifically, we study the problem of welfare maximization under different types of externality functions. Let n be the number of agents and m be the number of items. Our contributions are the following: (1) We show that welfare maximization is APX-hard; we show that even for step functions with 2-hop (and also with 1-hop) externalities it is NP-hard to approximate social welfare better than (1-1/e). (2) On the positive side we present (i) an O(sqrt n)-approximation algorithm for general concave externality functions,\r\n(ii) an O(\\log m)-approximation algorithm for linear externality functions, and (iii) an (1-1/e)\\frac{1}{6}-approximation algorithm for 2-hop step function externalities. We also improve the result from [6] for 1-hop step function externalities by giving a (1-1/e)/2-approximation algorithm."}],"citation":{"ista":"Bhattacharya S, Dvorák W, Henzinger M, Starnberger  Martin. 2015. Welfare maximization with friends-of-friends network externalities. 32nd International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 30, 90–102.","mla":"Bhattacharya, Sayan, et al. “Welfare Maximization with Friends-of-Friends Network Externalities.” <i>32nd International Symposium on Theoretical Aspects of Computer Science</i>, vol. 30, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102, doi:<a href=\"https://doi.org/10.4230/LIPICS.STACS.2015.90\">10.4230/LIPICS.STACS.2015.90</a>.","ieee":"S. Bhattacharya, W. Dvorák, M. Henzinger, and  Martin Starnberger, “Welfare maximization with friends-of-friends network externalities,” in <i>32nd International Symposium on Theoretical Aspects of Computer Science</i>, Garching, Germany, 2015, vol. 30, pp. 90–102.","apa":"Bhattacharya, S., Dvorák, W., Henzinger, M., &#38; Starnberger,  Martin. (2015). Welfare maximization with friends-of-friends network externalities. In <i>32nd International Symposium on Theoretical Aspects of Computer Science</i> (Vol. 30, pp. 90–102). Garching, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPICS.STACS.2015.90\">https://doi.org/10.4230/LIPICS.STACS.2015.90</a>","short":"S. Bhattacharya, W. Dvorák, M. Henzinger,  Martin Starnberger, in:, 32nd International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015, pp. 90–102.","chicago":"Bhattacharya, Sayan, Wolfgang Dvorák, Monika Henzinger, and  Martin Starnberger. “Welfare Maximization with Friends-of-Friends Network Externalities.” In <i>32nd International Symposium on Theoretical Aspects of Computer Science</i>, 30:90–102. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2015. <a href=\"https://doi.org/10.4230/LIPICS.STACS.2015.90\">https://doi.org/10.4230/LIPICS.STACS.2015.90</a>.","ama":"Bhattacharya S, Dvorák W, Henzinger M, Starnberger  Martin. Welfare maximization with friends-of-friends network externalities. In: <i>32nd International Symposium on Theoretical Aspects of Computer Science</i>. Vol 30. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2015:90-102. doi:<a href=\"https://doi.org/10.4230/LIPICS.STACS.2015.90\">10.4230/LIPICS.STACS.2015.90</a>"},"publication_status":"published","quality_controlled":"1","oa_version":"Published Version","related_material":{"record":[{"relation":"later_version","status":"public","id":"11903"}]},"_id":"11837","main_file_link":[{"open_access":"1","url":"https://doi.org/10.4230/LIPICS.STACS.2015.90"}],"extern":"1","volume":30,"publication_identifier":{"issn":["1868-8969"],"isbn":["978-3-939897-78-1"]},"language":[{"iso":"eng"}],"type":"conference","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","article_processing_charge":"No","title":"Welfare maximization with friends-of-friends network externalities","year":"2015","page":"90-102","doi":"10.4230/LIPICS.STACS.2015.90","intvolume":"        30","status":"public","day":"26","conference":{"end_date":"2015-03-07","location":"Garching, Germany","name":"STACS: Symposium on Theoretical Aspects of Computer Science","start_date":"2015-03-04"},"date_updated":"2024-11-06T12:24:23Z","date_created":"2022-08-12T11:39:40Z","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"ddc":["570"],"publisher":"Wiley","day":"01","date_updated":"2024-11-06T12:16:55Z","date_created":"2022-08-16T06:43:49Z","intvolume":"         6","status":"public","page":"83-91","year":"2015","external_id":{"pmid":["25893087"]},"doi":"10.1111/2041-210x.12299","tmp":{"short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_processing_charge":"No","article_type":"original","title":"Split diversity in constrained conservation prioritization using integer linear programming","scopus_import":"1","has_accepted_license":"1","file_date_updated":"2022-08-16T06:52:53Z","month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"880e78f09f0ac99cb351c48dc97623b6","creator":"asandaue","file_size":411415,"file_name":"2015_MethodsInEcologyAndEvolutionChernomor.pdf","access_level":"open_access","relation":"main_file","success":1,"content_type":"application/pdf","file_id":"11846","date_updated":"2022-08-16T06:52:53Z","date_created":"2022-08-16T06:52:53Z"}],"publication_identifier":{"eissn":["2041-210X"]},"issue":"1","extern":"1","volume":6,"pmid":1,"language":[{"iso":"eng"}],"type":"journal_article","_id":"11845","oa_version":"Published Version","citation":{"short":"O. Chernomor, B.Q. Minh, F. Forest, S. Klaere, T. Ingram, M. Henzinger, A. von Haeseler, Methods in Ecology and Evolution 6 (2015) 83–91.","ama":"Chernomor O, Minh BQ, Forest F, et al. Split diversity in constrained conservation prioritization using integer linear programming. <i>Methods in Ecology and Evolution</i>. 2015;6(1):83-91. doi:<a href=\"https://doi.org/10.1111/2041-210x.12299\">10.1111/2041-210x.12299</a>","chicago":"Chernomor, Olga, Bui Quang Minh, Félix Forest, Steffen Klaere, Travis Ingram, Monika Henzinger, and Arndt von Haeseler. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” <i>Methods in Ecology and Evolution</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/2041-210x.12299\">https://doi.org/10.1111/2041-210x.12299</a>.","apa":"Chernomor, O., Minh, B. Q., Forest, F., Klaere, S., Ingram, T., Henzinger, M., &#38; von Haeseler, A. (2015). Split diversity in constrained conservation prioritization using integer linear programming. <i>Methods in Ecology and Evolution</i>. Wiley. <a href=\"https://doi.org/10.1111/2041-210x.12299\">https://doi.org/10.1111/2041-210x.12299</a>","mla":"Chernomor, Olga, et al. “Split Diversity in Constrained Conservation Prioritization Using Integer Linear Programming.” <i>Methods in Ecology and Evolution</i>, vol. 6, no. 1, Wiley, 2015, pp. 83–91, doi:<a href=\"https://doi.org/10.1111/2041-210x.12299\">10.1111/2041-210x.12299</a>.","ieee":"O. Chernomor <i>et al.</i>, “Split diversity in constrained conservation prioritization using integer linear programming,” <i>Methods in Ecology and Evolution</i>, vol. 6, no. 1. Wiley, pp. 83–91, 2015.","ista":"Chernomor O, Minh BQ, Forest F, Klaere S, Ingram T, Henzinger M, von Haeseler A. 2015. Split diversity in constrained conservation prioritization using integer linear programming. Methods in Ecology and Evolution. 6(1), 83–91."},"publication_status":"published","quality_controlled":"1","abstract":[{"text":"Phylogenetic diversity (PD) is a measure of biodiversity based on the evolutionary history of species. Here, we discuss several optimization problems related to the use of PD, and the more general measure split diversity (SD), in conservation prioritization.\r\nDepending on the conservation goal and the information available about species, one can construct optimization routines that incorporate various conservation constraints. We demonstrate how this information can be used to select sets of species for conservation action. Specifically, we discuss the use of species' geographic distributions, the choice of candidates under economic pressure, and the use of predator–prey interactions between the species in a community to define viability constraints.\r\nDespite such optimization problems falling into the area of NP hard problems, it is possible to solve them in a reasonable amount of time using integer programming. We apply integer linear programming to a variety of models for conservation prioritization that incorporate the SD measure.\r\nWe exemplarily show the results for two data sets: the Cape region of South Africa and a Caribbean coral reef community. Finally, we provide user-friendly software at http://www.cibiv.at/software/pda.","lang":"eng"}],"author":[{"last_name":"Chernomor","first_name":"Olga","full_name":"Chernomor, Olga"},{"full_name":"Minh, Bui Quang","first_name":"Bui Quang","last_name":"Minh"},{"first_name":"Félix","full_name":"Forest, Félix","last_name":"Forest"},{"first_name":"Steffen","full_name":"Klaere, Steffen","last_name":"Klaere"},{"first_name":"Travis","full_name":"Ingram, Travis","last_name":"Ingram"},{"last_name":"Henzinger","orcid":"0000-0002-5008-6530","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H"},{"last_name":"von Haeseler","full_name":"von Haeseler, Arndt","first_name":"Arndt"}],"publication":"Methods in Ecology and Evolution","date_published":"2015-01-01T00:00:00Z","oa":1},{"publication_status":"published","citation":{"short":"M. Henzinger, S. Krinninger, D. Nanongkai, T. Saranurak, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015.","chicago":"Henzinger, Monika, Sebastian Krinninger, Danupon Nanongkai, and Thatchaphol Saranurak. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” In <i>47th Annual ACM Symposium on Theory of Computing</i>. Association for Computing Machinery, 2015. <a href=\"https://doi.org/10.1145/2746539.2746609\">https://doi.org/10.1145/2746539.2746609</a>.","ama":"Henzinger M, Krinninger S, Nanongkai D, Saranurak T. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In: <i>47th Annual ACM Symposium on Theory of Computing</i>. Association for Computing Machinery; 2015. doi:<a href=\"https://doi.org/10.1145/2746539.2746609\">10.1145/2746539.2746609</a>","apa":"Henzinger, M., Krinninger, S., Nanongkai, D., &#38; Saranurak, T. (2015). Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. In <i>47th Annual ACM Symposium on Theory of Computing</i>. Portland, OR, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/2746539.2746609\">https://doi.org/10.1145/2746539.2746609</a>","ieee":"M. Henzinger, S. Krinninger, D. Nanongkai, and T. Saranurak, “Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture,” in <i>47th Annual ACM Symposium on Theory of Computing</i>, Portland, OR, United States, 2015.","mla":"Henzinger, Monika, et al. “Unifying and Strengthening Hardness for Dynamic Problems via the Online Matrix-Vector Multiplication Conjecture.” <i>47th Annual ACM Symposium on Theory of Computing</i>, 21–30, Association for Computing Machinery, 2015, doi:<a href=\"https://doi.org/10.1145/2746539.2746609\">10.1145/2746539.2746609</a>.","ista":"Henzinger M, Krinninger S, Nanongkai D, Saranurak T. 2015. Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 21–30."},"quality_controlled":"1","oa_version":"Preprint","author":[{"first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","last_name":"Henzinger","orcid":"0000-0002-5008-6530"},{"full_name":"Krinninger, Sebastian","first_name":"Sebastian","last_name":"Krinninger"},{"last_name":"Nanongkai","first_name":"Danupon","full_name":"Nanongkai, Danupon"},{"last_name":"Saranurak","first_name":"Thatchaphol","full_name":"Saranurak, Thatchaphol"}],"publication":"47th Annual ACM Symposium on Theory of Computing","oa":1,"date_published":"2015-06-14T00:00:00Z","abstract":[{"lang":"eng","text":"Consider the following Online Boolean Matrix-Vector Multiplication problem: We are given an n x n matrix M and will receive n column-vectors of size n, denoted by v1, ..., vn, one by one. After seeing each vector vi, we have to output the product Mvi before we can see the next vector. A naive algorithm can solve this problem using O(n3) time in total, and its running time can be slightly improved to O(n3/log2 n) [Williams SODA'07]. We show that a conjecture that there is no truly subcubic (O(n3-ε)) time algorithm for this problem can be used to exhibit the underlying polynomial time hardness shared by many dynamic problems. For a number of problems, such as subgraph connectivity, Pagh's problem, d-failure connectivity, decremental single-source shortest paths, and decremental transitive closure, this conjecture implies tight hardness results. Thus, proving or disproving this conjecture will be very interesting as it will either imply several tight unconditional lower bounds or break through a common barrier that blocks progress with these problems. This conjecture might also be considered as strong evidence against any further improvement for these problems since refuting it will imply a major breakthrough for combinatorial Boolean matrix multiplication and other long-standing problems if the term \"combinatorial algorithms\" is interpreted as \"Strassen-like algorithms\" [Ballard et al. SPAA'11].\r\n\r\nThe conjecture also leads to hardness results for problems that were previously based on diverse problems and conjectures -- such as 3SUM, combinatorial Boolean matrix multiplication, triangle detection, and multiphase -- thus providing a uniform way to prove polynomial hardness results for dynamic algorithms; some of the new proofs are also simpler or even become trivial. The conjecture also leads to stronger and new, non-trivial, hardness results, e.g., for the fully-dynamic densest subgraph and diameter problems."}],"_id":"11868","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.06773"}],"publication_identifier":{"issn":["0737.8017"],"isbn":["978-145033536-2"]},"article_number":"21-30","extern":"1","type":"conference","language":[{"iso":"eng"}],"arxiv":1,"article_processing_charge":"No","title":"Unifying and strengthening hardness for dynamic problems via the online matrix-vector multiplication conjecture","year":"2015","external_id":{"arxiv":["1511.06773"]},"doi":"10.1145/2746539.2746609","month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","publisher":"Association for Computing Machinery","status":"public","day":"14","date_created":"2022-08-16T09:31:21Z","date_updated":"2024-11-06T12:19:48Z","conference":{"location":"Portland, OR, United States","end_date":"2015-06-17","name":"STOC: Symposium on Theory of Computing","start_date":"2015-06-14"}},{"publisher":"Association for Computing Machinery","status":"public","conference":{"end_date":"2015-06-17","location":"Portland, OR, United States","name":"STOC: Symposium on Theory of Computing","start_date":"2015-06-14"},"date_updated":"2024-11-06T12:20:01Z","date_created":"2022-08-16T09:36:48Z","day":"01","title":"Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams","article_processing_charge":"No","doi":"10.1145/2746539.2746592","external_id":{"arxiv":["1504.02268"]},"year":"2015","page":"173 - 182","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","scopus_import":"1","_id":"11869","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1504.02268"}],"language":[{"iso":"eng"}],"type":"conference","extern":"1","publication_identifier":{"isbn":["978-145033536-2"],"issn":["0737-8017"]},"arxiv":1,"quality_controlled":"1","publication_status":"published","citation":{"ieee":"S. Bhattacharya, M. Henzinger, D. Nanongkai, and C. Tsourakakis, “Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams,” in <i>47th Annual ACM Symposium on Theory of Computing</i>, Portland, OR, United States, 2015, pp. 173–182.","mla":"Bhattacharya, Sayan, et al. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” <i>47th Annual ACM Symposium on Theory of Computing</i>, Association for Computing Machinery, 2015, pp. 173–82, doi:<a href=\"https://doi.org/10.1145/2746539.2746592\">10.1145/2746539.2746592</a>.","ista":"Bhattacharya S, Henzinger M, Nanongkai D, Tsourakakis C. 2015. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. 47th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 173–182.","ama":"Bhattacharya S, Henzinger M, Nanongkai D, Tsourakakis C. Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In: <i>47th Annual ACM Symposium on Theory of Computing</i>. Association for Computing Machinery; 2015:173-182. doi:<a href=\"https://doi.org/10.1145/2746539.2746592\">10.1145/2746539.2746592</a>","chicago":"Bhattacharya, Sayan, Monika Henzinger, Danupon Nanongkai, and Charalampos Tsourakakis. “Space- and Time-Efficient Algorithm for Maintaining Dense Subgraphs on One-Pass Dynamic Streams.” In <i>47th Annual ACM Symposium on Theory of Computing</i>, 173–82. Association for Computing Machinery, 2015. <a href=\"https://doi.org/10.1145/2746539.2746592\">https://doi.org/10.1145/2746539.2746592</a>.","short":"S. Bhattacharya, M. Henzinger, D. Nanongkai, C. Tsourakakis, in:, 47th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2015, pp. 173–182.","apa":"Bhattacharya, S., Henzinger, M., Nanongkai, D., &#38; Tsourakakis, C. (2015). Space- and time-efficient algorithm for maintaining dense subgraphs on one-pass dynamic streams. In <i>47th Annual ACM Symposium on Theory of Computing</i> (pp. 173–182). Portland, OR, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/2746539.2746592\">https://doi.org/10.1145/2746539.2746592</a>"},"oa_version":"Preprint","oa":1,"date_published":"2015-06-01T00:00:00Z","publication":"47th Annual ACM Symposium on Theory of Computing","author":[{"first_name":"Sayan","full_name":"Bhattacharya, Sayan","last_name":"Bhattacharya"},{"orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"last_name":"Nanongkai","full_name":"Nanongkai, Danupon","first_name":"Danupon"},{"first_name":"Charalampos","full_name":"Tsourakakis, Charalampos","last_name":"Tsourakakis"}],"abstract":[{"text":"While in many graph mining applications it is crucial to handle a stream of updates efficiently in terms of both time and space, not much was known about achieving such type of algorithm. In this paper we study this issue for a problem which lies at the core of many graph mining applications called densest subgraph problem. We develop an algorithm that achieves time- and space-efficiency for this problem simultaneously. It is one of the first of its kind for graph problems to the best of our knowledge.\r\n\r\nGiven an input graph, the densest subgraph is the subgraph that maximizes the ratio between the number of edges and the number of nodes. For any ε>0, our algorithm can, with high probability, maintain a (4+ε)-approximate solution under edge insertions and deletions using ~O(n) space and ~O(1) amortized time per update; here, $n$ is the number of nodes in the graph and ~O hides the O(polylog_{1+ε} n) term. The approximation ratio can be improved to (2+ε) with more time. It can be extended to a (2+ε)-approximation sublinear-time algorithm and a distributed-streaming algorithm. Our algorithm is the first streaming algorithm that can maintain the densest subgraph in one pass. Prior to this, no algorithm could do so even in the special case of an incremental stream and even when there is no time restriction. The previously best algorithm in this setting required O(log n) passes [BahmaniKV12]. The space required by our algorithm is tight up to a polylogarithmic factor.","lang":"eng"}]},{"year":"2015","page":"1-15","doi":"10.1016/j.tcs.2015.01.033","article_processing_charge":"No","title":"Truthful unit-demand auctions with budgets revisited","article_type":"original","scopus_import":"1","month":"03","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","day":"30","date_created":"2022-08-17T09:06:53Z","date_updated":"2024-11-06T12:24:01Z","intvolume":"       573","status":"public","oa_version":"None","publication_status":"published","citation":{"apa":"Henzinger, M., &#38; Loitzenbauer, V. (2015). Truthful unit-demand auctions with budgets revisited. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2015.01.033\">https://doi.org/10.1016/j.tcs.2015.01.033</a>","short":"M. Henzinger, V. Loitzenbauer, Theoretical Computer Science 573 (2015) 1–15.","ama":"Henzinger M, Loitzenbauer V. Truthful unit-demand auctions with budgets revisited. <i>Theoretical Computer Science</i>. 2015;573:1-15. doi:<a href=\"https://doi.org/10.1016/j.tcs.2015.01.033\">10.1016/j.tcs.2015.01.033</a>","chicago":"Henzinger, Monika, and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” <i>Theoretical Computer Science</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.tcs.2015.01.033\">https://doi.org/10.1016/j.tcs.2015.01.033</a>.","ista":"Henzinger M, Loitzenbauer V. 2015. Truthful unit-demand auctions with budgets revisited. Theoretical Computer Science. 573, 1–15.","mla":"Henzinger, Monika, and Veronika Loitzenbauer. “Truthful Unit-Demand Auctions with Budgets Revisited.” <i>Theoretical Computer Science</i>, vol. 573, Elsevier, 2015, pp. 1–15, doi:<a href=\"https://doi.org/10.1016/j.tcs.2015.01.033\">10.1016/j.tcs.2015.01.033</a>.","ieee":"M. Henzinger and V. Loitzenbauer, “Truthful unit-demand auctions with budgets revisited,” <i>Theoretical Computer Science</i>, vol. 573. Elsevier, pp. 1–15, 2015."},"quality_controlled":"1","abstract":[{"text":"We consider auctions of indivisible items to unit-demand bidders with budgets. This setting was suggested as an expressive model for single sponsored search auctions. Prior work presented mechanisms that compute bidder-optimal outcomes and are truthful for a restricted set of inputs, i.e., inputs in so-called general position. This condition is easily violated. We provide the first mechanism that is truthful in expectation for all inputs and achieves for each bidder no worse utility than the bidder-optimal outcome. Additionally we give a complete characterization for which inputs mechanisms that compute bidder-optimal outcomes are truthful.","lang":"eng"}],"publication":"Theoretical Computer Science","author":[{"orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","full_name":"Henzinger, Monika H","first_name":"Monika H"},{"last_name":"Loitzenbauer","full_name":"Loitzenbauer, Veronika","first_name":"Veronika"}],"oa":1,"date_published":"2015-03-30T00:00:00Z","volume":573,"extern":"1","publication_identifier":{"issn":["0304-3975"]},"language":[{"iso":"eng"}],"type":"journal_article","_id":"11901","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.tcs.2015.01.033"}]},{"title":"Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs","article_type":"original","article_processing_charge":"No","doi":"10.1002/chem.201406439","external_id":{"pmid":["25655090"]},"page":"4368-4376","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"03","scopus_import":"1","publisher":"Wiley","status":"public","intvolume":"        21","date_updated":"2023-02-21T10:09:30Z","date_created":"2022-08-24T11:11:10Z","day":"09","quality_controlled":"1","publication_status":"published","citation":{"ista":"Pieber B, Glasnov T, Kappe CO. 2015. Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. Chemistry - A European Journal. 21(11), 4368–4376.","ieee":"B. Pieber, T. Glasnov, and C. O. Kappe, “Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs,” <i>Chemistry - A European Journal</i>, vol. 21, no. 11. Wiley, pp. 4368–4376, 2015.","mla":"Pieber, Bartholomäus, et al. “Continuous Flow Reduction of Artemisinic Acid Utilizing Multi-Injection Strategies-Closing the Gap towards a Fully Continuous Synthesis of Antimalarial Drugs.” <i>Chemistry - A European Journal</i>, vol. 21, no. 11, Wiley, 2015, pp. 4368–76, doi:<a href=\"https://doi.org/10.1002/chem.201406439\">10.1002/chem.201406439</a>.","apa":"Pieber, B., Glasnov, T., &#38; Kappe, C. O. (2015). Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. <i>Chemistry - A European Journal</i>. Wiley. <a href=\"https://doi.org/10.1002/chem.201406439\">https://doi.org/10.1002/chem.201406439</a>","ama":"Pieber B, Glasnov T, Kappe CO. Continuous flow reduction of artemisinic acid utilizing multi-injection strategies-closing the gap towards a fully continuous synthesis of antimalarial drugs. <i>Chemistry - A European Journal</i>. 2015;21(11):4368-4376. doi:<a href=\"https://doi.org/10.1002/chem.201406439\">10.1002/chem.201406439</a>","short":"B. Pieber, T. Glasnov, C.O. Kappe, Chemistry - A European Journal 21 (2015) 4368–4376.","chicago":"Pieber, Bartholomäus, Toma Glasnov, and C. Oliver Kappe. “Continuous Flow Reduction of Artemisinic Acid Utilizing Multi-Injection Strategies-Closing the Gap towards a Fully Continuous Synthesis of Antimalarial Drugs.” <i>Chemistry - A European Journal</i>. Wiley, 2015. <a href=\"https://doi.org/10.1002/chem.201406439\">https://doi.org/10.1002/chem.201406439</a>."},"oa_version":"None","date_published":"2015-03-09T00:00:00Z","author":[{"last_name":"Pieber","orcid":"0000-0001-8689-388X","first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","full_name":"Pieber, Bartholomäus"},{"last_name":"Glasnov","first_name":"Toma","full_name":"Glasnov, Toma"},{"last_name":"Kappe","first_name":"C. Oliver","full_name":"Kappe, C. Oliver"}],"publication":"Chemistry - A European Journal","abstract":[{"text":"One of the rare alternative reagents for the reduction of carbon–carbon double bonds is diimide (HNNH), which can be generated in situ from hydrazine hydrate (N2H4⋅H2O) and O2. Although this selective method is extremely clean and powerful, it is rarely used, as the rate-determining oxidation of hydrazine in the absence of a catalyst is relatively slow using conventional batch protocols. A continuous high-temperature/high-pressure methodology dramatically enhances the initial oxidation step, at the same time allowing for a safe and scalable processing of the hazardous reaction mixture. Simple alkenes can be selectively reduced within 10–20 min at 100–120 °C and 20 bar O2 pressure. The development of a multi-injection reactor platform for the periodic addition of N2H4⋅H2O enables the reduction of less reactive olefins even at lower reaction temperatures. This concept was utilized for the highly selective reduction of artemisinic acid to dihydroartemisinic acid, the precursor molecule for the semisynthesis of the antimalarial drug artemisinin. The industrially relevant reduction was achieved by using four consecutive liquid feeds (of N2H4⋅H2O) and residence time units resulting in a highly selective reduction within approximately 40 min at 60 °C and 20 bar O2 pressure, providing dihydroartemisinic acid in ≥93 % yield and ≥95 % selectivity.","lang":"eng"}],"_id":"11962","pmid":1,"language":[{"iso":"eng"}],"type":"journal_article","issue":"11","publication_identifier":{"eissn":["1521-3765"],"issn":["0947-6539"]},"extern":"1","volume":21},{"article_type":"original","title":"A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids","article_processing_charge":"No","external_id":{"pmid":["25842982"]},"doi":"10.1021/acs.joc.5b00445","year":"2015","page":"4590-4602","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"05","scopus_import":"1","publisher":"American Chemical Society","status":"public","intvolume":"        80","date_created":"2022-08-25T10:52:24Z","date_updated":"2023-02-21T10:10:04Z","day":"01","quality_controlled":"1","publication_status":"published","citation":{"apa":"Salvador, C. E. M., Pieber, B., Neu, P. M., Torvisco, A., Kleber Z. Andrade, C., &#38; Kappe, C. O. (2015). A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. <i>The Journal of Organic Chemistry</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.joc.5b00445\">https://doi.org/10.1021/acs.joc.5b00445</a>","chicago":"Salvador, Carlos Eduardo M., Bartholomäus Pieber, Philipp M. Neu, Ana Torvisco, Carlos Kleber Z. Andrade, and C. Oliver Kappe. “A Sequential Ugi Multicomponent/Cu-Catalyzed Azide–Alkyne Cycloaddition Approach for the Continuous Flow Generation of Cyclic Peptoids.” <i>The Journal of Organic Chemistry</i>. American Chemical Society, 2015. <a href=\"https://doi.org/10.1021/acs.joc.5b00445\">https://doi.org/10.1021/acs.joc.5b00445</a>.","ama":"Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z. Andrade C, Kappe CO. A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. <i>The Journal of Organic Chemistry</i>. 2015;80(9):4590-4602. doi:<a href=\"https://doi.org/10.1021/acs.joc.5b00445\">10.1021/acs.joc.5b00445</a>","short":"C.E.M. Salvador, B. Pieber, P.M. Neu, A. Torvisco, C. Kleber Z. Andrade, C.O. Kappe, The Journal of Organic Chemistry 80 (2015) 4590–4602.","ista":"Salvador CEM, Pieber B, Neu PM, Torvisco A, Kleber Z. Andrade C, Kappe CO. 2015. A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids. The Journal of Organic Chemistry. 80(9), 4590–4602.","mla":"Salvador, Carlos Eduardo M., et al. “A Sequential Ugi Multicomponent/Cu-Catalyzed Azide–Alkyne Cycloaddition Approach for the Continuous Flow Generation of Cyclic Peptoids.” <i>The Journal of Organic Chemistry</i>, vol. 80, no. 9, American Chemical Society, 2015, pp. 4590–602, doi:<a href=\"https://doi.org/10.1021/acs.joc.5b00445\">10.1021/acs.joc.5b00445</a>.","ieee":"C. E. M. Salvador, B. Pieber, P. M. Neu, A. Torvisco, C. Kleber Z. Andrade, and C. O. Kappe, “A sequential Ugi multicomponent/Cu-catalyzed azide–alkyne cycloaddition approach for the continuous flow generation of cyclic peptoids,” <i>The Journal of Organic Chemistry</i>, vol. 80, no. 9. American Chemical Society, pp. 4590–4602, 2015."},"oa_version":"None","date_published":"2015-05-01T00:00:00Z","publication":"The Journal of Organic Chemistry","author":[{"first_name":"Carlos Eduardo M.","full_name":"Salvador, Carlos Eduardo M.","last_name":"Salvador"},{"first_name":"Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","full_name":"Pieber, Bartholomäus","last_name":"Pieber","orcid":"0000-0001-8689-388X"},{"first_name":"Philipp M.","full_name":"Neu, Philipp M.","last_name":"Neu"},{"full_name":"Torvisco, Ana","first_name":"Ana","last_name":"Torvisco"},{"first_name":"Carlos","full_name":"Kleber Z. Andrade, Carlos","last_name":"Kleber Z. Andrade"},{"first_name":"C. Oliver","full_name":"Kappe, C. Oliver","last_name":"Kappe"}],"abstract":[{"text":"The development of a continuous flow multistep strategy for the synthesis of linear peptoids and their subsequent macrocyclization via Click chemistry is described. The central transformation of this process is an Ugi four-component reaction generating the peptidomimetic core structure. In order to avoid exposure to the often toxic and malodorous isocyanide building blocks, the continuous approach was telescoped by the dehydration of the corresponding formamide. In a concurrent operation, the highly energetic azide moiety required for the subsequent intramolecular copper-catalyzed azide–alkyne cycloaddition (Click reaction) was installed by nucleophilic substitution from a bromide precursor. All steps yielding to the linear core structures can be conveniently coupled without the need for purification steps resulting in a single process generating the desired peptidomimetics in good to excellent yields within a 25 min reaction time. The following macrocyclization was realized in a coil reactor made of copper without any additional additive. A careful process intensification study demonstrated that this transformation occurs quantitatively within 25 min at 140 °C. Depending on the resulting ring strain, either a dimeric or a monomeric form of the cyclic product was obtained.","lang":"eng"}],"_id":"11977","type":"journal_article","language":[{"iso":"eng"}],"pmid":1,"extern":"1","volume":80,"issue":"9","publication_identifier":{"issn":["0022-3263"],"eissn":["1520-6904"]}},{"author":[{"orcid":"0000-0001-8689-388X","last_name":"Pieber","full_name":"Pieber, Bartholomäus","id":"93e5e5b2-0da6-11ed-8a41-af589a024726","first_name":"Bartholomäus"},{"full_name":"Kappe, C. Oliver","first_name":"C. Oliver","last_name":"Kappe"}],"publication":"Organometallic Flow Chemistry","alternative_title":["Topics in Organometallic Chemistry"],"date_published":"2015-06-10T00:00:00Z","editor":[{"last_name":"Noël","full_name":"Noël, Timothy","first_name":"Timothy"}],"abstract":[{"lang":"eng","text":"In recent years, the high demand for sustainable processes resulted in the development of highly attractive oxidation protocols utilizing molecular oxygen or even air instead of more uneconomic and often toxic reagents. The application of these sustainable, gaseous oxidants in conventional batch reactors is often associated with severe safety risks and process challenges especially on larger scales. Continuous flow technology offers the possibility to minimize these safety hazards and concurrently allows working in high-temperature/high-pressure regimes to access highly efficient oxidation protocols. This review article critically discusses recent literature examples of flow methodologies for selective aerobic oxidations of organic compounds. Several technologies and reactor designs for biphasic gas/liquid as well as supercritical reaction media are presented in detail. © Springer International Publishing Switzerland 2015."}],"publication_status":"published","citation":{"ieee":"B. Pieber and C. O. Kappe, “Aerobic oxidations in continuous flow,” in <i>Organometallic Flow Chemistry</i>, 1st ed., vol. 57, T. Noël, Ed. Cham: Springer Nature, 2015, pp. 97–136.","mla":"Pieber, Bartholomäus, and C. Oliver Kappe. “Aerobic Oxidations in Continuous Flow.” <i>Organometallic Flow Chemistry</i>, edited by Timothy Noël, 1st ed., vol. 57, Springer Nature, 2015, pp. 97–136, doi:<a href=\"https://doi.org/10.1007/3418_2015_133\">10.1007/3418_2015_133</a>.","ista":"Pieber B, Kappe CO. 2015.Aerobic oxidations in continuous flow. In: Organometallic Flow Chemistry. Topics in Organometallic Chemistry, vol. 57, 97–136.","ama":"Pieber B, Kappe CO. Aerobic oxidations in continuous flow. In: Noël T, ed. <i>Organometallic Flow Chemistry</i>. Vol 57. 1st ed. TOPORGAN. Cham: Springer Nature; 2015:97–136. doi:<a href=\"https://doi.org/10.1007/3418_2015_133\">10.1007/3418_2015_133</a>","short":"B. Pieber, C.O. Kappe, in:, T. Noël (Ed.), Organometallic Flow Chemistry, 1st ed., Springer Nature, Cham, 2015, pp. 97–136.","chicago":"Pieber, Bartholomäus, and C. Oliver Kappe. “Aerobic Oxidations in Continuous Flow.” In <i>Organometallic Flow Chemistry</i>, edited by Timothy Noël, 1st ed., 57:97–136. TOPORGAN. Cham: Springer Nature, 2015. <a href=\"https://doi.org/10.1007/3418_2015_133\">https://doi.org/10.1007/3418_2015_133</a>.","apa":"Pieber, B., &#38; Kappe, C. O. (2015). Aerobic oxidations in continuous flow. In T. Noël (Ed.), <i>Organometallic Flow Chemistry</i> (1st ed., Vol. 57, pp. 97–136). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/3418_2015_133\">https://doi.org/10.1007/3418_2015_133</a>"},"edition":"1","quality_controlled":"1","oa_version":"None","series_title":"TOPORGAN","_id":"11989","publication_identifier":{"eissn":["1616-8534"],"eisbn":["9783319332437"],"isbn":["9783319332413"],"issn":["1436-6002"]},"volume":57,"extern":"1","type":"book_chapter","language":[{"iso":"eng"}],"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1","article_processing_charge":"No","title":"Aerobic oxidations in continuous flow","page":"97–136","year":"2015","doi":"10.1007/3418_2015_133","intvolume":"        57","status":"public","day":"10","place":"Cham","date_updated":"2023-02-21T10:10:35Z","date_created":"2022-08-25T11:58:38Z","publisher":"Springer Nature"},{"issue":"9","extern":"1","volume":11,"type":"journal_article","language":[{"iso":"eng"}],"_id":"120","publisher":"Nature Publishing Group","day":"13","date_created":"2018-12-11T11:44:44Z","date_updated":"2021-01-12T06:49:02Z","intvolume":"        11","status":"public","page":"733 - 737","year":"2015","oa_version":"None","doi":"10.1038/nphys3396","publist_id":"7934","citation":{"apa":"Lee, V., Waitukaitis, S. R., Miskin, M., &#38; Jaeger, H. (2015). Direct observation of particle interactions and clustering in charged granular streams. <i>Nature Physics</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nphys3396\">https://doi.org/10.1038/nphys3396</a>","ama":"Lee V, Waitukaitis SR, Miskin M, Jaeger H. Direct observation of particle interactions and clustering in charged granular streams. <i>Nature Physics</i>. 2015;11(9):733-737. doi:<a href=\"https://doi.org/10.1038/nphys3396\">10.1038/nphys3396</a>","short":"V. Lee, S.R. Waitukaitis, M. Miskin, H. Jaeger, Nature Physics 11 (2015) 733–737.","chicago":"Lee, Victor, Scott R Waitukaitis, Marc Miskin, and Heinrich Jaeger. “Direct Observation of Particle Interactions and Clustering in Charged Granular Streams.” <i>Nature Physics</i>. Nature Publishing Group, 2015. <a href=\"https://doi.org/10.1038/nphys3396\">https://doi.org/10.1038/nphys3396</a>.","ista":"Lee V, Waitukaitis SR, Miskin M, Jaeger H. 2015. Direct observation of particle interactions and clustering in charged granular streams. Nature Physics. 11(9), 733–737.","ieee":"V. Lee, S. R. Waitukaitis, M. Miskin, and H. Jaeger, “Direct observation of particle interactions and clustering in charged granular streams,” <i>Nature Physics</i>, vol. 11, no. 9. Nature Publishing Group, pp. 733–737, 2015.","mla":"Lee, Victor, et al. “Direct Observation of Particle Interactions and Clustering in Charged Granular Streams.” <i>Nature Physics</i>, vol. 11, no. 9, Nature Publishing Group, 2015, pp. 733–37, doi:<a href=\"https://doi.org/10.1038/nphys3396\">10.1038/nphys3396</a>."},"publication_status":"published","acknowledgement":"This research was supported by NSF through DMR-1309611. The Chicago MRSEC, supported by NSF DMR-1420709, is gratefully acknowledged for access to its shared experimental facilities.","quality_controlled":"1","title":"Direct observation of particle interactions and clustering in charged granular streams","abstract":[{"text":"Clustering of fine particles is of crucial importance in settings ranging from the early stages of planet formation to the coagulation of industrial powders and airborne pollutants. Models of such clustering typically focus on inelastic deformation and cohesion. However, even in charge-neutral particle systems comprising grains of the same dielectric material, tribocharging can generate large amounts of net positive or negative charge on individual particles, resulting in long-range electrostatic forces. The effects of such forces on cluster formation are not well understood and have so far not been studied in situ. Here we report the first observations of individual collide-and-capture events between charged submillimetre particles, including Kepler-like orbits. Charged particles can become trapped in their mutual electrostatic energy well and aggregate via multiple bounces. This enables the initiation of clustering at relative velocities much larger than the upper limit for sticking after a head-on collision, a long-standing issue known from pre-planetary dust aggregation. Moreover, Coulomb interactions together with dielectric polarization are found to stabilize characteristic molecule-like configurations, providing new insights for the modelling of clustering dynamics in a wide range of microscopic dielectric systems, such as charged polarizable ions, biomolecules and colloids.","lang":"eng"}],"author":[{"last_name":"Lee","full_name":"Lee, Victor","first_name":"Victor"},{"first_name":"Scott R","full_name":"Waitukaitis, Scott R","id":"3A1FFC16-F248-11E8-B48F-1D18A9856A87","last_name":"Waitukaitis","orcid":"0000-0002-2299-3176"},{"full_name":"Miskin, Marc","first_name":"Marc","last_name":"Miskin"},{"first_name":"Heinrich","full_name":"Jaeger, Heinrich","last_name":"Jaeger"}],"publication":"Nature Physics","month":"07","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2015-07-13T00:00:00Z"},{"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","month":"03","scopus_import":"1","title":"On the distribution of local extrema in quantum chaos","department":[{"_id":"HeEd"}],"publist_id":"5152","article_processing_charge":"No","external_id":{"isi":["000349586000006"]},"doi":"10.1016/j.physleta.2014.12.010","page":"535 - 541","year":"2015","status":"public","isi":1,"intvolume":"       379","date_created":"2018-12-11T11:54:49Z","date_updated":"2025-09-23T09:44:12Z","day":"06","publisher":"Elsevier","date_published":"2015-03-06T00:00:00Z","author":[{"full_name":"Pausinger, Florian","id":"2A77D7A2-F248-11E8-B48F-1D18A9856A87","first_name":"Florian","orcid":"0000-0002-8379-3768","last_name":"Pausinger"},{"last_name":"Steinerberger","first_name":"Stefan","full_name":"Steinerberger, Stefan"}],"publication":"Physics Letters, Section A","abstract":[{"text":"We numerically investigate the distribution of extrema of 'chaotic' Laplacian eigenfunctions on two-dimensional manifolds. Our contribution is two-fold: (a) we count extrema on grid graphs with a small number of randomly added edges and show the behavior to coincide with the 1957 prediction of Longuet-Higgins for the continuous case and (b) we compute the regularity of their spatial distribution using discrepancy, which is a classical measure from the theory of Monte Carlo integration. The first part suggests that grid graphs with randomly added edges should behave like two-dimensional surfaces with ergodic geodesic flow; in the second part we show that the extrema are more regularly distributed in space than the grid Z2.","lang":"eng"}],"quality_controlled":"1","acknowledgement":"F.P. was supported by the Graduate School of IST Austria. S.S. was partially supported by CRC1060 of the DFG\r\nThe authors thank Olga Symonova and Michael Kerber for sharing their implementation of the persistence algorithm. ","publication_status":"published","citation":{"apa":"Pausinger, F., &#38; Steinerberger, S. (2015). On the distribution of local extrema in quantum chaos. <i>Physics Letters, Section A</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.physleta.2014.12.010\">https://doi.org/10.1016/j.physleta.2014.12.010</a>","short":"F. Pausinger, S. Steinerberger, Physics Letters, Section A 379 (2015) 535–541.","ama":"Pausinger F, Steinerberger S. On the distribution of local extrema in quantum chaos. <i>Physics Letters, Section A</i>. 2015;379(6):535-541. doi:<a href=\"https://doi.org/10.1016/j.physleta.2014.12.010\">10.1016/j.physleta.2014.12.010</a>","chicago":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” <i>Physics Letters, Section A</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.physleta.2014.12.010\">https://doi.org/10.1016/j.physleta.2014.12.010</a>.","ista":"Pausinger F, Steinerberger S. 2015. On the distribution of local extrema in quantum chaos. Physics Letters, Section A. 379(6), 535–541.","mla":"Pausinger, Florian, and Stefan Steinerberger. “On the Distribution of Local Extrema in Quantum Chaos.” <i>Physics Letters, Section A</i>, vol. 379, no. 6, Elsevier, 2015, pp. 535–41, doi:<a href=\"https://doi.org/10.1016/j.physleta.2014.12.010\">10.1016/j.physleta.2014.12.010</a>.","ieee":"F. Pausinger and S. Steinerberger, “On the distribution of local extrema in quantum chaos,” <i>Physics Letters, Section A</i>, vol. 379, no. 6. Elsevier, pp. 535–541, 2015."},"oa_version":"None","_id":"1938","type":"journal_article","language":[{"iso":"eng"}],"issue":"6","volume":379},{"publication_status":"published","citation":{"ieee":"T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 91, no. 6. American Institute of Physics, 2015.","mla":"Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>, vol. 91, no. 6, 062710, American Institute of Physics, 2015, doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">10.1103/PhysRevE.91.062710</a>.","ista":"Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(6), 062710.","ama":"Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. 2015;91(6). doi:<a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">10.1103/PhysRevE.91.062710</a>","short":"T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015).","chicago":"Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics, 2015. <a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">https://doi.org/10.1103/PhysRevE.91.062710</a>.","apa":"Sokolowski, T. R., &#38; Tkačik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. <i>Physical Review E Statistical Nonlinear and Soft Matter Physics</i>. American Institute of Physics. <a href=\"https://doi.org/10.1103/PhysRevE.91.062710\">https://doi.org/10.1103/PhysRevE.91.062710</a>"},"quality_controlled":"1","oa_version":"Preprint","author":[{"first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","full_name":"Sokolowski, Thomas R","last_name":"Sokolowski","orcid":"0000-0002-1287-3779"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","first_name":"Gasper","orcid":"0000-0002-6699-1455","last_name":"Tkacik"}],"publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","oa":1,"date_published":"2015-06-15T00:00:00Z","abstract":[{"text":"We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the &quot;input&quot;) by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models.","lang":"eng"}],"_id":"1940","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1501.04015"}],"issue":"6","article_number":"062710","volume":91,"language":[{"iso":"eng"}],"type":"journal_article","arxiv":1,"publist_id":"5145","article_processing_charge":"No","department":[{"_id":"GaTk"}],"title":"Optimizing information flow in small genetic networks. IV. Spatial coupling","year":"2015","external_id":{"isi":["000356131600006"],"arxiv":["1501.04015"]},"doi":"10.1103/PhysRevE.91.062710","month":"06","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","publisher":"American Institute of Physics","intvolume":"        91","isi":1,"status":"public","day":"15","date_updated":"2025-09-23T09:46:10Z","date_created":"2018-12-11T11:54:49Z"},{"ec_funded":1,"publisher":"Elsevier","date_updated":"2025-09-23T09:23:09Z","date_created":"2018-12-11T11:54:51Z","day":"01","status":"public","isi":1,"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"intvolume":"        23","external_id":{"isi":["000349880900017"]},"doi":"10.1016/j.pbi.2014.12.002","year":"2015","page":"116 - 123","title":"Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants","department":[{"_id":"JiFr"}],"article_processing_charge":"No","publist_id":"5140","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","month":"02","type":"journal_article","language":[{"iso":"eng"}],"volume":23,"issue":"2","_id":"1944","oa_version":"None","quality_controlled":"1","acknowledgement":"This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP); the Agency for Innovation by Science and Technology (IWT) (predoctoral fellowship to H.R.); and the People Programme (Marie Curie Actions) of the European Union","citation":{"ista":"Rakusová H, Fendrych M, Friml J. 2015. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. Current Opinion in Plant Biology. 23(2), 116–123.","ieee":"H. Rakusová, M. Fendrych, and J. Friml, “Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants,” <i>Current Opinion in Plant Biology</i>, vol. 23, no. 2. Elsevier, pp. 116–123, 2015.","mla":"Rakusová, Hana, et al. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” <i>Current Opinion in Plant Biology</i>, vol. 23, no. 2, Elsevier, 2015, pp. 116–23, doi:<a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">10.1016/j.pbi.2014.12.002</a>.","apa":"Rakusová, H., Fendrych, M., &#38; Friml, J. (2015). Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. <i>Current Opinion in Plant Biology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">https://doi.org/10.1016/j.pbi.2014.12.002</a>","chicago":"Rakusová, Hana, Matyas Fendrych, and Jiří Friml. “Intracellular Trafficking and PIN-Mediated Cell Polarity during Tropic Responses in Plants.” <i>Current Opinion in Plant Biology</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">https://doi.org/10.1016/j.pbi.2014.12.002</a>.","short":"H. Rakusová, M. Fendrych, J. Friml, Current Opinion in Plant Biology 23 (2015) 116–123.","ama":"Rakusová H, Fendrych M, Friml J. Intracellular trafficking and PIN-mediated cell polarity during tropic responses in plants. <i>Current Opinion in Plant Biology</i>. 2015;23(2):116-123. doi:<a href=\"https://doi.org/10.1016/j.pbi.2014.12.002\">10.1016/j.pbi.2014.12.002</a>"},"publication_status":"published","date_published":"2015-02-01T00:00:00Z","publication":"Current Opinion in Plant Biology","author":[{"full_name":"Rakusová, Hana","first_name":"Hana","last_name":"Rakusová"},{"full_name":"Fendrych, Matyas","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas","orcid":"0000-0002-9767-8699","last_name":"Fendrych"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","first_name":"Jirí","full_name":"Friml, Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}]},{"DOAJ_listed":"1","main_file_link":[{"url":"https://doi.org/10.1126/sciadv.1500692","open_access":"1"}],"_id":"19805","type":"journal_article","language":[{"iso":"eng"}],"article_number":"1500692","issue":"9","publication_identifier":{"issn":["2375-2548"]},"volume":1,"extern":"1","OA_type":"gold","date_published":"2015-10-01T00:00:00Z","oa":1,"author":[{"full_name":"Kushwaha, Pallavi","first_name":"Pallavi","last_name":"Kushwaha"},{"last_name":"Sunko","orcid":"0000-0003-2724-3523","first_name":"Veronika","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3","full_name":"Sunko, Veronika"},{"first_name":"Philip J. W.","full_name":"Moll, Philip J. W.","last_name":"Moll"},{"last_name":"Bawden","first_name":"Lewis","full_name":"Bawden, Lewis"},{"first_name":"Jonathon M.","full_name":"Riley, Jonathon M.","last_name":"Riley"},{"full_name":"Nandi, Nabhanila","first_name":"Nabhanila","last_name":"Nandi"},{"first_name":"Helge","full_name":"Rosner, Helge","last_name":"Rosner"},{"full_name":"Schmidt, Marcus P.","first_name":"Marcus P.","last_name":"Schmidt"},{"first_name":"Frank","full_name":"Arnold, Frank","last_name":"Arnold"},{"first_name":"Elena","full_name":"Hassinger, Elena","last_name":"Hassinger"},{"last_name":"Kim","first_name":"Timur K.","full_name":"Kim, Timur K."},{"last_name":"Hoesch","first_name":"Moritz","full_name":"Hoesch, Moritz"},{"last_name":"Mackenzie","full_name":"Mackenzie, Andrew P.","first_name":"Andrew P."},{"last_name":"King","full_name":"King, Phil D. C.","first_name":"Phil D. C."}],"publication":"Science Advances","abstract":[{"lang":"eng","text":"Understanding the role of electron correlations in strong spin-orbit transition-metal oxides is key to the realization of numerous exotic phases including spin-orbit–assisted Mott insulators, correlated topological solids, and prospective new high-temperature superconductors. To date, most attention has been focused on the 5d iridium-based oxides. We instead consider the Pt-based delafossite oxide PtCoO2. Our transport measurements, performed on single-crystal samples etched to well-defined geometries using focused ion beam techniques, yield a room temperature resistivity of only 2.1 microhm·cm (μΩ-cm), establishing PtCoO2 as the most conductive oxide known. From angle-resolved photoemission and density functional theory, we show that the underlying Fermi surface is a single cylinder of nearly hexagonal cross-section, with very weak dispersion along kz. Despite being predominantly composed of d-orbital character, the conduction band is remarkably steep, with an average effective mass of only 1.14me. Moreover, the sharp spectral features observed in photoemission remain well defined with little additional broadening for more than 500 meV below EF, pointing to suppressed electron-electron scattering. Together, our findings establish PtCoO2 as a model nearly-free–electron system in a 5d delafossite transition-metal oxide."}],"OA_place":"publisher","quality_controlled":"1","publication_status":"published","citation":{"apa":"Kushwaha, P., Sunko, V., Moll, P. J. W., Bawden, L., Riley, J. M., Nandi, N., … King, P. D. C. (2015). Nearly free electrons in a 5d delafossite oxide metal. <i>Science Advances</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/sciadv.1500692\">https://doi.org/10.1126/sciadv.1500692</a>","chicago":"Kushwaha, Pallavi, Veronika Sunko, Philip J. W. Moll, Lewis Bawden, Jonathon M. Riley, Nabhanila Nandi, Helge Rosner, et al. “Nearly Free Electrons in a 5d Delafossite Oxide Metal.” <i>Science Advances</i>. American Association for the Advancement of Science, 2015. <a href=\"https://doi.org/10.1126/sciadv.1500692\">https://doi.org/10.1126/sciadv.1500692</a>.","short":"P. Kushwaha, V. Sunko, P.J.W. Moll, L. Bawden, J.M. Riley, N. Nandi, H. Rosner, M.P. Schmidt, F. Arnold, E. Hassinger, T.K. Kim, M. Hoesch, A.P. Mackenzie, P.D.C. King, Science Advances 1 (2015).","ama":"Kushwaha P, Sunko V, Moll PJW, et al. Nearly free electrons in a 5d delafossite oxide metal. <i>Science Advances</i>. 2015;1(9). doi:<a href=\"https://doi.org/10.1126/sciadv.1500692\">10.1126/sciadv.1500692</a>","ista":"Kushwaha P, Sunko V, Moll PJW, Bawden L, Riley JM, Nandi N, Rosner H, Schmidt MP, Arnold F, Hassinger E, Kim TK, Hoesch M, Mackenzie AP, King PDC. 2015. Nearly free electrons in a 5d delafossite oxide metal. Science Advances. 1(9), 1500692.","ieee":"P. Kushwaha <i>et al.</i>, “Nearly free electrons in a 5d delafossite oxide metal,” <i>Science Advances</i>, vol. 1, no. 9. American Association for the Advancement of Science, 2015.","mla":"Kushwaha, Pallavi, et al. “Nearly Free Electrons in a 5d Delafossite Oxide Metal.” <i>Science Advances</i>, vol. 1, no. 9, 1500692, American Association for the Advancement of Science, 2015, doi:<a href=\"https://doi.org/10.1126/sciadv.1500692\">10.1126/sciadv.1500692</a>."},"oa_version":"Published Version","status":"public","intvolume":"         1","date_created":"2025-06-10T09:09:54Z","date_updated":"2025-06-10T13:09:49Z","day":"01","ddc":["530"],"publisher":"American Association for the Advancement of Science","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"10","scopus_import":"1","article_type":"original","title":"Nearly free electrons in a 5d delafossite oxide metal","tmp":{"short":"CC BY-NC (4.0)","image":"/images/cc_by_nc.png","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"article_processing_charge":"No","doi":"10.1126/sciadv.1500692","year":"2015"},{"publisher":"Wiley","_id":"1981","language":[{"iso":"eng"}],"type":"journal_article","issue":"1","volume":53,"extern":"1","status":"public","intvolume":"        53","date_updated":"2025-08-05T14:47:50Z","date_created":"2018-12-11T11:55:02Z","day":"01","acknowledgement":"Funded by      University of Alaska Center for Global Change Student Research     Cooperative Institute for Alaska Research and the Rasmuson Foundation","title":"Review and meta-analysis of natural selection in mitochondrial complex I in metazoans","article_type":"review","citation":{"ista":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. 2015. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. Journal of Zoological Systematics and Evolutionary Research. 53(1), 1–17.","mla":"Garvin, Michael, et al. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” <i>Journal of Zoological Systematics and Evolutionary Research</i>, vol. 53, no. 1, Wiley, 2015, pp. 1–17, doi:<a href=\"https://doi.org/10.1111/jzs.12079\">10.1111/jzs.12079</a>.","ieee":"M. Garvin, J. Bielawski, L. A. Sazanov, and A. Gharrett, “Review and meta-analysis of natural selection in mitochondrial complex I in metazoans,” <i>Journal of Zoological Systematics and Evolutionary Research</i>, vol. 53, no. 1. Wiley, pp. 1–17, 2015.","apa":"Garvin, M., Bielawski, J., Sazanov, L. A., &#38; Gharrett, A. (2015). Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. <i>Journal of Zoological Systematics and Evolutionary Research</i>. Wiley. <a href=\"https://doi.org/10.1111/jzs.12079\">https://doi.org/10.1111/jzs.12079</a>","short":"M. Garvin, J. Bielawski, L.A. Sazanov, A. Gharrett, Journal of Zoological Systematics and Evolutionary Research 53 (2015) 1–17.","chicago":"Garvin, Michael, Joseph Bielawski, Leonid A Sazanov, and Anthony Gharrett. “Review and Meta-Analysis of Natural Selection in Mitochondrial Complex I in Metazoans.” <i>Journal of Zoological Systematics and Evolutionary Research</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/jzs.12079\">https://doi.org/10.1111/jzs.12079</a>.","ama":"Garvin M, Bielawski J, Sazanov LA, Gharrett A. Review and meta-analysis of natural selection in mitochondrial complex I in metazoans. <i>Journal of Zoological Systematics and Evolutionary Research</i>. 2015;53(1):1-17. doi:<a href=\"https://doi.org/10.1111/jzs.12079\">10.1111/jzs.12079</a>"},"publication_status":"published","publist_id":"5102","article_processing_charge":"No","doi":"10.1111/jzs.12079","page":"1 - 17","oa_version":"None","year":"2015","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2015-02-01T00:00:00Z","author":[{"first_name":"Michael","full_name":"Garvin, Michael","last_name":"Garvin"},{"last_name":"Bielawski","full_name":"Bielawski, Joseph","first_name":"Joseph"},{"first_name":"Leonid A","id":"338D39FE-F248-11E8-B48F-1D18A9856A87","full_name":"Sazanov, Leonid A","last_name":"Sazanov","orcid":"0000-0002-0977-7989"},{"first_name":"Anthony","full_name":"Gharrett, Anthony","last_name":"Gharrett"}],"publication":"Journal of Zoological Systematics and Evolutionary Research","month":"02","abstract":[{"text":"Variation in mitochondrial DNA is often assumed to be neutral and is used to construct the genealogical relationships among populations and species. However, if extant variation is the result of episodes of positive selection, these genealogies may be incorrect, although this information itself may pro-vide biologically and evolutionary meaningful information. In fact, positive Darwinian selection has been detected in the mitochondrial-encoded subunits that comprise complex I from diverse taxa with seemingly dissimilar bioenergetic life histories, but the functional implications of the selected sites are unknown. Complex I produces roughly 40% of the proton flux that is used to synthesize ATP from ADP, and a functional model based on the high-resolution structure of complex I described a unique biomechanical apparatus for proton translocation. We reported positive selection at sites in this apparatus during the evolution of Pacific salmon, and it appeared this was also the case in published reports from other taxa, but a comparison among studies was difficult because different statistical tests were used to detect selection and oftentimes, specific sites were not reported. Here we review the literature of positive selection in mitochondrial genomes, the statistical tests used to detect selection, and the structural and functional models that are currently available to study the physiological implications of selection. We then search for signatures of positive selection among the coding mitochondrial genomes of 237 species with a common set of tests and verify that the ND5 subunit of complex I is a repeated target of positive Darwinian selection in diverse taxa. We propose a novel hypothesis to explain the results based on their bioenergetic life histories and provide a guide for laboratory and field studies to test this hypothesis.","lang":"eng"}]},{"publist_id":"5091","article_processing_charge":"No","department":[{"_id":"ToHe"}],"title":"Succinct representation of concurrent trace sets","page":"433 - 444","year":"2015","doi":"10.1145/2676726.2677008","month":"01","file_date_updated":"2020-07-14T12:45:22Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"relation":"main_file","file_name":"IST-2015-317-v1+1_author_version.pdf","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:45:22Z","date_created":"2018-12-12T10:17:56Z","file_id":"5314","creator":"system","checksum":"f0d4395b600f410a191256ac0b73af32","file_size":399462}],"scopus_import":"1","has_accepted_license":"1","ddc":["005"],"publisher":"ACM","status":"public","day":"15","date_created":"2018-12-11T11:55:05Z","date_updated":"2025-03-07T08:44:29Z","conference":{"location":"Mumbai, India","end_date":"2015-01-17","name":"POPL: Principles of Programming Languages","start_date":"2015-01-15"},"publication_status":"published","citation":{"mla":"Gupta, Ashutosh, et al. <i>Succinct Representation of Concurrent Trace Sets</i>. ACM, 2015, pp. 433–44, doi:<a href=\"https://doi.org/10.1145/2676726.2677008\">10.1145/2676726.2677008</a>.","ieee":"A. Gupta, T. A. Henzinger, A. Radhakrishna, R. Samanta, and T. Tarrach, “Succinct representation of concurrent trace sets,” presented at the POPL: Principles of Programming Languages, Mumbai, India, 2015, pp. 433–444.","ista":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. 2015. Succinct representation of concurrent trace sets. POPL: Principles of Programming Languages, 433–444.","ama":"Gupta A, Henzinger TA, Radhakrishna A, Samanta R, Tarrach T. Succinct representation of concurrent trace sets. In: ACM; 2015:433-444. doi:<a href=\"https://doi.org/10.1145/2676726.2677008\">10.1145/2676726.2677008</a>","short":"A. Gupta, T.A. Henzinger, A. Radhakrishna, R. Samanta, T. Tarrach, in:, ACM, 2015, pp. 433–444.","chicago":"Gupta, Ashutosh, Thomas A Henzinger, Arjun Radhakrishna, Roopsha Samanta, and Thorsten Tarrach. “Succinct Representation of Concurrent Trace Sets,” 433–44. ACM, 2015. <a href=\"https://doi.org/10.1145/2676726.2677008\">https://doi.org/10.1145/2676726.2677008</a>.","apa":"Gupta, A., Henzinger, T. A., Radhakrishna, A., Samanta, R., &#38; Tarrach, T. (2015). Succinct representation of concurrent trace sets (pp. 433–444). Presented at the POPL: Principles of Programming Languages, Mumbai, India: ACM. <a href=\"https://doi.org/10.1145/2676726.2677008\">https://doi.org/10.1145/2676726.2677008</a>"},"quality_controlled":"1","oa_version":"Submitted Version","author":[{"last_name":"Gupta","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh","first_name":"Ashutosh"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724"},{"last_name":"Radhakrishna","full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun"},{"last_name":"Samanta","first_name":"Roopsha","full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"},{"id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","full_name":"Tarrach, Thorsten","first_name":"Thorsten","orcid":"0000-0003-4409-8487","last_name":"Tarrach"}],"oa":1,"date_published":"2015-01-15T00:00:00Z","abstract":[{"text":"We present a method and a tool for generating succinct representations of sets of concurrent traces. We focus on trace sets that contain all correct or all incorrect permutations of events from a given trace. We represent trace sets as HB-Formulas that are Boolean combinations of happens-before constraints between events. To generate a representation of incorrect interleavings, our method iteratively explores interleavings that violate the specification and gathers generalizations of the discovered interleavings into an HB-Formula; its complement yields a representation of correct interleavings.\r\n\r\nWe claim that our trace set representations can drive diverse verification, fault localization, repair, and synthesis techniques for concurrent programs. We demonstrate this by using our tool in three case studies involving synchronization synthesis, bug summarization, and abstraction refinement based verification. In each case study, our initial experimental results have been promising.\r\n\r\nIn the first case study, we present an algorithm for inferring missing synchronization from an HB-Formula representing correct interleavings of a given trace. The algorithm applies rules to rewrite specific patterns in the HB-Formula into locks, barriers, and wait-notify constructs. In the second case study, we use an HB-Formula representing incorrect interleavings for bug summarization. While the HB-Formula itself is a concise counterexample summary, we present additional inference rules to help identify specific concurrency bugs such as data races, define-use order violations, and two-stage access bugs. In the final case study, we present a novel predicate learning procedure that uses HB-Formulas representing abstract counterexamples to accelerate counterexample-guided abstraction refinement (CEGAR). In each iteration of the CEGAR loop, the procedure refines the abstraction to eliminate multiple spurious abstract counterexamples drawn from the HB-Formula.","lang":"eng"}],"_id":"1992","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"language":[{"iso":"eng"}],"type":"conference","pubrep_id":"317"},{"project":[{"grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425"},{"_id":"25DAF0B2-B435-11E9-9278-68D0E5697425","name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1"}],"intvolume":"       282","status":"public","isi":1,"day":"22","acknowledged_ssus":[{"_id":"EM-Fac"}],"date_updated":"2025-09-23T07:55:03Z","date_created":"2018-12-11T11:55:06Z","publisher":"The Royal Society","ec_funded":1,"month":"01","corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","scopus_import":"1","article_processing_charge":"No","publist_id":"5090","title":"Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","department":[{"_id":"SyCr"}],"article_type":"original","year":"2015","doi":"10.1098/rspb.2014.1976","external_id":{"pmid":["25473011"],"isi":["000345624600008"]},"related_material":{"record":[{"id":"9740","status":"public","relation":"research_data"}]},"main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/"}],"_id":"1993","volume":282,"publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"issue":"1799","article_number":"20141976","language":[{"iso":"eng"}],"type":"journal_article","pmid":1,"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","author":[{"first_name":"Matthias","full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad"},{"first_name":"Anna V","full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","last_name":"Grasse"},{"first_name":"Simon","full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust"},{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"oa":1,"date_published":"2015-01-22T00:00:00Z","abstract":[{"text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens. ","lang":"eng"}],"publication_status":"published","citation":{"apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2015). Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2014.1976\">https://doi.org/10.1098/rspb.2014.1976</a>","chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society, 2015. <a href=\"https://doi.org/10.1098/rspb.2014.1976\">https://doi.org/10.1098/rspb.2014.1976</a>.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2015;282(1799). doi:<a href=\"https://doi.org/10.1098/rspb.2014.1976\">10.1098/rspb.2014.1976</a>","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2015. Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Proceedings of the Royal Society of London Series B Biological Sciences. 282(1799), 20141976.","mla":"Konrad, Matthias, et al. “Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1799, 20141976, The Royal Society, 2015, doi:<a href=\"https://doi.org/10.1098/rspb.2014.1976\">10.1098/rspb.2014.1976</a>.","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 282, no. 1799. The Royal Society, 2015."},"acknowledgement":"Funding was obtained by the German Research Foundation (CR 118–2) and an ERC StG (243071) by the European Research Council (both to S.C.).\r\nWe thank Line V. Ugelvig for help with ant collection and statistical discussion, Xavier Espadaler for detailed information on the ant collection site, Birgit Lautenschläger for the electron microscopy images and Eva Sixt for ant drawings. We further thank Jørgen Eilenberg for the fungal strain, Meghan L. Vyleta for genetic strain characterization and immune gene primer development, Paul Schmid-Hempel for discussion, and Line V. Ugelvig, Xavier Espadaler and Christopher D. Pull for comments on the manuscript. S.C., M.K. and S.T. conceived the study; M.K. and A.V.G. performed the experiments; M.K. performed the statistical analysis; S.C. and M.K. wrote the manuscript with intense contributions of A.V.G. and S.T.; all authors approved the manuscript.","quality_controlled":"1","oa_version":"Submitted Version"},{"publisher":"Elsevier","day":"01","date_updated":"2025-09-23T14:17:34Z","date_created":"2018-12-11T11:55:07Z","status":"public","isi":1,"page":"285 - 296","year":"2015","external_id":{"arxiv":["1207.0077"],"isi":["000347767600016"]},"doi":"10.1016/j.jsc.2014.09.014","publist_id":"5082","article_processing_charge":"No","department":[{"_id":"CaUh"}],"title":"The three-state toric homogeneous Markov chain model has Markov degree two","scopus_import":"1","month":"05","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","corr_author":"1","issue":"May-June","volume":"68/Part 2","language":[{"iso":"eng"}],"type":"journal_article","main_file_link":[{"url":"http://arxiv.org/abs/1207.0077","open_access":"1"}],"_id":"1997","arxiv":1,"oa_version":"Preprint","publication_status":"published","citation":{"chicago":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>.","ama":"Noren P. The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. 2015;68/Part 2(May-June):285-296. doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>","short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.","apa":"Noren, P. (2015). The three-state toric homogeneous Markov chain model has Markov degree two. <i>Journal of Symbolic Computation</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">https://doi.org/10.1016/j.jsc.2014.09.014</a>","mla":"Noren, Patrik. “The Three-State Toric Homogeneous Markov Chain Model Has Markov Degree Two.” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June, Elsevier, 2015, pp. 285–96, doi:<a href=\"https://doi.org/10.1016/j.jsc.2014.09.014\">10.1016/j.jsc.2014.09.014</a>.","ieee":"P. Noren, “The three-state toric homogeneous Markov chain model has Markov degree two,” <i>Journal of Symbolic Computation</i>, vol. 68/Part 2, no. May-June. Elsevier, pp. 285–296, 2015.","ista":"Noren P. 2015. The three-state toric homogeneous Markov chain model has Markov degree two. Journal of Symbolic Computation. 68/Part 2(May-June), 285–296."},"quality_controlled":"1","abstract":[{"text":"We prove that the three-state toric homogeneous Markov chain model has Markov degree two. In algebraic terminology this means, that a certain class of toric ideals is generated by quadratic binomials. This was conjectured by Haws, Martin del Campo, Takemura and Yoshida, who proved that they are generated by degree six binomials.","lang":"eng"}],"author":[{"first_name":"Patrik","full_name":"Noren, Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87","last_name":"Noren"}],"publication":"Journal of Symbolic Computation","oa":1,"date_published":"2015-05-01T00:00:00Z"},{"publisher":"Taylor & Francis","date_updated":"2025-09-23T14:07:49Z","date_created":"2018-12-11T11:55:10Z","day":"23","isi":1,"status":"public","intvolume":"        24","external_id":{"arxiv":["1109.3436"],"isi":["000356873900001"]},"doi":"10.1080/10586458.2014.980044","year":"2015","page":"261 - 269","title":"The monotone secant conjecture in the real Schubert calculus","department":[{"_id":"CaUh"}],"article_processing_charge":"No","publist_id":"5070","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"06","language":[{"iso":"eng"}],"type":"journal_article","volume":24,"issue":"3","_id":"2006","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1109.3436"}],"arxiv":1,"oa_version":"Preprint","quality_controlled":"1","citation":{"ista":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. 2015. The monotone secant conjecture in the real Schubert calculus. Experimental Mathematics. 24(3), 261–269.","mla":"Hein, Nicolas, et al. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>, vol. 24, no. 3, Taylor &#38; Francis, 2015, pp. 261–69, doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>.","ieee":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, and Z. Teitler, “The monotone secant conjecture in the real Schubert calculus,” <i>Experimental Mathematics</i>, vol. 24, no. 3. Taylor &#38; Francis, pp. 261–269, 2015.","apa":"Hein, N., Hillar, C., Martin del Campo Sanchez, A., Sottile, F., &#38; Teitler, Z. (2015). The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>","chicago":"Hein, Nicolas, Christopher Hillar, Abraham Martin del Campo Sanchez, Frank Sottile, and Zach Teitler. “The Monotone Secant Conjecture in the Real Schubert Calculus.” <i>Experimental Mathematics</i>. Taylor &#38; Francis, 2015. <a href=\"https://doi.org/10.1080/10586458.2014.980044\">https://doi.org/10.1080/10586458.2014.980044</a>.","ama":"Hein N, Hillar C, Martin del Campo Sanchez A, Sottile F, Teitler Z. The monotone secant conjecture in the real Schubert calculus. <i>Experimental Mathematics</i>. 2015;24(3):261-269. doi:<a href=\"https://doi.org/10.1080/10586458.2014.980044\">10.1080/10586458.2014.980044</a>","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269."},"publication_status":"published","abstract":[{"text":"The monotone secant conjecture posits a rich class of polynomial systems, all of whose solutions are real. These systems come from the Schubert calculus on flag manifolds, and the monotone secant conjecture is a compelling generalization of the Shapiro conjecture for Grassmannians (Theorem of Mukhin, Tarasov, and Varchenko). We present some theoretical evidence for this conjecture, as well as computational evidence obtained by 1.9 teraHertz-years of computing, and we discuss some of the phenomena we observed in our data. ","lang":"eng"}],"oa":1,"date_published":"2015-06-23T00:00:00Z","publication":"Experimental Mathematics","author":[{"last_name":"Hein","full_name":"Hein, Nicolas","first_name":"Nicolas"},{"last_name":"Hillar","first_name":"Christopher","full_name":"Hillar, Christopher"},{"first_name":"Abraham","full_name":"Martin Del Campo Sanchez, Abraham","id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","last_name":"Martin Del Campo Sanchez"},{"last_name":"Sottile","full_name":"Sottile, Frank","first_name":"Frank"},{"last_name":"Teitler","first_name":"Zach","full_name":"Teitler, Zach"}]},{"arxiv":1,"_id":"2008","main_file_link":[{"url":"http://arxiv.org/abs/1307.3282","open_access":"1"}],"language":[{"iso":"eng"}],"type":"journal_article","volume":42,"issue":"3","oa":1,"date_published":"2015-09-01T00:00:00Z","publication":"Scandinavian Journal of Statistics","author":[{"last_name":"Klimova","first_name":"Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","full_name":"Klimova, Anna"},{"last_name":"Rudas","first_name":"Tamás","full_name":"Rudas, Tamás"}],"abstract":[{"text":"The paper describes a generalized iterative proportional fitting procedure that can be used for maximum likelihood estimation in a special class of the general log-linear model. The models in this class, called relational, apply to multivariate discrete sample spaces that do not necessarily have a Cartesian product structure and may not contain an overall effect. When applied to the cell probabilities, the models without the overall effect are curved exponential families and the values of the sufficient statistics are reproduced by the MLE only up to a constant of proportionality. The paper shows that Iterative Proportional Fitting, Generalized Iterative Scaling, and Improved Iterative Scaling fail to work for such models. The algorithm proposed here is based on iterated Bregman projections. As a by-product, estimates of the multiplicative parameters are also obtained. An implementation of the algorithm is available as an R-package.","lang":"eng"}],"quality_controlled":"1","acknowledgement":"Part of the material presented here was contained in the PhD thesis of the first author to which the second author and Thomas Richardson were advisers. The authors wish to thank him for several comments and suggestions. We also thank the reviewers and the Associate Editor for helpful comments. The proof of Proposition 1 uses the idea of Olga Klimova, to whom the authors are also indebted. The second author was supported in part by Grant K-106154 from the Hungarian National Scientific Research Fund (OTKA).","citation":{"mla":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3, Wiley, 2015, pp. 832–47, doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>.","ieee":"A. Klimova and T. Rudas, “Iterative scaling in curved exponential families,” <i>Scandinavian Journal of Statistics</i>, vol. 42, no. 3. Wiley, pp. 832–847, 2015.","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 832–847.","ama":"Klimova A, Rudas T. Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. 2015;42(3):832-847. doi:<a href=\"https://doi.org/10.1111/sjos.12139\">10.1111/sjos.12139</a>","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847.","chicago":"Klimova, Anna, and Tamás Rudas. “Iterative Scaling in Curved Exponential Families.” <i>Scandinavian Journal of Statistics</i>. Wiley, 2015. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>.","apa":"Klimova, A., &#38; Rudas, T. (2015). Iterative scaling in curved exponential families. <i>Scandinavian Journal of Statistics</i>. Wiley. <a href=\"https://doi.org/10.1111/sjos.12139\">https://doi.org/10.1111/sjos.12139</a>"},"publication_status":"published","oa_version":"Preprint","isi":1,"status":"public","intvolume":"        42","date_updated":"2025-09-23T09:25:01Z","date_created":"2018-12-11T11:55:11Z","day":"01","publisher":"Wiley","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"09","scopus_import":"1","department":[{"_id":"CaUh"}],"title":"Iterative scaling in curved exponential families","article_processing_charge":"No","publist_id":"5068","doi":"10.1111/sjos.12139","external_id":{"arxiv":["1307.3282"],"isi":["000360077100012"]},"year":"2015","page":"832 - 847"},{"oa":1,"date_published":"2015-07-01T00:00:00Z","author":[{"full_name":"Klimova, Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Klimova"},{"first_name":"Caroline","full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","last_name":"Uhler","orcid":"0000-0002-7008-0216"},{"last_name":"Rudas","full_name":"Rudas, Tamás","first_name":"Tamás"}],"publication":"Computational Statistics & Data Analysis","abstract":[{"lang":"eng","text":"The concepts of faithfulness and strong-faithfulness are important for statistical learning of graphical models. Graphs are not sufficient for describing the association structure of a discrete distribution. Hypergraphs representing hierarchical log-linear models are considered instead, and the concept of parametric (strong-) faithfulness with respect to a hypergraph is introduced. Strong-faithfulness ensures the existence of uniformly consistent parameter estimators and enables building uniformly consistent procedures for a hypergraph search. The strength of association in a discrete distribution can be quantified with various measures, leading to different concepts of strong-faithfulness. Lower and upper bounds for the proportions of distributions that do not satisfy strong-faithfulness are computed for different parameterizations and measures of association."}],"quality_controlled":"1","publication_status":"published","citation":{"mla":"Klimova, Anna, et al. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7, Elsevier, 2015, pp. 57–72, doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>.","ieee":"A. Klimova, C. Uhler, and T. Rudas, “Faithfulness and learning hypergraphs from discrete distributions,” <i>Computational Statistics &#38; Data Analysis</i>, vol. 87, no. 7. Elsevier, pp. 57–72, 2015.","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics &#38; Data Analysis. 87(7), 57–72.","short":"A. Klimova, C. Uhler, T. Rudas, Computational Statistics &#38; Data Analysis 87 (2015) 57–72.","chicago":"Klimova, Anna, Caroline Uhler, and Tamás Rudas. “Faithfulness and Learning Hypergraphs from Discrete Distributions.” <i>Computational Statistics &#38; Data Analysis</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>.","ama":"Klimova A, Uhler C, Rudas T. Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. 2015;87(7):57-72. doi:<a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">10.1016/j.csda.2015.01.017</a>","apa":"Klimova, A., Uhler, C., &#38; Rudas, T. (2015). Faithfulness and learning hypergraphs from discrete distributions. <i>Computational Statistics &#38; Data Analysis</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.csda.2015.01.017\">https://doi.org/10.1016/j.csda.2015.01.017</a>"},"oa_version":"Preprint","arxiv":1,"_id":"2014","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1404.6617"}],"type":"journal_article","language":[{"iso":"eng"}],"issue":"7","volume":87,"corr_author":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"07","scopus_import":"1","title":"Faithfulness and learning hypergraphs from discrete distributions","department":[{"_id":"CaUh"}],"publist_id":"5062","article_processing_charge":"No","doi":"10.1016/j.csda.2015.01.017","external_id":{"isi":["000352661000005"],"arxiv":["1404.6617"]},"page":"57 - 72","year":"2015","status":"public","isi":1,"intvolume":"        87","date_updated":"2025-09-23T08:45:54Z","date_created":"2018-12-11T11:55:13Z","day":"01","publisher":"Elsevier"}]