[{"type":"technical_report","publication_status":"published","pubrep_id":"344","ddc":["000"],"author":[{"full_name":"Anonymous, 1","last_name":"Anonymous","first_name":"1"},{"last_name":"Anonymous","first_name":"2","full_name":"Anonymous, 2"},{"last_name":"Anonymous","first_name":"3","full_name":"Anonymous, 3"},{"last_name":"Anonymous","first_name":"4","full_name":"Anonymous, 4"}],"oa_version":"Published Version","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"22","related_material":{"record":[{"status":"public","id":"5441","relation":"later_version"},{"relation":"later_version","id":"6009","status":"public"},{"status":"public","id":"1437","relation":"later_version"}]},"publication_identifier":{"issn":["2664-1690"]},"status":"public","abstract":[{"text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural properties that arise in program analysis.\r\nWe consider that each component of the concurrent system is a graph with constant treewidth, and it is known that the controlflow graphs of most programs have constant treewidth. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis problems (e.g., alias analysis). The study of multiple queries allows us to consider the tradeoff between the resource usage of the \\emph{one-time} preprocessing and for \\emph{each individual} query. The traditional approaches construct the product graph of all components and apply the best-known graph algorithm on the product. In the traditional approach, even the answer to a single query requires the transitive closure computation (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time.\r\n\r\nOur main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, \r\neach subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results that show that the worst-case running times of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (such as improving \r\nthe worst-case bounds for the shortest path problem in general graphs whose current best-known bound has not been improved in five decades). Finally, we provide a prototype implementation of our algorithms which significantly outperforms the existing algorithmic methods on several benchmarks.","lang":"eng"}],"month":"07","day":"14","alternative_title":["IST Austria Technical Report"],"date_updated":"2025-04-15T08:11:49Z","file_date_updated":"2020-07-14T12:46:57Z","date_published":"2015-07-14T00:00:00Z","year":"2015","date_created":"2018-12-12T11:39:21Z","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","_id":"5442","has_accepted_license":"1","language":[{"iso":"eng"}],"citation":{"chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, and 4 Anonymous. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. IST Austria, 2015.","ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. 2015. Algorithms for algebraic path properties in concurrent systems of constant treewidth components, IST Austria, 22p.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components, IST Austria, 2015.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, and 4 Anonymous, <i>Algorithms for algebraic path properties in concurrent systems of constant treewidth components</i>. IST Austria, 2015.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, &#38; Anonymous, 4. (2015). <i>Algorithms for algebraic path properties in concurrent systems of constant treewidth components</i>. IST Austria.","mla":"Anonymous, 1, et al. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. IST Austria, 2015.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. IST Austria; 2015."},"oa":1,"file":[{"content_type":"application/pdf","file_size":658747,"creator":"system","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T11:53:37Z","date_updated":"2020-07-14T12:46:57Z","file_name":"IST-2015-343-v2+1_main.pdf","checksum":"98fd936102f3e057fc321ef6d316001d","file_id":"5498"},{"date_updated":"2020-07-14T12:46:57Z","file_name":"IST-2015-343-v2+2_anonymous.txt","checksum":"b31d09b1241b59c75e1f42dadf09d258","file_id":"6316","content_type":"text/plain","file_size":139,"creator":"dernst","access_level":"closed","relation":"main_file","date_created":"2019-04-16T12:36:08Z"}],"publisher":"IST Austria"},{"pubrep_id":"362","publication_status":"published","type":"technical_report","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"full_name":"Chmelik, Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","last_name":"Chmelik"},{"last_name":"Davies","first_name":"Jessica","id":"378E0060-F248-11E8-B48F-1D18A9856A87","full_name":"Davies, Jessica"}],"ddc":["000"],"related_material":{"record":[{"status":"public","relation":"later_version","id":"1166"}]},"page":"23","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","status":"public","doi":"10.15479/AT:IST-2015-325-v2-1","publication_identifier":{"issn":["2664-1690"]},"alternative_title":["IST Austria Technical Report"],"month":"11","day":"06","abstract":[{"text":"POMDPs are standard models for probabilistic planning problems, where an agent interacts with an uncertain environment. We study the problem of almost-sure reachability, where given a set of target states, the question is to decide whether there is a policy to ensure that the target set is reached with probability 1 (almost-surely). While in general the problem is EXPTIME-complete, in many practical cases policies with a small amount of memory suffice. Moreover, the existing solution to the problem is explicit, which first requires to construct explicitly an exponential reduction to a belief-support MDP. In this work, we first study the existence of observation-stationary strategies, which is NP-complete, and then small-memory strategies. We present a symbolic algorithm by an efficient encoding to SAT and using a SAT solver for the problem. We report experimental results demonstrating the scalability of our symbolic (SAT-based) approach.","lang":"eng"}],"date_updated":"2025-06-25T11:52:13Z","_id":"5443","title":"A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs","date_created":"2018-12-12T11:39:22Z","year":"2015","file_date_updated":"2020-07-14T12:46:57Z","date_published":"2015-11-06T00:00:00Z","department":[{"_id":"KrCh"}],"publisher":"IST Austria","file":[{"file_id":"5466","checksum":"f0fa31ad8161ed655137e94012123ef9","file_name":"IST-2015-325-v2+1_main.pdf","date_updated":"2020-07-14T12:46:57Z","relation":"main_file","date_created":"2018-12-12T11:53:05Z","access_level":"open_access","creator":"system","content_type":"application/pdf","file_size":412379}],"language":[{"iso":"eng"}],"citation":{"short":"K. Chatterjee, M. Chmelik, J. Davies, A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs, IST Austria, 2015.","ista":"Chatterjee K, Chmelik M, Davies J. 2015. A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs, IST Austria, 23p.","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Jessica Davies. <i>A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-325-v2-1\">https://doi.org/10.15479/AT:IST-2015-325-v2-1</a>.","ama":"Chatterjee K, Chmelik M, Davies J. <i>A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-325-v2-1\">10.15479/AT:IST-2015-325-v2-1</a>","mla":"Chatterjee, Krishnendu, et al. <i>A Symbolic SAT-Based Algorithm for Almost-Sure Reachability with Small Strategies in POMDPs</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-325-v2-1\">10.15479/AT:IST-2015-325-v2-1</a>.","apa":"Chatterjee, K., Chmelik, M., &#38; Davies, J. (2015). <i>A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-325-v2-1\">https://doi.org/10.15479/AT:IST-2015-325-v2-1</a>","ieee":"K. Chatterjee, M. Chmelik, and J. Davies, <i>A symbolic SAT-based algorithm for almost-sure reachability with small strategies in POMDPs</i>. IST Austria, 2015."},"oa":1,"has_accepted_license":"1"},{"date_updated":"2020-07-14T23:05:07Z","month":"12","day":"30","alternative_title":["IST Austria Technical Report"],"abstract":[{"text":"A comprehensive understanding of the clonal evolution of cancer is critical for understanding neoplasia. Genome-wide sequencing data enables evolutionary studies at unprecedented depth. However, classical phylogenetic methods often struggle with noisy sequencing data of impure DNA samples and fail to detect subclones that have different evolutionary trajectories. We have developed a tool, called Treeomics, that allows us to reconstruct the phylogeny of a cancer with commonly available sequencing technologies. Using Bayesian inference and Integer Linear Programming, robust phylogenies consistent with the biological processes underlying cancer evolution were obtained for pancreatic, ovarian, and prostate cancers. Furthermore, Treeomics correctly identified sequencing artifacts such as those resulting from low statistical power; nearly 7% of variants were misclassified by conventional statistical methods. These artifacts can skew phylogenies by creating illusory tumor heterogeneity among distinct samples. Importantly, we show that the evolutionary trees generated with Treeomics are mathematically optimal.","lang":"eng"}],"file":[{"creator":"system","file_size":3533200,"content_type":"application/pdf","date_created":"2018-12-12T11:53:24Z","relation":"main_file","access_level":"open_access","file_name":"IST-2015-399-v1+1_treeomics.pdf","date_updated":"2020-07-14T12:46:58Z","checksum":"c47d33bdda06181753c0af36f16e7b5d","file_id":"5485"}],"publisher":"IST Austria","department":[{"_id":"KrCh"}],"has_accepted_license":"1","citation":{"short":"J. Reiter, A. Makohon-Moore, J. Gerold, I. Bozic, K. Chatterjee, C. Iacobuzio-Donahue, B. Vogelstein, M. Nowak, Reconstructing Robust Phylogenies of Metastatic Cancers, IST Austria, 2015.","chicago":"Reiter, Johannes, Alvin Makohon-Moore, Jeffrey Gerold, Ivana Bozic, Krishnendu Chatterjee, Christine Iacobuzio-Donahue, Bert Vogelstein, and Martin Nowak. <i>Reconstructing Robust Phylogenies of Metastatic Cancers</i>. IST Austria, 2015. <a href=\"https://doi.org/10.15479/AT:IST-2015-399-v1-1\">https://doi.org/10.15479/AT:IST-2015-399-v1-1</a>.","ista":"Reiter J, Makohon-Moore A, Gerold J, Bozic I, Chatterjee K, Iacobuzio-Donahue C, Vogelstein B, Nowak M. 2015. Reconstructing robust phylogenies of metastatic cancers, IST Austria, 25p.","ama":"Reiter J, Makohon-Moore A, Gerold J, et al. <i>Reconstructing Robust Phylogenies of Metastatic Cancers</i>. IST Austria; 2015. doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-399-v1-1\">10.15479/AT:IST-2015-399-v1-1</a>","ieee":"J. Reiter <i>et al.</i>, <i>Reconstructing robust phylogenies of metastatic cancers</i>. IST Austria, 2015.","apa":"Reiter, J., Makohon-Moore, A., Gerold, J., Bozic, I., Chatterjee, K., Iacobuzio-Donahue, C., … Nowak, M. (2015). <i>Reconstructing robust phylogenies of metastatic cancers</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2015-399-v1-1\">https://doi.org/10.15479/AT:IST-2015-399-v1-1</a>","mla":"Reiter, Johannes, et al. <i>Reconstructing Robust Phylogenies of Metastatic Cancers</i>. IST Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:IST-2015-399-v1-1\">10.15479/AT:IST-2015-399-v1-1</a>."},"language":[{"iso":"eng"}],"oa":1,"date_created":"2018-12-12T11:39:22Z","title":"Reconstructing robust phylogenies of metastatic cancers","_id":"5444","date_published":"2015-12-30T00:00:00Z","file_date_updated":"2020-07-14T12:46:58Z","year":"2015","ddc":["000","576"],"author":[{"orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Reiter"},{"last_name":"Makohon-Moore","first_name":"Alvin","full_name":"Makohon-Moore, Alvin"},{"full_name":"Gerold, Jeffrey","first_name":"Jeffrey","last_name":"Gerold"},{"last_name":"Bozic","first_name":"Ivana","full_name":"Bozic, Ivana"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee"},{"full_name":"Iacobuzio-Donahue, Christine","last_name":"Iacobuzio-Donahue","first_name":"Christine"},{"last_name":"Vogelstein","first_name":"Bert","full_name":"Vogelstein, Bert"},{"last_name":"Nowak","first_name":"Martin","full_name":"Nowak, Martin"}],"publication_status":"published","pubrep_id":"399","type":"technical_report","status":"public","publication_identifier":{"issn":["2664-1690"]},"doi":"10.15479/AT:IST-2015-399-v1-1","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"25"},{"file":[{"date_updated":"2020-07-14T12:47:00Z","file_name":"IST-2015-28-v1+2_Fellner_DataRep.zip","file_id":"5597","checksum":"b8bcb43c0893023cda66c1b69c16ac62","content_type":"application/zip","file_size":49557109,"creator":"system","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T13:02:31Z"}],"publisher":"Institute of Science and Technology Austria","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"has_accepted_license":"1","citation":{"ieee":"A. Fellner, “Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015.","mla":"Fellner, Andreas. <i>Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes</i>. Institute of Science and Technology Austria, 2015, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:28\">10.15479/AT:ISTA:28</a>.","apa":"Fellner, A. (2015). Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:28\">https://doi.org/10.15479/AT:ISTA:28</a>","ama":"Fellner A. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes. 2015. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:28\">10.15479/AT:ISTA:28</a>","chicago":"Fellner, Andreas. “Experimental Part of CAV 2015 Publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.” Institute of Science and Technology Austria, 2015. <a href=\"https://doi.org/10.15479/AT:ISTA:28\">https://doi.org/10.15479/AT:ISTA:28</a>.","ista":"Fellner A. 2015. Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:28\">10.15479/AT:ISTA:28</a>.","short":"A. Fellner, (2015)."},"keyword":["Markov Decision Process","Decision Tree","Probabilistic Verification","Counterexample Explanation"],"title":"Experimental part of CAV 2015 publication: Counterexample Explanation by Learning Small Strategies in Markov Decision Processes","_id":"5549","date_updated":"2025-09-23T08:23:15Z","day":"13","ec_funded":1,"status":"public","datarep_id":"28","doi":"10.15479/AT:ISTA:28","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","contributor":[{"first_name":"Jan","last_name":"Kretinsky","id":"44CEF464-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"record":[{"status":"public","relation":"popular_science","id":"1603"}]},"ddc":["004"],"article_processing_charge":"No","type":"research_data","oa":1,"license":"https://creativecommons.org/publicdomain/zero/1.0/","date_created":"2018-12-12T12:31:29Z","date_published":"2015-08-13T00:00:00Z","file_date_updated":"2020-07-14T12:47:00Z","publist_id":"5564","year":"2015","month":"08","abstract":[{"lang":"eng","text":"This repository contains the experimental part of the CAV 2015 publication Counterexample Explanation by Learning Small Strategies in Markov Decision Processes.\r\nWe extended the probabilistic model checker PRISM to represent strategies of Markov Decision Processes as Decision Trees.\r\nThe archive contains a java executable version of the extended tool (prism_dectree.jar) together with a few examples of the PRISM benchmark library.\r\nTo execute the program, please have a look at the README.txt, which provides instructions and further information on the archive.\r\nThe archive contains scripts that (if run often enough) reproduces the data presented in the publication."}],"project":[{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","grant_number":"279307"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"author":[{"id":"42BABFB4-F248-11E8-B48F-1D18A9856A87","full_name":"Fellner, Andreas","last_name":"Fellner","first_name":"Andreas"}],"tmp":{"short":"CC0 (1.0)","name":"Creative Commons Public Domain Dedication (CC0 1.0)","image":"/images/cc_0.png","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode"}},{"date_created":"2019-01-08T20:44:06Z","title":"From prima quadraginta octant to lattice sphere through primitive integer operations","_id":"5804","date_published":"2015-04-18T00:00:00Z","year":"2015","intvolume":"       624","publisher":"Elsevier","publication":"Theoretical Computer Science","language":[{"iso":"eng"}],"issue":"4","citation":{"ista":"Biswas R, Bhowmick P. 2015. From prima quadraginta octant to lattice sphere through primitive integer operations. Theoretical Computer Science. 624(4), 56–72.","chicago":"Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to Lattice Sphere through Primitive Integer Operations.” <i>Theoretical Computer Science</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.tcs.2015.11.018\">https://doi.org/10.1016/j.tcs.2015.11.018</a>.","short":"R. Biswas, P. Bhowmick, Theoretical Computer Science 624 (2015) 56–72.","apa":"Biswas, R., &#38; Bhowmick, P. (2015). From prima quadraginta octant to lattice sphere through primitive integer operations. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2015.11.018\">https://doi.org/10.1016/j.tcs.2015.11.018</a>","mla":"Biswas, Ranita, and Partha Bhowmick. “From Prima Quadraginta Octant to Lattice Sphere through Primitive Integer Operations.” <i>Theoretical Computer Science</i>, vol. 624, no. 4, Elsevier, 2015, pp. 56–72, doi:<a href=\"https://doi.org/10.1016/j.tcs.2015.11.018\">10.1016/j.tcs.2015.11.018</a>.","ieee":"R. Biswas and P. Bhowmick, “From prima quadraginta octant to lattice sphere through primitive integer operations,” <i>Theoretical Computer Science</i>, vol. 624, no. 4. Elsevier, pp. 56–72, 2015.","ama":"Biswas R, Bhowmick P. From prima quadraginta octant to lattice sphere through primitive integer operations. <i>Theoretical Computer Science</i>. 2015;624(4):56-72. doi:<a href=\"https://doi.org/10.1016/j.tcs.2015.11.018\">10.1016/j.tcs.2015.11.018</a>"},"day":"18","month":"04","abstract":[{"text":"We present here the first integer-based algorithm for constructing a well-defined lattice sphere specified by integer radius and integer center. The algorithm evolves from a unique correspondence between the lattice points comprising the sphere and the distribution of sum of three square numbers in integer intervals. We characterize these intervals to derive a useful set of recurrences, which, in turn, aids in efficient computation. Each point of the lattice sphere is determined by resorting to only a few primitive operations in the integer domain. The symmetry of its quadraginta octants provides an added advantage by confining the computation to its prima quadraginta octant. Detailed theoretical analysis and experimental results have been furnished to demonstrate its simplicity and elegance.","lang":"eng"}],"volume":624,"date_updated":"2021-01-12T08:03:36Z","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"56-72","status":"public","doi":"10.1016/j.tcs.2015.11.018","publication_identifier":{"issn":["0304-3975"]},"quality_controlled":"1","publication_status":"published","type":"journal_article","extern":"1","author":[{"last_name":"Biswas","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}]},{"_id":"5807","title":"On different topological classes of spherical geodesic paths and circles inZ3","date_created":"2019-01-08T20:44:52Z","year":"2015","date_published":"2015-11-09T00:00:00Z","publisher":"Elsevier","intvolume":"       605","language":[{"iso":"eng"}],"issue":"11","citation":{"apa":"Biswas, R., &#38; Bhowmick, P. (2015). On different topological classes of spherical geodesic paths and circles inZ3. <i>Theoretical Computer Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tcs.2015.09.003\">https://doi.org/10.1016/j.tcs.2015.09.003</a>","mla":"Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical Geodesic Paths and Circles InZ3.” <i>Theoretical Computer Science</i>, vol. 605, no. 11, Elsevier, 2015, pp. 146–63, doi:<a href=\"https://doi.org/10.1016/j.tcs.2015.09.003\">10.1016/j.tcs.2015.09.003</a>.","ieee":"R. Biswas and P. Bhowmick, “On different topological classes of spherical geodesic paths and circles inZ3,” <i>Theoretical Computer Science</i>, vol. 605, no. 11. Elsevier, pp. 146–163, 2015.","ama":"Biswas R, Bhowmick P. On different topological classes of spherical geodesic paths and circles inZ3. <i>Theoretical Computer Science</i>. 2015;605(11):146-163. doi:<a href=\"https://doi.org/10.1016/j.tcs.2015.09.003\">10.1016/j.tcs.2015.09.003</a>","ista":"Biswas R, Bhowmick P. 2015. On different topological classes of spherical geodesic paths and circles inZ3. Theoretical Computer Science. 605(11), 146–163.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On Different Topological Classes of Spherical Geodesic Paths and Circles InZ3.” <i>Theoretical Computer Science</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.tcs.2015.09.003\">https://doi.org/10.1016/j.tcs.2015.09.003</a>.","short":"R. Biswas, P. Bhowmick, Theoretical Computer Science 605 (2015) 146–163."},"publication":"Theoretical Computer Science","month":"11","day":"09","volume":605,"date_updated":"2021-01-12T08:03:37Z","page":"146-163","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","quality_controlled":"1","doi":"10.1016/j.tcs.2015.09.003","publication_identifier":{"issn":["0304-3975"]},"publication_status":"published","extern":"1","type":"journal_article","author":[{"first_name":"Ranita","last_name":"Biswas","full_name":"Biswas, Ranita","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"}]},{"volume":31,"date_updated":"2021-01-12T08:03:37Z","day":"08","month":"05","issue":"6-8","citation":{"ama":"Biswas R, Bhowmick P. Layer the sphere. <i>The Visual Computer</i>. 2015;31(6-8):787-797. doi:<a href=\"https://doi.org/10.1007/s00371-015-1101-3\">10.1007/s00371-015-1101-3</a>","ieee":"R. Biswas and P. Bhowmick, “Layer the sphere,” <i>The Visual Computer</i>, vol. 31, no. 6–8. Springer Nature, pp. 787–797, 2015.","apa":"Biswas, R., &#38; Bhowmick, P. (2015). Layer the sphere. <i>The Visual Computer</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00371-015-1101-3\">https://doi.org/10.1007/s00371-015-1101-3</a>","mla":"Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” <i>The Visual Computer</i>, vol. 31, no. 6–8, Springer Nature, 2015, pp. 787–97, doi:<a href=\"https://doi.org/10.1007/s00371-015-1101-3\">10.1007/s00371-015-1101-3</a>.","short":"R. Biswas, P. Bhowmick, The Visual Computer 31 (2015) 787–797.","chicago":"Biswas, Ranita, and Partha Bhowmick. “Layer the Sphere.” <i>The Visual Computer</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1007/s00371-015-1101-3\">https://doi.org/10.1007/s00371-015-1101-3</a>.","ista":"Biswas R, Bhowmick P. 2015. Layer the sphere. The Visual Computer. 31(6–8), 787–797."},"language":[{"iso":"eng"}],"publication":"The Visual Computer","publisher":"Springer Nature","intvolume":"        31","year":"2015","date_published":"2015-05-08T00:00:00Z","_id":"5808","title":"Layer the sphere","date_created":"2019-01-08T20:45:05Z","author":[{"orcid":"0000-0002-5372-7890","full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","first_name":"Ranita","last_name":"Biswas"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"}],"extern":"1","type":"journal_article","publication_status":"published","quality_controlled":"1","doi":"10.1007/s00371-015-1101-3","publication_identifier":{"issn":["0178-2789","1432-2315"]},"status":"public","page":"787-797","oa_version":"None","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Springer Nature","citation":{"ama":"Sainsbury S, Bernecky C, Cramer P. Structural basis of transcription initiation by RNA polymerase II. <i>Nature Reviews Molecular Cell Biology</i>. 2015;16(3):129-143. doi:<a href=\"https://doi.org/10.1038/nrm3952\">10.1038/nrm3952</a>","ieee":"S. Sainsbury, C. Bernecky, and P. Cramer, “Structural basis of transcription initiation by RNA polymerase II,” <i>Nature Reviews Molecular Cell Biology</i>, vol. 16, no. 3. Springer Nature, pp. 129–143, 2015.","mla":"Sainsbury, Sarah, et al. “Structural Basis of Transcription Initiation by RNA Polymerase II.” <i>Nature Reviews Molecular Cell Biology</i>, vol. 16, no. 3, Springer Nature, 2015, pp. 129–43, doi:<a href=\"https://doi.org/10.1038/nrm3952\">10.1038/nrm3952</a>.","apa":"Sainsbury, S., Bernecky, C., &#38; Cramer, P. (2015). Structural basis of transcription initiation by RNA polymerase II. <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/nrm3952\">https://doi.org/10.1038/nrm3952</a>","short":"S. Sainsbury, C. Bernecky, P. Cramer, Nature Reviews Molecular Cell Biology 16 (2015) 129–143.","chicago":"Sainsbury, Sarah, Carrie Bernecky, and Patrick Cramer. “Structural Basis of Transcription Initiation by RNA Polymerase II.” <i>Nature Reviews Molecular Cell Biology</i>. Springer Nature, 2015. <a href=\"https://doi.org/10.1038/nrm3952\">https://doi.org/10.1038/nrm3952</a>.","ista":"Sainsbury S, Bernecky C, Cramer P. 2015. Structural basis of transcription initiation by RNA polymerase II. Nature Reviews Molecular Cell Biology. 16(3), 129–143."},"publication":"Nature Reviews Molecular Cell Biology","_id":"594","title":"Structural basis of transcription initiation by RNA polymerase II","OA_type":"closed access","date_updated":"2026-05-19T08:24:08Z","day":"01","status":"public","quality_controlled":"1","publication_identifier":{"eissn":["1471-0080"],"issn":["1471-0072"]},"doi":"10.1038/nrm3952","page":"129 - 143","scopus_import":"1","oa_version":"None","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","article_processing_charge":"No","type":"journal_article","extern":"1","intvolume":"        16","issue":"3","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:47:23Z","publist_id":"7206","article_type":"review","year":"2015","date_published":"2015-03-01T00:00:00Z","volume":16,"month":"03","abstract":[{"text":"Transcription of eukaryotic protein-coding genes commences with the assembly of a conserved initiation complex, which consists of RNA polymerase II (Pol II) and the general transcription factors, at promoter DNA. After two decades of research, the structural basis of transcription initiation is emerging. Crystal structures of many components of the initiation complex have been resolved, and structural information on Pol II complexes with general transcription factors has recently been obtained. Although mechanistic details await elucidation, available data outline how Pol II cooperates with the general transcription factors to bind to and open promoter DNA, and how Pol II directs RNA synthesis and escapes from the promoter.","lang":"eng"}],"author":[{"full_name":"Sainsbury, Sarah","last_name":"Sainsbury","first_name":"Sarah"},{"first_name":"Carrie A","last_name":"Bernecky","orcid":"0000-0003-0893-7036","full_name":"Bernecky, Carrie A","id":"2CB9DFE2-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Cramer","first_name":"Patrick","full_name":"Cramer, Patrick"}],"pmid":1,"publication_status":"published","external_id":{"pmid":["25693126"]}},{"pmid":1,"publication_status":"published","external_id":{"pmid":["26100886"]},"author":[{"last_name":"Fenk","first_name":"Lorenz A.","full_name":"Fenk, Lorenz A."},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono","first_name":"Mario"}],"month":"07","abstract":[{"lang":"eng","text":"Carbon dioxide (CO2) gradients are ubiquitous and provide animals with information about their environment, such as the potential presence of prey or predators. The nematode Caenorhabditis elegans avoids elevated CO2, and previous work identified three neuron pairs called “BAG,” “AFD,” and “ASE” that respond to CO2 stimuli. Using in vivo Ca2+ imaging and behavioral analysis, we show that C. elegans can detect CO2 independently of these sensory pathways. Many of the C. elegans sensory neurons we examined, including the AWC olfactory neurons, the ASJ and ASK gustatory neurons, and the ASH and ADL nociceptors, respond to a rise in CO2 with a rise in Ca2+. In contrast, glial sheath cells harboring the sensory endings of C. elegans’ major chemosensory neurons exhibit strong and sustained decreases in Ca2+ in response to high CO2. Some of these CO2 responses appear to be cell intrinsic. Worms therefore may couple detection of CO2 to that of other cues at the earliest stages of sensory processing. We show that C. elegans persistently suppresses oviposition at high CO2. Hermaphrodite-specific neurons (HSNs), the executive neurons driving egg-laying, are tonically inhibited when CO2 is elevated. CO2 modulates the egg-laying system partly through the AWC olfactory neurons: High CO2 tonically activates AWC by a cGMP-dependent mechanism, and AWC output inhibits the HSNs. Our work shows that CO2 is a more complex sensory cue for C. elegans than previously thought, both in terms of behavior and neural circuitry."}],"volume":112,"date_created":"2019-03-19T14:15:50Z","year":"2015","file_date_updated":"2020-07-14T12:47:20Z","date_published":"2015-07-07T00:00:00Z","intvolume":"       112","oa":1,"language":[{"iso":"eng"}],"issue":"27","extern":"1","type":"journal_article","ddc":["570"],"page":"E3525-E3534","oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","quality_controlled":"1","publication_identifier":{"issn":["0027-8424","1091-6490"]},"doi":"10.1073/pnas.1423808112","day":"07","date_updated":"2021-01-12T08:06:12Z","_id":"6118","title":"Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity","publisher":"National Academy of Sciences","file":[{"creator":"kschuh","content_type":"application/pdf","file_size":2822681,"date_created":"2019-03-19T14:21:07Z","relation":"main_file","access_level":"open_access","file_name":"2015_PNAS_Fenk.pdf","date_updated":"2020-07-14T12:47:20Z","checksum":"3d2da5af8d72467e382a565abc2e003d","file_id":"6119"}],"citation":{"ama":"Fenk LA, de Bono M. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. <i>Proceedings of the National Academy of Sciences</i>. 2015;112(27):E3525-E3534. doi:<a href=\"https://doi.org/10.1073/pnas.1423808112\">10.1073/pnas.1423808112</a>","apa":"Fenk, L. A., &#38; de Bono, M. (2015). Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1423808112\">https://doi.org/10.1073/pnas.1423808112</a>","mla":"Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” <i>Proceedings of the National Academy of Sciences</i>, vol. 112, no. 27, National Academy of Sciences, 2015, pp. E3525–34, doi:<a href=\"https://doi.org/10.1073/pnas.1423808112\">10.1073/pnas.1423808112</a>.","ieee":"L. A. Fenk and M. de Bono, “Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity,” <i>Proceedings of the National Academy of Sciences</i>, vol. 112, no. 27. National Academy of Sciences, pp. E3525–E3534, 2015.","short":"L.A. Fenk, M. de Bono, Proceedings of the National Academy of Sciences 112 (2015) E3525–E3534.","ista":"Fenk LA, de Bono M. 2015. Environmental CO2 inhibits Caenorhabditis elegans egg-laying by modulating olfactory neurons and evokes widespread changes in neural activity. Proceedings of the National Academy of Sciences. 112(27), E3525–E3534.","chicago":"Fenk, Lorenz A., and Mario de Bono. “Environmental CO2 Inhibits Caenorhabditis Elegans Egg-Laying by Modulating Olfactory Neurons and Evokes Widespread Changes in Neural Activity.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2015. <a href=\"https://doi.org/10.1073/pnas.1423808112\">https://doi.org/10.1073/pnas.1423808112</a>."},"has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences"},{"external_id":{"pmid":["25760081"]},"publication_status":"published","article_number":"e04241","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"pmid":1,"author":[{"full_name":"Laurent, Patrick","last_name":"Laurent","first_name":"Patrick"},{"full_name":"Soltesz, Zoltan","first_name":"Zoltan","last_name":"Soltesz"},{"last_name":"Nelson","first_name":"Geoffrey M","full_name":"Nelson, Geoffrey M"},{"full_name":"Chen, Changchun","first_name":"Changchun","last_name":"Chen"},{"full_name":"Arellano-Carbajal, Fausto","first_name":"Fausto","last_name":"Arellano-Carbajal"},{"full_name":"Levy, Emmanuel","first_name":"Emmanuel","last_name":"Levy"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","full_name":"de Bono, Mario","orcid":"0000-0001-8347-0443","last_name":"de Bono","first_name":"Mario"}],"abstract":[{"lang":"eng","text":"Brains organize behavior and physiology to optimize the response to threats or opportunities. We dissect how 21% O2, an indicator of surface exposure, reprograms C. elegans' global state, inducing sustained locomotory arousal and altering expression of neuropeptides, metabolic enzymes, and other non-neural genes. The URX O2-sensing neurons drive arousal at 21% O2 by tonically activating the RMG interneurons. Stimulating RMG is sufficient to switch behavioral state. Ablating the ASH, ADL, or ASK sensory neurons connected to RMG by gap junctions does not disrupt arousal. However, disrupting cation currents in these neurons curtails RMG neurosecretion and arousal. RMG signals high O2 by peptidergic secretion. Neuropeptide reporters reveal neural circuit state, as neurosecretion stimulates neuropeptide expression. Neural imaging in unrestrained animals shows that URX and RMG encode O2 concentration rather than behavior, while the activity of downstream interneurons such as AVB and AIY reflect both O2 levels and the behavior being executed."}],"month":"03","volume":4,"date_published":"2015-03-11T00:00:00Z","file_date_updated":"2020-07-14T12:47:20Z","year":"2015","date_created":"2019-03-19T14:23:51Z","language":[{"iso":"eng"}],"oa":1,"intvolume":"         4","extern":"1","type":"journal_article","ddc":["570"],"oa_version":"Published Version","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["2050-084X"]},"doi":"10.7554/elife.04241","quality_controlled":"1","status":"public","day":"11","date_updated":"2021-01-12T08:06:13Z","_id":"6120","title":"Decoding a neural circuit controlling global animal state in C. elegans","publication":"eLife","has_accepted_license":"1","citation":{"chicago":"Laurent, Patrick, Zoltan Soltesz, Geoffrey M Nelson, Changchun Chen, Fausto Arellano-Carbajal, Emmanuel Levy, and Mario de Bono. “Decoding a Neural Circuit Controlling Global Animal State in C. Elegans.” <i>ELife</i>. eLife Sciences Publications, 2015. <a href=\"https://doi.org/10.7554/elife.04241\">https://doi.org/10.7554/elife.04241</a>.","ista":"Laurent P, Soltesz Z, Nelson GM, Chen C, Arellano-Carbajal F, Levy E, de Bono M. 2015. Decoding a neural circuit controlling global animal state in C. elegans. eLife. 4, e04241.","short":"P. Laurent, Z. Soltesz, G.M. Nelson, C. Chen, F. Arellano-Carbajal, E. Levy, M. de Bono, ELife 4 (2015).","ieee":"P. Laurent <i>et al.</i>, “Decoding a neural circuit controlling global animal state in C. elegans,” <i>eLife</i>, vol. 4. eLife Sciences Publications, 2015.","mla":"Laurent, Patrick, et al. “Decoding a Neural Circuit Controlling Global Animal State in C. Elegans.” <i>ELife</i>, vol. 4, e04241, eLife Sciences Publications, 2015, doi:<a href=\"https://doi.org/10.7554/elife.04241\">10.7554/elife.04241</a>.","apa":"Laurent, P., Soltesz, Z., Nelson, G. M., Chen, C., Arellano-Carbajal, F., Levy, E., &#38; de Bono, M. (2015). Decoding a neural circuit controlling global animal state in C. elegans. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.04241\">https://doi.org/10.7554/elife.04241</a>","ama":"Laurent P, Soltesz Z, Nelson GM, et al. Decoding a neural circuit controlling global animal state in C. elegans. <i>eLife</i>. 2015;4. doi:<a href=\"https://doi.org/10.7554/elife.04241\">10.7554/elife.04241</a>"},"file":[{"file_id":"6121","checksum":"cf641b7a363aecd0a101755d23dee7e0","file_name":"2015_elife_Laurent.pdf","date_updated":"2020-07-14T12:47:20Z","relation":"main_file","date_created":"2019-03-19T14:29:43Z","access_level":"open_access","creator":"kschuh","content_type":"application/pdf","file_size":6723528}],"publisher":"eLife Sciences Publications"},{"ddc":["530"],"extern":"1","type":"journal_article","article_processing_charge":"No","publication_identifier":{"issn":["2375-2548"]},"doi":"10.1126/sciadv.1500692","quality_controlled":"1","status":"public","oa_version":"Published Version","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-06-10T13:09:49Z","OA_type":"gold","day":"01","publication":"Science Advances","citation":{"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.","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>","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>.","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>","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>.","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.","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)."},"main_file_link":[{"url":"https://doi.org/10.1126/sciadv.1500692","open_access":"1"}],"publisher":"American Association for the Advancement of Science","OA_place":"publisher","title":"Nearly free electrons in a 5d delafossite oxide metal","_id":"19805","author":[{"full_name":"Kushwaha, Pallavi","last_name":"Kushwaha","first_name":"Pallavi"},{"first_name":"Veronika","last_name":"Sunko","full_name":"Sunko, Veronika","orcid":"0000-0003-2724-3523","id":"23cb1cf6-2c7a-11ef-91a4-f72fc19f20b3"},{"full_name":"Moll, Philip J. W.","first_name":"Philip J. W.","last_name":"Moll"},{"full_name":"Bawden, Lewis","first_name":"Lewis","last_name":"Bawden"},{"first_name":"Jonathon M.","last_name":"Riley","full_name":"Riley, Jonathon M."},{"full_name":"Nandi, Nabhanila","last_name":"Nandi","first_name":"Nabhanila"},{"full_name":"Rosner, Helge","last_name":"Rosner","first_name":"Helge"},{"full_name":"Schmidt, Marcus P.","first_name":"Marcus P.","last_name":"Schmidt"},{"full_name":"Arnold, Frank","last_name":"Arnold","first_name":"Frank"},{"full_name":"Hassinger, Elena","first_name":"Elena","last_name":"Hassinger"},{"full_name":"Kim, Timur K.","last_name":"Kim","first_name":"Timur K."},{"full_name":"Hoesch, Moritz","first_name":"Moritz","last_name":"Hoesch"},{"full_name":"Mackenzie, Andrew P.","last_name":"Mackenzie","first_name":"Andrew P."},{"full_name":"King, Phil D. C.","last_name":"King","first_name":"Phil D. C."}],"publication_status":"published","article_number":"1500692","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"DOAJ_listed":"1","volume":1,"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."}],"month":"10","issue":"9","oa":1,"language":[{"iso":"eng"}],"intvolume":"         1","date_published":"2015-10-01T00:00:00Z","article_type":"original","year":"2015","date_created":"2025-06-10T09:09:54Z"},{"year":"2015","article_type":"review","publist_id":"5102","date_published":"2015-02-01T00:00:00Z","title":"Review and meta-analysis of natural selection in mitochondrial complex I in metazoans","_id":"1981","date_created":"2018-12-11T11:55:02Z","language":[{"iso":"eng"}],"issue":"1","acknowledgement":"Funded by      University of Alaska Center for Global Change Student Research     Cooperative Institute for Alaska Research and the Rasmuson Foundation","citation":{"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>","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>","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.","short":"M. Garvin, J. Bielawski, L.A. Sazanov, A. Gharrett, Journal of Zoological Systematics and Evolutionary Research 53 (2015) 1–17.","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.","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>."},"publication":"Journal of Zoological Systematics and Evolutionary Research","publisher":"Wiley","intvolume":"        53","abstract":[{"lang":"eng","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."}],"month":"02","day":"01","volume":53,"date_updated":"2025-08-05T14:47:50Z","page":"1 - 17","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","doi":"10.1111/jzs.12079","status":"public","type":"journal_article","extern":"1","article_processing_charge":"No","publication_status":"published","author":[{"last_name":"Garvin","first_name":"Michael","full_name":"Garvin, Michael"},{"last_name":"Bielawski","first_name":"Joseph","full_name":"Bielawski, Joseph"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A","last_name":"Sazanov","first_name":"Leonid A"},{"first_name":"Anthony","last_name":"Gharrett","full_name":"Gharrett, Anthony"}]},{"citation":{"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>","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.","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>","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>.","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>.","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."},"has_accepted_license":"1","department":[{"_id":"ToHe"}],"publisher":"ACM","file":[{"date_updated":"2020-07-14T12:45:22Z","file_name":"IST-2015-317-v1+1_author_version.pdf","file_id":"5314","checksum":"f0d4395b600f410a191256ac0b73af32","content_type":"application/pdf","file_size":399462,"creator":"system","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:17:56Z"}],"_id":"1992","title":"Succinct representation of concurrent trace sets","date_updated":"2025-03-07T08:44:29Z","day":"15","quality_controlled":"1","publication_identifier":{"isbn":["978-1-4503-3300-9"]},"doi":"10.1145/2676726.2677008","status":"public","page":"433 - 444","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Submitted Version","scopus_import":"1","conference":{"name":"POPL: Principles of Programming Languages","start_date":"2015-01-15","location":"Mumbai, India","end_date":"2015-01-17"},"ddc":["005"],"type":"conference","article_processing_charge":"No","language":[{"iso":"eng"}],"oa":1,"publist_id":"5091","year":"2015","file_date_updated":"2020-07-14T12:45:22Z","date_published":"2015-01-15T00:00:00Z","date_created":"2018-12-11T11:55:05Z","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"}],"month":"01","author":[{"first_name":"Ashutosh","last_name":"Gupta","full_name":"Gupta, Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger","first_name":"Thomas A"},{"full_name":"Radhakrishna, Arjun","id":"3B51CAC4-F248-11E8-B48F-1D18A9856A87","first_name":"Arjun","last_name":"Radhakrishna"},{"id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","full_name":"Samanta, Roopsha","last_name":"Samanta","first_name":"Roopsha"},{"last_name":"Tarrach","first_name":"Thorsten","id":"3D6E8F2C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4409-8487","full_name":"Tarrach, Thorsten"}],"pubrep_id":"317","publication_status":"published"},{"citation":{"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>","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.","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>","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>.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, Proceedings of the Royal Society of London Series B Biological Sciences 282 (2015).","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>.","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."},"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","department":[{"_id":"SyCr"}],"publisher":"The Royal Society","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4286035/"}],"title":"Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","_id":"1993","date_updated":"2025-09-23T07:55:03Z","day":"22","quality_controlled":"1","doi":"10.1098/rspb.2014.1976","publication_identifier":{"eissn":["1471-2954"],"issn":["0962-8452"]},"ec_funded":1,"status":"public","related_material":{"record":[{"relation":"research_data","id":"9740","status":"public"}]},"scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Submitted Version","type":"journal_article","article_processing_charge":"No","issue":"1799","oa":1,"isi":1,"language":[{"iso":"eng"}],"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.","intvolume":"       282","article_type":"original","year":"2015","publist_id":"5090","date_published":"2015-01-22T00:00:00Z","date_created":"2018-12-11T11:55:06Z","volume":282,"abstract":[{"lang":"eng","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. "}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"month":"01","project":[{"_id":"25DC711C-B435-11E9-9278-68D0E5697425","grant_number":"243071","call_identifier":"FP7","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"},{"name":"Host-Parasite Coevolution","grant_number":"CR-118/3-1","_id":"25DAF0B2-B435-11E9-9278-68D0E5697425"}],"author":[{"full_name":"Konrad, Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","first_name":"Matthias","last_name":"Konrad"},{"full_name":"Grasse, Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V","last_name":"Grasse"},{"full_name":"Tragust, Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Tragust"},{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","last_name":"Cremer","first_name":"Sylvia"}],"corr_author":"1","external_id":{"pmid":["25473011"],"isi":["000345624600008"]},"pmid":1,"article_number":"20141976","publication_status":"published"},{"author":[{"first_name":"Patrik","last_name":"Noren","full_name":"Noren, Patrik","id":"46870C74-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","corr_author":"1","external_id":{"isi":["000347767600016"],"arxiv":["1207.0077"]},"oa":1,"language":[{"iso":"eng"}],"isi":1,"issue":"May-June","date_created":"2018-12-11T11:55:07Z","year":"2015","publist_id":"5082","date_published":"2015-05-01T00:00:00Z","volume":"68/Part 2","month":"05","abstract":[{"lang":"eng","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."}],"status":"public","quality_controlled":"1","doi":"10.1016/j.jsc.2014.09.014","page":"285 - 296","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","scopus_import":"1","arxiv":1,"article_processing_charge":"No","type":"journal_article","department":[{"_id":"CaUh"}],"publisher":"Elsevier","main_file_link":[{"url":"http://arxiv.org/abs/1207.0077","open_access":"1"}],"citation":{"short":"P. Noren, Journal of Symbolic Computation 68/Part 2 (2015) 285–296.","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>.","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.","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>","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.","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>."},"publication":"Journal of Symbolic Computation","title":"The three-state toric homogeneous Markov chain model has Markov degree two","_id":"1997","date_updated":"2025-09-23T14:17:34Z","day":"01"},{"volume":24,"month":"06","abstract":[{"lang":"eng","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. "}],"intvolume":"        24","language":[{"iso":"eng"}],"isi":1,"issue":"3","oa":1,"date_created":"2018-12-11T11:55:10Z","date_published":"2015-06-23T00:00:00Z","publist_id":"5070","year":"2015","author":[{"full_name":"Hein, Nicolas","last_name":"Hein","first_name":"Nicolas"},{"last_name":"Hillar","first_name":"Christopher","full_name":"Hillar, Christopher"},{"id":"4CF47F6A-F248-11E8-B48F-1D18A9856A87","full_name":"Martin Del Campo Sanchez, Abraham","last_name":"Martin Del Campo Sanchez","first_name":"Abraham"},{"first_name":"Frank","last_name":"Sottile","full_name":"Sottile, Frank"},{"full_name":"Teitler, Zach","last_name":"Teitler","first_name":"Zach"}],"publication_status":"published","external_id":{"arxiv":["1109.3436"],"isi":["000356873900001"]},"date_updated":"2025-09-23T14:07:49Z","day":"23","main_file_link":[{"url":"http://arxiv.org/abs/1109.3436","open_access":"1"}],"publisher":"Taylor & Francis","department":[{"_id":"CaUh"}],"publication":"Experimental Mathematics","citation":{"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>","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.","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>.","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>","short":"N. Hein, C. Hillar, A. Martin del Campo Sanchez, F. Sottile, Z. Teitler, Experimental Mathematics 24 (2015) 261–269.","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>.","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."},"title":"The monotone secant conjecture in the real Schubert calculus","_id":"2006","arxiv":1,"article_processing_charge":"No","type":"journal_article","status":"public","doi":"10.1080/10586458.2014.980044","quality_controlled":"1","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","page":"261 - 269"},{"date_created":"2018-12-11T11:55:11Z","publist_id":"5068","year":"2015","date_published":"2015-09-01T00:00:00Z","intvolume":"        42","oa":1,"language":[{"iso":"eng"}],"issue":"3","isi":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).","month":"09","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"}],"volume":42,"publication_status":"published","external_id":{"arxiv":["1307.3282"],"isi":["000360077100012"]},"author":[{"first_name":"Anna","last_name":"Klimova","full_name":"Klimova, Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Rudas","first_name":"Tamás","full_name":"Rudas, Tamás"}],"title":"Iterative scaling in curved exponential families","_id":"2008","department":[{"_id":"CaUh"}],"publisher":"Wiley","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1307.3282"}],"citation":{"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>","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.","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>","ista":"Klimova A, Rudas T. 2015. Iterative scaling in curved exponential families. Scandinavian Journal of Statistics. 42(3), 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>.","short":"A. Klimova, T. Rudas, Scandinavian Journal of Statistics 42 (2015) 832–847."},"publication":"Scandinavian Journal of Statistics","day":"01","date_updated":"2025-09-23T09:25:01Z","page":"832 - 847","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","scopus_import":"1","status":"public","quality_controlled":"1","doi":"10.1111/sjos.12139","article_processing_charge":"No","arxiv":1,"type":"journal_article"},{"type":"journal_article","article_processing_charge":"No","arxiv":1,"oa_version":"Preprint","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"57 - 72","doi":"10.1016/j.csda.2015.01.017","quality_controlled":"1","status":"public","day":"01","date_updated":"2025-09-23T08:45:54Z","title":"Faithfulness and learning hypergraphs from discrete distributions","_id":"2014","publication":"Computational Statistics & Data Analysis","citation":{"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>.","ista":"Klimova A, Uhler C, Rudas T. 2015. Faithfulness and learning hypergraphs from discrete distributions. Computational Statistics &#38; Data Analysis. 87(7), 57–72.","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>","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.","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>.","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>"},"main_file_link":[{"url":"http://arxiv.org/abs/1404.6617","open_access":"1"}],"publisher":"Elsevier","department":[{"_id":"CaUh"}],"external_id":{"isi":["000352661000005"],"arxiv":["1404.6617"]},"corr_author":"1","publication_status":"published","author":[{"full_name":"Klimova, Anna","id":"31934120-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Klimova"},{"orcid":"0000-0002-7008-0216","full_name":"Uhler, Caroline","id":"49ADD78E-F248-11E8-B48F-1D18A9856A87","first_name":"Caroline","last_name":"Uhler"},{"last_name":"Rudas","first_name":"Tamás","full_name":"Rudas, Tamás"}],"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."}],"month":"07","volume":87,"date_published":"2015-07-01T00:00:00Z","publist_id":"5062","year":"2015","date_created":"2018-12-11T11:55:13Z","isi":1,"issue":"7","oa":1,"language":[{"iso":"eng"}],"intvolume":"        87"},{"citation":{"mla":"Kawada, Daiki, et al. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 1, Elsevier, 2015, pp. 144–56, doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>.","apa":"Kawada, D., Kobayashi, H., Tomita, T., Nakata, E., Nagano, M., Siekhaus, D. E., … Toshimaa, J. (2015). The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>","ieee":"D. Kawada <i>et al.</i>, “The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins,” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>, vol. 1853, no. 1. Elsevier, pp. 144–156, 2015.","ama":"Kawada D, Kobayashi H, Tomita T, et al. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. 2015;1853(1):144-156. doi:<a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">10.1016/j.bbamcr.2014.10.009</a>","ista":"Kawada D, Kobayashi H, Tomita T, Nakata E, Nagano M, Siekhaus DE, Toshima J, Toshimaa J. 2015. The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins. Biochimica et Biophysica Acta - Molecular Cell Research. 1853(1), 144–156.","chicago":"Kawada, Daiki, Hiromu Kobayashi, Tsuyoshi Tomita, Eisuke Nakata, Makoto Nagano, Daria E Siekhaus, Junko Toshima, and Jiro Toshimaa. “The Yeast Arf-GAP Glo3p Is Required for the Endocytic Recycling of Cell Surface Proteins.” <i>Biochimica et Biophysica Acta - Molecular Cell Research</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.bbamcr.2014.10.009\">https://doi.org/10.1016/j.bbamcr.2014.10.009</a>.","short":"D. Kawada, H. Kobayashi, T. Tomita, E. Nakata, M. Nagano, D.E. Siekhaus, J. Toshima, J. Toshimaa, Biochimica et Biophysica Acta - Molecular Cell Research 1853 (2015) 144–156."},"publication":"Biochimica et Biophysica Acta - Molecular Cell Research","has_accepted_license":"1","publisher":"Elsevier","department":[{"_id":"DaSi"}],"file":[{"creator":"system","file_size":926685,"content_type":"application/pdf","date_created":"2018-12-12T10:12:18Z","relation":"main_file","access_level":"open_access","file_name":"IST-2016-615-v1+1_BBAMCR.pdf","date_updated":"2020-07-14T12:45:25Z","checksum":"5bb328edebb6a91337cadd7d63f961b7","file_id":"4936"}],"_id":"2025","title":"The yeast Arf-GAP Glo3p is required for the endocytic recycling of cell surface proteins","date_updated":"2025-09-23T14:51:55Z","day":"01","quality_controlled":"1","doi":"10.1016/j.bbamcr.2014.10.009","status":"public","page":"144 - 156","scopus_import":"1","oa_version":"Submitted Version","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ddc":["570"],"type":"journal_article","article_processing_charge":"No","oa":1,"issue":"1","isi":1,"language":[{"iso":"eng"}],"intvolume":"      1853","year":"2015","publist_id":"5047","file_date_updated":"2020-07-14T12:45:25Z","date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:55:17Z","volume":1853,"abstract":[{"lang":"eng","text":"Small GTP-binding proteins of the Ras superfamily play diverse roles in intracellular trafficking. Among them, the Rab, Arf, and Rho families function in successive steps of vesicle transport, in forming vesicles from donor membranes, directing vesicle trafficking toward target membranes and docking vesicles onto target membranes. These proteins act as molecular switches that are controlled by a cycle of GTP binding and hydrolysis regulated by guanine nucleotide exchange factors (GEFs) and GTPase-activating proteins (GAPs). In this study we explored the role of GAPs in the regulation of the endocytic pathway using fluorescently labeled yeast mating pheromone α-factor. Among 25 non-essential GAP mutants, we found that deletion of the GLO3 gene, encoding Arf-GAP protein, caused defective internalization of fluorescently labeled α-factor. Quantitative analysis revealed that glo3Δ cells show defective α-factor binding to the cell surface. Interestingly, Ste2p, the α-factor receptor, was mis-localized from the plasma membrane to the vacuole in glo3Δ cells. Domain deletion mutants of Glo3p revealed that a GAP-independent function, as well as the GAP activity, of Glo3p is important for both α-factor binding and Ste2p localization at the cell surface. Additionally, we found that deletion of the GLO3 gene affects the size and number of Arf1p-residing Golgi compartments and causes a defect in transport from the TGN to the plasma membrane. Furthermore, we demonstrated that glo3Δ cells were defective in the late endosome-to-TGN transport pathway, but not in the early endosome-to-TGN transport pathway. These findings suggest novel roles for Arf-GAP Glo3p in endocytic recycling of cell surface proteins."}],"month":"01","author":[{"full_name":"Kawada, Daiki","first_name":"Daiki","last_name":"Kawada"},{"last_name":"Kobayashi","first_name":"Hiromu","full_name":"Kobayashi, Hiromu"},{"first_name":"Tsuyoshi","last_name":"Tomita","full_name":"Tomita, Tsuyoshi"},{"first_name":"Eisuke","last_name":"Nakata","full_name":"Nakata, Eisuke"},{"full_name":"Nagano, Makoto","last_name":"Nagano","first_name":"Makoto"},{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","last_name":"Siekhaus","first_name":"Daria E"},{"full_name":"Toshima, Junko","first_name":"Junko","last_name":"Toshima"},{"last_name":"Toshimaa","first_name":"Jiro","full_name":"Toshimaa, Jiro"}],"external_id":{"isi":["000347598100014"]},"tmp":{"image":"/images/cc_by_nc_nd.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","short":"CC BY-NC-ND (4.0)"},"pubrep_id":"615","publication_status":"published"},{"title":"A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow","_id":"2030","citation":{"ista":"Shi L, Rampp M, Hof B, Avila M. 2015. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. Computers and Fluids. 106(1), 1–11.","chicago":"Shi, Liang, Markus Rampp, Björn Hof, and Marc Avila. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” <i>Computers and Fluids</i>. Elsevier, 2015. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>.","short":"L. Shi, M. Rampp, B. Hof, M. Avila, Computers and Fluids 106 (2015) 1–11.","mla":"Shi, Liang, et al. “A Hybrid MPI-OpenMP Parallel Implementation for Pseudospectral Simulations with Application to Taylor-Couette Flow.” <i>Computers and Fluids</i>, vol. 106, no. 1, Elsevier, 2015, pp. 1–11, doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>.","apa":"Shi, L., Rampp, M., Hof, B., &#38; Avila, M. (2015). A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. <i>Computers and Fluids</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">https://doi.org/10.1016/j.compfluid.2014.09.021</a>","ieee":"L. Shi, M. Rampp, B. Hof, and M. Avila, “A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow,” <i>Computers and Fluids</i>, vol. 106, no. 1. Elsevier, pp. 1–11, 2015.","ama":"Shi L, Rampp M, Hof B, Avila M. A hybrid MPI-OpenMP parallel implementation for pseudospectral simulations with application to Taylor-Couette flow. <i>Computers and Fluids</i>. 2015;106(1):1-11. doi:<a href=\"https://doi.org/10.1016/j.compfluid.2014.09.021\">10.1016/j.compfluid.2014.09.021</a>"},"publication":"Computers and Fluids","publisher":"Elsevier","department":[{"_id":"BjHo"}],"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1311.2481"}],"day":"01","date_updated":"2025-09-22T14:31:33Z","page":"1 - 11","oa_version":"Preprint","scopus_import":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","quality_controlled":"1","doi":"10.1016/j.compfluid.2014.09.021","status":"public","type":"journal_article","arxiv":1,"article_processing_charge":"No","year":"2015","publist_id":"5042","date_published":"2015-01-01T00:00:00Z","date_created":"2018-12-11T11:55:18Z","oa":1,"language":[{"iso":"eng"}],"issue":"1","isi":1,"intvolume":"       106","abstract":[{"text":"A hybrid-parallel direct-numerical-simulation method with application to turbulent Taylor-Couette flow is presented. The Navier-Stokes equations are discretized in cylindrical coordinates with the spectral Fourier-Galerkin method in the axial and azimuthal directions, and high-order finite differences in the radial direction. Time is advanced by a second-order, semi-implicit projection scheme, which requires the solution of five Helmholtz/Poisson equations, avoids staggered grids and renders very small slip velocities. Nonlinear terms are evaluated with the pseudospectral method. The code is parallelized using a hybrid MPI-OpenMP strategy, which, compared with a flat MPI parallelization, is simpler to implement, allows to reduce inter-node communications and MPI overhead that become relevant at high processor-core counts, and helps to contain the memory footprint. A strong scaling study shows that the hybrid code maintains scalability up to more than 20,000 processor cores and thus allows to perform simulations at higher resolutions than previously feasible. In particular, it opens up the possibility to simulate turbulent Taylor-Couette flows at Reynolds numbers up to O(105). This enables to probe hydrodynamic turbulence in Keplerian flows in experimentally relevant regimes.","lang":"eng"}],"month":"01","volume":106,"external_id":{"arxiv":["1311.2481"],"isi":["000346213200001"]},"publication_status":"published","author":[{"first_name":"Liang","last_name":"Shi","full_name":"Shi, Liang","id":"374A3F1A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Markus","last_name":"Rampp","full_name":"Rampp, Markus"},{"last_name":"Hof","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"},{"last_name":"Avila","first_name":"Marc","full_name":"Avila, Marc"}]}]