[{"external_id":{"pmid":["30936248"],"isi":["000470086100045"]},"day":"01","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"11626"},{"status":"public","id":"8822","relation":"dissertation_contains"}]},"publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"article_type":"original","acknowledgement":"We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis work was supported by the Ministry of Education, Culture, Sports, Science, and Technology (Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.), and the European Union’s Horizon2020 program (European Research Council grant agreement no. 742985 to J.F.).","title":"Pinstatic acid promotes auxin transport by inhibiting PIN internalization","date_updated":"2026-09-02T22:30:55Z","author":[{"full_name":"Oochi, A","first_name":"A","last_name":"Oochi"},{"first_name":"Jakub","orcid":"0000-0003-2140-7195","last_name":"Hajny","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","full_name":"Hajny, Jakub"},{"last_name":"Fukui","first_name":"K","full_name":"Fukui, K"},{"last_name":"Nakao","first_name":"Y","full_name":"Nakao, Y"},{"first_name":"Michelle C","last_name":"Gallei","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C","id":"35A03822-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Quareshy, M","first_name":"M","last_name":"Quareshy"},{"last_name":"Takahashi","first_name":"K","full_name":"Takahashi, K"},{"first_name":"T","last_name":"Kinoshita","full_name":"Kinoshita, T"},{"full_name":"Harborough, SR","last_name":"Harborough","first_name":"SR"},{"first_name":"S","last_name":"Kepinski","full_name":"Kepinski, S"},{"last_name":"Kasahara","first_name":"H","full_name":"Kasahara, H"},{"full_name":"Napier, RM","last_name":"Napier","first_name":"RM"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","orcid":"0000-0002-8302-7596"},{"first_name":"KI","last_name":"Hayashi","full_name":"Hayashi, KI"}],"doi":"10.1104/pp.19.00201","citation":{"ista":"Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 180(2), 1152–1165.","ama":"Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. <i>Plant Physiology</i>. 2019;180(2):1152-1165. doi:<a href=\"https://doi.org/10.1104/pp.19.00201\">10.1104/pp.19.00201</a>","apa":"Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., … Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN internalization. <i>Plant Physiology</i>. ASPB. <a href=\"https://doi.org/10.1104/pp.19.00201\">https://doi.org/10.1104/pp.19.00201</a>","mla":"Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” <i>Plant Physiology</i>, vol. 180, no. 2, ASPB, 2019, pp. 1152–65, doi:<a href=\"https://doi.org/10.1104/pp.19.00201\">10.1104/pp.19.00201</a>.","ieee":"A. Oochi <i>et al.</i>, “Pinstatic acid promotes auxin transport by inhibiting PIN internalization,” <i>Plant Physiology</i>, vol. 180, no. 2. ASPB, pp. 1152–1165, 2019.","short":"A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi, T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K. Hayashi, Plant Physiology 180 (2019) 1152–1165.","chicago":"Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy, K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” <i>Plant Physiology</i>. ASPB, 2019. <a href=\"https://doi.org/10.1104/pp.19.00201\">https://doi.org/10.1104/pp.19.00201</a>."},"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"}],"volume":180,"scopus_import":"1","department":[{"_id":"JiFr"}],"quality_controlled":"1","oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1104/pp.19.00201","open_access":"1"}],"_id":"6260","oa":1,"isi":1,"ec_funded":1,"type":"journal_article","page":"1152-1165","date_published":"2019-06-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","article_processing_charge":"No","year":"2019","intvolume":"       180","language":[{"iso":"eng"}],"publisher":"ASPB","pmid":1,"abstract":[{"lang":"eng","text":"Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport."}],"date_created":"2019-04-09T08:38:20Z","ddc":["580"],"status":"public","publication":"Plant Physiology","month":"06","issue":"2"},{"status":"public","month":"10","publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications ","ddc":["000"],"publisher":"ACM","abstract":[{"lang":"eng","text":"In this work, we consider the almost-sure termination problem for probabilistic programs that asks whether a\r\ngiven probabilistic program terminates with probability 1. Scalable approaches for program analysis often\r\nrely on modularity as their theoretical basis. In non-probabilistic programs, the classical variant rule (V-rule)\r\nof Floyd-Hoare logic provides the foundation for modular analysis. Extension of this rule to almost-sure\r\ntermination of probabilistic programs is quite tricky, and a probabilistic variant was proposed in [16]. While the\r\nproposed probabilistic variant cautiously addresses the key issue of integrability, we show that the proposed\r\nmodular rule is still not sound for almost-sure termination of probabilistic programs.\r\nBesides establishing unsoundness of the previous rule, our contributions are as follows: First, we present a\r\nsound modular rule for almost-sure termination of probabilistic programs. Our approach is based on a novel\r\nnotion of descent supermartingales. Second, for algorithmic approaches, we consider descent supermartingales\r\nthat are linear and show that they can be synthesized in polynomial time. Finally, we present experimental\r\nresults on a variety of benchmarks and several natural examples that model various types of nested while\r\nloops in probabilistic programs and demonstrate that our approach is able to efficiently prove their almost-sure\r\ntermination property"}],"date_created":"2019-08-09T09:54:20Z","has_accepted_license":"1","intvolume":"         3","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:40Z","file_id":"6807","file_size":1024643,"access_level":"open_access","content_type":"application/pdf","date_created":"2019-08-12T15:40:57Z","relation":"main_file","creator":"akafshda","checksum":"3482d8ace6fb4991eb7810e3b70f1b9f","file_name":"oopsla-2019.pdf"},{"file_id":"7821","date_updated":"2020-07-14T12:47:40Z","date_created":"2020-05-12T15:15:14Z","relation":"main_file","checksum":"4e5a6fb2b59a75222a4e8335a5a60eac","file_name":"2019_ACM_Huang.pdf","creator":"dernst","file_size":538579,"access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","year":"2019","article_processing_charge":"No","article_number":"129","date_published":"2019-10-01T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"type":"conference","ec_funded":1,"oa_version":"Published Version","quality_controlled":"1","_id":"6780","volume":3,"scopus_import":"1","department":[{"_id":"KrCh"}],"doi":"10.1145/3360555","tmp":{"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)","short":"CC BY-NC (4.0)"},"citation":{"chicago":"Huang, Mingzhang, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>, Vol. 3. ACM, 2019. <a href=\"https://doi.org/10.1145/3360555\">https://doi.org/10.1145/3360555</a>.","short":"M. Huang, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , ACM, 2019.","mla":"Huang, Mingzhang, et al. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>, vol. 3, 129, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3360555\">10.1145/3360555</a>.","ieee":"M. Huang, H. Fu, K. Chatterjee, and A. K. Goharshady, “Modular verification for almost-sure termination of probabilistic programs,” in <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>, Athens, Greece, 2019, vol. 3.","ista":"Huang M, Fu H, Chatterjee K, Goharshady AK. 2019. Modular verification for almost-sure termination of probabilistic programs. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications . OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 129.","apa":"Huang, M., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2019). Modular verification for almost-sure termination of probabilistic programs. In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i> (Vol. 3). Athens, Greece: ACM. <a href=\"https://doi.org/10.1145/3360555\">https://doi.org/10.1145/3360555</a>","ama":"Huang M, Fu H, Chatterjee K, Goharshady AK. Modular verification for almost-sure termination of probabilistic programs. In: <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>. Vol 3. ACM; 2019. doi:<a href=\"https://doi.org/10.1145/3360555\">10.1145/3360555</a>"},"project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Huang","first_name":"Mingzhang","full_name":"Huang, Mingzhang"},{"full_name":"Fu, Hongfei","last_name":"Fu","first_name":"Hongfei"},{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","first_name":"Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584"}],"title":"Modular verification for almost-sure termination of probabilistic programs","date_updated":"2026-09-02T22:30:57Z","arxiv":1,"day":"01","file_date_updated":"2020-07-14T12:47:40Z","related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"external_id":{"arxiv":["1901.06087"]},"conference":{"end_date":"2019-10-25","location":"Athens, Greece","name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications","start_date":"2019-10-23"},"license":"https://creativecommons.org/licenses/by-nc/4.0/"},{"pubrep_id":"1070","oa_version":"Submitted Version","quality_controlled":"1","_id":"6490","volume":"Part F147772","department":[{"_id":"KrCh"}],"scopus_import":"1","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “The Treewidth of Smart Contracts.” In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Part F147772:400–408. ACM, 2019. <a href=\"https://doi.org/10.1145/3297280.3297322\">https://doi.org/10.1145/3297280.3297322</a>.","short":"K. Chatterjee, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 400–408.","mla":"Chatterjee, Krishnendu, et al. “The Treewidth of Smart Contracts.” <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, vol. Part F147772, ACM, 2019, pp. 400–08, doi:<a href=\"https://doi.org/10.1145/3297280.3297322\">10.1145/3297280.3297322</a>.","ieee":"K. Chatterjee, A. K. Goharshady, and E. K. Goharshady, “The treewidth of smart contracts,” in <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Limassol, Cyprus, 2019, vol. Part F147772, pp. 400–408.","apa":"Chatterjee, K., Goharshady, A. K., &#38; Goharshady, E. K. (2019). The treewidth of smart contracts. In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i> (Vol. Part F147772, pp. 400–408). Limassol, Cyprus: ACM. <a href=\"https://doi.org/10.1145/3297280.3297322\">https://doi.org/10.1145/3297280.3297322</a>","ama":"Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts. In: <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>. Vol Part F147772. ACM; 2019:400-408. doi:<a href=\"https://doi.org/10.1145/3297280.3297322\">10.1145/3297280.3297322</a>","ista":"Chatterjee K, Goharshady AK, Goharshady EK. 2019. The treewidth of smart contracts. Proceedings of the 34th ACM Symposium on Applied Computing. SAC: Symposium on Applied Computing vol. Part F147772, 400–408."},"doi":"10.1145/3297280.3297322","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar"},{"full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady","first_name":"Ehsan Kafshdar"}],"date_updated":"2026-09-02T22:30:57Z","title":"The treewidth of smart contracts","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"publication_identifier":{"isbn":["9781450359337"]},"file_date_updated":"2020-07-14T12:47:32Z","day":"01","external_id":{"isi":["000474685800052"]},"conference":{"name":"SAC: Symposium on Applied Computing","location":"Limassol, Cyprus","start_date":"2019-04-08","end_date":"2019-04-12"},"ddc":["000"],"publication":"Proceedings of the 34th ACM Symposium on Applied Computing","status":"public","month":"04","corr_author":"1","publisher":"ACM","has_accepted_license":"1","date_created":"2019-05-26T21:59:15Z","abstract":[{"lang":"eng","text":"Smart contracts are programs that are stored and executed on the Blockchain and can receive, manage and transfer money (cryptocurrency units). Two important problems regarding smart contracts are formal analysis and compiler optimization. Formal analysis is extremely important, because smart contracts hold funds worth billions of dollars and their code is immutable after deployment. Hence, an undetected bug can cause significant financial losses. Compiler optimization is also crucial, because every action of a smart contract has to be executed by every node in the Blockchain network. Therefore, optimizations in compiling smart contracts can lead to significant savings in computation, time and energy.\r\n\r\nTwo classical approaches in program analysis and compiler optimization are intraprocedural and interprocedural analysis. In intraprocedural analysis, each function is analyzed separately, while interprocedural analysis considers the entire program. In both cases, the analyses are usually reduced to graph problems over the control flow graph (CFG) of the program. These graph problems are often computationally expensive. Hence, there has been ample research on exploiting structural properties of CFGs for efficient algorithms. One such well-studied property is the treewidth, which is a measure of tree-likeness of graphs. It is known that intraprocedural CFGs of structured programs have treewidth at most 6, whereas the interprocedural treewidth cannot be bounded. This result has been used as a basis for many efficient intraprocedural analyses.\r\n\r\nIn this paper, we explore the idea of exploiting the treewidth of smart contracts for formal analysis and compiler optimization. First, similar to classical programs, we show that the intraprocedural treewidth of structured Solidity and Vyper smart contracts is at most 9. Second, for global analysis, we prove that the interprocedural treewidth of structured smart contracts is bounded by 10 and, in sharp contrast with classical programs, treewidth-based algorithms can be easily applied for interprocedural analysis. Finally, we supplement our theoretical results with experiments using a tool we implemented for computing treewidth of smart contracts and show that the treewidth is much lower in practice. We use 36,764 real-world Ethereum smart contracts as benchmarks and find that they have an average treewidth of at most 3.35 for the intraprocedural case and 3.65 for the interprocedural case.\r\n"}],"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:47:32Z","file_id":"7827","file_size":6937138,"access_level":"open_access","content_type":"application/pdf","date_created":"2020-05-14T09:50:11Z","relation":"main_file","checksum":"dddc20f6d9881f23b8755eb720ec9d6f","file_name":"2019_ACM_Chatterjee.pdf","creator":"dernst"}],"article_processing_charge":"No","year":"2019","publication_status":"published","date_published":"2019-04-01T00:00:00Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"400-408","oa":1,"isi":1,"type":"conference"},{"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23","call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"doi":"10.1145/3363525","citation":{"short":"K. Chatterjee, A.K. Goharshady, P. Goyal, R. Ibsen-Jensen, A. Pavlogiannis, ACM Transactions on Programming Languages and Systems 41 (2019).","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Prateesh Goyal, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” <i>ACM Transactions on Programming Languages and Systems</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3363525\">https://doi.org/10.1145/3363525</a>.","ista":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. 2019. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. ACM Transactions on Programming Languages and Systems. 41(4), 23.","ama":"Chatterjee K, Goharshady AK, Goyal P, Ibsen-Jensen R, Pavlogiannis A. Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. <i>ACM Transactions on Programming Languages and Systems</i>. 2019;41(4). doi:<a href=\"https://doi.org/10.1145/3363525\">10.1145/3363525</a>","apa":"Chatterjee, K., Goharshady, A. K., Goyal, P., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2019). Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth. <i>ACM Transactions on Programming Languages and Systems</i>. ACM. <a href=\"https://doi.org/10.1145/3363525\">https://doi.org/10.1145/3363525</a>","ieee":"K. Chatterjee, A. K. Goharshady, P. Goyal, R. Ibsen-Jensen, and A. Pavlogiannis, “Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth,” <i>ACM Transactions on Programming Languages and Systems</i>, vol. 41, no. 4. ACM, 2019.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithms for Dynamic Algebraic Queries in Basic RSMs with Constant Treewidth.” <i>ACM Transactions on Programming Languages and Systems</i>, vol. 41, no. 4, 23, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3363525\">10.1145/3363525</a>."},"scopus_import":"1","department":[{"_id":"KrCh"}],"volume":41,"_id":"7158","quality_controlled":"1","oa_version":"Submitted Version","external_id":{"isi":["000564108400004"]},"file_date_updated":"2020-10-08T12:58:10Z","article_type":"original","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"publication_identifier":{"issn":["0164-0925"]},"day":"01","date_updated":"2026-09-02T22:30:57Z","title":"Faster algorithms for dynamic algebraic queries in basic RSMs with constant treewidth","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar"},{"first_name":"Prateesh","last_name":"Goyal","full_name":"Goyal, Prateesh"},{"full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87","first_name":"Rasmus","last_name":"Ibsen-Jensen","orcid":"0000-0003-4783-0389"},{"first_name":"Andreas","orcid":"0000-0002-8943-0722","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"}],"language":[{"iso":"eng"}],"intvolume":"        41","has_accepted_license":"1","abstract":[{"text":"Interprocedural analysis is at the heart of numerous applications in programming languages, such as alias analysis, constant propagation, and so on. Recursive state machines (RSMs) are standard models for interprocedural analysis. We consider a general framework with RSMs where the transitions are labeled from a semiring and path properties are algebraic with semiring operations. RSMs with algebraic path properties can model interprocedural dataflow analysis problems, the shortest path problem, the most probable path problem, and so on. The traditional algorithms for interprocedural analysis focus on path properties where the starting point is fixed as the entry point of a specific method. In this work, we consider possible multiple queries as required in many applications such as in alias analysis. The study of multiple queries allows us to bring in an important algorithmic distinction between the resource usage of the one-time preprocessing vs for each individual query. The second aspect we consider is that the control flow graphs for most programs have constant treewidth.\r\n\r\nOur main contributions are simple and implementable algorithms that support multiple queries for algebraic path properties for RSMs that have constant treewidth. Our theoretical results show that our algorithms have small additional one-time preprocessing but can answer subsequent queries significantly faster as compared to the current algorithmic solutions for interprocedural dataflow analysis. We have also implemented our algorithms and evaluated their performance for performing on-demand interprocedural dataflow analysis on various domains, such as for live variable analysis and reaching definitions, on a standard benchmark set. Our experimental results align with our theoretical statements and show that after a lightweight preprocessing, on-demand queries are answered much faster than the standard existing algorithmic approaches.\r\n","lang":"eng"}],"date_created":"2019-12-09T08:33:33Z","publisher":"ACM","publication":"ACM Transactions on Programming Languages and Systems","ddc":["000"],"month":"11","status":"public","issue":"4","ec_funded":1,"type":"journal_article","isi":1,"oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"23","date_published":"2019-11-01T00:00:00Z","article_processing_charge":"No","year":"2019","publication_status":"published","file":[{"date_created":"2020-10-08T12:58:10Z","relation":"main_file","creator":"dernst","checksum":"291cc86a07bd010d4815e177dac57b70","file_name":"2019_ACMTransactions_Chatterjee.pdf","file_size":667357,"access_level":"open_access","content_type":"application/pdf","file_id":"8632","success":1,"date_updated":"2020-10-08T12:58:10Z"}]},{"publication":"Proceedings of the 34th ACM Symposium on Applied Computing","month":"04","status":"public","ddc":["004"],"language":[{"iso":"eng"}],"publisher":"ACM","abstract":[{"lang":"eng","text":"In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin."}],"date_created":"2019-05-06T12:11:36Z","has_accepted_license":"1","date_published":"2019-04-01T00:00:00Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"6379","date_updated":"2020-07-14T12:47:29Z","relation":"main_file","date_created":"2019-05-06T12:09:27Z","file_name":"2019_ACM_Chatterjee.pdf","creator":"dernst","checksum":"fbfbcd5a0c7a743862bfc3045539a614","file_size":1023934,"content_type":"application/pdf","access_level":"open_access"}],"publication_status":"published","year":"2019","article_processing_charge":"No","oa":1,"isi":1,"type":"conference","ec_funded":1,"page":"374-381","oa_version":"Submitted Version","quality_controlled":"1","_id":"6378","pubrep_id":"1069","citation":{"chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Part F147772:374–81. ACM, 2019. <a href=\"https://doi.org/10.1145/3297280.3297319\">https://doi.org/10.1145/3297280.3297319</a>.","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381.","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving,” in <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Limassol, Cyprus, 2019, vol. Part F147772, pp. 374–381.","mla":"Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, vol. Part F147772, ACM, 2019, pp. 374–81, doi:<a href=\"https://doi.org/10.1145/3297280.3297319\">10.1145/3297280.3297319</a>.","ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In: <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>. Vol Part F147772. ACM; 2019:374-381. doi:<a href=\"https://doi.org/10.1145/3297280.3297319\">10.1145/3297280.3297319</a>","apa":"Chatterjee, K., Goharshady, A. K., &#38; Pourdamghani, A. (2019). Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i> (Vol. Part F147772, pp. 374–381). Limassol, Cyprus: ACM. <a href=\"https://doi.org/10.1145/3297280.3297319\">https://doi.org/10.1145/3297280.3297319</a>","ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. Proceedings of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing vol. Part F147772, 374–381."},"doi":"10.1145/3297280.3297319","project":[{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"volume":"Part F147772","department":[{"_id":"KrCh"}],"scopus_import":"1","title":"Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving","date_updated":"2026-09-02T22:30:58Z","author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar"},{"first_name":"Arash","last_name":"Pourdamghani","full_name":"Pourdamghani, Arash"}],"external_id":{"isi":["000474685800049"]},"conference":{"end_date":"2019-04-12","start_date":"2019-04-08","location":"Limassol, Cyprus","name":"ACM Symposium on Applied Computing"},"day":"01","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"publication_identifier":{"isbn":["9781450359337"]},"file_date_updated":"2020-07-14T12:47:29Z"},{"language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs,\r\nwhich aims at automated methods for analyzing the resource-usage of such programs.\r\nPrevious approaches for this problem could only handle nonnegative bounded costs.\r\nHowever, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols,\r\nboth positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the\r\nexpected accumulated cost of nondeterministic probabilistic programs.\r\nOur approach can handle (a) general positive and negative costs with bounded updates in\r\nvariables; and (b) nonnegative costs with general updates to variables.\r\nWe show that several natural examples which could not be\r\nhandled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no\r\nprevious approach for cost analysis of probabilistic programs could guarantee polynomial runtime.\r\nFinally, we show the effectiveness of our approach using experimental results on a variety of programs for which we efficiently synthesize tight resource-usage bounds."}],"date_created":"2019-03-25T10:13:25Z","has_accepted_license":"1","publisher":"Association for Computing Machinery","month":"06","status":"public","publication":"PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation","ddc":["000"],"ec_funded":1,"isi":1,"type":"conference","oa":1,"page":"204-220","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-06-08T00:00:00Z","year":"2019","keyword":["Program Cost Analysis","Program Termination","Probabilistic Programs","Martingales"],"article_processing_charge":"No","publication_status":"published","file":[{"date_updated":"2020-07-14T12:47:20Z","file_id":"6176","content_type":"application/pdf","access_level":"open_access","file_size":4051066,"checksum":"703a5e9b8c8587f2a44085ffd9a4db64","file_name":"paper.pdf","creator":"akafshda","relation":"main_file","date_created":"2019-03-25T10:11:22Z"}],"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"doi":"10.1145/3314221.3314581","citation":{"apa":"Wang, P., Fu, H., Goharshady, A. K., Chatterjee, K., Qin, X., &#38; Shi, W. (2019). Cost analysis of nondeterministic probabilistic programs. In <i>PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation</i> (pp. 204–220). Phoenix, AZ, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3314221.3314581\">https://doi.org/10.1145/3314221.3314581</a>","ama":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. Cost analysis of nondeterministic probabilistic programs. In: <i>PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>. Association for Computing Machinery; 2019:204-220. doi:<a href=\"https://doi.org/10.1145/3314221.3314581\">10.1145/3314221.3314581</a>","ista":"Wang P, Fu H, Goharshady AK, Chatterjee K, Qin X, Shi W. 2019. Cost analysis of nondeterministic probabilistic programs. PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation. PLDI: Conference on Programming Language Design and Implementation, 204–220.","mla":"Wang, Peixin, et al. “Cost Analysis of Nondeterministic Probabilistic Programs.” <i>PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, Association for Computing Machinery, 2019, pp. 204–20, doi:<a href=\"https://doi.org/10.1145/3314221.3314581\">10.1145/3314221.3314581</a>.","ieee":"P. Wang, H. Fu, A. K. Goharshady, K. Chatterjee, X. Qin, and W. Shi, “Cost analysis of nondeterministic probabilistic programs,” in <i>PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, Phoenix, AZ, United States, 2019, pp. 204–220.","short":"P. Wang, H. Fu, A.K. Goharshady, K. Chatterjee, X. Qin, W. Shi, in:, PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation, Association for Computing Machinery, 2019, pp. 204–220.","chicago":"Wang, Peixin, Hongfei Fu, Amir Kafshdar Goharshady, Krishnendu Chatterjee, Xudong Qin, and Wenjun Shi. “Cost Analysis of Nondeterministic Probabilistic Programs.” In <i>PLDI 2019: Proceedings of the 40th ACM SIGPLAN Conference on Programming Language Design and Implementation</i>, 204–20. Association for Computing Machinery, 2019. <a href=\"https://doi.org/10.1145/3314221.3314581\">https://doi.org/10.1145/3314221.3314581</a>."},"scopus_import":"1","department":[{"_id":"KrCh"}],"_id":"6175","quality_controlled":"1","oa_version":"Submitted Version","conference":{"name":"PLDI: Conference on Programming Language Design and Implementation","location":"Phoenix, AZ, United States","start_date":"2019-06-22","end_date":"2019-06-26"},"external_id":{"arxiv":["1902.04659"],"isi":["000523190300014"]},"file_date_updated":"2020-07-14T12:47:20Z","related_material":{"record":[{"status":"public","relation":"earlier_version","id":"5457"},{"id":"8934","relation":"dissertation_contains","status":"public"}]},"day":"08","arxiv":1,"date_updated":"2026-09-02T22:30:58Z","title":"Cost analysis of nondeterministic probabilistic programs","author":[{"last_name":"Wang","first_name":"Peixin","full_name":"Wang, Peixin"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei","id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar"},{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Qin, Xudong","first_name":"Xudong","last_name":"Qin"},{"full_name":"Shi, Wenjun","first_name":"Wenjun","last_name":"Shi"}]},{"doi":"10.1145/3339984","citation":{"mla":"Chatterjee, Krishnendu, et al. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” <i>ACM Transactions on Programming Languages and Systems</i>, vol. 41, no. 4, 20, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3339984\">10.1145/3339984</a>.","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst-case analysis of recursive programs,” <i>ACM Transactions on Programming Languages and Systems</i>, vol. 41, no. 4. ACM, 2019.","ista":"Chatterjee K, Fu H, Goharshady AK. 2019. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 41(4), 20.","apa":"Chatterjee, K., Fu, H., &#38; Goharshady, A. K. (2019). Non-polynomial worst-case analysis of recursive programs. <i>ACM Transactions on Programming Languages and Systems</i>. ACM. <a href=\"https://doi.org/10.1145/3339984\">https://doi.org/10.1145/3339984</a>","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst-case analysis of recursive programs. <i>ACM Transactions on Programming Languages and Systems</i>. 2019;41(4). doi:<a href=\"https://doi.org/10.1145/3339984\">10.1145/3339984</a>","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” <i>ACM Transactions on Programming Languages and Systems</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3339984\">https://doi.org/10.1145/3339984</a>.","short":"K. Chatterjee, H. Fu, A.K. Goharshady, ACM Transactions on Programming Languages and Systems 41 (2019)."},"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"volume":41,"department":[{"_id":"KrCh"}],"scopus_import":"1","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00317"}],"_id":"7014","external_id":{"isi":["000564108400001"],"arxiv":["1705.00317"]},"arxiv":1,"day":"01","related_material":{"record":[{"id":"639","relation":"earlier_version","status":"public"},{"relation":"dissertation_contains","id":"8934","status":"public"}]},"article_type":"original","title":"Non-polynomial worst-case analysis of recursive programs","date_updated":"2026-09-02T22:30:58Z","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee"},{"last_name":"Fu","first_name":"Hongfei","full_name":"Fu, Hongfei"},{"last_name":"Goharshady","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","full_name":"Goharshady, Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"}],"intvolume":"        41","language":[{"iso":"eng"}],"publisher":"ACM","date_created":"2019-11-13T08:33:43Z","abstract":[{"text":"We study the problem of developing efficient approaches for proving\r\nworst-case bounds of non-deterministic recursive programs. Ranking functions\r\nare sound and complete for proving termination and worst-case bounds of\r\nnonrecursive programs. First, we apply ranking functions to recursion,\r\nresulting in measure functions. We show that measure functions provide a sound\r\nand complete approach to prove worst-case bounds of non-deterministic recursive\r\nprograms. Our second contribution is the synthesis of measure functions in\r\nnonpolynomial forms. We show that non-polynomial measure functions with\r\nlogarithm and exponentiation can be synthesized through abstraction of\r\nlogarithmic or exponentiation terms, Farkas' Lemma, and Handelman's Theorem\r\nusing linear programming. While previous methods obtain worst-case polynomial\r\nbounds, our approach can synthesize bounds of the form $\\mathcal{O}(n\\log n)$\r\nas well as $\\mathcal{O}(n^r)$ where $r$ is not an integer. We present\r\nexperimental results to demonstrate that our approach can obtain efficiently\r\nworst-case bounds of classical recursive algorithms such as (i) Merge-Sort, the\r\ndivide-and-conquer algorithm for the Closest-Pair problem, where we obtain\r\n$\\mathcal{O}(n \\log n)$ worst-case bound, and (ii) Karatsuba's algorithm for\r\npolynomial multiplication and Strassen's algorithm for matrix multiplication,\r\nwhere we obtain $\\mathcal{O}(n^r)$ bound such that $r$ is not an integer and\r\nclose to the best-known bounds for the respective algorithms.","lang":"eng"}],"month":"10","publication":"ACM Transactions on Programming Languages and Systems","status":"public","issue":"4","oa":1,"ec_funded":1,"isi":1,"type":"journal_article","date_published":"2019-10-01T00:00:00Z","article_number":"20","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publication_status":"published","article_processing_charge":"No","year":"2019"},{"title":"Efficient parameterized algorithms for data packing","date_updated":"2026-09-02T22:30:58Z","author":[{"full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","orcid":"0000-0002-4561-241X"},{"first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar"},{"last_name":"Okati","first_name":"Nastaran","full_name":"Okati, Nastaran"},{"first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","id":"49704004-F248-11E8-B48F-1D18A9856A87"}],"OA_place":"publisher","day":"01","related_material":{"record":[{"status":"public","id":"8934","relation":"dissertation_contains"}]},"file_date_updated":"2020-07-14T12:47:29Z","publication_identifier":{"issn":["2475-1421"]},"article_type":"original","acknowledgement":"The research was partially supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), ERC\r\nStarting Grant (279307: Graph Games), and the IBM PhD Fellowship program.","oa_version":"Published Version","quality_controlled":"1","_id":"6380","pubrep_id":"1056","doi":"10.1145/3290366","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"citation":{"ista":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. 3(POPL), 53.","ama":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized algorithms for data packing. <i>Proceedings of the ACM on Programming Languages</i>. 2019;3(POPL). doi:<a href=\"https://doi.org/10.1145/3290366\">10.1145/3290366</a>","apa":"Chatterjee, K., Goharshady, A. K., Okati, N., &#38; Pavlogiannis, A. (2019). Efficient parameterized algorithms for data packing. <i>Proceedings of the ACM on Programming Languages</i>. ACM. <a href=\"https://doi.org/10.1145/3290366\">https://doi.org/10.1145/3290366</a>","mla":"Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data Packing.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 3, no. POPL, 53, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3290366\">10.1145/3290366</a>.","ieee":"K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient parameterized algorithms for data packing,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 3, no. POPL. ACM, 2019.","short":"K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 3 (2019).","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” <i>Proceedings of the ACM on Programming Languages</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3290366\">https://doi.org/10.1145/3290366</a>."},"project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"}],"volume":3,"department":[{"_id":"KrCh"}],"scopus_import":"1","date_published":"2019-01-01T00:00:00Z","article_number":"53","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"date_created":"2019-05-06T12:23:11Z","relation":"main_file","checksum":"c157752f96877b36685ad7063ada4524","file_name":"2019_ACM_POPL_Chatterjee.pdf","creator":"dernst","file_size":1294962,"access_level":"open_access","content_type":"application/pdf","file_id":"6381","date_updated":"2020-07-14T12:47:29Z"}],"publication_status":"published","year":"2019","article_processing_charge":"Yes (in subscription journal)","oa":1,"type":"journal_article","ec_funded":1,"month":"01","status":"public","publication":"Proceedings of the ACM on Programming Languages","ddc":["004"],"issue":"POPL","intvolume":"         3","language":[{"iso":"eng"}],"OA_type":"hybrid","publisher":"ACM","has_accepted_license":"1","date_created":"2019-05-06T12:18:17Z","abstract":[{"lang":"eng","text":"There is a huge gap between the speeds of modern caches and main memories, and therefore cache misses account for a considerable loss of efficiency in programs. The predominant technique to address this issue has been Data Packing: data elements that are frequently accessed within time proximity are packed into the same cache block, thereby minimizing accesses to the main memory. We consider the algorithmic problem of Data Packing on a two-level memory system. Given a reference sequence R of accesses to data elements, the task is to partition the elements into cache blocks such that the number of cache misses on R is minimized. The problem is notoriously difficult: it is NP-hard even when the cache has size 1, and is hard to approximate for any cache size larger than 4. Therefore, all existing techniques for Data Packing are based on heuristics and lack theoretical guarantees. In this work, we present the first positive theoretical results for Data Packing, along with new and stronger negative results. We consider the problem under the lens of the underlying access hypergraphs, which are hypergraphs of affinities between the data elements, where the order of an access hypergraph corresponds to the size of the affinity group. We study the problem parameterized by the treewidth of access hypergraphs, which is a standard notion in graph theory to measure the closeness of a graph to a tree. Our main results are as follows: We show there is a number q* depending on the cache parameters such that (a) if the access hypergraph of order q* has constant treewidth, then there is a linear-time algorithm for Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy depending on a single parameter, namely, the highest order among access hypegraphs that have constant treewidth; and establish the optimal value q* of this parameter. Finally, we present an experimental evaluation of a prototype implementation of our algorithm. Our results demonstrate that, in practice, access hypergraphs of many commonly-used algorithms have small treewidth. We compare our approach with several state-of-the-art heuristic-based algorithms and show that our algorithm leads to significantly fewer cache-misses. "}]},{"department":[{"_id":"KrCh"}],"scopus_import":"1","project":[{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"}],"doi":"10.1109/BLOC.2019.8751326","citation":{"ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Probabilistic smart contracts: Secure randomness on the blockchain. In: <i>IEEE International Conference on Blockchain and Cryptocurrency</i>. IEEE; 2019. doi:<a href=\"https://doi.org/10.1109/BLOC.2019.8751326\">10.1109/BLOC.2019.8751326</a>","ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Probabilistic smart contracts: Secure randomness on the blockchain. IEEE International Conference on Blockchain and Cryptocurrency. IEEE International Conference on Blockchain and Cryptocurrency, 8751326.","apa":"Chatterjee, K., Goharshady, A. K., &#38; Pourdamghani, A. (2019). Probabilistic smart contracts: Secure randomness on the blockchain. In <i>IEEE International Conference on Blockchain and Cryptocurrency</i>. Seoul, Korea: IEEE. <a href=\"https://doi.org/10.1109/BLOC.2019.8751326\">https://doi.org/10.1109/BLOC.2019.8751326</a>","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Probabilistic smart contracts: Secure randomness on the blockchain,” in <i>IEEE International Conference on Blockchain and Cryptocurrency</i>, Seoul, Korea, 2019.","mla":"Chatterjee, Krishnendu, et al. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” <i>IEEE International Conference on Blockchain and Cryptocurrency</i>, 8751326, IEEE, 2019, doi:<a href=\"https://doi.org/10.1109/BLOC.2019.8751326\">10.1109/BLOC.2019.8751326</a>.","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, IEEE International Conference on Blockchain and Cryptocurrency, IEEE, 2019.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Probabilistic Smart Contracts: Secure Randomness on the Blockchain.” In <i>IEEE International Conference on Blockchain and Cryptocurrency</i>. IEEE, 2019. <a href=\"https://doi.org/10.1109/BLOC.2019.8751326\">https://doi.org/10.1109/BLOC.2019.8751326</a>."},"_id":"6056","oa_version":"Preprint","quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/1902.07986","open_access":"1"}],"day":"01","related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"arxiv":1,"conference":{"start_date":"2019-05-14","name":"IEEE International Conference on Blockchain and Cryptocurrency","location":"Seoul, Korea","end_date":"2019-05-17"},"external_id":{"isi":["000491257000076"],"arxiv":["1902.07986"]},"author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","last_name":"Goharshady","first_name":"Amir Kafshdar"},{"first_name":"Arash","last_name":"Pourdamghani","full_name":"Pourdamghani, Arash"}],"title":"Probabilistic smart contracts: Secure randomness on the blockchain","date_updated":"2026-09-02T22:30:58Z","date_created":"2019-02-26T09:03:15Z","abstract":[{"lang":"eng","text":"In today's programmable blockchains, smart contracts are limited to being deterministic and non-probabilistic. This lack of randomness is a consequential limitation, given that a wide variety of real-world financial contracts, such as casino games and lotteries, depend entirely on randomness. As a result, several ad-hoc random number generation approaches have been developed to be used in smart contracts. These include ideas such as using an oracle or relying on the block hash. However, these approaches are manipulatable, i.e. their output can be tampered with by parties who might not be neutral, such as the owner of the oracle or the miners.We propose a novel game-theoretic approach for generating provably unmanipulatable pseudorandom numbers on the blockchain. Our approach allows smart contracts to access a trustworthy source of randomness that does not rely on potentially compromised miners or oracles, hence enabling the creation of a new generation of smart contracts that are not limited to being non-probabilistic and can be drawn from the much more general class of probabilistic programs."}],"publisher":"IEEE","language":[{"iso":"eng"}],"status":"public","month":"05","publication":"IEEE International Conference on Blockchain and Cryptocurrency","ec_funded":1,"type":"conference","isi":1,"oa":1,"publication_status":"published","article_processing_charge":"No","year":"2019","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","article_number":"8751326","date_published":"2019-05-01T00:00:00Z"},{"type":"dissertation","oa":1,"page":"142","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2019-10-09T00:00:00Z","year":"2019","article_processing_charge":"No","publication_status":"published","file":[{"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_size":214172667,"file_name":"PhDthesis_FrankAssen_revised2.docx","checksum":"53a739752a500f84d0f8ec953cbbd0b6","creator":"fassen","relation":"source_file","date_created":"2019-11-06T12:30:02Z","date_updated":"2020-11-07T23:30:03Z","embargo_to":"open_access","file_id":"6990"},{"embargo":"2020-11-06","file_id":"6991","date_updated":"2020-11-07T23:30:03Z","date_created":"2019-11-06T12:30:57Z","relation":"main_file","file_name":"PhDthesis_FrankAssen_revised2.pdf","creator":"fassen","checksum":"8c156b65d9347bb599623a4b09f15d15","file_size":83637532,"access_level":"open_access","content_type":"application/pdf"}],"supervisor":[{"first_name":"Michael K","last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"date_created":"2019-10-14T16:54:52Z","abstract":[{"text":"Lymph nodes  are es s ential organs  of the immune  s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular  cells (FRCs) are  the  main  stromal  cells and  form  a sponge-like extracellular matrix network,   called  conduits ,  which  they   thems elves   enwrap   and  contract.  Lymph,  containing  s oluble  antigens ,  arrive in  lymph  nodes  via afferent lymphatic  vessels that  connect  to  the  s ubcaps ular  s inus   and  conduit  network.  According  to  the  current  paradigm,  the  conduit  network   dis tributes   afferent  lymph  through   lymph  nodes   and  thus   provides   acces s   for  immune  cells to lymph-borne  antigens. An  elas tic  caps ule  s urrounds   the  organ  and  confines   the immune  cells and  FRC  network.   Lymph   nodes   are  completely  packed  with  lymphocytes   and  lymphocyte  numbers  directly  dictates  the size  of  the  organ.  Although  lymphocytes   cons tantly  enter  and  leave  the  lymph  node,  its   s ize  remains   remarkedly   s table  under  homeostatic conditions. It is only partly known  how the cellularity and s ize of the lymph node is regulated and  how  the  lymph  node  is able to swell in inflammation.  The role of the FRC network   in  lymph  node   s welling  and  trans fer  of  fluids   are  inves tigated in  this   thes is.  Furthermore,   we  s tudied  what  trafficking  routes   are  us ed  by  cancer  cells   in  lymph  nodes   to  form  distal metastases.We examined the role of a mechanical feedback in regulation of lymph  node swelling. Using parallel plate compression  and UV-las er  cutting  experiments   we  dis s ected  the  mechanical  force dynamics  of the whole lymph  node, and individually for FRCs  and the  caps ule. Physical forces   generated  by  packed  lymphocytes   directly  affect  the  tens ion  on  the  FRC  network  and  capsule,  which  increases  its  resistance  to   swelling.  This  implies  a  feedback  mechanism  between   tis s ue   pres s ure   and   ability   of   lymphocytes    to   enter   the   organ.   Following   inflammation,  the  lymph  node  swells ∼10 fold in two weeks . Yet, what  is  the role  for tens ion on  the  FRC  network   and  caps ule,  and  how  are  lymphocytes   able  to  enter  in  conditions  that resist swelling remain open ques tions . We s how that tens ion on the FRC network is  important to  limit  the  swelling  rate  of  the  organ  so  that  the  FRC  network  can  grow  in  a  coordinated  fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates  and a dis organized FRC network  in the inflamed lymph  node. Growth  of the FRC network  in  turn  is   expected  to  releas e  tens ion  on  thes e  s tructures   and  lowers   the  res is tance  to  swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of  swelling coincides   with  a  thickening  of  the  caps ule,  which  forms   a  thick  res is tant  band  around  the organ and lowers  tens ion on the FRC network  to form a new force equilibrium.The  FRC  and  conduit   network   are  further   believed  to  be  a  privileged  s ite  of  s oluble  information  within  the  lymph  node,  although  many  details   remain  uns olved.  We  s how  by  3D  ultra-recons truction   that  FRCs   and  antigen  pres enting  cells   cover  the  s urface  of  conduit  s ys tem for more  than 99% and we dis cus s  the implications  for s oluble information  exchangeat the conduit level.Finally, there  is an ongoing debate in the cancer field whether and how cancer cells  in lymph nodes   s eed  dis tal  metas tas es .  We  s how  that  cancer  cells   infus ed  into  the  lymph  node  can  utilize trafficking routes of immune  cells and  rapidly  migrate  to  blood  vessels. Once  in  the  blood circulation,  these cells are able to form  metastases in distal tissues.","lang":"eng"}],"has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"status":"public","corr_author":"1","ddc":["570"],"month":"10","degree_awarded":"PhD","OA_place":"publisher","file_date_updated":"2020-11-07T23:30:03Z","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"664","relation":"part_of_dissertation"},{"id":"402","relation":"part_of_dissertation","status":"public"}]},"day":"09","date_updated":"2026-06-18T18:47:59Z","title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","author":[{"first_name":"Frank P","last_name":"Assen","orcid":"0000-0003-3470-6119","full_name":"Assen, Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.15479/AT:ISTA:6947","citation":{"chicago":"Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>.","short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019.","mla":"Assen, Frank P. <i>Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>.","ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019.","apa":"Assen, F. P. (2019). <i>Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>","ista":"Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria.","ama":"Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>"},"department":[{"_id":"MiSi"}],"_id":"6947","oa_version":"Published Version"},{"department":[{"_id":"JoCs"},{"_id":"GradSch"}],"citation":{"short":"K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior, Institute of Science and Technology Austria, 2019.","chicago":"Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6825\">https://doi.org/10.15479/AT:ISTA:6825</a>.","apa":"Käfer, K. (2019). <i>The hippocampus and medial prefrontal cortex during flexible behavior</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6825\">https://doi.org/10.15479/AT:ISTA:6825</a>","ama":"Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6825\">10.15479/AT:ISTA:6825</a>","ista":"Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria.","mla":"Käfer, Karola. <i>The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6825\">10.15479/AT:ISTA:6825</a>.","ieee":"K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,” Institute of Science and Technology Austria, 2019."},"doi":"10.15479/AT:ISTA:6825","oa_version":"Published Version","_id":"6825","file_date_updated":"2024-04-10T22:30:48Z","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"5949"}]},"day":"24","OA_place":"publisher","author":[{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola","last_name":"Käfer","first_name":"Karola"}],"date_updated":"2026-04-08T13:56:14Z","title":"The hippocampus and medial prefrontal cortex during flexible behavior","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"date_created":"2019-08-21T15:00:57Z","has_accepted_license":"1","abstract":[{"text":"The solving of complex tasks requires the functions of more than one brain area and their interaction. Whilst spatial navigation and memory is dependent on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC). To further examine the roles of the hippocampus and mPFC, we recorded their neural activity during a task that depends on both of these brain regions.\r\nWith tetrodes, we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC neurons in Long-Evans rats performing a rule-switching task on the plus-maze. The plus-maze task had a spatial component since it required navigation along one of the two start arms and at the maze center a choice between one of the two goal arms. Which goal contained a reward depended on the rule currently in place. After an uncued rule change the animal had to abandon the old strategy and switch to the new rule, testing cognitive flexibility. Investigating the coordination of activity between the HPC and mPFC allows determination during which task stages their interaction is required. Additionally, comparing neural activity patterns in these two brain regions allows delineation of the specialized functions of the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC in terms of oscillatory interactions, rule coding and replay.\r\nWe found that theta coherence between the HPC and mPFC is increased at the center and goals of the maze, both when the rule was stable or has changed. Similar results were found for locking of HPC and mPFC neurons to HPC theta oscillations. However, no differences in HPC-mPFC theta coordination were observed between the spatially- and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations was not modulated by\r\nmaze position or rule type. We found that the HPC coded for the two different rules with cofiring relationships between\r\ncell pairs. However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective firing in the mPFC generalized between the two start and two goal arms. With Bayesian positional decoding, we found that the mPFC reactivated non-local positions during awake immobility periods. Replay of these non-local positions could represent entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore, mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently of each other. These results show that the mPFC can replay ordered patterns of activity during awake immobility, possibly underlying its role in flexible behavior. ","lang":"eng"}],"language":[{"iso":"eng"}],"supervisor":[{"first_name":"Jozsef L","last_name":"Csicsvari","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87"}],"degree_awarded":"PhD","month":"08","corr_author":"1","status":"public","ddc":["570"],"page":"89","oa":1,"type":"dissertation","file":[{"date_updated":"2020-09-06T22:30:03Z","request_a_copy":0,"file_id":"6846","embargo":"2020-09-05","file_size":3205202,"access_level":"open_access","content_type":"application/pdf","date_created":"2019-09-03T08:07:13Z","relation":"main_file","file_name":"Thesis_Kaefer_PDFA.pdf","checksum":"2664420e332a33338568f4f3bfc59287","creator":"kkaefer"},{"file_size":2506835,"content_type":"application/zip","access_level":"closed","relation":"source_file","date_created":"2019-09-03T08:07:17Z","creator":"kkaefer","checksum":"9a154eab6f07aa590a3d2651dc0d926a","file_name":"Thesis_Kaefer.zip","embargo_to":"open_access","date_updated":"2024-04-10T22:30:48Z","file_id":"6847"}],"year":"2019","article_processing_charge":"No","publication_status":"published","date_published":"2019-08-24T00:00:00Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd"},{"page":"802-816","ec_funded":1,"type":"journal_article","isi":1,"oa":1,"publication_status":"published","year":"2019","article_processing_charge":"Yes (via OA deal)","file":[{"date_updated":"2020-07-14T12:47:13Z","file_id":"5950","file_size":2132893,"access_level":"open_access","content_type":"application/pdf","date_created":"2019-02-11T10:42:51Z","relation":"main_file","checksum":"5e8de271ca04aef92a5de42d6aac4404","file_name":"2019_Hippocampus_Kaefer.pdf","creator":"dernst"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_published":"2019-09-01T00:00:00Z","date_created":"2019-02-10T22:59:18Z","abstract":[{"text":"Aberrant proteostasis of protein aggregation may lead to behavior disorders including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations that underlie CMI are not well understood. We recorded the local field potential and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein aggregation, disturbances in the dopaminergic system and attention-related deficits. Recordings were performed during exploration of familiar and novel open field environments and during sleep, allowing investigation of neuronal abnormalities in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited smaller place fields and decreased speed-modulation of their firing rates, demonstrating altered spatial coding and deficits in encoding location-independent sensory inputs. Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase locking strength during novelty, limiting their phase coding ability. However, their mean theta phases were more variable at the population level, reducing oscillatory network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced shift in their preferred theta and gamma firing phases, indicating deficits in coding of novel environments with oscillatory firing. By combining single cell and neuronal population analyses, we link DISC1 protein pathology with abnormal hippocampal neural coding and network synchrony, and thereby gain a more comprehensive understanding of CMI mechanisms.","lang":"eng"}],"has_accepted_license":"1","publisher":"Wiley","language":[{"iso":"eng"}],"intvolume":"        29","issue":"9","status":"public","ddc":["570"],"month":"09","publication":"Hippocampus","day":"01","related_material":{"record":[{"relation":"dissertation_contains","id":"6825","status":"public"}]},"article_type":"original","file_date_updated":"2020-07-14T12:47:13Z","external_id":{"isi":["000480635400003"]},"author":[{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola","first_name":"Karola","last_name":"Käfer"},{"full_name":"Malagon-Vina, Hugo","first_name":"Hugo","last_name":"Malagon-Vina"},{"id":"444EB89E-F248-11E8-B48F-1D18A9856A87","full_name":"Dickerson, Desiree","first_name":"Desiree","last_name":"Dickerson"},{"last_name":"O'Neill","first_name":"Joseph","full_name":"O'Neill, Joseph"},{"full_name":"Trossbach, Svenja V.","first_name":"Svenja V.","last_name":"Trossbach"},{"first_name":"Carsten","last_name":"Korth","full_name":"Korth, Carsten"},{"first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L"}],"title":"Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization","date_updated":"2026-09-02T22:31:00Z","scopus_import":"1","department":[{"_id":"JoCs"}],"volume":29,"project":[{"name":"inter-and intracellular signalling in schizophrenia","grant_number":"607616","call_identifier":"FP7","_id":"257BBB4C-B435-11E9-9278-68D0E5697425"}],"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1002/hipo.23076","citation":{"mla":"Käfer, Karola, et al. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” <i>Hippocampus</i>, vol. 29, no. 9, Wiley, 2019, pp. 802–16, doi:<a href=\"https://doi.org/10.1002/hipo.23076\">10.1002/hipo.23076</a>.","ieee":"K. Käfer <i>et al.</i>, “Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization,” <i>Hippocampus</i>, vol. 29, no. 9. Wiley, pp. 802–816, 2019.","ista":"Käfer K, Malagon-Vina H, Dickerson D, O’Neill J, Trossbach SV, Korth C, Csicsvari JL. 2019. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 29(9), 802–816.","ama":"Käfer K, Malagon-Vina H, Dickerson D, et al. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. <i>Hippocampus</i>. 2019;29(9):802-816. doi:<a href=\"https://doi.org/10.1002/hipo.23076\">10.1002/hipo.23076</a>","apa":"Käfer, K., Malagon-Vina, H., Dickerson, D., O’Neill, J., Trossbach, S. V., Korth, C., &#38; Csicsvari, J. L. (2019). Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. <i>Hippocampus</i>. Wiley. <a href=\"https://doi.org/10.1002/hipo.23076\">https://doi.org/10.1002/hipo.23076</a>","chicago":"Käfer, Karola, Hugo Malagon-Vina, Desiree Dickerson, Joseph O’Neill, Svenja V. Trossbach, Carsten Korth, and Jozsef L Csicsvari. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” <i>Hippocampus</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/hipo.23076\">https://doi.org/10.1002/hipo.23076</a>.","short":"K. Käfer, H. Malagon-Vina, D. Dickerson, J. O’Neill, S.V. Trossbach, C. Korth, J.L. Csicsvari, Hippocampus 29 (2019) 802–816."},"_id":"5949","oa_version":"Published Version","quality_controlled":"1"},{"intvolume":"         8","language":[{"iso":"eng"}],"publisher":"eLife Sciences Publications","has_accepted_license":"1","abstract":[{"text":"Aberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate a program governing migration steps important for both development and cancer metastasis.","lang":"eng"}],"date_created":"2019-03-28T13:37:45Z","acknowledged_ssus":[{"_id":"LifeSc"}],"publication":"eLife","status":"public","month":"03","ddc":["570"],"oa":1,"type":"journal_article","ec_funded":1,"isi":1,"article_number":"e41801","date_published":"2019-03-26T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","file":[{"file_id":"6188","date_updated":"2020-07-14T12:47:23Z","creator":"dernst","file_name":"2019_eLife_Valoskova.pdf","checksum":"cc0d1a512559d52e7e7cb0e9b9854b40","relation":"main_file","date_created":"2019-03-28T14:00:41Z","content_type":"application/pdf","access_level":"open_access","file_size":4496017}],"year":"2019","article_processing_charge":"No","publication_status":"published","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.7554/elife.41801","citation":{"apa":"Valosková, K., Bicher, J., Roblek, M., Emtenani, S., György, A., Misova, M., … Siekhaus, D. E. (2019). A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.41801\">https://doi.org/10.7554/elife.41801</a>","ama":"Valosková K, Bicher J, Roblek M, et al. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.41801\">10.7554/elife.41801</a>","ista":"Valosková K, Bicher J, Roblek M, Emtenani S, György A, Misova M, Ratheesh A, Dos Reis Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE. 2019. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife. 8, e41801.","mla":"Valosková, Katarina, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” <i>ELife</i>, vol. 8, e41801, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.41801\">10.7554/elife.41801</a>.","ieee":"K. Valosková <i>et al.</i>, “A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","short":"K. Valosková, J. Bicher, M. Roblek, S. Emtenani, A. György, M. Misova, A. Ratheesh, P. Dos Reis Rodrigues, K. Shkarina, I.S.B. Larsen, S.Y. Vakhrushev, H. Clausen, D.E. Siekhaus, ELife 8 (2019).","chicago":"Valosková, Katarina, Julia Bicher, Marko Roblek, Shamsi Emtenani, Attila György, Michaela Misova, Aparna Ratheesh, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.41801\">https://doi.org/10.7554/elife.41801</a>."},"project":[{"name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells","grant_number":"24283","_id":"253CDE40-B435-11E9-9278-68D0E5697425"},{"grant_number":"P29638","name":"The role of Drosophila TNF alpha in immune cell invasion","_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"334077","name":"Investigating the role of transporters in invasive migration through junctions"},{"grant_number":"329540","name":"Breaking barriers: Investigating the junctional and mechanobiological changes underlying the ability of Drosophila immune cells to invade an epithelium","_id":"25388084-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"International IST Doctoral Program","grant_number":"665385","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"volume":8,"scopus_import":"1","department":[{"_id":"DaSi"}],"quality_controlled":"1","oa_version":"Published Version","_id":"6187","external_id":{"isi":["000462530200001"]},"file_date_updated":"2020-07-14T12:47:23Z","publication_identifier":{"issn":["2050-084X"]},"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/new-gene-potentially-involved-in-metastasis-identified/","description":"News on IST Homepage"}],"record":[{"id":"6530","relation":"dissertation_contains"},{"id":"8983","relation":"dissertation_contains","status":"public"},{"relation":"dissertation_contains","id":"6546","status":"public"}]},"day":"26","date_updated":"2026-09-03T06:37:26Z","title":"A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion","author":[{"full_name":"Valosková, Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Valosková","orcid":"0000-0002-7926-0221"},{"last_name":"Biebl","first_name":"Julia","full_name":"Biebl, Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Marko","last_name":"Roblek","orcid":"0000-0001-9588-1389","full_name":"Roblek, Marko","id":"3047D808-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Emtenani","orcid":"0000-0001-6981-6938","first_name":"Shamsi","full_name":"Emtenani, Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Attila","orcid":"0000-0002-1819-198X","last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","full_name":"György, Attila"},{"id":"495A3C32-F248-11E8-B48F-1D18A9856A87","full_name":"Misova, Michaela","first_name":"Michaela","orcid":"0000-0003-2427-6856","last_name":"Misova"},{"first_name":"Aparna","last_name":"Ratheesh","orcid":"0000-0001-7190-0776","full_name":"Ratheesh, Aparna","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-1681-508X","last_name":"Dos Reis Rodrigues","first_name":"Patricia","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F","full_name":"Dos Reis Rodrigues, Patricia"},{"full_name":"Shkarina, Katerina","last_name":"Shkarina","first_name":"Katerina"},{"last_name":"Larsen","first_name":"Ida Signe Bohse","full_name":"Larsen, Ida Signe Bohse"},{"first_name":"Sergey Y","last_name":"Vakhrushev","full_name":"Vakhrushev, Sergey Y"},{"full_name":"Clausen, Henrik","last_name":"Clausen","first_name":"Henrik"},{"orcid":"0000-0001-8323-8353","last_name":"Siekhaus","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E"}]},{"publisher":"Institute of Science and Technology Austria","abstract":[{"lang":"eng","text":"Invasive migration plays a crucial role not only during development and homeostasis but also in pathological states, such as tumor metastasis. Drosophila macrophage migration into the extended germband is an interesting system to study invasive migration. It carries similarities to immune cell transmigration and cancer cell invasion, therefore studying this process could also bring new understanding of invasion in higher organisms. In our work, we uncover a highly conserved member of the major facilitator family that plays a role in tissue invasion through regulation of glycosylation on a subgroup of proteins and/or by aiding the precise timing of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator that orchestrates O-glycosylation on a protein subset to activate \r\na program governing migration steps important for both development and cancer metastasis. \r\n"}],"has_accepted_license":"1","date_created":"2019-06-07T12:49:19Z","alternative_title":["ISTA Thesis"],"language":[{"iso":"eng"}],"supervisor":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353","last_name":"Siekhaus","first_name":"Daria E"}],"degree_awarded":"PhD","corr_author":"1","status":"public","ddc":["570"],"month":"06","acknowledged_ssus":[{"_id":"Bio"}],"page":"141","oa":1,"type":"dissertation","file":[{"relation":"source_file","date_created":"2019-06-07T13:00:04Z","checksum":"68949c2d96210b45b981a23e9c9cd93c","file_name":"Katarina Valoskova_PhD thesis_final version.docx","creator":"khribikova","file_size":14110626,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","file_id":"6549","embargo_to":"open_access","date_updated":"2020-07-14T12:47:33Z"},{"date_created":"2019-06-07T13:00:08Z","relation":"main_file","checksum":"555329cd76e196c96f5278c480ee2e6e","file_name":"Katarina Valoskova_PhD thesis_final version.pdf","creator":"khribikova","file_size":10054156,"access_level":"open_access","content_type":"application/pdf","file_id":"6550","embargo":"2020-06-07","date_updated":"2021-02-11T11:17:14Z"}],"publication_status":"published","year":"2019","article_processing_charge":"No","date_published":"2019-06-07T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","department":[{"_id":"DaSi"},{"_id":"GradSch"}],"citation":{"short":"K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration, Institute of Science and Technology Austria, 2019.","chicago":"Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6546\">https://doi.org/10.15479/AT:ISTA:6546</a>.","ama":"Valosková K. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6546\">10.15479/AT:ISTA:6546</a>","ista":"Valosková K. 2019. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria.","apa":"Valosková, K. (2019). <i>The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6546\">https://doi.org/10.15479/AT:ISTA:6546</a>","mla":"Valosková, Katarina. <i>The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6546\">10.15479/AT:ISTA:6546</a>.","ieee":"K. Valosková, “The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration,” Institute of Science and Technology Austria, 2019."},"doi":"10.15479/AT:ISTA:6546","project":[{"_id":"253CDE40-B435-11E9-9278-68D0E5697425","name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells","grant_number":"24283"}],"doi_confirm":"1","oa_version":"Published Version","_id":"6546","day":"07","file_date_updated":"2021-02-11T11:17:14Z","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"544","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6187","status":"public"}]},"OA_place":"publisher","author":[{"full_name":"Valosková, Katarina","id":"46F146FC-F248-11E8-B48F-1D18A9856A87","last_name":"Valosková","orcid":"0000-0002-7926-0221","first_name":"Katarina"}],"title":"The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration","date_updated":"2026-09-03T06:37:27Z"},{"date_updated":"2026-09-03T06:34:45Z","title":"Design and characterization of methods and biological components to realize synthetic neurotransmission","author":[{"full_name":"Mckenzie, Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","last_name":"Mckenzie","first_name":"Catherine"}],"OA_place":"publisher","file_date_updated":"2020-07-14T12:47:50Z","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","relation":"old_edition","id":"6266"}]},"day":"27","_id":"7132","oa_version":"Published Version","doi":"10.15479/at:ista:7132","citation":{"chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:7132\">https://doi.org/10.15479/at:ista:7132</a>.","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria, 2019.","mla":"Mckenzie, Catherine. <i>Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:7132\">10.15479/at:ista:7132</a>.","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission,” Institute of Science and Technology Austria, 2019.","apa":"Mckenzie, C. (2019). <i>Design and characterization of methods and biological components to realize synthetic neurotransmission</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:7132\">https://doi.org/10.15479/at:ista:7132</a>","ista":"Mckenzie C. 2019. Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria.","ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission. 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:7132\">10.15479/at:ista:7132</a>"},"department":[{"_id":"HaJa"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_published":"2019-06-27T00:00:00Z","article_processing_charge":"No","year":"2019","publication_status":"published","file":[{"file_size":5054633,"access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_created":"2019-11-27T09:06:10Z","relation":"source_file","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.docx","creator":"dernst","checksum":"34d0fe0f6e0af97b5937205a3e350423","date_updated":"2020-07-14T12:47:50Z","file_id":"7133"},{"content_type":"application/pdf","access_level":"open_access","file_size":3231837,"file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.pdf","creator":"dernst","checksum":"140dfb5e3df7edca34f4b6fcc55d876f","relation":"main_file","date_created":"2019-11-27T09:06:10Z","date_updated":"2020-07-14T12:47:50Z","file_id":"7134"}],"type":"dissertation","oa":1,"page":"95","ddc":["571","573"],"corr_author":"1","status":"public","month":"06","degree_awarded":"PhD","supervisor":[{"last_name":"Janovjak","orcid":"0000-0002-8023-9315","first_name":"Harald L","full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"alternative_title":["ISTA Thesis"],"abstract":[{"text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing.","lang":"eng"}],"date_created":"2019-11-27T09:07:14Z","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria"},{"file":[{"date_updated":"2021-02-10T23:30:09Z","embargo_to":"open_access","file_id":"6865","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":18253100,"file_name":"Thesis_Damaris_Rangel_source.docx","creator":"drangel","checksum":"244dc4f74dbfc94f414156092298831f","date_created":"2019-09-09T13:09:45Z","relation":"source_file"},{"request_a_copy":0,"file_id":"6866","embargo":"2020-09-10","date_updated":"2020-09-11T22:30:04Z","date_created":"2019-09-09T13:09:52Z","relation":"main_file","checksum":"59c73be40eeaa1c4db24067270151555","creator":"drangel","file_name":"Thesis_Damaris_Rangel_pdfa.pdf","file_size":2160109,"access_level":"open_access","content_type":"application/pdf"}],"article_processing_charge":"No","year":"2019","publication_status":"published","date_published":"2019-09-09T00:00:00Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"97","oa":1,"type":"dissertation","degree_awarded":"PhD","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"M-Shop"}],"month":"09","ddc":["570"],"corr_author":"1","status":"public","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","date_created":"2019-09-06T06:54:16Z","abstract":[{"text":"Brain function is mediated by complex dynamical interactions between excitatory and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons) are one of the least studied types, despite being suspected to play important roles in cognitive processes. We studied the network effects of optogenetic silencing of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states. The cell firing pattern in response to light pulses allowed us to classify the recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal cell and interneurons, and the inhibited interneurons corresponding to the CCK group. The light application, which inhibited the activity of CCK interneurons triggered wider changes in the firing dynamics of cells. We observed rate changes (i.e. remapping) of pyramidal cells during the exploration session in which the light was applied relative to the previous control session that was not restricted neither in time nor space to the light delivery. Also, the disinhibited pyramidal cells had higher increase in bursting than in single spike firing rate as a result of CCK silencing. In addition, the firing activity patterns during exploratory periods were more weakly reactivated in sleep for those periods in which CCK-interneuron were silenced than in the unaffected periods. Furthermore, light pulses during sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK neurons during exploration suppressed the reactivation of waking firing patterns in sleep and CCK interneuron activity was also required during sleep for the normal reactivation of waking patterns. These findings demonstrate the involvement of CCK cells in reactivation-related memory consolidation. An important part of our analysis was to test the relationship of the identified CCKinterneurons to brain oscillations. Our findings showed that these cells exhibited different oscillatory behaviour during anaesthesia and natural waking and sleep conditions. We showed that: 1) Contrary to the past studies performed under anaesthesia, the identified CCKinterneurons fired on the descending portion of the theta phase in waking exploration. 2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3) Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons increased around the peak activity of the sharp-wave ripple (SWR) events in natural sleep, which is congruent with new reports about their functional connectivity. We also found that light driven CCK-interneuron silencing altered the dynamics on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted their preferred theta phases when the light was applied, while interneurons responses were less consistent. 2) As a population, pyramidal cells negatively shifted their preferred activity during gamma oscillations, albeit we did not find gamma modulation differences related to the light application when pyramidal cells were subdivided into the disinhibited and unaffected groups. 3) During the peak of SWR events, all but the CCK-interneurons had a reduction in their relative firing rate change during the light application as compared to the change observed at SWR initiation. Finally, regarding to the place field activity of the recorded pyramidal neurons, we showed that the disinhibited pyramidal cells had reduced place field similarity, coherence and spatial information, but only during the light application. The mechanisms behind such observed behaviours might involve eCB signalling and plastic changes in CCK-interneuron synapses. In conclusion, the observed changes related to the light-mediated silencing of CCKinterneurons have unravelled characteristics of this interneuron subpopulation that might change the understanding not only of their particular network interactions, but also of the current theories about the emergence of certain cognitive processes such as place coding needed for navigation or hippocampus-dependent memory consolidation. ","lang":"eng"}],"supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","last_name":"Csicsvari"}],"language":[{"iso":"eng"}],"author":[{"id":"4871BCE6-F248-11E8-B48F-1D18A9856A87","full_name":"Rangel Guerrero, Dámaris K","first_name":"Dámaris K","orcid":"0000-0002-8602-4374","last_name":"Rangel Guerrero"}],"date_updated":"2026-09-03T06:40:36Z","title":"The role of CCK-interneurons in regulating hippocampal network dynamics","file_date_updated":"2021-02-10T23:30:09Z","publication_identifier":{"isbn":["978-3-99078-003-9"],"issn":["2663-337X"]},"related_material":{"record":[{"status":"public","id":"5914","relation":"part_of_dissertation"}]},"day":"09","OA_place":"publisher","oa_version":"Published Version","doi_confirm":"1","_id":"6849","department":[{"_id":"JoCs"},{"_id":"GradSch"}],"citation":{"ista":"Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria.","ama":"Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal network dynamics. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6849\">10.15479/AT:ISTA:6849</a>","apa":"Rangel Guerrero, D. K. (2019). <i>The role of CCK-interneurons in regulating hippocampal network dynamics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6849\">https://doi.org/10.15479/AT:ISTA:6849</a>","mla":"Rangel Guerrero, Dámaris K. <i>The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6849\">10.15479/AT:ISTA:6849</a>.","ieee":"D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal network dynamics,” Institute of Science and Technology Austria, 2019.","short":"D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics, Institute of Science and Technology Austria, 2019.","chicago":"Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6849\">https://doi.org/10.15479/AT:ISTA:6849</a>."},"doi":"10.15479/AT:ISTA:6849"},{"arxiv":1,"acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","publication_identifier":{"eissn":["2211-2766"],"eisbn":["9783319747729"],"isbn":["9783319747712"],"issn":["2211-2758"]},"day":"21","external_id":{"arxiv":["1502.01072"]},"author":[{"last_name":"Kazda","first_name":"Alexandr","full_name":"Kazda, Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kozik, Marcin","first_name":"Marcin","last_name":"Kozik"},{"last_name":"McKenzie","first_name":"Ralph","full_name":"McKenzie, Ralph"},{"full_name":"Moore, Matthew","first_name":"Matthew","last_name":"Moore"}],"date_updated":"2024-10-09T21:01:50Z","title":"Absorption and directed Jónsson terms","volume":16,"scopus_import":"1","department":[{"_id":"VlKo"}],"doi":"10.1007/978-3-319-74772-9_7","citation":{"mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:<a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">10.1007/978-3-319-74772-9_7</a>.","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:<a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">10.1007/978-3-319-74772-9_7</a>","apa":"Kazda, A., Kozik, M., McKenzie, R., &#38; Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i> (Vol. 16, pp. 203–220). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">https://doi.org/10.1007/978-3-319-74772-9_7</a>","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">https://doi.org/10.1007/978-3-319-74772-9_7</a>.","short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220."},"main_file_link":[{"url":"https://arxiv.org/abs/1502.01072","open_access":"1"}],"oa_version":"Preprint","quality_controlled":"1","_id":"10864","page":"203-220","editor":[{"last_name":"Czelakowski","first_name":"J","full_name":"Czelakowski, J"}],"oa":1,"type":"book_chapter","series_title":"OCTR","article_processing_charge":"No","year":"2018","publication_status":"published","date_published":"2018-03-21T00:00:00Z","place":"Cham","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","abstract":[{"text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k.","lang":"eng"}],"date_created":"2022-03-18T10:30:32Z","intvolume":"        16","language":[{"iso":"eng"}],"publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","status":"public","corr_author":"1","month":"03"},{"language":[{"iso":"eng"}],"intvolume":"        17","pmid":1,"date_created":"2022-03-18T12:40:35Z","abstract":[{"lang":"eng","text":"Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Recently, it has been gradually revealed that WGD and subsequent fate changes of duplicated genes can facilitate phenotypic evolution. Here, we review the current understanding of the relationship between WGD and the acquisition of evolutionary novelties. We show some examples of this link and discuss how WGD and subsequent duplicated genes can facilitate phenotypic evolution as well as when such genomic doubling can be advantageous for adaptation."}],"publisher":"Oxford University Press","month":"09","corr_author":"1","ddc":["570"],"status":"public","publication":"Briefings in Functional Genomics","issue":"5","type":"journal_article","isi":1,"oa":1,"page":"329-338","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2018-09-01T00:00:00Z","year":"2018","article_processing_charge":"No","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"publication_status":"published","citation":{"chicago":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>.","short":"M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338.","mla":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>.","ieee":"M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications on the emergence of evolutionary novelties,” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.","apa":"Yuuta, M., &#38; Koshiba-Takeuchi, K. (2018). Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>","ama":"Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. 2018;17(5):329-338. doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>","ista":"Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 17(5), 329–338."},"doi":"10.1093/bfgp/ely007","scopus_import":"1","department":[{"_id":"CaHe"}],"volume":17,"_id":"10880","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/bfgp/ely007"}],"oa_version":"Published Version","quality_controlled":"1","external_id":{"pmid":["29579140"],"isi":["000456054400004"]},"article_type":"original","acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","publication_identifier":{"eissn":["2041-2657"],"issn":["2041-2649"]},"day":"01","date_updated":"2026-06-18T10:44:32Z","title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","author":[{"id":"4968E7C8-F248-11E8-B48F-1D18A9856A87","full_name":"Yuuta, Moriyama","orcid":"0000-0002-2853-8051","last_name":"Yuuta","first_name":"Moriyama"},{"last_name":"Koshiba-Takeuchi","first_name":"Kazuko","full_name":"Koshiba-Takeuchi, Kazuko"}]},{"_id":"10881","oa_version":"None","quality_controlled":"1","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"doi":"10.1093/jxb/ery097","citation":{"short":"T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378.","chicago":"Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>.","ama":"Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. 2018;69(9):2367-2378. doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>","ista":"Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S. 2018. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 69(9), 2367–2378.","apa":"Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml, J., &#38; Simon, S. (2018). Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>","ieee":"T. R. Moturu <i>et al.</i>, “Molecular evolution and diversification of the SMXL gene family,” <i>Journal of Experimental Botany</i>, vol. 69, no. 9. Oxford University Press, pp. 2367–2378, 2018.","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>, vol. 69, no. 9, Oxford University Press, 2018, pp. 2367–78, doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>."},"scopus_import":"1","department":[{"_id":"JiFr"}],"volume":69,"title":"Molecular evolution and diversification of the SMXL gene family","date_updated":"2025-04-15T07:48:01Z","author":[{"last_name":"Moturu","first_name":"Taraka Ramji","full_name":"Moturu, Taraka Ramji"},{"first_name":"Sravankumar","last_name":"Thula","full_name":"Thula, Sravankumar"},{"first_name":"Ravi Kumar","last_name":"Singh","full_name":"Singh, Ravi Kumar"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"full_name":"Vařeková, Radka Svobodová","last_name":"Vařeková","first_name":"Radka Svobodová"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří"},{"full_name":"Simon, Sibu","first_name":"Sibu","last_name":"Simon"}],"external_id":{"isi":["000430727000016"],"pmid":["29538714"]},"day":"13","publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"acknowledgement":"This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and it is co-financed by the South Moravian Region under grant agreement No. 665860 (SS). Access to computing and storage facilities owned by parties and projects contributing to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005) was greatly appreciated (RSV). The project was funded by The Ministry of Education, Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601) (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG 20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly the authors’ views, and the EU is not responsible for any use that may be made of the information it contains. ","article_type":"original","status":"public","publication":"Journal of Experimental Botany","month":"04","issue":"9","language":[{"iso":"eng"}],"intvolume":"        69","pmid":1,"abstract":[{"lang":"eng","text":"Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects of plant development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles for each, but very little is known about these repressors in terms of their sequence features. In this study, we performed an extensive comparative analysis of SMXLs and determined their phylogenetic and evolutionary history in the plant lineage. Our results show that SMXL family members can be sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1. Further, we identified the clade-specific motifs that have evolved and that might act as determinants of SL-KAR signalling specificity. These specificities resulted from functional diversities among the clades. Our results suggest that a gradual co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an increased specificity to both the SL perception and response in land plants."}],"date_created":"2022-03-18T12:43:22Z","publisher":"Oxford University Press","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-04-13T00:00:00Z","publication_status":"published","year":"2018","keyword":["Plant Science","Physiology"],"article_processing_charge":"No","type":"journal_article","ec_funded":1,"isi":1,"page":"2367-2378"},{"_id":"10882","main_file_link":[{"url":" https://doi.org/10.48550/arXiv.1712.08087","open_access":"1"}],"quality_controlled":"1","oa_version":"Preprint","scopus_import":"1","department":[{"_id":"ChLa"}],"doi":"10.1109/cvpr.2018.00956","citation":{"short":"J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.","chicago":"Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari. “Learning Intelligent Dialogs for Bounding Box Annotation.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 9175–84. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>.","apa":"Uijlings, J., Konyushkova, K., Lampert, C., &#38; Ferrari, V. (2018). Learning intelligent dialogs for bounding box annotation. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 9175–9184). Salt Lake City, UT, United States: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>","ista":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition, 9175–9184.","ama":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs for bounding box annotation. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:9175-9184. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>","ieee":"J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent dialogs for bounding box annotation,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, United States, 2018, pp. 9175–9184.","mla":"Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 9175–84, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>."},"author":[{"full_name":"Uijlings, Jasper","last_name":"Uijlings","first_name":"Jasper"},{"last_name":"Konyushkova","first_name":"Ksenia","full_name":"Konyushkova, Ksenia"},{"first_name":"Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","full_name":"Lampert, Christoph"},{"full_name":"Ferrari, Vittorio","first_name":"Vittorio","last_name":"Ferrari"}],"date_updated":"2024-10-09T21:02:26Z","title":"Learning intelligent dialogs for bounding box annotation","publication_identifier":{"isbn":["9781538664209"],"eissn":["2575-7075"]},"day":"17","arxiv":1,"conference":{"end_date":"2018-06-23","name":"CVF: Conference on Computer Vision and Pattern Recognition","location":"Salt Lake City, UT, United States","start_date":"2018-06-18"},"external_id":{"isi":["000457843609036"],"arxiv":["1712.08087"]},"publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","month":"12","corr_author":"1","status":"public","abstract":[{"text":"We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [34], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other based on reinforcement learning. We demonstrate that (1) our agents are able to learn efficient annotation strategies in several scenarios, automatically adapting to the image difficulty, the desired quality of the boxes, and the detector strength; (2) in all scenarios the resulting annotation dialogs speed up annotation compared to manual box drawing alone and box verification alone, while also outperforming any fixed combination of verification and drawing in most scenarios; (3) in a realistic scenario where the detector is iteratively re-trained, our agents evolve a series of strategies that reflect the shifting trade-off between verification and drawing as the detector grows stronger.","lang":"eng"}],"date_created":"2022-03-18T12:45:09Z","publisher":"IEEE","language":[{"iso":"eng"}],"article_processing_charge":"No","year":"2018","publication_status":"published","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-12-17T00:00:00Z","page":"9175-9184","type":"conference","isi":1,"oa":1}]