[{"publication_status":"published","type":"technical_report","department":[{"_id":"KrCh"}],"date_updated":"2023-02-23T11:23:11Z","language":[{"iso":"eng"}],"oa_version":"Published Version","_id":"5387","day":"16","date_published":"2011-02-16T00:00:00Z","month":"02","year":"2011","related_material":{"record":[{"id":"3345","relation":"later_version","status":"public"}]},"title":"Energy and mean-payoff parity Markov decision processes","has_accepted_license":"1","date_created":"2018-12-12T11:39:02Z","file":[{"content_type":"application/pdf","file_id":"5458","file_name":"IST-2011-0001_IST-2011-0001.pdf","creator":"system","access_level":"open_access","date_created":"2018-12-12T11:52:57Z","checksum":"824d6c70e6d3feb3e836b009e0b3cf73","file_size":329976,"relation":"main_file","date_updated":"2020-07-14T12:46:41Z"}],"pubrep_id":"23","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","alternative_title":["IST Austria Technical Report"],"doi":"10.15479/AT:IST-2011-0001","ddc":["000","005"],"publisher":"IST Austria","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"last_name":"Doyen","full_name":"Doyen, Laurent","first_name":"Laurent"}],"abstract":[{"text":"We consider Markov Decision Processes (MDPs) with mean-payoff parity and energy parity objectives. In system design, the parity objective is used to encode ω-regular specifications, and the mean-payoff and energy objectives can be used to model quantitative resource constraints. The energy condition re- quires that the resource level never drops below 0, and the mean-payoff condi- tion requires that the limit-average value of the resource consumption is within a threshold. While these two (energy and mean-payoff) classical conditions are equivalent for two-player games, we show that they differ for MDPs. We show that the problem of deciding whether a state is almost-sure winning (i.e., winning with probability 1) in energy parity MDPs is in NP ∩ coNP, while for mean- payoff parity MDPs, the problem is solvable in polynomial time, improving a recent PSPACE bound.","lang":"eng"}],"publication_identifier":{"issn":["2664-1690"]},"oa":1,"page":"20","citation":{"chicago":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>.","mla":"Chatterjee, Krishnendu, and Laurent Doyen. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>.","apa":"Chatterjee, K., &#38; Doyen, L. (2011). <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">https://doi.org/10.15479/AT:IST-2011-0001</a>","ieee":"K. Chatterjee and L. Doyen, <i>Energy and mean-payoff parity Markov decision processes</i>. IST Austria, 2011.","short":"K. Chatterjee, L. Doyen, Energy and Mean-Payoff Parity Markov Decision Processes, IST Austria, 2011.","ista":"Chatterjee K, Doyen L. 2011. Energy and mean-payoff parity Markov decision processes, IST Austria, 20p.","ama":"Chatterjee K, Doyen L. <i>Energy and Mean-Payoff Parity Markov Decision Processes</i>. IST Austria; 2011. doi:<a href=\"https://doi.org/10.15479/AT:IST-2011-0001\">10.15479/AT:IST-2011-0001</a>"},"file_date_updated":"2020-07-14T12:46:41Z"},{"abstract":[{"lang":"eng","text":"We report the switching behavior of the full bacterial flagellum system that includes the filament and the motor in wild-type Escherichia coli cells. In sorting the motor behavior by the clockwise bias, we find that the distributions of the clockwise (CW) and counterclockwise (CCW) intervals are either exponential or nonexponential with long tails. At low bias, CW intervals are exponentially distributed and CCW intervals exhibit long tails. At intermediate CW bias (0.5) both CW and CCW intervals are mainly exponentially distributed. A simple model suggests that these two distinct switching behaviors are governed by the presence of signaling noise within the chemotaxis network. Low noise yields exponentially distributed intervals, whereas large noise yields nonexponential behavior with long tails. These drastically different motor statistics may play a role in optimizing bacterial behavior for a wide range of environmental conditions."}],"author":[{"first_name":"Heungwon","full_name":"Park, Heungwon","last_name":"Park"},{"full_name":"Oikonomou, Panos","last_name":"Oikonomou","first_name":"Panos"},{"first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052"},{"first_name":"Philippe","last_name":"Cluzel","full_name":"Cluzel, Philippe"}],"publisher":"Elsevier","publication_identifier":{"issn":["0006-3495"]},"scopus_import":"1","status":"public","doi":"10.1016/j.bpj.2011.09.040","volume":101,"quality_controlled":"1","year":"2011","month":"11","title":"Noise underlies switching behavior of the bacterial flagellum","date_created":"2019-05-28T11:54:29Z","type":"journal_article","publication_status":"published","oa_version":"Published Version","oa":1,"citation":{"ama":"Park H, Oikonomou P, Guet CC, Cluzel P. Noise underlies switching behavior of the bacterial flagellum. <i>Biophysical Journal</i>. 2011;101(10):2336-2340. doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">10.1016/j.bpj.2011.09.040</a>","ista":"Park H, Oikonomou P, Guet CC, Cluzel P. 2011. Noise underlies switching behavior of the bacterial flagellum. Biophysical Journal. 101(10), 2336–2340.","ieee":"H. Park, P. Oikonomou, C. C. Guet, and P. Cluzel, “Noise underlies switching behavior of the bacterial flagellum,” <i>Biophysical Journal</i>, vol. 101, no. 10. Elsevier, pp. 2336–2340, 2011.","short":"H. Park, P. Oikonomou, C.C. Guet, P. Cluzel, Biophysical Journal 101 (2011) 2336–2340.","apa":"Park, H., Oikonomou, P., Guet, C. C., &#38; Cluzel, P. (2011). Noise underlies switching behavior of the bacterial flagellum. <i>Biophysical Journal</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">https://doi.org/10.1016/j.bpj.2011.09.040</a>","mla":"Park, Heungwon, et al. “Noise Underlies Switching Behavior of the Bacterial Flagellum.” <i>Biophysical Journal</i>, vol. 101, no. 10, Elsevier, 2011, pp. 2336–40, doi:<a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">10.1016/j.bpj.2011.09.040</a>.","chicago":"Park, Heungwon, Panos Oikonomou, Calin C Guet, and Philippe Cluzel. “Noise Underlies Switching Behavior of the Bacterial Flagellum.” <i>Biophysical Journal</i>. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.bpj.2011.09.040\">https://doi.org/10.1016/j.bpj.2011.09.040</a>."},"page":"2336-2340","intvolume":"       101","publication":"Biophysical Journal","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["22098731"]},"issue":"10","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218319/"}],"pmid":1,"date_published":"2011-11-16T00:00:00Z","date_updated":"2021-04-16T11:54:49Z","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"article_processing_charge":"No","day":"16","_id":"6496"},{"quality_controlled":"1","doi":"10.1073/pnas.1019273108","volume":108,"status":"public","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"scopus_import":"1","extern":"1","author":[{"full_name":"Hsieh, Tzung-Fu","last_name":"Hsieh","first_name":"Tzung-Fu"},{"full_name":"Shin, Juhyun","last_name":"Shin","first_name":"Juhyun"},{"full_name":"Uzawa, Rie","last_name":"Uzawa","first_name":"Rie"},{"full_name":"Silva, Pedro","last_name":"Silva","first_name":"Pedro"},{"full_name":"Cohen, Stephanie","last_name":"Cohen","first_name":"Stephanie"},{"last_name":"Bauer","full_name":"Bauer, Matthew J.","first_name":"Matthew J."},{"first_name":"Meryl","full_name":"Hashimoto, Meryl","last_name":"Hashimoto"},{"first_name":"Ryan C.","full_name":"Kirkbride, Ryan C.","last_name":"Kirkbride"},{"full_name":"Harada, John J.","last_name":"Harada","first_name":"John J."},{"first_name":"Daniel","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","full_name":"Zilberman, Daniel","last_name":"Zilberman","orcid":"0000-0002-0123-8649"},{"full_name":"Fischer, Robert L.","last_name":"Fischer","first_name":"Robert L."}],"publisher":"National Academy of Sciences","abstract":[{"lang":"eng","text":"Imprinted genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon that occurs in flowering plants and mammals. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes as well as by Polycomb group proteins. Currently, only 11 imprinted A. thaliana genes are known. Here, we use extensive sequencing of cDNA libraries to identify 9 paternally expressed and 34 maternally expressed imprinted genes in A. thaliana endosperm that are regulated by the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1, and/or the core Polycomb group protein FIE. These genes encode transcription factors, proteins involved in hormone signaling, components of the ubiquitin protein degradation pathway, regulators of histone and DNA methylation, and small RNA pathway proteins. We also identify maternally expressed genes that may be regulated by unknown mechanisms or deposited from maternal tissues. We did not detect any imprinted genes in the embryo. Our results show that imprinted gene expression is an extensive mechanistically complex phenomenon that likely affects multiple aspects of seed development."}],"oa_version":"Published Version","publication_status":"published","type":"journal_article","title":"Regulation of imprinted gene expression in Arabidopsis endosperm","date_created":"2021-06-07T07:40:38Z","article_type":"original","month":"02","year":"2011","issue":"5","external_id":{"pmid":["21257907"]},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"Proceedings of the National Academy of Sciences","intvolume":"       108","page":"1755-1762","citation":{"ista":"Hsieh T-F, Shin J, Uzawa R, Silva P, Cohen S, Bauer MJ, Hashimoto M, Kirkbride RC, Harada JJ, Zilberman D, Fischer RL. 2011. Regulation of imprinted gene expression in Arabidopsis endosperm. Proceedings of the National Academy of Sciences. 108(5), 1755–1762.","ama":"Hsieh T-F, Shin J, Uzawa R, et al. Regulation of imprinted gene expression in Arabidopsis endosperm. <i>Proceedings of the National Academy of Sciences</i>. 2011;108(5):1755-1762. doi:<a href=\"https://doi.org/10.1073/pnas.1019273108\">10.1073/pnas.1019273108</a>","short":"T.-F. Hsieh, J. Shin, R. Uzawa, P. Silva, S. Cohen, M.J. Bauer, M. Hashimoto, R.C. Kirkbride, J.J. Harada, D. Zilberman, R.L. Fischer, Proceedings of the National Academy of Sciences 108 (2011) 1755–1762.","ieee":"T.-F. Hsieh <i>et al.</i>, “Regulation of imprinted gene expression in Arabidopsis endosperm,” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 5. National Academy of Sciences, pp. 1755–1762, 2011.","mla":"Hsieh, Tzung-Fu, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” <i>Proceedings of the National Academy of Sciences</i>, vol. 108, no. 5, National Academy of Sciences, 2011, pp. 1755–62, doi:<a href=\"https://doi.org/10.1073/pnas.1019273108\">10.1073/pnas.1019273108</a>.","apa":"Hsieh, T.-F., Shin, J., Uzawa, R., Silva, P., Cohen, S., Bauer, M. J., … Fischer, R. L. (2011). Regulation of imprinted gene expression in Arabidopsis endosperm. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1019273108\">https://doi.org/10.1073/pnas.1019273108</a>","chicago":"Hsieh, Tzung-Fu, Juhyun Shin, Rie Uzawa, Pedro Silva, Stephanie Cohen, Matthew J. Bauer, Meryl Hashimoto, et al. “Regulation of Imprinted Gene Expression in Arabidopsis Endosperm.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2011. <a href=\"https://doi.org/10.1073/pnas.1019273108\">https://doi.org/10.1073/pnas.1019273108</a>."},"oa":1,"_id":"9483","day":"01","article_processing_charge":"No","language":[{"iso":"eng"}],"date_updated":"2021-12-14T08:33:49Z","department":[{"_id":"DaZi"}],"date_published":"2011-02-01T00:00:00Z","pmid":1,"main_file_link":[{"url":"https://doi.org/10.1073/pnas.1019273108","open_access":"1"}]},{"oa_version":"Published Version","type":"other_academic_publication","publication_status":"published","date_created":"2021-06-08T06:23:39Z","title":"Balancing parental contributions in plant embryonic gene activation","year":"2011","month":"06","volume":20,"quality_controlled":"1","doi":"10.1016/j.devcel.2011.05.018","status":"public","publication_identifier":{"issn":["1534-5807"],"eissn":["1878-1551"]},"abstract":[{"lang":"eng","text":"Little is known about chromatin remodeling events immediately after fertilization. A recent report by Autran et al. (2011) in Cell now shows that chromatin regulatory pathways that silence transposable elements are responsible for global delayed activation of gene expression in the early Arabidopsis embryo."}],"publisher":"Elsevier","author":[{"full_name":"Zilberman, Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","first_name":"Daniel"}],"extern":"1","article_processing_charge":"No","day":"14","_id":"9522","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:34:37Z","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.devcel.2011.05.018","open_access":"1"}],"pmid":1,"date_published":"2011-06-14T00:00:00Z","external_id":{"pmid":["21664571"]},"issue":"6","publication":"Developmental Cell","intvolume":"        20","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","oa":1,"page":"735-736","citation":{"apa":"Zilberman, D. (2011). <i>Balancing parental contributions in plant embryonic gene activation</i>. <i>Developmental Cell</i> (Vol. 20, pp. 735–736). Elsevier. <a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">https://doi.org/10.1016/j.devcel.2011.05.018</a>","mla":"Zilberman, Daniel. “Balancing Parental Contributions in Plant Embryonic Gene Activation.” <i>Developmental Cell</i>, vol. 20, no. 6, Elsevier, 2011, pp. 735–36, doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">10.1016/j.devcel.2011.05.018</a>.","chicago":"Zilberman, Daniel. <i>Balancing Parental Contributions in Plant Embryonic Gene Activation</i>. <i>Developmental Cell</i>. Vol. 20. Elsevier, 2011. <a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">https://doi.org/10.1016/j.devcel.2011.05.018</a>.","ista":"Zilberman D. 2011. Balancing parental contributions in plant embryonic gene activation, Elsevier,p.","ama":"Zilberman D. <i>Balancing Parental Contributions in Plant Embryonic Gene Activation</i>. Vol 20. Elsevier; 2011:735-736. doi:<a href=\"https://doi.org/10.1016/j.devcel.2011.05.018\">10.1016/j.devcel.2011.05.018</a>","ieee":"D. Zilberman, <i>Balancing parental contributions in plant embryonic gene activation</i>, vol. 20, no. 6. Elsevier, 2011, pp. 735–736.","short":"D. Zilberman, Balancing Parental Contributions in Plant Embryonic Gene Activation, Elsevier, 2011."}},{"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publication":"Computer Analysis of Images and Patterns","intvolume":"      6854","alternative_title":["LNCS"],"citation":{"ista":"Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. 2011. Incremental-decremental algorithm for computing AT-models and persistent homology. Computer Analysis of Images and Patterns. CAIP: International Conference on Computer Analysis of Images and Patterns, LNCS, vol. 6854, 286–293.","ama":"Gonzalez-Diaz R, Ion A, Jimenez MJ, Poyatos R. Incremental-decremental algorithm for computing AT-models and persistent homology. In: <i>Computer Analysis of Images and Patterns</i>. Vol 6854. Springer Nature; 2011:286-293. doi:<a href=\"https://doi.org/10.1007/978-3-642-23672-3_35\">10.1007/978-3-642-23672-3_35</a>","ieee":"R. Gonzalez-Diaz, A. Ion, M. J. Jimenez, and R. Poyatos, “Incremental-decremental algorithm for computing AT-models and persistent homology,” in <i>Computer Analysis of Images and Patterns</i>, Seville, Spain, 2011, vol. 6854, pp. 286–293.","short":"R. Gonzalez-Diaz, A. Ion, M.J. Jimenez, R. Poyatos, in:, Computer Analysis of Images and Patterns, Springer Nature, 2011, pp. 286–293.","apa":"Gonzalez-Diaz, R., Ion, A., Jimenez, M. J., &#38; Poyatos, R. (2011). Incremental-decremental algorithm for computing AT-models and persistent homology. In <i>Computer Analysis of Images and Patterns</i> (Vol. 6854, pp. 286–293). Seville, Spain: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-642-23672-3_35\">https://doi.org/10.1007/978-3-642-23672-3_35</a>","mla":"Gonzalez-Diaz, Rocio, et al. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” <i>Computer Analysis of Images and Patterns</i>, vol. 6854, Springer Nature, 2011, pp. 286–93, doi:<a href=\"https://doi.org/10.1007/978-3-642-23672-3_35\">10.1007/978-3-642-23672-3_35</a>.","chicago":"Gonzalez-Diaz, Rocio, Adrian Ion, Maria Jose Jimenez, and Regina Poyatos. “Incremental-Decremental Algorithm for Computing AT-Models and Persistent Homology.” In <i>Computer Analysis of Images and Patterns</i>, 6854:286–93. Springer Nature, 2011. <a href=\"https://doi.org/10.1007/978-3-642-23672-3_35\">https://doi.org/10.1007/978-3-642-23672-3_35</a>."},"page":"286-293","oa":1,"language":[{"iso":"eng"}],"date_updated":"2021-08-12T13:53:17Z","department":[{"_id":"HeEd"}],"_id":"9648","day":"01","article_processing_charge":"No","date_published":"2011-08-01T00:00:00Z","main_file_link":[{"url":"http://hdl.handle.net/11441/30766","open_access":"1"}],"status":"public","doi":"10.1007/978-3-642-23672-3_35","volume":6854,"quality_controlled":"1","publisher":"Springer Nature","author":[{"last_name":"Gonzalez-Diaz","full_name":"Gonzalez-Diaz, Rocio","first_name":"Rocio"},{"first_name":"Adrian","last_name":"Ion","full_name":"Ion, Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Maria Jose","full_name":"Jimenez, Maria Jose","last_name":"Jimenez"},{"first_name":"Regina","full_name":"Poyatos, Regina","last_name":"Poyatos"}],"abstract":[{"lang":"eng","text":"In this paper, we establish a correspondence between the incremental algorithm for computing AT-models [8,9] and the one for computing persistent homology [6,14,15]. We also present a decremental algorithm for computing AT-models that allows to extend the persistence computation to a wider setting. Finally, we show how to combine incremental and decremental techniques for persistent homology computation."}],"publication_identifier":{"eissn":["16113349"],"isbn":["9783642236716"],"issn":["03029743"]},"scopus_import":"1","conference":{"start_date":"2011-08-29","end_date":"2011-08-31","location":"Seville, Spain","name":"CAIP: International Conference on Computer Analysis of Images and Patterns"},"publication_status":"published","type":"conference","oa_version":"Published Version","month":"08","year":"2011","date_created":"2021-07-11T22:01:19Z","title":"Incremental-decremental algorithm for computing AT-models and persistent homology"},{"doi":"10.5061/dryad.299h8","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","status":"public","oa":1,"citation":{"ista":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. 2011. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas), IST Austria, <a href=\"https://doi.org/10.5061/dryad.299h8\">10.5061/dryad.299h8</a>.","ama":"Palero F, Abello P, Macpherson E, Beaumont M, Pascual M. Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). 2011. doi:<a href=\"https://doi.org/10.5061/dryad.299h8\">10.5061/dryad.299h8</a>","short":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, M. Pascual, (2011).","ieee":"F. Palero, P. Abello, E. Macpherson, M. Beaumont, and M. Pascual, “Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas).” IST Austria, 2011.","apa":"Palero, F., Abello, P., Macpherson, E., Beaumont, M., &#38; Pascual, M. (2011). Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas). IST Austria. <a href=\"https://doi.org/10.5061/dryad.299h8\">https://doi.org/10.5061/dryad.299h8</a>","mla":"Palero, Ferran, et al. <i>Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas)</i>. IST Austria, 2011, doi:<a href=\"https://doi.org/10.5061/dryad.299h8\">10.5061/dryad.299h8</a>.","chicago":"Palero, Ferran, Pere Abello, Enrique Macpherson, Mark Beaumont, and Marta Pascual. “Data from: Effect of Oceanographic Barriers and Overfishing on the Population Genetic Structure of the European Spiny Lobster (Palinurus Elephas).” IST Austria, 2011. <a href=\"https://doi.org/10.5061/dryad.299h8\">https://doi.org/10.5061/dryad.299h8</a>."},"abstract":[{"lang":"eng","text":"Defining population structure and genetic diversity levels is of the utmost importance for developing efficient conservation strategies. Overfishing has caused mean annual catches of the European spiny lobster (Palinurus elephas) to decrease alarmingly along its distribution area. In this context, there is a need for comprehensive studies to evaluate the genetic health of the exploited populations. The present work is based on a set of 10 nuclear markers amplified in 331 individuals from 10 different localities covering most of P. elephas distribution area. Samples from Atlantic and Mediterranean basins showed small but significant differences, indicating that P. elephas populations do not behave as a single panmictic unit but form two partially-overlapping groups. Despite intense overfishing, our dataset did not recover a recent bottleneck signal, and showed a large and stable historical effective size instead. This result could be accounted for by specific life history traits (reproduction and longevity) and the limitations of molecular markers in covering very recent timescales for non temporal samples. Our study emphasizes the necessity of integrating information on effective population sizes and life history parameters when evaluating population connectivity levels from genetic data."}],"author":[{"id":"3F0E2A22-F248-11E8-B48F-1D18A9856A87","last_name":"Palero","full_name":"Palero, Ferran","orcid":"0000-0002-0343-8329","first_name":"Ferran"},{"first_name":"Pere","full_name":"Abello, Pere","last_name":"Abello"},{"first_name":"Enrique","last_name":"Macpherson","full_name":"Macpherson, Enrique"},{"last_name":"Beaumont","full_name":"Beaumont, Mark","first_name":"Mark"},{"first_name":"Marta","full_name":"Pascual, Marta","last_name":"Pascual"}],"publisher":"IST Austria","article_processing_charge":"No","oa_version":"Published Version","_id":"9762","day":"12","department":[{"_id":"NiBa"}],"date_updated":"2023-02-23T11:25:25Z","type":"research_data_reference","related_material":{"record":[{"id":"3395","relation":"used_in_publication","status":"public"}]},"title":"Data from: Effect of oceanographic barriers and overfishing on the population genetic structure of the European spiny lobster (Palinurus elephas)","date_created":"2021-08-02T07:11:19Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.299h8"}],"year":"2011","date_published":"2011-05-12T00:00:00Z","month":"05"},{"_id":"9943","day":"09","oa_version":"Preprint","article_processing_charge":"No","publication_status":"published","language":[{"iso":"eng"}],"type":"conference","department":[{"_id":"Bio"}],"date_updated":"2023-02-23T14:13:38Z","title":"Ilastik: Interactive learning and segmentation toolkit","date_created":"2021-08-19T11:49:58Z","month":"06","date_published":"2011-06-09T00:00:00Z","year":"2011","main_file_link":[{"url":"https://www.researchgate.net/publication/224241106_Ilastik_Interactive_learning_and_segmentation_toolkit","open_access":"1"}],"quality_controlled":"1","doi":"10.1109/isbi.2011.5872394","status":"public","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publication":"2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro","keyword":["image segmentation","biomedical imaging","three dimensional displays","neurons","retina","observers","image color analysis"],"citation":{"chicago":"Sommer, Christoph M, Christoph Straehle, Ullrich Köthe, and Fred A. Hamprecht. “Ilastik: Interactive Learning and Segmentation Toolkit.” In <i>2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro</i>. Institute of Electrical and Electronics Engineers, 2011. <a href=\"https://doi.org/10.1109/isbi.2011.5872394\">https://doi.org/10.1109/isbi.2011.5872394</a>.","mla":"Sommer, Christoph M., et al. “Ilastik: Interactive Learning and Segmentation Toolkit.” <i>2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro</i>, Institute of Electrical and Electronics Engineers, 2011, doi:<a href=\"https://doi.org/10.1109/isbi.2011.5872394\">10.1109/isbi.2011.5872394</a>.","apa":"Sommer, C. M., Straehle, C., Köthe, U., &#38; Hamprecht, F. A. (2011). Ilastik: Interactive learning and segmentation toolkit. In <i>2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro</i>. Chicago, Illinois, USA: Institute of Electrical and Electronics Engineers. <a href=\"https://doi.org/10.1109/isbi.2011.5872394\">https://doi.org/10.1109/isbi.2011.5872394</a>","short":"C.M. Sommer, C. Straehle, U. Köthe, F.A. Hamprecht, in:, 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro, Institute of Electrical and Electronics Engineers, 2011.","ieee":"C. M. Sommer, C. Straehle, U. Köthe, and F. A. Hamprecht, “Ilastik: Interactive learning and segmentation toolkit,” in <i>2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro</i>, Chicago, Illinois, USA, 2011.","ista":"Sommer CM, Straehle C, Köthe U, Hamprecht FA. 2011. Ilastik: Interactive learning and segmentation toolkit. 2011 IEEE International Symposium on Biomedical Imaging: from Nano to Micro. ISBI: International Symposium on Biomedical Imaging.","ama":"Sommer CM, Straehle C, Köthe U, Hamprecht FA. Ilastik: Interactive learning and segmentation toolkit. In: <i>2011 IEEE International Symposium on Biomedical Imaging: From Nano to Micro</i>. Institute of Electrical and Electronics Engineers; 2011. doi:<a href=\"https://doi.org/10.1109/isbi.2011.5872394\">10.1109/isbi.2011.5872394</a>"},"oa":1,"publication_identifier":{"eissn":["1945-8452"],"isbn":["978-1-4244-4127-3"],"issn":["1945-7928"]},"conference":{"name":"ISBI: International Symposium on Biomedical Imaging","location":"Chicago, Illinois, USA","end_date":"2011-04-02","start_date":"2011-03-30"},"extern":"1","author":[{"orcid":"0000-0003-1216-9105","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","last_name":"Sommer","full_name":"Sommer, Christoph M","first_name":"Christoph M"},{"full_name":"Straehle, Christoph","last_name":"Straehle","first_name":"Christoph"},{"first_name":"Ullrich","full_name":"Köthe, Ullrich","last_name":"Köthe"},{"full_name":"Hamprecht, Fred A.","last_name":"Hamprecht","first_name":"Fred A."}],"publisher":"Institute of Electrical and Electronics Engineers","abstract":[{"lang":"eng","text":"Segmentation is the process of partitioning digital images into meaningful regions. The analysis of biological high content images often requires segmentation as a first step. We propose ilastik as an easy-to-use tool which allows the user without expertise in image processing to perform segmentation and classification in a unified way. ilastik learns from labels provided by the user through a convenient mouse interface. Based on these labels, ilastik infers a problem specific segmentation. A random forest classifier is used in the learning step, in which each pixel's neighborhood is characterized by a set of generic (nonlinear) features. ilastik supports up to three spatial plus one spectral dimension and makes use of all dimensions in the feature calculation. ilastik provides realtime feedback that enables the user to interactively refine the segmentation result and hence further fine-tune the classifier. An uncertainty measure guides the user to ambiguous regions in the images. Real time performance is achieved by multi-threading which fully exploits the capabilities of modern multi-core machines. Once a classifier has been trained on a set of representative images, it can be exported and used to automatically process a very large number of images (e.g. using the CellProfiler pipeline). ilastik is an open source project and released under the BSD license at www.ilastik.org."}]},{"date_published":"2011-06-01T00:00:00Z","language":[{"iso":"eng"}],"date_updated":"2023-09-05T14:10:15Z","department":[{"_id":"HeEd"}],"_id":"10907","day":"01","article_processing_charge":"No","citation":{"ista":"Artner NM, Ion A, Kropatsch WG. 2011. Spatio-temporal extraction of articulated models in a graph pyramid. Graph-Based Representations in Pattern Recognition. GbRPR: Graph-based Representations in Pattern RecognitionLNIP, LNCS, vol. 6658, 215–224.","ama":"Artner NM, Ion A, Kropatsch WG. Spatio-temporal extraction of articulated models in a graph pyramid. In: Jiang X, Ferrer M, Torsello A, eds. <i>Graph-Based Representations in Pattern Recognition</i>. Vol 6658. LNIP. Berlin, Heidelberg: Springer; 2011:215-224. doi:<a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">10.1007/978-3-642-20844-7_22</a>","short":"N.M. Artner, A. Ion, W.G. Kropatsch, in:, X. Jiang, M. Ferrer, A. Torsello (Eds.), Graph-Based Representations in Pattern Recognition, Springer, Berlin, Heidelberg, 2011, pp. 215–224.","ieee":"N. M. Artner, A. Ion, and W. G. Kropatsch, “Spatio-temporal extraction of articulated models in a graph pyramid,” in <i>Graph-Based Representations in Pattern Recognition</i>, Münster, Germany, 2011, vol. 6658, pp. 215–224.","mla":"Artner, Nicole M., et al. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” <i>Graph-Based Representations in Pattern Recognition</i>, edited by Xiaoyi Jiang et al., vol. 6658, Springer, 2011, pp. 215–24, doi:<a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">10.1007/978-3-642-20844-7_22</a>.","apa":"Artner, N. M., Ion, A., &#38; Kropatsch, W. G. (2011). Spatio-temporal extraction of articulated models in a graph pyramid. In X. Jiang, M. Ferrer, &#38; A. Torsello (Eds.), <i>Graph-Based Representations in Pattern Recognition</i> (Vol. 6658, pp. 215–224). Berlin, Heidelberg: Springer. <a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">https://doi.org/10.1007/978-3-642-20844-7_22</a>","chicago":"Artner, Nicole M., Adrian Ion, and Walter G. Kropatsch. “Spatio-Temporal Extraction of Articulated Models in a Graph Pyramid.” In <i>Graph-Based Representations in Pattern Recognition</i>, edited by Xiaoyi Jiang, Miquel Ferrer, and Andrea Torsello, 6658:215–24. LNIP. Berlin, Heidelberg: Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-20844-7_22\">https://doi.org/10.1007/978-3-642-20844-7_22</a>."},"page":"215-224","place":"Berlin, Heidelberg","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"      6658","publication":"Graph-Based Representations in Pattern Recognition","alternative_title":["LNCS"],"editor":[{"last_name":"Jiang","full_name":"Jiang, Xiaoyi","first_name":"Xiaoyi"},{"last_name":"Ferrer","full_name":"Ferrer, Miquel","first_name":"Miquel"},{"full_name":"Torsello, Andrea","last_name":"Torsello","first_name":"Andrea"}],"month":"06","year":"2011","date_created":"2022-03-21T08:08:35Z","title":"Spatio-temporal extraction of articulated models in a graph pyramid","series_title":"LNIP","publication_status":"published","type":"conference","oa_version":"None","author":[{"first_name":"Nicole M.","full_name":"Artner, Nicole M.","last_name":"Artner"},{"first_name":"Adrian","last_name":"Ion","full_name":"Ion, Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Walter G.","last_name":"Kropatsch","full_name":"Kropatsch, Walter G."}],"publisher":"Springer","abstract":[{"lang":"eng","text":"This paper presents a method to create a model of an articulated object using the planar motion in an initialization video. The model consists of rigid parts connected by points of articulation. The rigid parts are described by the positions of salient feature-points tracked throughout the video. Following a filtering step that identifies points that belong to different objects, rigid parts are found by a grouping process in a graph pyramid. Valid articulation points are selected by verifying multiple hypotheses for each pair of parts."}],"publication_identifier":{"issn":["0302-9743"],"eisbn":["9783642208447"],"isbn":["9783642208430"],"eissn":["1611-3349"]},"scopus_import":"1","conference":{"start_date":"2011-05-18","end_date":"2011-05-20","location":"Münster, Germany","name":"GbRPR: Graph-based Representations in Pattern Recognition"},"acknowledgement":"This work has been partially supported by the Austrian Science Fund under grants S9103-N13 and P18716-N13.","status":"public","quality_controlled":"1","volume":6658,"doi":"10.1007/978-3-642-20844-7_22"},{"quality_controlled":"1","status":"public","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"3522","citation":{"ista":"Lampert C. 2011. Maximum margin multi-label structured prediction. NIPS: Neural Information Processing Systems.","ama":"Lampert C. Maximum margin multi-label structured prediction. In: Neural Information Processing Systems; 2011.","short":"C. Lampert, in:, Neural Information Processing Systems, 2011.","ieee":"C. Lampert, “Maximum margin multi-label structured prediction,” presented at the NIPS: Neural Information Processing Systems, Granada, Spain, 2011.","apa":"Lampert, C. (2011). Maximum margin multi-label structured prediction. Presented at the NIPS: Neural Information Processing Systems, Granada, Spain: Neural Information Processing Systems.","mla":"Lampert, Christoph. <i>Maximum Margin Multi-Label Structured Prediction</i>. Neural Information Processing Systems, 2011.","chicago":"Lampert, Christoph. “Maximum Margin Multi-Label Structured Prediction.” Neural Information Processing Systems, 2011."},"scopus_import":1,"conference":{"start_date":"2011-12-12","location":"Granada, Spain","end_date":"2011-12-14","name":"NIPS: Neural Information Processing Systems"},"publisher":"Neural Information Processing Systems","author":[{"last_name":"Lampert","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"abstract":[{"text":"We study multi-label prediction for structured output sets, a problem that occurs, for example, in object detection in images, secondary structure prediction in computational biology, and graph matching with symmetries. Conventional multilabel classification techniques are typically not applicable in this situation, because they require explicit enumeration of the label set, which is infeasible in case of structured outputs. Relying on techniques originally designed for single-label structured prediction, in particular structured support vector machines, results in reduced prediction accuracy, or leads to infeasible optimization problems. In this work we derive a maximum-margin training formulation for multi-label structured prediction that remains computationally tractable while achieving high prediction accuracy. It also shares most beneficial properties with single-label maximum-margin approaches, in particular formulation as a convex optimization problem, efficient working set training, and PAC-Bayesian generalization bounds.","lang":"eng"}],"_id":"3163","day":"01","oa_version":"None","publication_status":"published","language":[{"iso":"eng"}],"date_updated":"2023-10-17T11:47:35Z","department":[{"_id":"ChLa"}],"type":"conference","date_created":"2018-12-11T12:01:45Z","title":"Maximum margin multi-label structured prediction","related_material":{"record":[{"status":"public","id":"3322","relation":"later_version"}]},"month":"12","date_published":"2011-12-01T00:00:00Z","year":"2011"},{"conference":{"name":"APLAS: Asian Symposium on Programming Languages and Systems","end_date":"2011-12-07","location":"Kenting, Taiwan","start_date":"2011-12-05"},"citation":{"chicago":"Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Solving Recursion-Free Horn Clauses over LI+UIF.” edited by Hongseok Yang, 7078:188–203. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">https://doi.org/10.1007/978-3-642-25318-8_16</a>.","apa":"Gupta, A., Popeea, C., &#38; Rybalchenko, A. (2011). Solving recursion-free Horn clauses over LI+UIF. In H. Yang (Ed.) (Vol. 7078, pp. 188–203). Presented at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan: Springer. <a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">https://doi.org/10.1007/978-3-642-25318-8_16</a>","mla":"Gupta, Ashutosh, et al. <i>Solving Recursion-Free Horn Clauses over LI+UIF</i>. Edited by Hongseok Yang, vol. 7078, Springer, 2011, pp. 188–203, doi:<a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">10.1007/978-3-642-25318-8_16</a>.","ieee":"A. Gupta, C. Popeea, and A. Rybalchenko, “Solving recursion-free Horn clauses over LI+UIF,” presented at the APLAS: Asian Symposium on Programming Languages and Systems, Kenting, Taiwan, 2011, vol. 7078, pp. 188–203.","short":"A. Gupta, C. Popeea, A. Rybalchenko, in:, H. Yang (Ed.), Springer, 2011, pp. 188–203.","ama":"Gupta A, Popeea C, Rybalchenko A. Solving recursion-free Horn clauses over LI+UIF. In: Yang H, ed. Vol 7078. Springer; 2011:188-203. doi:<a href=\"https://doi.org/10.1007/978-3-642-25318-8_16\">10.1007/978-3-642-25318-8_16</a>","ista":"Gupta A, Popeea C, Rybalchenko A. 2011. Solving recursion-free Horn clauses over LI+UIF. APLAS: Asian Symposium on Programming Languages and Systems, LNCS, vol. 7078, 188–203."},"page":"188 - 203","abstract":[{"lang":"eng","text":"Verification of programs with procedures, multi-threaded programs, and higher-order functional programs can be effectively au- tomated using abstraction and refinement schemes that rely on spurious counterexamples for abstraction discovery. The analysis of counterexam- ples can be automated by a series of interpolation queries, or, alterna- tively, as a constraint solving query expressed by a set of recursion free Horn clauses. (A set of interpolation queries can be formulated as a single constraint over Horn clauses with linear dependency structure between the unknown relations.) In this paper we present an algorithm for solving recursion free Horn clauses over a combined theory of linear real/rational arithmetic and uninterpreted functions. Our algorithm performs resolu- tion to deal with the clausal structure and relies on partial solutions to deal with (non-local) instances of functionality axioms."}],"publisher":"Springer","author":[{"first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","last_name":"Gupta","full_name":"Gupta, Ashutosh"},{"first_name":"Corneliu","last_name":"Popeea","full_name":"Popeea, Corneliu"},{"full_name":"Rybalchenko, Andrey","last_name":"Rybalchenko","first_name":"Andrey"}],"doi":"10.1007/978-3-642-25318-8_16","quality_controlled":"1","volume":7078,"editor":[{"first_name":"Hongseok","last_name":"Yang","full_name":"Yang, Hongseok"}],"alternative_title":["LNCS"],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"publist_id":"3383","intvolume":"      7078","status":"public","title":"Solving recursion-free Horn clauses over LI+UIF","date_created":"2018-12-11T12:02:20Z","year":"2011","month":"12","date_published":"2011-12-05T00:00:00Z","_id":"3264","day":"05","oa_version":"None","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling","call_identifier":"FP7","grant_number":"267989"}],"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"date_updated":"2021-01-12T07:42:15Z","type":"conference","publication_status":"published"},{"date_created":"2018-12-11T12:02:21Z","title":"Probabilistic joint image segmentation and labeling","month":"12","date_published":"2011-12-01T00:00:00Z","year":"2011","_id":"3266","day":"01","oa_version":"None","publication_status":"published","language":[{"iso":"eng"}],"date_updated":"2021-01-12T07:42:15Z","type":"conference","department":[{"_id":"HeEd"}],"citation":{"ista":"Ion A, Carreira J, Sminchisescu C. 2011. Probabilistic joint image segmentation and labeling. NIPS Proceedings. NIPS: Neural Information Processing Systems vol. 24, 1827–1835.","ama":"Ion A, Carreira J, Sminchisescu C. Probabilistic joint image segmentation and labeling. In: <i>NIPS Proceedings</i>. Vol 24. Neural Information Processing Systems Foundation; 2011:1827-1835.","short":"A. Ion, J. Carreira, C. Sminchisescu, in:, NIPS Proceedings, Neural Information Processing Systems Foundation, 2011, pp. 1827–1835.","ieee":"A. Ion, J. Carreira, and C. Sminchisescu, “Probabilistic joint image segmentation and labeling,” in <i>NIPS Proceedings</i>, Granada, Spain, 2011, vol. 24, pp. 1827–1835.","mla":"Ion, Adrian, et al. “Probabilistic Joint Image Segmentation and Labeling.” <i>NIPS Proceedings</i>, vol. 24, Neural Information Processing Systems Foundation, 2011, pp. 1827–35.","apa":"Ion, A., Carreira, J., &#38; Sminchisescu, C. (2011). Probabilistic joint image segmentation and labeling. In <i>NIPS Proceedings</i> (Vol. 24, pp. 1827–1835). Granada, Spain: Neural Information Processing Systems Foundation.","chicago":"Ion, Adrian, Joao Carreira, and Cristian Sminchisescu. “Probabilistic Joint Image Segmentation and Labeling.” In <i>NIPS Proceedings</i>, 24:1827–35. Neural Information Processing Systems Foundation, 2011."},"page":"1827 - 1835","scopus_import":1,"conference":{"end_date":"2011-12-14","name":"NIPS: Neural Information Processing Systems","location":"Granada, Spain","start_date":"2011-12-12"},"publisher":"Neural Information Processing Systems Foundation","author":[{"first_name":"Adrian","id":"29F89302-F248-11E8-B48F-1D18A9856A87","full_name":"Ion, Adrian","last_name":"Ion"},{"last_name":"Carreira","full_name":"Carreira, Joao","first_name":"Joao"},{"last_name":"Sminchisescu","full_name":"Sminchisescu, Cristian","first_name":"Cristian"}],"abstract":[{"lang":"eng","text":"We present a joint image segmentation and labeling model (JSL) which, given a bag of figure-ground segment hypotheses extracted at multiple image locations and scales, constructs a joint probability distribution over both the compatible image interpretations (tilings or image segmentations) composed from those segments, and over their labeling into categories. The process of drawing samples from the joint distribution can be interpreted as first sampling tilings, modeled as maximal cliques, from a graph connecting spatially non-overlapping segments in the bag [1], followed by sampling labels for those segments, conditioned on the choice of a particular tiling. We learn the segmentation and labeling parameters jointly, based on Maximum Likelihood with a novel Incremental Saddle Point estimation procedure. The partition function over tilings and labelings is increasingly more accurately approximated by including incorrect configurations that a not-yet-competent model rates probable during learning. We show that the proposed methodologymatches the current state of the art in the Stanford dataset [2], as well as in VOC2010, where 41.7% accuracy on the test set is achieved."}],"volume":24,"quality_controlled":"1","status":"public","publist_id":"3381","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        24","publication":"NIPS Proceedings"},{"date_published":"2011-01-14T00:00:00Z","month":"01","year":"2011","related_material":{"record":[{"status":"public","id":"10909","relation":"earlier_version"}]},"date_created":"2018-12-11T12:02:21Z","title":"Hardness results for homology localization","publication_status":"published","department":[{"_id":"HeEd"}],"date_updated":"2023-02-21T16:07:10Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"None","day":"14","_id":"3267","publisher":"Springer","author":[{"first_name":"Chao","full_name":"Chen, Chao","last_name":"Chen","id":"3E92416E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Freedman","full_name":"Freedman, Daniel","first_name":"Daniel"}],"abstract":[{"lang":"eng","text":"We address the problem of localizing homology classes, namely, finding the cycle representing a given class with the most concise geometric measure. We study the problem with different measures: volume, diameter and radius. For volume, that is, the 1-norm of a cycle, two main results are presented. First, we prove that the problem is NP-hard to approximate within any constant factor. Second, we prove that for homology of dimension two or higher, the problem is NP-hard to approximate even when the Betti number is O(1). The latter result leads to the inapproximability of the problem of computing the nonbounding cycle with the smallest volume and computing cycles representing a homology basis with the minimal total volume. As for the other two measures defined by pairwise geodesic distance, diameter and radius, we show that the localization problem is NP-hard for diameter but is polynomial for radius. Our work is restricted to homology over the ℤ2 field."}],"scopus_import":1,"citation":{"mla":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Discrete &#38; Computational Geometry</i>, vol. 45, no. 3, Springer, 2011, pp. 425–48, doi:<a href=\"https://doi.org/10.1007/s00454-010-9322-8\">10.1007/s00454-010-9322-8</a>.","apa":"Chen, C., &#38; Freedman, D. (2011). Hardness results for homology localization. <i>Discrete &#38; Computational Geometry</i>. Springer. <a href=\"https://doi.org/10.1007/s00454-010-9322-8\">https://doi.org/10.1007/s00454-010-9322-8</a>","chicago":"Chen, Chao, and Daniel Freedman. “Hardness Results for Homology Localization.” <i>Discrete &#38; Computational Geometry</i>. Springer, 2011. <a href=\"https://doi.org/10.1007/s00454-010-9322-8\">https://doi.org/10.1007/s00454-010-9322-8</a>.","ista":"Chen C, Freedman D. 2011. Hardness results for homology localization. Discrete &#38; Computational Geometry. 45(3), 425–448.","ama":"Chen C, Freedman D. Hardness results for homology localization. <i>Discrete &#38; Computational Geometry</i>. 2011;45(3):425-448. doi:<a href=\"https://doi.org/10.1007/s00454-010-9322-8\">10.1007/s00454-010-9322-8</a>","ieee":"C. Chen and D. Freedman, “Hardness results for homology localization,” <i>Discrete &#38; Computational Geometry</i>, vol. 45, no. 3. Springer, pp. 425–448, 2011.","short":"C. Chen, D. Freedman, Discrete &#38; Computational Geometry 45 (2011) 425–448."},"page":"425 - 448","status":"public","publication":"Discrete & Computational Geometry","intvolume":"        45","publist_id":"3379","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","doi":"10.1007/s00454-010-9322-8","quality_controlled":"1","volume":45},{"intvolume":"        30","publication":"Computer Graphics Forum","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3377","issue":"4","oa":1,"citation":{"apa":"Sheng, Y., Cutler, B., Chen, C., &#38; Nasman, J. (2011). Perceptual global illumination cancellation in complex projection environments. <i>Computer Graphics Forum</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">https://doi.org/10.1111/j.1467-8659.2011.01985.x</a>","mla":"Sheng, Yu, et al. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” <i>Computer Graphics Forum</i>, vol. 30, no. 4, Wiley-Blackwell, 2011, pp. 1261–68, doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">10.1111/j.1467-8659.2011.01985.x</a>.","chicago":"Sheng, Yu, Barbara Cutler, Chao Chen, and Joshua Nasman. “Perceptual Global Illumination Cancellation in Complex Projection Environments.” <i>Computer Graphics Forum</i>. Wiley-Blackwell, 2011. <a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">https://doi.org/10.1111/j.1467-8659.2011.01985.x</a>.","ama":"Sheng Y, Cutler B, Chen C, Nasman J. Perceptual global illumination cancellation in complex projection environments. <i>Computer Graphics Forum</i>. 2011;30(4):1261-1268. doi:<a href=\"https://doi.org/10.1111/j.1467-8659.2011.01985.x\">10.1111/j.1467-8659.2011.01985.x</a>","ista":"Sheng Y, Cutler B, Chen C, Nasman J. 2011. Perceptual global illumination cancellation in complex projection environments. Computer Graphics Forum. 30(4), 1261–1268.","ieee":"Y. Sheng, B. Cutler, C. Chen, and J. Nasman, “Perceptual global illumination cancellation in complex projection environments,” <i>Computer Graphics Forum</i>, vol. 30, no. 4. Wiley-Blackwell, pp. 1261–1268, 2011.","short":"Y. Sheng, B. Cutler, C. Chen, J. Nasman, Computer Graphics Forum 30 (2011) 1261–1268."},"page":"1261 - 1268","department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T07:42:16Z","language":[{"iso":"eng"}],"day":"19","_id":"3269","article_processing_charge":"No","date_published":"2011-07-19T00:00:00Z","main_file_link":[{"open_access":"1","url":"http://www.cs.cmu.edu/%7Eshengyu/download/egsr2011_paper.pdf"}],"status":"public","doi":"10.1111/j.1467-8659.2011.01985.x","quality_controlled":"1","volume":30,"author":[{"first_name":"Yu","full_name":"Sheng, Yu","last_name":"Sheng"},{"last_name":"Cutler","full_name":"Cutler, Barbara","first_name":"Barbara"},{"id":"3E92416E-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Chao","last_name":"Chen","first_name":"Chao"},{"full_name":"Nasman, Joshua","last_name":"Nasman","first_name":"Joshua"}],"publisher":"Wiley-Blackwell","abstract":[{"text":"The unintentional scattering of light between neighboring surfaces in complex projection environments increases the brightness and decreases the contrast, disrupting the appearance of the desired imagery. To achieve satisfactory projection results, the inverse problem of global illumination must be solved to cancel this secondary scattering. In this paper, we propose a global illumination cancellation method that minimizes the perceptual difference between the desired imagery and the actual total illumination in the resulting physical environment. Using Gauss-Newton and active set methods, we design a fast solver for the bound constrained nonlinear least squares problem raised by the perceptual error metrics. Our solver is further accelerated with a CUDA implementation and multi-resolution method to achieve 1–2 fps for problems with approximately 3000 variables. We demonstrate the global illumination cancellation algorithm with our multi-projector system. Results show that our method preserves the color fidelity of the desired imagery significantly better than previous methods.","lang":"eng"}],"scopus_import":1,"publication_status":"published","type":"journal_article","oa_version":"Published Version","month":"07","year":"2011","title":"Perceptual global illumination cancellation in complex projection environments","date_created":"2018-12-11T12:02:22Z","article_type":"original"},{"publisher":"TU Dortmund","author":[{"first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Chao"},{"full_name":"Kerber, Michael","last_name":"Kerber","id":"36E4574A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8030-9299","first_name":"Michael"}],"abstract":[{"text":"The persistence diagram of a filtered simplicial com- plex is usually computed by reducing the boundary matrix of the complex. We introduce a simple op- timization technique: by processing the simplices of the complex in decreasing dimension, we can “kill” columns (i.e., set them to zero) without reducing them. This technique completely avoids reduction on roughly half of the columns. We demonstrate that this idea significantly improves the running time of the reduction algorithm in practice. We also give an output-sensitive complexity analysis for the new al- gorithm which yields to sub-cubic asymptotic bounds under certain assumptions.","lang":"eng"}],"page":"197 - 200","citation":{"apa":"Chen, C., &#38; Kerber, M. (2011). Persistent homology computation with a twist (pp. 197–200). Presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland: TU Dortmund.","mla":"Chen, Chao, and Michael Kerber. <i>Persistent Homology Computation with a Twist</i>. TU Dortmund, 2011, pp. 197–200.","chicago":"Chen, Chao, and Michael Kerber. “Persistent Homology Computation with a Twist,” 197–200. TU Dortmund, 2011.","ista":"Chen C, Kerber M. 2011. Persistent homology computation with a twist. EuroCG: European Workshop on Computational Geometry, 197–200.","ama":"Chen C, Kerber M. Persistent homology computation with a twist. In: TU Dortmund; 2011:197-200.","ieee":"C. Chen and M. Kerber, “Persistent homology computation with a twist,” presented at the EuroCG: European Workshop on Computational Geometry, Morschach, Switzerland, 2011, pp. 197–200.","short":"C. Chen, M. Kerber, in:, TU Dortmund, 2011, pp. 197–200."},"conference":{"start_date":"2011-03-28","location":"Morschach, Switzerland","end_date":"2011-03-30","name":"EuroCG: European Workshop on Computational Geometry"},"status":"public","publist_id":"3376","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","month":"01","date_published":"2011-01-01T00:00:00Z","year":"2011","date_created":"2018-12-11T12:02:22Z","title":"Persistent homology computation with a twist","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"date_updated":"2021-01-12T07:42:17Z","type":"conference","day":"01","_id":"3270","oa_version":"None"},{"title":"Efficient computation of persistent homology for cubical data","date_created":"2018-12-11T12:02:23Z","year":"2011","date_published":"2011-11-14T00:00:00Z","month":"11","oa_version":"None","day":"14","_id":"3271","date_updated":"2021-01-12T07:42:18Z","department":[{"_id":"HeEd"}],"type":"book_chapter","language":[{"iso":"eng"}],"publication_status":"published","scopus_import":1,"citation":{"short":"H. Wagner, C. Chen, E. Vuçini, in:, R. Peikert, H. Hauser, H. Carr, R. Fuchs (Eds.), Topological Methods in Data Analysis and Visualization II, Springer, 2011, pp. 91–106.","ieee":"H. Wagner, C. Chen, and E. Vuçini, “Efficient computation of persistent homology for cubical data,” in <i>Topological Methods in Data Analysis and Visualization II</i>, R. Peikert, H. Hauser, H. Carr, and R. Fuchs, Eds. Springer, 2011, pp. 91–106.","ista":"Wagner H, Chen C, Vuçini E. 2011.Efficient computation of persistent homology for cubical data. In: Topological Methods in Data Analysis and Visualization II. Theory, Algorithms, and Applications, , 91–106.","ama":"Wagner H, Chen C, Vuçini E. Efficient computation of persistent homology for cubical data. In: Peikert R, Hauser H, Carr H, Fuchs R, eds. <i>Topological Methods in Data Analysis and Visualization II</i>. Springer; 2011:91-106. doi:<a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">10.1007/978-3-642-23175-9_7</a>","chicago":"Wagner, Hubert, Chao Chen, and Erald Vuçini. “Efficient Computation of Persistent Homology for Cubical Data.” In <i>Topological Methods in Data Analysis and Visualization II</i>, edited by Ronald Peikert, Helwig Hauser, Hamish Carr, and Raphael Fuchs, 91–106. Springer, 2011. <a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">https://doi.org/10.1007/978-3-642-23175-9_7</a>.","mla":"Wagner, Hubert, et al. “Efficient Computation of Persistent Homology for Cubical Data.” <i>Topological Methods in Data Analysis and Visualization II</i>, edited by Ronald Peikert et al., Springer, 2011, pp. 91–106, doi:<a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">10.1007/978-3-642-23175-9_7</a>.","apa":"Wagner, H., Chen, C., &#38; Vuçini, E. (2011). Efficient computation of persistent homology for cubical data. In R. Peikert, H. Hauser, H. Carr, &#38; R. Fuchs (Eds.), <i>Topological Methods in Data Analysis and Visualization II</i> (pp. 91–106). Springer. <a href=\"https://doi.org/10.1007/978-3-642-23175-9_7\">https://doi.org/10.1007/978-3-642-23175-9_7</a>"},"page":"91 - 106","abstract":[{"lang":"eng","text":"In this paper we present an efficient framework for computation of persis- tent homology of cubical data in arbitrary dimensions. An existing algorithm using simplicial complexes is adapted to the setting of cubical complexes. The proposed approach enables efficient application of persistent homology in domains where the data is naturally given in a cubical form. By avoiding triangulation of the data, we significantly reduce the size of the complex. We also present a data-structure de- signed to compactly store and quickly manipulate cubical complexes. By means of numerical experiments, we show high speed and memory efficiency of our ap- proach. We compare our framework to other available implementations, showing its superiority. Finally, we report performance on selected 3D and 4D data-sets."}],"author":[{"full_name":"Wagner, Hubert","last_name":"Wagner","first_name":"Hubert"},{"first_name":"Chao","id":"3E92416E-F248-11E8-B48F-1D18A9856A87","last_name":"Chen","full_name":"Chen, Chao"},{"first_name":"Erald","full_name":"Vuçini, Erald","last_name":"Vuçini"}],"publisher":"Springer","doi":"10.1007/978-3-642-23175-9_7","quality_controlled":"1","editor":[{"first_name":"Ronald","last_name":"Peikert","full_name":"Peikert, Ronald"},{"full_name":"Hauser, Helwig","last_name":"Hauser","first_name":"Helwig"},{"full_name":"Carr, Hamish","last_name":"Carr","first_name":"Hamish"},{"first_name":"Raphael","last_name":"Fuchs","full_name":"Fuchs, Raphael"}],"alternative_title":["Theory, Algorithms, and Applications"],"publication":"Topological Methods in Data Analysis and Visualization II","publist_id":"3375","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","status":"public"},{"degree_awarded":"PhD","title":"Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors","date_created":"2018-12-11T12:02:23Z","month":"12","date_published":"2011-12-12T00:00:00Z","year":"2011","_id":"3273","day":"12","oa_version":"None","article_processing_charge":"No","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"CaHe"}],"date_updated":"2023-09-07T11:30:16Z","type":"dissertation","citation":{"apa":"Maître, J.-L. (2011). <i>Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors</i>. Institute of Science and Technology Austria.","mla":"Maître, Jean-Léon. <i>Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors</i>. Institute of Science and Technology Austria, 2011.","chicago":"Maître, Jean-Léon. “Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors.” Institute of Science and Technology Austria, 2011.","ista":"Maître J-L. 2011. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. Institute of Science and Technology Austria.","ama":"Maître J-L. Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors. 2011.","short":"J.-L. Maître, Mechanics of Adhesion and De‐adhesion in Zebrafish Germ Layer Progenitors, Institute of Science and Technology Austria, 2011.","ieee":"J.-L. Maître, “Mechanics of adhesion and de‐adhesion in zebrafish germ layer progenitors,” Institute of Science and Technology Austria, 2011."},"publication_identifier":{"issn":["2663-337X"]},"publisher":"Institute of Science and Technology Austria","author":[{"last_name":"Maître","full_name":"Maître, Jean-Léon","id":"48F1E0D8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3688-1474","first_name":"Jean-Léon"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg","id":"39427864-F248-11E8-B48F-1D18A9856A87"}],"status":"public","publist_id":"3373","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"acknowledgement":"I would like to express my sincere gratitude to the following people who made with their continuous support and encouragement this thesis possible: First, I want to thank Prof. Dr. Michael Sixt for his excellent supervision and mentoring, especially for the nice, relaxed working atmosphere, a lot of brilliant ideas and the freedom to work in my own way.\r\n\r\nProf. Dr. Reinhard Fässler for his constant support of the Sixt lab and for providing excellent working conditions. \r\n\r\nProf. Dr. Sanjiv Luther and Prof. Dr. Tobias Bollenbach for agreeing to be member of my thesis committee and to evaluate my work.\r\n\r\nDr. Walther Göhring, Carmen Schmitz, the Recombinant Protein Production core facility and the animal care takers for providing the “infrastructure” for this thesis. \r\n\r\nProf. Dr. Daniel Legler, Markus Bruckner and Dr. Julien Polleux for very fruitful collaborations and discussions.\r\n\r\nMy labmates for their help, a lot of discussions and to make the Sixt lab to a convenient place to work : Karin Hirsch, Tim Lämmeramnn, Holger Pflicke, Jörg Renkawitz, Michele Weber and Alexander Eichner All members of the Department of Molecular Medicine for their help. Especially I want to thank Sarah Schmidt, Karin Hirsch and Raphael Ruppert for their friendship, nice chats and their uncensored point of view. ","status":"public","ddc":["570","579"],"supervisor":[{"first_name":"Michael K","orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"abstract":[{"lang":"eng","text":"Chemokines organize immune cell trafficking by inducing either directed (tactic) or random (kinetic) migration and by activating integrins in order to support surface adhesion (haptic). Beyond that the same chemokines can establish clearly defined functional areas in secondary lymphoid organs. Until now it is unclear how chemokines can fulfill such diverse functions. One decisive prerequisite to explain these capacities is to know how chemokines are presented in tissue. In theory chemokines could occur either soluble or immobilized, and could be distributed either homogenously or as a concentration gradient. To dissect if and how the presenting mode of chemokines influences immune cells, I tested the response of dendritic cells (DCs) to differentially displayed chemokines. DCs are antigen presenting cells that reside in the periphery and migrate into draining lymph nodes (LNs) once exposed to inflammatory stimuli to activate naïve T cells. DCs are guided to and within the LN by the chemokine receptor CCR7, which has two ligands, the chemokines CCL19 and CCL21. Both CCR7 ligands are expressed by fibroblastic reticular cells in the LN, but differ in their ability to bind to heparan sulfate residues. CCL21 has a highly charged C-terminal extension, which mediates binding to anionic surfaces, whereas CCL19 is lacking such residues and likely distributes as a soluble molecule. This study shows that surface-bound CCL21 causes random, haptokinetic DC motility, which is confined to the chemokine coated area by insideout activation of β2 integrins that mediate cell binding to the surface. CCL19 on the other hand forms concentration gradients which trigger directional, chemotactic movement, but no surface adhesion. In addition DCs can actively manipulate this system by recruiting and activating serine proteases on their surfaces, which create - by proteolytically removing the adhesive C-terminus - a solubilized variant of CCL21 that functionally resembles CCL19. By generating a CCL21 concentration gradient DCs establish a positive feedback loop to recruit further DCs from the periphery to the CCL21 coated region. In addition DCs can sense chemotactic gradients as well as immobilized haptokinetic fields at the same time and integrate these signals. The result is chemotactically biased haptokinesis - directional migration confined to a chemokine coated track or area - which could explain the dynamic but spatially tightly controlled swarming leukocyte locomotion patterns that have been observed in lymphatic organs by intravital microscopists. The finding that DCs can approach soluble cues in a non-adhesive manner while they attach to surfaces coated with immobilized cues raises the question how these cells transmit intracellular forces to the environment, especially in the non-adherent migration mode. In order to migrate, cells have to generate and transmit force to the extracellular substrate. Force transmission is the prerequisite to procure an expansion of the leading edge and a forward motion of the whole cell body. In the current conceptions actin polymerization at the leading edge is coupled to extracellular ligands via the integrin family of transmembrane receptors, which allows the transmission of intracellular force. Against the paradigm of force transmission during migration, leukocytes, like DCs, are able to migrate in threedimensional environments without using integrin transmembrane receptors (Lämmermann et al., 2008). This reflects the biological function of leukocytes, as they can invade almost all tissues, whereby their migration has to be independent from the extracellular environment. How the cells can achieve this is unclear. For this study I examined DC migration in a defined threedimensional environment and highlighted actin-dynamics with the probe Lifeact-GFP. The result was that chemotactic DCs can switch between integrin-dependent and integrin- independent locomotion and can thereby adapt to the adhesive properties of their environment. If the cells are able to couple their actin cytoskeleton to the substrate, actin polymerization is entirely converted into protrusion. Without coupling the actin cortex undergoes slippage and retrograde actin flow can be observed. But retrograde actin flow can be completely compensated by higher actin polymerization rate keeping the migration velocity and the shape of the cells unaltered. Mesenchymal cells like fibroblast cannot balance the loss of adhesive interaction, cannot protrude into open space and, therefore, strictly depend on integrinmediated force coupling. This leukocyte specific phenomenon of “adaptive force transmission” endows these cells with the unique ability to transit and invade almost every type of tissue. "}],"publisher":"Institute of Science and Technology Austria","author":[{"id":"F44D762E-4F9D-11E9-B64C-9EB26CEFFB5F","last_name":"Schumann","full_name":"Schumann, Kathrin","first_name":"Kathrin"}],"publication_identifier":{"issn":["2663-337X"]},"type":"dissertation","publication_status":"published","oa_version":"Published Version","year":"2011","month":"03","pubrep_id":"11","title":"The role of chemotactic gradients in dendritic cell migration","has_accepted_license":"1","date_created":"2018-12-11T12:02:24Z","publist_id":"3371","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["ISTA Thesis"],"file_date_updated":"2021-02-22T11:24:30Z","page":"141","citation":{"ieee":"K. Schumann, “The role of chemotactic gradients in dendritic cell migration,” Institute of Science and Technology Austria, 2011.","short":"K. Schumann, The Role of Chemotactic Gradients in Dendritic Cell Migration, Institute of Science and Technology Austria, 2011.","ama":"Schumann K. The role of chemotactic gradients in dendritic cell migration. 2011.","ista":"Schumann K. 2011. The role of chemotactic gradients in dendritic cell migration. Institute of Science and Technology Austria.","chicago":"Schumann, Kathrin. “The Role of Chemotactic Gradients in Dendritic Cell Migration.” Institute of Science and Technology Austria, 2011.","apa":"Schumann, K. (2011). <i>The role of chemotactic gradients in dendritic cell migration</i>. Institute of Science and Technology Austria.","mla":"Schumann, Kathrin. <i>The Role of Chemotactic Gradients in Dendritic Cell Migration</i>. Institute of Science and Technology Austria, 2011."},"oa":1,"language":[{"iso":"eng"}],"department":[{"_id":"MiSi"}],"date_updated":"2023-09-07T11:31:48Z","article_processing_charge":"No","_id":"3275","day":"01","date_published":"2011-03-01T00:00:00Z","file":[{"relation":"main_file","date_updated":"2020-07-14T12:46:06Z","file_size":4487708,"access_level":"closed","date_created":"2019-03-26T08:12:21Z","checksum":"e69eee6252660f0b694a2ea8923ddc72","creator":"dernst","file_name":"2011_Thesis_Kathrin_Schumann.pdf","file_id":"6177","content_type":"application/pdf"},{"relation":"main_file","date_updated":"2021-02-22T11:24:30Z","file_size":4313127,"file_id":"9175","file_name":"2011_Thesis_Schumann_noS.pdf","creator":"dernst","success":1,"content_type":"application/pdf","checksum":"71727d63f424b5b446f68f4b87ecadc0","access_level":"open_access","date_created":"2021-02-22T11:24:30Z"}],"degree_awarded":"PhD"},{"volume":12,"quality_controlled":"1","doi":"10.2174/138920311798841753","issue":"8","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"3358","publication":"Current Protein & Peptide Science","intvolume":"        12","status":"public","citation":{"mla":"Ruprecht, Verena, et al. “What Can We Learn from Single Molecule Trajectories?” <i>Current Protein &#38; Peptide Science</i>, vol. 12, no. 8, Bentham Science Publishers, 2011, pp. 714–24, doi:<a href=\"https://doi.org/10.2174/138920311798841753\">10.2174/138920311798841753</a>.","apa":"Ruprecht, V., Axmann, M., Wieser, S., &#38; Schuetz, G. (2011). What can we learn from single molecule trajectories? <i>Current Protein &#38; Peptide Science</i>. Bentham Science Publishers. <a href=\"https://doi.org/10.2174/138920311798841753\">https://doi.org/10.2174/138920311798841753</a>","chicago":"Ruprecht, Verena, Markus Axmann, Stefan Wieser, and Gerhard Schuetz. “What Can We Learn from Single Molecule Trajectories?” <i>Current Protein &#38; Peptide Science</i>. Bentham Science Publishers, 2011. <a href=\"https://doi.org/10.2174/138920311798841753\">https://doi.org/10.2174/138920311798841753</a>.","ista":"Ruprecht V, Axmann M, Wieser S, Schuetz G. 2011. What can we learn from single molecule trajectories? Current Protein &#38; Peptide Science. 12(8), 714–724.","ama":"Ruprecht V, Axmann M, Wieser S, Schuetz G. What can we learn from single molecule trajectories? <i>Current Protein &#38; Peptide Science</i>. 2011;12(8):714-724. doi:<a href=\"https://doi.org/10.2174/138920311798841753\">10.2174/138920311798841753</a>","short":"V. Ruprecht, M. Axmann, S. Wieser, G. Schuetz, Current Protein &#38; Peptide Science 12 (2011) 714–724.","ieee":"V. Ruprecht, M. Axmann, S. Wieser, and G. Schuetz, “What can we learn from single molecule trajectories?,” <i>Current Protein &#38; Peptide Science</i>, vol. 12, no. 8. Bentham Science Publishers, pp. 714–724, 2011."},"page":"714 - 724","scopus_import":1,"abstract":[{"lang":"eng","text":"Diffusing membrane constituents are constantly exposed to a variety of forces that influence their stochastic path. Single molecule experiments allow for resolving trajectories at extremely high spatial and temporal accuracy, thereby offering insights into en route interactions of the tracer. In this review we discuss approaches to derive information about the underlying processes, based on single molecule tracking experiments. In particular, we focus on a new versatile way to analyze single molecule diffusion in the absence of a full analytical treatment. The method is based on comprehensive comparison of an experimental data set against the hypothetical outcome of multiple experiments performed on the computer. Since Monte Carlo simulations can be easily and rapidly performed even on state-of-the-art PCs, our method provides a simple way for testing various - even complicated - diffusion models. We describe the new method in detail, and show the applicability on two specific examples: firstly, kinetic rate constants can be derived for the transient interaction of mobile membrane proteins; secondly, residence time and corral size can be extracted for confined diffusion."}],"author":[{"first_name":"Verena","full_name":"Ruprecht, Verena","last_name":"Ruprecht","id":"4D71A03A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4088-8633"},{"first_name":"Markus","last_name":"Axmann","full_name":"Axmann, Markus"},{"id":"355AA5A0-F248-11E8-B48F-1D18A9856A87","last_name":"Wieser","full_name":"Wieser, Stefan","orcid":"0000-0002-2670-2217","first_name":"Stefan"},{"full_name":"Schuetz, Gerhard","last_name":"Schuetz","first_name":"Gerhard"}],"publisher":"Bentham Science Publishers","_id":"3287","day":"01","oa_version":"None","language":[{"iso":"eng"}],"type":"journal_article","department":[{"_id":"CaHe"},{"_id":"MiSi"}],"date_updated":"2021-01-12T07:42:24Z","publication_status":"published","date_created":"2018-12-11T12:02:28Z","title":"What can we learn from single molecule trajectories?","year":"2011","month":"12","date_published":"2011-12-01T00:00:00Z"},{"date_created":"2018-12-11T12:02:28Z","has_accepted_license":"1","title":"Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens","month":"07","year":"2011","oa_version":"Published Version","publication_status":"published","type":"journal_article","author":[{"first_name":"Michael","orcid":"0000-0002-5920-9090","full_name":"Smutny, Michael","last_name":"Smutny","id":"3FE6E4E8-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Wu, Selwin","last_name":"Wu","first_name":"Selwin"},{"first_name":"Guillermo","full_name":"Gomez, Guillermo","last_name":"Gomez"},{"full_name":"Mangold, Sabine","last_name":"Mangold","first_name":"Sabine"},{"last_name":"Yap","full_name":"Yap, Alpha","first_name":"Alpha"},{"full_name":"Hamilton, Nicholas","last_name":"Hamilton","first_name":"Nicholas"}],"publisher":"Public Library of Science","abstract":[{"text":"The zonula adherens (ZA) of epithelial cells is a site of cell-cell adhesion where cellular forces are exerted and resisted. Increasing evidence indicates that E-cadherin adhesion molecules at the ZA serve to sense force applied on the junctions and coordinate cytoskeletal responses to those forces. Efforts to understand the role that cadherins play in mechanotransduction have been limited by the lack of assays to measure the impact of forces on the ZA. In this study we used 4D imaging of GFP-tagged E-cadherin to analyse the movement of the ZA. Junctions in confluent epithelial monolayers displayed prominent movements oriented orthogonal (perpendicular) to the ZA itself. Two components were identified in these movements: a relatively slow unidirectional (translational) component that could be readily fitted by least-squares regression analysis, upon which were superimposed more rapid oscillatory movements. Myosin IIB was a dominant factor responsible for driving the unilateral translational movements. In contrast, frequency spectrum analysis revealed that depletion of Myosin IIA increased the power of the oscillatory movements. This implies that Myosin IIA may serve to dampen oscillatory movements of the ZA. This extends our recent analysis of Myosin II at the ZA to demonstrate that Myosin IIA and Myosin IIB make distinct contributions to junctional movement at the ZA.","lang":"eng"}],"doi":"10.1371/journal.pone.0022458","quality_controlled":"1","volume":6,"ddc":["570"],"status":"public","acknowledgement":"his work was funded by the National Health and Medical Research Council (NHMRC) of Australia. M.S. was an Erwin Schroedinger postdoctoral fellow of the Austrian Science Fund (FWF), S.K.W. is supported by a UQ International Research Tuition Award and Research Scholarship, S.M .by an ANZ Trustees PhD Scholarship. A.S.Y. is a Research Fellow of the NHMRC. Confocal imaging was performed at the Australian Cancer Research Foundation (ACRF) Cancer Biology Imaging Centre at the Institute for Molecular Bioscience, established with the generous support of the ACRF.","file":[{"content_type":"application/pdf","file_id":"6399","file_name":"2011_PLOS_Smutny.PDF","creator":"dernst","checksum":"57a5eb11dd05241c48c44f492b3ec3ac","access_level":"open_access","date_created":"2019-05-10T10:51:43Z","file_size":1984567,"relation":"main_file","date_updated":"2020-07-14T12:46:06Z"}],"date_published":"2011-07-22T00:00:00Z","_id":"3288","day":"22","department":[{"_id":"CaHe"}],"date_updated":"2021-01-12T07:42:25Z","language":[{"iso":"eng"}],"oa":1,"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":{"ama":"Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. <i>PLoS One</i>. 2011;6(7). doi:<a href=\"https://doi.org/10.1371/journal.pone.0022458\">10.1371/journal.pone.0022458</a>","ista":"Smutny M, Wu S, Gomez G, Mangold S, Yap A, Hamilton N. 2011. Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. PLoS One. 6(7).","ieee":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, and N. Hamilton, “Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens,” <i>PLoS One</i>, vol. 6, no. 7. Public Library of Science, 2011.","short":"M. Smutny, S. Wu, G. Gomez, S. Mangold, A. Yap, N. Hamilton, PLoS One 6 (2011).","mla":"Smutny, Michael, et al. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” <i>PLoS One</i>, vol. 6, no. 7, Public Library of Science, 2011, doi:<a href=\"https://doi.org/10.1371/journal.pone.0022458\">10.1371/journal.pone.0022458</a>.","apa":"Smutny, M., Wu, S., Gomez, G., Mangold, S., Yap, A., &#38; Hamilton, N. (2011). Multicomponent analysis of junctional movements regulated by Myosin II isoforms at the epithelial zonula adherens. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0022458\">https://doi.org/10.1371/journal.pone.0022458</a>","chicago":"Smutny, Michael, Selwin Wu, Guillermo Gomez, Sabine Mangold, Alpha Yap, and Nicholas Hamilton. “Multicomponent Analysis of Junctional Movements Regulated by Myosin II Isoforms at the Epithelial Zonula Adherens.” <i>PLoS One</i>. Public Library of Science, 2011. <a href=\"https://doi.org/10.1371/journal.pone.0022458\">https://doi.org/10.1371/journal.pone.0022458</a>."},"file_date_updated":"2020-07-14T12:46:06Z","issue":"7","intvolume":"         6","publication":"PLoS One","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"3357"},{"oa_version":"Submitted Version","type":"journal_article","publication_status":"published","title":"A general method for calculating likelihoods under the coalescent process","date_created":"2018-12-11T12:02:29Z","year":"2011","month":"11","volume":189,"quality_controlled":"1","doi":"10.1534/genetics.111.129569","ec_funded":1,"status":"public","scopus_import":1,"abstract":[{"text":"Analysis of genomic data requires an efficient way to calculate likelihoods across very large numbers of loci. We describe a general method for finding the distribution of genealogies: we allow migration between demes, splitting of demes [as in the isolation-with-migration (IM) model], and recombination between linked loci. These processes are described by a set of linear recursions for the generating function of branch lengths. Under the infinite-sites model, the probability of any configuration of mutations can be found by differentiating this generating function. Such calculations are feasible for small numbers of sampled genomes: as an example, we show how the generating function can be derived explicitly for three genes under the two-deme IM model. This derivation is done automatically, using Mathematica. Given data from a large number of unlinked and nonrecombining blocks of sequence, these results can be used to find maximum-likelihood estimates of model parameters by tabulating the probabilities of all relevant mutational configurations and then multiplying across loci. The feasibility of the method is demonstrated by applying it to simulated data and to a data set previously analyzed by Wang and Hey (2010) consisting of 26,141 loci sampled from Drosophila simulans and D. melanogaster. Our results suggest that such likelihood calculations are scalable to genomic data as long as the numbers of sampled individuals and mutations per sequence block are small.","lang":"eng"}],"author":[{"full_name":"Lohse, Konrad","last_name":"Lohse","first_name":"Konrad"},{"first_name":"Richard","full_name":"Harrison, Richard","last_name":"Harrison"},{"first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publisher":"Genetics Society of America","day":"01","_id":"3290","project":[{"grant_number":"250152","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","_id":"25B07788-B435-11E9-9278-68D0E5697425"}],"language":[{"iso":"eng"}],"department":[{"_id":"NiBa"}],"date_updated":"2021-01-12T07:42:26Z","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3213358/","open_access":"1"}],"date_published":"2011-11-01T00:00:00Z","issue":"3","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publist_id":"3355","publication":"Genetics","intvolume":"       189","citation":{"chicago":"Lohse, Konrad, Richard Harrison, and Nicholas H Barton. “A General Method for Calculating Likelihoods under the Coalescent Process.” <i>Genetics</i>. Genetics Society of America, 2011. <a href=\"https://doi.org/10.1534/genetics.111.129569\">https://doi.org/10.1534/genetics.111.129569</a>.","mla":"Lohse, Konrad, et al. “A General Method for Calculating Likelihoods under the Coalescent Process.” <i>Genetics</i>, vol. 189, no. 3, Genetics Society of America, 2011, pp. 977–87, doi:<a href=\"https://doi.org/10.1534/genetics.111.129569\">10.1534/genetics.111.129569</a>.","apa":"Lohse, K., Harrison, R., &#38; Barton, N. H. (2011). A general method for calculating likelihoods under the coalescent process. <i>Genetics</i>. Genetics Society of America. <a href=\"https://doi.org/10.1534/genetics.111.129569\">https://doi.org/10.1534/genetics.111.129569</a>","short":"K. Lohse, R. Harrison, N.H. Barton, Genetics 189 (2011) 977–987.","ieee":"K. Lohse, R. Harrison, and N. H. Barton, “A general method for calculating likelihoods under the coalescent process,” <i>Genetics</i>, vol. 189, no. 3. Genetics Society of America, pp. 977–987, 2011.","ista":"Lohse K, Harrison R, Barton NH. 2011. A general method for calculating likelihoods under the coalescent process. Genetics. 189(3), 977–987.","ama":"Lohse K, Harrison R, Barton NH. A general method for calculating likelihoods under the coalescent process. <i>Genetics</i>. 2011;189(3):977-987. doi:<a href=\"https://doi.org/10.1534/genetics.111.129569\">10.1534/genetics.111.129569</a>"},"page":"977 - 987","oa":1}]