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Field and T. Ellis, “Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012.” Institute of Science and Technology Austria, 2016.","ista":"Field D, Ellis T. 2016. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>.","short":"D. Field, T. Ellis, (2016).","ama":"Field D, Ellis T. Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>","chicago":"Field, David, and Thomas Ellis. “Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>.","apa":"Field, D., &#38; Ellis, T. (2016). Inference of mating patterns among wild snapdragons in a natural hybrid zone in 2012. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:37\">https://doi.org/10.15479/AT:ISTA:37</a>","mla":"Field, David, and Thomas Ellis. <i>Inference of Mating Patterns among Wild Snapdragons in a Natural Hybrid Zone in 2012</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:37\">10.15479/AT:ISTA:37</a>."},"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","file":[{"content_type":"application/zip","date_updated":"2020-07-14T12:47:01Z","access_level":"open_access","file_size":132808,"file_name":"IST-2016-37-v1+1_paternity_archive.zip","file_id":"5620","relation":"main_file","checksum":"4ae751b1fa4897fa216241f975a57313","date_created":"2018-12-12T13:03:02Z","creator":"system"}]},{"oa":1,"keyword":["RNAP binding","de novo promoter evolution","lac promoter"],"date_updated":"2024-02-21T13:50:34Z","oa_version":"Published Version","datarep_id":"43","month":"05","day":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"used_in_publication","id":"1131","status":"public"}]},"year":"2016","author":[{"full_name":"Tugrul, Murat","id":"37C323C6-F248-11E8-B48F-1D18A9856A87","last_name":"Tugrul","first_name":"Murat","orcid":"0000-0002-8523-0758"}],"abstract":[{"lang":"eng","text":"The data stored here is used in Murat Tugrul's PhD thesis (Chapter 3), which is related to the evolution of bacterial RNA polymerase binding.\r\nMagdalena Steinrueck (PhD Student in Calin Guet's group at IST Austria) performed the experiments and created the data on de novo promoter evolution. Fabienne Jesse (PhD Student in Jon Bollback's group at IST Austria) performed the experiments and created the data on lac promoter evolution."}],"date_published":"2016-05-12T00:00:00Z","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:01Z","contributor":[{"id":"2C023F40-F248-11E8-B48F-1D18A9856A87","first_name":"Magdalena","last_name":"Steinrück","contributor_type":"researcher"},{"contributor_type":"researcher","first_name":"Fabienne","last_name":"Jesse","id":"4C8C26A4-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"NiBa"},{"_id":"JoBo"}],"date_created":"2018-12-12T12:31:30Z","doi":"10.15479/AT:ISTA:43","_id":"5554","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"title":"Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase","type":"research_data","status":"public","file":[{"file_id":"5626","date_created":"2018-12-12T13:03:08Z","creator":"system","checksum":"1fc0a10bb7ce110fcb5e1fbe3cf0c4e2","relation":"main_file","date_updated":"2020-07-14T12:47:01Z","content_type":"application/zip","file_name":"IST-2016-43-v1+1_DATA_MTugrul_PhDThesis_Chapter3.zip","file_size":1123495,"access_level":"open_access"}],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","citation":{"short":"M. Tugrul, (2016).","chicago":"Tugrul, Murat. “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>.","ama":"Tugrul M. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>","apa":"Tugrul, M. (2016). Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:43\">https://doi.org/10.15479/AT:ISTA:43</a>","mla":"Tugrul, Murat. <i>Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>.","ieee":"M. Tugrul, “Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase.” Institute of Science and Technology Austria, 2016.","ista":"Tugrul M. 2016. Experimental Data for Binding Site Evolution of Bacterial RNA Polymerase, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:43\">10.15479/AT:ISTA:43</a>."}},{"article_processing_charge":"No","citation":{"apa":"Hauschild, R. (2016). Fiji script to determine average speed and direction of migration of cells. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:44\">https://doi.org/10.15479/AT:ISTA:44</a>","mla":"Hauschild, Robert. <i>Fiji Script to Determine Average Speed and Direction of Migration of Cells</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>.","chicago":"Hauschild, Robert. “Fiji Script to Determine Average Speed and Direction of Migration of Cells.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:44\">https://doi.org/10.15479/AT:ISTA:44</a>.","ama":"Hauschild R. Fiji script to determine average speed and direction of migration of cells. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>","short":"R. Hauschild, (2016).","ieee":"R. Hauschild, “Fiji script to determine average speed and direction of migration of cells.” Institute of Science and Technology Austria, 2016.","ista":"Hauschild R. 2016. Fiji script to determine average speed and direction of migration of cells, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:44\">10.15479/AT:ISTA:44</a>."},"file":[{"date_updated":"2020-07-14T12:47:02Z","content_type":"application/zip","file_name":"IST-2016-44-v1+1_migrationAnalyzer.zip","access_level":"open_access","file_size":20692,"file_id":"5621","creator":"system","date_created":"2018-12-12T13:03:03Z","relation":"main_file","checksum":"9f96cddbcd4ed689f48712ffe234d5e5"}],"publisher":"Institute of Science and Technology Austria","status":"public","type":"research_data","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"title":"Fiji script to determine average speed and direction of migration of cells","_id":"5555","date_created":"2018-12-12T12:31:31Z","doi":"10.15479/AT:ISTA:44","department":[{"_id":"Bio"}],"has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:02Z","date_published":"2016-07-08T00:00:00Z","abstract":[{"text":"This FIJI script calculates the population average of the migration speed as a function of time of all cells from wide field microscopy movies.","lang":"eng"}],"author":[{"orcid":"0000-0001-9843-3522","last_name":"Hauschild","first_name":"Robert","full_name":"Hauschild, Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"}],"year":"2016","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"08","oa_version":"Published Version","month":"07","datarep_id":"44","date_updated":"2024-02-21T13:50:06Z","ddc":["570"],"keyword":["cell migration","wide field microscopy","FIJI"],"oa":1},{"title":"MATLAB analysis code for 'Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast'","tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","image":"/images/cc_by_sa.png","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode"},"type":"research_data","status":"public","publisher":"Institute of Science and Technology Austria","file":[{"file_id":"5616","relation":"main_file","checksum":"ee697f2b1ade4dc14d6ac0334dd832ab","creator":"system","date_created":"2018-12-12T13:02:58Z","content_type":"application/zip","date_updated":"2020-07-14T12:47:02Z","file_size":296722548,"access_level":"open_access","file_name":"IST-2016-45-v1+1_PaperCode.zip"}],"citation":{"ama":"Lukacisin M, Landon M, Jajoo R. MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>","short":"M. Lukacisin, M. Landon, R. Jajoo, (2016).","chicago":"Lukacisin, Martin, Matthieu Landon, and Rishi Jajoo. “MATLAB Analysis Code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>.","mla":"Lukacisin, Martin, et al. <i>MATLAB Analysis Code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.”</i> Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","apa":"Lukacisin, M., Landon, M., &#38; Jajoo, R. (2016). MATLAB analysis code for “Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:45\">https://doi.org/10.15479/AT:ISTA:45</a>","ista":"Lukacisin M, Landon M, Jajoo R. 2016. MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:45\">10.15479/AT:ISTA:45</a>.","ieee":"M. Lukacisin, M. Landon, and R. Jajoo, “MATLAB analysis code for ‘Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.’” Institute of Science and Technology Austria, 2016."},"article_processing_charge":"No","department":[{"_id":"ToBo"}],"doi":"10.15479/AT:ISTA:45","date_created":"2018-12-12T12:31:31Z","_id":"5556","license":"https://creativecommons.org/licenses/by-sa/4.0/","author":[{"orcid":"0000-0001-6549-4177","last_name":"Lukacisin","first_name":"Martin","full_name":"Lukacisin, Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Landon, Matthieu","first_name":"Matthieu","last_name":"Landon"},{"full_name":"Jajoo, Rishi","last_name":"Jajoo","first_name":"Rishi"}],"abstract":[{"lang":"eng","text":"MATLAB code and processed datasets available for reproducing the results in: \r\nLukačišin, M.*, Landon, M.*, Jajoo, R*. (2016) Sequence-Specific Thermodynamic Properties of Nucleic Acids Influence Both Transcriptional Pausing and Backtracking in Yeast.\r\n*equal contributions"}],"date_published":"2016-08-25T00:00:00Z","file_date_updated":"2020-07-14T12:47:02Z","has_accepted_license":"1","oa":1,"date_updated":"2024-02-21T13:51:53Z","keyword":["transcription","pausing","backtracking","polymerase","RNA","NET-seq","nucleosome","basepairing"],"ddc":["571"],"month":"08","oa_version":"Published Version","datarep_id":"45","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"25","related_material":{"record":[{"status":"deleted","id":"8431","relation":"used_in_publication"},{"status":"public","relation":"research_paper","id":"1029"}]},"year":"2016"},{"date_published":"2016-09-20T00:00:00Z","abstract":[{"text":"Small synthetic discrete tomography problems.\r\nSizes are 32x32, 64z64 and 256x256.\r\nProjection angles are 2, 4, and 6.\r\nNumber of labels are 3 and 5.","lang":"eng"}],"author":[{"last_name":"Swoboda","first_name":"Paul","full_name":"Swoboda, Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:02Z","has_accepted_license":"1","date_updated":"2024-02-21T13:50:21Z","ddc":["006"],"keyword":["discrete tomography"],"oa":1,"year":"2016","day":"20","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"09","datarep_id":"46","oa_version":"Published Version","status":"public","type":"research_data","tmp":{"name":"Creative Commons Public Domain Dedication (CC0 1.0)","short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png"},"title":"Synthetic discrete tomography problems","citation":{"ista":"Swoboda P. 2016. Synthetic discrete tomography problems, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>.","ieee":"P. Swoboda, “Synthetic discrete tomography problems.” Institute of Science and Technology Austria, 2016.","apa":"Swoboda, P. (2016). Synthetic discrete tomography problems. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>","mla":"Swoboda, Paul. <i>Synthetic Discrete Tomography Problems</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>.","short":"P. Swoboda, (2016).","chicago":"Swoboda, Paul. “Synthetic Discrete Tomography Problems.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:46\">https://doi.org/10.15479/AT:ISTA:46</a>.","ama":"Swoboda P. Synthetic discrete tomography problems. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:46\">10.15479/AT:ISTA:46</a>"},"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","file":[{"date_updated":"2020-07-14T12:47:02Z","content_type":"application/zip","file_name":"IST-2016-46-v1+1_discrete_tomography_synthetic.zip","file_size":36058401,"access_level":"open_access","file_id":"5645","creator":"system","date_created":"2018-12-12T13:05:19Z","relation":"main_file","checksum":"aa5a16a0dc888da7186fb8fc45e88439"}],"department":[{"_id":"VlKo"}],"contributor":[{"contributor_type":"data_collector","first_name":"Jan","last_name":"Kuske"}],"_id":"5557","doi":"10.15479/AT:ISTA:46","date_created":"2018-12-12T12:31:31Z"},{"datarep_id":"48","oa_version":"Published Version","month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"23","publist_id":"6238","related_material":{"record":[{"status":"public","relation":"other","id":"1122"}]},"year":"2016","oa":1,"ddc":["004"],"date_updated":"2024-02-21T13:50:48Z","file_date_updated":"2020-07-14T12:47:02Z","has_accepted_license":"1","author":[{"full_name":"Bojsen-Hansen, Morten","id":"439F0C8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4417-3224","first_name":"Morten","last_name":"Bojsen-Hansen"}],"abstract":[{"text":"PhD thesis LaTeX source code","lang":"eng"}],"date_published":"2016-09-23T00:00:00Z","doi":"10.15479/AT:ISTA:48","date_created":"2018-12-12T12:31:31Z","_id":"5558","department":[{"_id":"ChWo"}],"file":[{"date_created":"2018-12-12T13:02:18Z","creator":"system","checksum":"5b1b256ad796fbddb4b7729f5e45e444","relation":"main_file","file_id":"5589","file_name":"IST-2016-48-v1+1_2016_Bojsen-Hansen_TCaAWSW.tar.bz2","file_size":55237885,"access_level":"open_access","date_updated":"2020-07-14T12:47:02Z","content_type":"application/x-bzip2"}],"publisher":"Institute of Science and Technology Austria","citation":{"short":"M. Bojsen-Hansen, (2016).","chicago":"Bojsen-Hansen, Morten. “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>.","ama":"Bojsen-Hansen M. Tracking, Correcting and Absorbing Water Surface Waves. 2016. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>","apa":"Bojsen-Hansen, M. (2016). Tracking, Correcting and Absorbing Water Surface Waves. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:48\">https://doi.org/10.15479/AT:ISTA:48</a>","mla":"Bojsen-Hansen, Morten. <i>Tracking, Correcting and Absorbing Water Surface Waves</i>. Institute of Science and Technology Austria, 2016, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>.","ista":"Bojsen-Hansen M. 2016. Tracking, Correcting and Absorbing Water Surface Waves, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:48\">10.15479/AT:ISTA:48</a>.","ieee":"M. Bojsen-Hansen, “Tracking, Correcting and Absorbing Water Surface Waves.” Institute of Science and Technology Austria, 2016."},"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Tracking, Correcting and Absorbing Water Surface Waves","status":"public","type":"research_data","pubrep_id":"640"},{"publication":"Molecular Biology and Evolution","day":"01","year":"2016","language":[{"iso":"eng"}],"file_date_updated":"2020-07-14T12:47:10Z","issue":"3","author":[{"first_name":"Sébastien","last_name":"Wielgoss","full_name":"Wielgoss, Sébastien"},{"id":"2C471CFA-F248-11E8-B48F-1D18A9856A87","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","last_name":"Bergmiller","first_name":"Tobias"},{"full_name":"Bischofberger, Anna M.","first_name":"Anna M.","last_name":"Bischofberger"},{"full_name":"Hall, Alex R.","last_name":"Hall","first_name":"Alex R."}],"abstract":[{"text":"Parasitism creates selection for resistance mechanisms in host populations and is hypothesized to promote increased host evolvability. However, the influence of these traits on host evolution when parasites are no longer present is unclear. We used experimental evolution and whole-genome sequencing of Escherichia coli to determine the effects of past and present exposure to parasitic viruses (phages) on the spread of mutator alleles, resistance, and bacterial competitive fitness. We found that mutator alleles spread rapidly during adaptation to any of four different phage species, and this pattern was even more pronounced with multiple phages present simultaneously. However, hypermutability did not detectably accelerate adaptation in the absence of phages and recovery of fitness costs associated with resistance. Several lineages evolved phage resistance through elevated mucoidy, and during subsequent evolution in phage-free conditions they rapidly reverted to nonmucoid, phage-susceptible phenotypes. Genome sequencing revealed that this phenotypic reversion was achieved by additional genetic changes rather than by genotypic reversion of the initial resistance mutations. Insertion sequence (IS) elements played a key role in both the acquisition of resistance and adaptation in the absence of parasites; unlike single nucleotide polymorphisms, IS insertions were not more frequent in mutator lineages. Our results provide a genetic explanation for rapid reversion of mucoidy, a phenotype observed in other bacterial species including human pathogens. Moreover, this demonstrates that the types of genetic change underlying adaptation to fitness costs, and consequently the impact of evolvability mechanisms such as increased point-mutation rates, depend critically on the mechanism of resistance.","lang":"eng"}],"volume":33,"date_published":"2016-03-01T00:00:00Z","date_created":"2018-12-18T13:18:10Z","publisher":"Oxford University Press","file":[{"file_id":"5750","creator":"dernst","date_created":"2018-12-18T13:21:45Z","relation":"main_file","checksum":"47d9010690b6c5c17f2ac830cc63ac5c","date_updated":"2020-07-14T12:47:10Z","content_type":"application/pdf","file_name":"2016_MolBiolEvol_Wielgoss.pdf","file_size":634037,"access_level":"open_access"}],"pmid":1,"scopus_import":"1","oa_version":"Published Version","month":"03","related_material":{"record":[{"status":"public","relation":"research_data","id":"9719"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publication_status":"published","date_updated":"2023-09-05T13:46:05Z","ddc":["576"],"publication_identifier":{"issn":["0737-4038"],"eissn":["1537-1719"]},"has_accepted_license":"1","doi":"10.1093/molbev/msv270","external_id":{"pmid":["26609077"]},"_id":"5749","page":"770-782","intvolume":"        33","acknowledgement":"The authors thank three anonymous reviewers and the editor for helpful comments on the manuscript, as well as Dominique Schneider for feedback on an earlier draft, Jenna Gallie for lytic λ and Julien Capelle for T5 and T6. This work was supported by the Swiss National Science Foundation (PZ00P3_148255 to A.H.) and an EU Marie Curie PEOPLE Postdoctoral Fellowship for Career Development (FP7-PEOPLE-2012-IEF-331824 to S.W.).","quality_controlled":"1","department":[{"_id":"CaGu"}],"citation":{"mla":"Wielgoss, Sébastien, et al. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3, Oxford University Press, 2016, pp. 770–82, doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>.","apa":"Wielgoss, S., Bergmiller, T., Bischofberger, A. M., &#38; Hall, A. R. (2016). Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>","chicago":"Wielgoss, Sébastien, Tobias Bergmiller, Anna M. Bischofberger, and Alex R. Hall. “Adaptation to Parasites and Costs of Parasite Resistance in Mutator and Nonmutator Bacteria.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2016. <a href=\"https://doi.org/10.1093/molbev/msv270\">https://doi.org/10.1093/molbev/msv270</a>.","short":"S. Wielgoss, T. Bergmiller, A.M. Bischofberger, A.R. Hall, Molecular Biology and Evolution 33 (2016) 770–782.","ama":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. <i>Molecular Biology and Evolution</i>. 2016;33(3):770-782. doi:<a href=\"https://doi.org/10.1093/molbev/msv270\">10.1093/molbev/msv270</a>","ieee":"S. Wielgoss, T. Bergmiller, A. M. Bischofberger, and A. R. Hall, “Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria,” <i>Molecular Biology and Evolution</i>, vol. 33, no. 3. Oxford University Press, pp. 770–782, 2016.","ista":"Wielgoss S, Bergmiller T, Bischofberger AM, Hall AR. 2016. Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria. Molecular Biology and Evolution. 33(3), 770–782."},"article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","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)"},"title":"Adaptation to parasites and costs of parasite resistance in mutator and nonmutator bacteria","type":"journal_article","status":"public","pubrep_id":"587"},{"day":"02","language":[{"iso":"eng"}],"year":"2016","publication":"Computational Topology in Image Context","abstract":[{"lang":"eng","text":"Discretization of sphere in the integer space follows a particular discretization scheme, which, in principle, conforms to some topological model. This eventually gives rise to interesting topological properties of a discrete spherical surface, which need to be investigated for its analytical characterization. This paper presents some novel results on the local topological properties of the naive model of discrete sphere. They follow from the bijection of each quadraginta octant of naive sphere with its projection map called f -map on the corresponding functional plane and from the characterization of certain jumps in the f-map. As an application, we have shown how these properties can be used in designing an efficient reconstruction algorithm for a naive spherical surface from an input voxel set when it is sparse or noisy."}],"volume":9667,"date_published":"2016-06-02T00:00:00Z","author":[{"full_name":"Sen, Nabhasmita","last_name":"Sen","first_name":"Nabhasmita"},{"full_name":"Biswas, Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","last_name":"Biswas","first_name":"Ranita","orcid":"0000-0002-5372-7890"},{"full_name":"Bhowmick, Partha","last_name":"Bhowmick","first_name":"Partha"}],"date_created":"2019-01-08T20:44:24Z","publisher":"Springer Nature","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"06","oa_version":"None","date_updated":"2022-01-28T08:01:22Z","publication_identifier":{"isbn":["978-3-319-39440-4"],"eissn":["1611-3349"],"eisbn":["978-3-319-39441-1"],"issn":["0302-9743"]},"publication_status":"published","conference":{"name":"CTIC: Computational Topology in Image Context","end_date":"2016-06-17","start_date":"2016-06-15","location":"Marseille, France"},"alternative_title":["LNCS"],"page":"253-264","_id":"5805","intvolume":"      9667","doi":"10.1007/978-3-319-39441-1_23","department":[{"_id":"HeEd"}],"place":"Cham","quality_controlled":"1","article_processing_charge":"No","extern":"1","citation":{"ieee":"N. Sen, R. Biswas, and P. Bhowmick, “On some local topological properties of naive discrete sphere,” in <i>Computational Topology in Image Context</i>, vol. 9667, Cham: Springer Nature, 2016, pp. 253–264.","ista":"Sen N, Biswas R, Bhowmick P. 2016.On some local topological properties of naive discrete sphere. In: Computational Topology in Image Context. LNCS, vol. 9667, 253–264.","ama":"Sen N, Biswas R, Bhowmick P. On some local topological properties of naive discrete sphere. In: <i>Computational Topology in Image Context</i>. Vol 9667. Cham: Springer Nature; 2016:253-264. doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">10.1007/978-3-319-39441-1_23</a>","chicago":"Sen, Nabhasmita, Ranita Biswas, and Partha Bhowmick. “On Some Local Topological Properties of Naive Discrete Sphere.” In <i>Computational Topology in Image Context</i>, 9667:253–64. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">https://doi.org/10.1007/978-3-319-39441-1_23</a>.","short":"N. Sen, R. Biswas, P. Bhowmick, in:, Computational Topology in Image Context, Springer Nature, Cham, 2016, pp. 253–264.","mla":"Sen, Nabhasmita, et al. “On Some Local Topological Properties of Naive Discrete Sphere.” <i>Computational Topology in Image Context</i>, vol. 9667, Springer Nature, 2016, pp. 253–64, doi:<a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">10.1007/978-3-319-39441-1_23</a>.","apa":"Sen, N., Biswas, R., &#38; Bhowmick, P. (2016). On some local topological properties of naive discrete sphere. In <i>Computational Topology in Image Context</i> (Vol. 9667, pp. 253–264). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-39441-1_23\">https://doi.org/10.1007/978-3-319-39441-1_23</a>"},"status":"public","type":"book_chapter","title":"On some local topological properties of naive discrete sphere"},{"extern":"1","article_processing_charge":"No","citation":{"ista":"Biswas R, Bhowmick P. 2016. On functionality of quadraginta octants of naive sphere with application to circle drawing. Discrete Geometry for Computer Imagery. DGCI: International Conference on Discrete Geometry for Computer Imagery, LNCS, vol. 9647, 256–267.","ieee":"R. Biswas and P. Bhowmick, “On functionality of quadraginta octants of naive sphere with application to circle drawing,” in <i>Discrete Geometry for Computer Imagery</i>, Nantes, France, 2016, vol. 9647, pp. 256–267.","chicago":"Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing.” In <i>Discrete Geometry for Computer Imagery</i>, 9647:256–67. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">https://doi.org/10.1007/978-3-319-32360-2_20</a>.","short":"R. Biswas, P. Bhowmick, in:, Discrete Geometry for Computer Imagery, Springer Nature, Cham, 2016, pp. 256–267.","ama":"Biswas R, Bhowmick P. On functionality of quadraginta octants of naive sphere with application to circle drawing. In: <i>Discrete Geometry for Computer Imagery</i>. Vol 9647. Cham: Springer Nature; 2016:256-267. doi:<a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">10.1007/978-3-319-32360-2_20</a>","apa":"Biswas, R., &#38; Bhowmick, P. (2016). On functionality of quadraginta octants of naive sphere with application to circle drawing. In <i>Discrete Geometry for Computer Imagery</i> (Vol. 9647, pp. 256–267). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">https://doi.org/10.1007/978-3-319-32360-2_20</a>","mla":"Biswas, Ranita, and Partha Bhowmick. “On Functionality of Quadraginta Octants of Naive Sphere with Application to Circle Drawing.” <i>Discrete Geometry for Computer Imagery</i>, vol. 9647, Springer Nature, 2016, pp. 256–67, doi:<a href=\"https://doi.org/10.1007/978-3-319-32360-2_20\">10.1007/978-3-319-32360-2_20</a>."},"title":"On functionality of quadraginta octants of naive sphere with application to circle drawing","type":"conference","status":"public","doi":"10.1007/978-3-319-32360-2_20","intvolume":"      9647","page":"256-267","_id":"5806","quality_controlled":"1","place":"Cham","department":[{"_id":"HeEd"}],"alternative_title":["LNCS"],"month":"04","oa_version":"None","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","conference":{"start_date":"2016-04-18","name":"DGCI: International Conference on Discrete Geometry for Computer Imagery","end_date":"2016-04-20","location":"Nantes, France"},"publication_status":"published","publication_identifier":{"eisbn":["978-3-319-32360-2"],"issn":["0302-9743","1611-3349"],"isbn":["978-3-319-32359-6"]},"date_updated":"2022-01-28T08:10:11Z","publisher":"Springer Nature","date_created":"2019-01-08T20:44:37Z","author":[{"orcid":"0000-0002-5372-7890","last_name":"Biswas","first_name":"Ranita","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita"},{"last_name":"Bhowmick","first_name":"Partha","full_name":"Bhowmick, Partha"}],"date_published":"2016-04-09T00:00:00Z","abstract":[{"lang":"eng","text":"Although the concept of functional plane for naive plane is studied and reported in the literature in great detail, no similar study is yet found for naive sphere. This article exposes the first study in this line, opening up further prospects of analyzing the topological properties of sphere in the discrete space. We show that each quadraginta octant Q of a naive sphere forms a bijection with its projected pixel set on a unique coordinate plane, which thereby serves as the functional plane of Q, and hence gives rise to merely mono-jumps during back projection. The other two coordinate planes serve as para-functional and dia-functional planes for Q, as the former is ‘mono-jumping’ but not bijective, whereas the latter holds neither of the two. Owing to this, the quadraginta octants form symmetry groups and subgroups with equivalent jump conditions. We also show a potential application in generating a special class of discrete 3D circles based on back projection and jump bridging by Steiner voxels. A circle in this class possesses 4-symmetry, uniqueness, and bounded distance from the underlying real sphere and real plane."}],"volume":9647,"publication":"Discrete Geometry for Computer Imagery","language":[{"iso":"eng"}],"year":"2016","day":"09"},{"publisher":"Springer Nature","extern":"1","citation":{"ieee":"R. Biswas, P. Bhowmick, and V. E. Brimkov, “On the connectivity and smoothness of discrete spherical circles,” in <i>Combinatorial image analysis</i>, vol. 9448, Cham: Springer Nature, 2016, pp. 86–100.","ista":"Biswas R, Bhowmick P, Brimkov VE. 2016.On the connectivity and smoothness of discrete spherical circles. In: Combinatorial image analysis. vol. 9448, 86–100.","ama":"Biswas R, Bhowmick P, Brimkov VE. On the connectivity and smoothness of discrete spherical circles. In: <i>Combinatorial Image Analysis</i>. Vol 9448. Cham: Springer Nature; 2016:86-100. doi:<a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">10.1007/978-3-319-26145-4_7</a>","chicago":"Biswas, Ranita, Partha Bhowmick, and Valentin E. Brimkov. “On the Connectivity and Smoothness of Discrete Spherical Circles.” In <i>Combinatorial Image Analysis</i>, 9448:86–100. Cham: Springer Nature, 2016. <a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">https://doi.org/10.1007/978-3-319-26145-4_7</a>.","short":"R. Biswas, P. Bhowmick, V.E. Brimkov, in:, Combinatorial Image Analysis, Springer Nature, Cham, 2016, pp. 86–100.","mla":"Biswas, Ranita, et al. “On the Connectivity and Smoothness of Discrete Spherical Circles.” <i>Combinatorial Image Analysis</i>, vol. 9448, Springer Nature, 2016, pp. 86–100, doi:<a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">10.1007/978-3-319-26145-4_7</a>.","apa":"Biswas, R., Bhowmick, P., &#38; Brimkov, V. E. (2016). On the connectivity and smoothness of discrete spherical circles. In <i>Combinatorial image analysis</i> (Vol. 9448, pp. 86–100). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-26145-4_7\">https://doi.org/10.1007/978-3-319-26145-4_7</a>"},"article_processing_charge":"No","title":"On the connectivity and smoothness of discrete spherical circles","type":"book_chapter","status":"public","date_created":"2019-01-08T20:45:19Z","doi":"10.1007/978-3-319-26145-4_7","_id":"5809","page":"86-100","intvolume":"      9448","quality_controlled":"1","department":[{"_id":"HeEd"}],"place":"Cham","author":[{"first_name":"Ranita","last_name":"Biswas","orcid":"0000-0002-5372-7890","id":"3C2B033E-F248-11E8-B48F-1D18A9856A87","full_name":"Biswas, Ranita"},{"full_name":"Bhowmick, Partha","first_name":"Partha","last_name":"Bhowmick"},{"last_name":"Brimkov","first_name":"Valentin E.","full_name":"Brimkov, Valentin E."}],"volume":9448,"abstract":[{"lang":"eng","text":"A discrete spherical circle is a topologically well-connected 3D circle in the integer space, which belongs to a discrete sphere as well as a discrete plane. It is one of the most important 3D geometric primitives, but has not possibly yet been studied up to its merit. This paper is a maiden exposition of some of its elementary properties, which indicates a sense of its profound theoretical prospects in the framework of digital geometry. We have shown how different types of discretization can lead to forbidden and admissible classes, when one attempts to define the discretization of a spherical circle in terms of intersection between a discrete sphere and a discrete plane. Several fundamental theoretical results have been presented, the algorithm for construction of discrete spherical circles has been discussed, and some test results have been furnished to demonstrate its practicality and usefulness."}],"date_published":"2016-01-06T00:00:00Z","month":"01","publication":"Combinatorial image analysis","oa_version":"None","day":"06","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","language":[{"iso":"eng"}],"year":"2016","publication_status":"published","conference":{"name":"IWCIA: International Workshop on Combinatorial Image Analysis","end_date":"2015-11-27","start_date":"2015-11-24","location":"Kolkata, India"},"date_updated":"2022-01-28T08:13:03Z","publication_identifier":{"isbn":["978-3-319-26144-7"],"eissn":["1611-3349"],"eisbn":["978-3-319-26145-4"],"issn":["0302-9743"]}},{"oa":1,"publication_status":"published","date_updated":"2021-01-12T06:50:41Z","ddc":["570"],"oa_version":"Published Version","month":"01","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5767","article_number":"1865","has_accepted_license":"1","quality_controlled":"1","department":[{"_id":"SyCr"}],"doi":"10.7717/peerj.1865","_id":"1431","intvolume":"      2016","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon","status":"public","type":"journal_article","pubrep_id":"584","citation":{"ieee":"A. Tartally, A. Kelager, M. Fürst, and D. Nash, “Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon,” <i>PeerJ</i>, vol. 2016, no. 3. PeerJ, 2016.","ista":"Tartally A, Kelager A, Fürst M, Nash D. 2016. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. PeerJ. 2016(3), 1865.","mla":"Tartally, András, et al. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” <i>PeerJ</i>, vol. 2016, no. 3, 1865, PeerJ, 2016, doi:<a href=\"https://doi.org/10.7717/peerj.1865\">10.7717/peerj.1865</a>.","apa":"Tartally, A., Kelager, A., Fürst, M., &#38; Nash, D. (2016). Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. <i>PeerJ</i>. PeerJ. <a href=\"https://doi.org/10.7717/peerj.1865\">https://doi.org/10.7717/peerj.1865</a>","short":"A. Tartally, A. Kelager, M. Fürst, D. Nash, PeerJ 2016 (2016).","chicago":"Tartally, András, Andreas Kelager, Matthias Fürst, and David Nash. “Host Plant Use Drives Genetic Differentiation in Syntopic Populations of Maculinea Alcon.” <i>PeerJ</i>. PeerJ, 2016. <a href=\"https://doi.org/10.7717/peerj.1865\">https://doi.org/10.7717/peerj.1865</a>.","ama":"Tartally A, Kelager A, Fürst M, Nash D. Host plant use drives genetic differentiation in syntopic populations of Maculinea alcon. <i>PeerJ</i>. 2016;2016(3). doi:<a href=\"https://doi.org/10.7717/peerj.1865\">10.7717/peerj.1865</a>"},"publication":"PeerJ","day":"01","language":[{"iso":"eng"}],"year":"2016","author":[{"last_name":"Tartally","first_name":"András","full_name":"Tartally, András"},{"full_name":"Kelager, Andreas","first_name":"Andreas","last_name":"Kelager"},{"id":"393B1196-F248-11E8-B48F-1D18A9856A87","full_name":"Fürst, Matthias","last_name":"Fürst","first_name":"Matthias","orcid":"0000-0002-3712-925X"},{"first_name":"David","last_name":"Nash","full_name":"Nash, David"}],"volume":2016,"abstract":[{"text":"The rare socially parasitic butterfly Maculinea alcon occurs in two forms, which are characteristic of hygric or xeric habitats and which exploit different host plants and host ants. The status of these two forms has been the subject of considerable controversy. Populations of the two forms are usually spatially distinct, but at Răscruci in Romania both forms occur on the same site (syntopically). We examined the genetic differentiation between the two forms using eight microsatellite markers, and compared with a nearby hygric site, Şardu. Our results showed that while the two forms are strongly differentiated at Răscruci, it is the xeric form there that is most similar to the hygric form at Şardu, and Bayesian clustering algorithms suggest that these two populations have exchanged genes relatively recently. We found strong evidence for population substructuring, caused by high within host ant nest relatedness, indicating very limited dispersal of most ovipositing females, but not association with particular host ant species. Our results are consistent with the results of larger scale phylogeographic studies that suggest that the two forms represent local ecotypes specialising on different host plants, each with a distinct flowering phenology, providing a temporal rather than spatial barrier to gene flow.","lang":"eng"}],"date_published":"2016-01-01T00:00:00Z","file_date_updated":"2020-07-14T12:44:53Z","issue":"3","date_created":"2018-12-11T11:51:59Z","scopus_import":1,"publisher":"PeerJ","file":[{"relation":"main_file","checksum":"c27d898598a1e3d7f629607a309254e1","date_created":"2018-12-12T10:17:19Z","creator":"system","file_id":"5272","file_size":1216360,"access_level":"open_access","file_name":"IST-2016-584-v1+1_peerj-1865.pdf","content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z"}]},{"file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:44:53Z","file_size":4510512,"access_level":"open_access","file_name":"IST-2016-582-v1+1_ncomms11552.pdf","file_id":"5355","relation":"main_file","checksum":"7e84d0392348c874d473b62f1042de22","date_created":"2018-12-12T10:18:33Z","creator":"system"}],"publisher":"Nature Publishing Group","scopus_import":1,"project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P24909-B24"},{"call_identifier":"FP7","grant_number":"268548","_id":"25C0F108-B435-11E9-9278-68D0E5697425","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons"}],"date_created":"2018-12-11T11:51:59Z","file_date_updated":"2020-07-14T12:44:53Z","abstract":[{"lang":"eng","text":"CA3–CA3 recurrent excitatory synapses are thought to play a key role in memory storage and pattern completion. Whether the plasticity properties of these synapses are consistent with their proposed network functions remains unclear. Here, we examine the properties of spike timing-dependent plasticity (STDP) at CA3–CA3 synapses. Low-frequency pairing of excitatory postsynaptic potentials (EPSPs) and action potentials (APs) induces long-term potentiation (LTP), independent of temporal order. The STDP curve is symmetric and broad (half-width ~150 ms). Consistent with these STDP induction properties, AP–EPSP sequences lead to supralinear summation of spine [Ca2+] transients. Furthermore, afterdepolarizations (ADPs) following APs efficiently propagate into dendrites of CA3 pyramidal neurons, and EPSPs summate with dendritic ADPs. In autoassociative network models, storage and recall are more robust with symmetric than with asymmetric STDP rules. Thus, a specialized STDP induction rule allows reliable storage and recall of information in the hippocampal CA3 network."}],"volume":7,"date_published":"2016-05-13T00:00:00Z","author":[{"id":"46CB58F2-F248-11E8-B48F-1D18A9856A87","full_name":"Mishra, Rajiv Kumar","first_name":"Rajiv Kumar","last_name":"Mishra"},{"id":"394AB1C8-F248-11E8-B48F-1D18A9856A87","full_name":"Kim, Sooyun","first_name":"Sooyun","last_name":"Kim"},{"full_name":"Guzmán, José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2209-5242","first_name":"José","last_name":"Guzmán"},{"id":"353C1B58-F248-11E8-B48F-1D18A9856A87","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","orcid":"0000-0001-5001-4804"}],"day":"13","language":[{"iso":"eng"}],"year":"2016","publication":"Nature Communications","ec_funded":1,"citation":{"ieee":"R. K. Mishra, S. Kim, J. Guzmán, and P. M. Jonas, “Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks,” <i>Nature Communications</i>, vol. 7. Nature Publishing Group, 2016.","ista":"Mishra RK, Kim S, Guzmán J, Jonas PM. 2016. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. Nature Communications. 7, 11552.","mla":"Mishra, Rajiv Kumar, et al. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>, vol. 7, 11552, Nature Publishing Group, 2016, doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>.","apa":"Mishra, R. K., Kim, S., Guzmán, J., &#38; Jonas, P. M. (2016). Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>","ama":"Mishra RK, Kim S, Guzmán J, Jonas PM. Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks. <i>Nature Communications</i>. 2016;7. doi:<a href=\"https://doi.org/10.1038/ncomms11552\">10.1038/ncomms11552</a>","short":"R.K. Mishra, S. Kim, J. Guzmán, P.M. Jonas, Nature Communications 7 (2016).","chicago":"Mishra, Rajiv Kumar, Sooyun Kim, José Guzmán, and Peter M Jonas. “Symmetric Spike Timing-Dependent Plasticity at CA3–CA3 Synapses Optimizes Storage and Recall in Autoassociative Networks.” <i>Nature Communications</i>. Nature Publishing Group, 2016. <a href=\"https://doi.org/10.1038/ncomms11552\">https://doi.org/10.1038/ncomms11552</a>."},"status":"public","type":"journal_article","pubrep_id":"582","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Symmetric spike timing-dependent plasticity at CA3–CA3 synapses optimizes storage and recall in autoassociative networks","_id":"1432","intvolume":"         7","doi":"10.1038/ncomms11552","department":[{"_id":"PeJo"}],"acknowledgement":"We thank Jozsef Csicsvari and Nelson Spruston for critically reading the manuscript. We also thank A. Schlögl for programming, F. Marr for technical assistance and E. Kramberger for manuscript editing. ","quality_controlled":"1","has_accepted_license":"1","article_number":"11552","related_material":{"record":[{"status":"public","id":"1396","relation":"dissertation_contains"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5766","oa_version":"Published Version","month":"05","date_updated":"2023-09-07T11:55:25Z","ddc":["570"],"oa":1,"publication_status":"published"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publist_id":"5764","oa_version":"Preprint","month":"08","date_updated":"2021-01-12T06:50:42Z","oa":1,"publication_status":"published","intvolume":"       271","_id":"1434","page":"672 - 719","doi":"10.1016/j.jfa.2016.04.006","department":[{"_id":"LaEr"}],"quality_controlled":"1","citation":{"ista":"Bao Z, Erdös L, Schnelli K. 2016. Local stability of the free additive convolution. Journal of Functional Analysis. 271(3), 672–719.","ieee":"Z. Bao, L. Erdös, and K. Schnelli, “Local stability of the free additive convolution,” <i>Journal of Functional Analysis</i>, vol. 271, no. 3. Academic Press, pp. 672–719, 2016.","chicago":"Bao, Zhigang, László Erdös, and Kevin Schnelli. “Local Stability of the Free Additive Convolution.” <i>Journal of Functional Analysis</i>. Academic Press, 2016. <a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">https://doi.org/10.1016/j.jfa.2016.04.006</a>.","short":"Z. Bao, L. Erdös, K. Schnelli, Journal of Functional Analysis 271 (2016) 672–719.","ama":"Bao Z, Erdös L, Schnelli K. Local stability of the free additive convolution. <i>Journal of Functional Analysis</i>. 2016;271(3):672-719. doi:<a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">10.1016/j.jfa.2016.04.006</a>","apa":"Bao, Z., Erdös, L., &#38; Schnelli, K. (2016). Local stability of the free additive convolution. <i>Journal of Functional Analysis</i>. Academic Press. <a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">https://doi.org/10.1016/j.jfa.2016.04.006</a>","mla":"Bao, Zhigang, et al. “Local Stability of the Free Additive Convolution.” <i>Journal of Functional Analysis</i>, vol. 271, no. 3, Academic Press, 2016, pp. 672–719, doi:<a href=\"https://doi.org/10.1016/j.jfa.2016.04.006\">10.1016/j.jfa.2016.04.006</a>."},"type":"journal_article","status":"public","title":"Local stability of the free additive convolution","language":[{"iso":"eng"}],"year":"2016","day":"01","publication":"Journal of Functional Analysis","ec_funded":1,"issue":"3","date_published":"2016-08-01T00:00:00Z","volume":271,"abstract":[{"text":"We prove that the system of subordination equations, defining the free additive convolution of two probability measures, is stable away from the edges of the support and blow-up singularities by showing that the recent smoothness condition of Kargin is always satisfied. As an application, we consider the local spectral statistics of the random matrix ensemble A+UBU⁎A+UBU⁎, where U is a Haar distributed random unitary or orthogonal matrix, and A and B   are deterministic matrices. In the bulk regime, we prove that the empirical spectral distribution of A+UBU⁎A+UBU⁎ concentrates around the free additive convolution of the spectral distributions of A and B   on scales down to N−2/3N−2/3.","lang":"eng"}],"author":[{"full_name":"Bao, Zhigang","id":"442E6A6C-F248-11E8-B48F-1D18A9856A87","first_name":"Zhigang","last_name":"Bao","orcid":"0000-0003-3036-1475"},{"orcid":"0000-0001-5366-9603","last_name":"Erdös","first_name":"László","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László"},{"last_name":"Schnelli","first_name":"Kevin","orcid":"0000-0003-0954-3231","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","full_name":"Schnelli, Kevin"}],"project":[{"_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7"}],"date_created":"2018-12-11T11:52:00Z","main_file_link":[{"url":"http://arxiv.org/abs/1508.05905","open_access":"1"}],"publisher":"Academic Press","scopus_import":1},{"article_number":"1207393","has_accepted_license":"1","ddc":["570"],"date_updated":"2021-01-12T06:50:43Z","publication_status":"published","oa":1,"publist_id":"5762","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","month":"01","oa_version":"Published Version","status":"public","type":"journal_article","pubrep_id":"580","title":"P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"citation":{"chicago":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” <i>Neural Plasticity</i>. Hindawi Publishing Corporation, 2016. <a href=\"https://doi.org/10.1155/2016/1207393\">https://doi.org/10.1155/2016/1207393</a>.","ama":"Guzmán J, Gerevich Z. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. <i>Neural Plasticity</i>. 2016;2016. doi:<a href=\"https://doi.org/10.1155/2016/1207393\">10.1155/2016/1207393</a>","short":"J. Guzmán, Z. Gerevich, Neural Plasticity 2016 (2016).","mla":"Guzmán, José, and Zoltan Gerevich. “P2Y Receptors in Synaptic Transmission and Plasticity: Therapeutic Potential in Cognitive Dysfunction.” <i>Neural Plasticity</i>, vol. 2016, 1207393, Hindawi Publishing Corporation, 2016, doi:<a href=\"https://doi.org/10.1155/2016/1207393\">10.1155/2016/1207393</a>.","apa":"Guzmán, J., &#38; Gerevich, Z. (2016). P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. <i>Neural Plasticity</i>. Hindawi Publishing Corporation. <a href=\"https://doi.org/10.1155/2016/1207393\">https://doi.org/10.1155/2016/1207393</a>","ieee":"J. Guzmán and Z. Gerevich, “P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction,” <i>Neural Plasticity</i>, vol. 2016. Hindawi Publishing Corporation, 2016.","ista":"Guzmán J, Gerevich Z. 2016. P2Y receptors in synaptic transmission and plasticity: Therapeutic potential in cognitive dysfunction. Neural Plasticity. 2016, 1207393."},"department":[{"_id":"PeJo"}],"quality_controlled":"1","_id":"1435","intvolume":"      2016","doi":"10.1155/2016/1207393","volume":2016,"abstract":[{"text":"ATP released from neurons and astrocytes during neuronal activity or under pathophysiological circumstances is able to influence information flow in neuronal circuits by activation of ionotropic P2X and metabotropic P2Y receptors and subsequent modulation of cellular excitability, synaptic strength, and plasticity. In the present paper we review cellular and network effects of P2Y receptors in the brain. We show that P2Y receptors inhibit the release of neurotransmitters, modulate voltage- and ligand-gated ion channels, and differentially influence the induction of synaptic plasticity in the prefrontal cortex, hippocampus, and cerebellum. The findings discussed here may explain how P2Y1 receptor activation during brain injury, hypoxia, inflammation, schizophrenia, or Alzheimer's disease leads to an impairment of cognitive processes. Hence, it is suggested that the blockade of P2Y1 receptors may have therapeutic potential against cognitive disturbances in these states.","lang":"eng"}],"date_published":"2016-01-01T00:00:00Z","author":[{"last_name":"Guzmán","first_name":"José","id":"30CC5506-F248-11E8-B48F-1D18A9856A87","full_name":"Guzmán, José"},{"first_name":"Zoltan","last_name":"Gerevich","full_name":"Gerevich, Zoltan"}],"file_date_updated":"2020-07-14T12:44:54Z","day":"01","language":[{"iso":"eng"}],"year":"2016","publication":"Neural Plasticity","scopus_import":1,"file":[{"file_id":"4740","relation":"main_file","checksum":"8dc5c2f3d44d4775a6e7e3edb0d7a0da","creator":"system","date_created":"2018-12-12T10:09:17Z","content_type":"application/pdf","date_updated":"2020-07-14T12:44:54Z","access_level":"open_access","file_size":1395180,"file_name":"IST-2016-580-v1+1_1207393.pdf"}],"publisher":"Hindawi Publishing Corporation","date_created":"2018-12-11T11:52:00Z"},{"day":"01","language":[{"iso":"eng"}],"year":"2016","publication":"Journal de Mathématiques Pures et Appliquées","ec_funded":1,"issue":"1","file_date_updated":"2020-07-14T12:44:54Z","abstract":[{"text":"We study the time evolution of a system of N spinless fermions in R3 which interact through a pair potential, e.g., the Coulomb potential. We compare the dynamics given by the solution to Schrödinger's equation with the time-dependent Hartree-Fock approximation, and we give an estimate for the accuracy of this approximation in terms of the kinetic energy of the system. This leads, in turn, to bounds in terms of the initial total energy of the system.","lang":"eng"}],"volume":105,"date_published":"2016-01-01T00:00:00Z","author":[{"full_name":"Bach, Volker","first_name":"Volker","last_name":"Bach"},{"last_name":"Breteaux","first_name":"Sébastien","full_name":"Breteaux, Sébastien"},{"full_name":"Petrat, Sören P","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9166-5889","first_name":"Sören P","last_name":"Petrat"},{"last_name":"Pickl","first_name":"Peter","full_name":"Pickl, Peter"},{"full_name":"Tzaneteas, Tim","last_name":"Tzaneteas","first_name":"Tim"}],"date_created":"2018-12-11T11:52:00Z","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"file":[{"file_name":"IST-2016-581-v1+1_1-s2.0-S0021782415001191-main.pdf","file_size":658491,"access_level":"open_access","date_updated":"2020-07-14T12:44:54Z","content_type":"application/pdf","creator":"system","date_created":"2018-12-12T10:10:36Z","checksum":"c5afe1f6935bc7f2b546adbde1d31a35","relation":"main_file","file_id":"4825"}],"publisher":"Elsevier","scopus_import":1,"publist_id":"5763","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","month":"01","date_updated":"2021-01-12T06:50:43Z","ddc":["510","530"],"oa":1,"publication_status":"published","has_accepted_license":"1","_id":"1436","page":"1 - 30","intvolume":"       105","doi":"10.1016/j.matpur.2015.09.003","department":[{"_id":"RoSe"}],"quality_controlled":"1","citation":{"ista":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. 2016. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. Journal de Mathématiques Pures et Appliquées. 105(1), 1–30.","ieee":"V. Bach, S. Breteaux, S. P. Petrat, P. Pickl, and T. Tzaneteas, “Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction,” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 105, no. 1. Elsevier, pp. 1–30, 2016.","ama":"Bach V, Breteaux S, Petrat SP, Pickl P, Tzaneteas T. Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. <i>Journal de Mathématiques Pures et Appliquées</i>. 2016;105(1):1-30. doi:<a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">10.1016/j.matpur.2015.09.003</a>","chicago":"Bach, Volker, Sébastien Breteaux, Sören P Petrat, Peter Pickl, and Tim Tzaneteas. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier, 2016. <a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">https://doi.org/10.1016/j.matpur.2015.09.003</a>.","short":"V. Bach, S. Breteaux, S.P. Petrat, P. Pickl, T. Tzaneteas, Journal de Mathématiques Pures et Appliquées 105 (2016) 1–30.","mla":"Bach, Volker, et al. “Kinetic Energy Estimates for the Accuracy of the Time-Dependent Hartree-Fock Approximation with Coulomb Interaction.” <i>Journal de Mathématiques Pures et Appliquées</i>, vol. 105, no. 1, Elsevier, 2016, pp. 1–30, doi:<a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">10.1016/j.matpur.2015.09.003</a>.","apa":"Bach, V., Breteaux, S., Petrat, S. P., Pickl, P., &#38; Tzaneteas, T. (2016). Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction. <i>Journal de Mathématiques Pures et Appliquées</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.matpur.2015.09.003\">https://doi.org/10.1016/j.matpur.2015.09.003</a>"},"status":"public","type":"journal_article","pubrep_id":"581","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Kinetic energy estimates for the accuracy of the time-dependent Hartree-Fock approximation with Coulomb interaction"},{"date_created":"2018-12-11T11:52:01Z","project":[{"grant_number":"S 11407_N23","call_identifier":"FWF","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.07565"}],"publisher":"ACM","ec_funded":1,"year":"2016","language":[{"iso":"eng"}],"day":"11","date_published":"2016-01-11T00:00:00Z","abstract":[{"lang":"eng","text":"We study algorithmic questions for concurrent systems where the transitions are labeled from a complete, closed semiring, and path properties are algebraic with semiring operations. The algebraic path properties can model dataflow analysis problems, the shortest path problem, and many other natural problems that arise in program analysis. We consider that each component of the concurrent system is a graph with constant treewidth, a property satisfied by the controlflow graphs of most programs. We allow for multiple possible queries, which arise naturally in demand driven dataflow analysis. The study of multiple queries allows us to consider the tradeoff between the resource usage of the one-time preprocessing and for each individual query. The traditional approach constructs the product graph of all components and applies the best-known graph algorithm on the product. In this approach, even the answer to a single query requires the transitive closure (i.e., the results of all possible queries), which provides no room for tradeoff between preprocessing and query time. Our main contributions are algorithms that significantly improve the worst-case running time of the traditional approach, and provide various tradeoffs depending on the number of queries. For example, in a concurrent system of two components, the traditional approach requires hexic time in the worst case for answering one query as well as computing the transitive closure, whereas we show that with one-time preprocessing in almost cubic time, each subsequent query can be answered in at most linear time, and even the transitive closure can be computed in almost quartic time. Furthermore, we establish conditional optimality results showing that the worst-case running time of our algorithms cannot be improved without achieving major breakthroughs in graph algorithms (i.e., improving the worst-case bound for the shortest path problem in general graphs). Preliminary experimental results show that our algorithms perform favorably on several benchmarks."}],"volume":"20-22","author":[{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X"},{"last_name":"Goharshady","first_name":"Amir","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-4783-0389","last_name":"Ibsen-Jensen","first_name":"Rasmus","full_name":"Ibsen-Jensen, Rasmus","id":"3B699956-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722","id":"49704004-F248-11E8-B48F-1D18A9856A87","full_name":"Pavlogiannis, Andreas"}],"department":[{"_id":"KrCh"}],"quality_controlled":"1","_id":"1437","page":"733 - 747","external_id":{"arxiv":["1510.07565"]},"doi":"10.1145/2837614.2837624","status":"public","type":"conference","title":"Algorithms for algebraic path properties in concurrent systems of constant treewidth components","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components</i>. Vol. 20–22, ACM, 2016, pp. 733–47, doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>.","apa":"Chatterjee, K., Goharshady, A. K., Ibsen-Jensen, R., &#38; Pavlogiannis, A. (2016). Algorithms for algebraic path properties in concurrent systems of constant treewidth components (Vol. 20–22, pp. 733–747). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>","ama":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. In: Vol 20-22. ACM; 2016:733-747. doi:<a href=\"https://doi.org/10.1145/2837614.2837624\">10.1145/2837614.2837624</a>","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Rasmus Ibsen-Jensen, and Andreas Pavlogiannis. “Algorithms for Algebraic Path Properties in Concurrent Systems of Constant Treewidth Components,” 20–22:733–47. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837624\">https://doi.org/10.1145/2837614.2837624</a>.","short":"K. Chatterjee, A.K. Goharshady, R. Ibsen-Jensen, A. Pavlogiannis, in:, ACM, 2016, pp. 733–747.","ista":"Chatterjee K, Goharshady AK, Ibsen-Jensen R, Pavlogiannis A. 2016. Algorithms for algebraic path properties in concurrent systems of constant treewidth components. POPL: Principles of Programming Languages, POPL, vol. 20–22, 733–747.","ieee":"K. Chatterjee, A. K. Goharshady, R. Ibsen-Jensen, and A. Pavlogiannis, “Algorithms for algebraic path properties in concurrent systems of constant treewidth components,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 733–747."},"date_updated":"2024-03-25T23:30:18Z","conference":{"location":"St. Petersburg, FL, USA","name":"POPL: Principles of Programming Languages","start_date":"2016-01-20","end_date":"2016-01-22"},"publication_status":"published","oa":1,"publist_id":"5761","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"5441","relation":"earlier_version","status":"public"},{"relation":"earlier_version","id":"5442","status":"public"},{"status":"public","id":"821","relation":"dissertation_contains"},{"relation":"later_version","id":"6009","status":"public"},{"relation":"dissertation_contains","id":"8934","status":"public"}]},"oa_version":"Preprint","month":"01","alternative_title":["POPL"],"arxiv":1},{"publist_id":"5760","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"5993","relation":"later_version","status":"public"}]},"month":"01","oa_version":"Preprint","date_updated":"2023-09-19T14:38:41Z","conference":{"location":"St. Petersburg, FL, USA","start_date":"2016-01-20","name":"POPL: Principles of Programming Languages","end_date":"2016-01-22"},"oa":1,"publication_status":"published","alternative_title":["POPL"],"arxiv":1,"page":"327 - 342","_id":"1438","external_id":{"arxiv":["1510.08517"]},"doi":"10.1145/2837614.2837639","department":[{"_id":"KrCh"}],"quality_controlled":"1","acknowledgement":"Supported by the Natural Science Foundation of China (NSFC) under Grant No. 61532019 ","citation":{"chicago":"Chatterjee, Krishnendu, Hongfei Fu, Petr Novotný, and Rouzbeh Hasheminezhad. “Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs,” 20–22:327–42. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837639\">https://doi.org/10.1145/2837614.2837639</a>.","ama":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. In: Vol 20-22. ACM; 2016:327-342. doi:<a href=\"https://doi.org/10.1145/2837614.2837639\">10.1145/2837614.2837639</a>","short":"K. Chatterjee, H. Fu, P. Novotný, R. Hasheminezhad, in:, ACM, 2016, pp. 327–342.","apa":"Chatterjee, K., Fu, H., Novotný, P., &#38; Hasheminezhad, R. (2016). Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs (Vol. 20–22, pp. 327–342). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837639\">https://doi.org/10.1145/2837614.2837639</a>","mla":"Chatterjee, Krishnendu, et al. <i>Algorithmic Analysis of Qualitative and Quantitative Termination Problems for Affine Probabilistic Programs</i>. Vol. 20–22, ACM, 2016, pp. 327–42, doi:<a href=\"https://doi.org/10.1145/2837614.2837639\">10.1145/2837614.2837639</a>.","ieee":"K. Chatterjee, H. Fu, P. Novotný, and R. Hasheminezhad, “Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 327–342.","ista":"Chatterjee K, Fu H, Novotný P, Hasheminezhad R. 2016. Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs. POPL: Principles of Programming Languages, POPL, vol. 20–22, 327–342."},"status":"public","type":"conference","title":"Algorithmic analysis of qualitative and quantitative termination problems for affine probabilistic programs","year":"2016","language":[{"iso":"eng"}],"day":"11","ec_funded":1,"date_published":"2016-01-11T00:00:00Z","abstract":[{"lang":"eng","text":"In this paper, we consider termination of probabilistic programs with real-valued variables. The questions concerned are: (a) qualitative ones that ask (i) whether the program terminates with probability 1 (almost-sure termination) and (ii) whether the expected termination time is finite (finite termination); (b) quantitative ones that ask (i) to approximate the expected termination time (expectation problem) and (ii) to compute a bound B such that the probability to terminate after B steps decreases exponentially (concentration problem). To solve these questions, we utilize the notion of ranking supermartingales which is a powerful approach for proving termination of probabilistic programs. In detail, we focus on algorithmic synthesis of linear ranking-supermartingales over affine probabilistic programs (APP's) with both angelic and demonic non-determinism. An important subclass of APP's is LRAPP which is defined as the class of all APP's over which a linear ranking-supermartingale exists. Our main contributions are as follows. Firstly, we show that the membership problem of LRAPP (i) can be decided in polynomial time for APP's with at most demonic non-determinism, and (ii) is NP-hard and in PSPACE for APP's with angelic non-determinism; moreover, the NP-hardness result holds already for APP's without probability and demonic non-determinism. Secondly, we show that the concentration problem over LRAPP can be solved in the same complexity as for the membership problem of LRAPP. Finally, we show that the expectation problem over LRAPP can be solved in 2EXPTIME and is PSPACE-hard even for APP's without probability and non-determinism (i.e., deterministic programs). Our experimental results demonstrate the effectiveness of our approach to answer the qualitative and quantitative questions over APP's with at most demonic non-determinism."}],"volume":"20-22","author":[{"orcid":"0000-0002-4561-241X","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"id":"3AAD03D6-F248-11E8-B48F-1D18A9856A87","full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu"},{"full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny"},{"last_name":"Hasheminezhad","first_name":"Rouzbeh","full_name":"Hasheminezhad, Rouzbeh"}],"project":[{"call_identifier":"FWF","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"},{"call_identifier":"FP7","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"}],"date_created":"2018-12-11T11:52:01Z","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1510.08517"}],"publisher":"ACM","scopus_import":1},{"doi":"10.1145/2837614.2837650","_id":"1439","page":"400 - 415","acknowledgement":"Damien Zufferey was supported by DARPA (Grants FA8650-11-C-7192 and FA8650-15-C-7564) and NSF (Grant CCF-1138967). ","quality_controlled":"1","department":[{"_id":"ToHe"}],"citation":{"ieee":"C. Dragoi, T. A. Henzinger, and D. Zufferey, “PSYNC: A partially synchronous language for fault-tolerant distributed algorithms,” presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA, 2016, vol. 20–22, pp. 400–415.","ista":"Dragoi C, Henzinger TA, Zufferey D. 2016. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. POPL: Principles of Programming Languages, ACM SIGPLAN Notices, vol. 20–22, 400–415.","mla":"Dragoi, Cezara, et al. <i>PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms</i>. Vol. 20–22, ACM, 2016, pp. 400–15, doi:<a href=\"https://doi.org/10.1145/2837614.2837650\">10.1145/2837614.2837650</a>.","apa":"Dragoi, C., Henzinger, T. A., &#38; Zufferey, D. (2016). PSYNC: A partially synchronous language for fault-tolerant distributed algorithms (Vol. 20–22, pp. 400–415). Presented at the POPL: Principles of Programming Languages, St. Petersburg, FL, USA: ACM. <a href=\"https://doi.org/10.1145/2837614.2837650\">https://doi.org/10.1145/2837614.2837650</a>","short":"C. Dragoi, T.A. Henzinger, D. Zufferey, in:, ACM, 2016, pp. 400–415.","chicago":"Dragoi, Cezara, Thomas A Henzinger, and Damien Zufferey. “PSYNC: A Partially Synchronous Language for Fault-Tolerant Distributed Algorithms,” 20–22:400–415. ACM, 2016. <a href=\"https://doi.org/10.1145/2837614.2837650\">https://doi.org/10.1145/2837614.2837650</a>.","ama":"Dragoi C, Henzinger TA, Zufferey D. PSYNC: A partially synchronous language for fault-tolerant distributed algorithms. In: Vol 20-22. ACM; 2016:400-415. doi:<a href=\"https://doi.org/10.1145/2837614.2837650\">10.1145/2837614.2837650</a>"},"title":"PSYNC: A partially synchronous language for fault-tolerant distributed algorithms","status":"public","type":"conference","oa_version":"Preprint","month":"01","publist_id":"5759","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"conference":{"location":"St. Petersburg, FL, USA","end_date":"2016-01-22","start_date":"2016-01-20","name":"POPL: Principles of Programming Languages"},"date_updated":"2021-01-12T06:50:45Z","alternative_title":["ACM SIGPLAN Notices"],"date_created":"2018-12-11T11:52:01Z","project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"},{"name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211","call_identifier":"FWF"},{"grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering"}],"publisher":"ACM","main_file_link":[{"open_access":"1","url":"https://hal.inria.fr/hal-01251199/"}],"scopus_import":1,"day":"11","year":"2016","language":[{"iso":"eng"}],"ec_funded":1,"author":[{"last_name":"Dragoi","first_name":"Cezara","id":"2B2B5ED0-F248-11E8-B48F-1D18A9856A87","full_name":"Dragoi, Cezara"},{"first_name":"Thomas A","last_name":"Henzinger","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A"},{"id":"4397AC76-F248-11E8-B48F-1D18A9856A87","full_name":"Zufferey, Damien","first_name":"Damien","last_name":"Zufferey","orcid":"0000-0002-3197-8736"}],"volume":"20-22","abstract":[{"lang":"eng","text":"Fault-tolerant distributed algorithms play an important role in many critical/high-availability applications. These algorithms are notoriously difficult to implement correctly, due to asynchronous communication and the occurrence of faults, such as the network dropping messages or computers crashing. We introduce PSYNC, a domain specific language based on the Heard-Of model, which views asynchronous faulty systems as synchronous ones with an adversarial environment that simulates asynchrony and faults by dropping messages. We define a runtime system for PSYNC that efficiently executes on asynchronous networks. We formalize the relation between the runtime system and PSYNC in terms of observational refinement. The high-level lockstep abstraction introduced by PSYNC simplifies the design and implementation of fault-tolerant distributed algorithms and enables automated formal verification. We have implemented an embedding of PSYNC in the SCALA programming language with a runtime system for asynchronous networks. We show the applicability of PSYNC by implementing several important fault-tolerant distributed algorithms and we compare the implementation of consensus algorithms in PSYNC against implementations in other languages in terms of code size, runtime efficiency, and verification."}],"date_published":"2016-01-11T00:00:00Z"},{"citation":{"chicago":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” <i>Structure</i>. Cell Press, 2016. <a href=\"https://doi.org/10.1016/j.str.2016.01.002\">https://doi.org/10.1016/j.str.2016.01.002</a>.","short":"H.L. Janovjak, Structure 24 (2016) 213–215.","ama":"Janovjak HL. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. <i>Structure</i>. 2016;24(2):213-215. doi:<a href=\"https://doi.org/10.1016/j.str.2016.01.002\">10.1016/j.str.2016.01.002</a>","mla":"Janovjak, Harald L. “Light at the End of the Protein: Crystal Structure of a C-Terminal Light-Sensing Domain.” <i>Structure</i>, vol. 24, no. 2, Cell Press, 2016, pp. 213–15, doi:<a href=\"https://doi.org/10.1016/j.str.2016.01.002\">10.1016/j.str.2016.01.002</a>.","apa":"Janovjak, H. L. (2016). Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. <i>Structure</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.str.2016.01.002\">https://doi.org/10.1016/j.str.2016.01.002</a>","ieee":"H. L. Janovjak, “Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain,” <i>Structure</i>, vol. 24, no. 2. Cell Press, pp. 213–215, 2016.","ista":"Janovjak HL. 2016. Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain. Structure. 24(2), 213–215."},"publisher":"Cell Press","status":"public","type":"journal_article","title":"Light at the end of the protein: Crystal structure of a C-terminal light-sensing domain","scopus_import":1,"intvolume":"        24","page":"213 - 215","_id":"1440","date_created":"2018-12-11T11:52:02Z","doi":"10.1016/j.str.2016.01.002","project":[{"grant_number":"RGY0084/2012","_id":"255BFFFA-B435-11E9-9278-68D0E5697425","name":"In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator)"},{"call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"W1232-B24","name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"HaJa"}],"quality_controlled":"1","acknowledgement":"The author thanks Banerjee et al. (2016) for providing coordinates prior to public release and apologizes to colleagues whose work was not cited or discussed due to the limited space available. The author is supported by grants from EU FP7 (CIG-303564), HFSP (RGY0084_2012), and FWF (W1232).","issue":"2","date_published":"2016-02-02T00:00:00Z","volume":24,"author":[{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","first_name":"Harald L","last_name":"Janovjak"}],"language":[{"iso":"eng"}],"year":"2016","day":"02","publist_id":"5756","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","publication":"Structure","month":"02","ec_funded":1,"date_updated":"2021-01-12T06:50:46Z","publication_status":"published"},{"has_accepted_license":"1","oa_version":"Submitted Version","month":"05","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"5755","related_material":{"record":[{"status":"public","id":"418","relation":"dissertation_contains"}]},"publication_status":"published","oa":1,"ddc":["571","576"],"date_updated":"2023-09-07T12:49:08Z","citation":{"short":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, H.L. Janovjak, Angewandte Chemie - International Edition 55 (2016) 6339–6342.","chicago":"Gschaider-Reichhart, Eva, Álvaro Inglés Prieto, Alexandra-Madelaine Tichy, Catherine Mckenzie, and Harald L Janovjak. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>. Wiley, 2016. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>.","ama":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. 2016;55(21):6339-6342. doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>","mla":"Gschaider-Reichhart, Eva, et al. “A Phytochrome Sensory Domain Permits Receptor Activation by Red Light.” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21, Wiley, 2016, pp. 6339–42, doi:<a href=\"https://doi.org/10.1002/anie.201601736\">10.1002/anie.201601736</a>.","apa":"Gschaider-Reichhart, E., Inglés Prieto, Á., Tichy, A.-M., Mckenzie, C., &#38; Janovjak, H. L. (2016). A phytochrome sensory domain permits receptor activation by red light. <i>Angewandte Chemie - International Edition</i>. Wiley. <a href=\"https://doi.org/10.1002/anie.201601736\">https://doi.org/10.1002/anie.201601736</a>","ista":"Gschaider-Reichhart E, Inglés Prieto Á, Tichy A-M, Mckenzie C, Janovjak HL. 2016. A phytochrome sensory domain permits receptor activation by red light. Angewandte Chemie - International Edition. 55(21), 6339–6342.","ieee":"E. Gschaider-Reichhart, Á. Inglés Prieto, A.-M. Tichy, C. Mckenzie, and H. L. Janovjak, “A phytochrome sensory domain permits receptor activation by red light,” <i>Angewandte Chemie - International Edition</i>, vol. 55, no. 21. Wiley, pp. 6339–6342, 2016."},"title":"A phytochrome sensory domain permits receptor activation by red light","type":"journal_article","status":"public","pubrep_id":"840","doi":"10.1002/anie.201601736","_id":"1441","page":"6339 - 6342","intvolume":"        55","acknowledgement":"A.I.-P. was supported by a Ramon Areces fellowship, and E.R. by the graduate program MolecularDrugTargets (Austrian Science Fund (FWF): W1232) and a FemTech fellowship (Austrian Research Promotion Agency: 3580812).","quality_controlled":"1","department":[{"_id":"HaJa"}],"file_date_updated":"2020-07-14T12:44:55Z","issue":"21","author":[{"last_name":"Gschaider-Reichhart","first_name":"Eva","orcid":"0000-0002-7218-7738","id":"3FEE232A-F248-11E8-B48F-1D18A9856A87","full_name":"Gschaider-Reichhart, Eva"},{"full_name":"Inglés Prieto, Álvaro","id":"2A9DB292-F248-11E8-B48F-1D18A9856A87","first_name":"Álvaro","last_name":"Inglés Prieto","orcid":"0000-0002-5409-8571"},{"full_name":"Tichy, Alexandra-Madelaine","id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","last_name":"Tichy","first_name":"Alexandra-Madelaine"},{"last_name":"Mckenzie","first_name":"Catherine","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87","full_name":"Mckenzie, Catherine"},{"full_name":"Janovjak, Harald L","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8023-9315","last_name":"Janovjak","first_name":"Harald L"}],"volume":55,"abstract":[{"text":"Optogenetics and photopharmacology enable the spatio-temporal control of cell and animal behavior by light. Although red light offers deep-tissue penetration and minimal phototoxicity, very few red-light-sensitive optogenetic methods are currently available. We have now developed a red-light-induced homodimerization domain. We first showed that an optimized sensory domain of the cyanobacterial phytochrome 1 can be expressed robustly and without cytotoxicity in human cells. We then applied this domain to induce the dimerization of two receptor tyrosine kinases—the fibroblast growth factor receptor 1 and the neurotrophin receptor trkB. This new optogenetic method was then used to activate the MAPK/ERK pathway non-invasively in mammalian tissue and in multicolor cell-signaling experiments. The light-controlled dimerizer and red-light-activated receptor tyrosine kinases will prove useful to regulate a variety of cellular processes with light. Go deep with red: The sensory domain (S) of the cyanobacterial phytochrome 1 (CPH1) was repurposed to induce the homodimerization of proteins in living cells by red light. By using this domain, light-activated protein kinases were engineered that can be activated orthogonally from many fluorescent proteins and through mammalian tissue. Pr/Pfr=red-/far-red-absorbing state of CPH1.","lang":"eng"}],"date_published":"2016-05-17T00:00:00Z","publication":"Angewandte Chemie - International Edition","day":"17","language":[{"iso":"eng"}],"year":"2016","ec_funded":1,"publisher":"Wiley","file":[{"file_id":"5255","checksum":"26da07960e57ac4750b54179197ce57f","relation":"main_file","creator":"system","date_created":"2018-12-12T10:17:03Z","content_type":"application/pdf","date_updated":"2020-07-14T12:44:55Z","file_size":1268662,"access_level":"open_access","file_name":"IST-2017-840-v1+1_reichhart.pdf"}],"scopus_import":1,"project":[{"call_identifier":"FP7","grant_number":"303564","name":"Microbial Ion Channels for Synthetic Neurobiology","_id":"25548C20-B435-11E9-9278-68D0E5697425"},{"grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets","_id":"255A6082-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:52:02Z"}]