[{"project":[{"_id":"265E2996-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20"}],"article_processing_charge":"No","author":[{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja","full_name":"Kopf, Aglaja","orcid":"0000-0002-2187-6656","last_name":"Kopf"}],"title":"The implication of cytoskeletal dynamics on leukocyte migration","citation":{"ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria.","chicago":"Kopf, Aglaja. “The Implication of Cytoskeletal Dynamics on Leukocyte Migration.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6891.","ieee":"A. Kopf, “The implication of cytoskeletal dynamics on leukocyte migration,” Institute of Science and Technology Austria, 2019.","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019.","apa":"Kopf, A. (2019). The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6891","ama":"Kopf A. The implication of cytoskeletal dynamics on leukocyte migration. 2019. doi:10.15479/AT:ISTA:6891","mla":"Kopf, Aglaja. The Implication of Cytoskeletal Dynamics on Leukocyte Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6891."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Institute of Science and Technology Austria","page":"171","date_created":"2019-09-19T08:19:44Z","date_published":"2019-07-24T00:00:00Z","doi":"10.15479/AT:ISTA:6891","year":"2019","has_accepted_license":"1","day":"24","type":"dissertation","keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"status":"public","_id":"6891","file_date_updated":"2020-10-17T22:30:03Z","department":[{"_id":"MiSi"}],"date_updated":"2023-10-18T08:49:17Z","supervisor":[{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"ddc":["570"],"alternative_title":["ISTA Thesis"],"month":"07","abstract":[{"text":"While cells of mesenchymal or epithelial origin perform their effector functions in a purely anchorage dependent manner, cells derived from the hematopoietic lineage are not committed to operate only within a specific niche. Instead, these cells are able to function autonomously of the molecular composition in a broad range of tissue compartments. By this means, cells of the hematopoietic lineage retain the capacity to disseminate into connective tissue and recirculate between organs, building the foundation for essential processes such as tissue regeneration or immune surveillance. \r\nCells of the immune system, specifically leukocytes, are extraordinarily good at performing this task. These cells are able to flexibly shift their mode of migration between an adhesion-mediated and an adhesion-independent manner, instantaneously accommodating for any changes in molecular composition of the external scaffold. The key component driving directed leukocyte migration is the chemokine receptor 7, which guides the cell along gradients of chemokine ligand. Therefore, the physical destination of migrating leukocytes is purely deterministic, i.e. given by global directional cues such as chemokine gradients. \r\nNevertheless, these cells typically reside in three-dimensional scaffolds of inhomogeneous complexity, raising the question whether cells are able to locally discriminate between multiple optional migration routes. Current literature provides evidence that leukocytes, specifically dendritic cells, do indeed probe their surrounding by virtue of multiple explorative protrusions. However, it remains enigmatic how these cells decide which one is the more favorable route to follow and what are the key players involved in performing this task. Due to the heterogeneous environment of most tissues, and the vast adaptability of migrating leukocytes, at this time it is not clear to what extent leukocytes are able to optimize their migratory strategy by adapting their level of adhesiveness. And, given the fact that leukocyte migration is characterized by branched cell shapes in combination with high migration velocities, it is reasonable to assume that these cells require fine tuned shape maintenance mechanisms that tightly coordinate protrusion and adhesion dynamics in a spatiotemporal manner. \r\nTherefore, this study aimed to elucidate how rapidly migrating leukocytes opt for an ideal migratory path while maintaining a continuous cell shape and balancing adhesive forces to efficiently navigate through complex microenvironments. \r\nThe results of this study unraveled a role for the microtubule cytoskeleton in promoting the decision making process during path finding and for the first time point towards a microtubule-mediated function in cell shape maintenance of highly ramified cells such as dendritic cells. Furthermore, we found that migrating low-adhesive leukocytes are able to instantaneously adapt to increased tensile load by engaging adhesion receptors. This response was only occurring tangential to the substrate while adhesive properties in the vertical direction were not increased. As leukocytes are primed for rapid migration velocities, these results demonstrate that leukocyte integrins are able to confer a high level of traction forces parallel to the cell membrane along the direction of migration without wasting energy in gluing the cell to the substrate. \r\nThus, the data in the here presented thesis provide new insights into the pivotal role of cytoskeletal dynamics and the mechanisms of force transduction during leukocyte migration. \r\nThereby the here presented results help to further define fundamental principles underlying leukocyte migration and open up potential therapeutic avenues of clinical relevance.\r\n","lang":"eng"}],"oa_version":"Published Version","related_material":{"link":[{"url":"https://ist.ac.at/en/news/feeling-like-a-cell/","relation":"press_release"}],"record":[{"id":"6328","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"15","status":"public"},{"id":"6877","status":"public","relation":"part_of_dissertation"}]},"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"isbn":["978-3-99078-002-2"],"eissn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"00d100d6468e31e583051e0a006b640c","file_id":"6950","file_size":74735267,"date_updated":"2020-10-17T22:30:03Z","creator":"akopf","file_name":"Kopf_PhD_Thesis.docx","date_created":"2019-10-15T05:28:42Z"},{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6951","checksum":"5d1baa899993ae6ca81aebebe1797000","embargo":"2020-10-16","date_updated":"2020-10-17T22:30:03Z","file_size":52787224,"creator":"akopf","date_created":"2019-10-15T05:28:47Z","file_name":"Kopf_PhD_Thesis1.pdf"}]},{"quality_controlled":"1","publisher":"Springer Nature","oa":1,"page":"546-550","date_published":"2019-04-25T00:00:00Z","doi":"10.1038/s41586-019-1087-5","date_created":"2019-04-17T06:52:28Z","isi":1,"year":"2019","day":"25","publication":"Nature","project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373"},{"_id":"265FAEBA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25A48D24-B435-11E9-9278-68D0E5697425","name":"Molecular and system level view of immune cell migration","grant_number":"ALTF 1396-2014"}],"author":[{"last_name":"Renkawitz","orcid":"0000-0003-2856-3369","full_name":"Renkawitz, Jörg","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kopf","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja"},{"id":"489E3F00-F248-11E8-B48F-1D18A9856A87","first_name":"Julian A","full_name":"Stopp, Julian A","last_name":"Stopp"},{"full_name":"de Vries, Ingrid","last_name":"de Vries","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid"},{"first_name":"Meghan K.","last_name":"Driscoll","full_name":"Driscoll, Meghan K."},{"last_name":"Merrin","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert"},{"last_name":"Welf","full_name":"Welf, Erik S.","first_name":"Erik S."},{"full_name":"Danuser, Gaudenz","last_name":"Danuser","first_name":"Gaudenz"},{"first_name":"Reto","last_name":"Fiolka","full_name":"Fiolka, Reto"},{"first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","last_name":"Sixt"}],"article_processing_charge":"No","external_id":{"pmid":["30944468"],"isi":["000465594200050"]},"title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","citation":{"ista":"Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550.","chicago":"Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5.","short":"J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550.","ieee":"J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” Nature, vol. 568. Springer Nature, pp. 546–550, 2019.","ama":"Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 2019;568:546-550. doi:10.1038/s41586-019-1087-5","apa":"Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5","mla":"Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature, vol. 568, Springer Nature, 2019, pp. 546–50, doi:10.1038/s41586-019-1087-5."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/"}],"month":"04","intvolume":" 568","acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"text":"During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","volume":568,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/"}],"record":[{"id":"14697","status":"public","relation":"dissertation_contains"},{"status":"public","id":"6891","relation":"dissertation_contains"}]},"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"letter_note","status":"public","_id":"6328","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"date_updated":"2024-03-27T23:30:39Z"},{"date_updated":"2024-03-27T23:30:41Z","department":[{"_id":"SiHi"}],"_id":"6830","status":"public","article_type":"letter_note","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["08966273"],"eissn":["10974199"]},"issue":"5","volume":103,"related_material":{"record":[{"id":"7902","status":"public","relation":"part_of_dissertation"}]},"oa_version":"Published Version","pmid":1,"intvolume":" 103","month":"09","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.021"}],"scopus_import":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"apa":"Contreras, X., & Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.021","ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. Neuron. 2019;103(5):750-752. doi:10.1016/j.neuron.2019.08.021","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” Neuron, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752.","mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:10.1016/j.neuron.2019.08.021.","ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752.","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.021."},"title":"Memo1 tiles the radial glial cell grid","article_processing_charge":"No","external_id":{"pmid":["31487522"],"isi":["000484400200002"]},"author":[{"last_name":"Contreras","full_name":"Contreras, Ximena","first_name":"Ximena","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"}],"publication":"Neuron","day":"04","year":"2019","isi":1,"date_created":"2019-08-25T22:00:50Z","doi":"10.1016/j.neuron.2019.08.021","date_published":"2019-09-04T00:00:00Z","page":"750-752","oa":1,"publisher":"Elsevier","quality_controlled":"1"},{"file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"JiFr"}],"ddc":["580"],"date_updated":"2024-03-27T23:30:43Z","status":"public","type":"journal_article","article_type":"original","tmp":{"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)","short":"CC BY (4.0)"},"_id":"6627","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"10083"}]},"volume":20,"issue":"13","ec_funded":1,"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"dd9d1cbb933a72ceb666c9667890ac51","file_id":"6645","creator":"dernst","date_updated":"2020-07-14T12:47:34Z","file_size":3330291,"date_created":"2019-07-17T06:17:15Z","file_name":"2019_JournalMolecularScience_Adamowski.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1422-0067"]},"publication_status":"published","month":"07","intvolume":" 20","scopus_import":"1","oa_version":"Published Version","pmid":1,"abstract":[{"text":"Cortical microtubule arrays in elongating epidermal cells in both the root and stem of plants have the propensity of dynamic reorientations that are correlated with the activation or inhibition of growth. Factors regulating plant growth, among them the hormone auxin, have been recognized as regulators of microtubule array orientations. Some previous work in the field has aimed at elucidating the causal relationship between cell growth, the signaling of auxin or other growth-regulating factors, and microtubule array reorientations, with various conclusions. Here, we revisit this problem of causality with a comprehensive set of experiments in Arabidopsis thaliana, using the now available pharmacological and genetic tools. We use isolated, auxin-depleted hypocotyls, an experimental system allowing for full control of both growth and auxin signaling. We demonstrate that reorientation of microtubules is not directly triggered by an auxin signal during growth activation. Instead, reorientation is triggered by the activation of the growth process itself and is auxin-independent in its nature. We discuss these findings in the context of previous relevant work, including that on the mechanical regulation of microtubule array orientation.","lang":"eng"}],"title":"Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling","author":[{"last_name":"Adamowski","full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","id":"45F536D2-F248-11E8-B48F-1D18A9856A87","first_name":"Maciek"},{"orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","last_name":"Li","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87","first_name":"Lanxin"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["31284661"],"isi":["000477041100221"]},"article_processing_charge":"Yes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"chicago":"Adamowski, Maciek, Lanxin Li, and Jiří Friml. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences. MDPI, 2019. https://doi.org/10.3390/ijms20133337.","ista":"Adamowski M, Li L, Friml J. 2019. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 20(13), 3337.","mla":"Adamowski, Maciek, et al. “Reorientation of Cortical Microtubule Arrays in the Hypocotyl of Arabidopsis Thaliana Is Induced by the Cell Growth Process and Independent of Auxin Signaling.” International Journal of Molecular Sciences, vol. 20, no. 13, 3337, MDPI, 2019, doi:10.3390/ijms20133337.","ieee":"M. Adamowski, L. Li, and J. Friml, “Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling,” International Journal of Molecular Sciences, vol. 20, no. 13. MDPI, 2019.","short":"M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019).","ama":"Adamowski M, Li L, Friml J. Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. 2019;20(13). doi:10.3390/ijms20133337","apa":"Adamowski, M., Li, L., & Friml, J. (2019). Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms20133337"},"project":[{"name":"Polarity and subcellular dynamics in plants","grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"article_number":"3337","date_published":"2019-07-07T00:00:00Z","doi":"10.3390/ijms20133337","date_created":"2019-07-11T12:00:32Z","day":"07","publication":"International Journal of Molecular Sciences","isi":1,"has_accepted_license":"1","year":"2019","publisher":"MDPI","quality_controlled":"1","oa":1},{"scopus_import":"1","intvolume":" 38","month":"11","abstract":[{"text":"We propose a novel generic shape optimization method for CAD models based on the eXtended Finite Element Method (XFEM). Our method works directly on the intersection between the model and a regular simulation grid, without the need to mesh or remesh, thus removing a bottleneck of classical shape optimization strategies. This is made possible by a novel hierarchical integration scheme that accurately integrates finite element quantities with sub-element precision. For optimization, we efficiently compute analytical shape derivatives of the entire framework, from model intersection to integration rule generation and XFEM simulation. Moreover, we describe a differentiable projection of shape parameters onto a constraint manifold spanned by user-specified shape preservation, consistency, and manufacturability constraints. We demonstrate the utility of our approach by optimizing mass distribution, strength-to-weight ratio, and inverse elastic shape design objectives directly on parameterized 3D CAD models.","lang":"eng"}],"oa_version":"Submitted Version","ec_funded":1,"related_material":{"record":[{"status":"public","id":"12897","relation":"dissertation_contains"}]},"issue":"6","volume":38,"publication_status":"published","publication_identifier":{"issn":["0730-0301"]},"language":[{"iso":"eng"}],"file":[{"relation":"supplementary_material","access_level":"open_access","content_type":"application/pdf","file_id":"7119","checksum":"56a2fb019adcb556d2b022f5e5acb68c","creator":"bbickel","file_size":1673176,"date_updated":"2020-07-14T12:47:49Z","file_name":"xcad_sup_mat_siga19.pdf","date_created":"2019-11-26T14:24:26Z","title":"X-CAD Supplemental Material"},{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","description":"This is the author's version of the work.","file_id":"7120","checksum":"5f29d76aceb5102e766cbab9b17d776e","creator":"bbickel","date_updated":"2020-07-14T12:47:49Z","file_size":14563618,"date_created":"2019-11-26T14:24:27Z","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","file_name":"XCAD_authors_version.pdf"},{"date_created":"2019-11-26T14:27:37Z","file_name":"XCAD_video.mp4","creator":"bbickel","date_updated":"2020-07-14T12:47:49Z","file_size":259979129,"checksum":"0d31e123286cbec9e28b2001c2bb0d55","file_id":"7121","access_level":"open_access","relation":"main_file","content_type":"video/mp4"}],"article_type":"original","type":"journal_article","status":"public","_id":"7117","file_date_updated":"2020-07-14T12:47:49Z","department":[{"_id":"BeBi"}],"date_updated":"2024-03-27T23:30:46Z","ddc":["000"],"oa":1,"publisher":"ACM","quality_controlled":"1","date_created":"2019-11-26T14:22:09Z","date_published":"2019-11-06T00:00:00Z","doi":"10.1145/3355089.3356576","year":"2019","isi":1,"has_accepted_license":"1","publication":"ACM Transactions on Graphics","day":"06","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767","_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"157","article_processing_charge":"No","external_id":{"isi":["000498397300007"]},"author":[{"id":"400429CC-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","last_name":"Hafner","full_name":"Hafner, Christian"},{"first_name":"Christian","last_name":"Schumacher","full_name":"Schumacher, Christian"},{"first_name":"Espen","full_name":"Knoop, Espen","last_name":"Knoop"},{"full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","last_name":"Auzinger","first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd"},{"first_name":"Moritz","full_name":"Bächer, Moritz","last_name":"Bächer"}],"title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","citation":{"mla":"Hafner, Christian, et al. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics, vol. 38, no. 6, 157, ACM, 2019, doi:10.1145/3355089.3356576.","apa":"Hafner, C., Schumacher, C., Knoop, E., Auzinger, T., Bickel, B., & Bächer, M. (2019). X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3355089.3356576","ama":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 2019;38(6). doi:10.1145/3355089.3356576","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","ieee":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, and M. Bächer, “X-CAD: Optimizing CAD Models with Extended Finite Elements,” ACM Transactions on Graphics, vol. 38, no. 6. ACM, 2019.","chicago":"Hafner, Christian, Christian Schumacher, Espen Knoop, Thomas Auzinger, Bernd Bickel, and Moritz Bächer. “X-CAD: Optimizing CAD Models with Extended Finite Elements.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3355089.3356576.","ista":"Hafner C, Schumacher C, Knoop E, Auzinger T, Bickel B, Bächer M. 2019. X-CAD: Optimizing CAD Models with Extended Finite Elements. ACM Transactions on Graphics. 38(6), 157."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_created":"2019-03-31T21:59:12Z","doi":"10.1103/PhysRevLett.122.114502","date_published":"2019-03-22T00:00:00Z","year":"2019","isi":1,"publication":"Physical Review Letters","day":"22","oa":1,"quality_controlled":"1","publisher":"American Physical Society","external_id":{"isi":["000461922000006"],"arxiv":["1809.06358"]},"article_processing_charge":"No","author":[{"full_name":"Agrawal, Nishchal","last_name":"Agrawal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Choueiri, George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"title":"Transition to turbulence in particle laden flows","citation":{"chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters. American Physical Society, 2019. https://doi.org/10.1103/PhysRevLett.122.114502.","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” Physical Review Letters, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:10.1103/PhysRevLett.122.114502.","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” Physical Review Letters, vol. 122, no. 11. American Physical Society, 2019.","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019).","apa":"Agrawal, N., Choueiri, G. H., & Hof, B. (2019). Transition to turbulence in particle laden flows. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.122.114502","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. Physical Review Letters. 2019;122(11). doi:10.1103/PhysRevLett.122.114502"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"114502","issue":"11","volume":122,"related_material":{"record":[{"id":"9728","status":"public","relation":"dissertation_contains"}]},"publication_status":"published","publication_identifier":{"issn":["00319007"],"eissn":["10797114"]},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.06358"}],"scopus_import":"1","intvolume":" 122","month":"03","abstract":[{"lang":"eng","text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations."}],"oa_version":"Preprint","department":[{"_id":"BjHo"}],"date_updated":"2024-03-27T23:30:47Z","type":"journal_article","status":"public","_id":"6189"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Igler, Claudia. On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6371.","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:10.15479/AT:ISTA:6371","apa":"Igler, C. (2019). On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6371","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6371.","ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria."},"title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","article_processing_charge":"No","author":[{"last_name":"Igler","full_name":"Igler, Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"}],"project":[{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"day":"03","year":"2019","has_accepted_license":"1","date_created":"2019-05-03T11:55:51Z","doi":"10.15479/AT:ISTA:6371","date_published":"2019-05-03T00:00:00Z","page":"152","oa":1,"publisher":"Institute of Science and Technology Austria","ddc":["576","579"],"date_updated":"2024-02-21T13:45:52Z","supervisor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","first_name":"Calin C","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet"}],"department":[{"_id":"CaGu"}],"file_date_updated":"2021-02-11T11:17:13Z","_id":"6371","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"status":"public","type":"dissertation","language":[{"iso":"eng"}],"file":[{"file_id":"6373","checksum":"c0085d47c58c9cbcab1b0a783480f6da","embargo":"2020-05-02","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-05-03T11:54:52Z","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","creator":"cigler","date_updated":"2021-02-11T11:17:13Z","file_size":12597663},{"access_level":"closed","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","file_id":"6374","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","creator":"cigler","date_updated":"2020-07-14T12:47:28Z","file_size":34644426,"date_created":"2019-05-03T11:54:54Z","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"related_material":{"record":[{"relation":"part_of_dissertation","id":"67","status":"public"},{"relation":"popular_science","status":"public","id":"5585"}]},"oa_version":"Published Version","abstract":[{"text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation. \r\n","lang":"eng"}],"month":"05","alternative_title":["ISTA Thesis"]},{"oa":1,"quality_controlled":"1","publisher":"International Association for Cryptologic Research","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","day":"01","year":"2018","has_accepted_license":"1","date_created":"2021-11-14T23:01:25Z","date_published":"2018-01-01T00:00:00Z","doi":"10.13154/tches.v2018.i3.214-242","page":"214-242","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"ama":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018;2018(3):214-242. doi:10.13154/tches.v2018.i3.214-242","apa":"Allini, E. N., Skórski, M., Petura, O., Bernard, F., Laban, M., & Fischer, V. (2018). Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research. https://doi.org/10.13154/tches.v2018.i3.214-242","ieee":"E. N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, and V. Fischer, “Evaluation and monitoring of free running oscillators serving as source of randomness,” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3. International Association for Cryptologic Research, pp. 214–242, 2018.","short":"E.N. Allini, M. Skórski, O. Petura, F. Bernard, M. Laban, V. Fischer, IACR Transactions on Cryptographic Hardware and Embedded Systems 2018 (2018) 214–242.","mla":"Allini, Elie Noumon, et al. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems, vol. 2018, no. 3, International Association for Cryptologic Research, 2018, pp. 214–42, doi:10.13154/tches.v2018.i3.214-242.","ista":"Allini EN, Skórski M, Petura O, Bernard F, Laban M, Fischer V. 2018. Evaluation and monitoring of free running oscillators serving as source of randomness. IACR Transactions on Cryptographic Hardware and Embedded Systems. 2018(3), 214–242.","chicago":"Allini, Elie Noumon, Maciej Skórski, Oto Petura, Florent Bernard, Marek Laban, and Viktor Fischer. “Evaluation and Monitoring of Free Running Oscillators Serving as Source of Randomness.” IACR Transactions on Cryptographic Hardware and Embedded Systems. International Association for Cryptologic Research, 2018. https://doi.org/10.13154/tches.v2018.i3.214-242."},"title":"Evaluation and monitoring of free running oscillators serving as source of randomness","article_processing_charge":"No","author":[{"first_name":"Elie Noumon","last_name":"Allini","full_name":"Allini, Elie Noumon"},{"last_name":"Skórski","full_name":"Skórski, Maciej","first_name":"Maciej","id":"EC09FA6A-02D0-11E9-8223-86B7C91467DD"},{"first_name":"Oto","full_name":"Petura, Oto","last_name":"Petura"},{"full_name":"Bernard, Florent","last_name":"Bernard","first_name":"Florent"},{"last_name":"Laban","full_name":"Laban, Marek","first_name":"Marek"},{"last_name":"Fischer","full_name":"Fischer, Viktor","first_name":"Viktor"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this paper, we evaluate clock signals generated in ring oscillators and self-timed rings and the way their jitter can be transformed into random numbers. We show that counting the periods of the jittery clock signal produces random numbers of significantly better quality than the methods in which the jittery signal is simply sampled (the case in almost all current methods). Moreover, we use the counter values to characterize and continuously monitor the source of randomness. However, instead of using the widely used statistical variance, we propose to use Allan variance to do so. There are two main advantages: Allan variance is insensitive to low frequency noises such as flicker noise that are known to be autocorrelated and significantly less circuitry is required for its computation than that used to compute commonly used variance. We also show that it is essential to use a differential principle of randomness extraction from the jitter based on the use of two identical oscillators to avoid autocorrelations originating from external and internal global jitter sources and that this fact is valid for both kinds of rings. Last but not least, we propose a method of statistical testing based on high order Markov model to show the reduced dependencies when the proposed randomness extraction is applied."}],"intvolume":" 2018","month":"01","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"success":1,"file_id":"10289","checksum":"b816b848f046c48a8357700d9305dce5","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_IACR_Allini.pdf","date_created":"2021-11-15T10:27:29Z","file_size":955755,"date_updated":"2021-11-15T10:27:29Z","creator":"cchlebak"}],"publication_status":"published","publication_identifier":{"eissn":["2569-2925"]},"volume":2018,"issue":"3","_id":"10286","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["000"],"date_updated":"2021-11-15T10:48:49Z","department":[{"_id":"KrPi"}],"file_date_updated":"2021-11-15T10:27:29Z"},{"publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","day":"23","year":"2018","has_accepted_license":"1","date_created":"2022-03-18T12:46:32Z","date_published":"2018-10-23T00:00:00Z","doi":"10.29007/5z5k","page":"233-253","acknowledgement":"A. S. is fully supported by the Vienna Science and Technology Fund (WWTF) through project ICT15-003. K.C. is supported by the Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE) and an ERC Starting grant (279307: Graph Games). For M.H the research leading to these results has received funding from the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013) /ERC Grant Agreement no. 340506.","oa":1,"publisher":"EasyChair","quality_controlled":"1","user_id":"72615eeb-f1f3-11ec-aa25-d4573ddc34fd","citation":{"chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika H Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k.","ista":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k.","ieee":"K. Chatterjee, W. Dvořák, M. H. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","short":"K. Chatterjee, W. Dvořák, M.H. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","ama":"Chatterjee K, Dvořák W, Henzinger MH, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k","apa":"Chatterjee, K., Dvořák, W., Henzinger, M. H., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k"},"title":"Quasipolynomial set-based symbolic algorithms for parity games","article_processing_charge":"No","external_id":{"arxiv":["1909.04983"]},"author":[{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Wolfgang","full_name":"Dvořák, Wolfgang","last_name":"Dvořák"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","first_name":"Monika H"},{"full_name":"Svozil, Alexander","last_name":"Svozil","first_name":"Alexander"}],"project":[{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"1229aa8640bd6db610c85decf2265480","file_id":"11392","success":1,"creator":"dernst","date_updated":"2022-05-17T07:51:08Z","file_size":720893,"date_created":"2022-05-17T07:51:08Z","file_name":"2018_EPiCs_Chatterjee.pdf"}],"publication_status":"published","publication_identifier":{"issn":["2398-7340"]},"ec_funded":1,"volume":57,"oa_version":"Published Version","abstract":[{"text":"Solving parity games, which are equivalent to modal μ-calculus model checking, is a central algorithmic problem in formal methods, with applications in reactive synthesis, program repair, verification of branching-time properties, etc. Besides the standard compu- tation model with the explicit representation of games, another important theoretical model of computation is that of set-based symbolic algorithms. Set-based symbolic algorithms use basic set operations and one-step predecessor operations on the implicit description of games, rather than the explicit representation. The significance of symbolic algorithms is that they provide scalable algorithms for large finite-state systems, as well as for infinite-state systems with finite quotient. Consider parity games on graphs with n vertices and parity conditions with d priorities. While there is a rich literature of explicit algorithms for parity games, the main results for set-based symbolic algorithms are as follows: (a) the basic algorithm that requires O(nd) symbolic operations and O(d) symbolic space; and (b) an improved algorithm that requires O(nd/3+1) symbolic operations and O(n) symbolic space. In this work, our contributions are as follows: (1) We present a black-box set-based symbolic algorithm based on the explicit progress measure algorithm. Two important consequences of our algorithm are as follows: (a) a set-based symbolic algorithm for parity games that requires quasi-polynomially many symbolic operations and O(n) symbolic space; and (b) any future improvement in progress measure based explicit algorithms immediately imply an efficiency improvement in our set-based symbolic algorithm for parity games. (2) We present a set-based symbolic algorithm that requires quasi-polynomially many symbolic operations and O(d · log n) symbolic space. Moreover, for the important special case of d ≤ log n, our algorithm requires only polynomially many symbolic operations and poly-logarithmic symbolic space.","lang":"eng"}],"intvolume":" 57","month":"10","scopus_import":"1","alternative_title":["EPiC Series in Computing"],"ddc":["000"],"date_updated":"2022-07-29T09:24:31Z","department":[{"_id":"KrCh"}],"file_date_updated":"2022-05-17T07:51:08Z","_id":"10883","status":"public","conference":{"name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning","start_date":"2018-11-17","end_date":"2018-11-21","location":"Awassa, Ethiopia"},"type":"conference"},{"_id":"11","type":"conference","conference":{"name":"MaLiQS: Macroscopic Limits of Quantum Systems","location":"Munich, Germany","end_date":"2017-04-01","start_date":"2017-03-30"},"status":"public","date_updated":"2021-01-12T06:48:16Z","department":[{"_id":"RoSe"}],"abstract":[{"lang":"eng","text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm."}],"oa_version":"Preprint","scopus_import":1,"main_file_link":[{"url":"https://arxiv.org/abs/1806.10843","open_access":"1"}],"month":"10","intvolume":" 270","publication_status":"published","language":[{"iso":"eng"}],"volume":270,"ec_funded":1,"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"citation":{"ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214.","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9.","ieee":"N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.","short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9","apa":"Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9","mla":"Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K","orcid":"0000-0002-0495-6822","full_name":"Leopold, Nikolai K","last_name":"Leopold"},{"first_name":"Peter","last_name":"Pickl","full_name":"Pickl, Peter"}],"publist_id":"8045","external_id":{"arxiv":["1806.10843"]},"title":"Mean-field limits of particles in interaction with quantised radiation fields","quality_controlled":"1","publisher":"Springer","oa":1,"year":"2018","day":"27","page":"185 - 214","doi":"10.1007/978-3-030-01602-9_9","date_published":"2018-10-27T00:00:00Z","date_created":"2018-12-11T11:44:08Z"},{"_id":"1215","pubrep_id":"712","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["519"],"date_updated":"2021-01-12T06:49:09Z","department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:44:39Z","oa_version":"Published Version","abstract":[{"text":"Two generalizations of Itô formula to infinite-dimensional spaces are given.\r\nThe first one, in Hilbert spaces, extends the classical one by taking advantage of\r\ncancellations when they occur in examples and it is applied to the case of a group\r\ngenerator. The second one, based on the previous one and a limit procedure, is an Itô\r\nformula in a special class of Banach spaces having a product structure with the noise\r\nin a Hilbert component; again the key point is the extension due to a cancellation. This\r\nextension to Banach spaces and in particular the specific cancellation are motivated\r\nby path-dependent Itô calculus.","lang":"eng"}],"intvolume":" 31","month":"06","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"checksum":"47686d58ec21c164540f1a980ff2163f","file_id":"5266","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:17:13Z","file_name":"IST-2016-712-v1+1_s10959-016-0724-2.pdf","creator":"system","date_updated":"2020-07-14T12:44:39Z","file_size":671125}],"publication_status":"published","issue":"2","volume":31,"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Flandoli, Franco, et al. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability, vol. 31, no. 2, Springer, 2018, pp. 789–826, doi:10.1007/s10959-016-0724-2.","ama":"Flandoli F, Russo F, Zanco GA. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 2018;31(2):789-826. doi:10.1007/s10959-016-0724-2","apa":"Flandoli, F., Russo, F., & Zanco, G. A. (2018). Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. Springer. https://doi.org/10.1007/s10959-016-0724-2","short":"F. Flandoli, F. Russo, G.A. Zanco, Journal of Theoretical Probability 31 (2018) 789–826.","ieee":"F. Flandoli, F. Russo, and G. A. Zanco, “Infinite-dimensional calculus under weak spatial regularity of the processes,” Journal of Theoretical Probability, vol. 31, no. 2. Springer, pp. 789–826, 2018.","chicago":"Flandoli, Franco, Francesco Russo, and Giovanni A Zanco. “Infinite-Dimensional Calculus under Weak Spatial Regularity of the Processes.” Journal of Theoretical Probability. Springer, 2018. https://doi.org/10.1007/s10959-016-0724-2.","ista":"Flandoli F, Russo F, Zanco GA. 2018. Infinite-dimensional calculus under weak spatial regularity of the processes. Journal of Theoretical Probability. 31(2), 789–826."},"title":"Infinite-dimensional calculus under weak spatial regularity of the processes","article_processing_charge":"Yes (via OA deal)","publist_id":"6119","author":[{"first_name":"Franco","full_name":"Flandoli, Franco","last_name":"Flandoli"},{"last_name":"Russo","full_name":"Russo, Francesco","first_name":"Francesco"},{"first_name":"Giovanni A","id":"47491882-F248-11E8-B48F-1D18A9856A87","full_name":"Zanco, Giovanni A","last_name":"Zanco"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The second named author benefited partially from the support of the “FMJH Program Gaspard Monge in Optimization and Operations Research” (Project 2014-1607H). He is also grateful for the invitation to the Department of Mathematics of the University of Pisa. The third named author is grateful for the invitation to ENSTA.","oa":1,"publisher":"Springer","quality_controlled":"1","publication":"Journal of Theoretical Probability","day":"01","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:50:45Z","doi":"10.1007/s10959-016-0724-2","date_published":"2018-06-01T00:00:00Z","page":"789-826"},{"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","has_accepted_license":"1","day":"01","date_created":"2018-12-11T11:45:04Z","date_published":"2018-01-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.39","article_number":"39","project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"citation":{"chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.39.","ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.","mla":"Fulek, Radoslav, and Jan Kynčl. Hanani-Tutte for Approximating Maps of Graphs. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.39.","ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.39","apa":"Fulek, R., & Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.39","ieee":"R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7735","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"}],"title":"Hanani-Tutte for approximating maps of graphs","abstract":[{"text":"We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint "pipes" corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once.","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"intvolume":" 99","month":"01","publication_status":"published","publication_identifier":{"isbn":["978-3-95977-066-8"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-17T12:33:52Z","file_name":"2018_LIPIcs_Fulek.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:19Z","file_size":718857,"file_id":"5701","checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"volume":99,"_id":"185","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2018-06-11","location":"Budapest, Hungary","end_date":"2018-06-14"},"tmp":{"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)","short":"CC BY (4.0)"},"type":"conference","status":"public","date_updated":"2021-01-12T06:53:36Z","ddc":["510"],"file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"UlWa"}]},{"acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2018","day":"11","page":"35:1 - 35:13","doi":"10.4230/LIPIcs.SoCG.2018.35","date_published":"2018-06-11T00:00:00Z","date_created":"2018-12-11T11:45:05Z","project":[{"call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"citation":{"mla":"Edelsbrunner, Herbert, et al. Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:10.4230/LIPIcs.SoCG.2018.35.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.","apa":"Edelsbrunner, H., Virk, Z., & Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.35","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:10.4230/LIPIcs.SoCG.2018.35","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.35.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Virk","full_name":"Virk, Ziga","first_name":"Ziga"},{"first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","last_name":"Wagner","full_name":"Wagner, Hubert"}],"publist_id":"7733","title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","abstract":[{"lang":"eng","text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex."}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"month":"06","intvolume":" 99","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7509403803b3ac1aee94bbc2ad293d21","file_id":"5724","file_size":489080,"date_updated":"2020-07-14T12:45:20Z","creator":"dernst","file_name":"2018_LIPIcs_Edelsbrunner.pdf","date_created":"2018-12-17T16:31:31Z"}],"language":[{"iso":"eng"}],"volume":99,"_id":"188","type":"conference","conference":{"end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"tmp":{"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)","short":"CC BY (4.0)"},"status":"public","date_updated":"2021-01-12T06:53:48Z","ddc":["000"],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:20Z"},{"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"67010cf5e3b3e0637c659371714a715a","file_id":"5929","creator":"dernst","date_updated":"2020-07-14T12:45:59Z","file_size":994490,"date_created":"2019-02-06T07:36:24Z","file_name":"2018_Heliyon_DeMartino.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"4","volume":4,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A cornerstone of statistical inference, the maximum entropy framework is being increasingly applied to construct descriptive and predictive models of biological systems, especially complex biological networks, from large experimental data sets. Both its broad applicability and the success it obtained in different contexts hinge upon its conceptual simplicity and mathematical soundness. Here we try to concisely review the basic elements of the maximum entropy principle, starting from the notion of ‘entropy’, and describe its usefulness for the analysis of biological systems. As examples, we focus specifically on the problem of reconstructing gene interaction networks from expression data and on recent work attempting to expand our system-level understanding of bacterial metabolism. Finally, we highlight some extensions and potential limitations of the maximum entropy approach, and point to more recent developments that are likely to play a key role in the upcoming challenges of extracting structures and information from increasingly rich, high-throughput biological data."}],"month":"04","intvolume":" 4","scopus_import":1,"ddc":["530"],"date_updated":"2021-01-12T07:40:46Z","file_date_updated":"2020-07-14T12:45:59Z","department":[{"_id":"GaTk"}],"_id":"306","status":"public","type":"journal_article","tmp":{"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)","short":"CC BY (4.0)"},"day":"01","publication":"Heliyon","has_accepted_license":"1","year":"2018","doi":"10.1016/j.heliyon.2018.e00596","date_published":"2018-04-01T00:00:00Z","date_created":"2018-12-11T11:45:44Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"De Martino A, De Martino D. 2018. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 4(4), e00596.","chicago":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon. Elsevier, 2018. https://doi.org/10.1016/j.heliyon.2018.e00596.","apa":"De Martino, A., & De Martino, D. (2018). An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. Elsevier. https://doi.org/10.1016/j.heliyon.2018.e00596","ama":"De Martino A, De Martino D. An introduction to the maximum entropy approach and its application to inference problems in biology. Heliyon. 2018;4(4). doi:10.1016/j.heliyon.2018.e00596","ieee":"A. De Martino and D. De Martino, “An introduction to the maximum entropy approach and its application to inference problems in biology,” Heliyon, vol. 4, no. 4. Elsevier, 2018.","short":"A. De Martino, D. De Martino, Heliyon 4 (2018).","mla":"De Martino, Andrea, and Daniele De Martino. “An Introduction to the Maximum Entropy Approach and Its Application to Inference Problems in Biology.” Heliyon, vol. 4, no. 4, e00596, Elsevier, 2018, doi:10.1016/j.heliyon.2018.e00596."},"title":"An introduction to the maximum entropy approach and its application to inference problems in biology","author":[{"last_name":"De Martino","full_name":"De Martino, Andrea","first_name":"Andrea"},{"last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87"}],"article_number":"e00596","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}]},{"project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"author":[{"orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"}],"publist_id":"8018","article_processing_charge":"No","title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","citation":{"chicago":"Zagórski, Marcin P, and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” In Morphogen Gradients , 1863:47–63. MIMB. Springer Nature, 2018. https://doi.org/10.1007/978-1-4939-8772-6_4.","ista":"Zagórski MP, Kicheva A. 2018.Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Methods in Molecular Biology, vol. 1863, 47–63.","mla":"Zagórski, Marcin P., and Anna Kicheva. “Measuring Dorsoventral Pattern and Morphogen Signaling Profiles in the Growing Neural Tube.” Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63, doi:10.1007/978-1-4939-8772-6_4.","ieee":"M. P. Zagórski and A. Kicheva, “Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube,” in Morphogen Gradients , vol. 1863, Springer Nature, 2018, pp. 47–63.","short":"M.P. Zagórski, A. Kicheva, in:, Morphogen Gradients , Springer Nature, 2018, pp. 47–63.","apa":"Zagórski, M. P., & Kicheva, A. (2018). Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In Morphogen Gradients (Vol. 1863, pp. 47–63). Springer Nature. https://doi.org/10.1007/978-1-4939-8772-6_4","ama":"Zagórski MP, Kicheva A. Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube. In: Morphogen Gradients . Vol 1863. MIMB. Springer Nature; 2018:47-63. doi:10.1007/978-1-4939-8772-6_4"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Springer Nature","oa":1,"page":"47 - 63","doi":"10.1007/978-1-4939-8772-6_4","date_published":"2018-10-16T00:00:00Z","date_created":"2018-12-11T11:44:17Z","has_accepted_license":"1","year":"2018","day":"16","publication":"Morphogen Gradients ","type":"book_chapter","status":"public","_id":"37","series_title":"MIMB","department":[{"_id":"AnKi"}],"file_date_updated":"2020-10-13T14:20:37Z","date_updated":"2021-01-12T07:49:03Z","ddc":["570"],"alternative_title":["Methods in Molecular Biology"],"scopus_import":"1","month":"10","intvolume":" 1863","abstract":[{"text":"Developmental processes are inherently dynamic and understanding them requires quantitative measurements of gene and protein expression levels in space and time. While live imaging is a powerful approach for obtaining such data, it is still a challenge to apply it over long periods of time to large tissues, such as the embryonic spinal cord in mouse and chick. Nevertheless, dynamics of gene expression and signaling activity patterns in this organ can be studied by collecting tissue sections at different developmental stages. In combination with immunohistochemistry, this allows for measuring the levels of multiple developmental regulators in a quantitative manner with high spatiotemporal resolution. The mean protein expression levels over time, as well as embryo-to-embryo variability can be analyzed. A key aspect of the approach is the ability to compare protein levels across different samples. This requires a number of considerations in sample preparation, imaging and data analysis. Here we present a protocol for obtaining time course data of dorsoventral expression patterns from mouse and chick neural tube in the first 3 days of neural tube development. The described workflow starts from embryo dissection and ends with a processed dataset. Software scripts for data analysis are included. The protocol is adaptable and instructions that allow the user to modify different steps are provided. Thus, the procedure can be altered for analysis of time-lapse images and applied to systems other than the neural tube.","lang":"eng"}],"oa_version":"Submitted Version","volume":1863,"ec_funded":1,"publication_identifier":{"issn":["1064-3745"],"isbn":["978-1-4939-8771-9"]},"publication_status":"published","file":[{"date_created":"2020-10-13T14:20:37Z","file_name":"2018_MIMB_Zagorski.pdf","creator":"dernst","date_updated":"2020-10-13T14:20:37Z","file_size":4906815,"file_id":"8656","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}]},{"issue":"POPL","volume":2,"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.04037"}],"intvolume":" 2","month":"01","abstract":[{"text":"Probabilistic programs extend classical imperative programs with real-valued random variables and random branching. The most basic liveness property for such programs is the termination property. The qualitative (aka almost-sure) termination problem asks whether a given program program terminates with probability 1. While ranking functions provide a sound and complete method for non-probabilistic programs, the extension of them to probabilistic programs is achieved via ranking supermartingales (RSMs). Although deep theoretical results have been established about RSMs, their application to probabilistic programs with nondeterminism has been limited only to programs of restricted control-flow structure. For non-probabilistic programs, lexicographic ranking functions provide a compositional and practical approach for termination analysis of real-world programs. In this work we introduce lexicographic RSMs and show that they present a sound method for almost-sure termination of probabilistic programs with nondeterminism. We show that lexicographic RSMs provide a tool for compositional reasoning about almost-sure termination, and for probabilistic programs with linear arithmetic they can be synthesized efficiently (in polynomial time). We also show that with additional restrictions even asymptotic bounds on expected termination time can be obtained through lexicographic RSMs. Finally, we present experimental results on benchmarks adapted from previous work to demonstrate the effectiveness of our approach.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"KrCh"}],"date_updated":"2021-01-12T07:42:07Z","conference":{"name":"POPL: Principles of Programming Languages","start_date":"2018-01-07","location":"Los Angeles, CA, USA","end_date":"2018-01-13"},"type":"conference","status":"public","_id":"325","date_created":"2018-12-11T11:45:50Z","date_published":"2018-01-01T00:00:00Z","doi":"10.1145/3158122","year":"2018","day":"01","oa":1,"quality_controlled":"1","publisher":"ACM","external_id":{"arxiv":["1709.04037"]},"publist_id":"7540","author":[{"first_name":"Sheshansh","full_name":"Agrawal, Sheshansh","last_name":"Agrawal"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Novotny, Petr","last_name":"Novotny","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"}],"title":"Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs","citation":{"ieee":"S. Agrawal, K. Chatterjee, and P. Novotný, “Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs,” presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA, 2018, vol. 2, no. POPL.","short":"S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.","ama":"Agrawal S, Chatterjee K, Novotný P. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. In: Vol 2. ACM; 2018. doi:10.1145/3158122","apa":"Agrawal, S., Chatterjee, K., & Novotný, P. (2018). Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs (Vol. 2). Presented at the POPL: Principles of Programming Languages, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/3158122","mla":"Agrawal, Sheshansh, et al. Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs. Vol. 2, no. POPL, 34, ACM, 2018, doi:10.1145/3158122.","ista":"Agrawal S, Chatterjee K, Novotný P. 2018. Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs. POPL: Principles of Programming Languages vol. 2, 34.","chicago":"Agrawal, Sheshansh, Krishnendu Chatterjee, and Petr Novotný. “Lexicographic Ranking Supermartingales: An Efficient Approach to Termination of Probabilistic Programs,” Vol. 2. ACM, 2018. https://doi.org/10.1145/3158122."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"34"},{"publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","oa":1,"page":"199 - 206","doi":"10.31263/voebm.v71i1.1993","date_published":"2018-10-01T00:00:00Z","date_created":"2018-12-11T11:44:22Z","has_accepted_license":"1","year":"2018","day":"01","publication":"VÖB Mitteilungen","author":[{"first_name":"Barbara","id":"406048EC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2724-4614","full_name":"Petritsch, Barbara","last_name":"Petritsch"},{"first_name":"Jana","id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","full_name":"Porsche, Jana","last_name":"Porsche"}],"publist_id":"8001","title":"IST PubRep and IST DataRep: the institutional repositories at IST Austria","citation":{"mla":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen, vol. 71, no. 1, Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018, pp. 199–206, doi:10.31263/voebm.v71i1.1993.","short":"B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206.","ieee":"B. Petritsch and J. Porsche, “IST PubRep and IST DataRep: the institutional repositories at IST Austria,” VÖB Mitteilungen, vol. 71, no. 1. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, pp. 199–206, 2018.","ama":"Petritsch B, Porsche J. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 2018;71(1):199-206. doi:10.31263/voebm.v71i1.1993","apa":"Petritsch, B., & Porsche, J. (2018). IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. https://doi.org/10.31263/voebm.v71i1.1993","chicago":"Petritsch, Barbara, and Jana Porsche. “IST PubRep and IST DataRep: The Institutional Repositories at IST Austria.” VÖB Mitteilungen. Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare, 2018. https://doi.org/10.31263/voebm.v71i1.1993.","ista":"Petritsch B, Porsche J. 2018. IST PubRep and IST DataRep: the institutional repositories at IST Austria. VÖB Mitteilungen. 71(1), 199–206."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"10","intvolume":" 71","abstract":[{"text":"In 2013, a publication repository was implemented at IST Austria and 2015 after a thorough preparation phase a data repository was implemented - both based on the Open Source Software EPrints. In this text, designed as field report, we will reflect on our experiences with Open Source Software in general and specifically with EPrints regarding technical aspects but also regarding their characteristics of the user community. The second part is a pleading for including the end users in the process of implementation, adaption and evaluation.","lang":"eng"}],"oa_version":"Published Version","issue":"1","volume":71,"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"7ac61bade5f37db011ca435ebcf86797","file_id":"5702","file_size":509434,"date_updated":"2020-07-14T12:46:38Z","creator":"dernst","file_name":"2018_VOEB_Petritsch.pdf","date_created":"2018-12-17T12:40:27Z"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","_id":"53","department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:46:38Z","date_updated":"2021-01-12T08:01:26Z","ddc":["020"]},{"tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","_id":"536","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:46:38Z","date_updated":"2023-02-23T12:23:25Z","ddc":["000"],"scopus_import":1,"intvolume":" 31","month":"11","abstract":[{"text":"We consider the problem of consensus in the challenging classic model. In this model, the adversary is adaptive; it can choose which processors crash at any point during the course of the algorithm. Further, communication is via asynchronous message passing: there is no known upper bound on the time to send a message from one processor to another, and all messages and coin flips are seen by the adversary. We describe a new randomized consensus protocol with expected message complexity O(n2log2n) when fewer than n / 2 processes may fail by crashing. This is an almost-linear improvement over the best previously known protocol, and within logarithmic factors of a known Ω(n2) message lower bound. The protocol further ensures that no process sends more than O(nlog3n) messages in expectation, which is again within logarithmic factors of optimal. We also present a generalization of the algorithm to an arbitrary number of failures t, which uses expected O(nt+t2log2t) total messages. Our approach is to build a message-efficient, resilient mechanism for aggregating individual processor votes, implementing the message-passing equivalent of a weak shared coin. Roughly, in our protocol, a processor first announces its votes to small groups, then propagates them to increasingly larger groups as it generates more and more votes. To bound the number of messages that an individual process might have to send or receive, the protocol progressively increases the weight of generated votes. The main technical challenge is bounding the impact of votes that are still “in flight” (generated, but not fully propagated) on the final outcome of the shared coin, especially since such votes might have different weights. We achieve this by leveraging the structure of the algorithm, and a technical argument based on martingale concentration bounds. Overall, we show that it is possible to build an efficient message-passing implementation of a shared coin, and in the process (almost-optimally) solve the classic consensus problem in the asynchronous message-passing model.","lang":"eng"}],"oa_version":"Published Version","volume":31,"issue":"6","publication_status":"published","publication_identifier":{"issn":["01782770"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","date_updated":"2020-07-14T12:46:38Z","file_size":595707,"date_created":"2019-01-22T07:25:51Z","file_name":"2017_DistribComp_Alistarh.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"69b46e537acdcac745237ddb853fcbb5","file_id":"5867"}],"project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"article_processing_charge":"Yes (via OA deal)","publist_id":"7281","author":[{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X"},{"last_name":"Aspnes","full_name":"Aspnes, James","first_name":"James"},{"full_name":"King, Valerie","last_name":"King","first_name":"Valerie"},{"last_name":"Saia","full_name":"Saia, Jared","first_name":"Jared"}],"title":"Communication-efficient randomized consensus","citation":{"ista":"Alistarh D-A, Aspnes J, King V, Saia J. 2018. Communication-efficient randomized consensus. Distributed Computing. 31(6), 489–501.","chicago":"Alistarh, Dan-Adrian, James Aspnes, Valerie King, and Jared Saia. “Communication-Efficient Randomized Consensus.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-017-0315-1.","apa":"Alistarh, D.-A., Aspnes, J., King, V., & Saia, J. (2018). Communication-efficient randomized consensus. Distributed Computing. Springer. https://doi.org/10.1007/s00446-017-0315-1","ama":"Alistarh D-A, Aspnes J, King V, Saia J. Communication-efficient randomized consensus. Distributed Computing. 2018;31(6):489-501. doi:10.1007/s00446-017-0315-1","ieee":"D.-A. Alistarh, J. Aspnes, V. King, and J. Saia, “Communication-efficient randomized consensus,” Distributed Computing, vol. 31, no. 6. Springer, pp. 489–501, 2018.","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 489–501.","mla":"Alistarh, Dan-Adrian, et al. “Communication-Efficient Randomized Consensus.” Distributed Computing, vol. 31, no. 6, Springer, 2018, pp. 489–501, doi:10.1007/s00446-017-0315-1."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Springer","page":"489-501","date_created":"2018-12-11T11:47:01Z","date_published":"2018-11-01T00:00:00Z","doi":"10.1007/s00446-017-0315-1","year":"2018","has_accepted_license":"1","publication":"Distributed Computing","day":"01"},{"year":"2018","publication":"Communications in Mathematical Physics","day":"01","page":"347-403","date_created":"2018-12-11T11:47:09Z","doi":"10.1007/s00220-017-3064-x","date_published":"2018-05-01T00:00:00Z","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 360(1), 347–403.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s00220-017-3064-x.","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “The Bogoliubov free energy functional II: The dilute Limit,” Communications in Mathematical Physics, vol. 360, no. 1. Springer, pp. 347–403, 2018.","short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, Communications in Mathematical Physics 360 (2018) 347–403.","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-017-3064-x","ama":"Napiórkowski MM, Reuvers R, Solovej J. The Bogoliubov free energy functional II: The dilute Limit. Communications in Mathematical Physics. 2018;360(1):347-403. doi:10.1007/s00220-017-3064-x","mla":"Napiórkowski, Marcin M., et al. “The Bogoliubov Free Energy Functional II: The Dilute Limit.” Communications in Mathematical Physics, vol. 360, no. 1, Springer, 2018, pp. 347–403, doi:10.1007/s00220-017-3064-x."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1511.05953"]},"author":[{"last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin M"},{"first_name":"Robin","full_name":"Reuvers, Robin","last_name":"Reuvers"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"publist_id":"7260","title":"The Bogoliubov free energy functional II: The dilute Limit","project":[{"call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems"}],"publication_status":"published","publication_identifier":{"issn":["00103616"]},"language":[{"iso":"eng"}],"volume":360,"issue":"1","abstract":[{"lang":"eng","text":"We analyse the canonical Bogoliubov free energy functional in three dimensions at low temperatures in the dilute limit. We prove existence of a first-order phase transition and, in the limit (Formula presented.), we determine the critical temperature to be (Formula presented.) to leading order. Here, (Formula presented.) is the critical temperature of the free Bose gas, ρ is the density of the gas and a is the scattering length of the pair-interaction potential V. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee–Huang–Yang formula in the limit (Formula presented.)."}],"oa_version":"Submitted Version","main_file_link":[{"url":"https://arxiv.org/abs/1511.05953","open_access":"1"}],"scopus_import":1,"intvolume":" 360","month":"05","date_updated":"2021-01-12T08:02:35Z","department":[{"_id":"RoSe"}],"_id":"554","type":"journal_article","status":"public"},{"article_processing_charge":"No","external_id":{"pmid":["29222783"]},"author":[{"last_name":"Dimitrov","full_name":"Dimitrov, Dimitar","first_name":"Dimitar"},{"last_name":"Guillaud","full_name":"Guillaud, Laurent","first_name":"Laurent"},{"orcid":"0000-0002-6170-2546","full_name":"Eguchi, Kohgaku","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku"},{"last_name":"Takahashi","full_name":"Takahashi, Tomoyuki","first_name":"Tomoyuki"}],"publist_id":"7252","title":"Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses","editor":[{"full_name":"Skaper, Stephen D.","last_name":"Skaper","first_name":"Stephen D."}],"citation":{"chicago":"Dimitrov, Dimitar, Laurent Guillaud, Kohgaku Eguchi, and Tomoyuki Takahashi. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” In Neurotrophic Factors, edited by Stephen D. Skaper, 1727:201–15. Springer, 2018. https://doi.org/10.1007/978-1-4939-7571-6_15.","ista":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. 2018.Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Neurotrophic Factors. Methods in Molecular Biology, vol. 1727, 201–215.","mla":"Dimitrov, Dimitar, et al. “Culture of Mouse Giant Central Nervous System Synapses and Application for Imaging and Electrophysiological Analyses.” Neurotrophic Factors, edited by Stephen D. Skaper, vol. 1727, Springer, 2018, pp. 201–15, doi:10.1007/978-1-4939-7571-6_15.","short":"D. Dimitrov, L. Guillaud, K. Eguchi, T. Takahashi, in:, S.D. Skaper (Ed.), Neurotrophic Factors, Springer, 2018, pp. 201–215.","ieee":"D. Dimitrov, L. Guillaud, K. Eguchi, and T. Takahashi, “Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses,” in Neurotrophic Factors, vol. 1727, S. D. Skaper, Ed. Springer, 2018, pp. 201–215.","ama":"Dimitrov D, Guillaud L, Eguchi K, Takahashi T. Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In: Skaper SD, ed. Neurotrophic Factors. Vol 1727. Springer; 2018:201-215. doi:10.1007/978-1-4939-7571-6_15","apa":"Dimitrov, D., Guillaud, L., Eguchi, K., & Takahashi, T. (2018). Culture of mouse giant central nervous system synapses and application for imaging and electrophysiological analyses. In S. D. Skaper (Ed.), Neurotrophic Factors (Vol. 1727, pp. 201–215). Springer. https://doi.org/10.1007/978-1-4939-7571-6_15"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publisher":"Springer","quality_controlled":"1","page":"201 - 215","date_created":"2018-12-11T11:47:11Z","doi":"10.1007/978-1-4939-7571-6_15","date_published":"2018-01-01T00:00:00Z","year":"2018","has_accepted_license":"1","publication":"Neurotrophic Factors","day":"01","type":"book_chapter","status":"public","_id":"562","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:09Z","date_updated":"2021-01-12T08:03:05Z","ddc":["570"],"scopus_import":1,"alternative_title":["Methods in Molecular Biology"],"intvolume":" 1727","month":"01","abstract":[{"lang":"eng","text":"Primary neuronal cell culture preparations are widely used to investigate synaptic functions. This chapter describes a detailed protocol for the preparation of a neuronal cell culture in which giant calyx-type synaptic terminals are formed. This chapter also presents detailed protocols for utilizing the main technical advantages provided by such a preparation, namely, labeling and imaging of synaptic organelles and electrophysiological recordings directly from presynaptic terminals."}],"oa_version":"Submitted Version","pmid":1,"volume":1727,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"date_created":"2019-11-19T07:47:43Z","file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:09Z","file_size":787407,"checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","file_id":"7046","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}]},{"month":"09","intvolume":" 8","abstract":[{"text":"Blood platelets are critical for hemostasis and thrombosis, but also play diverse roles during immune responses. We have recently reported that platelets migrate at sites of infection in vitro and in vivo. Importantly, platelets use their ability to migrate to collect and bundle fibrin (ogen)-bound bacteria accomplishing efficient intravascular bacterial trapping. Here, we describe a method that allows analyzing platelet migration in vitro, focusing on their ability to collect bacteria and trap bacteria under flow.","lang":"eng"}],"oa_version":"Published Version","volume":8,"issue":"18","ec_funded":1,"publication_identifier":{"issn":["2331-8325"]},"publication_status":"published","file":[{"file_id":"6360","checksum":"d4588377e789da7f360b553ae02c5119","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-04-30T08:04:33Z","file_name":"2018_BioProtocol_Fan.pdf","date_updated":"2020-07-14T12:47:28Z","file_size":2928337,"creator":"dernst"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"_id":"6354","file_date_updated":"2020-07-14T12:47:28Z","department":[{"_id":"MiSi"}],"date_updated":"2021-01-12T08:07:12Z","ddc":["570"],"quality_controlled":"1","publisher":"Bio-Protocol","oa":1,"acknowledgement":" FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)","date_published":"2018-09-20T00:00:00Z","doi":"10.21769/bioprotoc.3018","date_created":"2019-04-29T09:40:33Z","has_accepted_license":"1","year":"2018","day":"20","publication":"Bio-Protocol","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","call_identifier":"H2020","_id":"260AA4E2-B435-11E9-9278-68D0E5697425"}],"article_number":"e3018","author":[{"full_name":"Fan, Shuxia","last_name":"Fan","first_name":"Shuxia"},{"first_name":"Michael","last_name":"Lorenz","full_name":"Lorenz, Michael"},{"first_name":"Steffen","full_name":"Massberg, Steffen","last_name":"Massberg"},{"first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","last_name":"Gärtner","full_name":"Gärtner, Florian R","orcid":"0000-0001-6120-3723"}],"title":"Platelet migration and bacterial trapping assay under flow","citation":{"chicago":"Fan, Shuxia, Michael Lorenz, Steffen Massberg, and Florian R Gärtner. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol. Bio-Protocol, 2018. https://doi.org/10.21769/bioprotoc.3018.","ista":"Fan S, Lorenz M, Massberg S, Gärtner FR. 2018. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 8(18), e3018.","mla":"Fan, Shuxia, et al. “Platelet Migration and Bacterial Trapping Assay under Flow.” Bio-Protocol, vol. 8, no. 18, e3018, Bio-Protocol, 2018, doi:10.21769/bioprotoc.3018.","ama":"Fan S, Lorenz M, Massberg S, Gärtner FR. Platelet migration and bacterial trapping assay under flow. Bio-Protocol. 2018;8(18). doi:10.21769/bioprotoc.3018","apa":"Fan, S., Lorenz, M., Massberg, S., & Gärtner, F. R. (2018). Platelet migration and bacterial trapping assay under flow. Bio-Protocol. Bio-Protocol. https://doi.org/10.21769/bioprotoc.3018","ieee":"S. Fan, M. Lorenz, S. Massberg, and F. R. Gärtner, “Platelet migration and bacterial trapping assay under flow,” Bio-Protocol, vol. 8, no. 18. Bio-Protocol, 2018.","short":"S. Fan, M. Lorenz, S. Massberg, F.R. Gärtner, Bio-Protocol 8 (2018)."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"publisher":"IST Austria","oa":1,"month":"09","oa_version":"Published Version","date_published":"2018-09-24T00:00:00Z","doi":"10.5281/zenodo.1410279","date_created":"2019-05-16T07:27:14Z","has_accepted_license":"1","year":"2018","publication_status":"published","file":[{"file_size":1967778,"date_updated":"2020-07-14T12:47:30Z","creator":"dernst","file_name":"Poster_Beitrag_125_Petritsch.pdf","date_created":"2019-05-16T07:26:25Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"6460","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1"}],"day":"24","language":[{"iso":"eng"}],"type":"conference_poster","tmp":{"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)","short":"CC BY (4.0)"},"conference":{"start_date":"2018-09-24","end_date":"2018-09-26","location":"Graz, Austria","name":"Open-Access-Tage"},"status":"public","keyword":["Open Access","Publication Analysis"],"_id":"6459","author":[{"id":"406048EC-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","last_name":"Petritsch","full_name":"Petritsch, Barbara","orcid":"0000-0003-2724-4614"}],"file_date_updated":"2020-07-14T12:47:30Z","title":"Open Access at IST Austria 2009-2017","department":[{"_id":"E-Lib"}],"date_updated":"2020-07-14T23:06:21Z","citation":{"apa":"Petritsch, B. (2018). Open Access at IST Austria 2009-2017. Presented at the Open-Access-Tage, Graz, Austria: IST Austria. https://doi.org/10.5281/zenodo.1410279","ama":"Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018. doi:10.5281/zenodo.1410279","ieee":"B. Petritsch, Open Access at IST Austria 2009-2017. IST Austria, 2018.","short":"B. Petritsch, Open Access at IST Austria 2009-2017, IST Austria, 2018.","mla":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018, doi:10.5281/zenodo.1410279.","ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.","chicago":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018. https://doi.org/10.5281/zenodo.1410279."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["020"]},{"_id":"690","type":"journal_article","status":"public","date_updated":"2021-01-12T08:09:33Z","department":[{"_id":"LaEr"}],"abstract":[{"text":"We consider spectral properties and the edge universality of sparse random matrices, the class of random matrices that includes the adjacency matrices of the Erdős–Rényi graph model G(N, p). We prove a local law for the eigenvalue density up to the spectral edges. Under a suitable condition on the sparsity, we also prove that the rescaled extremal eigenvalues exhibit GOE Tracy–Widom fluctuations if a deterministic shift of the spectral edge due to the sparsity is included. For the adjacency matrix of the Erdős–Rényi graph this establishes the Tracy–Widom fluctuations of the second largest eigenvalue when p is much larger than N−2/3 with a deterministic shift of order (Np)−1.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"url":"https://arxiv.org/abs/1605.08767","open_access":"1"}],"scopus_import":1,"intvolume":" 171","month":"06","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":171,"issue":"1-2","article_number":"543-616","project":[{"name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","call_identifier":"FP7","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).","ieee":"J. Lee and K. Schnelli, “Local law and Tracy–Widom limit for sparse random matrices,” Probability Theory and Related Fields, vol. 171, no. 1–2. Springer, 2018.","apa":"Lee, J., & Schnelli, K. (2018). Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. Springer. https://doi.org/10.1007/s00440-017-0787-8","ama":"Lee J, Schnelli K. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 2018;171(1-2). doi:10.1007/s00440-017-0787-8","mla":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields, vol. 171, no. 1–2, 543–616, Springer, 2018, doi:10.1007/s00440-017-0787-8.","ista":"Lee J, Schnelli K. 2018. Local law and Tracy–Widom limit for sparse random matrices. Probability Theory and Related Fields. 171(1–2), 543–616.","chicago":"Lee, Jii, and Kevin Schnelli. “Local Law and Tracy–Widom Limit for Sparse Random Matrices.” Probability Theory and Related Fields. Springer, 2018. https://doi.org/10.1007/s00440-017-0787-8."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1605.08767"]},"author":[{"last_name":"Lee","full_name":"Lee, Jii","first_name":"Jii"},{"first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","last_name":"Schnelli"}],"publist_id":"7017","title":"Local law and Tracy–Widom limit for sparse random matrices","oa":1,"publisher":"Springer","quality_controlled":"1","year":"2018","publication":"Probability Theory and Related Fields","day":"14","date_created":"2018-12-11T11:47:56Z","date_published":"2018-06-14T00:00:00Z","doi":"10.1007/s00440-017-0787-8"},{"page":"1668-1682","date_published":"2018-07-01T00:00:00Z","doi":"10.1109/TPAMI.2017.2730884","date_created":"2018-12-11T11:48:01Z","year":"2018","day":"01","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","quality_controlled":"1","publisher":"IEEE","oa":1,"author":[{"first_name":"Alexander","last_name":"Shekhovtsov","full_name":"Shekhovtsov, Alexander"},{"first_name":"Paul","id":"446560C6-F248-11E8-B48F-1D18A9856A87","full_name":"Swoboda, Paul","last_name":"Swoboda"},{"full_name":"Savchynskyy, Bogdan","last_name":"Savchynskyy","first_name":"Bogdan"}],"publist_id":"6992","external_id":{"arxiv":["1508.07902"]},"title":"Maximum persistency via iterative relaxed inference with graphical models","citation":{"mla":"Shekhovtsov, Alexander, et al. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7, IEEE, 2018, pp. 1668–82, doi:10.1109/TPAMI.2017.2730884.","short":"A. Shekhovtsov, P. Swoboda, B. Savchynskyy, IEEE Transactions on Pattern Analysis and Machine Intelligence 40 (2018) 1668–1682.","ieee":"A. Shekhovtsov, P. Swoboda, and B. Savchynskyy, “Maximum persistency via iterative relaxed inference with graphical models,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 40, no. 7. IEEE, pp. 1668–1682, 2018.","apa":"Shekhovtsov, A., Swoboda, P., & Savchynskyy, B. (2018). Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/TPAMI.2017.2730884","ama":"Shekhovtsov A, Swoboda P, Savchynskyy B. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2018;40(7):1668-1682. doi:10.1109/TPAMI.2017.2730884","chicago":"Shekhovtsov, Alexander, Paul Swoboda, and Bogdan Savchynskyy. “Maximum Persistency via Iterative Relaxed Inference with Graphical Models.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2018. https://doi.org/10.1109/TPAMI.2017.2730884.","ista":"Shekhovtsov A, Swoboda P, Savchynskyy B. 2018. Maximum persistency via iterative relaxed inference with graphical models. IEEE Transactions on Pattern Analysis and Machine Intelligence. 40(7), 1668–1682."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":40,"issue":"7","publication_identifier":{"issn":["01628828"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1508.07902"}],"month":"07","intvolume":" 40","abstract":[{"lang":"eng","text":"We consider the NP-hard problem of MAP-inference for undirected discrete graphical models. We propose a polynomial time and practically efficient algorithm for finding a part of its optimal solution. Specifically, our algorithm marks some labels of the considered graphical model either as (i) optimal, meaning that they belong to all optimal solutions of the inference problem; (ii) non-optimal if they provably do not belong to any solution. With access to an exact solver of a linear programming relaxation to the MAP-inference problem, our algorithm marks the maximal possible (in a specified sense) number of labels. We also present a version of the algorithm, which has access to a suboptimal dual solver only and still can ensure the (non-)optimality for the marked labels, although the overall number of the marked labels may decrease. We propose an efficient implementation, which runs in time comparable to a single run of a suboptimal dual solver. Our method is well-scalable and shows state-of-the-art results on computational benchmarks from machine learning and computer vision."}],"oa_version":"Preprint","department":[{"_id":"VlKo"}],"date_updated":"2021-01-12T08:11:32Z","type":"journal_article","status":"public","_id":"703"},{"ddc":["000"],"date_updated":"2023-02-23T12:59:17Z","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:47:49Z","_id":"7116","status":"public","type":"conference","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (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"},"conference":{"name":"EDBT: Conference on Extending Database Technology","start_date":"2018-03-26","end_date":"2018-03-29","location":"Vienna, Austria"},"file":[{"file_id":"7118","checksum":"ec979b56abc71016d6e6adfdadbb4afe","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-11-26T14:23:04Z","file_name":"2018_OpenProceedings_Grubic.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:49Z","file_size":1603204}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783893180783"],"issn":["2367-2005"]},"publication_status":"published","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Training deep learning models has received tremendous research interest recently. In particular, there has been intensive research on reducing the communication cost of training when using multiple computational devices, through reducing the precision of the underlying data representation. Naturally, such methods induce system trade-offs—lowering communication precision could de-crease communication overheads and improve scalability; but, on the other hand, it can also reduce the accuracy of training. In this paper, we study this trade-off space, and ask:Can low-precision communication consistently improve the end-to-end performance of training modern neural networks, with no accuracy loss?From the performance point of view, the answer to this question may appear deceptively easy: compressing communication through low precision should help when the ratio between communication and computation is high. However, this answer is less straightforward when we try to generalize this principle across various neural network architectures (e.g., AlexNet vs. ResNet),number of GPUs (e.g., 2 vs. 8 GPUs), machine configurations(e.g., EC2 instances vs. NVIDIA DGX-1), communication primitives (e.g., MPI vs. NCCL), and even different GPU architectures(e.g., Kepler vs. Pascal). Currently, it is not clear how a realistic realization of all these factors maps to the speed up provided by low-precision communication. In this paper, we conduct an empirical study to answer this question and report the insights."}],"month":"03","scopus_import":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Grubic, Demjan, Leo Tam, Dan-Adrian Alistarh, and Ce Zhang. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” In Proceedings of the 21st International Conference on Extending Database Technology, 145–56. OpenProceedings, 2018. https://doi.org/10.5441/002/EDBT.2018.14.","ista":"Grubic D, Tam L, Alistarh D-A, Zhang C. 2018. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. Proceedings of the 21st International Conference on Extending Database Technology. EDBT: Conference on Extending Database Technology, 145–156.","mla":"Grubic, Demjan, et al. “Synchronous Multi-GPU Training for Deep Learning with Low-Precision Communications: An Empirical Study.” Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–56, doi:10.5441/002/EDBT.2018.14.","ama":"Grubic D, Tam L, Alistarh D-A, Zhang C. Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In: Proceedings of the 21st International Conference on Extending Database Technology. OpenProceedings; 2018:145-156. doi:10.5441/002/EDBT.2018.14","apa":"Grubic, D., Tam, L., Alistarh, D.-A., & Zhang, C. (2018). Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study. In Proceedings of the 21st International Conference on Extending Database Technology (pp. 145–156). Vienna, Austria: OpenProceedings. https://doi.org/10.5441/002/EDBT.2018.14","short":"D. Grubic, L. Tam, D.-A. Alistarh, C. Zhang, in:, Proceedings of the 21st International Conference on Extending Database Technology, OpenProceedings, 2018, pp. 145–156.","ieee":"D. Grubic, L. Tam, D.-A. Alistarh, and C. Zhang, “Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study,” in Proceedings of the 21st International Conference on Extending Database Technology, Vienna, Austria, 2018, pp. 145–156."},"title":"Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study","author":[{"full_name":"Grubic, Demjan","last_name":"Grubic","first_name":"Demjan"},{"last_name":"Tam","full_name":"Tam, Leo","first_name":"Leo"},{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"},{"full_name":"Zhang, Ce","last_name":"Zhang","first_name":"Ce"}],"article_processing_charge":"No","day":"26","publication":"Proceedings of the 21st International Conference on Extending Database Technology","has_accepted_license":"1","year":"2018","doi":"10.5441/002/EDBT.2018.14","date_published":"2018-03-26T00:00:00Z","date_created":"2019-11-26T14:19:11Z","page":"145-156","quality_controlled":"1","publisher":"OpenProceedings","oa":1},{"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"has_accepted_license":"1","year":"2018","day":"31","publication":"10th Innovations in Theoretical Computer Science Conference (ITCS 2019)","page":"59:1-59:25","doi":"10.4230/LIPICS.ITCS.2019.59","date_published":"2018-12-31T00:00:00Z","date_created":"2020-01-30T09:16:05Z","project":[{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"citation":{"ama":"Pietrzak KZ. Proofs of catalytic space. In: 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). Vol 124. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:59:1-59:25. doi:10.4230/LIPICS.ITCS.2019.59","apa":"Pietrzak, K. Z. (2018). Proofs of catalytic space. In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019) (Vol. 124, p. 59:1-59:25). San Diego, CA, United States: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.ITCS.2019.59","ieee":"K. Z. Pietrzak, “Proofs of catalytic space,” in 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), San Diego, CA, United States, 2018, vol. 124, p. 59:1-59:25.","short":"K.Z. Pietrzak, in:, 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25.","mla":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), vol. 124, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 59:1-59:25, doi:10.4230/LIPICS.ITCS.2019.59.","ista":"Pietrzak KZ. 2018. Proofs of catalytic space. 10th Innovations in Theoretical Computer Science Conference (ITCS 2019). ITCS: Innovations in theoretical Computer Science Conference, LIPIcs, vol. 124, 59:1-59:25.","chicago":"Pietrzak, Krzysztof Z. “Proofs of Catalytic Space.” In 10th Innovations in Theoretical Computer Science Conference (ITCS 2019), 124:59:1-59:25. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.ITCS.2019.59."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"Proofs of catalytic space","abstract":[{"text":"Proofs of space (PoS) [Dziembowski et al., CRYPTO'15] are proof systems where a prover can convince a verifier that he \"wastes\" disk space. PoS were introduced as a more ecological and economical replacement for proofs of work which are currently used to secure blockchains like Bitcoin. In this work we investigate extensions of PoS which allow the prover to embed useful data into the dedicated space, which later can be recovered. Our first contribution is a security proof for the original PoS from CRYPTO'15 in the random oracle model (the original proof only applied to a restricted class of adversaries which can store a subset of the data an honest prover would store). When this PoS is instantiated with recent constructions of maximally depth robust graphs, our proof implies basically optimal security. As a second contribution we show three different extensions of this PoS where useful data can be embedded into the space required by the prover. Our security proof for the PoS extends (non-trivially) to these constructions. We discuss how some of these variants can be used as proofs of catalytic space (PoCS), a notion we put forward in this work, and which basically is a PoS where most of the space required by the prover can be used to backup useful data. Finally we discuss how one of the extensions is a candidate construction for a proof of replication (PoR), a proof system recently suggested in the Filecoin whitepaper. ","lang":"eng"}],"oa_version":"Published Version","scopus_import":1,"alternative_title":["LIPIcs"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/194"}],"month":"12","intvolume":" 124","publication_identifier":{"isbn":["978-3-95977-095-8"],"issn":["1868-8969"]},"publication_status":"published","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"5cebb7f7849a3beda898f697d755dd96","file_id":"7443","date_updated":"2020-07-14T12:47:57Z","file_size":822884,"creator":"dernst","date_created":"2020-02-04T08:17:52Z","file_name":"2018_LIPIcs_Pietrzak.pdf"}],"language":[{"iso":"eng"}],"volume":124,"ec_funded":1,"_id":"7407","type":"conference","conference":{"name":"ITCS: Innovations in theoretical Computer Science Conference","location":"San Diego, CA, United States","end_date":"2019-01-12","start_date":"2019-01-10"},"tmp":{"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)","short":"CC BY (4.0)"},"status":"public","date_updated":"2021-01-12T08:13:26Z","ddc":["000"],"department":[{"_id":"KrPi"}],"file_date_updated":"2020-07-14T12:47:57Z"},{"_id":"7812","status":"public","conference":{"start_date":"2018-04-30","end_date":"2018-05-03","location":"Vancouver, Canada","name":"ICLR: International Conference on Learning Representations"},"type":"conference","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 6th International Conference on Learning Representations, 2018.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018.","apa":"Polino, A., Pascanu, R., & Alistarh, D.-A. (2018). Model compression via distillation and quantization. In 6th International Conference on Learning Representations. Vancouver, Canada.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, in:, 6th International Conference on Learning Representations, 2018.","ieee":"A. Polino, R. Pascanu, and D.-A. Alistarh, “Model compression via distillation and quantization,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018.","chicago":"Polino, Antonio, Razvan Pascanu, and Dan-Adrian Alistarh. “Model Compression via Distillation and Quantization.” In 6th International Conference on Learning Representations, 2018.","ista":"Polino A, Pascanu R, Alistarh D-A. 2018. Model compression via distillation and quantization. 6th International Conference on Learning Representations. ICLR: International Conference on Learning Representations."},"date_updated":"2023-02-23T13:18:41Z","title":"Model compression via distillation and quantization","file_date_updated":"2020-07-14T12:48:03Z","department":[{"_id":"DaAl"}],"external_id":{"arxiv":["1802.05668"]},"article_processing_charge":"No","author":[{"first_name":"Antonio","full_name":"Polino, Antonio","last_name":"Polino"},{"full_name":"Pascanu, Razvan","last_name":"Pascanu","first_name":"Razvan"},{"id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}],"oa_version":"Published Version","abstract":[{"text":"Deep neural networks (DNNs) continue to make significant advances, solving tasks from image classification to translation or reinforcement learning. One aspect of the field receiving considerable attention is efficiently executing deep models in resource-constrained environments, such as mobile or embedded devices. This paper focuses on this problem, and proposes two new compression methods, which jointly leverage weight quantization and distillation of larger teacher networks into smaller student networks. The first method we propose is called quantized distillation and leverages distillation during the training process, by incorporating distillation loss, expressed with respect to the teacher, into the training of a student network whose weights are quantized to a limited set of levels. The second method, differentiable quantization, optimizes the location of quantization points through stochastic gradient descent, to better fit the behavior of the teacher model. We validate both methods through experiments on convolutional and recurrent architectures. We show that quantized shallow students can reach similar accuracy levels to full-precision teacher models, while providing order of magnitude compression, and inference speedup that is linear in the depth reduction. In sum, our results enable DNNs for resource-constrained environments to leverage architecture and accuracy advances developed on more powerful devices.","lang":"eng"}],"month":"05","oa":1,"quality_controlled":"1","scopus_import":1,"publication":"6th International Conference on Learning Representations","language":[{"iso":"eng"}],"day":"01","file":[{"date_created":"2020-05-26T13:02:00Z","file_name":"2018_ICLR_Polino.pdf","date_updated":"2020-07-14T12:48:03Z","file_size":308339,"creator":"dernst","file_id":"7894","checksum":"a4336c167978e81891970e4e4517a8c3","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"year":"2018","publication_status":"published","has_accepted_license":"1","date_created":"2020-05-10T22:00:51Z","date_published":"2018-05-01T00:00:00Z"},{"month":"12","main_file_link":[{"url":"https://doi.org/10.1101/494088","open_access":"1"}],"oa":1,"publisher":"Cold Spring Harbor Laboratory","acknowledgement":"We thank I. Andrew and S.E. Bae for excellent technical assistance, F. Gage for plasmids, and K. Nave (Nex-Cre) for mouse colonies. We thank members of the Marín and Rico laboratories for stimulating discussions and ideas. Our research on this topic is supported by grants from the European Research Council (ERC-2017-AdG 787355 to O.M and ERC2016-CoG 725780 to S.H.) and Wellcome Trust (103714MA) to O.M. L.L. was the recipient of an EMBO long-term postdoctoral fellowship, R.B. received support from FWF Lise-Meitner program (M 2416) and F.K.W. was supported by an EMBO postdoctoral fellowship and is currently a Marie Skłodowska-Curie Fellow from the European Commission under the H2020 Programme.","oa_version":"Preprint","abstract":[{"lang":"eng","text":"The cerebral cortex contains multiple hierarchically organized areas with distinctive cytoarchitectonical patterns, but the cellular mechanisms underlying the emergence of this diversity remain unclear. Here, we have quantitatively investigated the neuronal output of individual progenitor cells in the ventricular zone of the developing mouse neocortex using a combination of methods that together circumvent the biases and limitations of individual approaches. We found that individual cortical progenitor cells show a high degree of stochasticity and generate pyramidal cell lineages that adopt a wide range of laminar configurations. Mathematical modelling these lineage data suggests that a small number of progenitor cell populations, each generating pyramidal cells following different stochastic developmental programs, suffice to generate the heterogenous complement of pyramidal cell lineages that collectively build the complex cytoarchitecture of the neocortex."}],"date_created":"2020-09-21T12:01:50Z","ec_funded":1,"date_published":"2018-12-13T00:00:00Z","doi":"10.1101/494088","language":[{"iso":"eng"}],"publication":"bioRxiv","day":"13","publication_status":"submitted","year":"2018","status":"public","project":[{"grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","_id":"260018B0-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416"}],"type":"preprint","_id":"8547","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","department":[{"_id":"SiHi"}],"article_processing_charge":"No","author":[{"full_name":"Llorca, Alfredo","last_name":"Llorca","first_name":"Alfredo"},{"full_name":"Ciceri, Gabriele","last_name":"Ciceri","first_name":"Gabriele"},{"first_name":"Robert J","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","last_name":"Beattie","full_name":"Beattie, Robert J","orcid":"0000-0002-8483-8753"},{"last_name":"Wong","full_name":"Wong, Fong K.","first_name":"Fong K."},{"first_name":"Giovanni","last_name":"Diana","full_name":"Diana, Giovanni"},{"first_name":"Eleni","full_name":"Serafeimidou, Eleni","last_name":"Serafeimidou"},{"first_name":"Marian","last_name":"Fernández-Otero","full_name":"Fernández-Otero, Marian"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen","last_name":"Streicher"},{"first_name":"Sebastian J.","full_name":"Arnold, Sebastian J.","last_name":"Arnold"},{"first_name":"Martin","full_name":"Meyer, Martin","last_name":"Meyer"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","last_name":"Hippenmeyer"},{"last_name":"Maravall","full_name":"Maravall, Miguel","first_name":"Miguel"},{"last_name":"Marín","full_name":"Marín, Oscar","first_name":"Oscar"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2021-01-12T08:20:00Z","citation":{"chicago":"Llorca, Alfredo, Gabriele Ciceri, Robert J Beattie, Fong K. Wong, Giovanni Diana, Eleni Serafeimidou, Marian Fernández-Otero, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv. Cold Spring Harbor Laboratory, n.d. https://doi.org/10.1101/494088.","ista":"Llorca A, Ciceri G, Beattie RJ, Wong FK, Diana G, Serafeimidou E, Fernández-Otero M, Streicher C, Arnold SJ, Meyer M, Hippenmeyer S, Maravall M, Marín O. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv, 10.1101/494088.","mla":"Llorca, Alfredo, et al. “Heterogeneous Progenitor Cell Behaviors Underlie the Assembly of Neocortical Cytoarchitecture.” BioRxiv, Cold Spring Harbor Laboratory, doi:10.1101/494088.","short":"A. Llorca, G. Ciceri, R.J. Beattie, F.K. Wong, G. Diana, E. Serafeimidou, M. Fernández-Otero, C. Streicher, S.J. Arnold, M. Meyer, S. Hippenmeyer, M. Maravall, O. Marín, BioRxiv (n.d.).","ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory.","apa":"Llorca, A., Ciceri, G., Beattie, R. J., Wong, F. K., Diana, G., Serafeimidou, E., … Marín, O. (n.d.). Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/494088","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088"}},{"acknowledgement":"This research was supported in part by the Austrian Science Fund (FWF) under grants S11402-N23, S11407-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), ERC Start grant (279307: Graph Games), Vienna Science and Technology Fund (WWTF) through project ICT15-003 and by the National Science Centre (NCN), Poland under grant 2014/15/D/ST6/04543.","oa":1,"quality_controlled":"1","publisher":"Springer","publication":"Principles of Modeling","day":"20","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:44:33Z","doi":"10.1007/978-3-319-95246-8_9","date_published":"2018-07-20T00:00:00Z","page":"143 - 161","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z211","name":"The Wittgenstein Prize","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, and Jan Otop. “Computing Average Response Time.” In Principles of Modeling, edited by Marten Lohstroh, Patricia Derler, and Marjan Sirjani, 10760:143–61. Springer, 2018. https://doi.org/10.1007/978-3-319-95246-8_9.","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","mla":"Chatterjee, Krishnendu, et al. “Computing Average Response Time.” Principles of Modeling, edited by Marten Lohstroh et al., vol. 10760, Springer, 2018, pp. 143–61, doi:10.1007/978-3-319-95246-8_9.","short":"K. Chatterjee, T.A. Henzinger, J. Otop, in:, M. Lohstroh, P. Derler, M. Sirjani (Eds.), Principles of Modeling, Springer, 2018, pp. 143–161.","ieee":"K. Chatterjee, T. A. Henzinger, and J. Otop, “Computing average response time,” in Principles of Modeling, vol. 10760, M. Lohstroh, P. Derler, and M. Sirjani, Eds. Springer, 2018, pp. 143–161.","ama":"Chatterjee K, Henzinger TA, Otop J. Computing average response time. In: Lohstroh M, Derler P, Sirjani M, eds. Principles of Modeling. Vol 10760. Springer; 2018:143-161. doi:10.1007/978-3-319-95246-8_9","apa":"Chatterjee, K., Henzinger, T. A., & Otop, J. (2018). Computing average response time. In M. Lohstroh, P. Derler, & M. Sirjani (Eds.), Principles of Modeling (Vol. 10760, pp. 143–161). Springer. https://doi.org/10.1007/978-3-319-95246-8_9"},"editor":[{"first_name":"Marten","full_name":"Lohstroh, Marten","last_name":"Lohstroh"},{"last_name":"Derler","full_name":"Derler, Patricia","first_name":"Patricia"},{"first_name":"Marjan","full_name":"Sirjani, Marjan","last_name":"Sirjani"}],"title":"Computing average response time","publist_id":"7968","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A"},{"full_name":"Otop, Jan","last_name":"Otop","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","first_name":"Jan"}],"oa_version":"Submitted Version","abstract":[{"text":"Responsiveness—the requirement that every request to a system be eventually handled—is one of the fundamental liveness properties of a reactive system. Average response time is a quantitative measure for the responsiveness requirement used commonly in performance evaluation. We show how average response time can be computed on state-transition graphs, on Markov chains, and on game graphs. In all three cases, we give polynomial-time algorithms.","lang":"eng"}],"intvolume":" 10760","month":"07","scopus_import":1,"alternative_title":["LNCS"],"language":[{"iso":"eng"}],"file":[{"file_name":"2018_PrinciplesModeling_Chatterjee.pdf","date_created":"2019-11-19T08:22:18Z","creator":"dernst","file_size":516307,"date_updated":"2020-07-14T12:48:14Z","checksum":"9995c6ce6957333baf616fc4f20be597","file_id":"7053","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","ec_funded":1,"volume":10760,"_id":"86","status":"public","type":"book_chapter","ddc":["000"],"date_updated":"2021-01-12T08:20:14Z","file_date_updated":"2020-07-14T12:48:14Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}]},{"department":[{"_id":"JoDa"}],"date_updated":"2021-12-03T07:31:05Z","type":"journal_article","article_type":"letter_note","status":"public","_id":"9229","volume":4,"issue":"S1","publication_identifier":{"eissn":["2500-2295"],"issn":["2500-2287"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","alternative_title":["Molecular and cellular neuroscience"],"main_file_link":[{"url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience","open_access":"1"}],"month":"06","intvolume":" 4","oa_version":"Published Version","author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","full_name":"Danzl, Johann G","orcid":"0000-0001-8559-3973"}],"article_processing_charge":"No","title":"Diffraction-unlimited optical imaging for synaptic physiology","citation":{"ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11.","chicago":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod, 2018. https://doi.org/10.20388/omp2018.00s1.001.","ieee":"J. G. Danzl, “Diffraction-unlimited optical imaging for synaptic physiology,” Opera Medica et Physiologica, vol. 4, no. S1. Lobachevsky State University of Nizhny Novgorod, p. 11, 2018.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","ama":"Danzl JG. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 2018;4(S1):11. doi:10.20388/omp2018.00s1.001","apa":"Danzl, J. G. (2018). Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. Lobachevsky State University of Nizhny Novgorod. https://doi.org/10.20388/omp2018.00s1.001","mla":"Danzl, Johann G. “Diffraction-Unlimited Optical Imaging for Synaptic Physiology.” Opera Medica et Physiologica, vol. 4, no. S1, Lobachevsky State University of Nizhny Novgorod, 2018, p. 11, doi:10.20388/omp2018.00s1.001."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"11","doi":"10.20388/omp2018.00s1.001","date_published":"2018-06-30T00:00:00Z","date_created":"2021-03-07T23:01:25Z","year":"2018","day":"30","publication":"Opera Medica et Physiologica","quality_controlled":"1","publisher":"Lobachevsky State University of Nizhny Novgorod","oa":1},{"publication_status":"published","publication_identifier":{"issn":["1868-8969"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":542889,"date_updated":"2020-07-14T12:47:15Z","file_name":"2018_LIPIcs_Avni.pdf","date_created":"2019-02-14T14:22:04Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","file_id":"6007"}],"volume":117,"related_material":{"record":[{"relation":"earlier_version","id":"963","status":"public"}]},"abstract":[{"lang":"eng","text":"Network games are widely used as a model for selfish resource-allocation problems. In the classicalmodel, each player selects a path connecting her source and target vertices. The cost of traversingan edge depends on theload; namely, number of players that traverse it. Thus, it abstracts the factthat different users may use a resource at different times and for different durations, which playsan important role in determining the costs of the users in reality. For example, when transmittingpackets in a communication network, routing traffic in a road network, or processing a task in aproduction system, actual sharing and congestion of resources crucially depends on time.In [13], we introducedtimed network games, which add a time component to network games.Each vertexvin the network is associated with a cost function, mapping the load onvto theprice that a player pays for staying invfor one time unit with this load. Each edge in thenetwork is guarded by the time intervals in which it can be traversed, which forces the players tospend time in the vertices. In this work we significantly extend the way time can be referred toin timed network games. In the model we study, the network is equipped withclocks, and, as intimed automata, edges are guarded by constraints on the values of the clocks, and their traversalmay involve a reset of some clocks. We argue that the stronger model captures many realisticnetworks. The addition of clocks breaks the techniques we developed in [13] and we developnew techniques in order to show that positive results on classic network games carry over to thestronger timed setting."}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":"1","intvolume":" 117","month":"08","date_updated":"2023-02-23T14:02:58Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:15Z","_id":"6005","tmp":{"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)","short":"CC BY (4.0)"},"conference":{"start_date":"2018-08-27","location":"Liverpool, United Kingdom","end_date":"2018-08-31","name":"MFCS: Mathematical Foundations of Computer Science"},"type":"conference","status":"public","year":"2018","has_accepted_license":"1","day":"01","date_created":"2019-02-14T14:12:09Z","date_published":"2018-08-01T00:00:00Z","doi":"10.4230/LIPICS.MFCS.2018.23","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","citation":{"ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23.","chicago":"Avni, Guy, Shibashis Guha, and Orna Kupferman. “Timed Network Games with Clocks,” Vol. 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPICS.MFCS.2018.23.","apa":"Avni, G., Guha, S., & Kupferman, O. (2018). Timed network games with clocks (Vol. 117). Presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPICS.MFCS.2018.23","ama":"Avni G, Guha S, Kupferman O. Timed network games with clocks. In: Vol 117. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPICS.MFCS.2018.23","ieee":"G. Avni, S. Guha, and O. Kupferman, “Timed network games with clocks,” presented at the MFCS: Mathematical Foundations of Computer Science, Liverpool, United Kingdom, 2018, vol. 117.","short":"G. Avni, S. Guha, O. Kupferman, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","mla":"Avni, Guy, et al. Timed Network Games with Clocks. Vol. 117, 23, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPICS.MFCS.2018.23."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","last_name":"Avni","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"full_name":"Guha, Shibashis","last_name":"Guha","first_name":"Shibashis"},{"full_name":"Kupferman, Orna","last_name":"Kupferman","first_name":"Orna"}],"title":"Timed network games with clocks","article_number":"23","project":[{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"25F42A32-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize","grant_number":"Z211"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"M02369","name":"Formal Methods meets Algorithmic Game Theory"}]},{"article_number":"e2005372","citation":{"chicago":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005372.","ista":"Polechova J. 2018. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 16(6), e2005372.","mla":"Polechova, Jitka. “Is the Sky the Limit? On the Expansion Threshold of a Species’ Range.” PLoS Biology, vol. 16, no. 6, e2005372, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005372.","ieee":"J. Polechova, “Is the sky the limit? On the expansion threshold of a species’ range,” PLoS Biology, vol. 16, no. 6. Public Library of Science, 2018.","short":"J. Polechova, PLoS Biology 16 (2018).","apa":"Polechova, J. (2018). Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005372","ama":"Polechova J. Is the sky the limit? On the expansion threshold of a species’ range. PLoS Biology. 2018;16(6). doi:10.1371/journal.pbio.2005372"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7550","author":[{"full_name":"Polechova, Jitka","orcid":"0000-0003-0951-3112","last_name":"Polechova","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"}],"title":"Is the sky the limit? On the expansion threshold of a species’ range","oa":1,"quality_controlled":"1","publisher":"Public Library of Science","year":"2018","has_accepted_license":"1","publication":"PLoS Biology","day":"15","date_created":"2018-12-11T11:45:46Z","date_published":"2018-06-15T00:00:00Z","doi":"10.1371/journal.pbio.2005372","_id":"315","tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","status":"public","date_updated":"2023-02-23T14:10:16Z","ddc":["576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:01Z","abstract":[{"lang":"eng","text":"More than 100 years after Grigg’s influential analysis of species’ borders, the causes of limits to species’ ranges still represent a puzzle that has never been understood with clarity. The topic has become especially important recently as many scientists have become interested in the potential for species’ ranges to shift in response to climate change—and yet nearly all of those studies fail to recognise or incorporate evolutionary genetics in a way that relates to theoretical developments. I show that range margins can be understood based on just two measurable parameters: (i) the fitness cost of dispersal—a measure of environmental heterogeneity—and (ii) the strength of genetic drift, which reduces genetic diversity. Together, these two parameters define an ‘expansion threshold’: adaptation fails when genetic drift reduces genetic diversity below that required for adaptation to a heterogeneous environment. When the key parameters drop below this expansion threshold locally, a sharp range margin forms. When they drop below this threshold throughout the species’ range, adaptation collapses everywhere, resulting in either extinction or formation of a fragmented metapopulation. Because the effects of dispersal differ fundamentally with dimension, the second parameter—the strength of genetic drift—is qualitatively different compared to a linear habitat. In two-dimensional habitats, genetic drift becomes effectively independent of selection. It decreases with ‘neighbourhood size’—the number of individuals accessible by dispersal within one generation. Moreover, in contrast to earlier predictions, which neglected evolution of genetic variance and/or stochasticity in two dimensions, dispersal into small marginal populations aids adaptation. This is because the reduction of both genetic and demographic stochasticity has a stronger effect than the cost of dispersal through increased maladaptation. The expansion threshold thus provides a novel, theoretically justified, and testable prediction for formation of the range margin and collapse of the species’ range."}],"oa_version":"Published Version","scopus_import":1,"intvolume":" 16","month":"06","publication_status":"published","publication_identifier":{"issn":["15449173"]},"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"908c52751bba30c55ed36789e5e4c84d","file_id":"5870","creator":"dernst","file_size":6968201,"date_updated":"2020-07-14T12:46:01Z","file_name":"2017_PLOS_Polechova.pdf","date_created":"2019-01-22T08:30:03Z"}],"volume":16,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9839"}]},"issue":"6"},{"project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Fulek, R., & Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.40","ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:10.4230/LIPIcs.SoCG.2018.40","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","mla":"Fulek, Radoslav, and Jan Kynčl. The ℤ2-Genus of Kuratowski Minors. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:10.4230/LIPIcs.SoCG.2018.40.","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.","chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.40."},"title":"The ℤ2-Genus of Kuratowski minors","article_processing_charge":"No","external_id":{"arxiv":["1803.05085"]},"publist_id":"7734","author":[{"id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek"},{"first_name":"Jan","last_name":"Kynčl","full_name":"Kynčl, Jan"}],"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","day":"11","year":"2018","date_created":"2018-12-11T11:45:05Z","date_published":"2018-06-11T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.40","page":"40.1 - 40.14","_id":"186","status":"public","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2018-06-11","end_date":"2018-06-14","location":"Budapest, Hungary"},"type":"conference","date_updated":"2023-08-14T12:43:51Z","department":[{"_id":"UlWa"}],"oa_version":"Submitted Version","abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces.","lang":"eng"}],"intvolume":" 99","month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1803.05085"}],"alternative_title":["LIPIcs"],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"later_version","id":"11593","status":"public"}]},"volume":99},{"status":"public","conference":{"name":"GD 2017: Graph Drawing and Network Visualization","start_date":"201-09-25","location":"Boston, MA, United States","end_date":"2017-09-27"},"type":"conference","_id":"433","department":[{"_id":"UlWa"}],"date_updated":"2023-08-24T14:39:32Z","intvolume":" 10692","month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"alternative_title":["LNCS"],"scopus_import":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"A thrackle is a graph drawn in the plane so that every pair of its edges meet exactly once: either at a common end vertex or in a proper crossing. We prove that any thrackle of n vertices has at most 1.3984n edges. Quasi-thrackles are defined similarly, except that every pair of edges that do not share a vertex are allowed to cross an odd number of times. It is also shown that the maximum number of edges of a quasi-thrackle on n vertices is 3/2(n-1), and that this bound is best possible for infinitely many values of n."}],"volume":10692,"related_material":{"record":[{"relation":"later_version","status":"public","id":"5857"}]},"language":[{"iso":"eng"}],"publication_status":"published","title":"Thrackles: An improved upper bound","external_id":{"arxiv":["1708.08037"]},"author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek"},{"full_name":"Pach, János","last_name":"Pach","first_name":"János"}],"publist_id":"7390","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Fulek, Radoslav, and János Pach. “Thrackles: An Improved Upper Bound,” 10692:160–66. Springer, 2018. https://doi.org/10.1007/978-3-319-73915-1_14.","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","mla":"Fulek, Radoslav, and János Pach. Thrackles: An Improved Upper Bound. Vol. 10692, Springer, 2018, pp. 160–66, doi:10.1007/978-3-319-73915-1_14.","ieee":"R. Fulek and J. Pach, “Thrackles: An improved upper bound,” presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States, 2018, vol. 10692, pp. 160–166.","short":"R. Fulek, J. Pach, in:, Springer, 2018, pp. 160–166.","ama":"Fulek R, Pach J. Thrackles: An improved upper bound. In: Vol 10692. Springer; 2018:160-166. doi:10.1007/978-3-319-73915-1_14","apa":"Fulek, R., & Pach, J. (2018). Thrackles: An improved upper bound (Vol. 10692, pp. 160–166). Presented at the GD 2017: Graph Drawing and Network Visualization, Boston, MA, United States: Springer. https://doi.org/10.1007/978-3-319-73915-1_14"},"oa":1,"publisher":"Springer","quality_controlled":"1","date_created":"2018-12-11T11:46:27Z","doi":"10.1007/978-3-319-73915-1_14","date_published":"2018-01-21T00:00:00Z","page":"160 - 166","day":"21","year":"2018"},{"department":[{"_id":"NiBa"}],"title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","article_processing_charge":"No","author":[{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"},{"first_name":"Pragya","last_name":"Chaube","full_name":"Chaube, Pragya"},{"full_name":"Morales, Hernán E.","last_name":"Morales","first_name":"Hernán E."},{"full_name":"Larsson, Tomas","last_name":"Larsson","first_name":"Tomas"},{"first_name":"Alan R.","full_name":"Lemmon, Alan R.","last_name":"Lemmon"},{"first_name":"Emily M.","last_name":"Lemmon","full_name":"Lemmon, Emily M."},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"last_name":"Panova","full_name":"Panova, Marina","first_name":"Marina"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"first_name":"Kerstin","full_name":"Johannesson, Kerstin","last_name":"Johannesson"},{"last_name":"Westram","full_name":"Westram, Anja M","orcid":"0000-0003-1050-4969","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"mla":"Faria, Rui, et al. Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes. Dryad, 2018, doi:10.5061/dryad.72cg113.","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","short":"R. Faria, P. Chaube, H.E. Morales, T. Larsson, A.R. Lemmon, E.M. Lemmon, M. Rafajlović, M. Panova, M. Ravinet, K. Johannesson, A.M. Westram, R.K. Butlin, (2018).","apa":"Faria, R., Chaube, P., Morales, H. E., Larsson, T., Lemmon, A. R., Lemmon, E. M., … Butlin, R. K. (2018). Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. Dryad. https://doi.org/10.5061/dryad.72cg113","ama":"Faria R, Chaube P, Morales HE, et al. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes. 2018. doi:10.5061/dryad.72cg113","chicago":"Faria, Rui, Pragya Chaube, Hernán E. Morales, Tomas Larsson, Alan R. Lemmon, Emily M. Lemmon, Marina Rafajlović, et al. “Data from: Multiple Chromosomal Rearrangements in a Hybrid Zone between Littorina Saxatilis Ecotypes.” Dryad, 2018. https://doi.org/10.5061/dryad.72cg113.","ista":"Faria R, Chaube P, Morales HE, Larsson T, Lemmon AR, Lemmon EM, Rafajlović M, Panova M, Ravinet M, Johannesson K, Westram AM, Butlin RK. 2018. Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes, Dryad, 10.5061/dryad.72cg113."},"date_updated":"2023-08-24T14:50:26Z","status":"public","type":"research_data_reference","_id":"9837","date_created":"2021-08-09T12:46:39Z","doi":"10.5061/dryad.72cg113","date_published":"2018-10-09T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"6095"}]},"day":"09","year":"2018","month":"10","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.72cg113"}],"oa":1,"publisher":"Dryad","oa_version":"Published Version","abstract":[{"text":"Both classical and recent studies suggest that chromosomal inversion polymorphisms are important in adaptation and speciation. However, biases in discovery and reporting of inversions make it difficult to assess their prevalence and biological importance. Here, we use an approach based on linkage disequilibrium among markers genotyped for samples collected across a transect between contrasting habitats to detect chromosomal rearrangements de novo. We report 17 polymorphic rearrangements in a single locality for the coastal marine snail, Littorina saxatilis. Patterns of diversity in the field and of recombination in controlled crosses provide strong evidence that at least the majority of these rearrangements are inversions. Most show clinal changes in frequency between habitats, suggestive of divergent selection, but only one appears to be fixed for different arrangements in the two habitats. Consistent with widespread evidence for balancing selection on inversion polymorphisms, we argue that a combination of heterosis and divergent selection can explain the observed patterns and should be considered in other systems spanning environmental gradients.","lang":"eng"}]},{"_id":"5457","pubrep_id":"1066","status":"public","type":"technical_report","ddc":["000"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. 2018. Cost analysis of nondeterministic probabilistic programs, IST Austria, 27p.","chicago":"Anonymous, 1, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria, 2018.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous, Cost analysis of nondeterministic probabilistic programs. IST Austria, 2018.","short":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, 6 Anonymous, Cost Analysis of Nondeterministic Probabilistic Programs, IST Austria, 2018.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria; 2018.","apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, Anonymous, 4, Anonymous, 5, & Anonymous, 6. (2018). Cost analysis of nondeterministic probabilistic programs. IST Austria.","mla":"Anonymous, 1, et al. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria, 2018."},"date_updated":"2023-08-25T08:07:48Z","title":"Cost analysis of nondeterministic probabilistic programs","file_date_updated":"2020-07-14T12:47:00Z","author":[{"full_name":"Anonymous, 1","last_name":"Anonymous","first_name":"1"},{"first_name":"2","last_name":"Anonymous","full_name":"Anonymous, 2"},{"last_name":"Anonymous","full_name":"Anonymous, 3","first_name":"3"},{"first_name":"4","full_name":"Anonymous, 4","last_name":"Anonymous"},{"first_name":"5","last_name":"Anonymous","full_name":"Anonymous, 5"},{"first_name":"6","last_name":"Anonymous","full_name":"Anonymous, 6"}],"oa_version":"Published Version","abstract":[{"text":"We consider the problem of expected cost analysis over nondeterministic probabilistic programs, which aims at automated methods for analyzing the resource-usage of such programs. Previous approaches for this problem could only handle nonnegative bounded costs. However, in many scenarios, such as queuing networks or analysis of cryptocurrency protocols, both positive and negative costs are necessary and the costs are unbounded as well.\r\n\r\nIn this work, we present a sound and efficient approach to obtain polynomial bounds on the expected accumulated cost of nondeterministic probabilistic programs. Our approach can handle (a) general positive and negative costs with bounded updates in variables; and (b) nonnegative costs with general updates to variables. We show that several natural examples which could not be handled by previous approaches are captured in our framework.\r\n\r\nMoreover, our approach leads to an efficient polynomial-time algorithm, while no previous approach for cost analysis of probabilistic programs could guarantee polynomial runtime. Finally, we show the effectiveness of our approach by presenting experimental results on a variety of programs, motivated by real-world applications, for which we efficiently synthesize tight resource-usage bounds.","lang":"eng"}],"month":"11","oa":1,"scopus_import":1,"alternative_title":["IST Austria Technical Report"],"publisher":"IST Austria","language":[{"iso":"eng"}],"day":"11","file":[{"file_id":"5493","checksum":"ba3adafd36fe200385ccda583063b9eb","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-1066-v1+1_techreport.pdf","date_created":"2018-12-12T11:53:32Z","file_size":4202966,"date_updated":"2020-07-14T12:47:00Z","creator":"system"},{"date_created":"2019-05-10T13:22:12Z","file_name":"authors-names.txt","date_updated":"2020-07-14T12:47:00Z","file_size":322,"creator":"dernst","file_id":"6402","checksum":"6cf3a19164bb8e5048a9c8c84dfd9fa3","content_type":"text/plain","access_level":"closed","relation":"main_file"}],"publication_status":"published","year":"2018","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"date_created":"2018-12-12T11:39:26Z","date_published":"2018-11-11T00:00:00Z","related_material":{"record":[{"relation":"later_version","id":"6175","status":"public"}]},"page":"27"},{"type":"book_chapter","status":"public","_id":"10864","series_title":"OCTR","department":[{"_id":"VlKo"}],"date_updated":"2023-09-05T15:37:18Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.01072"}],"month":"03","place":"Cham","intvolume":" 16","abstract":[{"text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k.","lang":"eng"}],"oa_version":"Preprint","volume":16,"publication_identifier":{"eissn":["2211-2766"],"isbn":["9783319747712"],"issn":["2211-2758"],"eisbn":["9783319747729"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"last_name":"Kazda","full_name":"Kazda, Alexandr","id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","first_name":"Alexandr"},{"last_name":"Kozik","full_name":"Kozik, Marcin","first_name":"Marcin"},{"first_name":"Ralph","last_name":"McKenzie","full_name":"McKenzie, Ralph"},{"full_name":"Moore, Matthew","last_name":"Moore","first_name":"Matthew"}],"external_id":{"arxiv":["1502.01072"]},"article_processing_charge":"No","editor":[{"first_name":"J","last_name":"Czelakowski","full_name":"Czelakowski, J"}],"title":"Absorption and directed Jónsson terms","citation":{"ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7","apa":"Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7","short":"A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220.","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","mla":"Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7.","ista":"Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Springer Nature","quality_controlled":"1","oa":1,"acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","page":"203-220","doi":"10.1007/978-3-319-74772-9_7","date_published":"2018-03-21T00:00:00Z","date_created":"2022-03-18T10:30:32Z","year":"2018","day":"21","publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science"},{"file":[{"file_name":"2018_LIPIcs_Goaoc.pdf","date_created":"2018-12-17T16:35:02Z","file_size":718414,"date_updated":"2020-07-14T12:45:18Z","creator":"dernst","file_id":"5725","checksum":"d12bdd60f04a57307867704b5f930afd","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"status":"public","id":"7108","relation":"later_version"}]},"volume":99,"oa_version":"Published Version","abstract":[{"text":"We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes.","lang":"eng"}],"month":"06","intvolume":" 99","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"scopus_import":1,"ddc":["516","000"],"date_updated":"2023-09-06T11:10:57Z","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:45:18Z","_id":"184","status":"public","type":"conference","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11"},"tmp":{"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)","short":"CC BY (4.0)"},"day":"11","has_accepted_license":"1","year":"2018","doi":"10.4230/LIPIcs.SoCG.2018.41","date_published":"2018-06-11T00:00:00Z","date_created":"2018-12-11T11:45:04Z","page":"41:1 - 41:16","acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16.","ieee":"X. Goaoc, P. Paták, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 41:1-41:16.","apa":"Goaoc, X., Paták, P., Patakova, Z., Tancer, M., & Wagner, U. (2018). Shellability is NP-complete (Vol. 99, p. 41:1-41:16). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.41","ama":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:41:1-41:16. doi:10.4230/LIPIcs.SoCG.2018.41","mla":"Goaoc, Xavier, et al. Shellability Is NP-Complete. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 41:1-41:16, doi:10.4230/LIPIcs.SoCG.2018.41.","ista":"Goaoc X, Paták P, Patakova Z, Tancer M, Wagner U. 2018. Shellability is NP-complete. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 41:1-41:16.","chicago":"Goaoc, Xavier, Pavel Paták, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete,” 99:41:1-41:16. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.41."},"title":"Shellability is NP-complete","author":[{"full_name":"Goaoc, Xavier","last_name":"Goaoc","first_name":"Xavier"},{"first_name":"Pavel","last_name":"Paták","full_name":"Paták, Pavel"},{"first_name":"Zuzana","id":"48B57058-F248-11E8-B48F-1D18A9856A87","last_name":"Patakova","orcid":"0000-0002-3975-1683","full_name":"Patakova, Zuzana"},{"orcid":"0000-0002-1191-6714","full_name":"Tancer, Martin","last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"}],"publist_id":"7736"},{"_id":"285","type":"conference","conference":{"end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"tmp":{"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)","short":"CC BY (4.0)"},"status":"public","date_updated":"2023-09-06T11:13:41Z","ddc":["516","000"],"department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:45:51Z","abstract":[{"lang":"eng","text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how "simple" or "thin" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth. In view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs). We derive these results from work of Agol and of Scharlemann and Thompson, by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 48(k+1) (resp. 4(3k+1))."}],"oa_version":"Submitted Version","alternative_title":["LIPIcs"],"scopus_import":1,"month":"06","intvolume":" 99","publication_identifier":{"issn":["18688969"]},"publication_status":"published","file":[{"file_name":"2018_LIPIcs_Huszar.pdf","date_created":"2018-12-17T15:32:38Z","creator":"dernst","file_size":642522,"date_updated":"2020-07-14T12:45:51Z","file_id":"5713","checksum":"530d084116778135d5bffaa317479cac","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"7093"}]},"volume":99,"article_number":"46","citation":{"ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.46","apa":"Huszár, K., Spreer, J., & Wagner, U. (2018). On the treewidth of triangulated 3-manifolds (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.46","mla":"Huszár, Kristóf, et al. On the Treewidth of Triangulated 3-Manifolds. Vol. 99, 46, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.46.","ista":"Huszár K, Spreer J, Wagner U. 2018. On the treewidth of triangulated 3-manifolds. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 46.","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.46."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Huszár","full_name":"Huszár, Kristóf","orcid":"0000-0002-5445-5057","first_name":"Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jonathan","last_name":"Spreer","full_name":"Spreer, Jonathan"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli"}],"publist_id":"7614","external_id":{"arxiv":["1712.00434"]},"article_processing_charge":"No","title":"On the treewidth of triangulated 3-manifolds","acknowledgement":"Research of the second author was supported by the Einstein Foundation (project “Einstein Visiting Fellow Santos”) and by the Simons Foundation (“Simons Visiting Professors” program).","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2018","day":"01","date_published":"2018-06-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.46","date_created":"2018-12-11T11:45:37Z"},{"_id":"13059","status":"public","type":"research_data_reference","tmp":{"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)","short":"CC BY (4.0)"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"citation":{"apa":"Garriga, E., di Tommaso, P., Magis, C., Erb, I., Mansouri, L., Baltzis, A., … Notredame, C. (2018). Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. Zenodo. https://doi.org/10.5281/ZENODO.2025846","ama":"Garriga E, di Tommaso P, Magis C, et al. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method. 2018. doi:10.5281/ZENODO.2025846","short":"E. Garriga, P. di Tommaso, C. Magis, I. Erb, L. Mansouri, A. Baltzis, H. Laayouni, F. Kondrashov, E. Floden, C. Notredame, (2018).","ieee":"E. Garriga et al., “Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method.” Zenodo, 2018.","mla":"Garriga, Edgar, et al. Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method. Zenodo, 2018, doi:10.5281/ZENODO.2025846.","ista":"Garriga E, di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, Laayouni H, Kondrashov F, Floden E, Notredame C. 2018. Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method, Zenodo, 10.5281/ZENODO.2025846.","chicago":"Garriga, Edgar, Paolo di Tommaso, Cedrik Magis, Ionas Erb, Leila Mansouri, Athanasios Baltzis, Hafid Laayouni, Fyodor Kondrashov, Evan Floden, and Cedric Notredame. “Fast and Accurate Large Multiple Sequence Alignments with a Root-to-Leaf Regressive Method.” Zenodo, 2018. https://doi.org/10.5281/ZENODO.2025846."},"date_updated":"2023-09-06T14:32:51Z","title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","department":[{"_id":"FyKo"}],"author":[{"full_name":"Garriga, Edgar","last_name":"Garriga","first_name":"Edgar"},{"first_name":"Paolo","full_name":"di Tommaso, Paolo","last_name":"di Tommaso"},{"last_name":"Magis","full_name":"Magis, Cedrik","first_name":"Cedrik"},{"full_name":"Erb, Ionas","last_name":"Erb","first_name":"Ionas"},{"first_name":"Leila","full_name":"Mansouri, Leila","last_name":"Mansouri"},{"first_name":"Athanasios","full_name":"Baltzis, Athanasios","last_name":"Baltzis"},{"full_name":"Laayouni, Hafid","last_name":"Laayouni","first_name":"Hafid"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694"},{"first_name":"Evan","full_name":"Floden, Evan","last_name":"Floden"},{"last_name":"Notredame","full_name":"Notredame, Cedric","first_name":"Cedric"}],"article_processing_charge":"No","oa_version":"Published Version","abstract":[{"text":"This dataset contains a GitHub repository containing all the data, analysis, Nextflow workflows and Jupyter notebooks to replicate the manuscript titled \"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method\".\r\nIt also contains the Multiple Sequence Alignments (MSAs) generated and well as the main figures and tables from the manuscript.\r\nThe repository is also available at GitHub (https://github.com/cbcrg/dpa-analysis) release `v1.2`.\r\nFor details on how to use the regressive alignment algorithm, see the T-Coffee software suite (https://github.com/cbcrg/tcoffee).","lang":"eng"}],"month":"12","publisher":"Zenodo","oa":1,"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.3271452","open_access":"1"}],"day":"07","year":"2018","doi":"10.5281/ZENODO.2025846","date_published":"2018-12-07T00:00:00Z","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"7181"}]},"date_created":"2023-05-23T16:08:20Z"},{"ddc":["530"],"date_updated":"2023-09-07T12:27:43Z","supervisor":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"department":[{"_id":"GeKa"}],"file_date_updated":"2020-07-14T12:46:35Z","_id":"49","pubrep_id":"1033","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"type":"dissertation","language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:46:35Z","file_size":85539748,"creator":"dernst","date_created":"2019-04-09T07:13:28Z","file_name":"2018_Thesis_Watzinger.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","file_id":"6249","checksum":"b653b5216251f938ddbeafd1de88667c"},{"creator":"dernst","file_size":21830697,"date_updated":"2020-07-14T12:46:35Z","file_name":"2018_Thesis_Watzinger_source.zip","date_created":"2019-04-09T07:13:27Z","relation":"source_file","access_level":"closed","content_type":"application/zip","checksum":"39bcf8de7ac5b1bb516b11ce2f966785","file_id":"6250"}],"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Nowadays, quantum computation is receiving more and more attention as an alternative to the classical way of computing. For realizing a quantum computer, different devices are investigated as potential quantum bits. In this thesis, the focus is on Ge hut wires, which turned out to be promising candidates for implementing hole spin quantum bits. The advantages of Ge as a material system are the low hyperfine interaction for holes and the strong spin orbit coupling, as well as the compatibility with the highly developed CMOS processes in industry. In addition, Ge can also be isotopically purified which is expected to boost the spin coherence times. The strong spin orbit interaction for holes in Ge on the one hand enables the full electrical control of the quantum bit and on the other hand should allow short spin manipulation times. Starting with a bare Si wafer, this work covers the entire process reaching from growth over the fabrication and characterization of hut wire devices up to the demonstration of hole spin resonance. From experiments with single quantum dots, a large g-factor anisotropy between the in-plane and the out-of-plane direction was found. A comparison to a theoretical model unveiled the heavy-hole character of the lowest energy states. The second part of the thesis addresses double quantum dot devices, which were realized by adding two gate electrodes to a hut wire. In such devices, Pauli spin blockade was observed, which can serve as a read-out mechanism for spin quantum bits. Applying oscillating electric fields in spin blockade allowed the demonstration of continuous spin rotations and the extraction of a lower bound for the spin dephasing time. Despite the strong spin orbit coupling in Ge, the obtained value for the dephasing time is comparable to what has been recently reported for holes in Si. All in all, the presented results point out the high potential of Ge hut wires as a platform for long-lived, fast and fully electrically tunable hole spin quantum bits."}],"month":"07","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Watzinger H. 2018. Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria.","chicago":"Watzinger, Hannes. “Ge Hut Wires - from Growth to Hole Spin Resonance.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1033.","apa":"Watzinger, H. (2018). Ge hut wires - from growth to hole spin resonance. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1033","ama":"Watzinger H. Ge hut wires - from growth to hole spin resonance. 2018. doi:10.15479/AT:ISTA:th_1033","short":"H. Watzinger, Ge Hut Wires - from Growth to Hole Spin Resonance, Institute of Science and Technology Austria, 2018.","ieee":"H. Watzinger, “Ge hut wires - from growth to hole spin resonance,” Institute of Science and Technology Austria, 2018.","mla":"Watzinger, Hannes. Ge Hut Wires - from Growth to Hole Spin Resonance. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1033."},"title":"Ge hut wires - from growth to hole spin resonance","article_processing_charge":"No","author":[{"id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes","full_name":"Watzinger, Hannes","last_name":"Watzinger"}],"publist_id":"8005","day":"30","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:44:21Z","date_published":"2018-07-30T00:00:00Z","doi":"10.15479/AT:ISTA:th_1033","page":"77","oa":1,"publisher":"Institute of Science and Technology Austria"},{"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"file_id":"5918","checksum":"dd699303623e96d1478a6ae07210dd05","content_type":"application/zip","relation":"source_file","access_level":"closed","file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip","date_created":"2019-02-05T07:43:31Z","file_size":11827713,"date_updated":"2020-07-14T12:45:24Z","creator":"kschuh"},{"file_size":4783846,"date_updated":"2020-07-14T12:45:24Z","creator":"kschuh","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf","date_created":"2019-02-05T07:43:45Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5919","checksum":"ba163849a190d2b41d66fef0e4983294"}],"alternative_title":["ISTA Thesis"],"month":"06","abstract":[{"lang":"eng","text":"We describe arrangements of three-dimensional spheres from a geometrical and topological point of view. Real data (fitting this setup) often consist of soft spheres which show certain degree of deformation while strongly packing against each other. In this context, we answer the following questions: If we model a soft packing of spheres by hard spheres that are allowed to overlap, can we measure the volume in the overlapped areas? Can we be more specific about the overlap volume, i.e. quantify how much volume is there covered exactly twice, three times, or k times? What would be a good optimization criteria that rule the arrangement of soft spheres while making a good use of the available space? Fixing a particular criterion, what would be the optimal sphere configuration? The first result of this thesis are short formulas for the computation of volumes covered by at least k of the balls. The formulas exploit information contained in the order-k Voronoi diagrams and its closely related Level-k complex. The used complexes lead to a natural generalization into poset diagrams, a theoretical formalism that contains the order-k and degree-k diagrams as special cases. In parallel, we define different criteria to determine what could be considered an optimal arrangement from a geometrical point of view. Fixing a criterion, we find optimal soft packing configurations in 2D and 3D where the ball centers lie on a lattice. As a last step, we use tools from computational topology on real physical data, to show the potentials of higher-order diagrams in the description of melting crystals. The results of the experiments leaves us with an open window to apply the theories developed in this thesis in real applications."}],"oa_version":"Published Version","file_date_updated":"2020-07-14T12:45:24Z","department":[{"_id":"HeEd"}],"date_updated":"2023-09-07T12:25:32Z","supervisor":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"}],"ddc":["514","516"],"type":"dissertation","pubrep_id":"1026","status":"public","_id":"201","page":"171","date_created":"2018-12-11T11:45:10Z","doi":"10.15479/AT:ISTA:th_1026","date_published":"2018-06-11T00:00:00Z","year":"2018","has_accepted_license":"1","day":"11","oa":1,"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","publist_id":"7712","author":[{"id":"41B58C0C-F248-11E8-B48F-1D18A9856A87","first_name":"Mabel","last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel"}],"title":"Multiple covers with balls","citation":{"chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1026.","ista":"Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria.","mla":"Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026.","short":"M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018.","ieee":"M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018.","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026","apa":"Iglesias Ham, M. (2018). Multiple covers with balls. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1026"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"alternative_title":["ISTA Thesis"],"month":"09","abstract":[{"lang":"eng","text":"The most common assumption made in statistical learning theory is the assumption of the independent and identically distributed (i.i.d.) data. While being very convenient mathematically, it is often very clearly violated in practice. This disparity between the machine learning theory and applications underlies a growing demand in the development of algorithms that learn from dependent data and theory that can provide generalization guarantees similar to the independent situations. This thesis is dedicated to two variants of dependencies that can arise in practice. One is a dependence on the level of samples in a single learning task. Another dependency type arises in the multi-task setting when the tasks are dependent on each other even though the data for them can be i.i.d. In both cases we model the data (samples or tasks) as stochastic processes and introduce new algorithms for both settings that take into account and exploit the resulting dependencies. We prove the theoretical guarantees on the performance of the introduced algorithms under different evaluation criteria and, in addition, we compliment the theoretical study by the empirical one, where we evaluate some of the algorithms on two real world datasets to highlight their practical applicability."}],"oa_version":"Published Version","ec_funded":1,"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","file":[{"file_id":"6253","checksum":"e849dd40a915e4d6c5572b51b517f098","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-04-09T07:32:47Z","file_name":"2018_Thesis_Zimin.pdf","date_updated":"2020-07-14T12:47:40Z","file_size":1036137,"creator":"dernst"},{"creator":"dernst","date_updated":"2020-07-14T12:47:40Z","file_size":637490,"date_created":"2019-04-09T07:32:47Z","file_name":"2018_Thesis_Zimin_Source.zip","access_level":"closed","relation":"source_file","content_type":"application/zip","checksum":"da092153cec55c97461bd53c45c5d139","file_id":"6254"}],"language":[{"iso":"eng"}],"type":"dissertation","status":"public","pubrep_id":"1048","_id":"68","file_date_updated":"2020-07-14T12:47:40Z","department":[{"_id":"ChLa"}],"supervisor":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph"}],"date_updated":"2023-09-07T12:29:07Z","ddc":["004","519"],"publisher":"Institute of Science and Technology Austria","oa":1,"page":"92","doi":"10.15479/AT:ISTA:TH1048","date_published":"2018-09-01T00:00:00Z","date_created":"2018-12-11T11:44:27Z","has_accepted_license":"1","year":"2018","day":"01","project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"author":[{"first_name":"Alexander","id":"37099E9C-F248-11E8-B48F-1D18A9856A87","full_name":"Zimin, Alexander","last_name":"Zimin"}],"publist_id":"7986","article_processing_charge":"No","title":"Learning from dependent data","citation":{"ama":"Zimin A. Learning from dependent data. 2018. doi:10.15479/AT:ISTA:TH1048","apa":"Zimin, A. (2018). Learning from dependent data. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH1048","short":"A. Zimin, Learning from Dependent Data, Institute of Science and Technology Austria, 2018.","ieee":"A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018.","mla":"Zimin, Alexander. Learning from Dependent Data. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH1048.","ista":"Zimin A. 2018. Learning from dependent data. Institute of Science and Technology Austria.","chicago":"Zimin, Alexander. “Learning from Dependent Data.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH1048."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"project":[{"grant_number":"259668","name":"Provable Security for Physical Cryptography","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Abusalah, Hamza M. Proof Systems for Sustainable Decentralized Cryptocurrencies. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:TH_1046.","short":"H.M. Abusalah, Proof Systems for Sustainable Decentralized Cryptocurrencies, Institute of Science and Technology Austria, 2018.","ieee":"H. M. Abusalah, “Proof systems for sustainable decentralized cryptocurrencies,” Institute of Science and Technology Austria, 2018.","ama":"Abusalah HM. Proof systems for sustainable decentralized cryptocurrencies. 2018. doi:10.15479/AT:ISTA:TH_1046","apa":"Abusalah, H. M. (2018). Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:TH_1046","chicago":"Abusalah, Hamza M. “Proof Systems for Sustainable Decentralized Cryptocurrencies.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:TH_1046.","ista":"Abusalah HM. 2018. Proof systems for sustainable decentralized cryptocurrencies. Institute of Science and Technology Austria."},"title":"Proof systems for sustainable decentralized cryptocurrencies","publist_id":"7971","author":[{"id":"40297222-F248-11E8-B48F-1D18A9856A87","first_name":"Hamza M","full_name":"Abusalah, Hamza M","last_name":"Abusalah"}],"article_processing_charge":"No","publisher":"Institute of Science and Technology Austria","oa":1,"day":"05","has_accepted_license":"1","year":"2018","doi":"10.15479/AT:ISTA:TH_1046","date_published":"2018-09-05T00:00:00Z","date_created":"2018-12-11T11:44:32Z","page":"59","_id":"83","status":"public","pubrep_id":"1046","type":"dissertation","ddc":["004"],"supervisor":[{"orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z"}],"date_updated":"2023-09-07T12:30:23Z","file_date_updated":"2020-07-14T12:48:11Z","department":[{"_id":"KrPi"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"A proof system is a protocol between a prover and a verifier over a common input in which an honest prover convinces the verifier of the validity of true statements. Motivated by the success of decentralized cryptocurrencies, exemplified by Bitcoin, the focus of this thesis will be on proof systems which found applications in some sustainable alternatives to Bitcoin, such as the Spacemint and Chia cryptocurrencies. In particular, we focus on proofs of space and proofs of sequential work.\r\nProofs of space (PoSpace) were suggested as more ecological, economical, and egalitarian alternative to the energy-wasteful proof-of-work mining of Bitcoin. However, the state-of-the-art constructions of PoSpace are based on sophisticated graph pebbling lower bounds, and are therefore complex. Moreover, when these PoSpace are used in cryptocurrencies like Spacemint, miners can only start mining after ensuring that a commitment to their space is already added in a special transaction to the blockchain. Proofs of sequential work (PoSW) are proof systems in which a prover, upon receiving a statement x and a time parameter T, computes a proof which convinces the verifier that T time units had passed since x was received. Whereas Spacemint assumes synchrony to retain some interesting Bitcoin dynamics, Chia requires PoSW with unique proofs, i.e., PoSW in which it is hard to come up with more than one accepting proof for any true statement. In this thesis we construct simple and practically-efficient PoSpace and PoSW. When using our PoSpace in cryptocurrencies, miners can start mining on the fly, like in Bitcoin, and unlike current constructions of PoSW, which either achieve efficient verification of sequential work, or faster-than-recomputing verification of correctness of proofs, but not both at the same time, ours achieve the best of these two worlds."}],"month":"09","alternative_title":["ISTA Thesis"],"file":[{"file_id":"6245","checksum":"c4b5f7d111755d1396787f41886fc674","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-04-09T06:43:41Z","file_name":"2018_Thesis_Abusalah.pdf","creator":"dernst","date_updated":"2020-07-14T12:48:11Z","file_size":876241},{"creator":"dernst","date_updated":"2020-07-14T12:48:11Z","file_size":2029190,"date_created":"2019-04-09T06:43:41Z","file_name":"2018_Thesis_Abusalah_source.tar.gz","access_level":"closed","relation":"source_file","content_type":"application/x-gzip","checksum":"0f382ac56b471c48fd907d63eb87dafe","file_id":"6246"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","related_material":{"record":[{"id":"1229","status":"public","relation":"part_of_dissertation"},{"id":"1235","status":"public","relation":"part_of_dissertation"},{"id":"1236","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"559"}]},"ec_funded":1},{"publisher":"Institute of Science and Technology Austria","oa":1,"acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","date_published":"2018-05-25T00:00:00Z","doi":"10.15479/AT:ISTA:th_1021","date_created":"2018-12-11T11:45:09Z","page":"113","day":"25","has_accepted_license":"1","year":"2018","project":[{"name":"Lifelong Learning of Visual Scene Understanding","grant_number":"308036","_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"title":"Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images","publist_id":"7718","author":[{"full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ieee":"A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018.","short":"A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018.","apa":"Kolesnikov, A. (2018). Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:th_1021","ama":"Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. 2018. doi:10.15479/AT:ISTA:th_1021","mla":"Kolesnikov, Alexander. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1021.","ista":"Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria.","chicago":"Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. https://doi.org/10.15479/AT:ISTA:th_1021."},"month":"05","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task."}],"ec_funded":1,"file":[{"checksum":"bc678e02468d8ebc39dc7267dfb0a1c4","file_id":"5113","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:14:57Z","file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf","creator":"system","date_updated":"2020-07-14T12:45:22Z","file_size":12918758},{"access_level":"closed","relation":"source_file","content_type":"application/zip","checksum":"bc66973b086da5a043f1162dcfb1fde4","file_id":"6225","creator":"dernst","date_updated":"2020-07-14T12:45:22Z","file_size":55973760,"date_created":"2019-04-05T09:34:49Z","file_name":"2018_Thesis_Kolesnikov_source.zip"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publication_status":"published","status":"public","pubrep_id":"1021","type":"dissertation","_id":"197","file_date_updated":"2020-07-14T12:45:22Z","department":[{"_id":"ChLa"}],"ddc":["004"],"supervisor":[{"full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2023-09-07T12:51:46Z"},{"title":"Computing simplicial representatives of homotopy group elements","author":[{"full_name":"Filakovský, Marek","last_name":"Filakovský","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","first_name":"Marek"},{"full_name":"Franek, Peter","orcid":"0000-0001-8878-8397","last_name":"Franek","first_name":"Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhechev, Stephan Y","last_name":"Zhechev","first_name":"Stephan Y","id":"3AA52972-F248-11E8-B48F-1D18A9856A87"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Filakovský M, Franek P, Wagner U, Zhechev SY. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2018;2(3-4):177-231. doi:10.1007/s41468-018-0021-5","apa":"Filakovský, M., Franek, P., Wagner, U., & Zhechev, S. Y. (2018). Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. Springer. https://doi.org/10.1007/s41468-018-0021-5","short":"M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and Computational Topology 2 (2018) 177–231.","ieee":"M. Filakovský, P. Franek, U. Wagner, and S. Y. Zhechev, “Computing simplicial representatives of homotopy group elements,” Journal of Applied and Computational Topology, vol. 2, no. 3–4. Springer, pp. 177–231, 2018.","mla":"Filakovský, Marek, et al. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology, vol. 2, no. 3–4, Springer, 2018, pp. 177–231, doi:10.1007/s41468-018-0021-5.","ista":"Filakovský M, Franek P, Wagner U, Zhechev SY. 2018. Computing simplicial representatives of homotopy group elements. Journal of Applied and Computational Topology. 2(3–4), 177–231.","chicago":"Filakovský, Marek, Peter Franek, Uli Wagner, and Stephan Y Zhechev. “Computing Simplicial Representatives of Homotopy Group Elements.” Journal of Applied and Computational Topology. Springer, 2018. https://doi.org/10.1007/s41468-018-0021-5."},"project":[{"grant_number":"M01980","name":"Robust invariants of Nonlinear Systems","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF","name":"FWF Open Access Fund"}],"doi":"10.1007/s41468-018-0021-5","date_published":"2018-12-01T00:00:00Z","date_created":"2019-08-08T06:47:40Z","page":"177-231","day":"01","publication":"Journal of Applied and Computational Topology","has_accepted_license":"1","year":"2018","quality_controlled":"1","publisher":"Springer","oa":1,"file_date_updated":"2020-07-14T12:47:40Z","department":[{"_id":"UlWa"}],"ddc":["514"],"date_updated":"2023-09-07T13:10:36Z","status":"public","article_type":"original","type":"journal_article","tmp":{"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)","short":"CC BY (4.0)"},"_id":"6774","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6681"}]},"issue":"3-4","volume":2,"file":[{"date_created":"2019-08-08T06:55:21Z","file_name":"2018_JourAppliedComputTopology_Filakovsky.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:40Z","file_size":1056278,"file_id":"6775","checksum":"cf9e7fcd2a113dd4828774fc75cdb7e8","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2367-1734"],"issn":["2367-1726"]},"publication_status":"published","month":"12","intvolume":" 2","oa_version":"Published Version","abstract":[{"text":"A central problem of algebraic topology is to understand the homotopy groups 𝜋𝑑(𝑋) of a topological space X. For the computational version of the problem, it is well known that there is no algorithm to decide whether the fundamental group 𝜋1(𝑋) of a given finite simplicial complex X is trivial. On the other hand, there are several algorithms that, given a finite simplicial complex X that is simply connected (i.e., with 𝜋1(𝑋) trivial), compute the higher homotopy group 𝜋𝑑(𝑋) for any given 𝑑≥2 . However, these algorithms come with a caveat: They compute the isomorphism type of 𝜋𝑑(𝑋) , 𝑑≥2 as an abstract finitely generated abelian group given by generators and relations, but they work with very implicit representations of the elements of 𝜋𝑑(𝑋) . Converting elements of this abstract group into explicit geometric maps from the d-dimensional sphere 𝑆𝑑 to X has been one of the main unsolved problems in the emerging field of computational homotopy theory. Here we present an algorithm that, given a simply connected space X, computes 𝜋𝑑(𝑋) and represents its elements as simplicial maps from a suitable triangulation of the d-sphere 𝑆𝑑 to X. For fixed d, the algorithm runs in time exponential in size(𝑋) , the number of simplices of X. Moreover, we prove that this is optimal: For every fixed 𝑑≥2 , we construct a family of simply connected spaces X such that for any simplicial map representing a generator of 𝜋𝑑(𝑋) , the size of the triangulation of 𝑆𝑑 on which the map is defined, is exponential in size(𝑋) .","lang":"eng"}]},{"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:44:44Z","ddc":["000"],"date_updated":"2023-09-07T13:18:00Z","pubrep_id":"1039","status":"public","conference":{"location":"Beijing, China","end_date":"2018-09-07","start_date":"2018-09-04","name":"CONCUR: International Conference on Concurrency Theory"},"tmp":{"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)","short":"CC BY (4.0)"},"type":"conference","_id":"133","volume":118,"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"6426"},{"relation":"dissertation_contains","status":"public","id":"8332"}]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"c90895f4c5fafc18ddc54d1c8848077e","file_id":"5368","file_size":745438,"date_updated":"2020-07-14T12:44:44Z","creator":"system","file_name":"IST-2018-853-v2+2_concur2018.pdf","date_created":"2018-12-12T10:18:46Z"}],"publication_status":"published","publication_identifier":{"issn":["18688969"]},"intvolume":" 118","month":"08","alternative_title":["LIPIcs"],"scopus_import":1,"oa_version":"Published Version","abstract":[{"text":"Synchronous programs are easy to specify because the side effects of an operation are finished by the time the invocation of the operation returns to the caller. Asynchronous programs, on the other hand, are difficult to specify because there are side effects due to pending computation scheduled as a result of the invocation of an operation. They are also difficult to verify because of the large number of possible interleavings of concurrent computation threads. We present synchronization, a new proof rule that simplifies the verification of asynchronous programs by introducing the fiction, for proof purposes, that asynchronous operations complete synchronously. Synchronization summarizes an asynchronous computation as immediate atomic effect. Modular verification is enabled via pending asynchronous calls in atomic summaries, and a complementary proof rule that eliminates pending asynchronous calls when components and their specifications are composed. We evaluate synchronization in the context of a multi-layer refinement verification methodology on a collection of benchmark programs.","lang":"eng"}],"title":"Synchronizing the asynchronous","publist_id":"7790","author":[{"first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard"},{"first_name":"Shaz","last_name":"Qadeer","full_name":"Qadeer, Shaz"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","full_name":"Henzinger, Thomas A","last_name":"Henzinger"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 21.","chicago":"Kragl, Bernhard, Shaz Qadeer, and Thomas A Henzinger. “Synchronizing the Asynchronous,” Vol. 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21.","ieee":"B. Kragl, S. Qadeer, and T. A. Henzinger, “Synchronizing the asynchronous,” presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China, 2018, vol. 118.","short":"B. Kragl, S. Qadeer, T.A. Henzinger, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","apa":"Kragl, B., Qadeer, S., & Henzinger, T. A. (2018). Synchronizing the asynchronous (Vol. 118). Presented at the CONCUR: International Conference on Concurrency Theory, Beijing, China: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.CONCUR.2018.21","ama":"Kragl B, Qadeer S, Henzinger TA. Synchronizing the asynchronous. In: Vol 118. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.CONCUR.2018.21","mla":"Kragl, Bernhard, et al. Synchronizing the Asynchronous. Vol. 118, 21, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.CONCUR.2018.21."},"project":[{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S11402-N23"},{"grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms","call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425"}],"article_number":"21","date_created":"2018-12-11T11:44:48Z","date_published":"2018-08-13T00:00:00Z","doi":"10.4230/LIPIcs.CONCUR.2018.21","day":"13","year":"2018","has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik"},{"project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"article_number":"34","title":"The multi-cover persistence of Euclidean balls","publist_id":"7732","author":[{"full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner","first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","last_name":"Osang"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34.","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. https://doi.org/10.4230/LIPIcs.SoCG.2018.34.","apa":"Edelsbrunner, H., & Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.SoCG.2018.34","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:10.4230/LIPIcs.SoCG.2018.34","short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. The Multi-Cover Persistence of Euclidean Balls. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:10.4230/LIPIcs.SoCG.2018.34."},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","oa":1,"acknowledgement":"This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","doi":"10.4230/LIPIcs.SoCG.2018.34","date_published":"2018-06-11T00:00:00Z","date_created":"2018-12-11T11:45:05Z","day":"11","has_accepted_license":"1","year":"2018","status":"public","type":"conference","tmp":{"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)","short":"CC BY (4.0)"},"conference":{"end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"_id":"187","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"HeEd"}],"ddc":["516"],"date_updated":"2023-09-07T13:29:00Z","month":"06","intvolume":" 99","scopus_import":1,"alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"text":"Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. ","lang":"eng"}],"volume":99,"related_material":{"record":[{"status":"public","id":"9317","relation":"later_version"},{"id":"9056","status":"public","relation":"dissertation_contains"}]},"file":[{"date_created":"2018-12-18T09:27:22Z","file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:19Z","file_size":528018,"file_id":"5738","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"publication_status":"published"},{"citation":{"chicago":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata. Springer, 2018. https://doi.org/10.1007/s10711-017-0265-6.","ista":"Akopyan A. 2018. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 194(1), 55–64.","mla":"Akopyan, Arseniy. “3-Webs Generated by Confocal Conics and Circles.” Geometriae Dedicata, vol. 194, no. 1, Springer, 2018, pp. 55–64, doi:10.1007/s10711-017-0265-6.","ieee":"A. Akopyan, “3-Webs generated by confocal conics and circles,” Geometriae Dedicata, vol. 194, no. 1. Springer, pp. 55–64, 2018.","short":"A. Akopyan, Geometriae Dedicata 194 (2018) 55–64.","ama":"Akopyan A. 3-Webs generated by confocal conics and circles. Geometriae Dedicata. 2018;194(1):55-64. doi:10.1007/s10711-017-0265-6","apa":"Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. Geometriae Dedicata. Springer. https://doi.org/10.1007/s10711-017-0265-6"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"}],"publist_id":"7014","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000431418800004"]},"title":"3-Webs generated by confocal conics and circles","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"isi":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"Geometriae Dedicata","page":"55 - 64","doi":"10.1007/s10711-017-0265-6","date_published":"2018-06-01T00:00:00Z","date_created":"2018-12-11T11:47:57Z","publisher":"Springer","quality_controlled":"1","oa":1,"date_updated":"2023-09-08T11:40:29Z","ddc":["510"],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:47:44Z","_id":"692","type":"journal_article","article_type":"original","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","publication_status":"published","file":[{"date_created":"2020-01-03T11:35:08Z","file_name":"2018_Springer_Akopyan.pdf","date_updated":"2020-07-14T12:47:44Z","file_size":1140860,"creator":"kschuh","file_id":"7222","checksum":"1febcfc1266486053a069e3425ea3713","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"issue":"1","volume":194,"ec_funded":1,"abstract":[{"text":"We consider families of confocal conics and two pencils of Apollonian circles having the same foci. We will show that these families of curves generate trivial 3-webs and find the exact formulas describing them.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","month":"06","intvolume":" 194"},{"scopus_import":"1","intvolume":" 9","month":"09","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"abstract":[{"lang":"eng","text":"Holes confined in quantum dots have gained considerable interest in the past few years due to their potential as spin qubits. Here we demonstrate two-axis control of a spin 3/2 qubit in natural Ge. The qubit is formed in a hut wire double quantum dot device. The Pauli spin blockade principle allowed us to demonstrate electric dipole spin resonance by applying a radio frequency electric field to one of the electrodes defining the double quantum dot. Coherent hole spin oscillations with Rabi frequencies reaching 140 MHz are demonstrated and dephasing times of 130 ns are measured. The reported results emphasize the potential of Ge as a platform for fast and electrically tunable hole spin qubit devices."}],"oa_version":"Published Version","ec_funded":1,"volume":9,"issue":"3902 ","related_material":{"record":[{"relation":"popular_science","id":"7977"},{"status":"public","id":"7996","relation":"dissertation_contains"}]},"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"e7148c10a64497e279c4de570b6cc544","file_id":"5687","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-17T10:28:30Z","file_name":"2018_NatureComm_Watzinger.pdf","date_updated":"2020-07-14T12:48:02Z","file_size":1063469,"creator":"dernst"}],"tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"77","department":[{"_id":"GeKa"}],"file_date_updated":"2020-07-14T12:48:02Z","date_updated":"2023-09-08T11:44:02Z","ddc":["530"],"oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_created":"2018-12-11T11:44:30Z","doi":"10.1038/s41467-018-06418-4","date_published":"2018-09-25T00:00:00Z","year":"2018","has_accepted_license":"1","isi":1,"publication":"Nature Communications","day":"25","project":[{"grant_number":"335497","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"_id":"2552F888-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium","grant_number":"Y00715"}],"external_id":{"isi":["000445560800010"]},"article_processing_charge":"Yes","author":[{"full_name":"Watzinger, Hannes","last_name":"Watzinger","first_name":"Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87"},{"id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada","orcid":"0000-0003-2424-8636","full_name":"Vukusic, Lada","last_name":"Vukusic"},{"first_name":"Fei","full_name":"Gao, Fei","last_name":"Gao"},{"full_name":"Wang, Ting","last_name":"Wang","first_name":"Ting"},{"full_name":"Schäffler, Friedrich","last_name":"Schäffler","first_name":"Friedrich"},{"full_name":"Zhang, Jian","last_name":"Zhang","first_name":"Jian"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios"}],"title":"A germanium hole spin qubit","citation":{"apa":"Watzinger, H., Kukucka, J., Vukušić, L., Gao, F., Wang, T., Schäffler, F., … Katsaros, G. (2018). A germanium hole spin qubit. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-06418-4","ama":"Watzinger H, Kukucka J, Vukušić L, et al. A germanium hole spin qubit. Nature Communications. 2018;9(3902). doi:10.1038/s41467-018-06418-4","short":"H. Watzinger, J. Kukucka, L. Vukušić, F. Gao, T. Wang, F. Schäffler, J. Zhang, G. Katsaros, Nature Communications 9 (2018).","ieee":"H. Watzinger et al., “A germanium hole spin qubit,” Nature Communications, vol. 9, no. 3902. Nature Publishing Group, 2018.","mla":"Watzinger, Hannes, et al. “A Germanium Hole Spin Qubit.” Nature Communications, vol. 9, no. 3902, Nature Publishing Group, 2018, doi:10.1038/s41467-018-06418-4.","ista":"Watzinger H, Kukucka J, Vukušić L, Gao F, Wang T, Schäffler F, Zhang J, Katsaros G. 2018. A germanium hole spin qubit. Nature Communications. 9(3902).","chicago":"Watzinger, Hannes, Josip Kukucka, Lada Vukušić, Fei Gao, Ting Wang, Friedrich Schäffler, Jian Zhang, and Georgios Katsaros. “A Germanium Hole Spin Qubit.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-06418-4."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"volume":9,"issue":"1","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4902","checksum":"87a427bc2e8724be3dd22a4efdd21a33","creator":"system","file_size":3780491,"date_updated":"2020-07-14T12:46:22Z","file_name":"IST-2018-996-v1+1_2018_Hannezo_A-biochemical.pdf","date_created":"2018-12-12T10:11:45Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"03","intvolume":" 9","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The actomyosin cytoskeleton, a key stress-producing unit in epithelial cells, oscillates spontaneously in a wide variety of systems. Although much of the signal cascade regulating myosin activity has been characterized, the origin of such oscillatory behavior is still unclear. Here, we show that basal myosin II oscillation in Drosophila ovarian epithelium is not controlled by actomyosin cortical tension, but instead relies on a biochemical oscillator involving ROCK and myosin phosphatase. Key to this oscillation is a diffusive ROCK flow, linking junctional Rho1 to medial actomyosin cortex, and dynamically maintained by a self-activation loop reliant on ROCK kinase activity. In response to the resulting myosin II recruitment, myosin phosphatase is locally enriched and shuts off ROCK and myosin II signals. Coupling Drosophila genetics, live imaging, modeling, and optogenetics, we uncover an intrinsic biochemical oscillator at the core of myosin II regulatory network, shedding light on the spatio-temporal dynamics of force generation."}],"file_date_updated":"2020-07-14T12:46:22Z","department":[{"_id":"EdHa"}],"ddc":["539","570"],"date_updated":"2023-09-08T11:41:45Z","status":"public","pubrep_id":"996","type":"journal_article","tmp":{"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)","short":"CC BY (4.0)"},"_id":"401","date_published":"2018-03-23T00:00:00Z","doi":"10.1038/s41467-018-03574-5","date_created":"2018-12-11T11:46:16Z","day":"23","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2018","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"title":"A biochemical network controlling basal myosin oscillation","author":[{"full_name":"Qin, Xiang","last_name":"Qin","first_name":"Xiang"},{"last_name":"Hannezo","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"},{"first_name":"Thomas","full_name":"Mangeat, Thomas","last_name":"Mangeat"},{"first_name":"Chang","full_name":"Liu, Chang","last_name":"Liu"},{"last_name":"Majumder","full_name":"Majumder, Pralay","first_name":"Pralay"},{"first_name":"Jjiaying","last_name":"Liu","full_name":"Liu, Jjiaying"},{"full_name":"Choesmel Cadamuro, Valerie","last_name":"Choesmel Cadamuro","first_name":"Valerie"},{"first_name":"Jocelyn","full_name":"Mcdonald, Jocelyn","last_name":"Mcdonald"},{"full_name":"Liu, Yinyao","last_name":"Liu","first_name":"Yinyao"},{"last_name":"Yi","full_name":"Yi, Bin","first_name":"Bin"},{"last_name":"Wang","full_name":"Wang, Xiaobo","first_name":"Xiaobo"}],"publist_id":"7427","article_processing_charge":"No","external_id":{"isi":["000428165400009"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Qin X, Hannezo EB, Mangeat T, Liu C, Majumder P, Liu J, Choesmel Cadamuro V, Mcdonald J, Liu Y, Yi B, Wang X. 2018. A biochemical network controlling basal myosin oscillation. Nature Communications. 9(1), 1210.","chicago":"Qin, Xiang, Edouard B Hannezo, Thomas Mangeat, Chang Liu, Pralay Majumder, Jjiaying Liu, Valerie Choesmel Cadamuro, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-018-03574-5.","short":"X. Qin, E.B. Hannezo, T. Mangeat, C. Liu, P. Majumder, J. Liu, V. Choesmel Cadamuro, J. Mcdonald, Y. Liu, B. Yi, X. Wang, Nature Communications 9 (2018).","ieee":"X. Qin et al., “A biochemical network controlling basal myosin oscillation,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","apa":"Qin, X., Hannezo, E. B., Mangeat, T., Liu, C., Majumder, P., Liu, J., … Wang, X. (2018). A biochemical network controlling basal myosin oscillation. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-018-03574-5","ama":"Qin X, Hannezo EB, Mangeat T, et al. A biochemical network controlling basal myosin oscillation. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-03574-5","mla":"Qin, Xiang, et al. “A Biochemical Network Controlling Basal Myosin Oscillation.” Nature Communications, vol. 9, no. 1, 1210, Nature Publishing Group, 2018, doi:10.1038/s41467-018-03574-5."},"article_number":"1210"},{"oa":1,"quality_controlled":"1","publisher":"Cell Press","acknowledgement":"Short Survey","page":"405 - 406","date_created":"2018-12-11T11:45:47Z","date_published":"2018-02-26T00:00:00Z","doi":"10.1016/j.devcel.2018.02.009","year":"2018","isi":1,"publication":"Developmental Cell","day":"26","article_processing_charge":"No","external_id":{"pmid":["29486189"],"isi":["000426150700002"]},"author":[{"first_name":"Alessandra M","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87","last_name":"Casano","full_name":"Casano, Alessandra M","orcid":"0000-0002-6009-6804"},{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7547","title":"A fat lot of good for wound healing","citation":{"ieee":"A. M. Casano and M. K. Sixt, “A fat lot of good for wound healing,” Developmental Cell, vol. 44, no. 4. Cell Press, pp. 405–406, 2018.","short":"A.M. Casano, M.K. Sixt, Developmental Cell 44 (2018) 405–406.","ama":"Casano AM, Sixt MK. A fat lot of good for wound healing. Developmental Cell. 2018;44(4):405-406. doi:10.1016/j.devcel.2018.02.009","apa":"Casano, A. M., & Sixt, M. K. (2018). A fat lot of good for wound healing. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.02.009","mla":"Casano, Alessandra M., and Michael K. Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell, vol. 44, no. 4, Cell Press, 2018, pp. 405–06, doi:10.1016/j.devcel.2018.02.009.","ista":"Casano AM, Sixt MK. 2018. A fat lot of good for wound healing. Developmental Cell. 44(4), 405–406.","chicago":"Casano, Alessandra M, and Michael K Sixt. “A Fat Lot of Good for Wound Healing.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.02.009."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29486189"}],"scopus_import":"1","intvolume":" 44","month":"02","abstract":[{"lang":"eng","text":"The insect’s fat body combines metabolic and immunological functions. In this issue of Developmental Cell, Franz et al. (2018) show that in Drosophila, cells of the fat body are not static, but can actively “swim” toward sites of epithelial injury, where they physically clog the wound and locally secrete antimicrobial peptides."}],"oa_version":"Published Version","pmid":1,"volume":44,"issue":"4","publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","status":"public","_id":"318","department":[{"_id":"MiSi"}],"date_updated":"2023-09-08T11:42:28Z"},{"article_number":"5184","external_id":{"isi":["000428234100005"]},"article_processing_charge":"No","publist_id":"7419","author":[{"full_name":"Masís, Javier","last_name":"Masís","first_name":"Javier"},{"last_name":"Mankus","full_name":"Mankus, David","first_name":"David"},{"first_name":"Steffen","last_name":"Wolff","full_name":"Wolff, Steffen"},{"first_name":"Grigori","last_name":"Guitchounts","full_name":"Guitchounts, Grigori"},{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"},{"full_name":"Cox, David","last_name":"Cox","first_name":"David"}],"title":"A micro-CT-based method for quantitative brain lesion characterization and electrode localization","citation":{"ista":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. 2018. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 8(1), 5184.","chicago":"Masís, Javier, David Mankus, Steffen Wolff, Grigori Guitchounts, Maximilian A Jösch, and David Cox. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-23247-z.","short":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M.A. Jösch, D. Cox, Scientific Reports 8 (2018).","ieee":"J. Masís, D. Mankus, S. Wolff, G. Guitchounts, M. A. Jösch, and D. Cox, “A micro-CT-based method for quantitative brain lesion characterization and electrode localization,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","ama":"Masís J, Mankus D, Wolff S, Guitchounts G, Jösch MA, Cox D. A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-23247-z","apa":"Masís, J., Mankus, D., Wolff, S., Guitchounts, G., Jösch, M. A., & Cox, D. (2018). A micro-CT-based method for quantitative brain lesion characterization and electrode localization. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-23247-z","mla":"Masís, Javier, et al. “A Micro-CT-Based Method for Quantitative Brain Lesion Characterization and Electrode Localization.” Scientific Reports, vol. 8, no. 1, 5184, Nature Publishing Group, 2018, doi:10.1038/s41598-018-23247-z."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","date_created":"2018-12-11T11:46:19Z","date_published":"2018-03-26T00:00:00Z","doi":"10.1038/s41598-018-23247-z","year":"2018","has_accepted_license":"1","isi":1,"publication":"Scientific Reports","day":"26","tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"994","status":"public","_id":"410","department":[{"_id":"MaJö"}],"file_date_updated":"2020-07-14T12:46:23Z","date_updated":"2023-09-08T11:48:39Z","ddc":["571","572"],"scopus_import":"1","intvolume":" 8","month":"03","abstract":[{"text":"Lesion verification and quantification is traditionally done via histological examination of sectioned brains, a time-consuming process that relies heavily on manual estimation. Such methods are particularly problematic in posterior cortical regions (e.g. visual cortex), where sectioning leads to significant damage and distortion of tissue. Even more challenging is the post hoc localization of micro-electrodes, which relies on the same techniques, suffers from similar drawbacks and requires even higher precision. Here, we propose a new, simple method for quantitative lesion characterization and electrode localization that is less labor-intensive and yields more detailed results than conventional methods. We leverage staining techniques standard in electron microscopy with the use of commodity micro-CT imaging. We stain whole rat and zebra finch brains in osmium tetroxide, embed these in resin and scan entire brains in a micro-CT machine. The scans result in 3D reconstructions of the brains with section thickness dependent on sample size (12–15 and 5–6 microns for rat and zebra finch respectively) that can be segmented manually or automatically. Because the method captures the entire intact brain volume, comparisons within and across studies are more tractable, and the extent of lesions and electrodes may be studied with higher accuracy than with current methods.","lang":"eng"}],"oa_version":"Published Version","volume":8,"issue":"1","publication_status":"published","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"4831","checksum":"653fcb852f899c75b00ceee2a670d738","file_size":2359430,"date_updated":"2020-07-14T12:46:23Z","creator":"system","file_name":"IST-2018-994-v1+1_2018_Joesch_A-micro-CT-based.pdf","date_created":"2018-12-12T10:10:42Z"}]},{"ddc":["580"],"date_updated":"2023-09-08T13:21:05Z","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:45:45Z","_id":"277","status":"public","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"file":[{"checksum":"451ae47616e6af2533099f596b2a47fb","file_id":"7834","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_PlantMolecBio_Dokladal.pdf","date_created":"2020-05-14T12:23:08Z","file_size":1150679,"date_updated":"2020-07-14T12:45:45Z","creator":"dernst"}],"publication_status":"published","volume":97,"issue":"5","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions."}],"intvolume":" 97","month":"06","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:10.1007/s11103-018-0747-4.","short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420.","ieee":"L. Dokládal et al., “An armadillo-domain protein participates in a telomerase interaction network,” Plant Molecular Biology, vol. 97, no. 5. Springer, pp. 407–420, 2018.","apa":"Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., & Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. Springer. https://doi.org/10.1007/s11103-018-0747-4","ama":"Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 2018;97(5):407-420. doi:10.1007/s11103-018-0747-4","chicago":"Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” Plant Molecular Biology. Springer, 2018. https://doi.org/10.1007/s11103-018-0747-4.","ista":"Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420."},"title":"An armadillo-domain protein participates in a telomerase interaction network","article_processing_charge":"No","external_id":{"isi":["000438981700009"]},"publist_id":"7625","author":[{"last_name":"Dokládal","full_name":"Dokládal, Ladislav","first_name":"Ladislav"},{"orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Honys","full_name":"Honys, David","first_name":"David"},{"full_name":"Dupláková, Nikoleta","last_name":"Dupláková","first_name":"Nikoleta"},{"last_name":"Lee","full_name":"Lee, Lan","first_name":"Lan"},{"last_name":"Gelvin","full_name":"Gelvin, Stanton","first_name":"Stanton"},{"last_name":"Sýkorová","full_name":"Sýkorová, Eva","first_name":"Eva"}],"publication":"Plant Molecular Biology","day":"12","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:45:34Z","date_published":"2018-06-12T00:00:00Z","doi":"10.1007/s11103-018-0747-4","page":"407 - 420","oa":1,"quality_controlled":"1","publisher":"Springer"},{"oa":1,"quality_controlled":"1","publisher":"Springer","page":"303 - 319","date_created":"2018-12-11T11:45:41Z","doi":"10.1007/978-3-319-89963-3_18","date_published":"2018-04-14T00:00:00Z","year":"2018","has_accepted_license":"1","isi":1,"day":"14","external_id":{"isi":["00445822600018"]},"article_processing_charge":"No","publist_id":"7582","author":[{"full_name":"Nickovic, Dejan","last_name":"Nickovic","first_name":"Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lebeltel","full_name":"Lebeltel, Olivier","first_name":"Olivier"},{"first_name":"Oded","last_name":"Maler","full_name":"Maler, Oded"},{"last_name":"Ferrere","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143","first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dogan","last_name":"Ulus","full_name":"Ulus, Dogan"}],"title":"AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic","editor":[{"first_name":"Dirk","last_name":"Beyer","full_name":"Beyer, Dirk"},{"first_name":"Marieke","full_name":"Huisman, Marieke","last_name":"Huisman"}],"citation":{"apa":"Nickovic, D., Lebeltel, O., Maler, O., Ferrere, T., & Ulus, D. (2018). AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In D. Beyer & M. Huisman (Eds.) (Vol. 10806, pp. 303–319). Presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89963-3_18","ama":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. In: Beyer D, Huisman M, eds. Vol 10806. Springer; 2018:303-319. doi:10.1007/978-3-319-89963-3_18","ieee":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, and D. Ulus, “AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic,” presented at the TACAS: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10806, pp. 303–319.","short":"D. Nickovic, O. Lebeltel, O. Maler, T. Ferrere, D. Ulus, in:, D. Beyer, M. Huisman (Eds.), Springer, 2018, pp. 303–319.","mla":"Nickovic, Dejan, et al. AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic. Edited by Dirk Beyer and Marieke Huisman, vol. 10806, Springer, 2018, pp. 303–19, doi:10.1007/978-3-319-89963-3_18.","ista":"Nickovic D, Lebeltel O, Maler O, Ferrere T, Ulus D. 2018. AMT 2.0: Qualitative and quantitative trace analysis with extended signal temporal logic. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10806, 303–319.","chicago":"Nickovic, Dejan, Olivier Lebeltel, Oded Maler, Thomas Ferrere, and Dogan Ulus. “AMT 2.0: Qualitative and Quantitative Trace Analysis with Extended Signal Temporal Logic.” edited by Dirk Beyer and Marieke Huisman, 10806:303–19. Springer, 2018. https://doi.org/10.1007/978-3-319-89963-3_18."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","alternative_title":["LNCS"],"intvolume":" 10806","month":"04","abstract":[{"lang":"eng","text":"We introduce in this paper AMT 2.0 , a tool for qualitative and quantitative analysis of hybrid continuous and Boolean signals that combine numerical values and discrete events. The evaluation of the signals is based on rich temporal specifications expressed in extended Signal Temporal Logic (xSTL), which integrates Timed Regular Expressions (TRE) within Signal Temporal Logic (STL). The tool features qualitative monitoring (property satisfaction checking), trace diagnostics for explaining and justifying property violations and specification-driven measurement of quantitative features of the signal."}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"10861","relation":"later_version"}]},"volume":10806,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"e11db3b9c8e27a1c7d1c738cc5e4d25a","file_id":"5928","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_LNCS_Nickovic.pdf","date_created":"2019-02-06T07:33:05Z","creator":"dernst","file_size":3267209,"date_updated":"2020-07-14T12:45:58Z"}],"conference":{"start_date":"2018-04-14","location":"Thessaloniki, Greece","end_date":"2018-04-20","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"tmp":{"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)","short":"CC BY (4.0)"},"type":"conference","status":"public","_id":"299","department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:45:58Z","date_updated":"2023-09-08T11:52:02Z","ddc":["000"]},{"language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/helping-in-spite-of-risk-ants-perform-risk-averse-sanitary-care-of-infectious-nest-mates/","description":"News on IST Homepage"}]},"issue":"11","volume":115,"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Being cared for when sick is a benefit of sociality that can reduce disease and improve survival of group members. However, individuals providing care risk contracting infectious diseases themselves. If they contract a low pathogen dose, they may develop low-level infections that do not cause disease but still affect host immunity by either decreasing or increasing the host’s vulnerability to subsequent infections. Caring for contagious individuals can thus significantly alter the future disease susceptibility of caregivers. Using ants and their fungal pathogens as a model system, we tested if the altered disease susceptibility of experienced caregivers, in turn, affects their expression of sanitary care behavior. We found that low-level infections contracted during sanitary care had protective or neutral effects on secondary exposure to the same (homologous) pathogen but consistently caused high mortality on superinfection with a different (heterologous) pathogen. In response to this risk, the ants selectively adjusted the expression of their sanitary care. Specifically, the ants performed less grooming and more antimicrobial disinfection when caring for nestmates contaminated with heterologous pathogens compared with homologous ones. By modulating the components of sanitary care in this way the ants acquired less infectious particles of the heterologous pathogens, resulting in reduced superinfection. The performance of risk-adjusted sanitary care reveals the remarkable capacity of ants to react to changes in their disease susceptibility, according to their own infection history and to flexibly adjust collective care to individual risk.","lang":"eng"}],"intvolume":" 115","month":"03","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29463746"}],"scopus_import":"1","date_updated":"2023-09-08T13:22:21Z","department":[{"_id":"SyCr"}],"_id":"413","status":"public","type":"journal_article","publication":"PNAS","day":"13","year":"2018","isi":1,"date_created":"2018-12-11T11:46:20Z","date_published":"2018-03-13T00:00:00Z","doi":"10.1073/pnas.1713501115","page":"2782 - 2787","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Konrad M, Pull C, Metzler S, Seif K, Naderlinger E, Grasse AV, Cremer S. 2018. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 115(11), 2782–2787.","chicago":"Konrad, Matthias, Christopher Pull, Sina Metzler, Katharina Seif, Elisabeth Naderlinger, Anna V Grasse, and Sylvia Cremer. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1713501115.","ieee":"M. Konrad et al., “Ants avoid superinfections by performing risk-adjusted sanitary care,” PNAS, vol. 115, no. 11. National Academy of Sciences, pp. 2782–2787, 2018.","short":"M. Konrad, C. Pull, S. Metzler, K. Seif, E. Naderlinger, A.V. Grasse, S. Cremer, PNAS 115 (2018) 2782–2787.","ama":"Konrad M, Pull C, Metzler S, et al. Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. 2018;115(11):2782-2787. doi:10.1073/pnas.1713501115","apa":"Konrad, M., Pull, C., Metzler, S., Seif, K., Naderlinger, E., Grasse, A. V., & Cremer, S. (2018). Ants avoid superinfections by performing risk-adjusted sanitary care. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1713501115","mla":"Konrad, Matthias, et al. “Ants Avoid Superinfections by Performing Risk-Adjusted Sanitary Care.” PNAS, vol. 115, no. 11, National Academy of Sciences, 2018, pp. 2782–87, doi:10.1073/pnas.1713501115."},"title":"Ants avoid superinfections by performing risk-adjusted sanitary care","external_id":{"isi":["000427245400069"],"pmid":["29463746"]},"article_processing_charge":"No","author":[{"first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","full_name":"Konrad, Matthias","last_name":"Konrad"},{"full_name":"Pull, Christopher","orcid":"0000-0003-1122-3982","last_name":"Pull","first_name":"Christopher","id":"3C7F4840-F248-11E8-B48F-1D18A9856A87"},{"id":"48204546-F248-11E8-B48F-1D18A9856A87","first_name":"Sina","last_name":"Metzler","full_name":"Metzler, Sina","orcid":"0000-0002-9547-2494"},{"id":"90F7894A-02CF-11E9-976E-E38CFE5CBC1D","first_name":"Katharina","last_name":"Seif","full_name":"Seif, Katharina"},{"last_name":"Naderlinger","full_name":"Naderlinger, Elisabeth","id":"31757262-F248-11E8-B48F-1D18A9856A87","first_name":"Elisabeth"},{"full_name":"Grasse, Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia"}],"publist_id":"7416","project":[{"_id":"25DC711C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"243071","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects"}]},{"date_updated":"2023-09-08T13:22:57Z","department":[{"_id":"MiLe"}],"_id":"195","status":"public","type":"journal_article","language":[{"iso":"eng"}],"publication_status":"published","volume":98,"issue":"4","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases.","lang":"eng"}],"month":"07","intvolume":" 98","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1712.00308","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.045402.","ista":"Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4), 045402.","mla":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4, 045402, American Physical Society, 2018, doi:10.1103/PhysRevB.98.045402.","short":"E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 98 (2018).","ieee":"E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in two dimensions,” Physical Review B - Condensed Matter and Materials Physics, vol. 98, no. 4. American Physical Society, 2018.","apa":"Yakaboylu, E., & Lemeshko, M. (2018). Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. American Physical Society. https://doi.org/10.1103/PhysRevB.98.045402","ama":"Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 2018;98(4). doi:10.1103/PhysRevB.98.045402"},"title":"Anyonic statistics of quantum impurities in two dimensions","author":[{"id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","first_name":"Enderalp","last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"}],"external_id":{"arxiv":["1712.00308"],"isi":["000436939100007"]},"article_processing_charge":"No","article_number":"045402","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425"}],"day":"15","publication":"Physical Review B - Condensed Matter and Materials Physics","isi":1,"year":"2018","date_published":"2018-07-15T00:00:00Z","doi":"10.1103/PhysRevB.98.045402","date_created":"2018-12-11T11:45:08Z","publisher":"American Physical Society","quality_controlled":"1","oa":1},{"date_created":"2018-12-11T11:45:11Z","doi":"10.1073/pnas.1806565115","date_published":"2018-06-26T00:00:00Z","page":"6864-6869","publication":"PNAS","day":"26","year":"2018","isi":1,"oa":1,"publisher":"National Academy of Sciences","quality_controlled":"1","title":"Auxin methylation is required for differential growth in Arabidopsis","article_processing_charge":"No","external_id":{"isi":["000436245000096"]},"publist_id":"7710","author":[{"first_name":"Mohamad","id":"47E8FC1C-F248-11E8-B48F-1D18A9856A87","full_name":"Abbas, Mohamad","last_name":"Abbas"},{"first_name":"García J","full_name":"Hernández, García J","last_name":"Hernández"},{"first_name":"Stephan","full_name":"Pollmann, Stephan","last_name":"Pollmann"},{"first_name":"Sophia L","last_name":"Samodelov","full_name":"Samodelov, Sophia L"},{"first_name":"Martina","last_name":"Kolb","full_name":"Kolb, Martina"},{"first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml"},{"last_name":"Hammes","full_name":"Hammes, Ulrich Z","first_name":"Ulrich Z"},{"full_name":"Zurbriggen, Matias D","last_name":"Zurbriggen","first_name":"Matias D"},{"first_name":"Miguel","last_name":"Blázquez","full_name":"Blázquez, Miguel"},{"first_name":"David","full_name":"Alabadí, David","last_name":"Alabadí"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Abbas M, Hernández GJ, Pollmann S, Samodelov SL, Kolb M, Friml J, Hammes UZ, Zurbriggen MD, Blázquez M, Alabadí D. 2018. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 115(26), 6864–6869.","chicago":"Abbas, Mohamad, García J Hernández, Stephan Pollmann, Sophia L Samodelov, Martina Kolb, Jiří Friml, Ulrich Z Hammes, Matias D Zurbriggen, Miguel Blázquez, and David Alabadí. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1806565115.","ama":"Abbas M, Hernández GJ, Pollmann S, et al. Auxin methylation is required for differential growth in Arabidopsis. PNAS. 2018;115(26):6864-6869. doi:10.1073/pnas.1806565115","apa":"Abbas, M., Hernández, G. J., Pollmann, S., Samodelov, S. L., Kolb, M., Friml, J., … Alabadí, D. (2018). Auxin methylation is required for differential growth in Arabidopsis. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1806565115","short":"M. Abbas, G.J. Hernández, S. Pollmann, S.L. Samodelov, M. Kolb, J. Friml, U.Z. Hammes, M.D. Zurbriggen, M. Blázquez, D. Alabadí, PNAS 115 (2018) 6864–6869.","ieee":"M. Abbas et al., “Auxin methylation is required for differential growth in Arabidopsis,” PNAS, vol. 115, no. 26. National Academy of Sciences, pp. 6864–6869, 2018.","mla":"Abbas, Mohamad, et al. “Auxin Methylation Is Required for Differential Growth in Arabidopsis.” PNAS, vol. 115, no. 26, National Academy of Sciences, 2018, pp. 6864–69, doi:10.1073/pnas.1806565115."},"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"282300","name":"Polarity and subcellular dynamics in plants"}],"ec_funded":1,"issue":"26","volume":115,"language":[{"iso":"eng"}],"publication_status":"published","intvolume":" 115","month":"06","main_file_link":[{"url":"http://eprints.nottingham.ac.uk/52388/","open_access":"1"}],"scopus_import":"1","oa_version":"None","abstract":[{"text":"Asymmetric auxin distribution is instrumental for the differential growth that causes organ bending on tropic stimuli and curvatures during plant development. Local differences in auxin concentrations are achieved mainly by polarized cellular distribution of PIN auxin transporters, but whether other mechanisms involving auxin homeostasis are also relevant for the formation of auxin gradients is not clear. Here we show that auxin methylation is required for asymmetric auxin distribution across the hypocotyl, particularly during its response to gravity. We found that loss-of-function mutants in Arabidopsis IAA CARBOXYL METHYLTRANSFERASE1 (IAMT1) prematurely unfold the apical hook, and that their hypocotyls are impaired in gravitropic reorientation. This defect is linked to an auxin-dependent increase in PIN gene expression, leading to an increased polar auxin transport and lack of asymmetric distribution of PIN3 in the iamt1 mutant. Gravitropic reorientation in the iamt1 mutant could be restored with either endodermis-specific expression of IAMT1 or partial inhibition of polar auxin transport, which also results in normal PIN gene expression levels. We propose that IAA methylation is necessary in gravity-sensing cells to restrict polar auxin transport within the range of auxin levels that allow for differential responses.","lang":"eng"}],"department":[{"_id":"JiFr"}],"date_updated":"2023-09-08T13:24:40Z","status":"public","type":"journal_article","_id":"203"},{"date_updated":"2023-09-08T13:30:51Z","department":[{"_id":"RoSe"}],"_id":"399","type":"journal_article","article_type":"original","status":"public","publication_status":"published","language":[{"iso":"eng"}],"volume":121,"issue":"1","abstract":[{"text":"Following an earlier calculation in 3D, we calculate the 2D critical temperature of a dilute, translation-invariant Bose gas using a variational formulation of the Bogoliubov approximation introduced by Critchley and Solomon in 1976. This provides the first analytical calculation of the Kosterlitz-Thouless transition temperature that includes the constant in the logarithm.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1706.01822","open_access":"1"}],"month":"01","intvolume":" 121","citation":{"short":"M.M. Napiórkowski, R. Reuvers, J. Solovej, EPL 121 (2018).","ieee":"M. M. Napiórkowski, R. Reuvers, and J. Solovej, “Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation,” EPL, vol. 121, no. 1. IOP Publishing Ltd., 2018.","ama":"Napiórkowski MM, Reuvers R, Solovej J. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 2018;121(1). doi:10.1209/0295-5075/121/10007","apa":"Napiórkowski, M. M., Reuvers, R., & Solovej, J. (2018). Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. IOP Publishing Ltd. https://doi.org/10.1209/0295-5075/121/10007","mla":"Napiórkowski, Marcin M., et al. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL, vol. 121, no. 1, 10007, IOP Publishing Ltd., 2018, doi:10.1209/0295-5075/121/10007.","ista":"Napiórkowski MM, Reuvers R, Solovej J. 2018. Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation. EPL. 121(1), 10007.","chicago":"Napiórkowski, Marcin M, Robin Reuvers, and Jan Solovej. “Calculation of the Critical Temperature of a Dilute Bose Gas in the Bogoliubov Approximation.” EPL. IOP Publishing Ltd., 2018. https://doi.org/10.1209/0295-5075/121/10007."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"full_name":"Napiórkowski, Marcin M","last_name":"Napiórkowski","first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Robin","full_name":"Reuvers, Robin","last_name":"Reuvers"},{"first_name":"Jan","full_name":"Solovej, Jan","last_name":"Solovej"}],"publist_id":"7432","external_id":{"isi":["000460003000003"],"arxiv":["1706.01822"]},"article_processing_charge":"No","title":"Calculation of the critical temperature of a dilute Bose gas in the Bogoliubov approximation","article_number":"10007","project":[{"grant_number":"P27533_N27","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"isi":1,"year":"2018","day":"01","publication":"EPL","doi":"10.1209/0295-5075/121/10007","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:46:15Z","acknowledgement":"We thank Robert Seiringer and Daniel Ueltschi for bringing the issue of the change in critical temperature to our attention. We also thank the Erwin Schrödinger Institute (all authors) and the Department of Mathematics, University of Copenhagen (MN) for the hospitality during the period this work was carried out. We gratefully acknowledge the financial support by the European Unions Seventh Framework Programme under the ERC Grant Agreement Nos. 321029 (JPS and RR) and 337603 (RR) as well as support by the VIL-LUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059) (JPS and RR), by the National Science Center (NCN) under grant No. 2016/21/D/ST1/02430 and the Austrian Science Fund (FWF) through project No. P 27533-N27 (MN).","quality_controlled":"1","publisher":"IOP Publishing Ltd.","oa":1},{"type":"journal_article","status":"public","_id":"5830","article_processing_charge":"No","external_id":{"isi":["000459014800021"],"pmid":["30378140"]},"author":[{"full_name":"Zhang, Luosha","last_name":"Zhang","first_name":"Luosha"},{"first_name":"Xiong","full_name":"Shi, Xiong","last_name":"Shi"},{"first_name":"Yutao","last_name":"Zhang","full_name":"Zhang, Yutao"},{"first_name":"Jiajing","last_name":"Wang","full_name":"Wang, Jiajing"},{"full_name":"Yang, Jingwei","last_name":"Yang","first_name":"Jingwei"},{"first_name":"Takashi","last_name":"Ishida","full_name":"Ishida, Takashi"},{"last_name":"Jiang","full_name":"Jiang, Wenqian","first_name":"Wenqian"},{"first_name":"Xiangyu","full_name":"Han, Xiangyu","last_name":"Han"},{"last_name":"Kang","full_name":"Kang, Jingke","first_name":"Jingke"},{"full_name":"Wang, Xuening","last_name":"Wang","first_name":"Xuening"},{"first_name":"Lixia","last_name":"Pan","full_name":"Pan, Lixia"},{"full_name":"Lv, Shuo","last_name":"Lv","first_name":"Shuo"},{"first_name":"Bing","last_name":"Cao","full_name":"Cao, Bing"},{"first_name":"Yonghong","last_name":"Zhang","full_name":"Zhang, Yonghong"},{"first_name":"Jinbin","full_name":"Wu, Jinbin","last_name":"Wu"},{"full_name":"Han, Huibin","last_name":"Han","id":"31435098-F248-11E8-B48F-1D18A9856A87","first_name":"Huibin"},{"full_name":"Hu, Zhubing","last_name":"Hu","first_name":"Zhubing"},{"full_name":"Cui, Langjun","last_name":"Cui","first_name":"Langjun"},{"first_name":"Shinichiro","full_name":"Sawa, Shinichiro","last_name":"Sawa"},{"last_name":"He","full_name":"He, Junmin","first_name":"Junmin"},{"first_name":"Guodong","full_name":"Wang, Guodong","last_name":"Wang"}],"title":"CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana","department":[{"_id":"JiFr"}],"date_updated":"2023-09-11T12:43:31Z","citation":{"ista":"Zhang L, Shi X, Zhang Y, Wang J, Yang J, Ishida T, Jiang W, Han X, Kang J, Wang X, Pan L, Lv S, Cao B, Zhang Y, Wu J, Han H, Hu Z, Cui L, Sawa S, He J, Wang G. 2018. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment.","chicago":"Zhang, Luosha, Xiong Shi, Yutao Zhang, Jiajing Wang, Jingwei Yang, Takashi Ishida, Wenqian Jiang, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment. Wiley, 2018. https://doi.org/10.1111/pce.13475.","apa":"Zhang, L., Shi, X., Zhang, Y., Wang, J., Yang, J., Ishida, T., … Wang, G. (2018). CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. Wiley. https://doi.org/10.1111/pce.13475","ama":"Zhang L, Shi X, Zhang Y, et al. CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana. Plant Cell and Environment. 2018. doi:10.1111/pce.13475","ieee":"L. Zhang et al., “CLE9 peptide-induced stomatal closure is mediated by abscisic acid, hydrogen peroxide, and nitric oxide in arabidopsis thaliana,” Plant Cell and Environment. Wiley, 2018.","short":"L. Zhang, X. Shi, Y. Zhang, J. Wang, J. Yang, T. Ishida, W. Jiang, X. Han, J. Kang, X. Wang, L. Pan, S. Lv, B. Cao, Y. Zhang, J. Wu, H. Han, Z. Hu, L. Cui, S. Sawa, J. He, G. Wang, Plant Cell and Environment (2018).","mla":"Zhang, Luosha, et al. “CLE9 Peptide-Induced Stomatal Closure Is Mediated by Abscisic Acid, Hydrogen Peroxide, and Nitric Oxide in Arabidopsis Thaliana.” Plant Cell and Environment, Wiley, 2018, doi:10.1111/pce.13475."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/30378140","open_access":"1"}],"oa":1,"publisher":"Wiley","quality_controlled":"1","scopus_import":"1","month":"10","abstract":[{"text":"CLE peptides have been implicated in various developmental processes of plants and mediate their responses to environmental stimuli. However, the biological relevance of most CLE genes remains to be functionally characterized. Here, we report that CLE9, which is expressed in stomata, acts as an essential regulator in the induction of stomatal closure. Exogenous application of CLE9 peptides or overexpression of CLE9 effectively led to stomatal closure and enhanced drought tolerance, whereas CLE9 loss-of-function mutants were sensitivity to drought stress. CLE9-induced stomatal closure was impaired in abscisic acid (ABA)-deficient mutants, indicating that ABA is required for CLE9-medaited guard cell signalling. We further deciphered that two guard cell ABA-signalling components, OST1 and SLAC1, were responsible for CLE9-induced stomatal closure. MPK3 and MPK6 were activated by the CLE9 peptide, and CLE9 peptides failed to close stomata in mpk3 and mpk6 mutants. In addition, CLE9 peptides stimulated the induction of hydrogen peroxide (H2O2) and nitric oxide (NO) synthesis associated with stomatal closure, which was abolished in the NADPH oxidase-deficient mutants or nitric reductase mutants, respectively. Collectively, our results reveal a novel ABA-dependent function of CLE9 in the regulation of stomatal apertures, thereby suggesting a potential role of CLE9 in the stress acclimatization of plants.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"date_created":"2019-01-13T22:59:11Z","date_published":"2018-10-31T00:00:00Z","doi":"10.1111/pce.13475","year":"2018","publication_status":"epub_ahead","publication_identifier":{"issn":["01407791"]},"isi":1,"publication":"Plant Cell and Environment","language":[{"iso":"eng"}],"day":"31"},{"page":"677 - 687","date_published":"2018-05-21T00:00:00Z","doi":"10.1038/s41556-018-0108-1","date_created":"2018-12-11T11:45:38Z","isi":1,"year":"2018","day":"21","publication":"Nature Cell Biology","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"publist_id":"7594","author":[{"first_name":"Anna","last_name":"Lilja","full_name":"Lilja, Anna"},{"last_name":"Rodilla","full_name":"Rodilla, Veronica","first_name":"Veronica"},{"full_name":"Huyghe, Mathilde","last_name":"Huyghe","first_name":"Mathilde"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B","orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo"},{"first_name":"Camille","full_name":"Landragin, Camille","last_name":"Landragin"},{"first_name":"Olivier","last_name":"Renaud","full_name":"Renaud, Olivier"},{"first_name":"Olivier","full_name":"Leroy, Olivier","last_name":"Leroy"},{"first_name":"Steffen","full_name":"Rulands, Steffen","last_name":"Rulands"},{"first_name":"Benjamin","full_name":"Simons, Benjamin","last_name":"Simons"},{"first_name":"Silvia","full_name":"Fré, Silvia","last_name":"Fré"}],"article_processing_charge":"No","external_id":{"pmid":["29784917"],"isi":["000433237300003"]},"title":"Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland","citation":{"ista":"Lilja A, Rodilla V, Huyghe M, Hannezo EB, Landragin C, Renaud O, Leroy O, Rulands S, Simons B, Fré S. 2018. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 20(6), 677–687.","chicago":"Lilja, Anna, Veronica Rodilla, Mathilde Huyghe, Edouard B Hannezo, Camille Landragin, Olivier Renaud, Olivier Leroy, Steffen Rulands, Benjamin Simons, and Silvia Fré. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41556-018-0108-1.","ieee":"A. Lilja et al., “Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland,” Nature Cell Biology, vol. 20, no. 6. Nature Publishing Group, pp. 677–687, 2018.","short":"A. Lilja, V. Rodilla, M. Huyghe, E.B. Hannezo, C. Landragin, O. Renaud, O. Leroy, S. Rulands, B. Simons, S. Fré, Nature Cell Biology 20 (2018) 677–687.","ama":"Lilja A, Rodilla V, Huyghe M, et al. Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. 2018;20(6):677-687. doi:10.1038/s41556-018-0108-1","apa":"Lilja, A., Rodilla, V., Huyghe, M., Hannezo, E. B., Landragin, C., Renaud, O., … Fré, S. (2018). Clonal analysis of Notch1-expressing cells reveals the existence of unipotent stem cells that retain long-term plasticity in the embryonic mammary gland. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/s41556-018-0108-1","mla":"Lilja, Anna, et al. “Clonal Analysis of Notch1-Expressing Cells Reveals the Existence of Unipotent Stem Cells That Retain Long-Term Plasticity in the Embryonic Mammary Gland.” Nature Cell Biology, vol. 20, no. 6, Nature Publishing Group, 2018, pp. 677–87, doi:10.1038/s41556-018-0108-1."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","issue":"6","volume":20,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6984964","open_access":"1"}],"month":"05","intvolume":" 20","abstract":[{"lang":"eng","text":"Recent lineage tracing studies have revealed that mammary gland homeostasis relies on unipotent stem cells. However, whether and when lineage restriction occurs during embryonic mammary development, and which signals orchestrate cell fate specification, remain unknown. Using a combination of in vivo clonal analysis with whole mount immunofluorescence and mathematical modelling of clonal dynamics, we found that embryonic multipotent mammary cells become lineage-restricted surprisingly early in development, with evidence for unipotency as early as E12.5 and no statistically discernable bipotency after E15.5. To gain insights into the mechanisms governing the switch from multipotency to unipotency, we used gain-of-function Notch1 mice and demonstrated that Notch activation cell autonomously dictates luminal cell fate specification to both embryonic and basally committed mammary cells. These functional studies have important implications for understanding the signals underlying cell plasticity and serve to clarify how reactivation of embryonic programs in adult cells can lead to cancer."}],"oa_version":"Submitted Version","pmid":1,"department":[{"_id":"EdHa"}],"date_updated":"2023-09-11T12:44:08Z","article_type":"original","type":"journal_article","status":"public","_id":"288"},{"file":[{"date_created":"2018-12-12T10:18:14Z","file_name":"IST-2018-1024-v1+1_NanoStructColor-Auzinger-paper.pdf","creator":"system","date_updated":"2020-07-14T12:45:59Z","file_size":10751684,"checksum":"dcdcc955a4c1c6d2599aeebb97d2e7b9","file_id":"5334","access_level":"open_access","relation":"main_file","content_type":"application/pdf"},{"checksum":"cae52b3a8d5e97be84771cd61ea2f75e","file_id":"5335","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:18:15Z","file_name":"IST-2018-1024-v1+2_NanoStructColor-Auzinger-supplemental.pdf","date_updated":"2020-07-14T12:45:59Z","file_size":20755095,"creator":"system"},{"checksum":"76dd90648f75779d3f64e324b6daaffe","file_id":"5336","relation":"main_file","access_level":"open_access","content_type":"image/jpeg","file_name":"IST-2018-1024-v1+3_NanoStructColor-Auzinger-image.jpg","date_created":"2018-12-12T10:18:16Z","creator":"system","file_size":2186944,"date_updated":"2020-07-14T12:45:59Z"},{"checksum":"c3a5b775a0ecdb20ccefb8d9646ec140","file_id":"5337","content_type":"application/x-7z-compressed","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:18:17Z","file_name":"IST-2018-1024-v1+4_NanoStructColor-Auzinger-blueprint.7z","date_updated":"2020-07-14T12:45:59Z","file_size":2734352,"creator":"system"},{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5338","checksum":"dcdcc955a4c1c6d2599aeebb97d2e7b9","file_size":10751684,"date_updated":"2020-07-14T12:45:59Z","creator":"system","file_name":"IST-2018-1024-v2+1_NanoStructColor-Auzinger-paper.pdf","date_created":"2018-12-12T10:18:18Z"},{"file_name":"IST-2018-1024-v2+3_NanoStructColor-Auzinger-image.jpg","date_created":"2018-12-12T10:18:19Z","creator":"system","file_size":2186944,"date_updated":"2020-07-14T12:45:59Z","checksum":"76dd90648f75779d3f64e324b6daaffe","file_id":"5339","relation":"main_file","access_level":"open_access","content_type":"image/jpeg"},{"date_created":"2018-12-12T10:18:20Z","file_name":"IST-2018-1024-v2+4_NanoStructColor-Auzinger-blueprint.7z","date_updated":"2020-07-14T12:45:59Z","file_size":2734352,"creator":"system","checksum":"c3a5b775a0ecdb20ccefb8d9646ec140","file_id":"5340","content_type":"application/x-7z-compressed","access_level":"open_access","relation":"main_file"},{"file_id":"5341","checksum":"667e91b686db41e44d855a4fb2137402","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:18:21Z","file_name":"IST-2018-1024-v2+5_NanoStructColor-Auzinger-supplemental.pdf","date_updated":"2020-07-14T12:45:59Z","file_size":20755762,"creator":"system"},{"file_id":"5342","checksum":"dcdcc955a4c1c6d2599aeebb97d2e7b9","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-1024-v3+1_NanoStructColor-Auzinger-paper.pdf","date_created":"2018-12-12T10:18:22Z","file_size":10751684,"date_updated":"2020-07-14T12:45:59Z","creator":"system"},{"date_updated":"2020-07-14T12:45:59Z","file_size":2186944,"creator":"system","date_created":"2018-12-12T10:18:22Z","file_name":"IST-2018-1024-v3+3_NanoStructColor-Auzinger-image.jpg","content_type":"image/jpeg","access_level":"open_access","relation":"main_file","checksum":"76dd90648f75779d3f64e324b6daaffe","file_id":"5343"},{"relation":"main_file","access_level":"open_access","content_type":"application/x-7z-compressed","file_id":"5344","checksum":"c3a5b775a0ecdb20ccefb8d9646ec140","creator":"system","file_size":2734352,"date_updated":"2020-07-14T12:45:59Z","file_name":"IST-2018-1024-v3+4_NanoStructColor-Auzinger-blueprint.7z","date_created":"2018-12-12T10:18:23Z"},{"checksum":"667e91b686db41e44d855a4fb2137402","file_id":"5345","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-1024-v3+5_NanoStructColor-Auzinger-supplemental.pdf","date_created":"2018-12-12T10:18:24Z","file_size":20755762,"date_updated":"2020-07-14T12:45:59Z","creator":"system"},{"content_type":"application/vnd.openxmlformats-officedocument.presentationml.presentation","relation":"main_file","access_level":"open_access","file_id":"5346","checksum":"72dce35388fb1aa7953df4d9ae3d02f1","file_size":69698068,"date_updated":"2020-07-14T12:45:59Z","creator":"system","file_name":"IST-2018-1024-v3+6_NanoStructColor-Auzinger-presentation.pptx","date_created":"2018-12-12T10:18:25Z"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":37,"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/color-effects-from-transparent-3d-printed-nanostructures/"}]},"issue":"4","ec_funded":1,"oa_version":"Submitted Version","abstract":[{"text":"Additive manufacturing has recently seen drastic improvements in resolution, making it now possible to fabricate features at scales of hundreds or even dozens of nanometers, which previously required very expensive lithographic methods.\r\nAs a result, additive manufacturing now seems poised for optical applications, including those relevant to computer graphics, such as material design, as well as display and imaging applications.\r\n \r\nIn this work, we explore the use of additive manufacturing for generating structural colors, where the structures are designed using a fabrication-aware optimization process.\r\nThis requires a combination of full-wave simulation, a feasible parameterization of the design space, and a tailored optimization procedure.\r\nMany of these components should be re-usable for the design of other optical structures at this scale.\r\n \r\nWe show initial results of material samples fabricated based on our designs.\r\nWhile these suffer from the prototype character of state-of-the-art fabrication hardware, we believe they clearly demonstrate the potential of additive nanofabrication for structural colors and other graphics applications.","lang":"eng"}],"month":"08","intvolume":" 37","alternative_title":["ACM Transactions on Graphics"],"scopus_import":"1","ddc":["000","535","680"],"date_updated":"2023-09-11T12:46:13Z","file_date_updated":"2020-07-14T12:45:59Z","department":[{"_id":"BeBi"}],"_id":"304","status":"public","pubrep_id":"1028","type":"journal_article","day":"01","publication":"ACM Transactions on Graphics","isi":1,"has_accepted_license":"1","year":"2018","date_published":"2018-08-01T00:00:00Z","doi":"10.1145/3197517.3201376","date_created":"2018-12-11T11:45:43Z","acknowledgement":"This work was in part supported by King Abdullah University of Science and Technology Baseline Funding.","publisher":"ACM","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Auzinger T, Heidrich W, Bickel B. 2018. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 37(4), 159.","chicago":"Auzinger, Thomas, Wolfgang Heidrich, and Bernd Bickel. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201376.","ama":"Auzinger T, Heidrich W, Bickel B. Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. 2018;37(4). doi:10.1145/3197517.3201376","apa":"Auzinger, T., Heidrich, W., & Bickel, B. (2018). Computational design of nanostructural color for additive manufacturing. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3197517.3201376","short":"T. Auzinger, W. Heidrich, B. Bickel, ACM Transactions on Graphics 37 (2018).","ieee":"T. Auzinger, W. Heidrich, and B. Bickel, “Computational design of nanostructural color for additive manufacturing,” ACM Transactions on Graphics, vol. 37, no. 4. ACM, 2018.","mla":"Auzinger, Thomas, et al. “Computational Design of Nanostructural Color for Additive Manufacturing.” ACM Transactions on Graphics, vol. 37, no. 4, 159, ACM, 2018, doi:10.1145/3197517.3201376."},"title":"Computational design of nanostructural color for additive manufacturing","author":[{"first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas"},{"last_name":"Heidrich","full_name":"Heidrich, Wolfgang","first_name":"Wolfgang"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"}],"external_id":{"isi":["000448185000120"]},"article_processing_charge":"No","article_number":"159","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","grant_number":"715767"}]},{"article_number":"135","project":[{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"_id":"2508E324-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"642841","name":"Distributed 3D Object Design"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, B. Bickel, ACM Transaction on Graphics 37 (2018).","ieee":"K. Nakashima, T. Auzinger, E. Iarussi, R. Zhang, T. Igarashi, and B. Bickel, “CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds,” ACM Transaction on Graphics, vol. 37, no. 4. ACM, 2018.","apa":"Nakashima, K., Auzinger, T., Iarussi, E., Zhang, R., Igarashi, T., & Bickel, B. (2018). CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. ACM. https://doi.org/10.1145/3197517.3201341","ama":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 2018;37(4). doi:10.1145/3197517.3201341","mla":"Nakashima, Kazutaka, et al. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics, vol. 37, no. 4, 135, ACM, 2018, doi:10.1145/3197517.3201341.","ista":"Nakashima K, Auzinger T, Iarussi E, Zhang R, Igarashi T, Bickel B. 2018. CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds. ACM Transaction on Graphics. 37(4), 135.","chicago":"Nakashima, Kazutaka, Thomas Auzinger, Emmanuel Iarussi, Ran Zhang, Takeo Igarashi, and Bernd Bickel. “CoreCavity: Interactive Shell Decomposition for Fabrication with Two-Piece Rigid Molds.” ACM Transaction on Graphics. ACM, 2018. https://doi.org/10.1145/3197517.3201341."},"title":"CoreCavity: Interactive shell decomposition for fabrication with two-piece rigid molds","external_id":{"isi":["000448185000096"]},"article_processing_charge":"No","publist_id":"8044","author":[{"last_name":"Nakashima","full_name":"Nakashima, Kazutaka","first_name":"Kazutaka"},{"first_name":"Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","last_name":"Auzinger","orcid":"0000-0002-1546-3265","full_name":"Auzinger, Thomas"},{"last_name":"Iarussi","full_name":"Iarussi, Emmanuel","id":"33F19F16-F248-11E8-B48F-1D18A9856A87","first_name":"Emmanuel"},{"id":"4DDBCEB0-F248-11E8-B48F-1D18A9856A87","first_name":"Ran","last_name":"Zhang","full_name":"Zhang, Ran","orcid":"0000-0002-3808-281X"},{"full_name":"Igarashi, Takeo","last_name":"Igarashi","first_name":"Takeo"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel","first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"publisher":"ACM","quality_controlled":"1","publication":"ACM Transaction on Graphics","day":"04","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:09Z","doi":"10.1145/3197517.3201341","date_published":"2018-08-04T00:00:00Z","_id":"12","pubrep_id":"1037","status":"public","type":"journal_article","ddc":["004","516","670"],"date_updated":"2023-09-11T12:48:09Z","department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:44:38Z","oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Molding is a popular mass production method, in which the initial expenses for the mold are offset by the low per-unit production cost. However, the physical fabrication constraints of the molding technique commonly restrict the shape of moldable objects. For a complex shape, a decomposition of the object into moldable parts is a common strategy to address these constraints, with plastic model kits being a popular and illustrative example. However, conducting such a decomposition requires considerable expertise, and it depends on the technical aspects of the fabrication technique, as well as aesthetic considerations. We present an interactive technique to create such decompositions for two-piece molding, in which each part of the object is cast between two rigid mold pieces. Given the surface description of an object, we decompose its thin-shell equivalent into moldable parts by first performing a coarse decomposition and then utilizing an active contour model for the boundaries between individual parts. Formulated as an optimization problem, the movement of the contours is guided by an energy reflecting fabrication constraints to ensure the moldability of each part. Simultaneously, the user is provided with editing capabilities to enforce aesthetic guidelines. Our interactive interface provides control of the contour positions by allowing, for example, the alignment of part boundaries with object features. Our technique enables a novel workflow, as it empowers novice users to explore the design space, and it generates fabrication-ready two-piece molds that can be used either for casting or industrial injection molding of free-form objects."}],"intvolume":" 37","month":"08","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_size":104225664,"date_updated":"2020-07-14T12:44:38Z","creator":"system","file_name":"IST-2018-1037-v1+1_CoreCavity-AuthorVersion.pdf","date_created":"2018-12-12T10:18:38Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"6a5368bc86c4e1a9fcfe588fd1f14ee8","file_id":"5360"},{"file_id":"5361","checksum":"3861e693ba47c51f3ec7b7867d573a61","relation":"main_file","access_level":"open_access","content_type":"application/zip","file_name":"IST-2018-1037-v1+2_CoreCavity-Supplemental.zip","date_created":"2018-12-12T10:18:39Z","creator":"system","file_size":377743553,"date_updated":"2020-07-14T12:44:38Z"},{"relation":"main_file","access_level":"open_access","content_type":"video/vnd.objectvideo","file_id":"5362","checksum":"490040c685ed869536e2a18f5a906b94","creator":"system","file_size":162634396,"date_updated":"2020-07-14T12:44:38Z","file_name":"IST-2018-1037-v1+3_CoreCavity-Video.mp4","date_created":"2018-12-12T10:18:41Z"},{"checksum":"be7fc8b229adda727419b6504b3b9352","file_id":"5363","content_type":"image/jpeg","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:18:42Z","file_name":"IST-2018-1037-v1+4_CoreCavity-RepresentativeImage.jpg","date_updated":"2020-07-14T12:44:38Z","file_size":527972,"creator":"system"}],"publication_status":"published","ec_funded":1,"volume":37,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/interactive-software-tool-makes-complex-mold-design-simple/","relation":"press_release","description":"News on IST Homepage"}]},"issue":"4"},{"article_processing_charge":"No","external_id":{"isi":["000424318200001"]},"publist_id":"7368","author":[{"first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0170-7353","full_name":"Reiter, Johannes","last_name":"Reiter"},{"first_name":"Christian","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5116-955X","full_name":"Hilbe, Christian","last_name":"Hilbe"},{"first_name":"David","last_name":"Rand","full_name":"Rand, David"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Martin","full_name":"Nowak, Martin","last_name":"Nowak"}],"title":"Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness","citation":{"ista":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. 2018. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 9(1), 555.","chicago":"Reiter, Johannes, Christian Hilbe, David Rand, Krishnendu Chatterjee, and Martin Nowak. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications. Nature Publishing Group, 2018. https://doi.org/10.1038/s41467-017-02721-8.","ama":"Reiter J, Hilbe C, Rand D, Chatterjee K, Nowak M. Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. 2018;9(1). doi:10.1038/s41467-017-02721-8","apa":"Reiter, J., Hilbe, C., Rand, D., Chatterjee, K., & Nowak, M. (2018). Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/s41467-017-02721-8","ieee":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, and M. Nowak, “Crosstalk in concurrent repeated games impedes direct reciprocity and requires stronger levels of forgiveness,” Nature Communications, vol. 9, no. 1. Nature Publishing Group, 2018.","short":"J. Reiter, C. Hilbe, D. Rand, K. Chatterjee, M. Nowak, Nature Communications 9 (2018).","mla":"Reiter, Johannes, et al. “Crosstalk in Concurrent Repeated Games Impedes Direct Reciprocity and Requires Stronger Levels of Forgiveness.” Nature Communications, vol. 9, no. 1, 555, Nature Publishing Group, 2018, doi:10.1038/s41467-017-02721-8."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification"},{"name":"Game Theory","grant_number":"S11407","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"555","date_created":"2018-12-11T11:46:34Z","doi":"10.1038/s41467-017-02721-8","date_published":"2018-02-07T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Nature Communications","day":"07","oa":1,"publisher":"Nature Publishing Group","quality_controlled":"1","acknowledgement":"This work was supported by the European Research Council (ERC) start grant 279307: Graph Games (C.K.), Austrian Science Fund (FWF) grant no P23499-N23 (C.K.), FWF\r\nNFN grant no S11407-N23 RiSE/SHiNE (C.K.), Office of Naval Research grant N00014-16-1-2914 (M.A.N.), National Cancer Institute grant CA179991 (M.A.N.) and by the John Templeton Foundation. J.G.R. is supported by an Erwin Schrödinger fellowship\r\n(Austrian Science Fund FWF J-3996). C.H. acknowledges generous support from the\r\nISTFELLOW program. The Program for Evolutionary Dynamics is supported in part by\r\na gift from B Wu and Eric Larson.","file_date_updated":"2020-07-14T12:46:31Z","department":[{"_id":"KrCh"}],"date_updated":"2023-09-11T12:51:03Z","ddc":["004"],"tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"964","status":"public","_id":"454","ec_funded":1,"issue":"1","volume":9,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"b6b90367545b4c615891c960ab0567f1","file_id":"4741","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-12T10:09:18Z","file_name":"IST-2018-964-v1+1_2018_Hilbe_Crosstalk_in.pdf","date_updated":"2020-07-14T12:46:31Z","file_size":843646,"creator":"system"}],"scopus_import":"1","intvolume":" 9","month":"02","abstract":[{"lang":"eng","text":"Direct reciprocity is a mechanism for cooperation among humans. Many of our daily interactions are repeated. We interact repeatedly with our family, friends, colleagues, members of the local and even global community. In the theory of repeated games, it is a tacit assumption that the various games that a person plays simultaneously have no effect on each other. Here we introduce a general framework that allows us to analyze “crosstalk” between a player’s concurrent games. In the presence of crosstalk, the action a person experiences in one game can alter the person’s decision in another. We find that crosstalk impedes the maintenance of cooperation and requires stronger levels of forgiveness. The magnitude of the effect depends on the population structure. In more densely connected social groups, crosstalk has a stronger effect. A harsh retaliator, such as Tit-for-Tat, is unable to counteract crosstalk. The crosstalk framework provides a unified interpretation of direct and upstream reciprocity in the context of repeated games."}],"oa_version":"Published Version"},{"oa":1,"publisher":"Elsevier","quality_controlled":"1","publication":"Neuron","day":"04","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:45:48Z","date_published":"2018-04-04T00:00:00Z","doi":"10.1016/j.neuron.2018.02.024","page":"156 - 165","project":[{"grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"grant_number":"692692","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"name":"The Wittgenstein Prize","grant_number":"Z00312","_id":"25C5A090-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"H. Hu, F. Roth, D.H. Vandael, P.M. Jonas, Neuron 98 (2018) 156–165.","ieee":"H. Hu, F. Roth, D. H. Vandael, and P. M. Jonas, “Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons,” Neuron, vol. 98, no. 1. Elsevier, pp. 156–165, 2018.","apa":"Hu, H., Roth, F., Vandael, D. H., & Jonas, P. M. (2018). Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2018.02.024","ama":"Hu H, Roth F, Vandael DH, Jonas PM. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 2018;98(1):156-165. doi:10.1016/j.neuron.2018.02.024","mla":"Hu, Hua, et al. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron, vol. 98, no. 1, Elsevier, 2018, pp. 156–65, doi:10.1016/j.neuron.2018.02.024.","ista":"Hu H, Roth F, Vandael DH, Jonas PM. 2018. Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons. Neuron. 98(1), 156–165.","chicago":"Hu, Hua, Fabian Roth, David H Vandael, and Peter M Jonas. “Complementary Tuning of Na+ and K+ Channel Gating Underlies Fast and Energy-Efficient Action Potentials in GABAergic Interneuron Axons.” Neuron. Elsevier, 2018. https://doi.org/10.1016/j.neuron.2018.02.024."},"title":"Complementary tuning of Na+ and K+ channel gating underlies fast and energy-efficient action potentials in GABAergic interneuron axons","external_id":{"isi":["000429192100016"]},"article_processing_charge":"Yes (in subscription journal)","publist_id":"7545","author":[{"first_name":"Hua","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","full_name":"Hu, Hua","last_name":"Hu"},{"first_name":"Fabian","last_name":"Roth","full_name":"Roth, Fabian"},{"last_name":"Vandael","orcid":"0000-0001-7577-1676","full_name":"Vandael, David H","first_name":"David H","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Fast-spiking, parvalbumin-expressing GABAergic interneurons (PV+-BCs) express a complex machinery of rapid signaling mechanisms, including specialized voltage-gated ion channels to generate brief action potentials (APs). However, short APs are associated with overlapping Na+ and K+ fluxes and are therefore energetically expensive. How the potentially vicious combination of high AP frequency and inefficient spike generation can be reconciled with limited energy supply is presently unclear. To address this question, we performed direct recordings from the PV+-BC axon, the subcellular structure where active conductances for AP initiation and propagation are located. Surprisingly, the energy required for the AP was, on average, only ∼1.6 times the theoretical minimum. High energy efficiency emerged from the combination of fast inactivation of Na+ channels and delayed activation of Kv3-type K+ channels, which minimized ion flux overlap during APs. Thus, the complementary tuning of axonal Na+ and K+ channel gating optimizes both fast signaling properties and metabolic efficiency. Hu et al. demonstrate that action potentials in parvalbumin-expressing GABAergic interneuron axons are energetically efficient, which is highly unexpected given their brief duration. High energy efficiency emerges from the combination of fast inactivation of voltage-gated Na+ channels and delayed activation of Kv3 channels in the axon. "}],"intvolume":" 98","month":"04","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"file_size":3180444,"date_updated":"2020-07-14T12:46:03Z","creator":"dernst","file_name":"2018_Neuron_Hu.pdf","date_created":"2018-12-17T10:37:50Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"76070f3729f9c603e1080d0151aa2b11","file_id":"5690"}],"publication_status":"published","ec_funded":1,"volume":98,"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/a-certain-type-of-neurons-is-more-energy-efficient-than-previously-assumed/","description":"News on IST Homepage"}]},"issue":"1","_id":"320","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","ddc":["570"],"date_updated":"2023-09-11T12:45:10Z","file_date_updated":"2020-07-14T12:46:03Z","department":[{"_id":"PeJo"}]},{"file_date_updated":"2020-07-14T12:46:25Z","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"ddc":["576"],"date_updated":"2023-09-11T12:49:17Z","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","_id":"423","ec_funded":1,"related_material":{"record":[{"status":"public","id":"9840","relation":"research_data"}]},"volume":7,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5689","checksum":"447cf6e680bdc3c01062a8737d876569","creator":"dernst","date_updated":"2020-07-14T12:46:25Z","file_size":3533881,"date_created":"2018-12-17T10:36:07Z","file_name":"2018_eLife_Payne.pdf"}],"publication_status":"published","intvolume":" 7","month":"03","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity."}],"title":"CRISPR-based herd immunity can limit phage epidemics in bacterial populations","external_id":{"isi":["000431035800001"]},"article_processing_charge":"No","publist_id":"7400","author":[{"id":"35F78294-F248-11E8-B48F-1D18A9856A87","first_name":"Pavel","last_name":"Payne","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton"},{"first_name":"Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","last_name":"Bollback"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32035.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 7, e32035.","mla":"Payne, Pavel, et al. “CRISPR-Based Herd Immunity Can Limit Phage Epidemics in Bacterial Populations.” ELife, vol. 7, e32035, eLife Sciences Publications, 2018, doi:10.7554/eLife.32035.","apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). CRISPR-based herd immunity can limit phage epidemics in bacterial populations. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32035","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. CRISPR-based herd immunity can limit phage epidemics in bacterial populations. eLife. 2018;7. doi:10.7554/eLife.32035","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “CRISPR-based herd immunity can limit phage epidemics in bacterial populations,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, ELife 7 (2018)."},"project":[{"call_identifier":"H2020","_id":"2578D616-B435-11E9-9278-68D0E5697425","name":"Selective Barriers to Horizontal Gene Transfer","grant_number":"648440"}],"article_number":"e32035","date_created":"2018-12-11T11:46:23Z","doi":"10.7554/eLife.32035","date_published":"2018-03-09T00:00:00Z","publication":"eLife","day":"09","year":"2018","has_accepted_license":"1","isi":1,"oa":1,"publisher":"eLife Sciences Publications","quality_controlled":"1","acknowledgement":"We are grateful to Remy Chait for his help and assistance with establishing our experimental setups and to Tobias Bergmiller for valuable insights into some specific experimental details. We thank Luciano Marraffini for donating us the pCas9 plasmid used in this study. We also want to express our gratitude to Seth Barribeau, Andrea Betancourt, Călin Guet, Mato Lagator, Tiago Paixão and Maroš Pleška for valuable discussions on the manuscript. Finally, we would like to thank the \r\neditors and reviewers for their helpful comments and suggestions."},{"title":"Crossing minimization in perturbed drawings","author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"full_name":"Tóth, Csaba D.","last_name":"Tóth","first_name":"Csaba D."}],"article_processing_charge":"No","external_id":{"isi":["000672802500016"],"arxiv":["1808.07608"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Fulek R, Tóth CD. 2018. Crossing minimization in perturbed drawings. Graph Drawing and Network Visualization, LNCS, vol. 11282, 229–241.","chicago":"Fulek, Radoslav, and Csaba D. Tóth. “Crossing Minimization in Perturbed Drawings,” 11282:229–41. Springer, 2018. https://doi.org/10.1007/978-3-030-04414-5_16.","ama":"Fulek R, Tóth CD. Crossing minimization in perturbed drawings. In: Vol 11282. Springer; 2018:229-241. doi:10.1007/978-3-030-04414-5_16","apa":"Fulek, R., & Tóth, C. D. (2018). Crossing minimization in perturbed drawings (Vol. 11282, pp. 229–241). Presented at the Graph Drawing and Network Visualization, Barcelona, Spain: Springer. https://doi.org/10.1007/978-3-030-04414-5_16","short":"R. Fulek, C.D. Tóth, in:, Springer, 2018, pp. 229–241.","ieee":"R. Fulek and C. D. Tóth, “Crossing minimization in perturbed drawings,” presented at the Graph Drawing and Network Visualization, Barcelona, Spain, 2018, vol. 11282, pp. 229–241.","mla":"Fulek, Radoslav, and Csaba D. Tóth. Crossing Minimization in Perturbed Drawings. Vol. 11282, Springer, 2018, pp. 229–41, doi:10.1007/978-3-030-04414-5_16."},"publisher":"Springer","quality_controlled":"1","oa":1,"doi":"10.1007/978-3-030-04414-5_16","date_published":"2018-12-18T00:00:00Z","date_created":"2018-12-30T22:59:15Z","page":"229-241","day":"18","isi":1,"year":"2018","status":"public","type":"conference","conference":{"end_date":"2018-09-28","location":"Barcelona, Spain","start_date":"2018-09-26","name":"Graph Drawing and Network Visualization"},"_id":"5791","department":[{"_id":"UlWa"}],"date_updated":"2023-09-11T12:49:55Z","month":"12","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1808.07608"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Due to data compression or low resolution, nearby vertices and edges of a graph drawing may be bundled to a common node or arc. We model such a “compromised” drawing by a piecewise linear map φ:G → ℝ. We wish to perturb φ by an arbitrarily small ε>0 into a proper drawing (in which the vertices are distinct points, any two edges intersect in finitely many points, and no three edges have a common interior point) that minimizes the number of crossings. An ε-perturbation, for every ε>0, is given by a piecewise linear map (Formula Presented), where with ||·|| is the uniform norm (i.e., sup norm). We present a polynomial-time solution for this optimization problem when G is a cycle and the map φ has no spurs (i.e., no two adjacent edges are mapped to overlapping arcs). We also show that the problem becomes NP-complete (i) when G is an arbitrary graph and φ has no spurs, and (ii) when φ may have spurs and G is a cycle or a union of disjoint paths."}],"volume":"11282 ","language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783030044138"]},"publication_status":"published"},{"issue":"5","volume":3,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1802.01918","open_access":"1"}],"month":"05","intvolume":" 3","abstract":[{"text":"Over the past decade, the edge of chaos has proven to be a fruitful starting point for investigations of shear flows when the laminar base flow is linearly stable. Numerous computational studies of shear flows demonstrated the existence of states that separate laminar and turbulent regions of the state space. In addition, some studies determined invariant solutions that reside on this edge. In this paper, we study the unstable manifold of one such solution with the aid of continuous symmetry reduction, which we formulate here for the simultaneous quotiening of axial and azimuthal symmetries. Upon our investigation of the unstable manifold, we discover a previously unknown traveling-wave solution on the laminar-turbulent boundary with a relatively complex structure. By means of low-dimensional projections, we visualize different dynamical paths that connect these solutions to the turbulence. Our numerical experiments demonstrate that the laminar-turbulent boundary exhibits qualitatively different regions whose properties are influenced by the nearby invariant solutions.","lang":"eng"}],"oa_version":"Preprint","department":[{"_id":"BjHo"}],"date_updated":"2023-09-11T12:45:44Z","type":"journal_article","status":"public","_id":"291","date_published":"2018-05-30T00:00:00Z","doi":"10.1103/PhysRevFluids.3.054401","date_created":"2018-12-11T11:45:39Z","isi":1,"year":"2018","day":"30","publication":"Physical Review Fluids","quality_controlled":"1","publisher":"American Physical Society","oa":1,"publist_id":"7590","author":[{"full_name":"Budanur, Nazmi B","orcid":"0000-0003-0423-5010","last_name":"Budanur","first_name":"Nazmi B","id":"3EA1010E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Hof","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000433426200001"],"arxiv":["1802.01918"]},"article_processing_charge":"No","title":"Complexity of the laminar-turbulent boundary in pipe flow","citation":{"mla":"Budanur, Nazmi B., and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids, vol. 3, no. 5, 054401, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.054401.","ieee":"N. B. Budanur and B. Hof, “Complexity of the laminar-turbulent boundary in pipe flow,” Physical Review Fluids, vol. 3, no. 5. American Physical Society, 2018.","short":"N.B. Budanur, B. Hof, Physical Review Fluids 3 (2018).","ama":"Budanur NB, Hof B. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 2018;3(5). doi:10.1103/PhysRevFluids.3.054401","apa":"Budanur, N. B., & Hof, B. (2018). Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.054401","chicago":"Budanur, Nazmi B, and Björn Hof. “Complexity of the Laminar-Turbulent Boundary in Pipe Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.054401.","ista":"Budanur NB, Hof B. 2018. Complexity of the laminar-turbulent boundary in pipe flow. Physical Review Fluids. 3(5), 054401."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_number":"054401"},{"project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"title":"Counting blanks in polygonal arrangements","article_processing_charge":"No","external_id":{"isi":["000450810500036"],"arxiv":["1604.00960"]},"publist_id":"7996","author":[{"full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X","last_name":"Akopyan","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy"},{"full_name":"Segal Halevi, Erel","last_name":"Segal Halevi","first_name":"Erel"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M110407X.","ista":"Akopyan A, Segal Halevi E. 2018. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 32(3), 2242–2257.","mla":"Akopyan, Arseniy, and Erel Segal Halevi. “Counting Blanks in Polygonal Arrangements.” SIAM Journal on Discrete Mathematics, vol. 32, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 2242–57, doi:10.1137/16M110407X.","apa":"Akopyan, A., & Segal Halevi, E. (2018). Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M110407X","ama":"Akopyan A, Segal Halevi E. Counting blanks in polygonal arrangements. SIAM Journal on Discrete Mathematics. 2018;32(3):2242-2257. doi:10.1137/16M110407X","ieee":"A. Akopyan and E. Segal Halevi, “Counting blanks in polygonal arrangements,” SIAM Journal on Discrete Mathematics, vol. 32, no. 3. Society for Industrial and Applied Mathematics , pp. 2242–2257, 2018.","short":"A. Akopyan, E. Segal Halevi, SIAM Journal on Discrete Mathematics 32 (2018) 2242–2257."},"oa":1,"publisher":"Society for Industrial and Applied Mathematics ","quality_controlled":"1","date_created":"2018-12-11T11:44:24Z","date_published":"2018-09-06T00:00:00Z","doi":"10.1137/16M110407X","page":"2242 - 2257","publication":"SIAM Journal on Discrete Mathematics","day":"06","year":"2018","isi":1,"status":"public","type":"journal_article","_id":"58","department":[{"_id":"HeEd"}],"date_updated":"2023-09-11T12:48:39Z","intvolume":" 32","month":"09","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.00960"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"Inside a two-dimensional region (``cake""), there are m nonoverlapping tiles of a certain kind (``toppings""). We want to expand the toppings while keeping them nonoverlapping, and possibly add some blank pieces of the same ``certain kind,"" such that the entire cake is covered. How many blanks must we add? We study this question in several cases: (1) The cake and toppings are general polygons. (2) The cake and toppings are convex figures. (3) The cake and toppings are axis-parallel rectangles. (4) The cake is an axis-parallel rectilinear polygon and the toppings are axis-parallel rectangles. In all four cases, we provide tight bounds on the number of blanks.","lang":"eng"}],"ec_funded":1,"issue":"3","volume":32,"language":[{"iso":"eng"}],"publication_status":"published"},{"date_updated":"2023-09-11T12:49:17Z","citation":{"apa":"Payne, P., Geyrhofer, L., Barton, N. H., & Bollback, J. P. (2018). Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. Dryad. https://doi.org/10.5061/dryad.42n44","ama":"Payne P, Geyrhofer L, Barton NH, Bollback JP. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations. 2018. doi:10.5061/dryad.42n44","short":"P. Payne, L. Geyrhofer, N.H. Barton, J.P. Bollback, (2018).","ieee":"P. Payne, L. Geyrhofer, N. H. Barton, and J. P. Bollback, “Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations.” Dryad, 2018.","mla":"Payne, Pavel, et al. Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations. Dryad, 2018, doi:10.5061/dryad.42n44.","ista":"Payne P, Geyrhofer L, Barton NH, Bollback JP. 2018. Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations, Dryad, 10.5061/dryad.42n44.","chicago":"Payne, Pavel, Lukas Geyrhofer, Nicholas H Barton, and Jonathan P Bollback. “Data from: CRISPR-Based Herd Immunity Limits Phage Epidemics in Bacterial Populations.” Dryad, 2018. https://doi.org/10.5061/dryad.42n44."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","author":[{"first_name":"Pavel","id":"35F78294-F248-11E8-B48F-1D18A9856A87","last_name":"Payne","full_name":"Payne, Pavel","orcid":"0000-0002-2711-9453"},{"full_name":"Geyrhofer, Lukas","last_name":"Geyrhofer","first_name":"Lukas"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bollback","orcid":"0000-0002-4624-4612","full_name":"Bollback, Jonathan P","id":"2C6FA9CC-F248-11E8-B48F-1D18A9856A87","first_name":"Jonathan P"}],"article_processing_charge":"No","title":"Data from: CRISPR-based herd immunity limits phage epidemics in bacterial populations","department":[{"_id":"NiBa"},{"_id":"JoBo"}],"_id":"9840","type":"research_data_reference","status":"public","year":"2018","day":"12","related_material":{"record":[{"relation":"used_in_publication","id":"423","status":"public"}]},"doi":"10.5061/dryad.42n44","date_published":"2018-03-12T00:00:00Z","date_created":"2021-08-09T13:10:02Z","abstract":[{"text":"Herd immunity, a process in which resistant individuals limit the spread of a pathogen among susceptible hosts has been extensively studied in eukaryotes. Even though bacteria have evolved multiple immune systems against their phage pathogens, herd immunity in bacteria remains unexplored. Here we experimentally demonstrate that herd immunity arises during phage epidemics in structured and unstructured Escherichia coli populations consisting of differing frequencies of susceptible and resistant cells harboring CRISPR immunity. In addition, we develop a mathematical model that quantifies how herd immunity is affected by spatial population structure, bacterial growth rate, and phage replication rate. Using our model we infer a general epidemiological rule describing the relative speed of an epidemic in partially resistant spatially structured populations. Our experimental and theoretical findings indicate that herd immunity may be important in bacterial communities, allowing for stable coexistence of bacteria and their phages and the maintenance of polymorphism in bacterial immunity.","lang":"eng"}],"oa_version":"Published Version","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.42n44"}],"oa":1,"month":"03"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Pull, Christopher, et al. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife, vol. 7, e32073, eLife Sciences Publications, 2018, doi:10.7554/eLife.32073.","ieee":"C. Pull et al., “Destructive disinfection of infected brood prevents systemic disease spread in ant colonies,” eLife, vol. 7. eLife Sciences Publications, 2018.","short":"C. Pull, L.V. Ugelvig, F. Wiesenhofer, A.V. Grasse, S. Tragust, T. Schmitt, M. Brown, S. Cremer, ELife 7 (2018).","apa":"Pull, C., Ugelvig, L. V., Wiesenhofer, F., Grasse, A. V., Tragust, S., Schmitt, T., … Cremer, S. (2018). Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.32073","ama":"Pull C, Ugelvig LV, Wiesenhofer F, et al. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 2018;7. doi:10.7554/eLife.32073","chicago":"Pull, Christopher, Line V Ugelvig, Florian Wiesenhofer, Anna V Grasse, Simon Tragust, Thomas Schmitt, Mark Brown, and Sylvia Cremer. “Destructive Disinfection of Infected Brood Prevents Systemic Disease Spread in Ant Colonies.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.32073.","ista":"Pull C, Ugelvig LV, Wiesenhofer F, Grasse AV, Tragust S, Schmitt T, Brown M, Cremer S. 2018. Destructive disinfection of infected brood prevents systemic disease spread in ant colonies. eLife. 7, e32073."},"title":"Destructive disinfection of infected brood prevents systemic disease spread in ant colonies","author":[{"id":"3C7F4840-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher","last_name":"Pull","orcid":"0000-0003-1122-3982","full_name":"Pull, Christopher"},{"first_name":"Line V","id":"3DC97C8E-F248-11E8-B48F-1D18A9856A87","last_name":"Ugelvig","orcid":"0000-0003-1832-8883","full_name":"Ugelvig, Line V"},{"first_name":"Florian","id":"39523C54-F248-11E8-B48F-1D18A9856A87","full_name":"Wiesenhofer, Florian","last_name":"Wiesenhofer"},{"full_name":"Grasse, Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"full_name":"Tragust, Simon","last_name":"Tragust","first_name":"Simon","id":"35A7A418-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Schmitt","full_name":"Schmitt, Thomas","first_name":"Thomas"},{"first_name":"Mark","full_name":"Brown, Mark","last_name":"Brown"},{"last_name":"Cremer","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"}],"publist_id":"7188","external_id":{"isi":["000419601300001"]},"article_processing_charge":"Yes","article_number":"e32073","project":[{"call_identifier":"FP7","_id":"25DC711C-B435-11E9-9278-68D0E5697425","name":"Social Vaccination in Ant Colonies: from Individual Mechanisms to Society Effects","grant_number":"243071"},{"_id":"25DDF0F0-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Pathogen Detectors Collective disease defence and pathogen detection abilities in ant societies: a chemo-neuro-immunological approach","grant_number":"302004"}],"day":"09","publication":"eLife","isi":1,"has_accepted_license":"1","year":"2018","doi":"10.7554/eLife.32073","date_published":"2018-01-09T00:00:00Z","date_created":"2018-12-11T11:47:31Z","quality_controlled":"1","publisher":"eLife Sciences Publications","oa":1,"ddc":["570","590"],"date_updated":"2023-09-11T12:54:26Z","file_date_updated":"2020-07-14T12:47:20Z","department":[{"_id":"SyCr"}],"_id":"616","status":"public","pubrep_id":"978","type":"journal_article","tmp":{"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)","short":"CC BY (4.0)"},"file":[{"file_id":"4832","checksum":"540f941e8d3530a9441e4affd94f07d7","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"IST-2018-978-v1+1_elife-32073-v1.pdf","date_created":"2018-12-12T10:10:43Z","file_size":1435585,"date_updated":"2020-07-14T12:47:20Z","creator":"system"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":7,"related_material":{"record":[{"relation":"dissertation_contains","id":"819","status":"public"}]},"ec_funded":1,"oa_version":"Published Version","abstract":[{"text":"Social insects protect their colonies from infectious disease through collective defences that result in social immunity. In ants, workers first try to prevent infection of colony members. Here, we show that if this fails and a pathogen establishes an infection, ants employ an efficient multicomponent behaviour − "destructive disinfection" − to prevent further spread of disease through the colony. Ants specifically target infected pupae during the pathogen's non-contagious incubation period, relying on chemical 'sickness cues' emitted by pupae. They then remove the pupal cocoon, perforate its cuticle and administer antimicrobial poison, which enters the body and prevents pathogen replication from the inside out. Like the immune system of a body that specifically targets and eliminates infected cells, this social immunity measure sacrifices infected brood to stop the pathogen completing its lifecycle, thus protecting the rest of the colony. Hence, the same principles of disease defence apply at different levels of biological organisation.","lang":"eng"}],"month":"01","intvolume":" 7","scopus_import":"1"},{"status":"public","type":"journal_article","article_type":"original","tmp":{"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)","short":"CC BY (4.0)"},"_id":"132","department":[{"_id":"EdHa"}],"file_date_updated":"2020-07-14T12:44:43Z","ddc":["570"],"date_updated":"2023-09-11T12:52:41Z","month":"08","intvolume":" 46","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Pancreas development involves a coordinated process in which an early phase of cell segregation is followed by a longer phase of lineage restriction, expansion, and tissue remodeling. By combining clonal tracing and whole-mount reconstruction with proliferation kinetics and single-cell transcriptional profiling, we define the functional basis of pancreas morphogenesis. We show that the large-scale organization of mouse pancreas can be traced to the activity of self-renewing precursors positioned at the termini of growing ducts, which act collectively to drive serial rounds of stochastic ductal bifurcation balanced by termination. During this phase of branching morphogenesis, multipotent precursors become progressively fate-restricted, giving rise to self-renewing acinar-committed precursors that are conveyed with growing ducts, as well as ductal progenitors that expand the trailing ducts and give rise to delaminating endocrine cells. These findings define quantitatively how the functional behavior and lineage progression of precursor pools determine the large-scale patterning of pancreatic sub-compartments.","lang":"eng"}],"issue":"3","volume":46,"file":[{"date_updated":"2020-07-14T12:44:43Z","file_size":8948384,"creator":"dernst","date_created":"2018-12-17T10:49:49Z","file_name":"2018_DevelopmentalCell_Sznurkowska.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"78d2062b9e3c3b90fe71545aeb6d2f65","file_id":"5694"}],"language":[{"iso":"eng"}],"publication_status":"published","title":"Defining lineage potential and fate behavior of precursors during pancreas development","author":[{"full_name":"Sznurkowska, Magdalena","last_name":"Sznurkowska","first_name":"Magdalena"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","first_name":"Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Azzarelli","full_name":"Azzarelli, Roberta","first_name":"Roberta"},{"first_name":"Steffen","full_name":"Rulands, Steffen","last_name":"Rulands"},{"first_name":"Sonia","full_name":"Nestorowa, Sonia","last_name":"Nestorowa"},{"last_name":"Hindley","full_name":"Hindley, Christopher","first_name":"Christopher"},{"last_name":"Nichols","full_name":"Nichols, Jennifer","first_name":"Jennifer"},{"full_name":"Göttgens, Berthold","last_name":"Göttgens","first_name":"Berthold"},{"last_name":"Huch","full_name":"Huch, Meritxell","first_name":"Meritxell"},{"last_name":"Philpott","full_name":"Philpott, Anna","first_name":"Anna"},{"full_name":"Simons, Benjamin","last_name":"Simons","first_name":"Benjamin"}],"publist_id":"7791","article_processing_charge":"No","external_id":{"isi":["000441327300012"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Sznurkowska, M., Hannezo, E. B., Azzarelli, R., Rulands, S., Nestorowa, S., Hindley, C., … Simons, B. (2018). Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.06.028","ama":"Sznurkowska M, Hannezo EB, Azzarelli R, et al. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 2018;46(3):360-375. doi:10.1016/j.devcel.2018.06.028","ieee":"M. Sznurkowska et al., “Defining lineage potential and fate behavior of precursors during pancreas development,” Developmental Cell, vol. 46, no. 3. Cell Press, pp. 360–375, 2018.","short":"M. Sznurkowska, E.B. Hannezo, R. Azzarelli, S. Rulands, S. Nestorowa, C. Hindley, J. Nichols, B. Göttgens, M. Huch, A. Philpott, B. Simons, Developmental Cell 46 (2018) 360–375.","mla":"Sznurkowska, Magdalena, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell, vol. 46, no. 3, Cell Press, 2018, pp. 360–75, doi:10.1016/j.devcel.2018.06.028.","ista":"Sznurkowska M, Hannezo EB, Azzarelli R, Rulands S, Nestorowa S, Hindley C, Nichols J, Göttgens B, Huch M, Philpott A, Simons B. 2018. Defining lineage potential and fate behavior of precursors during pancreas development. Developmental Cell. 46(3), 360–375.","chicago":"Sznurkowska, Magdalena, Edouard B Hannezo, Roberta Azzarelli, Steffen Rulands, Sonia Nestorowa, Christopher Hindley, Jennifer Nichols, et al. “Defining Lineage Potential and Fate Behavior of Precursors during Pancreas Development.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.06.028."},"quality_controlled":"1","publisher":"Cell Press","oa":1,"acknowledgement":"E.H. is funded by a Junior Research Fellowship from Trinity College, Cam-bridge, a Sir Henry Wellcome Fellowship from the Wellcome Trust, and theBettencourt-Schueller Young Researcher Prize for support.","doi":"10.1016/j.devcel.2018.06.028","date_published":"2018-08-06T00:00:00Z","date_created":"2018-12-11T11:44:48Z","page":"360 - 375","day":"06","publication":"Developmental Cell","isi":1,"has_accepted_license":"1","year":"2018"},{"ddc":["575"],"date_updated":"2023-09-11T12:52:03Z","department":[{"_id":"EvBe"}],"file_date_updated":"2020-07-14T12:46:25Z","_id":"42","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","language":[{"iso":"eng"}],"file":[{"file_name":"2018_JournalExperimBotany_Cucinotta.pdf","date_created":"2018-12-17T10:44:16Z","file_size":1292128,"date_updated":"2020-07-14T12:46:25Z","creator":"dernst","checksum":"ca3b6711040b1662488aeb3d1f961f13","file_id":"5691","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"publication_status":"published","volume":69,"issue":"21","oa_version":"Published Version","abstract":[{"text":"Seeds derive from ovules upon fertilization and therefore the total number of ovules determines the final seed yield, a fundamental trait in crop plants. Among the factors that co-ordinate the process of ovule formation, the transcription factors CUP-SHAPED COTYLEDON 1 (CUC1) and CUC2 and the hormone cytokinin (CK) have a particularly prominent role. Indeed, the absence of both CUC1 and CUC2 causes a severe reduction in ovule number, a phenotype that can be rescued by CK treatment. In this study, we combined CK quantification with an integrative genome-wide target identification approach to select Arabidopsis genes regulated by CUCs that are also involved in CK metabolism. We focused our attention on the functional characterization of UDP-GLUCOSYL TRANSFERASE 85A3 (UGT85A3) and UGT73C1, which are up-regulated in the absence of CUC1 and CUC2 and encode enzymes able to catalyse CK inactivation by O-glucosylation. Our results demonstrate a role for these UGTs as a link between CUCs and CK homeostasis, and highlight the importance of CUCs and CKs in the determination of seed yield.","lang":"eng"}],"intvolume":" 69","month":"07","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Cucinotta, Mara, Silvia Manrique, Candela Cuesta, Eva Benková, Ondřej Novák, and Lucia Colombo. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery281.","ista":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. 2018. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 69(21), 5169–5176.","mla":"Cucinotta, Mara, et al. “Cup-Shaped Cotyledon1 (CUC1) and CU2 Regulate Cytokinin Homeostasis to Determine Ovule Number in Arabidopsis.” Journal of Experimental Botany, vol. 69, no. 21, Oxford University Press, 2018, pp. 5169–76, doi:10.1093/jxb/ery281.","apa":"Cucinotta, M., Manrique, S., Cuesta, C., Benková, E., Novák, O., & Colombo, L. (2018). Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery281","ama":"Cucinotta M, Manrique S, Cuesta C, Benková E, Novák O, Colombo L. Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis. Journal of Experimental Botany. 2018;69(21):5169-5176. doi:10.1093/jxb/ery281","short":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, L. Colombo, Journal of Experimental Botany 69 (2018) 5169–5176.","ieee":"M. Cucinotta, S. Manrique, C. Cuesta, E. Benková, O. Novák, and L. Colombo, “Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis,” Journal of Experimental Botany, vol. 69, no. 21. Oxford University Press, pp. 5169–5176, 2018."},"title":"Cup-shaped Cotyledon1 (CUC1) and CU2 regulate cytokinin homeostasis to determine ovule number in arabidopsis","article_processing_charge":"No","external_id":{"isi":["000448163900015"]},"author":[{"first_name":"Mara","last_name":"Cucinotta","full_name":"Cucinotta, Mara"},{"first_name":"Silvia","full_name":"Manrique, Silvia","last_name":"Manrique"},{"last_name":"Cuesta","full_name":"Cuesta, Candela","orcid":"0000-0003-1923-2410","first_name":"Candela","id":"33A3C818-F248-11E8-B48F-1D18A9856A87"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"},{"last_name":"Novák","full_name":"Novák, Ondřej","first_name":"Ondřej"},{"first_name":"Lucia","full_name":"Colombo, Lucia","last_name":"Colombo"}],"publist_id":"8012","publication":"Journal of Experimental Botany","day":"26","year":"2018","has_accepted_license":"1","isi":1,"date_created":"2018-12-11T11:44:19Z","doi":"10.1093/jxb/ery281","date_published":"2018-07-26T00:00:00Z","page":"5169 - 5176","acknowledgement":"This work was funded by the Ministry of Education, Youth and Sports of the Czech Republic through the National Program of Sustainability (grant no. LO1204).","oa":1,"publisher":"Oxford University Press","quality_controlled":"1"},{"doi":"10.1103/PhysRevB.98.161122","date_published":"2018-10-15T00:00:00Z","date_created":"2018-12-11T11:44:20Z","day":"15","publication":"Physical Review B","isi":1,"year":"2018","quality_controlled":"1","publisher":"American Physical Society","oa":1,"acknowledgement":"F.P. acknowledges the sup- port of the DFG Research Unit FOR 1807 through Grants No. PO 1370/2-1 and No. TRR80, the Nanosystems Initiative Munich (NIM) by the German Excellence Initiative, and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 771537). N.Y.Y. acknowledges support from the NSF (PHY-1654740), the ARO STIR program, and a Google research award.","title":"Detection and characterization of many-body localization in central spin models","author":[{"last_name":"Hetterich","full_name":"Hetterich, Daniel","first_name":"Daniel"},{"first_name":"Norman","last_name":"Yao","full_name":"Yao, Norman"},{"last_name":"Serbyn","full_name":"Serbyn, Maksym","orcid":"0000-0002-2399-5827","first_name":"Maksym","id":"47809E7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Frank","full_name":"Pollmann, Frank","last_name":"Pollmann"},{"first_name":"Björn","full_name":"Trauzettel, Björn","last_name":"Trauzettel"}],"publist_id":"8008","article_processing_charge":"No","external_id":{"arxiv":["1806.08316"],"isi":["000448596500002"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. 2018. Detection and characterization of many-body localization in central spin models. Physical Review B. 98(16), 161122.","chicago":"Hetterich, Daniel, Norman Yao, Maksym Serbyn, Frank Pollmann, and Björn Trauzettel. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.98.161122.","ieee":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, and B. Trauzettel, “Detection and characterization of many-body localization in central spin models,” Physical Review B, vol. 98, no. 16. American Physical Society, 2018.","short":"D. Hetterich, N. Yao, M. Serbyn, F. Pollmann, B. Trauzettel, Physical Review B 98 (2018).","apa":"Hetterich, D., Yao, N., Serbyn, M., Pollmann, F., & Trauzettel, B. (2018). Detection and characterization of many-body localization in central spin models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.98.161122","ama":"Hetterich D, Yao N, Serbyn M, Pollmann F, Trauzettel B. Detection and characterization of many-body localization in central spin models. Physical Review B. 2018;98(16). doi:10.1103/PhysRevB.98.161122","mla":"Hetterich, Daniel, et al. “Detection and Characterization of Many-Body Localization in Central Spin Models.” Physical Review B, vol. 98, no. 16, 161122, American Physical Society, 2018, doi:10.1103/PhysRevB.98.161122."},"article_number":"161122","issue":"16","volume":98,"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 98","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.08316"}],"oa_version":"Preprint","abstract":[{"text":"We analyze a disordered central spin model, where a central spin interacts equally with each spin in a periodic one-dimensional (1D) random-field Heisenberg chain. If the Heisenberg chain is initially in the many-body localized (MBL) phase, we find that the coupling to the central spin suffices to delocalize the chain for a substantial range of coupling strengths. We calculate the phase diagram of the model and identify the phase boundary between the MBL and ergodic phase. Within the localized phase, the central spin significantly enhances the rate of the logarithmic entanglement growth and its saturation value. We attribute the increase in entanglement entropy to a nonextensive enhancement of magnetization fluctuations induced by the central spin. Finally, we demonstrate that correlation functions of the central spin can be utilized to distinguish between MBL and ergodic phases of the 1D chain. Hence, we propose the use of a central spin as a possible experimental probe to identify the MBL phase.","lang":"eng"}],"department":[{"_id":"MaSe"}],"date_updated":"2023-09-11T12:55:03Z","status":"public","type":"journal_article","article_type":"original","_id":"46"},{"publication_status":"published","language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/cells-change-tension-to-make-tissue-barriers-easier-to-get-through/","relation":"press_release","description":"News on IST Homepage"}]},"volume":45,"issue":"3","ec_funded":1,"abstract":[{"lang":"eng","text":"Migrating cells penetrate tissue barriers during development, inflammatory responses, and tumor metastasis. We study if migration in vivo in such three-dimensionally confined environments requires changes in the mechanical properties of the surrounding cells using embryonic Drosophila melanogaster hemocytes, also called macrophages, as a model. We find that macrophage invasion into the germband through transient separation of the apposing ectoderm and mesoderm requires cell deformations and reductions in apical tension in the ectoderm. Interestingly, the genetic pathway governing these mechanical shifts acts downstream of the only known tumor necrosis factor superfamily member in Drosophila, Eiger, and its receptor, Grindelwald. Eiger-Grindelwald signaling reduces levels of active Myosin in the germband ectodermal cortex through the localization of a Crumbs complex component, Patj (Pals-1-associated tight junction protein). We therefore elucidate a distinct molecular pathway that controls tissue tension and demonstrate the importance of such regulation for invasive migration in vivo."}],"acknowledged_ssus":[{"_id":"SSU"}],"oa_version":"Published Version","pmid":1,"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.devcel.2018.04.002"}],"month":"05","intvolume":" 45","date_updated":"2023-09-11T13:22:13Z","department":[{"_id":"DaSi"},{"_id":"CaHe"},{"_id":"Bio"},{"_id":"EM-Fac"},{"_id":"MiSi"}],"_id":"308","type":"journal_article","article_type":"original","status":"public","isi":1,"year":"2018","day":"07","publication":"Developmental Cell","page":"331 - 346","date_published":"2018-05-07T00:00:00Z","doi":"10.1016/j.devcel.2018.04.002","date_created":"2018-12-11T11:45:44Z","publisher":"Elsevier","quality_controlled":"1","oa":1,"citation":{"mla":"Ratheesh, Aparna, et al. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell, vol. 45, no. 3, Elsevier, 2018, pp. 331–46, doi:10.1016/j.devcel.2018.04.002.","ama":"Ratheesh A, Bicher J, Smutny M, et al. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 2018;45(3):331-346. doi:10.1016/j.devcel.2018.04.002","apa":"Ratheesh, A., Bicher, J., Smutny, M., Veselá, J., Papusheva, E., Krens, G., … Siekhaus, D. E. (2018). Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2018.04.002","ieee":"A. Ratheesh et al., “Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration,” Developmental Cell, vol. 45, no. 3. Elsevier, pp. 331–346, 2018.","short":"A. Ratheesh, J. Bicher, M. Smutny, J. Veselá, E. Papusheva, G. Krens, W. Kaufmann, A. György, A.M. Casano, D.E. Siekhaus, Developmental Cell 45 (2018) 331–346.","chicago":"Ratheesh, Aparna, Julia Bicher, Michael Smutny, Jana Veselá, Ekaterina Papusheva, Gabriel Krens, Walter Kaufmann, Attila György, Alessandra M Casano, and Daria E Siekhaus. “Drosophila TNF Modulates Tissue Tension in the Embryo to Facilitate Macrophage Invasive Migration.” Developmental Cell. Elsevier, 2018. https://doi.org/10.1016/j.devcel.2018.04.002.","ista":"Ratheesh A, Bicher J, Smutny M, Veselá J, Papusheva E, Krens G, Kaufmann W, György A, Casano AM, Siekhaus DE. 2018. Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration. Developmental Cell. 45(3), 331–346."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"orcid":"0000-0001-7190-0776","full_name":"Ratheesh, Aparna","last_name":"Ratheesh","id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","first_name":"Aparna"},{"full_name":"Biebl, Julia","last_name":"Biebl","first_name":"Julia","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Michael","last_name":"Smutny","full_name":"Smutny, Michael"},{"id":"433253EE-F248-11E8-B48F-1D18A9856A87","first_name":"Jana","last_name":"Veselá","full_name":"Veselá, Jana"},{"id":"41DB591E-F248-11E8-B48F-1D18A9856A87","first_name":"Ekaterina","last_name":"Papusheva","full_name":"Papusheva, Ekaterina"},{"first_name":"Gabriel","id":"2B819732-F248-11E8-B48F-1D18A9856A87","full_name":"Krens, Gabriel","orcid":"0000-0003-4761-5996","last_name":"Krens"},{"full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","first_name":"Walter"},{"id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","first_name":"Attila","full_name":"György, Attila","orcid":"0000-0002-1819-198X","last_name":"György"},{"orcid":"0000-0002-6009-6804","full_name":"Casano, Alessandra M","last_name":"Casano","first_name":"Alessandra M","id":"3DBA3F4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Siekhaus","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E","first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"isi":["000432461400009"],"pmid":["29738712"]},"article_processing_charge":"No","title":"Drosophila TNF modulates tissue tension in the embryo to facilitate macrophage invasive migration","project":[{"grant_number":"P29638","name":"Drosophila TNFa´s Funktion in Immunzellen","_id":"253B6E48-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"name":"Investigating the role of transporters in invasive migration through junctions","grant_number":"334077","_id":"2536F660-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"title":"Drag enhancement and drag reduction in viscoelastic flow","publist_id":"8038","author":[{"id":"2A2006B2-F248-11E8-B48F-1D18A9856A87","first_name":"Atul","last_name":"Varshney","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999"},{"first_name":"Victor","last_name":"Steinberg","full_name":"Steinberg, Victor"}],"article_processing_charge":"No","external_id":{"isi":["000447311500001"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302.","chicago":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103302.","apa":"Varshney, A., & Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103302","ama":"Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103302","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","ieee":"A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018.","mla":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103302."},"project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships"}],"article_number":"103302 ","date_published":"2018-10-15T00:00:00Z","doi":"10.1103/PhysRevFluids.3.103302","date_created":"2018-12-11T11:44:11Z","day":"15","publication":"Physical Review Fluids","isi":1,"has_accepted_license":"1","year":"2018","publisher":"American Physical Society","quality_controlled":"1","oa":1,"file_date_updated":"2020-07-14T12:45:12Z","department":[{"_id":"BjHo"}],"ddc":["532"],"date_updated":"2023-09-11T12:59:28Z","status":"public","pubrep_id":"1061","type":"journal_article","_id":"17","volume":3,"issue":"10","ec_funded":1,"file":[{"file_id":"4800","checksum":"e1445be33e8165114e96246275600750","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2018-12-12T10:10:14Z","file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf","creator":"system","date_updated":"2020-07-14T12:45:12Z","file_size":1409040}],"language":[{"iso":"eng"}],"publication_status":"published","month":"10","intvolume":" 3","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow.","lang":"eng"}]},{"abstract":[{"text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.","lang":"eng"}],"oa_version":"Preprint","pmid":1,"main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/09/21/192039","open_access":"1"}],"scopus_import":"1","intvolume":" 115","month":"06","publication_status":"published","language":[{"iso":"eng"}],"volume":115,"issue":"23","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"6473"}]},"_id":"281","article_type":"original","type":"journal_article","status":"public","date_updated":"2023-09-11T12:58:24Z","department":[{"_id":"GaTk"}],"acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","year":"2018","isi":1,"publication":"PNAS","day":"05","page":"6088 - 6093","date_created":"2018-12-11T11:45:35Z","date_published":"2018-06-05T00:00:00Z","doi":"10.1073/pnas.1716659115","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"citation":{"chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1716659115.","ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.","apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., & Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1716659115","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. PNAS. 2018;115(23):6088-6093. doi:10.1073/pnas.1716659115","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.","ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” PNAS, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"pmid":["29784812"],"isi":["000434114900071"]},"publist_id":"7618","author":[{"first_name":"Alejandro","full_name":"Granados, Alejandro","last_name":"Granados"},{"last_name":"Pietsch","full_name":"Pietsch, Julian","first_name":"Julian"},{"first_name":"Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","last_name":"Cepeda Humerez","full_name":"Cepeda Humerez, Sarah A"},{"last_name":"Farquhar","full_name":"Farquhar, Isebail","first_name":"Isebail"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper","orcid":"0000-0002-6699-1455"},{"first_name":"Peter","last_name":"Swain","full_name":"Swain, Peter"}],"title":"Distributed and dynamic intracellular organization of extracellular information"},{"type":"journal_article","status":"public","_id":"620","department":[{"_id":"DaSi"}],"date_updated":"2023-09-11T12:57:13Z","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/29192062"}],"month":"01","intvolume":" 131","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis requires the coordinated assembly of various endocytic proteins and lipids at the plasma membrane. Accumulating evidence demonstrates a crucial role for phosphatidylinositol-4,5-bisphosphate (PtdIns(4,5)P2) in endocytosis, but specific roles for PtdIns(4)P other than as the biosynthetic precursor of PtdIns(4,5)P2 have not been clarified. In this study we investigated the role of PtdIns(4)P or PtdIns(4,5)P2 in receptor-mediated endocytosis through the construction of temperature-sensitive (ts) mutants for the PI 4-kinases Stt4p and Pik1p and the PtdIns(4) 5-kinase Mss4p. Quantitative analyses of endocytosis revealed that both the stt4(ts)pik1(ts) and mss4(ts) mutants have a severe defect in endocytic internalization. Live-cell imaging of endocytic protein dynamics in stt4(ts)pik1(ts) and mss4(ts) mutants revealed that PtdIns(4)P is required for the recruitment of the alpha-factor receptor Ste2p to clathrin-coated pits whereas PtdIns(4,5)P2 is required for membrane internalization. We also found that the localization to endocytic sites of the ENTH/ANTH domain-bearing clathrin adaptors, Ent1p/Ent2p and Yap1801p/Yap1802p, is significantly impaired in the stt4(ts)pik1(ts) mutant, but not in the mss4(ts) mutant. These results suggest distinct roles in successive steps for PtdIns(4)P and PtdIns(4,5)P2 during receptor-mediated endocytosis."}],"oa_version":"Published Version","pmid":1,"issue":"1","volume":131,"publication_status":"published","language":[{"iso":"eng"}],"article_number":"jcs207696","publist_id":"7184","author":[{"first_name":"Wataru","full_name":"Yamamoto, Wataru","last_name":"Yamamoto"},{"first_name":"Suguru","full_name":"Wada, Suguru","last_name":"Wada"},{"last_name":"Nagano","full_name":"Nagano, Makoto","first_name":"Makoto"},{"first_name":"Kaito","full_name":"Aoshima, Kaito","last_name":"Aoshima"},{"first_name":"Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","orcid":"0000-0001-8323-8353"},{"first_name":"Junko","last_name":"Toshima","full_name":"Toshima, Junko"},{"first_name":"Jiro","full_name":"Toshima, Jiro","last_name":"Toshima"}],"external_id":{"pmid":["29192062"],"isi":["000424786900012"]},"article_processing_charge":"No","title":"Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis","citation":{"mla":"Yamamoto, Wataru, et al. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science, vol. 131, no. 1, jcs207696, Company of Biologists, 2018, doi:10.1242/jcs.207696.","apa":"Yamamoto, W., Wada, S., Nagano, M., Aoshima, K., Siekhaus, D. E., Toshima, J., & Toshima, J. (2018). Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.207696","ama":"Yamamoto W, Wada S, Nagano M, et al. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 2018;131(1). doi:10.1242/jcs.207696","short":"W. Yamamoto, S. Wada, M. Nagano, K. Aoshima, D.E. Siekhaus, J. Toshima, J. Toshima, Journal of Cell Science 131 (2018).","ieee":"W. Yamamoto et al., “Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis,” Journal of Cell Science, vol. 131, no. 1. Company of Biologists, 2018.","chicago":"Yamamoto, Wataru, Suguru Wada, Makoto Nagano, Kaito Aoshima, Daria E Siekhaus, Junko Toshima, and Jiro Toshima. “Distinct Roles for Plasma Membrane PtdIns 4 P and PtdIns 4 5 P2 during Yeast Receptor Mediated Endocytosis.” Journal of Cell Science. Company of Biologists, 2018. https://doi.org/10.1242/jcs.207696.","ista":"Yamamoto W, Wada S, Nagano M, Aoshima K, Siekhaus DE, Toshima J, Toshima J. 2018. Distinct roles for plasma membrane PtdIns 4 P and PtdIns 4 5 P2 during yeast receptor mediated endocytosis. Journal of Cell Science. 131(1), jcs207696."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","publisher":"Company of Biologists","oa":1,"date_published":"2018-01-04T00:00:00Z","doi":"10.1242/jcs.207696","date_created":"2018-12-11T11:47:32Z","isi":1,"year":"2018","day":"04","publication":"Journal of Cell Science"},{"oa":1,"quality_controlled":"1","publisher":"ACM","page":"177 - 186","date_created":"2018-12-11T11:45:04Z","doi":"10.1145/3178126.3178132","date_published":"2018-04-11T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"Proceedings of the 21st International Conference on Hybrid Systems","day":"11","project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"article_processing_charge":"No","external_id":{"isi":["000474781600020"]},"author":[{"first_name":"Alexey","last_name":"Bakhirkin","full_name":"Bakhirkin, Alexey"},{"orcid":"0000-0001-5199-3143","full_name":"Ferrere, Thomas","last_name":"Ferrere","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"full_name":"Maler, Oded","last_name":"Maler","first_name":"Oded"}],"publist_id":"7739","title":"Efficient parametric identification for STL","citation":{"mla":"Bakhirkin, Alexey, et al. “Efficient Parametric Identification for STL.” Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–86, doi:10.1145/3178126.3178132.","ama":"Bakhirkin A, Ferrere T, Maler O. Efficient parametric identification for STL. In: Proceedings of the 21st International Conference on Hybrid Systems. ACM; 2018:177-186. doi:10.1145/3178126.3178132","apa":"Bakhirkin, A., Ferrere, T., & Maler, O. (2018). Efficient parametric identification for STL. In Proceedings of the 21st International Conference on Hybrid Systems (pp. 177–186). Porto, Portugal: ACM. https://doi.org/10.1145/3178126.3178132","short":"A. Bakhirkin, T. Ferrere, O. Maler, in:, Proceedings of the 21st International Conference on Hybrid Systems, ACM, 2018, pp. 177–186.","ieee":"A. Bakhirkin, T. Ferrere, and O. Maler, “Efficient parametric identification for STL,” in Proceedings of the 21st International Conference on Hybrid Systems, Porto, Portugal, 2018, pp. 177–186.","chicago":"Bakhirkin, Alexey, Thomas Ferrere, and Oded Maler. “Efficient Parametric Identification for STL.” In Proceedings of the 21st International Conference on Hybrid Systems, 177–86. ACM, 2018. https://doi.org/10.1145/3178126.3178132.","ista":"Bakhirkin A, Ferrere T, Maler O. 2018. Efficient parametric identification for STL. Proceedings of the 21st International Conference on Hybrid Systems. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 177–186."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","alternative_title":["HSCC Proceedings"],"scopus_import":"1","month":"04","abstract":[{"text":"We describe a new algorithm for the parametric identification problem for signal temporal logic (STL), stated as follows. Given a densetime real-valued signal w and a parameterized temporal logic formula φ, compute the subset of the parameter space that renders the formula satisfied by the signal. Unlike previous solutions, which were based on search in the parameter space or quantifier elimination, our procedure works recursively on φ and computes the evolution over time of the set of valid parameter assignments. This procedure is similar to that of monitoring or computing the robustness of φ relative to w. Our implementation and experiments demonstrate that this approach can work well in practice.","lang":"eng"}],"oa_version":"Submitted Version","publication_status":"published","publication_identifier":{"isbn":["978-1-4503-5642-8 "]},"language":[{"iso":"eng"}],"file":[{"checksum":"81eabc96430e84336ea88310ac0a1ad0","file_id":"7833","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2020-05-14T12:18:29Z","file_name":"2018_HSCC_Bakhirkin.pdf","date_updated":"2020-07-14T12:45:17Z","file_size":5900421,"creator":"dernst"}],"conference":{"name":"HSCC: Hybrid Systems: Computation and Control","end_date":"2018-04-13","location":"Porto, Portugal","start_date":"2018-04-11"},"type":"conference","status":"public","_id":"182","file_date_updated":"2020-07-14T12:45:17Z","department":[{"_id":"ToHe"}],"date_updated":"2023-09-11T13:30:51Z","ddc":["000"]},{"conference":{"name":"LICS: Logic in Computer Science","start_date":"2018-07-09","location":"Oxford, United Kingdom","end_date":"2018-07-12"},"type":"conference","status":"public","_id":"143","department":[{"_id":"KrCh"}],"date_updated":"2023-09-11T13:23:42Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.10985"}],"scopus_import":"1","alternative_title":["ACM/IEEE Symposium on Logic in Computer Science"],"month":"07","abstract":[{"text":"Vector Addition Systems with States (VASS) provide a well-known and fundamental model for the analysis of concurrent processes, parameterized systems, and are also used as abstract models of programs in resource bound analysis. In this paper we study the problem of obtaining asymptotic bounds on the termination time of a given VASS. In particular, we focus on the practically important case of obtaining polynomial bounds on termination time. Our main contributions are as follows: First, we present a polynomial-time algorithm for deciding whether a given VASS has a linear asymptotic complexity. We also show that if the complexity of a VASS is not linear, it is at least quadratic. Second, we classify VASS according to quantitative properties of their cycles. We show that certain singularities in these properties are the key reason for non-polynomial asymptotic complexity of VASS. In absence of singularities, we show that the asymptotic complexity is always polynomial and of the form Θ(nk), for some integer k d, where d is the dimension of the VASS. We present a polynomial-time algorithm computing the optimal k. For general VASS, the same algorithm, which is based on a complete technique for the construction of ranking functions in VASS, produces a valid lower bound, i.e., a k such that the termination complexity is (nk). Our results are based on new insights into the geometry of VASS dynamics, which hold the potential for further applicability to VASS analysis.","lang":"eng"}],"oa_version":"Preprint","ec_funded":1,"volume":"F138033","publication_status":"published","publication_identifier":{"isbn":["978-1-4503-5583-4"]},"language":[{"iso":"eng"}],"project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"external_id":{"isi":["000545262800020"]},"article_processing_charge":"No","publist_id":"7780","author":[{"first_name":"Tomáš","last_name":"Brázdil","full_name":"Brázdil, Tomáš"},{"last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"full_name":"Kučera, Antonín","last_name":"Kučera","first_name":"Antonín"},{"first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","full_name":"Novotny, Petr"},{"first_name":"Dominik","full_name":"Velan, Dominik","last_name":"Velan"},{"last_name":"Zuleger","full_name":"Zuleger, Florian","first_name":"Florian"}],"title":"Efficient algorithms for asymptotic bounds on termination time in VASS","citation":{"chicago":"Brázdil, Tomáš, Krishnendu Chatterjee, Antonín Kučera, Petr Novotný, Dominik Velan, and Florian Zuleger. “Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS,” F138033:185–94. IEEE, 2018. https://doi.org/10.1145/3209108.3209191.","ista":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. 2018. Efficient algorithms for asymptotic bounds on termination time in VASS. LICS: Logic in Computer Science, ACM/IEEE Symposium on Logic in Computer Science, vol. F138033, 185–194.","mla":"Brázdil, Tomáš, et al. Efficient Algorithms for Asymptotic Bounds on Termination Time in VASS. Vol. F138033, IEEE, 2018, pp. 185–94, doi:10.1145/3209108.3209191.","ieee":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, and F. Zuleger, “Efficient algorithms for asymptotic bounds on termination time in VASS,” presented at the LICS: Logic in Computer Science, Oxford, United Kingdom, 2018, vol. F138033, pp. 185–194.","short":"T. Brázdil, K. Chatterjee, A. Kučera, P. Novotný, D. Velan, F. Zuleger, in:, IEEE, 2018, pp. 185–194.","ama":"Brázdil T, Chatterjee K, Kučera A, Novotný P, Velan D, Zuleger F. Efficient algorithms for asymptotic bounds on termination time in VASS. In: Vol F138033. IEEE; 2018:185-194. doi:10.1145/3209108.3209191","apa":"Brázdil, T., Chatterjee, K., Kučera, A., Novotný, P., Velan, D., & Zuleger, F. (2018). Efficient algorithms for asymptotic bounds on termination time in VASS (Vol. F138033, pp. 185–194). Presented at the LICS: Logic in Computer Science, Oxford, United Kingdom: IEEE. https://doi.org/10.1145/3209108.3209191"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"publisher":"IEEE","quality_controlled":"1","page":"185 - 194","date_created":"2018-12-11T11:44:51Z","doi":"10.1145/3209108.3209191","date_published":"2018-07-09T00:00:00Z","year":"2018","isi":1,"day":"09"},{"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:3693-3701. doi:10.1109/cvpr.2018.00389","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., & Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. https://doi.org/10.1109/cvpr.2018.00389","ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, USA, 2018, pp. 3693–3701.","short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701.","mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–701, doi:10.1109/cvpr.2018.00389.","ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 3693–3701. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00389."},"title":"Efficient optimization for rank-based loss functions","external_id":{"arxiv":["1604.08269"],"isi":["000457843603087"]},"article_processing_charge":"No","author":[{"first_name":"Pritish","full_name":"Mohapatra, Pritish","last_name":"Mohapatra"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","first_name":"Michal","full_name":"Rolinek, Michal","last_name":"Rolinek"},{"first_name":"C V","full_name":"Jawahar, C V","last_name":"Jawahar"},{"last_name":"Kolmogorov","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir"},{"first_name":"M Pawan","full_name":"Kumar, M Pawan","last_name":"Kumar"}],"oa":1,"quality_controlled":"1","publisher":"IEEE","publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","day":"28","year":"2018","isi":1,"date_created":"2018-12-11T11:45:33Z","date_published":"2018-06-28T00:00:00Z","doi":"10.1109/cvpr.2018.00389","page":"3693-3701","_id":"273","status":"public","conference":{"location":"Salt Lake City, UT, USA","end_date":"2018-06-22","start_date":"2018-06-18","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"type":"conference","date_updated":"2023-09-11T13:24:43Z","department":[{"_id":"VlKo"}],"oa_version":"Preprint","abstract":[{"lang":"eng","text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time."}],"month":"06","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08269"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["9781538664209"]},"ec_funded":1},{"publisher":"American Physical Society","quality_controlled":"1","oa":1,"acknowledgement":"The experimental work at UCSB was funded by the National Science Foundation under Grant No. DMR- 1654186. Work at Columbia was supported by the National Science Foundation under Grant No. DMR- 1507788. K. W. and T. T. acknowledge support from the Elemental Strategy Initiative conducted by the Ministry of Education, Culture, Sports, Science and Technology, Japan, and the Japan Society for the Promotion of Science KAKENHI Grant No. JP15K21722. E. M. S. acknowledges the support of the Elings Fellowship from the California Nanosystems Institute at the University of California, Santa Barbara. A. F. Y. acknowledges the support of the David and Lucile Packard foundation and the Sloan Foundation. Measurements made use of a dilution refrigerator funded through the Major Research Instrumentation program of the U.S. National Science Foundation under Grant No. DMR- 1531389, and the MRL Shared Experimental Facilities, which are supported by the MRSEC Program of the U.S. National Science Foundation under Grant No. DMR- 1720256.","date_published":"2018-10-19T00:00:00Z","doi":"10.1103/PhysRevLett.121.167601","date_created":"2018-12-11T11:45:38Z","day":"19","publication":"Physical Review Letters","isi":1,"year":"2018","article_number":"167601","title":"Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene","author":[{"last_name":"Zibrov","full_name":"Zibrov, Alexander","first_name":"Alexander"},{"first_name":"Rao","id":"47C23AC6-02D0-11E9-BD0E-99399A5D3DEB","last_name":"Peng","orcid":"0000-0003-1250-0021","full_name":"Peng, Rao"},{"last_name":"Kometter","full_name":"Kometter, Carlos","first_name":"Carlos"},{"full_name":"Li, Jia","last_name":"Li","first_name":"Jia"},{"full_name":"Dean, Cory","last_name":"Dean","first_name":"Cory"},{"first_name":"Takashi","full_name":"Taniguchi, Takashi","last_name":"Taniguchi"},{"first_name":"Kenji","last_name":"Watanabe","full_name":"Watanabe, Kenji"},{"orcid":"0000-0002-2399-5827","full_name":"Serbyn, Maksym","last_name":"Serbyn","id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym"},{"first_name":"Andrea","last_name":"Young","full_name":"Young, Andrea"}],"external_id":{"isi":["000447307500007"],"arxiv":["1805.01038"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"chicago":"Zibrov, Alexander, Peng Rao, Carlos Kometter, Jia Li, Cory Dean, Takashi Taniguchi, Kenji Watanabe, Maksym Serbyn, and Andrea Young. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.167601.","ista":"Zibrov A, Rao P, Kometter C, Li J, Dean C, Taniguchi T, Watanabe K, Serbyn M, Young A. 2018. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 121(16), 167601.","mla":"Zibrov, Alexander, et al. “Emergent Dirac Gullies and Gully-Symmetry-Breaking Quantum Hall States in ABA Trilayer Graphene.” Physical Review Letters, vol. 121, no. 16, 167601, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.167601.","apa":"Zibrov, A., Rao, P., Kometter, C., Li, J., Dean, C., Taniguchi, T., … Young, A. (2018). Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.167601","ama":"Zibrov A, Rao P, Kometter C, et al. Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene. Physical Review Letters. 2018;121(16). doi:10.1103/PhysRevLett.121.167601","short":"A. Zibrov, P. Rao, C. Kometter, J. Li, C. Dean, T. Taniguchi, K. Watanabe, M. Serbyn, A. Young, Physical Review Letters 121 (2018).","ieee":"A. Zibrov et al., “Emergent dirac gullies and gully-symmetry-breaking quantum hall states in ABA trilayer graphene,” Physical Review Letters, vol. 121, no. 16. American Physical Society, 2018."},"month":"10","intvolume":" 121","scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1805.01038","open_access":"1"}],"oa_version":"Preprint","abstract":[{"text":"We report on quantum capacitance measurements of high quality, graphite- and hexagonal boron nitride encapsulated Bernal stacked trilayer graphene devices. At zero applied magnetic field, we observe a number of electron density- and electrical displacement-tuned features in the electronic compressibility associated with changes in Fermi surface topology. At high displacement field and low density, strong trigonal warping gives rise to emergent Dirac gullies centered near the corners of the hexagonal Brillouin and related by three fold rotation symmetry. At low magnetic fields of B=1.25~T, the gullies manifest as a change in the degeneracy of the Landau levels from two to three. Weak incompressible states are also observed at integer filling within these triplets Landau levels, which a Hartree-Fock analysis indicates are associated with Coulomb-driven nematic phases that spontaneously break rotation symmetry.","lang":"eng"}],"issue":"16","volume":121,"language":[{"iso":"eng"}],"publication_status":"published","status":"public","article_type":"original","type":"journal_article","_id":"289","department":[{"_id":"MaSe"}],"date_updated":"2023-09-11T13:39:50Z"},{"project":[{"call_identifier":"H2020","_id":"258047B6-B435-11E9-9278-68D0E5697425","name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM","grant_number":"707438"}],"title":"Electromagnetic fields and optomechanics In cancer diagnostics and treatment","author":[{"first_name":"Vahid","full_name":"Salari, Vahid","last_name":"Salari"},{"id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","first_name":"Shabir","last_name":"Barzanjeh","orcid":"0000-0003-0415-1423","full_name":"Barzanjeh, Shabir"},{"full_name":"Cifra, Michal","last_name":"Cifra","first_name":"Michal"},{"first_name":"Christoph","full_name":"Simon, Christoph","last_name":"Simon"},{"full_name":"Scholkmann, Felix","last_name":"Scholkmann","first_name":"Felix"},{"first_name":"Zahra","last_name":"Alirezaei","full_name":"Alirezaei, Zahra"},{"first_name":"Jack","last_name":"Tuszynski","full_name":"Tuszynski, Jack"}],"external_id":{"isi":["000439042800001"],"pmid":["29293441"]},"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Salari, Vahid, et al. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark, vol. 23, no. 8, Frontiers in Bioscience, 2018, pp. 1391–406, doi:10.2741/4651.","short":"V. Salari, S. Barzanjeh, M. Cifra, C. Simon, F. Scholkmann, Z. Alirezaei, J. Tuszynski, Frontiers in Bioscience - Landmark 23 (2018) 1391–1406.","ieee":"V. Salari et al., “Electromagnetic fields and optomechanics In cancer diagnostics and treatment,” Frontiers in Bioscience - Landmark, vol. 23, no. 8. Frontiers in Bioscience, pp. 1391–1406, 2018.","ama":"Salari V, Barzanjeh S, Cifra M, et al. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 2018;23(8):1391-1406. doi:10.2741/4651","apa":"Salari, V., Barzanjeh, S., Cifra, M., Simon, C., Scholkmann, F., Alirezaei, Z., & Tuszynski, J. (2018). Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. Frontiers in Bioscience. https://doi.org/10.2741/4651","chicago":"Salari, Vahid, Shabir Barzanjeh, Michal Cifra, Christoph Simon, Felix Scholkmann, Zahra Alirezaei, and Jack Tuszynski. “Electromagnetic Fields and Optomechanics In Cancer Diagnostics and Treatment.” Frontiers in Bioscience - Landmark. Frontiers in Bioscience, 2018. https://doi.org/10.2741/4651.","ista":"Salari V, Barzanjeh S, Cifra M, Simon C, Scholkmann F, Alirezaei Z, Tuszynski J. 2018. Electromagnetic fields and optomechanics In cancer diagnostics and treatment. Frontiers in Bioscience - Landmark. 23(8), 1391–1406."},"quality_controlled":"1","publisher":"Frontiers in Bioscience","oa":1,"acknowledgement":"The work of SB has been supported by the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska Curie grant agreement No MSC-IF 707438 SUPEREOM. JAT gratefully acknowledges funding support from NSERC (Canada) for his research. MC acknowledges support from the Czech Science Foundation, projects 15-17102S and 17-11898S and he participates in COST Action BM1309, CA15211 and bilateral exchange project between Czech and Slovak Academies of Sciences, SAV-15-22.","doi":"10.2741/4651","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:45:37Z","page":"1391 - 1406","day":"01","publication":"Frontiers in Bioscience - Landmark","isi":1,"year":"2018","status":"public","type":"journal_article","_id":"287","department":[{"_id":"JoFi"}],"date_updated":"2023-09-11T13:38:14Z","month":"03","intvolume":" 23","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.bioscience.org/2018/v23/af/4651/fulltext.htm"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"text":"In this paper, we discuss biological effects of electromagnetic (EM) fields in the context of cancer biology. In particular, we review the nanomechanical properties of microtubules (MTs), the latter being one of the most successful targets for cancer therapy. We propose an investigation on the coupling of electromagnetic radiation to mechanical vibrations of MTs as an important basis for biological and medical applications. In our opinion, optomechanical methods can accurately monitor and control the mechanical properties of isolated MTs in a liquid environment. Consequently, studying nanomechanical properties of MTs may give useful information for future applications to diagnostic and therapeutic technologies involving non-invasive externally applied physical fields. For example, electromagnetic fields or high intensity ultrasound can be used therapeutically avoiding harmful side effects of chemotherapeutic agents or classical radiation therapy.","lang":"eng"}],"issue":"8","volume":23,"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"published"},{"citation":{"ama":"Matoušek J, Sedgwick E, Tancer M, Wagner U. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 2018;65(1). doi:10.1145/3078632","apa":"Matoušek, J., Sedgwick, E., Tancer, M., & Wagner, U. (2018). Embeddability in the 3-Sphere is decidable. Journal of the ACM. ACM. https://doi.org/10.1145/3078632","short":"J. Matoušek, E. Sedgwick, M. Tancer, U. Wagner, Journal of the ACM 65 (2018).","ieee":"J. Matoušek, E. Sedgwick, M. Tancer, and U. Wagner, “Embeddability in the 3-Sphere is decidable,” Journal of the ACM, vol. 65, no. 1. ACM, 2018.","mla":"Matoušek, Jiří, et al. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM, vol. 65, no. 1, 5, ACM, 2018, doi:10.1145/3078632.","ista":"Matoušek J, Sedgwick E, Tancer M, Wagner U. 2018. Embeddability in the 3-Sphere is decidable. Journal of the ACM. 65(1), 5.","chicago":"Matoušek, Jiří, Eric Sedgwick, Martin Tancer, and Uli Wagner. “Embeddability in the 3-Sphere Is Decidable.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3078632."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"arxiv":["1402.0815"],"isi":["000425685900006"]},"publist_id":"7398","author":[{"first_name":"Jiří","last_name":"Matoušek","full_name":"Matoušek, Jiří"},{"first_name":"Eric","last_name":"Sedgwick","full_name":"Sedgwick, Eric"},{"full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","last_name":"Tancer","id":"38AC689C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"title":"Embeddability in the 3-Sphere is decidable","article_number":"5","project":[{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"}],"year":"2018","isi":1,"publication":"Journal of the ACM","day":"01","date_created":"2018-12-11T11:46:24Z","doi":"10.1145/3078632","date_published":"2018-01-01T00:00:00Z","oa":1,"quality_controlled":"1","publisher":"ACM","date_updated":"2023-09-11T13:38:49Z","department":[{"_id":"UlWa"}],"_id":"425","article_type":"original","type":"journal_article","status":"public","publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"issue":"1","related_material":{"record":[{"id":"2157","status":"public","relation":"earlier_version"}]},"volume":65,"abstract":[{"text":"We show that the following algorithmic problem is decidable: given a 2-dimensional simplicial complex, can it be embedded (topologically, or equivalently, piecewise linearly) in R3? By a known reduction, it suffices to decide the embeddability of a given triangulated 3-manifold X into the 3-sphere S3. The main step, which allows us to simplify X and recurse, is in proving that if X can be embedded in S3, then there is also an embedding in which X has a short meridian, that is, an essential curve in the boundary of X bounding a disk in S3 \\ X with length bounded by a computable function of the number of tetrahedra of X.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1402.0815"}],"scopus_import":"1","intvolume":" 65","month":"01"},{"date_updated":"2023-09-11T13:41:22Z","ddc":["519","576"],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:47:09Z","_id":"564","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","publication_status":"published","file":[{"date_updated":"2020-07-14T12:47:09Z","file_size":2287682,"creator":"nbarton","date_created":"2019-12-21T09:36:39Z","file_name":"bartonetheridge.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"0b96f6db47e3e91b5e7d103b847c239d","file_id":"7199"}],"language":[{"iso":"eng"}],"issue":"7","volume":122,"related_material":{"record":[{"relation":"research_data","status":"public","id":"9842"}]},"ec_funded":1,"abstract":[{"lang":"eng","text":"Maladapted individuals can only colonise a new habitat if they can evolve a\r\npositive growth rate fast enough to avoid extinction, a process known as evolutionary\r\nrescue. We treat log fitness at low density in the new habitat as a\r\nsingle polygenic trait and thus use the infinitesimal model to follow the evolution\r\nof the growth rate; this assumes that the trait values of offspring of a\r\nsexual union are normally distributed around the mean of the parents’ trait\r\nvalues, with variance that depends only on the parents’ relatedness. The\r\nprobability that a single migrant can establish depends on just two parameters:\r\nthe mean and genetic variance of the trait in the source population.\r\nThe chance of success becomes small if migrants come from a population\r\nwith mean growth rate in the new habitat more than a few standard deviations\r\nbelow zero; this chance depends roughly equally on the probability\r\nthat the initial founder is unusually fit, and on the subsequent increase in\r\ngrowth rate of its offspring as a result of selection. The loss of genetic variation\r\nduring the founding event is substantial, but highly variable. With\r\ncontinued migration at rate M, establishment is inevitable; when migration\r\nis rare, the expected time to establishment decreases inversely with M.\r\nHowever, above a threshold migration rate, the population may be trapped\r\nin a ‘sink’ state, in which adaptation is held back by gene flow; above this\r\nthreshold, the expected time to establishment increases exponentially with M. This threshold behaviour is captured by a deterministic approximation,\r\nwhich assumes a Gaussian distribution of the trait in the founder population\r\nwith mean and variance evolving deterministically. By assuming a constant\r\ngenetic variance, we also develop a diffusion approximation for the joint distribution\r\nof population size and trait mean, which extends to include stabilising\r\nselection and density regulation. Divergence of the population from its\r\nancestors causes partial reproductive isolation, which we measure through\r\nthe reproductive value of migrants into the newly established population."}],"oa_version":"Submitted Version","scopus_import":"1","month":"07","intvolume":" 122","citation":{"ista":"Barton NH, Etheridge A. 2018. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 122(7), 110–127.","chicago":"Barton, Nicholas H, and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology. Academic Press, 2018. https://doi.org/10.1016/j.tpb.2017.11.007.","ama":"Barton NH, Etheridge A. Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. 2018;122(7):110-127. doi:10.1016/j.tpb.2017.11.007","apa":"Barton, N. H., & Etheridge, A. (2018). Establishment in a new habitat by polygenic adaptation. Theoretical Population Biology. Academic Press. https://doi.org/10.1016/j.tpb.2017.11.007","short":"N.H. Barton, A. Etheridge, Theoretical Population Biology 122 (2018) 110–127.","ieee":"N. H. Barton and A. Etheridge, “Establishment in a new habitat by polygenic adaptation,” Theoretical Population Biology, vol. 122, no. 7. Academic Press, pp. 110–127, 2018.","mla":"Barton, Nicholas H., and Alison Etheridge. “Establishment in a New Habitat by Polygenic Adaptation.” Theoretical Population Biology, vol. 122, no. 7, Academic Press, 2018, pp. 110–27, doi:10.1016/j.tpb.2017.11.007."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7250","author":[{"orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"full_name":"Etheridge, Alison","last_name":"Etheridge","first_name":"Alison"}],"external_id":{"isi":["000440392900014"]},"article_processing_charge":"No","title":"Establishment in a new habitat by polygenic adaptation","project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Theoretical Population Biology","page":"110-127","doi":"10.1016/j.tpb.2017.11.007","date_published":"2018-07-01T00:00:00Z","date_created":"2018-12-11T11:47:12Z","publisher":"Academic Press","quality_controlled":"1","oa":1},{"language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"011ab905cf9a410bc2b96f15174d654d","file_id":"7049","creator":"dernst","file_size":2834442,"date_updated":"2020-07-14T12:45:02Z","file_name":"2018_Nature_Hilbe.pdf","date_created":"2019-11-19T08:09:57Z"}],"publication_status":"published","ec_funded":1,"issue":"7713","volume":559,"related_material":{"link":[{"url":"https://ist.ac.at/en/news/engineering-cooperation/","relation":"press_release","description":"News on IST Homepage"}]},"oa_version":"Submitted Version","abstract":[{"lang":"eng","text":"Social dilemmas occur when incentives for individuals are misaligned with group interests 1-7 . According to the 'tragedy of the commons', these misalignments can lead to overexploitation and collapse of public resources. The resulting behaviours can be analysed with the tools of game theory 8 . The theory of direct reciprocity 9-15 suggests that repeated interactions can alleviate such dilemmas, but previous work has assumed that the public resource remains constant over time. Here we introduce the idea that the public resource is instead changeable and depends on the strategic choices of individuals. An intuitive scenario is that cooperation increases the public resource, whereas defection decreases it. Thus, cooperation allows the possibility of playing a more valuable game with higher payoffs, whereas defection leads to a less valuable game. We analyse this idea using the theory of stochastic games 16-19 and evolutionary game theory. We find that the dependence of the public resource on previous interactions can greatly enhance the propensity for cooperation. For these results, the interaction between reciprocity and payoff feedback is crucial: neither repeated interactions in a constant environment nor single interactions in a changing environment yield similar cooperation rates. Our framework shows which feedbacks between exploitation and environment - either naturally occurring or designed - help to overcome social dilemmas."}],"intvolume":" 559","month":"07","scopus_import":"1","ddc":["000"],"date_updated":"2023-09-11T13:43:22Z","department":[{"_id":"KrCh"}],"file_date_updated":"2020-07-14T12:45:02Z","_id":"157","status":"public","type":"journal_article","publication":"Nature","day":"04","year":"2018","isi":1,"has_accepted_license":"1","date_created":"2018-12-11T11:44:56Z","doi":"10.1038/s41586-018-0277-x","date_published":"2018-07-04T00:00:00Z","page":"246 - 249","acknowledgement":"European Research Council Start Grant 279307, Austrian Science Fund (FWF) grant P23499-N23, \r\nC.H. acknowledges support from the ISTFELLOW programme.","oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Hilbe, Christian, et al. “Evolution of Cooperation in Stochastic Games.” Nature, vol. 559, no. 7713, Nature Publishing Group, 2018, pp. 246–49, doi:10.1038/s41586-018-0277-x.","ieee":"C. Hilbe, Š. Šimsa, K. Chatterjee, and M. Nowak, “Evolution of cooperation in stochastic games,” Nature, vol. 559, no. 7713. Nature Publishing Group, pp. 246–249, 2018.","short":"C. Hilbe, Š. Šimsa, K. Chatterjee, M. Nowak, Nature 559 (2018) 246–249.","apa":"Hilbe, C., Šimsa, Š., Chatterjee, K., & Nowak, M. (2018). Evolution of cooperation in stochastic games. Nature. Nature Publishing Group. https://doi.org/10.1038/s41586-018-0277-x","ama":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. Evolution of cooperation in stochastic games. Nature. 2018;559(7713):246-249. doi:10.1038/s41586-018-0277-x","chicago":"Hilbe, Christian, Štepán Šimsa, Krishnendu Chatterjee, and Martin Nowak. “Evolution of Cooperation in Stochastic Games.” Nature. Nature Publishing Group, 2018. https://doi.org/10.1038/s41586-018-0277-x.","ista":"Hilbe C, Šimsa Š, Chatterjee K, Nowak M. 2018. Evolution of cooperation in stochastic games. Nature. 559(7713), 246–249."},"title":"Evolution of cooperation in stochastic games","article_processing_charge":"No","external_id":{"isi":["000438240900054"]},"publist_id":"7764","author":[{"id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hilbe, Christian","orcid":"0000-0001-5116-955X","last_name":"Hilbe"},{"first_name":"Štepán","last_name":"Šimsa","full_name":"Šimsa, Štepán"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Nowak","full_name":"Nowak, Martin","first_name":"Martin"}],"project":[{"call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425","name":"Game Theory","grant_number":"S11407"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"2584A770-B435-11E9-9278-68D0E5697425","name":"Modern Graph Algorithmic Techniques in Formal Verification","grant_number":"P 23499-N23"},{"name":"Rigorous Systems Engineering","grant_number":"S 11407_N23","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"citation":{"mla":"Hönigschmid, Peter, et al. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution, vol. 10, no. 3, Oxford University Press, 2018, pp. 928–38, doi:10.1093/gbe/evy049.","short":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, D. Frishman, Genome Biology and Evolution 10 (2018) 928–938.","ieee":"P. Hönigschmid, N. Bykova, R. Schneider, D. Ivankov, and D. Frishman, “Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss,” Genome Biology and Evolution, vol. 10, no. 3. Oxford University Press, pp. 928–938, 2018.","ama":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 2018;10(3):928-938. doi:10.1093/gbe/evy049","apa":"Hönigschmid, P., Bykova, N., Schneider, R., Ivankov, D., & Frishman, D. (2018). Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. Oxford University Press. https://doi.org/10.1093/gbe/evy049","chicago":"Hönigschmid, Peter, Nadya Bykova, René Schneider, Dmitry Ivankov, and Dmitrij Frishman. “Evolutionary Interplay between Symbiotic Relationships and Patterns of Signal Peptide Gain and Loss.” Genome Biology and Evolution. Oxford University Press, 2018. https://doi.org/10.1093/gbe/evy049.","ista":"Hönigschmid P, Bykova N, Schneider R, Ivankov D, Frishman D. 2018. Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss. Genome Biology and Evolution. 10(3), 928–938."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","external_id":{"isi":["000429483700022"]},"article_processing_charge":"No","author":[{"last_name":"Hönigschmid","full_name":"Hönigschmid, Peter","first_name":"Peter"},{"first_name":"Nadya","full_name":"Bykova, Nadya","last_name":"Bykova"},{"full_name":"Schneider, René","last_name":"Schneider","first_name":"René"},{"full_name":"Ivankov, Dmitry","last_name":"Ivankov","first_name":"Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Dmitrij","last_name":"Frishman","full_name":"Frishman, Dmitrij"}],"publist_id":"7445","title":"Evolutionary interplay between symbiotic relationships and patterns of signal peptide gain and loss","acknowledgement":"his work was supported by the Deutsche Forschungsgemeinschaft (grant number FR 1411/9-1). This work was supported by the German Research Foundation (DFG) and the Technical University of Munich within the fund- ing programme Open Access Publish\r\nWe thank Goar Frishman for help with the annotation of the\r\nsymbiont status of the organisms and Michael Galperin for\r\nuseful comments. T","oa":1,"publisher":"Oxford University Press","quality_controlled":"1","year":"2018","has_accepted_license":"1","isi":1,"publication":"Genome Biology and Evolution","day":"01","page":"928 - 938","date_created":"2018-12-11T11:46:10Z","date_published":"2018-03-01T00:00:00Z","doi":"10.1093/gbe/evy049","_id":"384","tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","pubrep_id":"999","status":"public","date_updated":"2023-09-11T13:56:52Z","ddc":["576"],"department":[{"_id":"FyKo"}],"file_date_updated":"2020-07-14T12:46:16Z","abstract":[{"lang":"eng","text":"Can orthologous proteins differ in terms of their ability to be secreted? To answer this question, we investigated the distribution of signal peptides within the orthologous groups of Enterobacterales. Parsimony analysis and sequence comparisons revealed a large number of signal peptide gain and loss events, in which signal peptides emerge or disappear in the course of evolution. Signal peptide losses prevail over gains, an effect which is especially pronounced in the transition from the free-living or commensal to the endosymbiotic lifestyle. The disproportionate decline in the number of signal peptide-containing proteins in endosymbionts cannot be explained by the overall reduction of their genomes. Signal peptides can be gained and lost either by acquisition/elimination of the corresponding N-terminal regions or by gradual accumulation of mutations. The evolutionary dynamics of signal peptides in bacterial proteins represents a powerful mechanism of functional diversification."}],"oa_version":"Published Version","scopus_import":"1","intvolume":" 10","month":"03","publication_status":"published","language":[{"iso":"eng"}],"file":[{"creator":"system","date_updated":"2020-07-14T12:46:16Z","file_size":691602,"date_created":"2018-12-12T10:08:07Z","file_name":"IST-2018-999-v1+1_2018_Ivankov_Evolutionary_interplay.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"4667","checksum":"458a7c2c2e79528567edfeb0f326cbe0"}],"issue":"3","volume":10},{"language":[{"iso":"eng"}],"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"200"}]},"issue":"3","volume":208,"oa_version":"Preprint","abstract":[{"text":"In continuous populations with local migration, nearby pairs of individuals have on average more similar genotypes\r\nthan geographically well separated pairs. A barrier to gene flow distorts this classical pattern of isolation by distance. Genetic similarity is decreased for sample pairs on different sides of the barrier and increased for pairs on the same side near the barrier. Here, we introduce an inference scheme that utilizes this signal to detect and estimate the strength of a linear barrier to gene flow in two-dimensions. We use a diffusion approximation to model the effects of a barrier on the geographical spread of ancestry backwards in time. This approach allows us to calculate the chance of recent coalescence and probability of identity by descent. We introduce an inference scheme that fits these theoretical results to the geographical covariance structure of bialleleic genetic markers. It can estimate the strength of the barrier as well as several demographic parameters. We investigate the power of our inference scheme to detect barriers by applying it to a wide range of simulated data. We also showcase an example application to a Antirrhinum majus (snapdragon) flower color hybrid zone, where we do not detect any signal of a strong genome wide barrier to gene flow.","lang":"eng"}],"month":"03","intvolume":" 208","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://www.biorxiv.org/content/10.1101/205484v1"}],"date_updated":"2023-09-11T13:42:38Z","department":[{"_id":"NiBa"},{"_id":"ChLa"}],"_id":"563","status":"public","type":"journal_article","day":"01","publication":"Genetics","isi":1,"year":"2018","doi":"10.1534/genetics.117.300638","date_published":"2018-03-01T00:00:00Z","date_created":"2018-12-11T11:47:12Z","page":"1231-1245","publisher":"Genetics Society of America","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Ringbauer, Harald, et al. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics, vol. 208, no. 3, Genetics Society of America, 2018, pp. 1231–45, doi:10.1534/genetics.117.300638.","short":"H. Ringbauer, A. Kolesnikov, D. Field, N.H. Barton, Genetics 208 (2018) 1231–1245.","ieee":"H. Ringbauer, A. Kolesnikov, D. Field, and N. H. Barton, “Estimating barriers to gene flow from distorted isolation-by-distance patterns,” Genetics, vol. 208, no. 3. Genetics Society of America, pp. 1231–1245, 2018.","ama":"Ringbauer H, Kolesnikov A, Field D, Barton NH. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 2018;208(3):1231-1245. doi:10.1534/genetics.117.300638","apa":"Ringbauer, H., Kolesnikov, A., Field, D., & Barton, N. H. (2018). Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.117.300638","chicago":"Ringbauer, Harald, Alexander Kolesnikov, David Field, and Nicholas H Barton. “Estimating Barriers to Gene Flow from Distorted Isolation-by-Distance Patterns.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.117.300638.","ista":"Ringbauer H, Kolesnikov A, Field D, Barton NH. 2018. Estimating barriers to gene flow from distorted isolation-by-distance patterns. Genetics. 208(3), 1231–1245."},"title":"Estimating barriers to gene flow from distorted isolation-by-distance patterns","author":[{"first_name":"Harald","id":"417FCFF4-F248-11E8-B48F-1D18A9856A87","full_name":"Ringbauer, Harald","orcid":"0000-0002-4884-9682","last_name":"Ringbauer"},{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov"},{"first_name":"David","last_name":"Field","full_name":"Field, David"},{"last_name":"Barton","full_name":"Barton, Nicholas H","orcid":"0000-0002-8548-5240","first_name":"Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7251","external_id":{"isi":["000426219600025"]},"article_processing_charge":"No"},{"project":[{"grant_number":"638176","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","_id":"2533E772-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"author":[{"first_name":"Takahiro","full_name":"Sato, Takahiro","last_name":"Sato"},{"id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J","last_name":"Wojtan","orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"first_name":"Takeo","last_name":"Igarashi","full_name":"Igarashi, Takeo"},{"first_name":"Ryoichi","last_name":"Ando","full_name":"Ando, Ryoichi"}],"external_id":{"isi":["000434085600016"]},"article_processing_charge":"No","title":"Extended narrow band FLIP for liquid simulations","citation":{"ista":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. 2018. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 37(2), 169–177.","chicago":"Sato, Takahiro, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum. Wiley, 2018. https://doi.org/10.1111/cgf.13351.","apa":"Sato, T., Wojtan, C., Thuerey, N., Igarashi, T., & Ando, R. (2018). Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.13351","ama":"Sato T, Wojtan C, Thuerey N, Igarashi T, Ando R. Extended narrow band FLIP for liquid simulations. Computer Graphics Forum. 2018;37(2):169-177. doi:10.1111/cgf.13351","ieee":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Extended narrow band FLIP for liquid simulations,” Computer Graphics Forum, vol. 37, no. 2. Wiley, pp. 169–177, 2018.","short":"T. Sato, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, Computer Graphics Forum 37 (2018) 169–177.","mla":"Sato, Takahiro, et al. “Extended Narrow Band FLIP for Liquid Simulations.” Computer Graphics Forum, vol. 37, no. 2, Wiley, 2018, pp. 169–77, doi:10.1111/cgf.13351."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley","quality_controlled":"1","oa":1,"page":"169 - 177","doi":"10.1111/cgf.13351","date_published":"2018-05-22T00:00:00Z","date_created":"2018-12-11T11:44:49Z","has_accepted_license":"1","isi":1,"year":"2018","day":"22","publication":"Computer Graphics Forum","type":"journal_article","article_type":"original","status":"public","_id":"135","department":[{"_id":"ChWo"}],"file_date_updated":"2020-10-08T08:38:23Z","date_updated":"2023-09-11T14:00:26Z","ddc":["006"],"scopus_import":"1","alternative_title":["Eurographics"],"month":"05","intvolume":" 37","abstract":[{"lang":"eng","text":"The Fluid Implicit Particle method (FLIP) reduces numerical dissipation by combining particles with grids. To improve performance, the subsequent narrow band FLIP method (NB‐FLIP) uses a FLIP‐based fluid simulation only near the liquid surface and a traditional grid‐based fluid simulation away from the surface. This spatially‐limited FLIP simulation significantly reduces the number of particles and alleviates a computational bottleneck. In this paper, we extend the NB‐FLIP idea even further, by allowing a simulation to transition between a FLIP‐like fluid simulation and a grid‐based simulation in arbitrary locations, not just near the surface. This approach leads to even more savings in memory and computation, because we can concentrate the particles only in areas where they are needed. More importantly, this new method allows us to seamlessly transition to smooth implicit surface geometry wherever the particle‐based simulation is unnecessary. Consequently, our method leads to a practical algorithm for avoiding the noisy surface artifacts associated with particle‐based liquid simulations, while simultaneously maintaining the benefits of a FLIP simulation in regions of dynamic motion."}],"oa_version":"Submitted Version","volume":37,"issue":"2","ec_funded":1,"publication_identifier":{"issn":["0167-7055"]},"publication_status":"published","file":[{"date_created":"2020-10-08T08:38:23Z","file_name":"exnbflip.pdf","creator":"wojtan","date_updated":"2020-10-08T08:38:23Z","file_size":54309947,"checksum":"8edb90da8a72395eb5d970580e0925b6","file_id":"8627","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"language":[{"iso":"eng"}]},{"page":"861-883","date_published":"2018-07-01T00:00:00Z","doi":"10.1534/genetics.118.300748","date_created":"2018-12-11T11:45:47Z","isi":1,"year":"2018","day":"01","publication":"Genetics","quality_controlled":"1","publisher":"Genetics Society of America","oa":1,"author":[{"id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","first_name":"Katarina","last_name":"Bodova","full_name":"Bodova, Katarina","orcid":"0000-0002-7214-0171"},{"id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas","full_name":"Priklopil, Tadeas","last_name":"Priklopil"},{"last_name":"Field","orcid":"0000-0002-4014-8478","full_name":"Field, David","id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","external_id":{"isi":["000437171700017"]},"title":"Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system","citation":{"ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 209(3), 861–883.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300748.","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system,” Genetics, vol. 209, no. 3. Genetics Society of America, pp. 861–883, 2018.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, Genetics 209 (2018) 861–883.","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. 2018;209(3):861-883. doi:10.1534/genetics.118.300748","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Evolutionary pathways for the generation of new self-incompatibility haplotypes in a non-self recognition system. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300748","mla":"Bodova, Katarina, et al. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.” Genetics, vol. 209, no. 3, Genetics Society of America, 2018, pp. 861–83, doi:10.1534/genetics.118.300748."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","project":[{"_id":"25B36484-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Mating system and the evolutionary dynamics of hybrid zones","grant_number":"329960"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"250152","name":"Limits to selection in biology and in evolutionary computation"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"volume":209,"issue":"3","related_material":{"record":[{"status":"public","id":"9813","relation":"research_data"}],"link":[{"url":"https://ist.ac.at/en/news/recognizing-others-but-not-yourself-new-insights-into-the-evolution-of-plant-mating/","relation":"press_release","description":"News on IST Homepage"}]},"ec_funded":1,"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"url":"https://www.biorxiv.org/node/80098.abstract","open_access":"1"}],"month":"07","intvolume":" 209","abstract":[{"lang":"eng","text":"Self-incompatibility (SI) is a genetically based recognition system that functions to prevent self-fertilization and mating among related plants. An enduring puzzle in SI is how the high diversity observed in nature arises and is maintained. Based on the underlying recognition mechanism, SI can be classified into two main groups: self- and non-self recognition. Most work has focused on diversification within self-recognition systems despite expected differences between the two groups in the evolutionary pathways and outcomes of diversification. Here, we use a deterministic population genetic model and stochastic simulations to investigate how novel S-haplotypes evolve in a gametophytic non-self recognition (SRNase/S Locus F-box (SLF)) SI system. For this model the pathways for diversification involve either the maintenance or breakdown of SI and can vary in the order of mutations of the female (SRNase) and male (SLF) components. We show analytically that diversification can occur with high inbreeding depression and self-pollination, but this varies with evolutionary pathway and level of completeness (which determines the number of potential mating partners in the population), and in general is more likely for lower haplotype number. The conditions for diversification are broader in stochastic simulations of finite population size. However, the number of haplotypes observed under high inbreeding and moderate to high self-pollination is less than that commonly observed in nature. Diversification was observed through pathways that maintain SI as well as through self-compatible intermediates. Yet the lifespan of diversified haplotypes was sensitive to their level of completeness. By examining diversification in a non-self recognition SI system, this model extends our understanding of the evolution and maintenance of haplotype diversity observed in a self recognition system common in flowering plants."}],"oa_version":"Preprint","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"date_updated":"2023-09-11T13:57:43Z","type":"journal_article","article_type":"original","status":"public","_id":"316"},{"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264.","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley, 2018. https://doi.org/10.1002/jez.b.22824.","ieee":"M. Harrison et al., “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 330. Wiley, pp. 254–264, 2018.","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 2018;330:254-264. doi:10.1002/jez.b.22824","apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. Wiley. https://doi.org/10.1002/jez.b.22824","mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, vol. 330, Wiley, 2018, pp. 254–64, doi:10.1002/jez.b.22824."},"title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","publist_id":"7730","author":[{"first_name":"Mark","full_name":"Harrison, Mark","last_name":"Harrison"},{"last_name":"Arning","full_name":"Arning, Nicolas","first_name":"Nicolas"},{"full_name":"Kremer, Lucas","last_name":"Kremer","first_name":"Lucas"},{"first_name":"Guillem","full_name":"Ylla, Guillem","last_name":"Ylla"},{"last_name":"Belles","full_name":"Belles, Xavier","first_name":"Xavier"},{"last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich","first_name":"Erich"},{"full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","last_name":"Huylmans","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jongepier, Evelien","last_name":"Jongepier","first_name":"Evelien"},{"full_name":"Puilachs, Maria","last_name":"Puilachs","first_name":"Maria"},{"first_name":"Stephen","last_name":"Richards","full_name":"Richards, Stephen"},{"first_name":"Coby","last_name":"Schal","full_name":"Schal, Coby"}],"article_processing_charge":"No","external_id":{"isi":["000443231000002"],"pmid":["29998472"]},"quality_controlled":"1","publisher":"Wiley","oa":1,"day":"11","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","isi":1,"year":"2018","doi":"10.1002/jez.b.22824","date_published":"2018-07-11T00:00:00Z","date_created":"2018-12-11T11:45:06Z","page":"254-264","_id":"190","status":"public","type":"journal_article","article_type":"original","date_updated":"2023-09-11T13:59:54Z","department":[{"_id":"BeVi"}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control."}],"month":"07","intvolume":" 330","scopus_import":"1","main_file_link":[{"url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824","open_access":"1"}],"language":[{"iso":"eng"}],"publication_status":"published","volume":330},{"day":"30","publication":"SIAM Journal on Mathematical Analysis","isi":1,"has_accepted_license":"1","year":"2018","date_published":"2018-01-30T00:00:00Z","doi":"10.1137/16M1098796","date_created":"2018-12-11T11:46:17Z","page":"411 - 455","publisher":"Society for Industrial and Applied Mathematics ","quality_controlled":"1","oa":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"apa":"Fischer, J. L., & Grün, G. (2018). Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1098796","ama":"Fischer JL, Grün G. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 2018;50(1):411-455. doi:10.1137/16M1098796","short":"J.L. Fischer, G. Grün, SIAM Journal on Mathematical Analysis 50 (2018) 411–455.","ieee":"J. L. Fischer and G. Grün, “Existence of positive solutions to stochastic thin-film equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 1. Society for Industrial and Applied Mathematics , pp. 411–455, 2018.","mla":"Fischer, Julian L., and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 411–55, doi:10.1137/16M1098796.","ista":"Fischer JL, Grün G. 2018. Existence of positive solutions to stochastic thin-film equations. SIAM Journal on Mathematical Analysis. 50(1), 411–455.","chicago":"Fischer, Julian L, and Günther Grün. “Existence of Positive Solutions to Stochastic Thin-Film Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1098796."},"title":"Existence of positive solutions to stochastic thin-film equations","author":[{"id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","last_name":"Fischer","full_name":"Fischer, Julian L","orcid":"0000-0002-0479-558X"},{"first_name":"Günther","last_name":"Grün","full_name":"Grün, Günther"}],"publist_id":"7425","article_processing_charge":"No","external_id":{"isi":["000426630900015"]},"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"89a8eae7c52bb356c04f52b44bff4b5a","file_id":"6992","date_updated":"2020-07-14T12:46:22Z","file_size":557338,"creator":"dernst","date_created":"2019-11-07T12:20:25Z","file_name":"2018_SIAM_Fischer.pdf"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"1","volume":50,"oa_version":"Published Version","abstract":[{"text":"We construct martingale solutions to stochastic thin-film equations by introducing a (spatial) semidiscretization and establishing convergence. The discrete scheme allows for variants of the energy and entropy estimates in the continuous setting as long as the discrete energy does not exceed certain threshold values depending on the spatial grid size $h$. Using a stopping time argument to prolongate high-energy paths constant in time, arbitrary moments of coupled energy/entropy functionals can be controlled. Having established Hölder regularity of approximate solutions, the convergence proof is then based on compactness arguments---in particular on Jakubowski's generalization of Skorokhod's theorem---weak convergence methods, and recent tools on martingale convergence.\r\n\r\n","lang":"eng"}],"month":"01","intvolume":" 50","scopus_import":"1","ddc":["510"],"date_updated":"2023-09-11T13:59:22Z","department":[{"_id":"JuFi"}],"file_date_updated":"2020-07-14T12:46:22Z","_id":"404","status":"public","type":"journal_article","article_type":"original"},{"status":"public","type":"research_data_reference","_id":"9813","title":"Supplemental material for Bodova et al., 2018","department":[{"_id":"NiBa"},{"_id":"GaTk"}],"author":[{"orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína","last_name":"Bod'ová","first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Priklopil, Tadeas","last_name":"Priklopil","id":"3C869AA0-F248-11E8-B48F-1D18A9856A87","first_name":"Tadeas"},{"id":"419049E2-F248-11E8-B48F-1D18A9856A87","first_name":"David","full_name":"Field, David","orcid":"0000-0002-4014-8478","last_name":"Field"},{"last_name":"Barton","orcid":"0000-0002-8548-5240","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","first_name":"Nicholas H"},{"last_name":"Pickup","full_name":"Pickup, Melinda","orcid":"0000-0001-6118-0541","first_name":"Melinda","id":"2C78037E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","citation":{"ista":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. 2018. Supplemental material for Bodova et al., 2018, Genetics Society of America, 10.25386/genetics.6148304.v1.","chicago":"Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.” Genetics Society of America, 2018. https://doi.org/10.25386/genetics.6148304.v1.","apa":"Bodova, K., Priklopil, T., Field, D., Barton, N. H., & Pickup, M. (2018). Supplemental material for Bodova et al., 2018. Genetics Society of America. https://doi.org/10.25386/genetics.6148304.v1","ama":"Bodova K, Priklopil T, Field D, Barton NH, Pickup M. Supplemental material for Bodova et al., 2018. 2018. doi:10.25386/genetics.6148304.v1","ieee":"K. Bodova, T. Priklopil, D. Field, N. H. Barton, and M. Pickup, “Supplemental material for Bodova et al., 2018.” Genetics Society of America, 2018.","short":"K. Bodova, T. Priklopil, D. Field, N.H. Barton, M. Pickup, (2018).","mla":"Bodova, Katarina, et al. Supplemental Material for Bodova et Al., 2018. Genetics Society of America, 2018, doi:10.25386/genetics.6148304.v1."},"date_updated":"2023-09-11T13:57:42Z","month":"04","publisher":"Genetics Society of America","main_file_link":[{"open_access":"1","url":"https://doi.org/10.25386/genetics.6148304.v1"}],"oa":1,"oa_version":"Published Version","abstract":[{"text":"File S1 contains figures that clarify the following features: (i) effect of population size on the average number/frequency of SI classes, (ii) changes in the minimal completeness deficit in time for a single class, and (iii) diversification diagrams for all studied pathways, including the summary figure for k = 8. File S2 contains the code required for a stochastic simulation of the SLF system with an example. This file also includes the output in the form of figures and tables.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"316","relation":"used_in_publication"}]},"date_published":"2018-04-30T00:00:00Z","doi":"10.25386/genetics.6148304.v1","date_created":"2021-08-06T13:04:32Z","day":"30","year":"2018"},{"oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","page":"12728-12732","date_created":"2018-12-23T22:59:18Z","date_published":"2018-12-11T00:00:00Z","doi":"10.1073/pnas.1803615115","year":"2018","isi":1,"has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","day":"11","article_processing_charge":"No","external_id":{"isi":["000452866000068"]},"author":[{"last_name":"Kotlobay","full_name":"Kotlobay, Alexey A.","first_name":"Alexey A."},{"full_name":"Sarkisyan, Karen","orcid":"0000-0002-5375-6341","last_name":"Sarkisyan","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"first_name":"Yuliana A.","last_name":"Mokrushina","full_name":"Mokrushina, Yuliana A."},{"first_name":"Marina","full_name":"Marcet-Houben, Marina","last_name":"Marcet-Houben"},{"full_name":"Serebrovskaya, Ekaterina O.","last_name":"Serebrovskaya","first_name":"Ekaterina O."},{"first_name":"Nadezhda M.","full_name":"Markina, Nadezhda M.","last_name":"Markina"},{"first_name":"Louisa","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","last_name":"Gonzalez Somermeyer"},{"first_name":"Andrey Y.","full_name":"Gorokhovatsky, Andrey Y.","last_name":"Gorokhovatsky"},{"first_name":"Andrey","full_name":"Vvedensky, Andrey","last_name":"Vvedensky"},{"first_name":"Konstantin V.","last_name":"Purtov","full_name":"Purtov, Konstantin V."},{"last_name":"Petushkov","full_name":"Petushkov, Valentin N.","first_name":"Valentin N."},{"first_name":"Natalja S.","full_name":"Rodionova, Natalja S.","last_name":"Rodionova"},{"first_name":"Tatiana V.","full_name":"Chepurnyh, Tatiana V.","last_name":"Chepurnyh"},{"first_name":"Liliia","last_name":"Fakhranurova","full_name":"Fakhranurova, Liliia"},{"first_name":"Elena B.","last_name":"Guglya","full_name":"Guglya, Elena B."},{"first_name":"Rustam","last_name":"Ziganshin","full_name":"Ziganshin, Rustam"},{"last_name":"Tsarkova","full_name":"Tsarkova, Aleksandra S.","first_name":"Aleksandra S."},{"last_name":"Kaskova","full_name":"Kaskova, Zinaida M.","first_name":"Zinaida M."},{"first_name":"Victoria","full_name":"Shender, Victoria","last_name":"Shender"},{"last_name":"Abakumov","full_name":"Abakumov, Maxim","first_name":"Maxim"},{"last_name":"Abakumova","full_name":"Abakumova, Tatiana O.","first_name":"Tatiana O."},{"full_name":"Povolotskaya, Inna S.","last_name":"Povolotskaya","first_name":"Inna S."},{"full_name":"Eroshkin, Fedor M.","last_name":"Eroshkin","first_name":"Fedor M."},{"first_name":"Andrey G.","full_name":"Zaraisky, Andrey G.","last_name":"Zaraisky"},{"last_name":"Mishin","full_name":"Mishin, Alexander S.","first_name":"Alexander S."},{"full_name":"Dolgov, Sergey V.","last_name":"Dolgov","first_name":"Sergey V."},{"full_name":"Mitiouchkina, Tatiana Y.","last_name":"Mitiouchkina","first_name":"Tatiana Y."},{"last_name":"Kopantzev","full_name":"Kopantzev, Eugene P.","first_name":"Eugene P."},{"last_name":"Waldenmaier","full_name":"Waldenmaier, Hans E.","first_name":"Hans E."},{"full_name":"Oliveira, Anderson G.","last_name":"Oliveira","first_name":"Anderson G."},{"first_name":"Yuichi","last_name":"Oba","full_name":"Oba, Yuichi"},{"full_name":"Barsova, Ekaterina","last_name":"Barsova","first_name":"Ekaterina"},{"first_name":"Ekaterina A.","full_name":"Bogdanova, Ekaterina A.","last_name":"Bogdanova"},{"last_name":"Gabaldón","full_name":"Gabaldón, Toni","first_name":"Toni"},{"last_name":"Stevani","full_name":"Stevani, Cassius V.","first_name":"Cassius V."},{"first_name":"Sergey","last_name":"Lukyanov","full_name":"Lukyanov, Sergey"},{"full_name":"Smirnov, Ivan V.","last_name":"Smirnov","first_name":"Ivan V."},{"full_name":"Gitelson, Josef I.","last_name":"Gitelson","first_name":"Josef I."},{"first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","orcid":"0000-0001-8243-4694","full_name":"Kondrashov, Fyodor"},{"first_name":"Ilia V.","last_name":"Yampolsky","full_name":"Yampolsky, Ilia V."}],"title":"Genetically encodable bioluminescent system from fungi","citation":{"chicago":"Kotlobay, Alexey A., Karen Sarkisyan, Yuliana A. Mokrushina, Marina Marcet-Houben, Ekaterina O. Serebrovskaya, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1803615115.","ista":"Kotlobay AA, Sarkisyan K, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova L, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov F, Yampolsky IV. 2018. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 115(50), 12728–12732.","mla":"Kotlobay, Alexey A., et al. “Genetically Encodable Bioluminescent System from Fungi.” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50, National Academy of Sciences, 2018, pp. 12728–32, doi:10.1073/pnas.1803615115.","ama":"Kotlobay AA, Sarkisyan K, Mokrushina YA, et al. Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. 2018;115(50):12728-12732. doi:10.1073/pnas.1803615115","apa":"Kotlobay, A. A., Sarkisyan, K., Mokrushina, Y. A., Marcet-Houben, M., Serebrovskaya, E. O., Markina, N. M., … Yampolsky, I. V. (2018). Genetically encodable bioluminescent system from fungi. Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1803615115","short":"A.A. Kotlobay, K. Sarkisyan, Y.A. Mokrushina, M. Marcet-Houben, E.O. Serebrovskaya, N.M. Markina, L. Gonzalez Somermeyer, A.Y. Gorokhovatsky, A. Vvedensky, K.V. Purtov, V.N. Petushkov, N.S. Rodionova, T.V. Chepurnyh, L. Fakhranurova, E.B. Guglya, R. Ziganshin, A.S. Tsarkova, Z.M. Kaskova, V. Shender, M. Abakumov, T.O. Abakumova, I.S. Povolotskaya, F.M. Eroshkin, A.G. Zaraisky, A.S. Mishin, S.V. Dolgov, T.Y. Mitiouchkina, E.P. Kopantzev, H.E. Waldenmaier, A.G. Oliveira, Y. Oba, E. Barsova, E.A. Bogdanova, T. Gabaldón, C.V. Stevani, S. Lukyanov, I.V. Smirnov, J.I. Gitelson, F. Kondrashov, I.V. Yampolsky, Proceedings of the National Academy of Sciences of the United States of America 115 (2018) 12728–12732.","ieee":"A. A. Kotlobay et al., “Genetically encodable bioluminescent system from fungi,” Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 50. National Academy of Sciences, pp. 12728–12732, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","intvolume":" 115","month":"12","abstract":[{"lang":"eng","text":"Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit light when enzymatically oxidized, are known. However, just one biochemical pathway for luciferin biosynthesis has been described in full, which is found only in bacteria. Here, we report identification of the fungal luciferase and three other key enzymes that together form the biosynthetic cycle of the fungal luciferin from caffeic acid, a simple and widespread metabolite. Introduction of the identified genes into the genome of the yeast Pichia pastoris along with caffeic acid biosynthesis genes resulted in a strain that is autoluminescent in standard media. We analyzed evolution of the enzymes of the luciferin biosynthesis cycle and found that fungal bioluminescence emerged through a series of events that included two independent gene duplications. The retention of the duplicated enzymes of the luciferin pathway in nonluminescent fungi shows that the gene duplication was followed by functional sequence divergence of enzymes of at least one gene in the biosynthetic pathway and suggests that the evolution of fungal bioluminescence proceeded through several closely related stepping stone nonluminescent biochemical reactions with adaptive roles. The availability of a complete eukaryotic luciferin biosynthesis pathway provides several applications in biomedicine and bioengineering."}],"oa_version":"Published Version","volume":115,"issue":"50","publication_status":"published","publication_identifier":{"issn":["00278424"]},"language":[{"iso":"eng"}],"file":[{"file_id":"5926","checksum":"46b2c12185eb2ddb598f4c7b4bd267bf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_PNAS_Kotlobay.pdf","date_created":"2019-02-05T15:21:40Z","file_size":1271988,"date_updated":"2020-07-14T12:47:11Z","creator":"dernst"}],"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (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"},"type":"journal_article","status":"public","_id":"5780","file_date_updated":"2020-07-14T12:47:11Z","department":[{"_id":"FyKo"}],"date_updated":"2023-09-11T14:04:05Z","ddc":["580"]},{"tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (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"},"type":"journal_article","status":"public","_id":"428","file_date_updated":"2020-07-14T12:46:26Z","department":[{"_id":"JiFr"}],"date_updated":"2023-09-11T14:06:34Z","ddc":["580"],"scopus_import":"1","intvolume":" 115","month":"04","abstract":[{"text":"The plant hormone gibberellic acid (GA) is a crucial regulator of growth and development. The main paradigm of GA signaling puts forward transcriptional regulation via the degradation of DELLA transcriptional repressors. GA has also been shown to regulate tropic responses by modulation of the plasma membrane incidence of PIN auxin transporters by an unclear mechanism. Here we uncovered the cellular and molecular mechanisms by which GA redirects protein trafficking and thus regulates cell surface functionality. Photoconvertible reporters revealed that GA balances the protein traffic between the vacuole degradation route and recycling back to the cell surface. Low GA levels promote vacuolar delivery and degradation of multiple cargos, including PIN proteins, whereas high GA levels promote their recycling to the plasma membrane. This GA effect requires components of the retromer complex, such as Sorting Nexin 1 (SNX1) and its interacting, microtubule (MT)-associated protein, the Cytoplasmic Linker-Associated Protein (CLASP1). Accordingly, GA regulates the subcellular distribution of SNX1 and CLASP1, and the intact MT cytoskeleton is essential for the GA effect on trafficking. This GA cellular action occurs through DELLA proteins that regulate the MT and retromer presumably via their interaction partners Prefoldins (PFDs). Our study identified a branching of the GA signaling pathway at the level of DELLA proteins, which, in parallel to regulating transcription, also target by a nontranscriptional mechanism the retromer complex acting at the intersection of the degradation and recycling trafficking routes. By this mechanism, GA can redirect receptors and transporters to the cell surface, thus coregulating multiple processes, including PIN-dependent auxin fluxes during tropic responses.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"issue":"14","volume":115,"publication_status":"published","language":[{"iso":"eng"}],"file":[{"file_size":1924101,"date_updated":"2020-07-14T12:46:26Z","creator":"dernst","file_name":"2018_PNAS_Salanenka.pdf","date_created":"2018-12-17T12:30:14Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5700","checksum":"1fcf7223fb8f99559cfa80bd6f24ce44"}],"project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_processing_charge":"No","external_id":{"isi":["000429012500073"]},"publist_id":"7395","author":[{"last_name":"Salanenka","full_name":"Salanenka, Yuliya","first_name":"Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87"},{"id":"362BF7FE-F248-11E8-B48F-1D18A9856A87","first_name":"Inge","full_name":"Verstraeten, Inge","orcid":"0000-0001-7241-2328","last_name":"Verstraeten"},{"full_name":"Löfke, Christian","last_name":"Löfke","first_name":"Christian"},{"last_name":"Tabata","full_name":"Tabata, Kaori","first_name":"Kaori","id":"7DAAEDA4-02D0-11E9-B11A-A5A4D7DFFFD0"},{"first_name":"Satoshi","last_name":"Naramoto","full_name":"Naramoto, Satoshi"},{"id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","first_name":"Matous","last_name":"Glanc","orcid":"0000-0003-0619-7783","full_name":"Glanc, Matous"},{"orcid":"0000-0002-8302-7596","full_name":"Friml, Jirí","last_name":"Friml","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"title":"Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane","citation":{"apa":"Salanenka, Y., Verstraeten, I., Löfke, C., Tabata, K., Naramoto, S., Glanc, M., & Friml, J. (2018). Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721760115","ama":"Salanenka Y, Verstraeten I, Löfke C, et al. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 2018;115(14):3716-3721. doi:10.1073/pnas.1721760115","ieee":"Y. Salanenka et al., “Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane,” PNAS, vol. 115, no. 14. National Academy of Sciences, pp. 3716–3721, 2018.","short":"Y. Salanenka, I. Verstraeten, C. Löfke, K. Tabata, S. Naramoto, M. Glanc, J. Friml, PNAS 115 (2018) 3716–3721.","mla":"Salanenka, Yuliya, et al. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS, vol. 115, no. 14, National Academy of Sciences, 2018, pp. 3716–21, doi:10.1073/pnas.1721760115.","ista":"Salanenka Y, Verstraeten I, Löfke C, Tabata K, Naramoto S, Glanc M, Friml J. 2018. Gibberellin DELLA signaling targets the retromer complex to redirect protein trafficking to the plasma membrane. PNAS. 115(14), 3716–3721.","chicago":"Salanenka, Yuliya, Inge Verstraeten, Christian Löfke, Kaori Tabata, Satoshi Naramoto, Matous Glanc, and Jiří Friml. “Gibberellin DELLA Signaling Targets the Retromer Complex to Redirect Protein Trafficking to the Plasma Membrane.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721760115."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa":1,"quality_controlled":"1","publisher":"National Academy of Sciences","acknowledgement":"We gratefully acknowledge M. Blázquez (Instituto de Biología Molecular y Celular de Plantas), M. Fendrych, C. Cuesta Moliner (Institute of Science and Technology Austria), M. Vanstraelen, M. Nowack (Center for Plant Systems Biology, Ghent), C. Luschnig (Universitat fur Bodenkultur Wien, Vienna), S. Simon (Central European Institute of Technology, Brno), C. Sommerville (Carnegie Institution for Science), and Y. Gu (Penn State University) for making available the materials used in this study;\r\n...funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP7/2007-2013)/ERC Grant Agreement 282300.\r\nCC BY NC ND","page":" 3716 - 3721","date_created":"2018-12-11T11:46:25Z","doi":"10.1073/pnas.1721760115","date_published":"2018-04-03T00:00:00Z","year":"2018","isi":1,"has_accepted_license":"1","publication":"PNAS","day":"03"},{"article_number":"14247","title":"Flexible learning-free segmentation and reconstruction of neural volumes","article_processing_charge":"No","external_id":{"isi":["000445336600015"]},"author":[{"first_name":"Ali","last_name":"Shabazi","full_name":"Shabazi, Ali"},{"first_name":"Jeffery","last_name":"Kinnison","full_name":"Kinnison, Jeffery"},{"full_name":"Vescovi, Rafael","last_name":"Vescovi","first_name":"Rafael"},{"first_name":"Ming","full_name":"Du, Ming","last_name":"Du"},{"last_name":"Hill","full_name":"Hill, Robert","first_name":"Robert"},{"full_name":"Jösch, Maximilian A","orcid":"0000-0002-3937-1330","last_name":"Jösch","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","first_name":"Maximilian A"},{"first_name":"Marc","full_name":"Takeno, Marc","last_name":"Takeno"},{"first_name":"Hongkui","last_name":"Zeng","full_name":"Zeng, Hongkui"},{"first_name":"Nuno","last_name":"Da Costa","full_name":"Da Costa, Nuno"},{"full_name":"Grutzendler, Jaime","last_name":"Grutzendler","first_name":"Jaime"},{"full_name":"Kasthuri, Narayanan","last_name":"Kasthuri","first_name":"Narayanan"},{"first_name":"Walter","full_name":"Scheirer, Walter","last_name":"Scheirer"}],"publist_id":"7992","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Shabazi, Ali, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports, vol. 8, no. 1, 14247, Nature Publishing Group, 2018, doi:10.1038/s41598-018-32628-3.","ieee":"A. Shabazi et al., “Flexible learning-free segmentation and reconstruction of neural volumes,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018.","short":"A. Shabazi, J. Kinnison, R. Vescovi, M. Du, R. Hill, M.A. Jösch, M. Takeno, H. Zeng, N. Da Costa, J. Grutzendler, N. Kasthuri, W. Scheirer, Scientific Reports 8 (2018).","apa":"Shabazi, A., Kinnison, J., Vescovi, R., Du, M., Hill, R., Jösch, M. A., … Scheirer, W. (2018). Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-32628-3","ama":"Shabazi A, Kinnison J, Vescovi R, et al. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-32628-3","chicago":"Shabazi, Ali, Jeffery Kinnison, Rafael Vescovi, Ming Du, Robert Hill, Maximilian A Jösch, Marc Takeno, et al. “Flexible Learning-Free Segmentation and Reconstruction of Neural Volumes.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-32628-3.","ista":"Shabazi A, Kinnison J, Vescovi R, Du M, Hill R, Jösch MA, Takeno M, Zeng H, Da Costa N, Grutzendler J, Kasthuri N, Scheirer W. 2018. Flexible learning-free segmentation and reconstruction of neural volumes. Scientific Reports. 8(1), 14247."},"oa":1,"quality_controlled":"1","publisher":"Nature Publishing Group","acknowledgement":"Equipment was generously donated by the NVIDIA Corporation, and made available by the National Science Foundation (NSF) through grant #CNS-1629914. This research used resources of the Argonne Leadership Computing Facility, which is a DOE Office of Science User Facility supported under Contract DE-AC02-06CH11357.","date_created":"2018-12-11T11:44:25Z","doi":"10.1038/s41598-018-32628-3","date_published":"2018-09-24T00:00:00Z","publication":"Scientific Reports","day":"24","year":"2018","isi":1,"has_accepted_license":"1","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"62","department":[{"_id":"MaJö"}],"file_date_updated":"2020-07-14T12:47:24Z","ddc":["570"],"date_updated":"2023-09-11T14:02:55Z","intvolume":" 8","month":"09","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Imaging is a dominant strategy for data collection in neuroscience, yielding stacks of images that often scale to gigabytes of data for a single experiment. Machine learning algorithms from computer vision can serve as a pair of virtual eyes that tirelessly processes these images, automatically detecting and identifying microstructures. Unlike learning methods, our Flexible Learning-free Reconstruction of Imaged Neural volumes (FLoRIN) pipeline exploits structure-specific contextual clues and requires no training. This approach generalizes across different modalities, including serially-sectioned scanning electron microscopy (sSEM) of genetically labeled and contrast enhanced processes, spectral confocal reflectance (SCoRe) microscopy, and high-energy synchrotron X-ray microtomography (μCT) of large tissue volumes. We deploy the FLoRIN pipeline on newly published and novel mouse datasets, demonstrating the high biological fidelity of the pipeline’s reconstructions. FLoRIN reconstructions are of sufficient quality for preliminary biological study, for example examining the distribution and morphology of cells or extracting single axons from functional data. Compared to existing supervised learning methods, FLoRIN is one to two orders of magnitude faster and produces high-quality reconstructions that are tolerant to noise and artifacts, as is shown qualitatively and quantitatively."}],"related_material":{"link":[{"url":"http://doi.org/10.1038/s41598-018-36220-7","relation":"erratum"}]},"volume":8,"issue":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":4141645,"date_updated":"2020-07-14T12:47:24Z","file_name":"2018_ScientificReports_Shahbazi.pdf","date_created":"2018-12-17T12:22:24Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"1a14ae0666b82fbaa04bef110e3f6bf2","file_id":"5699"}],"publication_status":"published"},{"project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373"}],"author":[{"id":"3B1B77E4-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander F","full_name":"Leithner, Alexander F","orcid":"0000-0002-1073-744X","last_name":"Leithner"},{"full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","last_name":"Renkawitz","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"last_name":"De Vries","full_name":"De Vries, Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","first_name":"Ingrid"},{"full_name":"Hauschild, Robert","orcid":"0000-0001-9843-3522","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"last_name":"Haecker","full_name":"Haecker, Hans","first_name":"Hans"},{"last_name":"Sixt","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","first_name":"Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7386","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000434963700016"]},"title":"Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration","citation":{"mla":"Leithner, Alexander F., et al. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology, vol. 48, no. 6, Wiley-Blackwell, 2018, pp. 1074–77, doi:10.1002/eji.201747358.","short":"A.F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, M.K. Sixt, European Journal of Immunology 48 (2018) 1074–1077.","ieee":"A. F. Leithner, J. Renkawitz, I. de Vries, R. Hauschild, H. Haecker, and M. K. Sixt, “Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration,” European Journal of Immunology, vol. 48, no. 6. Wiley-Blackwell, pp. 1074–1077, 2018.","ama":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 2018;48(6):1074-1077. doi:10.1002/eji.201747358","apa":"Leithner, A. F., Renkawitz, J., de Vries, I., Hauschild, R., Haecker, H., & Sixt, M. K. (2018). Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201747358","chicago":"Leithner, Alexander F, Jörg Renkawitz, Ingrid de Vries, Robert Hauschild, Hans Haecker, and Michael K Sixt. “Fast and Efficient Genetic Engineering of Hematopoietic Precursor Cells for the Study of Dendritic Cell Migration.” European Journal of Immunology. Wiley-Blackwell, 2018. https://doi.org/10.1002/eji.201747358.","ista":"Leithner AF, Renkawitz J, de Vries I, Hauschild R, Haecker H, Sixt MK. 2018. Fast and efficient genetic engineering of hematopoietic precursor cells for the study of dendritic cell migration. European Journal of Immunology. 48(6), 1074–1077."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Wiley-Blackwell","quality_controlled":"1","oa":1,"acknowledgement":"This work was supported by grants of the European Research Council (ERC CoG 724373) and the Austrian Science Fund (FWF) to M.S. We thank the scientific support units at IST Austria for excellent technical support.\r\nWe thank the scientific support units at IST Austria for excellent technical support. ","page":"1074 - 1077","date_published":"2018-02-13T00:00:00Z","doi":"10.1002/eji.201747358","date_created":"2018-12-11T11:46:28Z","isi":1,"has_accepted_license":"1","year":"2018","day":"13","publication":"European Journal of Immunology","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)"},"status":"public","pubrep_id":"1067","_id":"437","department":[{"_id":"MiSi"},{"_id":"Bio"}],"file_date_updated":"2020-07-14T12:46:27Z","date_updated":"2023-09-11T14:01:18Z","ddc":["570"],"scopus_import":"1","month":"02","intvolume":" 48","acknowledged_ssus":[{"_id":"SSU"}],"abstract":[{"text":"Dendritic cells (DCs) are sentinels of the adaptive immune system that reside in peripheral organs of mammals. Upon pathogen encounter, they undergo maturation and up-regulate the chemokine receptor CCR7 that guides them along gradients of its chemokine ligands CCL19 and 21 to the next draining lymph node. There, DCs present peripherally acquired antigen to naïve T cells, thereby triggering adaptive immunity.","lang":"eng"}],"oa_version":"Published Version","issue":"6","volume":48,"ec_funded":1,"publication_status":"published","file":[{"date_created":"2018-12-12T10:13:56Z","file_name":"IST-2018-1067-v1+2_Leithner_et_al-2018-European_Journal_of_Immunology.pdf","date_updated":"2020-07-14T12:46:27Z","file_size":590106,"creator":"system","file_id":"5044","checksum":"9d5b74cd016505aeb9a4c2d33bbedaeb","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}]},{"doi":"10.1111/jeb.13211","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:47:31Z","page":"159 - 171","day":"01","publication":"Journal of Evolutionary Biology","isi":1,"year":"2018","publisher":"Wiley","quality_controlled":"1","oa":1,"acknowledgement":"We would like to thank Susann Wicke for performing the genome-wide SNP/indel analyses, as well as Veronica Alves, Kevin Ferro, Momir Futo, Barbara Hasert, Dafne Maximo, Nora Schulz, Marlene Sroka, and Barth Wieczorek for technical help. We thank Brian Lazzaro for the L. lactis strain and Bruno Lemaitre for the Pseudomonas entomophila strain. We would like to thank two anonymous reviewers for their helpful comments. We are grateful to the Deutsche Forschungsgemeinschaft (DFG) priority programme 1399 ‘Host parasite coevolution’ for funding this project (AR 872/1-1). ","title":"Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance","author":[{"first_name":"Megan","id":"29D0B332-F248-11E8-B48F-1D18A9856A87","last_name":"Kutzer","full_name":"Kutzer, Megan","orcid":"0000-0002-8696-6978"},{"first_name":"Joachim","full_name":"Kurtz, Joachim","last_name":"Kurtz"},{"last_name":"Armitage","full_name":"Armitage, Sophie","first_name":"Sophie"}],"publist_id":"7187","article_processing_charge":"No","external_id":{"pmid":["29150962"],"isi":["000419307000014"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Kutzer M, Kurtz J, Armitage S. 2018. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 31(1), 159–171.","chicago":"Kutzer, Megan, Joachim Kurtz, and Sophie Armitage. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology. Wiley, 2018. https://doi.org/10.1111/jeb.13211.","apa":"Kutzer, M., Kurtz, J., & Armitage, S. (2018). Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.13211","ama":"Kutzer M, Kurtz J, Armitage S. Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance. Journal of Evolutionary Biology. 2018;31(1):159-171. doi:10.1111/jeb.13211","ieee":"M. Kutzer, J. Kurtz, and S. Armitage, “Genotype and diet affect resistance, survival, and fecundity but not fecundity tolerance,” Journal of Evolutionary Biology, vol. 31, no. 1. Wiley, pp. 159–171, 2018.","short":"M. Kutzer, J. Kurtz, S. Armitage, Journal of Evolutionary Biology 31 (2018) 159–171.","mla":"Kutzer, Megan, et al. “Genotype and Diet Affect Resistance, Survival, and Fecundity but Not Fecundity Tolerance.” Journal of Evolutionary Biology, vol. 31, no. 1, Wiley, 2018, pp. 159–71, doi:10.1111/jeb.13211."},"volume":31,"issue":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1010-061X"],"eissn":["1420-9101"]},"publication_status":"published","month":"01","intvolume":" 31","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/jeb.13211"}],"oa_version":"Published Version","pmid":1,"abstract":[{"text":"Insects are exposed to a variety of potential pathogens in their environment, many of which can severely impact fitness and health. Consequently, hosts have evolved resistance and tolerance strategies to suppress or cope with infections. Hosts utilizing resistance improve fitness by clearing or reducing pathogen loads, and hosts utilizing tolerance reduce harmful fitness effects per pathogen load. To understand variation in, and selective pressures on, resistance and tolerance, we asked to what degree they are shaped by host genetic background, whether plasticity in these responses depends upon dietary environment, and whether there are interactions between these two factors. Females from ten wild-type Drosophila melanogaster genotypes were kept on high- or low-protein (yeast) diets and infected with one of two opportunistic bacterial pathogens, Lactococcus lactis or Pseudomonas entomophila. We measured host resistance as the inverse of bacterial load in the early infection phase. The relationship (slope) between fly fecundity and individual-level bacteria load provided our fecundity tolerance measure. Genotype and dietary yeast determined host fecundity and strongly affected survival after infection with pathogenic P. entomophila. There was considerable genetic variation in host resistance, a commonly found phenomenon resulting from for example varying resistance costs or frequency-dependent selection. Despite this variation and the reproductive cost of higher P. entomophila loads, fecundity tolerance did not vary across genotypes. The absence of genetic variation in tolerance may suggest that at this early infection stage, fecundity tolerance is fixed or that any evolved tolerance mechanisms are not expressed under these infection conditions.","lang":"eng"}],"department":[{"_id":"SyCr"}],"date_updated":"2023-09-11T14:06:04Z","status":"public","type":"journal_article","article_type":"original","_id":"617"},{"department":[{"_id":"GaNo"}],"file_date_updated":"2020-07-14T12:47:13Z","ddc":["570"],"date_updated":"2023-09-11T14:04:41Z","status":"public","tmp":{"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)","short":"CC BY (4.0)"},"type":"journal_article","_id":"5888","volume":50,"issue":"8","language":[{"iso":"eng"}],"file":[{"file_size":1237482,"date_updated":"2020-07-14T12:47:13Z","creator":"dernst","file_name":"2018_EMM_Tarlungeanu.pdf","date_created":"2019-01-28T15:18:02Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"4498301c8c53097c9a1a8ef990936eb5","file_id":"5893"}],"publication_status":"published","publication_identifier":{"issn":["2092-6413"]},"intvolume":" 50","month":"08","scopus_import":"1","pmid":1,"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Despite the remarkable number of scientific breakthroughs of the last 100 years, the treatment of neurodevelopmental\r\ndisorders (e.g., autism spectrum disorder, intellectual disability) remains a great challenge. Recent advancements in\r\ngenomics, such as whole-exome or whole-genome sequencing, have enabled scientists to identify numerous\r\nmutations underlying neurodevelopmental disorders. Given the few hundred risk genes that have been discovered,\r\nthe etiological variability and the heterogeneous clinical presentation, the need for genotype — along with phenotype-\r\nbased diagnosis of individual patients has become a requisite. In this review we look at recent advancements in\r\ngenomic analysis and their translation into clinical practice."}],"title":"Genomics in neurodevelopmental disorders: an avenue to personalized medicine","external_id":{"pmid":["30089840"],"isi":["000441266700006"]},"article_processing_charge":"No","author":[{"last_name":"Tarlungeanu","full_name":"Tarlungeanu, Dora-Clara","id":"2ABCE612-F248-11E8-B48F-1D18A9856A87","first_name":"Dora-Clara"},{"first_name":"Gaia","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","last_name":"Novarino","full_name":"Novarino, Gaia","orcid":"0000-0002-7673-7178"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"short":"D.-C. Tarlungeanu, G. Novarino, Experimental & Molecular Medicine 50 (2018).","ieee":"D.-C. Tarlungeanu and G. Novarino, “Genomics in neurodevelopmental disorders: an avenue to personalized medicine,” Experimental & Molecular Medicine, vol. 50, no. 8. Springer Nature, 2018.","apa":"Tarlungeanu, D.-C., & Novarino, G. (2018). Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. Springer Nature. https://doi.org/10.1038/s12276-018-0129-7","ama":"Tarlungeanu D-C, Novarino G. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 2018;50(8). doi:10.1038/s12276-018-0129-7","mla":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine, vol. 50, no. 8, 100, Springer Nature, 2018, doi:10.1038/s12276-018-0129-7.","ista":"Tarlungeanu D-C, Novarino G. 2018. Genomics in neurodevelopmental disorders: an avenue to personalized medicine. Experimental & Molecular Medicine. 50(8), 100.","chicago":"Tarlungeanu, Dora-Clara, and Gaia Novarino. “Genomics in Neurodevelopmental Disorders: An Avenue to Personalized Medicine.” Experimental & Molecular Medicine. Springer Nature, 2018. https://doi.org/10.1038/s12276-018-0129-7."},"article_number":"100","date_created":"2019-01-27T22:59:11Z","date_published":"2018-08-07T00:00:00Z","doi":"10.1038/s12276-018-0129-7","publication":"Experimental & Molecular Medicine","day":"07","year":"2018","isi":1,"has_accepted_license":"1","oa":1,"quality_controlled":"1","publisher":"Springer Nature"},{"quality_controlled":"1","publisher":"Springer","oa":1,"acknowledgement":"Financial support from the Swedish Research Council, grant no. 2013-4734 (D. L.), the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 694227, R. S.), and by the Austrian Science Fund (FWF), project Nr. P 27533-N27 (R. S.), is gratefully acknowledged.","page":"2523-2541","doi":"10.1007/s11005-018-1091-y","date_published":"2018-05-11T00:00:00Z","date_created":"2018-12-11T11:45:40Z","has_accepted_license":"1","isi":1,"year":"2018","day":"11","publication":"Letters in Mathematical Physics","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27","call_identifier":"FWF","_id":"25C878CE-B435-11E9-9278-68D0E5697425"}],"publist_id":"7586","author":[{"first_name":"Douglas","full_name":"Lundholm, Douglas","last_name":"Lundholm"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0002-6781-0521","full_name":"Seiringer, Robert","last_name":"Seiringer"}],"article_processing_charge":"No","external_id":{"isi":["000446491500008"],"arxiv":["1712.06218"]},"title":"Fermionic behavior of ideal anyons","citation":{"ama":"Lundholm D, Seiringer R. Fermionic behavior of ideal anyons. Letters in Mathematical Physics. 2018;108(11):2523-2541. doi:10.1007/s11005-018-1091-y","apa":"Lundholm, D., & Seiringer, R. (2018). Fermionic behavior of ideal anyons. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-018-1091-y","short":"D. Lundholm, R. Seiringer, Letters in Mathematical Physics 108 (2018) 2523–2541.","ieee":"D. Lundholm and R. Seiringer, “Fermionic behavior of ideal anyons,” Letters in Mathematical Physics, vol. 108, no. 11. Springer, pp. 2523–2541, 2018.","mla":"Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.” Letters in Mathematical Physics, vol. 108, no. 11, Springer, 2018, pp. 2523–41, doi:10.1007/s11005-018-1091-y.","ista":"Lundholm D, Seiringer R. 2018. Fermionic behavior of ideal anyons. Letters in Mathematical Physics. 108(11), 2523–2541.","chicago":"Lundholm, Douglas, and Robert Seiringer. “Fermionic Behavior of Ideal Anyons.” Letters in Mathematical Physics. Springer, 2018. https://doi.org/10.1007/s11005-018-1091-y."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","month":"05","intvolume":" 108","abstract":[{"lang":"eng","text":"We prove upper and lower bounds on the ground-state energy of the ideal two-dimensional anyon gas. Our bounds are extensive in the particle number, as for fermions, and linear in the statistics parameter (Formula presented.). The lower bounds extend to Lieb–Thirring inequalities for all anyons except bosons."}],"oa_version":"Published Version","issue":"11","volume":108,"ec_funded":1,"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5698","checksum":"8beb9632fa41bbd19452f55f31286a31","creator":"dernst","file_size":551996,"date_updated":"2020-07-14T12:45:55Z","file_name":"2018_LettMathPhys_Lundholm.pdf","date_created":"2018-12-17T12:14:17Z"}],"language":[{"iso":"eng"}],"type":"journal_article","tmp":{"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)","short":"CC BY (4.0)"},"status":"public","_id":"295","file_date_updated":"2020-07-14T12:45:55Z","department":[{"_id":"RoSe"}],"date_updated":"2023-09-11T14:01:57Z","ddc":["510"]}]