[{"project":[{"call_identifier":"FWF","_id":"265E2996-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems","grant_number":"W01250-B20"}],"title":"The implication of cytoskeletal dynamics on leukocyte migration","author":[{"orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja","last_name":"Kopf","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja"}],"article_processing_charge":"No","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"mla":"Kopf, Aglaja. The Implication of Cytoskeletal Dynamics on Leukocyte Migration. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6891.","short":"A. Kopf, The Implication of Cytoskeletal Dynamics on Leukocyte Migration, Institute of Science and Technology Austria, 2019.","ieee":"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","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.","ista":"Kopf A. 2019. The implication of cytoskeletal dynamics on leukocyte migration. Institute of Science and Technology Austria."},"publisher":"Institute of Science and Technology Austria","oa":1,"date_published":"2019-07-24T00:00:00Z","doi":"10.15479/AT:ISTA:6891","date_created":"2019-09-19T08:19:44Z","page":"171","day":"24","has_accepted_license":"1","year":"2019","status":"public","keyword":["cell biology","immunology","leukocyte","migration","microfluidics"],"type":"dissertation","_id":"6891","file_date_updated":"2020-10-17T22:30:03Z","department":[{"_id":"MiSi"}],"ddc":["570"],"supervisor":[{"last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"date_updated":"2023-10-18T08:49:17Z","month":"07","alternative_title":["ISTA Thesis"],"oa_version":"Published Version","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"}],"related_material":{"link":[{"relation":"press_release","url":"https://ist.ac.at/en/news/feeling-like-a-cell/"}],"record":[{"relation":"part_of_dissertation","id":"6328","status":"public"},{"relation":"part_of_dissertation","id":"15","status":"public"},{"id":"6877","status":"public","relation":"part_of_dissertation"}]},"file":[{"file_id":"6950","checksum":"00d100d6468e31e583051e0a006b640c","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","file_name":"Kopf_PhD_Thesis.docx","date_created":"2019-10-15T05:28:42Z","file_size":74735267,"date_updated":"2020-10-17T22:30:03Z","creator":"akopf"},{"file_name":"Kopf_PhD_Thesis1.pdf","date_created":"2019-10-15T05:28:47Z","file_size":52787224,"date_updated":"2020-10-17T22:30:03Z","creator":"akopf","embargo":"2020-10-16","checksum":"5d1baa899993ae6ca81aebebe1797000","file_id":"6951","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2663-337X"],"isbn":["978-3-99078-002-2"]},"degree_awarded":"PhD","publication_status":"published"},{"project":[{"call_identifier":"FP7","_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes (EU)","grant_number":"281556"},{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"724373","name":"Cellular navigation along spatial gradients"},{"_id":"265FAEBA-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"W01250-B20","name":"Nano-Analytics of Cellular Systems"},{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"grant_number":"ALTF 1396-2014","name":"Molecular and system level view of immune cell migration","_id":"25A48D24-B435-11E9-9278-68D0E5697425"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","citation":{"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","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","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.","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.","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."},"title":"Nuclear positioning facilitates amoeboid migration along the path of least resistance","article_processing_charge":"No","external_id":{"isi":["000465594200050"],"pmid":["30944468"]},"author":[{"last_name":"Renkawitz","full_name":"Renkawitz, Jörg","orcid":"0000-0003-2856-3369","first_name":"Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87"},{"id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","first_name":"Aglaja","last_name":"Kopf","orcid":"0000-0002-2187-6656","full_name":"Kopf, Aglaja"},{"first_name":"Julian A","id":"489E3F00-F248-11E8-B48F-1D18A9856A87","full_name":"Stopp, Julian A","last_name":"Stopp"},{"first_name":"Ingrid","id":"4C7D837E-F248-11E8-B48F-1D18A9856A87","last_name":"de Vries","full_name":"de Vries, Ingrid"},{"full_name":"Driscoll, Meghan K.","last_name":"Driscoll","first_name":"Meghan K."},{"orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack"},{"orcid":"0000-0001-9843-3522","full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert"},{"first_name":"Erik S.","last_name":"Welf","full_name":"Welf, Erik S."},{"first_name":"Gaudenz","full_name":"Danuser, Gaudenz","last_name":"Danuser"},{"full_name":"Fiolka, Reto","last_name":"Fiolka","first_name":"Reto"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179"}],"oa":1,"publisher":"Springer Nature","quality_controlled":"1","publication":"Nature","day":"25","year":"2019","isi":1,"date_created":"2019-04-17T06:52:28Z","date_published":"2019-04-25T00:00:00Z","doi":"10.1038/s41586-019-1087-5","page":"546-550","_id":"6328","status":"public","article_type":"letter_note","type":"journal_article","date_updated":"2024-03-27T23:30:39Z","department":[{"_id":"MiSi"},{"_id":"NanoFab"},{"_id":"Bio"}],"oa_version":"Submitted Version","pmid":1,"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"}],"acknowledged_ssus":[{"_id":"SSU"}],"intvolume":" 568","month":"04","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","ec_funded":1,"volume":568,"related_material":{"record":[{"relation":"dissertation_contains","id":"14697","status":"public"},{"status":"public","id":"6891","relation":"dissertation_contains"}],"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/","relation":"press_release"}]}},{"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.08.021","open_access":"1"}],"month":"09","intvolume":" 103","pmid":1,"oa_version":"Published Version","issue":"5","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"7902"}]},"volume":103,"publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"publication_status":"published","language":[{"iso":"eng"}],"article_type":"letter_note","type":"journal_article","status":"public","_id":"6830","department":[{"_id":"SiHi"}],"date_updated":"2024-03-27T23:30:41Z","quality_controlled":"1","publisher":"Elsevier","oa":1,"page":"750-752","doi":"10.1016/j.neuron.2019.08.021","date_published":"2019-09-04T00:00:00Z","date_created":"2019-08-25T22:00:50Z","isi":1,"year":"2019","day":"04","publication":"Neuron","author":[{"id":"475990FE-F248-11E8-B48F-1D18A9856A87","first_name":"Ximena","last_name":"Contreras","full_name":"Contreras, Ximena"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer"}],"external_id":{"pmid":["31487522"],"isi":["000484400200002"]},"article_processing_charge":"No","title":"Memo1 tiles the radial glial cell grid","citation":{"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.","ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 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.","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.","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"},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"publisher":"MDPI","quality_controlled":"1","oa":1,"has_accepted_license":"1","isi":1,"year":"2019","day":"07","publication":"International Journal of Molecular Sciences","date_published":"2019-07-07T00:00:00Z","doi":"10.3390/ijms20133337","date_created":"2019-07-11T12:00:32Z","article_number":"3337","project":[{"grant_number":"282300","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","_id":"25716A02-B435-11E9-9278-68D0E5697425"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"665385","name":"International IST Doctoral Program"},{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"citation":{"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.","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.","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","short":"M. Adamowski, L. Li, J. Friml, International Journal of Molecular Sciences 20 (2019).","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.","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."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"full_name":"Adamowski, Maciek","orcid":"0000-0001-6463-5257","last_name":"Adamowski","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","title":"Reorientation of cortical microtubule arrays in the hypocotyl of arabidopsis thaliana is induced by the cell growth process and independent of auxin signaling","abstract":[{"lang":"eng","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."}],"pmid":1,"oa_version":"Published Version","scopus_import":"1","month":"07","intvolume":" 20","publication_identifier":{"eissn":["1422-0067"]},"publication_status":"published","file":[{"checksum":"dd9d1cbb933a72ceb666c9667890ac51","file_id":"6645","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2019-07-17T06:17:15Z","file_name":"2019_JournalMolecularScience_Adamowski.pdf","creator":"dernst","date_updated":"2020-07-14T12:47:34Z","file_size":3330291}],"language":[{"iso":"eng"}],"issue":"13","related_material":{"record":[{"relation":"dissertation_contains","id":"10083","status":"public"}]},"volume":20,"license":"https://creativecommons.org/licenses/by/4.0/","ec_funded":1,"_id":"6627","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","date_updated":"2024-03-27T23:30:43Z","ddc":["580"],"file_date_updated":"2020-07-14T12:47:34Z","department":[{"_id":"JiFr"}]},{"ddc":["000"],"date_updated":"2024-03-27T23:30:46Z","department":[{"_id":"BeBi"}],"file_date_updated":"2020-07-14T12:47:49Z","_id":"7117","status":"public","article_type":"original","type":"journal_article","file":[{"title":"X-CAD Supplemental Material","date_created":"2019-11-26T14:24:26Z","file_name":"xcad_sup_mat_siga19.pdf","creator":"bbickel","date_updated":"2020-07-14T12:47:49Z","file_size":1673176,"file_id":"7119","checksum":"56a2fb019adcb556d2b022f5e5acb68c","access_level":"open_access","relation":"supplementary_material","content_type":"application/pdf"},{"file_id":"7120","checksum":"5f29d76aceb5102e766cbab9b17d776e","access_level":"open_access","relation":"main_file","content_type":"application/pdf","description":"This is the author's version of the work.","title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","date_created":"2019-11-26T14:24:27Z","file_name":"XCAD_authors_version.pdf","creator":"bbickel","date_updated":"2020-07-14T12:47:49Z","file_size":14563618},{"date_created":"2019-11-26T14:27:37Z","file_name":"XCAD_video.mp4","date_updated":"2020-07-14T12:47:49Z","file_size":259979129,"creator":"bbickel","file_id":"7121","checksum":"0d31e123286cbec9e28b2001c2bb0d55","content_type":"video/mp4","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0730-0301"]},"publication_status":"published","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"12897"}]},"issue":"6","volume":38,"ec_funded":1,"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"month":"11","intvolume":" 38","scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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.","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.","short":"C. Hafner, C. Schumacher, E. Knoop, T. Auzinger, B. Bickel, M. Bächer, ACM Transactions on Graphics 38 (2019).","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","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","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."},"title":"X-CAD: Optimizing CAD Models with Extended Finite Elements","author":[{"full_name":"Hafner, Christian","last_name":"Hafner","first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Christian","full_name":"Schumacher, Christian","last_name":"Schumacher"},{"first_name":"Espen","full_name":"Knoop, Espen","last_name":"Knoop"},{"last_name":"Auzinger","full_name":"Auzinger, Thomas","orcid":"0000-0002-1546-3265","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas"},{"orcid":"0000-0001-6511-9385","full_name":"Bickel, Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87","first_name":"Bernd"},{"first_name":"Moritz","last_name":"Bächer","full_name":"Bächer, Moritz"}],"external_id":{"isi":["000498397300007"]},"article_processing_charge":"No","article_number":"157","project":[{"grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425"}],"day":"06","publication":"ACM Transactions on Graphics","isi":1,"has_accepted_license":"1","year":"2019","date_published":"2019-11-06T00:00:00Z","doi":"10.1145/3355089.3356576","date_created":"2019-11-26T14:22:09Z","publisher":"ACM","quality_controlled":"1","oa":1},{"issue":"11","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"9728"}]},"volume":122,"publication_identifier":{"eissn":["10797114"],"issn":["00319007"]},"publication_status":"published","language":[{"iso":"eng"}],"scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.06358"}],"month":"03","intvolume":" 122","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","doi":"10.1103/PhysRevLett.122.114502","date_published":"2019-03-22T00:00:00Z","date_created":"2019-03-31T21:59:12Z","isi":1,"year":"2019","day":"22","publication":"Physical Review Letters","publisher":"American Physical Society","quality_controlled":"1","oa":1,"author":[{"last_name":"Agrawal","full_name":"Agrawal, Nishchal","first_name":"Nishchal","id":"469E6004-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Choueiri","full_name":"Choueiri, George H","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87","first_name":"George H"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","last_name":"Hof"}],"external_id":{"isi":["000461922000006"],"arxiv":["1809.06358"]},"article_processing_charge":"No","title":"Transition to turbulence in particle laden flows","citation":{"ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","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.","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"114502"},{"project":[{"_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture (DOC Fellowship)","grant_number":"24573"}],"author":[{"last_name":"Igler","full_name":"Igler, Claudia","first_name":"Claudia","id":"46613666-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","citation":{"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.","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.","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","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.","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"Institute of Science and Technology Austria","oa":1,"page":"152","doi":"10.15479/AT:ISTA:6371","date_published":"2019-05-03T00:00:00Z","date_created":"2019-05-03T11:55:51Z","has_accepted_license":"1","year":"2019","day":"03","type":"dissertation","status":"public","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"_id":"6371","department":[{"_id":"CaGu"}],"file_date_updated":"2021-02-11T11:17:13Z","supervisor":[{"orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C","last_name":"Guet","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"date_updated":"2024-02-21T13:45:52Z","ddc":["576","579"],"alternative_title":["ISTA Thesis"],"month":"05","abstract":[{"lang":"eng","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"}],"oa_version":"Published Version","related_material":{"record":[{"relation":"part_of_dissertation","id":"67","status":"public"},{"relation":"popular_science","status":"public","id":"5585"}]},"publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","date_created":"2019-05-03T11:54:52Z","creator":"cigler","file_size":12597663,"date_updated":"2021-02-11T11:17:13Z","embargo":"2020-05-02","file_id":"6373","checksum":"c0085d47c58c9cbcab1b0a783480f6da","relation":"main_file","access_level":"open_access","content_type":"application/pdf"},{"file_size":34644426,"date_updated":"2020-07-14T12:47:28Z","creator":"cigler","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","date_created":"2019-05-03T11:54:54Z","embargo_to":"open_access","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","access_level":"closed","checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","file_id":"6374"}],"language":[{"iso":"eng"}]},{"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"},{"full_name":"Petura, Oto","last_name":"Petura","first_name":"Oto"},{"full_name":"Bernard, Florent","last_name":"Bernard","first_name":"Florent"},{"full_name":"Laban, Marek","last_name":"Laban","first_name":"Marek"},{"full_name":"Fischer, Viktor","last_name":"Fischer","first_name":"Viktor"}],"title":"Evaluation and monitoring of free running oscillators serving as source of randomness","citation":{"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.","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","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."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","page":"214-242","date_created":"2021-11-14T23:01:25Z","doi":"10.13154/tches.v2018.i3.214-242","date_published":"2018-01-01T00:00:00Z","year":"2018","has_accepted_license":"1","publication":"IACR Transactions on Cryptographic Hardware and Embedded Systems","day":"01","oa":1,"publisher":"International Association for Cryptologic Research","quality_controlled":"1","file_date_updated":"2021-11-15T10:27:29Z","department":[{"_id":"KrPi"}],"date_updated":"2021-11-15T10:48:49Z","ddc":["000"],"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","status":"public","_id":"10286","volume":2018,"issue":"3","publication_status":"published","publication_identifier":{"eissn":["2569-2925"]},"language":[{"iso":"eng"}],"file":[{"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","success":1,"checksum":"b816b848f046c48a8357700d9305dce5","file_id":"10289","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"scopus_import":"1","intvolume":" 2018","month":"01","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version"},{"file_date_updated":"2022-05-17T07:51:08Z","department":[{"_id":"KrCh"}],"ddc":["000"],"date_updated":"2022-07-29T09:24:31Z","status":"public","type":"conference","conference":{"end_date":"2018-11-21","location":"Awassa, Ethiopia","start_date":"2018-11-17","name":"LPAR: Conference on Logic for Programming, Artificial Intelligence and Reasoning"},"_id":"10883","volume":57,"ec_funded":1,"file":[{"success":1,"file_id":"11392","checksum":"1229aa8640bd6db610c85decf2265480","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_EPiCs_Chatterjee.pdf","date_created":"2022-05-17T07:51:08Z","file_size":720893,"date_updated":"2022-05-17T07:51:08Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2398-7340"]},"publication_status":"published","month":"10","intvolume":" 57","alternative_title":["EPiC Series in Computing"],"scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"title":"Quasipolynomial set-based symbolic algorithms for parity games","author":[{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"},{"last_name":"Dvořák","full_name":"Dvořák, Wolfgang","first_name":"Wolfgang"},{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","last_name":"Henzinger","first_name":"Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"first_name":"Alexander","last_name":"Svozil","full_name":"Svozil, Alexander"}],"article_processing_charge":"No","external_id":{"arxiv":["1909.04983"]},"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.","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","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."},"project":[{"_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11407","name":"Game Theory"},{"grant_number":"279307","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"doi":"10.29007/5z5k","date_published":"2018-10-23T00:00:00Z","date_created":"2022-03-18T12:46:32Z","page":"233-253","day":"23","publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","has_accepted_license":"1","year":"2018","publisher":"EasyChair","quality_controlled":"1","oa":1,"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."},{"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"volume":270,"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10843"}],"scopus_import":1,"intvolume":" 270","month":"10","date_updated":"2021-01-12T06:48:16Z","department":[{"_id":"RoSe"}],"_id":"11","conference":{"location":"Munich, Germany","end_date":"2017-04-01","start_date":"2017-03-30","name":"MaLiQS: Macroscopic Limits of Quantum Systems"},"type":"conference","status":"public","year":"2018","day":"27","page":"185 - 214","date_created":"2018-12-11T11:44:08Z","doi":"10.1007/978-3-030-01602-9_9","date_published":"2018-10-27T00:00:00Z","oa":1,"publisher":"Springer","quality_controlled":"1","citation":{"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.","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.","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.","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.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["1806.10843"]},"publist_id":"8045","author":[{"id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K","full_name":"Leopold, Nikolai K","orcid":"0000-0002-0495-6822","last_name":"Leopold"},{"full_name":"Pickl, Peter","last_name":"Pickl","first_name":"Peter"}],"title":"Mean-field limits of particles in interaction with quantised radiation fields","project":[{"grant_number":"694227","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}]},{"publist_id":"6119","author":[{"last_name":"Flandoli","full_name":"Flandoli, Franco","first_name":"Franco"},{"full_name":"Russo, Francesco","last_name":"Russo","first_name":"Francesco"},{"last_name":"Zanco","full_name":"Zanco, Giovanni A","id":"47491882-F248-11E8-B48F-1D18A9856A87","first_name":"Giovanni A"}],"article_processing_charge":"Yes (via OA deal)","title":"Infinite-dimensional calculus under weak spatial regularity of the processes","citation":{"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.","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.","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","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","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.","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"page":"789-826","doi":"10.1007/s10959-016-0724-2","date_published":"2018-06-01T00:00:00Z","date_created":"2018-12-11T11:50:45Z","has_accepted_license":"1","year":"2018","day":"01","publication":"Journal of Theoretical Probability","quality_controlled":"1","publisher":"Springer","oa":1,"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.","department":[{"_id":"JaMa"}],"file_date_updated":"2020-07-14T12:44:39Z","date_updated":"2021-01-12T06:49:09Z","ddc":["519"],"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","pubrep_id":"712","_id":"1215","issue":"2","volume":31,"publication_status":"published","file":[{"file_name":"IST-2016-712-v1+1_s10959-016-0724-2.pdf","date_created":"2018-12-12T10:17:13Z","file_size":671125,"date_updated":"2020-07-14T12:44:39Z","creator":"system","file_id":"5266","checksum":"47686d58ec21c164540f1a980ff2163f","content_type":"application/pdf","relation":"main_file","access_level":"open_access"}],"language":[{"iso":"eng"}],"scopus_import":1,"month":"06","intvolume":" 31","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"}],"oa_version":"Published Version"},{"ddc":["510"],"date_updated":"2021-01-12T06:53:36Z","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:45:19Z","_id":"185","status":"public","conference":{"start_date":"2018-06-11","end_date":"2018-06-14","location":"Budapest, Hungary","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)"},"type":"conference","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","file_id":"5701","creator":"dernst","date_updated":"2020-07-14T12:45:19Z","file_size":718857,"date_created":"2018-12-17T12:33:52Z","file_name":"2018_LIPIcs_Fulek.pdf"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-95977-066-8"]},"volume":99,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 99","month":"01","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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."},"title":"Hanani-Tutte for approximating maps of graphs","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Kynčl","full_name":"Kynčl, Jan","first_name":"Jan"}],"publist_id":"7735","article_number":"39","project":[{"call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"day":"01","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:45:04Z","date_published":"2018-01-01T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.39","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1"},{"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"],"intvolume":" 99","month":"06","publication_status":"published","language":[{"iso":"eng"}],"file":[{"checksum":"7509403803b3ac1aee94bbc2ad293d21","file_id":"5724","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2018-12-17T16:31:31Z","file_name":"2018_LIPIcs_Edelsbrunner.pdf","date_updated":"2020-07-14T12:45:20Z","file_size":489080,"creator":"dernst"}],"volume":99,"_id":"188","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":{"location":"Budapest, Hungary","end_date":"2018-06-14","start_date":"2018-06-11","name":"SoCG: Symposium on Computational Geometry"},"type":"conference","status":"public","date_updated":"2021-01-12T06:53:48Z","ddc":["000"],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:45:20Z","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","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","year":"2018","has_accepted_license":"1","day":"11","page":"35:1 - 35:13","date_created":"2018-12-11T11:45:05Z","doi":"10.4230/LIPIcs.SoCG.2018.35","date_published":"2018-06-11T00:00:00Z","project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"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.","short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, 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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7733","author":[{"first_name":"Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"last_name":"Virk","full_name":"Virk, Ziga","first_name":"Ziga"},{"id":"379CA8B8-F248-11E8-B48F-1D18A9856A87","first_name":"Hubert","last_name":"Wagner","full_name":"Wagner, Hubert"}],"title":"Smallest enclosing spheres and Chernoff points in Bregman geometry"},{"_id":"306","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","date_updated":"2021-01-12T07:40:46Z","ddc":["530"],"department":[{"_id":"GaTk"}],"file_date_updated":"2020-07-14T12:45:59Z","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."}],"oa_version":"Published Version","scopus_import":1,"month":"04","intvolume":" 4","publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5929","checksum":"67010cf5e3b3e0637c659371714a715a","file_size":994490,"date_updated":"2020-07-14T12:45:59Z","creator":"dernst","file_name":"2018_Heliyon_DeMartino.pdf","date_created":"2019-02-06T07:36:24Z"}],"language":[{"iso":"eng"}],"issue":"4","volume":4,"ec_funded":1,"article_number":"e00596","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"citation":{"short":"A. De Martino, D. De Martino, Heliyon 4 (2018).","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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Andrea","full_name":"De Martino, Andrea","last_name":"De Martino"},{"last_name":"De Martino","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"}],"title":"An introduction to the maximum entropy approach and its application to inference problems in biology","publisher":"Elsevier","quality_controlled":"1","oa":1,"has_accepted_license":"1","year":"2018","day":"01","publication":"Heliyon","doi":"10.1016/j.heliyon.2018.e00596","date_published":"2018-04-01T00:00:00Z","date_created":"2018-12-11T11:45:44Z"},{"file_date_updated":"2020-10-13T14:20:37Z","department":[{"_id":"AnKi"}],"date_updated":"2021-01-12T07:49:03Z","ddc":["570"],"type":"book_chapter","status":"public","_id":"37","series_title":"MIMB","volume":1863,"ec_funded":1,"publication_identifier":{"isbn":["978-1-4939-8771-9"],"issn":["1064-3745"]},"publication_status":"published","file":[{"file_id":"8656","checksum":"2a97d0649fdcfcf1bdca7c8ad1dce71b","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","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}],"language":[{"iso":"eng"}],"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","publist_id":"8018","author":[{"orcid":"0000-0001-7896-7762","full_name":"Zagórski, Marcin P","last_name":"Zagórski","id":"343DA0DC-F248-11E8-B48F-1D18A9856A87","first_name":"Marcin P"},{"orcid":"0000-0003-4509-4998","full_name":"Kicheva, Anna","last_name":"Kicheva","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","first_name":"Anna"}],"article_processing_charge":"No","title":"Measuring dorsoventral pattern and morphogen signaling profiles in the growing neural tube","citation":{"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.","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.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"680037","name":"Coordination of Patterning And Growth In the Spinal Cord","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"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 ","publisher":"Springer Nature","quality_controlled":"1","oa":1},{"article_number":"34","project":[{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","short":"S. Agrawal, K. Chatterjee, P. Novotný, in:, ACM, 2018.","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.","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."},"title":"Lexicographic ranking supermartingales: an efficient approach to termination of probabilistic programs","author":[{"first_name":"Sheshansh","full_name":"Agrawal, Sheshansh","last_name":"Agrawal"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","first_name":"Petr","last_name":"Novotny","full_name":"Novotny, Petr"}],"publist_id":"7540","external_id":{"arxiv":["1709.04037"]},"publisher":"ACM","quality_controlled":"1","oa":1,"day":"01","year":"2018","doi":"10.1145/3158122","date_published":"2018-01-01T00:00:00Z","date_created":"2018-12-11T11:45:50Z","_id":"325","status":"public","type":"conference","conference":{"location":"Los Angeles, CA, USA","end_date":"2018-01-13","start_date":"2018-01-07","name":"POPL: Principles of Programming Languages"},"date_updated":"2021-01-12T07:42:07Z","department":[{"_id":"KrCh"}],"oa_version":"Preprint","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"}],"month":"01","intvolume":" 2","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.04037"}],"language":[{"iso":"eng"}],"publication_status":"published","issue":"POPL","volume":2},{"publication":"VÖB Mitteilungen","day":"01","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:44:22Z","doi":"10.31263/voebm.v71i1.1993","date_published":"2018-10-01T00:00:00Z","page":"199 - 206","oa":1,"publisher":"Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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","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","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.","short":"B. Petritsch, J. Porsche, VÖB Mitteilungen 71 (2018) 199–206.","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."},"title":"IST PubRep and IST DataRep: the institutional repositories at IST Austria","publist_id":"8001","author":[{"orcid":"0000-0003-2724-4614","full_name":"Petritsch, Barbara","last_name":"Petritsch","id":"406048EC-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara"},{"id":"3252EDC2-F248-11E8-B48F-1D18A9856A87","first_name":"Jana","full_name":"Porsche, Jana","last_name":"Porsche"}],"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":509434,"date_updated":"2020-07-14T12:46:38Z","file_name":"2018_VOEB_Petritsch.pdf","date_created":"2018-12-17T12:40:27Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"5702","checksum":"7ac61bade5f37db011ca435ebcf86797"}],"publication_status":"published","volume":71,"issue":"1","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 71","month":"10","scopus_import":1,"ddc":["020"],"date_updated":"2021-01-12T08:01:26Z","file_date_updated":"2020-07-14T12:46:38Z","department":[{"_id":"E-Lib"}],"_id":"53","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"},{"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","citation":{"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","short":"D.-A. Alistarh, J. Aspnes, V. King, J. Saia, Distributed Computing 31 (2018) 489–501.","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.","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.","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."},"title":"Communication-efficient randomized consensus","article_processing_charge":"Yes (via OA deal)","publist_id":"7281","author":[{"last_name":"Alistarh","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Aspnes, James","last_name":"Aspnes","first_name":"James"},{"full_name":"King, Valerie","last_name":"King","first_name":"Valerie"},{"first_name":"Jared","full_name":"Saia, Jared","last_name":"Saia"}],"oa":1,"quality_controlled":"1","publisher":"Springer","publication":"Distributed Computing","day":"01","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:47:01Z","doi":"10.1007/s00446-017-0315-1","date_published":"2018-11-01T00:00:00Z","page":"489-501","_id":"536","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":["000"],"date_updated":"2023-02-23T12:23:25Z","file_date_updated":"2020-07-14T12:46:38Z","department":[{"_id":"DaAl"}],"oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 31","month":"11","scopus_import":1,"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"5867","checksum":"69b46e537acdcac745237ddb853fcbb5","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"}],"publication_status":"published","publication_identifier":{"issn":["01782770"]},"volume":31,"issue":"6"},{"title":"The Bogoliubov free energy functional II: The dilute Limit","external_id":{"arxiv":["1511.05953"]},"publist_id":"7260","author":[{"first_name":"Marcin M","id":"4197AD04-F248-11E8-B48F-1D18A9856A87","last_name":"Napiórkowski","full_name":"Napiórkowski, Marcin M"},{"full_name":"Reuvers, Robin","last_name":"Reuvers","first_name":"Robin"},{"full_name":"Solovej, Jan","last_name":"Solovej","first_name":"Jan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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.","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","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","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.","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."},"project":[{"_id":"25C878CE-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","grant_number":"P27533_N27"}],"date_created":"2018-12-11T11:47:09Z","doi":"10.1007/s00220-017-3064-x","date_published":"2018-05-01T00:00:00Z","page":"347-403","publication":"Communications in Mathematical Physics","day":"01","year":"2018","oa":1,"quality_controlled":"1","publisher":"Springer","department":[{"_id":"RoSe"}],"date_updated":"2021-01-12T08:02:35Z","status":"public","type":"journal_article","_id":"554","issue":"1","volume":360,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["00103616"]},"intvolume":" 360","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1511.05953"}],"scopus_import":1,"oa_version":"Submitted Version","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.)."}]},{"page":"201 - 215","date_published":"2018-01-01T00:00:00Z","doi":"10.1007/978-1-4939-7571-6_15","date_created":"2018-12-11T11:47:11Z","has_accepted_license":"1","year":"2018","day":"01","publication":"Neurotrophic Factors","quality_controlled":"1","publisher":"Springer","oa":1,"author":[{"first_name":"Dimitar","full_name":"Dimitrov, Dimitar","last_name":"Dimitrov"},{"first_name":"Laurent","last_name":"Guillaud","full_name":"Guillaud, Laurent"},{"last_name":"Eguchi","orcid":"0000-0002-6170-2546","full_name":"Eguchi, Kohgaku","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","first_name":"Kohgaku"},{"first_name":"Tomoyuki","full_name":"Takahashi, Tomoyuki","last_name":"Takahashi"}],"publist_id":"7252","external_id":{"pmid":["29222783"]},"article_processing_charge":"No","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":{"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","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.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":1727,"publication_status":"published","file":[{"file_id":"7046","checksum":"8aa174ca65a56fbb19e9f88cff3ac3fd","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_NeurotrophicFactors_Dimitrov.pdf","date_created":"2019-11-19T07:47:43Z","file_size":787407,"date_updated":"2020-07-14T12:47:09Z","creator":"dernst"}],"language":[{"iso":"eng"}],"alternative_title":["Methods in Molecular Biology"],"scopus_import":1,"month":"01","intvolume":" 1727","abstract":[{"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.","lang":"eng"}],"pmid":1,"oa_version":"Submitted Version","department":[{"_id":"RySh"}],"file_date_updated":"2020-07-14T12:47:09Z","date_updated":"2021-01-12T08:03:05Z","ddc":["570"],"type":"book_chapter","status":"public","_id":"562"},{"intvolume":" 8","month":"09","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","ec_funded":1,"volume":8,"issue":"18","publication_status":"published","publication_identifier":{"issn":["2331-8325"]},"language":[{"iso":"eng"}],"file":[{"checksum":"d4588377e789da7f360b553ae02c5119","file_id":"6360","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2018_BioProtocol_Fan.pdf","date_created":"2019-04-30T08:04:33Z","file_size":2928337,"date_updated":"2020-07-14T12:47:28Z","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","keyword":["Platelets","Cell migration","Bacteria","Shear flow","Fibrinogen","E. coli"],"status":"public","_id":"6354","file_date_updated":"2020-07-14T12:47:28Z","department":[{"_id":"MiSi"}],"date_updated":"2021-01-12T08:07:12Z","ddc":["570"],"oa":1,"quality_controlled":"1","publisher":"Bio-Protocol","acknowledgement":" FöFoLe project 947 (F.G.), the Friedrich-Baur-Stiftung project 41/16 (F.G.)","date_created":"2019-04-29T09:40:33Z","date_published":"2018-09-20T00:00:00Z","doi":"10.21769/bioprotoc.3018","year":"2018","has_accepted_license":"1","publication":"Bio-Protocol","day":"20","project":[{"name":"Mechanical Adaptation of Lamellipodial Actin Networks in Migrating Cells","grant_number":"747687","_id":"260AA4E2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"article_number":"e3018","author":[{"full_name":"Fan, Shuxia","last_name":"Fan","first_name":"Shuxia"},{"first_name":"Michael","full_name":"Lorenz, Michael","last_name":"Lorenz"},{"full_name":"Massberg, Steffen","last_name":"Massberg","first_name":"Steffen"},{"first_name":"Florian R","id":"397A88EE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6120-3723","full_name":"Gärtner, Florian R","last_name":"Gärtner"}],"title":"Platelet migration and bacterial trapping assay under flow","citation":{"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.","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).","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","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","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."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"author":[{"id":"406048EC-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara","last_name":"Petritsch","orcid":"0000-0003-2724-4614","full_name":"Petritsch, Barbara"}],"department":[{"_id":"E-Lib"}],"file_date_updated":"2020-07-14T12:47:30Z","title":"Open Access at IST Austria 2009-2017","citation":{"chicago":"Petritsch, Barbara. Open Access at IST Austria 2009-2017. IST Austria, 2018. https://doi.org/10.5281/zenodo.1410279.","ista":"Petritsch B. 2018. Open Access at IST Austria 2009-2017, IST Austria,p.","mla":"Petritsch, Barbara. 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.","ama":"Petritsch B. Open Access at IST Austria 2009-2017. IST Austria; 2018. doi:10.5281/zenodo.1410279","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"},"date_updated":"2020-07-14T23:06:21Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["020"],"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","doi":"10.5281/zenodo.1410279","date_published":"2018-09-24T00:00:00Z","date_created":"2019-05-16T07:27:14Z","has_accepted_license":"1","year":"2018","publication_status":"published","day":"24","file":[{"date_created":"2019-05-16T07:26:25Z","file_name":"Poster_Beitrag_125_Petritsch.pdf","date_updated":"2020-07-14T12:47:30Z","file_size":1967778,"creator":"dernst","file_id":"6460","checksum":"9063ab4d10ea93353c3a03bbf53fbcf1","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publisher":"IST Austria","oa":1,"month":"09","oa_version":"Published Version"},{"department":[{"_id":"LaEr"}],"date_updated":"2021-01-12T08:09:33Z","type":"journal_article","status":"public","_id":"690","ec_funded":1,"volume":171,"issue":"1-2","publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1605.08767"}],"scopus_import":1,"intvolume":" 171","month":"06","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","external_id":{"arxiv":["1605.08767"]},"author":[{"first_name":"Jii","full_name":"Lee, Jii","last_name":"Lee"},{"last_name":"Schnelli","full_name":"Schnelli, Kevin","orcid":"0000-0003-0954-3231","first_name":"Kevin","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7017","title":"Local law and Tracy–Widom limit for sparse random matrices","citation":{"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.","short":"J. Lee, K. Schnelli, Probability Theory and Related Fields 171 (2018).","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","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","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","project":[{"grant_number":"338804","name":"Random matrices, universality and disordered quantum systems","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"article_number":"543-616","date_created":"2018-12-11T11:47:56Z","doi":"10.1007/s00440-017-0787-8","date_published":"2018-06-14T00:00:00Z","year":"2018","publication":"Probability Theory and Related Fields","day":"14","oa":1,"publisher":"Springer","quality_controlled":"1"},{"oa":1,"quality_controlled":"1","publisher":"IEEE","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","day":"01","year":"2018","date_created":"2018-12-11T11:48:01Z","date_published":"2018-07-01T00:00:00Z","doi":"10.1109/TPAMI.2017.2730884","page":"1668-1682","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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."},"title":"Maximum persistency via iterative relaxed inference with graphical models","external_id":{"arxiv":["1508.07902"]},"publist_id":"6992","author":[{"full_name":"Shekhovtsov, Alexander","last_name":"Shekhovtsov","first_name":"Alexander"},{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","full_name":"Swoboda, Paul","last_name":"Swoboda"},{"first_name":"Bogdan","last_name":"Savchynskyy","full_name":"Savchynskyy, Bogdan"}],"oa_version":"Preprint","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."}],"intvolume":" 40","month":"07","main_file_link":[{"url":"https://arxiv.org/abs/1508.07902","open_access":"1"}],"scopus_import":1,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["01628828"]},"volume":40,"issue":"7","_id":"703","status":"public","type":"journal_article","date_updated":"2021-01-12T08:11:32Z","department":[{"_id":"VlKo"}]},{"quality_controlled":"1","publisher":"OpenProceedings","oa":1,"page":"145-156","date_published":"2018-03-26T00:00:00Z","doi":"10.5441/002/EDBT.2018.14","date_created":"2019-11-26T14:19:11Z","has_accepted_license":"1","year":"2018","day":"26","publication":"Proceedings of the 21st International Conference on Extending Database Technology","author":[{"full_name":"Grubic, Demjan","last_name":"Grubic","first_name":"Demjan"},{"last_name":"Tam","full_name":"Tam, Leo","first_name":"Leo"},{"last_name":"Alistarh","orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Ce","last_name":"Zhang","full_name":"Zhang, Ce"}],"article_processing_charge":"No","title":"Synchronous multi-GPU training for deep learning with low-precision communications: An empirical study","citation":{"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.","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"month":"03","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."}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication_identifier":{"issn":["2367-2005"],"isbn":["9783893180783"]},"publication_status":"published","file":[{"file_id":"7118","checksum":"ec979b56abc71016d6e6adfdadbb4afe","content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2019-11-26T14:23:04Z","file_name":"2018_OpenProceedings_Grubic.pdf","date_updated":"2020-07-14T12:47:49Z","file_size":1603204,"creator":"dernst"}],"language":[{"iso":"eng"}],"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":{"start_date":"2018-03-26","end_date":"2018-03-29","location":"Vienna, Austria","name":"EDBT: Conference on Extending Database Technology"},"status":"public","_id":"7116","department":[{"_id":"DaAl"}],"file_date_updated":"2020-07-14T12:47:49Z","date_updated":"2023-02-23T12:59:17Z","ddc":["000"]},{"file":[{"checksum":"5cebb7f7849a3beda898f697d755dd96","file_id":"7443","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_LIPIcs_Pietrzak.pdf","date_created":"2020-02-04T08:17:52Z","creator":"dernst","file_size":822884,"date_updated":"2020-07-14T12:47:57Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["978-3-95977-095-8"],"issn":["1868-8969"]},"publication_status":"published","volume":124,"ec_funded":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"month":"12","intvolume":" 124","scopus_import":1,"alternative_title":["LIPIcs"],"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/194"}],"ddc":["000"],"date_updated":"2021-01-12T08:13:26Z","file_date_updated":"2020-07-14T12:47:57Z","department":[{"_id":"KrPi"}],"_id":"7407","status":"public","type":"conference","conference":{"location":"San Diego, CA, United States","end_date":"2019-01-12","start_date":"2019-01-10","name":"ITCS: Innovations in theoretical Computer Science 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)"},"day":"31","publication":"10th Innovations in Theoretical Computer Science Conference (ITCS 2019)","has_accepted_license":"1","year":"2018","date_published":"2018-12-31T00:00:00Z","doi":"10.4230/LIPICS.ITCS.2019.59","date_created":"2020-01-30T09:16:05Z","page":"59:1-59:25","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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."},"title":"Proofs of catalytic space","author":[{"last_name":"Pietrzak","orcid":"0000-0002-9139-1654","full_name":"Pietrzak, Krzysztof Z","first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","project":[{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}]},{"file_date_updated":"2020-07-14T12:48:03Z","title":"Model compression via distillation and quantization","department":[{"_id":"DaAl"}],"author":[{"first_name":"Antonio","full_name":"Polino, Antonio","last_name":"Polino"},{"full_name":"Pascanu, Razvan","last_name":"Pascanu","first_name":"Razvan"},{"first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh"}],"article_processing_charge":"No","external_id":{"arxiv":["1802.05668"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"date_updated":"2023-02-23T13:18:41Z","citation":{"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.","mla":"Polino, Antonio, et al. “Model Compression via Distillation and Quantization.” 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.","short":"A. Polino, R. Pascanu, D.-A. Alistarh, 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.","ama":"Polino A, Pascanu R, Alistarh D-A. Model compression via distillation and quantization. In: 6th International Conference on Learning Representations. ; 2018."},"status":"public","type":"conference","conference":{"start_date":"2018-04-30","end_date":"2018-05-03","location":"Vancouver, Canada","name":"ICLR: International Conference on Learning Representations"},"_id":"7812","date_published":"2018-05-01T00:00:00Z","date_created":"2020-05-10T22:00:51Z","file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"a4336c167978e81891970e4e4517a8c3","file_id":"7894","date_updated":"2020-07-14T12:48:03Z","file_size":308339,"creator":"dernst","date_created":"2020-05-26T13:02:00Z","file_name":"2018_ICLR_Polino.pdf"}],"day":"01","language":[{"iso":"eng"}],"publication":"6th International Conference on Learning Representations","has_accepted_license":"1","year":"2018","publication_status":"published","month":"05","quality_controlled":"1","scopus_import":1,"oa":1,"oa_version":"Published Version","abstract":[{"lang":"eng","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."}]},{"year":"2018","publication_status":"submitted","day":"13","language":[{"iso":"eng"}],"publication":"bioRxiv","doi":"10.1101/494088","date_published":"2018-12-13T00:00:00Z","date_created":"2020-09-21T12:01:50Z","ec_funded":1,"abstract":[{"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.","lang":"eng"}],"oa_version":"Preprint","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.","publisher":"Cold Spring Harbor Laboratory","oa":1,"main_file_link":[{"url":"https://doi.org/10.1101/494088","open_access":"1"}],"month":"12","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.","ama":"Llorca A, Ciceri G, Beattie RJ, et al. Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture. bioRxiv. doi:10.1101/494088","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","ieee":"A. Llorca et al., “Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture,” bioRxiv. Cold Spring Harbor Laboratory.","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.)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Alfredo","full_name":"Llorca, Alfredo","last_name":"Llorca"},{"full_name":"Ciceri, Gabriele","last_name":"Ciceri","first_name":"Gabriele"},{"orcid":"0000-0002-8483-8753","full_name":"Beattie, Robert J","last_name":"Beattie","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","first_name":"Robert J"},{"first_name":"Fong K.","last_name":"Wong","full_name":"Wong, Fong K."},{"last_name":"Diana","full_name":"Diana, Giovanni","first_name":"Giovanni"},{"first_name":"Eleni","last_name":"Serafeimidou","full_name":"Serafeimidou, Eleni"},{"full_name":"Fernández-Otero, Marian","last_name":"Fernández-Otero","first_name":"Marian"},{"id":"36BCB99C-F248-11E8-B48F-1D18A9856A87","first_name":"Carmen","full_name":"Streicher, Carmen","last_name":"Streicher"},{"first_name":"Sebastian J.","last_name":"Arnold","full_name":"Arnold, Sebastian J."},{"full_name":"Meyer, Martin","last_name":"Meyer","first_name":"Martin"},{"first_name":"Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon"},{"first_name":"Miguel","full_name":"Maravall, Miguel","last_name":"Maravall"},{"last_name":"Marín","full_name":"Marín, Oscar","first_name":"Oscar"}],"article_processing_charge":"No","title":"Heterogeneous progenitor cell behaviors underlie the assembly of neocortical cytoarchitecture","department":[{"_id":"SiHi"}],"_id":"8547","type":"preprint","project":[{"call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","grant_number":"725780","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"},{"call_identifier":"FWF","_id":"264E56E2-B435-11E9-9278-68D0E5697425","grant_number":"M02416","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex"}],"status":"public"},{"editor":[{"last_name":"Lohstroh","full_name":"Lohstroh, Marten","first_name":"Marten"},{"last_name":"Derler","full_name":"Derler, Patricia","first_name":"Patricia"},{"first_name":"Marjan","last_name":"Sirjani","full_name":"Sirjani, Marjan"}],"title":"Computing average response time","publist_id":"7968","author":[{"last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","last_name":"Otop","full_name":"Otop, Jan"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","ista":"Chatterjee K, Henzinger TA, Otop J. 2018.Computing average response time. In: Principles of Modeling. LNCS, vol. 10760, 143–161.","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."},"project":[{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"name":"Game Theory","grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"Z211","name":"The Wittgenstein Prize","_id":"25F42A32-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"},{"name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425"}],"doi":"10.1007/978-3-319-95246-8_9","date_published":"2018-07-20T00:00:00Z","date_created":"2018-12-11T11:44:33Z","page":"143 - 161","day":"20","publication":"Principles of Modeling","has_accepted_license":"1","year":"2018","publisher":"Springer","quality_controlled":"1","oa":1,"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.","file_date_updated":"2020-07-14T12:48:14Z","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"ddc":["000"],"date_updated":"2021-01-12T08:20:14Z","status":"public","type":"book_chapter","_id":"86","volume":10760,"ec_funded":1,"file":[{"date_created":"2019-11-19T08:22:18Z","file_name":"2018_PrinciplesModeling_Chatterjee.pdf","date_updated":"2020-07-14T12:48:14Z","file_size":516307,"creator":"dernst","file_id":"7053","checksum":"9995c6ce6957333baf616fc4f20be597","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"07","intvolume":" 10760","scopus_import":1,"alternative_title":["LNCS"],"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}]},{"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"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.","ista":"Danzl JG. 2018. Diffraction-unlimited optical imaging for synaptic physiology. Opera Medica et Physiologica. 4(S1), 11.","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.","short":"J.G. Danzl, Opera Medica et Physiologica 4 (2018) 11.","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.","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"},"title":"Diffraction-unlimited optical imaging for synaptic physiology","author":[{"id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johann G","last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G"}],"article_processing_charge":"No","quality_controlled":"1","publisher":"Lobachevsky State University of Nizhny Novgorod","oa":1,"day":"30","publication":"Opera Medica et Physiologica","year":"2018","date_published":"2018-06-30T00:00:00Z","doi":"10.20388/omp2018.00s1.001","date_created":"2021-03-07T23:01:25Z","page":"11","_id":"9229","status":"public","article_type":"letter_note","type":"journal_article","date_updated":"2021-12-03T07:31:05Z","department":[{"_id":"JoDa"}],"oa_version":"Published Version","month":"06","intvolume":" 4","alternative_title":["Molecular and cellular neuroscience"],"scopus_import":"1","main_file_link":[{"url":"http://operamedphys.org/content/molecular-and-cellular-neuroscience","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["2500-2287"],"eissn":["2500-2295"]},"publication_status":"published","volume":4,"issue":"S1"},{"oa":1,"quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","year":"2018","has_accepted_license":"1","day":"01","date_created":"2019-02-14T14:12:09Z","doi":"10.4230/LIPICS.MFCS.2018.23","date_published":"2018-08-01T00:00:00Z","article_number":"23","project":[{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"},{"call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","grant_number":"Z211"},{"_id":"264B3912-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Formal Methods meets Algorithmic Game Theory","grant_number":"M02369"}],"citation":{"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.","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.","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","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","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.","ista":"Avni G, Guha S, Kupferman O. 2018. Timed network games with clocks. MFCS: Mathematical Foundations of Computer Science, LIPIcs, vol. 117, 23."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"last_name":"Avni","orcid":"0000-0001-5588-8287","full_name":"Avni, Guy","id":"463C8BC2-F248-11E8-B48F-1D18A9856A87","first_name":"Guy"},{"first_name":"Shibashis","full_name":"Guha, Shibashis","last_name":"Guha"},{"first_name":"Orna","full_name":"Kupferman, Orna","last_name":"Kupferman"}],"title":"Timed network games with clocks","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":"1","intvolume":" 117","month":"08","publication_status":"published","publication_identifier":{"issn":["1868-8969"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"41ab2ae9b63f5eb49fa995250c0ba128","file_id":"6007","date_updated":"2020-07-14T12:47:15Z","file_size":542889,"creator":"dernst","date_created":"2019-02-14T14:22:04Z","file_name":"2018_LIPIcs_Avni.pdf"}],"volume":117,"related_material":{"record":[{"id":"963","status":"public","relation":"earlier_version"}]},"_id":"6005","conference":{"name":"MFCS: Mathematical Foundations of Computer Science","start_date":"2018-08-27","end_date":"2018-08-31","location":"Liverpool, United Kingdom"},"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":"2023-02-23T14:02:58Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:47:15Z"},{"issue":"6","volume":16,"related_material":{"record":[{"id":"9839","status":"public","relation":"research_data"}]},"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"908c52751bba30c55ed36789e5e4c84d","file_id":"5870","date_updated":"2020-07-14T12:46:01Z","file_size":6968201,"creator":"dernst","date_created":"2019-01-22T08:30:03Z","file_name":"2017_PLOS_Polechova.pdf"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["15449173"]},"publication_status":"published","month":"06","intvolume":" 16","scopus_import":1,"oa_version":"Published Version","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."}],"department":[{"_id":"NiBa"}],"file_date_updated":"2020-07-14T12:46:01Z","ddc":["576"],"date_updated":"2023-02-23T14:10:16Z","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)"},"_id":"315","date_published":"2018-06-15T00:00:00Z","doi":"10.1371/journal.pbio.2005372","date_created":"2018-12-11T11:45:46Z","day":"15","publication":"PLoS Biology","has_accepted_license":"1","year":"2018","quality_controlled":"1","publisher":"Public Library of Science","oa":1,"title":"Is the sky the limit? On the expansion threshold of a species’ range","author":[{"last_name":"Polechova","orcid":"0000-0003-0951-3112","full_name":"Polechova, Jitka","first_name":"Jitka","id":"3BBFB084-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7550","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","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"},"article_number":"e2005372"},{"scopus_import":"1","alternative_title":["LIPIcs"],"main_file_link":[{"url":"https://arxiv.org/abs/1803.05085","open_access":"1"}],"month":"06","intvolume":" 99","abstract":[{"lang":"eng","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."}],"oa_version":"Submitted Version","volume":99,"related_material":{"record":[{"relation":"later_version","status":"public","id":"11593"}]},"publication_status":"published","language":[{"iso":"eng"}],"type":"conference","conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2018-06-11","end_date":"2018-06-14","location":"Budapest, Hungary"},"status":"public","_id":"186","department":[{"_id":"UlWa"}],"date_updated":"2023-08-14T12:43:51Z","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"page":"40.1 - 40.14","date_published":"2018-06-11T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.40","date_created":"2018-12-11T11:45:05Z","year":"2018","day":"11","project":[{"_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Eliminating intersections in drawings of graphs","grant_number":"M02281"}],"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"}],"external_id":{"arxiv":["1803.05085"]},"article_processing_charge":"No","title":"The ℤ2-Genus of Kuratowski minors","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","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.","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, 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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"publisher":"Springer","quality_controlled":"1","oa":1,"year":"2018","day":"21","page":"160 - 166","doi":"10.1007/978-3-319-73915-1_14","date_published":"2018-01-21T00:00:00Z","date_created":"2018-12-11T11:46:27Z","citation":{"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","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.","ista":"Fulek R, Pach J. 2018. Thrackles: An improved upper bound. GD 2017: Graph Drawing and Network Visualization, LNCS, vol. 10692, 160–166.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"7390","author":[{"last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"first_name":"János","last_name":"Pach","full_name":"Pach, János"}],"external_id":{"arxiv":["1708.08037"]},"title":"Thrackles: An improved upper bound","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."}],"oa_version":"Submitted Version","scopus_import":1,"alternative_title":["LNCS"],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1708.08037"}],"month":"01","intvolume":" 10692","publication_status":"published","language":[{"iso":"eng"}],"volume":10692,"related_material":{"record":[{"relation":"later_version","status":"public","id":"5857"}]},"_id":"433","type":"conference","conference":{"name":"GD 2017: Graph Drawing and Network Visualization","start_date":"201-09-25","location":"Boston, MA, United States","end_date":"2017-09-27"},"status":"public","date_updated":"2023-08-24T14:39:32Z","department":[{"_id":"UlWa"}]},{"date_updated":"2023-08-24T14:50:26Z","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.","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).","ieee":"R. Faria et al., “Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes.” Dryad, 2018.","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","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","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."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","article_processing_charge":"No","author":[{"first_name":"Rui","last_name":"Faria","full_name":"Faria, Rui"},{"first_name":"Pragya","full_name":"Chaube, Pragya","last_name":"Chaube"},{"last_name":"Morales","full_name":"Morales, Hernán E.","first_name":"Hernán E."},{"first_name":"Tomas","last_name":"Larsson","full_name":"Larsson, Tomas"},{"first_name":"Alan R.","full_name":"Lemmon, Alan R.","last_name":"Lemmon"},{"full_name":"Lemmon, Emily M.","last_name":"Lemmon","first_name":"Emily M."},{"first_name":"Marina","full_name":"Rafajlović, Marina","last_name":"Rafajlović"},{"first_name":"Marina","full_name":"Panova, Marina","last_name":"Panova"},{"first_name":"Mark","full_name":"Ravinet, Mark","last_name":"Ravinet"},{"first_name":"Kerstin","last_name":"Johannesson","full_name":"Johannesson, Kerstin"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","id":"3C147470-F248-11E8-B48F-1D18A9856A87","first_name":"Anja M"},{"first_name":"Roger K.","last_name":"Butlin","full_name":"Butlin, Roger K."}],"department":[{"_id":"NiBa"}],"title":"Data from: Multiple chromosomal rearrangements in a hybrid zone between Littorina saxatilis ecotypes","_id":"9837","type":"research_data_reference","status":"public","year":"2018","day":"09","date_created":"2021-08-09T12:46:39Z","date_published":"2018-10-09T00:00:00Z","doi":"10.5061/dryad.72cg113","related_material":{"record":[{"status":"public","id":"6095","relation":"used_in_publication"}]},"abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","oa":1,"main_file_link":[{"url":"https://doi.org/10.5061/dryad.72cg113","open_access":"1"}],"publisher":"Dryad","month":"10"},{"type":"technical_report","status":"public","pubrep_id":"1066","_id":"5457","author":[{"first_name":"1","last_name":"Anonymous","full_name":"Anonymous, 1"},{"first_name":"2","full_name":"Anonymous, 2","last_name":"Anonymous"},{"first_name":"3","last_name":"Anonymous","full_name":"Anonymous, 3"},{"first_name":"4","last_name":"Anonymous","full_name":"Anonymous, 4"},{"first_name":"5","full_name":"Anonymous, 5","last_name":"Anonymous"},{"first_name":"6","full_name":"Anonymous, 6","last_name":"Anonymous"}],"file_date_updated":"2020-07-14T12:47:00Z","title":"Cost analysis of nondeterministic probabilistic programs","citation":{"apa":"Anonymous, 1, Anonymous, 2, Anonymous, 3, Anonymous, 4, Anonymous, 5, & Anonymous, 6. (2018). Cost analysis of nondeterministic probabilistic programs. IST Austria.","ama":"Anonymous 1, Anonymous 2, Anonymous 3, Anonymous 4, Anonymous 5, Anonymous 6. 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.","ieee":"1 Anonymous, 2 Anonymous, 3 Anonymous, 4 Anonymous, 5 Anonymous, and 6 Anonymous, Cost analysis of nondeterministic probabilistic programs. IST Austria, 2018.","mla":"Anonymous, 1, et al. Cost Analysis of Nondeterministic Probabilistic Programs. IST Austria, 2018.","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."},"date_updated":"2023-08-25T08:07:48Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["000"],"alternative_title":["IST Austria Technical Report"],"scopus_import":1,"publisher":"IST Austria","oa":1,"month":"11","abstract":[{"lang":"eng","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."}],"oa_version":"Published Version","page":"27","related_material":{"record":[{"id":"6175","status":"public","relation":"later_version"}]},"date_published":"2018-11-11T00:00:00Z","date_created":"2018-12-12T11:39:26Z","has_accepted_license":"1","publication_identifier":{"issn":["2664-1690"]},"publication_status":"published","year":"2018","day":"11","file":[{"date_updated":"2020-07-14T12:47:00Z","file_size":4202966,"creator":"system","date_created":"2018-12-12T11:53:32Z","file_name":"IST-2018-1066-v1+1_techreport.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"ba3adafd36fe200385ccda583063b9eb","file_id":"5493"},{"content_type":"text/plain","access_level":"closed","relation":"main_file","checksum":"6cf3a19164bb8e5048a9c8c84dfd9fa3","file_id":"6402","date_updated":"2020-07-14T12:47:00Z","file_size":322,"creator":"dernst","date_created":"2019-05-10T13:22:12Z","file_name":"authors-names.txt"}],"language":[{"iso":"eng"}]},{"acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","oa":1,"publisher":"Springer Nature","quality_controlled":"1","year":"2018","publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","day":"21","page":"203-220","date_created":"2022-03-18T10:30:32Z","date_published":"2018-03-21T00:00:00Z","doi":"10.1007/978-3-319-74772-9_7","citation":{"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.","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.","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.","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.","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"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","external_id":{"arxiv":["1502.01072"]},"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","full_name":"McKenzie, Ralph","last_name":"McKenzie"},{"full_name":"Moore, Matthew","last_name":"Moore","first_name":"Matthew"}],"title":"Absorption and directed Jónsson terms","editor":[{"first_name":"J","last_name":"Czelakowski","full_name":"Czelakowski, J"}],"abstract":[{"lang":"eng","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."}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1502.01072"}],"scopus_import":"1","intvolume":" 16","month":"03","place":"Cham","publication_status":"published","publication_identifier":{"eissn":["2211-2766"],"isbn":["9783319747712"],"issn":["2211-2758"],"eisbn":["9783319747729"]},"language":[{"iso":"eng"}],"volume":16,"series_title":"OCTR","_id":"10864","type":"book_chapter","status":"public","date_updated":"2023-09-05T15:37:18Z","department":[{"_id":"VlKo"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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.","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","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."},"title":"Shellability is NP-complete","author":[{"first_name":"Xavier","full_name":"Goaoc, Xavier","last_name":"Goaoc"},{"last_name":"Paták","full_name":"Paták, Pavel","first_name":"Pavel"},{"id":"48B57058-F248-11E8-B48F-1D18A9856A87","first_name":"Zuzana","full_name":"Patakova, Zuzana","orcid":"0000-0002-3975-1683","last_name":"Patakova"},{"last_name":"Tancer","full_name":"Tancer, Martin","orcid":"0000-0002-1191-6714","first_name":"Martin","id":"38AC689C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7736","acknowledgement":"Partially supported by the project EMBEDS II (CZ: 7AMB17FR029, FR: 38087RM) of Czech-French collaboration.","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","day":"11","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:45:04Z","date_published":"2018-06-11T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.41","page":"41:1 - 41:16","_id":"184","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)"},"conference":{"name":"SoCG: Symposium on Computational Geometry","start_date":"2018-06-11","location":"Budapest, Hungary","end_date":"2018-06-14"},"type":"conference","ddc":["516","000"],"date_updated":"2023-09-06T11:10:57Z","department":[{"_id":"UlWa"}],"file_date_updated":"2020-07-14T12:45:18Z","oa_version":"Published Version","abstract":[{"lang":"eng","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."}],"intvolume":" 99","month":"06","scopus_import":1,"alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"d12bdd60f04a57307867704b5f930afd","file_id":"5725","creator":"dernst","date_updated":"2020-07-14T12:45:18Z","file_size":718414,"date_created":"2018-12-17T16:35:02Z","file_name":"2018_LIPIcs_Goaoc.pdf"}],"publication_status":"published","volume":99,"related_material":{"record":[{"status":"public","id":"7108","relation":"later_version"}]}},{"volume":99,"related_material":{"record":[{"relation":"later_version","id":"7093","status":"public"}]},"publication_status":"published","publication_identifier":{"issn":["18688969"]},"language":[{"iso":"eng"}],"file":[{"date_created":"2018-12-17T15:32:38Z","file_name":"2018_LIPIcs_Huszar.pdf","creator":"dernst","date_updated":"2020-07-14T12:45:51Z","file_size":642522,"checksum":"530d084116778135d5bffaa317479cac","file_id":"5713","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"scopus_import":1,"alternative_title":["LIPIcs"],"intvolume":" 99","month":"06","abstract":[{"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)).","lang":"eng"}],"oa_version":"Submitted Version","file_date_updated":"2020-07-14T12:45:51Z","department":[{"_id":"UlWa"}],"date_updated":"2023-09-06T11:13:41Z","ddc":["516","000"],"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":"2018-06-11","end_date":"2018-06-14","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"type":"conference","status":"public","_id":"285","date_created":"2018-12-11T11:45:37Z","doi":"10.4230/LIPIcs.SoCG.2018.46","date_published":"2018-06-01T00:00:00Z","year":"2018","has_accepted_license":"1","day":"01","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"1","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).","article_processing_charge":"No","external_id":{"arxiv":["1712.00434"]},"publist_id":"7614","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"},{"first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","last_name":"Wagner"}],"title":"On the treewidth of triangulated 3-manifolds","citation":{"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.","short":"K. Huszár, J. Spreer, U. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_number":"46"},{"citation":{"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.","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","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","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.","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.","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."},"date_updated":"2023-09-06T14:32:51Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Edgar","last_name":"Garriga","full_name":"Garriga, Edgar"},{"first_name":"Paolo","full_name":"di Tommaso, Paolo","last_name":"di Tommaso"},{"full_name":"Magis, Cedrik","last_name":"Magis","first_name":"Cedrik"},{"last_name":"Erb","full_name":"Erb, Ionas","first_name":"Ionas"},{"last_name":"Mansouri","full_name":"Mansouri, Leila","first_name":"Leila"},{"first_name":"Athanasios","last_name":"Baltzis","full_name":"Baltzis, Athanasios"},{"last_name":"Laayouni","full_name":"Laayouni, Hafid","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","last_name":"Floden","full_name":"Floden, Evan"},{"first_name":"Cedric","full_name":"Notredame, Cedric","last_name":"Notredame"}],"article_processing_charge":"No","title":"Fast and accurate large multiple sequence alignments with a root-to-leaf regressive method","department":[{"_id":"FyKo"}],"_id":"13059","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)"},"status":"public","year":"2018","day":"07","date_published":"2018-12-07T00:00:00Z","doi":"10.5281/ZENODO.2025846","related_material":{"record":[{"status":"public","id":"7181","relation":"used_in_publication"}]},"date_created":"2023-05-23T16:08:20Z","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"}],"oa_version":"Published Version","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/zenodo.3271452"}],"oa":1,"month":"12"},{"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","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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.","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."},"date_created":"2018-12-11T11:44:21Z","date_published":"2018-07-30T00:00:00Z","doi":"10.15479/AT:ISTA:th_1033","page":"77","day":"30","year":"2018","has_accepted_license":"1","oa":1,"publisher":"Institute of Science and Technology Austria","file_date_updated":"2020-07-14T12:46:35Z","department":[{"_id":"GeKa"}],"ddc":["530"],"date_updated":"2023-09-07T12:27:43Z","supervisor":[{"first_name":"Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","full_name":"Katsaros, Georgios","last_name":"Katsaros"}],"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","_id":"49","language":[{"iso":"eng"}],"file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","checksum":"b653b5216251f938ddbeafd1de88667c","file_id":"6249","creator":"dernst","file_size":85539748,"date_updated":"2020-07-14T12:46:35Z","file_name":"2018_Thesis_Watzinger.pdf","date_created":"2019-04-09T07:13:28Z"},{"date_updated":"2020-07-14T12:46:35Z","file_size":21830697,"creator":"dernst","date_created":"2019-04-09T07:13:27Z","file_name":"2018_Thesis_Watzinger_source.zip","content_type":"application/zip","access_level":"closed","relation":"source_file","file_id":"6250","checksum":"39bcf8de7ac5b1bb516b11ce2f966785"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"month":"07","alternative_title":["ISTA Thesis"],"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."}]},{"ddc":["514","516"],"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"}],"file_date_updated":"2020-07-14T12:45:24Z","department":[{"_id":"HeEd"}],"_id":"201","pubrep_id":"1026","status":"public","type":"dissertation","language":[{"iso":"eng"}],"file":[{"file_id":"5918","checksum":"dd699303623e96d1478a6ae07210dd05","content_type":"application/zip","access_level":"closed","relation":"source_file","date_created":"2019-02-05T07:43:31Z","file_name":"IST-2018-1025-v2+5_ist-thesis-iglesias-11June2018(1).zip","date_updated":"2020-07-14T12:45:24Z","file_size":11827713,"creator":"kschuh"},{"date_created":"2019-02-05T07:43:45Z","file_name":"IST-2018-1025-v2+4_ThesisIglesiasFinal11June2018.pdf","creator":"kschuh","date_updated":"2020-07-14T12:45:24Z","file_size":4783846,"checksum":"ba163849a190d2b41d66fef0e4983294","file_id":"5919","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"oa_version":"Published Version","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."}],"month":"06","alternative_title":["ISTA Thesis"],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"ista":"Iglesias Ham M. 2018. Multiple covers with balls. Institute of Science and Technology Austria.","chicago":"Iglesias Ham, Mabel. “Multiple Covers with Balls.” Institute of Science and Technology Austria, 2018. https://doi.org/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","ama":"Iglesias Ham M. Multiple covers with balls. 2018. doi:10.15479/AT:ISTA:th_1026","ieee":"M. Iglesias Ham, “Multiple covers with balls,” Institute of Science and Technology Austria, 2018.","short":"M. Iglesias Ham, Multiple Covers with Balls, Institute of Science and Technology Austria, 2018.","mla":"Iglesias Ham, Mabel. Multiple Covers with Balls. Institute of Science and Technology Austria, 2018, doi:10.15479/AT:ISTA:th_1026."},"title":"Multiple covers with balls","article_processing_charge":"No","publist_id":"7712","author":[{"last_name":"Iglesias Ham","full_name":"Iglesias Ham, Mabel","first_name":"Mabel","id":"41B58C0C-F248-11E8-B48F-1D18A9856A87"}],"day":"11","year":"2018","has_accepted_license":"1","date_created":"2018-12-11T11:45:10Z","date_published":"2018-06-11T00:00:00Z","doi":"10.15479/AT:ISTA:th_1026","page":"171","oa":1,"publisher":"Institute of Science and Technology Austria"},{"publication_status":"published","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"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","checksum":"e849dd40a915e4d6c5572b51b517f098","file_id":"6253","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"date_updated":"2020-07-14T12:47:40Z","file_size":637490,"creator":"dernst","date_created":"2019-04-09T07:32:47Z","file_name":"2018_Thesis_Zimin_Source.zip","content_type":"application/zip","access_level":"closed","relation":"source_file","file_id":"6254","checksum":"da092153cec55c97461bd53c45c5d139"}],"ec_funded":1,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","date_updated":"2023-09-07T12:29:07Z","supervisor":[{"last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"ddc":["004","519"],"file_date_updated":"2020-07-14T12:47:40Z","department":[{"_id":"ChLa"}],"_id":"68","type":"dissertation","pubrep_id":"1048","status":"public","year":"2018","has_accepted_license":"1","day":"01","page":"92","date_created":"2018-12-11T11:44:27Z","doi":"10.15479/AT:ISTA:TH1048","date_published":"2018-09-01T00:00:00Z","oa":1,"publisher":"Institute of Science and Technology Austria","citation":{"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.","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","ieee":"A. Zimin, “Learning from dependent data,” Institute of Science and Technology Austria, 2018.","short":"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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","publist_id":"7986","author":[{"first_name":"Alexander","id":"37099E9C-F248-11E8-B48F-1D18A9856A87","last_name":"Zimin","full_name":"Zimin, Alexander"}],"title":"Learning from dependent data","project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}]},{"supervisor":[{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","last_name":"Pietrzak","full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654"}],"date_updated":"2023-09-07T12:30:23Z","ddc":["004"],"file_date_updated":"2020-07-14T12:48:11Z","department":[{"_id":"KrPi"}],"_id":"83","type":"dissertation","status":"public","pubrep_id":"1046","publication_identifier":{"issn":["2663-337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"date_created":"2019-04-09T06:43:41Z","file_name":"2018_Thesis_Abusalah.pdf","date_updated":"2020-07-14T12:48:11Z","file_size":876241,"creator":"dernst","checksum":"c4b5f7d111755d1396787f41886fc674","file_id":"6245","content_type":"application/pdf","access_level":"open_access","relation":"main_file"},{"content_type":"application/x-gzip","access_level":"closed","relation":"source_file","checksum":"0f382ac56b471c48fd907d63eb87dafe","file_id":"6246","date_updated":"2020-07-14T12:48:11Z","file_size":2029190,"creator":"dernst","date_created":"2019-04-09T06:43:41Z","file_name":"2018_Thesis_Abusalah_source.tar.gz"}],"language":[{"iso":"eng"}],"related_material":{"record":[{"relation":"part_of_dissertation","id":"1229","status":"public"},{"status":"public","id":"1235","relation":"part_of_dissertation"},{"id":"1236","status":"public","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"559","status":"public"}]},"ec_funded":1,"abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","alternative_title":["ISTA Thesis"],"month":"09","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.","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","author":[{"first_name":"Hamza M","id":"40297222-F248-11E8-B48F-1D18A9856A87","full_name":"Abusalah, Hamza M","last_name":"Abusalah"}],"publist_id":"7971","article_processing_charge":"No","title":"Proof systems for sustainable decentralized cryptocurrencies","project":[{"name":"Provable Security for Physical Cryptography","grant_number":"259668","_id":"258C570E-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"},{"call_identifier":"H2020","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","grant_number":"682815","name":"Teaching Old Crypto New Tricks"}],"has_accepted_license":"1","year":"2018","day":"05","page":"59","date_published":"2018-09-05T00:00:00Z","doi":"10.15479/AT:ISTA:TH_1046","date_created":"2018-12-11T11:44:32Z","publisher":"Institute of Science and Technology Austria","oa":1},{"alternative_title":["ISTA Thesis"],"month":"05","abstract":[{"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.","lang":"eng"}],"oa_version":"Published Version","ec_funded":1,"degree_awarded":"PhD","publication_status":"published","publication_identifier":{"issn":["2663-337X"]},"language":[{"iso":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:22Z","file_size":12918758,"creator":"system","date_created":"2018-12-12T10:14:57Z","file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"bc678e02468d8ebc39dc7267dfb0a1c4","file_id":"5113"},{"file_id":"6225","checksum":"bc66973b086da5a043f1162dcfb1fde4","access_level":"closed","relation":"source_file","content_type":"application/zip","date_created":"2019-04-05T09:34:49Z","file_name":"2018_Thesis_Kolesnikov_source.zip","creator":"dernst","date_updated":"2020-07-14T12:45:22Z","file_size":55973760}],"type":"dissertation","pubrep_id":"1021","status":"public","_id":"197","department":[{"_id":"ChLa"}],"file_date_updated":"2020-07-14T12:45:22Z","date_updated":"2023-09-07T12:51:46Z","supervisor":[{"orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","last_name":"Lampert","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"ddc":["004"],"oa":1,"publisher":"Institute of Science and Technology Austria","acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","page":"113","date_created":"2018-12-11T11:45:09Z","date_published":"2018-05-25T00:00:00Z","doi":"10.15479/AT:ISTA:th_1021","year":"2018","has_accepted_license":"1","day":"25","project":[{"grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding","call_identifier":"FP7","_id":"2532554C-B435-11E9-9278-68D0E5697425"}],"article_processing_charge":"No","author":[{"last_name":"Kolesnikov","full_name":"Kolesnikov, Alexander","first_name":"Alexander","id":"2D157DB6-F248-11E8-B48F-1D18A9856A87"}],"publist_id":"7718","title":"Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images","citation":{"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.","ista":"Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria.","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.","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","short":"A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018.","ieee":"A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1"},{"date_updated":"2023-09-07T13:10:36Z","ddc":["514"],"file_date_updated":"2020-07-14T12:47:40Z","department":[{"_id":"UlWa"}],"_id":"6774","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","publication_status":"published","publication_identifier":{"issn":["2367-1726"],"eissn":["2367-1734"]},"language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"6775","checksum":"cf9e7fcd2a113dd4828774fc75cdb7e8","creator":"dernst","date_updated":"2020-07-14T12:47:40Z","file_size":1056278,"date_created":"2019-08-08T06:55:21Z","file_name":"2018_JourAppliedComputTopology_Filakovsky.pdf"}],"issue":"3-4","related_material":{"record":[{"relation":"dissertation_contains","id":"6681","status":"public"}]},"volume":2,"abstract":[{"lang":"eng","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) ."}],"oa_version":"Published Version","intvolume":" 2","month":"12","citation":{"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.","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.","short":"M. Filakovský, P. Franek, U. Wagner, S.Y. Zhechev, Journal of Applied and Computational Topology 2 (2018) 177–231.","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","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.","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Filakovský","full_name":"Filakovský, Marek","first_name":"Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Peter","id":"473294AE-F248-11E8-B48F-1D18A9856A87","last_name":"Franek","orcid":"0000-0001-8878-8397","full_name":"Franek, Peter"},{"id":"36690CA2-F248-11E8-B48F-1D18A9856A87","first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner"},{"full_name":"Zhechev, Stephan Y","last_name":"Zhechev","id":"3AA52972-F248-11E8-B48F-1D18A9856A87","first_name":"Stephan Y"}],"title":"Computing simplicial representatives of homotopy group elements","project":[{"call_identifier":"FWF","_id":"25F8B9BC-B435-11E9-9278-68D0E5697425","name":"Robust invariants of Nonlinear Systems","grant_number":"M01980"},{"name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","call_identifier":"FWF"}],"year":"2018","has_accepted_license":"1","publication":"Journal of Applied and Computational Topology","day":"01","page":"177-231","date_created":"2019-08-08T06:47:40Z","date_published":"2018-12-01T00:00:00Z","doi":"10.1007/s41468-018-0021-5","oa":1,"quality_controlled":"1","publisher":"Springer"},{"article_number":"21","project":[{"call_identifier":"FWF","_id":"25F2ACDE-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","name":"Rigorous Systems Engineering"},{"_id":"25F5A88A-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"S11402-N23","name":"Moderne Concurrency Paradigms"}],"citation":{"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.","ista":"Kragl B, Qadeer S, Henzinger TA. 2018. Synchronizing the asynchronous. CONCUR: International Conference on Concurrency Theory, LIPIcs, vol. 118, 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.","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.","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","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"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Kragl","orcid":"0000-0001-7745-9117","full_name":"Kragl, Bernhard","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Qadeer","full_name":"Qadeer, Shaz","first_name":"Shaz"},{"id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","last_name":"Henzinger","full_name":"Henzinger, Thomas A","orcid":"0000−0002−2985−7724"}],"publist_id":"7790","title":"Synchronizing the asynchronous","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","oa":1,"has_accepted_license":"1","year":"2018","day":"13","date_published":"2018-08-13T00:00:00Z","doi":"10.4230/LIPIcs.CONCUR.2018.21","date_created":"2018-12-11T11:44:48Z","_id":"133","type":"conference","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)"},"status":"public","pubrep_id":"1039","date_updated":"2023-09-07T13:18:00Z","ddc":["000"],"department":[{"_id":"ToHe"}],"file_date_updated":"2020-07-14T12:44:44Z","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"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"scopus_import":1,"month":"08","intvolume":" 118","publication_identifier":{"issn":["18688969"]},"publication_status":"published","file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_id":"5368","checksum":"c90895f4c5fafc18ddc54d1c8848077e","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"}],"language":[{"iso":"eng"}],"volume":118,"related_material":{"record":[{"status":"public","id":"6426","relation":"earlier_version"},{"id":"8332","status":"public","relation":"dissertation_contains"}]}},{"intvolume":" 99","month":"06","scopus_import":1,"alternative_title":["LIPIcs"],"oa_version":"Published Version","abstract":[{"lang":"eng","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. "}],"volume":99,"related_material":{"record":[{"status":"public","id":"9317","relation":"later_version"},{"id":"9056","status":"public","relation":"dissertation_contains"}]},"language":[{"iso":"eng"}],"file":[{"file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","date_created":"2018-12-18T09:27:22Z","creator":"dernst","file_size":528018,"date_updated":"2020-07-14T12:45:19Z","file_id":"5738","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","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)"},"conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","end_date":"2018-06-14","start_date":"2018-06-11"},"type":"conference","_id":"187","file_date_updated":"2020-07-14T12:45:19Z","department":[{"_id":"HeEd"}],"ddc":["516"],"date_updated":"2023-09-07T13:29:00Z","oa":1,"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","quality_controlled":"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).","date_created":"2018-12-11T11:45:05Z","date_published":"2018-06-11T00:00:00Z","doi":"10.4230/LIPIcs.SoCG.2018.34","day":"11","year":"2018","has_accepted_license":"1","project":[{"grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"article_number":"34","title":"The multi-cover persistence of Euclidean balls","publist_id":"7732","author":[{"last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert"},{"id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","last_name":"Osang"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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","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","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.","short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","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.","ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34."}},{"citation":{"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.","apa":"Akopyan, A. (2018). 3-Webs generated by confocal conics and circles. Geometriae Dedicata. Springer. https://doi.org/10.1007/s10711-017-0265-6","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","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.","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."},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publist_id":"7014","author":[{"id":"430D2C90-F248-11E8-B48F-1D18A9856A87","first_name":"Arseniy","orcid":"0000-0002-2548-617X","full_name":"Akopyan, Arseniy","last_name":"Akopyan"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["000431418800004"]},"title":"3-Webs generated by confocal conics and circles","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"has_accepted_license":"1","isi":1,"year":"2018","day":"01","publication":"Geometriae Dedicata","page":"55 - 64","date_published":"2018-06-01T00:00:00Z","doi":"10.1007/s10711-017-0265-6","date_created":"2018-12-11T11:47:57Z","quality_controlled":"1","publisher":"Springer","oa":1,"date_updated":"2023-09-08T11:40:29Z","ddc":["510"],"department":[{"_id":"HeEd"}],"file_date_updated":"2020-07-14T12:47:44Z","_id":"692","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)"},"status":"public","publication_status":"published","file":[{"checksum":"1febcfc1266486053a069e3425ea3713","file_id":"7222","access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2020-01-03T11:35:08Z","file_name":"2018_Springer_Akopyan.pdf","creator":"kschuh","date_updated":"2020-07-14T12:47:44Z","file_size":1140860}],"language":[{"iso":"eng"}],"volume":194,"issue":"1","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"},{"doi":"10.1038/s41467-018-06418-4","date_published":"2018-09-25T00:00:00Z","date_created":"2018-12-11T11:44:30Z","day":"25","publication":"Nature Communications","has_accepted_license":"1","isi":1,"year":"2018","publisher":"Nature Publishing Group","quality_controlled":"1","oa":1,"title":"A germanium hole spin qubit","author":[{"full_name":"Watzinger, Hannes","last_name":"Watzinger","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","first_name":"Hannes"},{"first_name":"Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","full_name":"Kukucka, Josip","last_name":"Kukucka"},{"last_name":"Vukusic","full_name":"Vukusic, Lada","orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","first_name":"Lada"},{"first_name":"Fei","last_name":"Gao","full_name":"Gao, Fei"},{"first_name":"Ting","last_name":"Wang","full_name":"Wang, Ting"},{"first_name":"Friedrich","last_name":"Schäffler","full_name":"Schäffler, Friedrich"},{"first_name":"Jian","last_name":"Zhang","full_name":"Zhang, Jian"},{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","first_name":"Georgios","full_name":"Katsaros, Georgios","orcid":"0000-0001-8342-202X","last_name":"Katsaros"}],"article_processing_charge":"Yes","external_id":{"isi":["000445560800010"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","citation":{"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.","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","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","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.","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.","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)."},"project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires","grant_number":"335497"},{"_id":"2552F888-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"Y00715","name":"Loch Spin-Qubits und Majorana-Fermionen in Germanium"}],"issue":"3902 ","volume":9,"related_material":{"record":[{"id":"7977","relation":"popular_science"},{"status":"public","id":"7996","relation":"dissertation_contains"}]},"ec_funded":1,"file":[{"checksum":"e7148c10a64497e279c4de570b6cc544","file_id":"5687","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2018_NatureComm_Watzinger.pdf","date_created":"2018-12-17T10:28:30Z","creator":"dernst","file_size":1063469,"date_updated":"2020-07-14T12:48:02Z"}],"language":[{"iso":"eng"}],"publication_status":"published","month":"09","intvolume":" 9","scopus_import":"1","oa_version":"Published Version","abstract":[{"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.","lang":"eng"}],"acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"file_date_updated":"2020-07-14T12:48:02Z","department":[{"_id":"GeKa"}],"ddc":["530"],"date_updated":"2023-09-08T11:44:02Z","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":"77"}]