[{"alternative_title":["ISTA Thesis"],"date_published":"2019-10-09T00:00:00Z","oa":1,"year":"2019","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"664"},{"id":"402","status":"public","relation":"part_of_dissertation"}]},"file_date_updated":"2020-11-07T23:30:03Z","abstract":[{"lang":"eng","text":"Lymph nodes  are es s ential organs  of the immune  s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular  cells (FRCs) are  the  main  stromal  cells and  form  a sponge-like extracellular matrix network,   called  conduits ,  which  they   thems elves   enwrap   and  contract.  Lymph,  containing  s oluble  antigens ,  arrive in  lymph  nodes  via afferent lymphatic  vessels that  connect  to  the  s ubcaps ular  s inus   and  conduit  network.  According  to  the  current  paradigm,  the  conduit  network   dis tributes   afferent  lymph  through   lymph  nodes   and  thus   provides   acces s   for  immune  cells to lymph-borne  antigens. An  elas tic  caps ule  s urrounds   the  organ  and  confines   the immune  cells and  FRC  network.   Lymph   nodes   are  completely  packed  with  lymphocytes   and  lymphocyte  numbers  directly  dictates  the size  of  the  organ.  Although  lymphocytes   cons tantly  enter  and  leave  the  lymph  node,  its   s ize  remains   remarkedly   s table  under  homeostatic conditions. It is only partly known  how the cellularity and s ize of the lymph node is regulated and  how  the  lymph  node  is able to swell in inflammation.  The role of the FRC network   in  lymph  node   s welling  and  trans fer  of  fluids   are  inves tigated in  this   thes is.  Furthermore,   we  s tudied  what  trafficking  routes   are  us ed  by  cancer  cells   in  lymph  nodes   to  form  distal metastases.We examined the role of a mechanical feedback in regulation of lymph  node swelling. Using parallel plate compression  and UV-las er  cutting  experiments   we  dis s ected  the  mechanical  force dynamics  of the whole lymph  node, and individually for FRCs  and the  caps ule. Physical forces   generated  by  packed  lymphocytes   directly  affect  the  tens ion  on  the  FRC  network  and  capsule,  which  increases  its  resistance  to   swelling.  This  implies  a  feedback  mechanism  between   tis s ue   pres s ure   and   ability   of   lymphocytes    to   enter   the   organ.   Following   inflammation,  the  lymph  node  swells ∼10 fold in two weeks . Yet, what  is  the role  for tens ion on  the  FRC  network   and  caps ule,  and  how  are  lymphocytes   able  to  enter  in  conditions  that resist swelling remain open ques tions . We s how that tens ion on the FRC network is  important to  limit  the  swelling  rate  of  the  organ  so  that  the  FRC  network  can  grow  in  a  coordinated  fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates  and a dis organized FRC network  in the inflamed lymph  node. Growth  of the FRC network  in  turn  is   expected  to  releas e  tens ion  on  thes e  s tructures   and  lowers   the  res is tance  to  swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of  swelling coincides   with  a  thickening  of  the  caps ule,  which  forms   a  thick  res is tant  band  around  the organ and lowers  tens ion on the FRC network  to form a new force equilibrium.The  FRC  and  conduit   network   are  further   believed  to  be  a  privileged  s ite  of  s oluble  information  within  the  lymph  node,  although  many  details   remain  uns olved.  We  s how  by  3D  ultra-recons truction   that  FRCs   and  antigen  pres enting  cells   cover  the  s urface  of  conduit  s ys tem for more  than 99% and we dis cus s  the implications  for s oluble information  exchangeat the conduit level.Finally, there  is an ongoing debate in the cancer field whether and how cancer cells  in lymph nodes   s eed  dis tal  metas tas es .  We  s how  that  cancer  cells   infus ed  into  the  lymph  node  can  utilize trafficking routes of immune  cells and  rapidly  migrate  to  blood  vessels. Once  in  the  blood circulation,  these cells are able to form  metastases in distal tissues."}],"publication_status":"published","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"oa_version":"Published Version","day":"09","OA_place":"publisher","has_accepted_license":"1","month":"10","author":[{"full_name":"Assen, Frank P","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3470-6119","first_name":"Frank P","last_name":"Assen"}],"date_created":"2019-10-14T16:54:52Z","doi":"10.15479/AT:ISTA:6947","type":"dissertation","file":[{"file_id":"6990","relation":"source_file","checksum":"53a739752a500f84d0f8ec953cbbd0b6","access_level":"closed","file_size":214172667,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","creator":"fassen","date_created":"2019-11-06T12:30:02Z","file_name":"PhDthesis_FrankAssen_revised2.docx","date_updated":"2020-11-07T23:30:03Z"},{"file_id":"6991","relation":"main_file","checksum":"8c156b65d9347bb599623a4b09f15d15","access_level":"open_access","file_size":83637532,"content_type":"application/pdf","embargo":"2020-11-06","file_name":"PhDthesis_FrankAssen_revised2.pdf","date_created":"2019-11-06T12:30:57Z","creator":"fassen","date_updated":"2020-11-07T23:30:03Z"}],"supervisor":[{"last_name":"Sixt","first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87"}],"_id":"6947","publisher":"Institute of Science and Technology Austria","status":"public","page":"142","citation":{"ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019.","apa":"Assen, F. P. (2019). <i>Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>","ama":"Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>","ista":"Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria.","mla":"Assen, Frank P. <i>Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>.","chicago":"Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>.","short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019."},"degree_awarded":"PhD","corr_author":"1","ddc":["570"],"department":[{"_id":"MiSi"}],"title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","date_updated":"2026-06-18T18:47:59Z","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}]},{"alternative_title":["ISTA Thesis"],"date_published":"2019-08-24T00:00:00Z","year":"2019","oa":1,"related_material":{"record":[{"relation":"part_of_dissertation","id":"5949","status":"public"}]},"file_date_updated":"2024-04-10T22:30:48Z","abstract":[{"lang":"eng","text":"The solving of complex tasks requires the functions of more than one brain area and their interaction. Whilst spatial navigation and memory is dependent on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC). To further examine the roles of the hippocampus and mPFC, we recorded their neural activity during a task that depends on both of these brain regions.\r\nWith tetrodes, we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC neurons in Long-Evans rats performing a rule-switching task on the plus-maze. The plus-maze task had a spatial component since it required navigation along one of the two start arms and at the maze center a choice between one of the two goal arms. Which goal contained a reward depended on the rule currently in place. After an uncued rule change the animal had to abandon the old strategy and switch to the new rule, testing cognitive flexibility. Investigating the coordination of activity between the HPC and mPFC allows determination during which task stages their interaction is required. Additionally, comparing neural activity patterns in these two brain regions allows delineation of the specialized functions of the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC in terms of oscillatory interactions, rule coding and replay.\r\nWe found that theta coherence between the HPC and mPFC is increased at the center and goals of the maze, both when the rule was stable or has changed. Similar results were found for locking of HPC and mPFC neurons to HPC theta oscillations. However, no differences in HPC-mPFC theta coordination were observed between the spatially- and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations was not modulated by\r\nmaze position or rule type. We found that the HPC coded for the two different rules with cofiring relationships between\r\ncell pairs. However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective firing in the mPFC generalized between the two start and two goal arms. With Bayesian positional decoding, we found that the mPFC reactivated non-local positions during awake immobility periods. Replay of these non-local positions could represent entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore, mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently of each other. These results show that the mPFC can replay ordered patterns of activity during awake immobility, possibly underlying its role in flexible behavior. "}],"publication_status":"published","oa_version":"Published Version","day":"24","OA_place":"publisher","has_accepted_license":"1","month":"08","author":[{"first_name":"Karola","last_name":"Käfer","full_name":"Käfer, Karola","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"}],"date_created":"2019-08-21T15:00:57Z","doi":"10.15479/AT:ISTA:6825","type":"dissertation","file":[{"content_type":"application/pdf","request_a_copy":0,"access_level":"open_access","file_size":3205202,"checksum":"2664420e332a33338568f4f3bfc59287","relation":"main_file","file_id":"6846","date_updated":"2020-09-06T22:30:03Z","creator":"kkaefer","date_created":"2019-09-03T08:07:13Z","file_name":"Thesis_Kaefer_PDFA.pdf","embargo":"2020-09-05"},{"content_type":"application/zip","embargo_to":"open_access","access_level":"closed","file_size":2506835,"relation":"source_file","checksum":"9a154eab6f07aa590a3d2651dc0d926a","file_id":"6847","date_updated":"2024-04-10T22:30:48Z","creator":"kkaefer","date_created":"2019-09-03T08:07:17Z","file_name":"Thesis_Kaefer.zip"}],"_id":"6825","supervisor":[{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"publisher":"Institute of Science and Technology Austria","status":"public","page":"89","citation":{"ista":"Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria.","mla":"Käfer, Karola. <i>The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6825\">10.15479/AT:ISTA:6825</a>.","chicago":"Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6825\">https://doi.org/10.15479/AT:ISTA:6825</a>.","short":"K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior, Institute of Science and Technology Austria, 2019.","ieee":"K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,” Institute of Science and Technology Austria, 2019.","ama":"Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6825\">10.15479/AT:ISTA:6825</a>","apa":"Käfer, K. (2019). <i>The hippocampus and medial prefrontal cortex during flexible behavior</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6825\">https://doi.org/10.15479/AT:ISTA:6825</a>"},"degree_awarded":"PhD","ddc":["570"],"corr_author":"1","department":[{"_id":"JoCs"},{"_id":"GradSch"}],"title":"The hippocampus and medial prefrontal cortex during flexible behavior","date_updated":"2026-04-08T13:56:14Z","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","language":[{"iso":"eng"}]},{"month":"09","has_accepted_license":"1","day":"01","ec_funded":1,"external_id":{"isi":["000480635400003"]},"oa_version":"Published Version","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Aberrant proteostasis of protein aggregation may lead to behavior disorders including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations that underlie CMI are not well understood. We recorded the local field potential and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein aggregation, disturbances in the dopaminergic system and attention-related deficits. Recordings were performed during exploration of familiar and novel open field environments and during sleep, allowing investigation of neuronal abnormalities in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited smaller place fields and decreased speed-modulation of their firing rates, demonstrating altered spatial coding and deficits in encoding location-independent sensory inputs. Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase locking strength during novelty, limiting their phase coding ability. However, their mean theta phases were more variable at the population level, reducing oscillatory network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced shift in their preferred theta and gamma firing phases, indicating deficits in coding of novel environments with oscillatory firing. By combining single cell and neuronal population analyses, we link DISC1 protein pathology with abnormal hippocampal neural coding and network synchrony, and thereby gain a more comprehensive understanding of CMI mechanisms."}],"file_date_updated":"2020-07-14T12:47:13Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"6825"}]},"year":"2019","oa":1,"volume":29,"date_published":"2019-09-01T00:00:00Z","publisher":"Wiley","_id":"5949","file":[{"creator":"dernst","date_created":"2019-02-11T10:42:51Z","file_name":"2019_Hippocampus_Kaefer.pdf","date_updated":"2020-07-14T12:47:13Z","file_id":"5950","checksum":"5e8de271ca04aef92a5de42d6aac4404","relation":"main_file","file_size":2132893,"access_level":"open_access","content_type":"application/pdf"}],"intvolume":"        29","type":"journal_article","doi":"10.1002/hipo.23076","project":[{"grant_number":"607616","name":"inter-and intracellular signalling in schizophrenia","call_identifier":"FP7","_id":"257BBB4C-B435-11E9-9278-68D0E5697425"}],"date_created":"2019-02-10T22:59:18Z","author":[{"id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87","full_name":"Käfer, Karola","last_name":"Käfer","first_name":"Karola"},{"full_name":"Malagon-Vina, Hugo","first_name":"Hugo","last_name":"Malagon-Vina"},{"id":"444EB89E-F248-11E8-B48F-1D18A9856A87","full_name":"Dickerson, Desiree","first_name":"Desiree","last_name":"Dickerson"},{"last_name":"O'Neill","first_name":"Joseph","full_name":"O'Neill, Joseph"},{"last_name":"Trossbach","first_name":"Svenja V.","full_name":"Trossbach, Svenja V."},{"full_name":"Korth, Carsten","first_name":"Carsten","last_name":"Korth"},{"full_name":"Csicsvari, Jozsef L","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5193-4036","first_name":"Jozsef L","last_name":"Csicsvari"}],"department":[{"_id":"JoCs"}],"issue":"9","ddc":["570"],"scopus_import":"1","isi":1,"publication":"Hippocampus","page":"802-816","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"K. Käfer, H. Malagon-Vina, D. Dickerson, J. O’Neill, S.V. Trossbach, C. Korth, J.L. Csicsvari, Hippocampus 29 (2019) 802–816.","chicago":"Käfer, Karola, Hugo Malagon-Vina, Desiree Dickerson, Joseph O’Neill, Svenja V. Trossbach, Carsten Korth, and Jozsef L Csicsvari. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” <i>Hippocampus</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/hipo.23076\">https://doi.org/10.1002/hipo.23076</a>.","ista":"Käfer K, Malagon-Vina H, Dickerson D, O’Neill J, Trossbach SV, Korth C, Csicsvari JL. 2019. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 29(9), 802–816.","mla":"Käfer, Karola, et al. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” <i>Hippocampus</i>, vol. 29, no. 9, Wiley, 2019, pp. 802–16, doi:<a href=\"https://doi.org/10.1002/hipo.23076\">10.1002/hipo.23076</a>.","apa":"Käfer, K., Malagon-Vina, H., Dickerson, D., O’Neill, J., Trossbach, S. V., Korth, C., &#38; Csicsvari, J. L. (2019). Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. <i>Hippocampus</i>. Wiley. <a href=\"https://doi.org/10.1002/hipo.23076\">https://doi.org/10.1002/hipo.23076</a>","ama":"Käfer K, Malagon-Vina H, Dickerson D, et al. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. <i>Hippocampus</i>. 2019;29(9):802-816. doi:<a href=\"https://doi.org/10.1002/hipo.23076\">10.1002/hipo.23076</a>","ieee":"K. Käfer <i>et al.</i>, “Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization,” <i>Hippocampus</i>, vol. 29, no. 9. Wiley, pp. 802–816, 2019."},"status":"public","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"Yes (via OA deal)","date_updated":"2026-08-27T22:31:05Z","title":"Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization"},{"scopus_import":"1","publication":"Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science","citation":{"apa":"Kazda, A., Kozik, M., McKenzie, R., &#38; Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i> (Vol. 16, pp. 203–220). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">https://doi.org/10.1007/978-3-319-74772-9_7</a>","ama":"Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:<a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">10.1007/978-3-319-74772-9_7</a>","ieee":"A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.","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.","chicago":"Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. <a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">https://doi.org/10.1007/978-3-319-74772-9_7</a>.","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.” <i>Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science</i>, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:<a href=\"https://doi.org/10.1007/978-3-319-74772-9_7\">10.1007/978-3-319-74772-9_7</a>."},"page":"203-220","status":"public","department":[{"_id":"VlKo"}],"corr_author":"1","article_processing_charge":"No","publication_identifier":{"eisbn":["9783319747729"],"issn":["2211-2758"],"eissn":["2211-2766"],"isbn":["9783319747712"]},"acknowledgement":"The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006.","date_updated":"2024-10-09T21:01:50Z","title":"Absorption and directed Jónsson terms","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"publication_status":"published","abstract":[{"text":"We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k.","lang":"eng"}],"year":"2018","oa":1,"volume":16,"date_published":"2018-03-21T00:00:00Z","arxiv":1,"month":"03","series_title":"OCTR","day":"21","external_id":{"arxiv":["1502.01072"]},"place":"Cham","oa_version":"Preprint","intvolume":"        16","type":"book_chapter","doi":"10.1007/978-3-319-74772-9_7","editor":[{"last_name":"Czelakowski","first_name":"J","full_name":"Czelakowski, J"}],"author":[{"id":"3B32BAA8-F248-11E8-B48F-1D18A9856A87","full_name":"Kazda, Alexandr","first_name":"Alexandr","last_name":"Kazda"},{"last_name":"Kozik","first_name":"Marcin","full_name":"Kozik, Marcin"},{"full_name":"McKenzie, Ralph","last_name":"McKenzie","first_name":"Ralph"},{"last_name":"Moore","first_name":"Matthew","full_name":"Moore, Matthew"}],"date_created":"2022-03-18T10:30:32Z","publisher":"Springer Nature","main_file_link":[{"url":"https://arxiv.org/abs/1502.01072","open_access":"1"}],"_id":"10864"},{"title":"Significance of whole-genome duplications on the emergence of evolutionary novelties","publication_identifier":{"issn":["2041-2649"],"eissn":["2041-2657"]},"acknowledgement":"This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.).","date_updated":"2026-06-18T10:44:32Z","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","keyword":["Genetics","Molecular Biology","Biochemistry","General Medicine"],"status":"public","publication":"Briefings in Functional Genomics","page":"329-338","citation":{"ieee":"M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications on the emergence of evolutionary novelties,” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018.","ama":"Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. 2018;17(5):329-338. doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>","apa":"Yuuta, M., &#38; Koshiba-Takeuchi, K. (2018). Significance of whole-genome duplications on the emergence of evolutionary novelties. <i>Briefings in Functional Genomics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>","ista":"Yuuta M, Koshiba-Takeuchi K. 2018. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 17(5), 329–338.","mla":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:<a href=\"https://doi.org/10.1093/bfgp/ely007\">10.1093/bfgp/ely007</a>.","chicago":"Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” <i>Briefings in Functional Genomics</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/bfgp/ely007\">https://doi.org/10.1093/bfgp/ely007</a>.","short":"M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338."},"scopus_import":"1","isi":1,"issue":"5","corr_author":"1","ddc":["570"],"pmid":1,"department":[{"_id":"CaHe"}],"author":[{"last_name":"Yuuta","first_name":"Moriyama","orcid":"0000-0002-2853-8051","full_name":"Yuuta, Moriyama","id":"4968E7C8-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kazuko","last_name":"Koshiba-Takeuchi","full_name":"Koshiba-Takeuchi, Kazuko"}],"date_created":"2022-03-18T12:40:35Z","doi":"10.1093/bfgp/ely007","intvolume":"        17","type":"journal_article","_id":"10880","main_file_link":[{"url":"https://doi.org/10.1093/bfgp/ely007","open_access":"1"}],"publisher":"Oxford University Press","year":"2018","oa":1,"date_published":"2018-09-01T00:00:00Z","volume":17,"publication_status":"published","article_type":"original","abstract":[{"text":"Acquisition of evolutionary novelties is a fundamental process for adapting to the external environment and invading new niches and results in the diversification of life, which we can see in the world today. How such novel phenotypic traits are acquired in the course of evolution and are built up in developing embryos has been a central question in biology. Whole-genome duplication (WGD) is a process of genome doubling that supplies raw genetic materials and increases genome complexity. Recently, it has been gradually revealed that WGD and subsequent fate changes of duplicated genes can facilitate phenotypic evolution. Here, we review the current understanding of the relationship between WGD and the acquisition of evolutionary novelties. We show some examples of this link and discuss how WGD and subsequent duplicated genes can facilitate phenotypic evolution as well as when such genomic doubling can be advantageous for adaptation.","lang":"eng"}],"external_id":{"pmid":["29579140"],"isi":["000456054400004"]},"oa_version":"Published Version","day":"01","month":"09"},{"date_updated":"2025-04-15T07:48:01Z","acknowledgement":"This project received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Actions and it is co-financed by the South Moravian Region under grant agreement No. 665860 (SS). Access to computing and storage facilities owned by parties and projects contributing to the national grid infrastructure, MetaCentrum, provided under the program ‘Projects of Large Infrastructure for Research, Development, and Innovations’ (LM2010005) was greatly appreciated (RSV). The project was funded by The Ministry of Education, Youth and Sports/MES of the Czech Republic under the project CEITEC 2020 (LQ1601) (TN, TRM). JF was supported by the European Research Council (project ERC-2011-StG 20101109-PSDP) and the Czech Science Foundation GAČR (GA13-40637S). We thank Dr Kamel Chibani for active discussions on the evolutionary analysis and Nandan Mysore Vardarajan for his critical comments on the manuscript. This article reflects\r\nonly the authors’ views, and the EU is not responsible for any use that may be made of the information it contains. ","publication_identifier":{"issn":["0022-0957"],"eissn":["1460-2431"]},"title":"Molecular evolution and diversification of the SMXL gene family","article_processing_charge":"No","quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","keyword":["Plant Science","Physiology"],"isi":1,"scopus_import":"1","page":"2367-2378","citation":{"chicago":"Moturu, Taraka Ramji, Sravankumar Thula, Ravi Kumar Singh, Tomasz Nodzyński, Radka Svobodová Vařeková, Jiří Friml, and Sibu Simon. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>.","ista":"Moturu TR, Thula S, Singh RK, Nodzyński T, Vařeková RS, Friml J, Simon S. 2018. Molecular evolution and diversification of the SMXL gene family. Journal of Experimental Botany. 69(9), 2367–2378.","mla":"Moturu, Taraka Ramji, et al. “Molecular Evolution and Diversification of the SMXL Gene Family.” <i>Journal of Experimental Botany</i>, vol. 69, no. 9, Oxford University Press, 2018, pp. 2367–78, doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>.","short":"T.R. Moturu, S. Thula, R.K. Singh, T. Nodzyński, R.S. Vařeková, J. Friml, S. Simon, Journal of Experimental Botany 69 (2018) 2367–2378.","apa":"Moturu, T. R., Thula, S., Singh, R. K., Nodzyński, T., Vařeková, R. S., Friml, J., &#38; Simon, S. (2018). Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/jxb/ery097\">https://doi.org/10.1093/jxb/ery097</a>","ama":"Moturu TR, Thula S, Singh RK, et al. Molecular evolution and diversification of the SMXL gene family. <i>Journal of Experimental Botany</i>. 2018;69(9):2367-2378. doi:<a href=\"https://doi.org/10.1093/jxb/ery097\">10.1093/jxb/ery097</a>","ieee":"T. R. Moturu <i>et al.</i>, “Molecular evolution and diversification of the SMXL gene family,” <i>Journal of Experimental Botany</i>, vol. 69, no. 9. Oxford University Press, pp. 2367–2378, 2018."},"publication":"Journal of Experimental Botany","issue":"9","department":[{"_id":"JiFr"}],"pmid":1,"doi":"10.1093/jxb/ery097","project":[{"grant_number":"282300","_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7"}],"author":[{"last_name":"Moturu","first_name":"Taraka Ramji","full_name":"Moturu, Taraka Ramji"},{"last_name":"Thula","first_name":"Sravankumar","full_name":"Thula, Sravankumar"},{"full_name":"Singh, Ravi Kumar","last_name":"Singh","first_name":"Ravi Kumar"},{"full_name":"Nodzyński, Tomasz","last_name":"Nodzyński","first_name":"Tomasz"},{"last_name":"Vařeková","first_name":"Radka Svobodová","full_name":"Vařeková, Radka Svobodová"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"},{"last_name":"Simon","first_name":"Sibu","full_name":"Simon, Sibu"}],"date_created":"2022-03-18T12:43:22Z","type":"journal_article","intvolume":"        69","publisher":"Oxford University Press","_id":"10881","volume":69,"date_published":"2018-04-13T00:00:00Z","year":"2018","abstract":[{"text":"Strigolactones (SLs) are a relatively recent addition to the list of plant hormones that control different aspects of plant development. SL signalling is perceived by an α/β hydrolase, DWARF 14 (D14). A close homolog of D14, KARRIKIN INSENSTIVE2 (KAI2), is involved in perception of an uncharacterized molecule called karrikin (KAR). Recent studies in Arabidopsis identified the SUPPRESSOR OF MAX2 1 (SMAX1) and SMAX1-LIKE 7 (SMXL7) to be potential SCF–MAX2 complex-mediated proteasome targets of KAI2 and D14, respectively. Genetic studies on SMXL7 and SMAX1 demonstrated distinct developmental roles for each, but very little is known about these repressors in terms of their sequence features. In this study, we performed an extensive comparative analysis of SMXLs and determined their phylogenetic and evolutionary history in the plant lineage. Our results show that SMXL family members can be sub-divided into four distinct phylogenetic clades/classes, with an ancient SMAX1. Further, we identified the clade-specific motifs that have evolved and that might act as determinants of SL-KAR signalling specificity. These specificities resulted from functional diversities among the clades. Our results suggest that a gradual co-evolution of SMXL members with their upstream receptors D14/KAI2 provided an increased specificity to both the SL perception and response in land plants.","lang":"eng"}],"article_type":"original","publication_status":"published","day":"13","oa_version":"None","ec_funded":1,"external_id":{"isi":["000430727000016"],"pmid":["29538714"]},"month":"04"},{"abstract":[{"lang":"eng","text":"We introduce Intelligent Annotation Dialogs for bounding box annotation. We train an agent to automatically choose a sequence of actions for a human annotator to produce a bounding box in a minimal amount of time. Specifically, we consider two actions: box verification [34], where the annotator verifies a box generated by an object detector, and manual box drawing. We explore two kinds of agents, one based on predicting the probability that a box will be positively verified, and the other based on reinforcement learning. We demonstrate that (1) our agents are able to learn efficient annotation strategies in several scenarios, automatically adapting to the image difficulty, the desired quality of the boxes, and the detector strength; (2) in all scenarios the resulting annotation dialogs speed up annotation compared to manual box drawing alone and box verification alone, while also outperforming any fixed combination of verification and drawing in most scenarios; (3) in a realistic scenario where the detector is iteratively re-trained, our agents evolve a series of strategies that reflect the shifting trade-off between verification and drawing as the detector grows stronger."}],"publication_status":"published","date_published":"2018-12-17T00:00:00Z","year":"2018","oa":1,"arxiv":1,"month":"12","day":"17","oa_version":"Preprint","external_id":{"isi":["000457843609036"],"arxiv":["1712.08087"]},"type":"conference","doi":"10.1109/cvpr.2018.00956","author":[{"full_name":"Uijlings, Jasper","first_name":"Jasper","last_name":"Uijlings"},{"last_name":"Konyushkova","first_name":"Ksenia","full_name":"Konyushkova, Ksenia"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"},{"full_name":"Ferrari, Vittorio","last_name":"Ferrari","first_name":"Vittorio"}],"date_created":"2022-03-18T12:45:09Z","main_file_link":[{"open_access":"1","url":" https://doi.org/10.48550/arXiv.1712.08087"}],"publisher":"IEEE","_id":"10882","isi":1,"scopus_import":"1","page":"9175-9184","citation":{"short":"J. Uijlings, K. Konyushkova, C. Lampert, V. Ferrari, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–9184.","chicago":"Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari. “Learning Intelligent Dialogs for Bounding Box Annotation.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 9175–84. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>.","mla":"Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 9175–84, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>.","ista":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. 2018. Learning intelligent dialogs for bounding box annotation. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVF: Conference on Computer Vision and Pattern Recognition, 9175–9184.","ama":"Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs for bounding box annotation. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:9175-9184. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00956\">10.1109/cvpr.2018.00956</a>","apa":"Uijlings, J., Konyushkova, K., Lampert, C., &#38; Ferrari, V. (2018). Learning intelligent dialogs for bounding box annotation. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 9175–9184). Salt Lake City, UT, United States: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00956\">https://doi.org/10.1109/cvpr.2018.00956</a>","ieee":"J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent dialogs for bounding box annotation,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, United States, 2018, pp. 9175–9184."},"publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","status":"public","department":[{"_id":"ChLa"}],"corr_author":"1","article_processing_charge":"No","date_updated":"2024-10-09T21:02:26Z","publication_identifier":{"isbn":["9781538664209"],"eissn":["2575-7075"]},"title":"Learning intelligent dialogs for bounding box annotation","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"conference":{"start_date":"2018-06-18","name":"CVF: Conference on Computer Vision and Pattern Recognition","location":"Salt Lake City, UT, United States","end_date":"2018-06-23"}},{"_id":"10883","publisher":"EasyChair","file":[{"file_id":"11392","success":1,"relation":"main_file","checksum":"1229aa8640bd6db610c85decf2265480","file_size":720893,"access_level":"open_access","content_type":"application/pdf","date_created":"2022-05-17T07:51:08Z","file_name":"2018_EPiCs_Chatterjee.pdf","creator":"dernst","date_updated":"2022-05-17T07:51:08Z"}],"intvolume":"        57","type":"conference","author":[{"last_name":"Chatterjee","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu"},{"full_name":"Dvořák, Wolfgang","last_name":"Dvořák","first_name":"Wolfgang"},{"last_name":"Henzinger","first_name":"Monika H","orcid":"0000-0002-5008-6530","full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630"},{"full_name":"Svozil, Alexander","first_name":"Alexander","last_name":"Svozil"}],"date_created":"2022-03-18T12:46:32Z","project":[{"grant_number":"S11407","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Game Theory"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"doi":"10.29007/5z5k","month":"10","has_accepted_license":"1","ec_funded":1,"external_id":{"arxiv":["1909.04983"]},"oa_version":"Published Version","day":"23","file_date_updated":"2022-05-17T07:51:08Z","publication_status":"published","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."}],"arxiv":1,"alternative_title":["EPiC Series in Computing"],"year":"2018","oa":1,"date_published":"2018-10-23T00:00:00Z","volume":57,"conference":{"start_date":"2018-11-17","name":"LPAR: Logic for Programming, Artificial Intelligence and Reasoning","end_date":"2018-11-21","location":"Awassa, Ethiopia"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"quality_controlled":"1","article_processing_charge":"No","title":"Quasipolynomial set-based symbolic algorithms for parity games","publication_identifier":{"issn":["2398-7340"]},"date_updated":"2025-07-10T11:50:02Z","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.","department":[{"_id":"KrCh"}],"ddc":["000"],"publication":"22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning","citation":{"apa":"Chatterjee, K., Dvořák, W., Henzinger, M., &#38; Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i> (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. <a href=\"https://doi.org/10.29007/5z5k\">https://doi.org/10.29007/5z5k</a>","ama":"Chatterjee K, Dvořák W, Henzinger M, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>. Vol 57. EasyChair; 2018:233-253. doi:<a href=\"https://doi.org/10.29007/5z5k\">10.29007/5z5k</a>","ieee":"K. Chatterjee, W. Dvořák, M. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253.","short":"K. Chatterjee, W. Dvořák, M. Henzinger, A. Svozil, in:, 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, EasyChair, 2018, pp. 233–253.","chicago":"Chatterjee, Krishnendu, Wolfgang Dvořák, Monika Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, 57:233–53. EasyChair, 2018. <a href=\"https://doi.org/10.29007/5z5k\">https://doi.org/10.29007/5z5k</a>.","mla":"Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” <i>22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning</i>, vol. 57, EasyChair, 2018, pp. 233–53, doi:<a href=\"https://doi.org/10.29007/5z5k\">10.29007/5z5k</a>.","ista":"Chatterjee K, Dvořák W, Henzinger M, Svozil A. 2018. Quasipolynomial set-based symbolic algorithms for parity games. 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. LPAR: Logic for Programming, Artificial Intelligence and Reasoning, EPiC Series in Computing, vol. 57, 233–253."},"page":"233-253","scopus_import":"1","status":"public"},{"status":"public","citation":{"short":"N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214.","mla":"Leopold, Nikolai K., and Peter Pickl. <i>Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields</i>. Vol. 270, Springer, 2018, pp. 185–214, doi:<a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">10.1007/978-3-030-01602-9_9</a>.","ista":"Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214.","chicago":"Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">https://doi.org/10.1007/978-3-030-01602-9_9</a>.","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.","apa":"Leopold, N. K., &#38; 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. <a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">https://doi.org/10.1007/978-3-030-01602-9_9</a>","ama":"Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:<a href=\"https://doi.org/10.1007/978-3-030-01602-9_9\">10.1007/978-3-030-01602-9_9</a>"},"page":"185 - 214","scopus_import":1,"department":[{"_id":"RoSe"}],"title":"Mean-field limits of particles in interaction with quantised radiation fields","date_updated":"2021-01-12T06:48:16Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"conference":{"start_date":"2017-03-30","location":"Munich, Germany","end_date":"2017-04-01","name":"MaLiQS: Macroscopic Limits of Quantum Systems"},"quality_controlled":"1","arxiv":1,"year":"2018","oa":1,"date_published":"2018-10-27T00:00:00Z","volume":270,"publist_id":"8045","publication_status":"published","abstract":[{"lang":"eng","text":"We report on a novel strategy to derive mean-field limits of quantum mechanical systems in which a large number of particles weakly couple to a second-quantized radiation field. The technique combines the method of counting and the coherent state approach to study the growth of the correlations among the particles and in the radiation field. As an instructional example, we derive the Schrödinger–Klein–Gordon system of equations from the Nelson model with ultraviolet cutoff and possibly massless scalar field. In particular, we prove the convergence of the reduced density matrices (of the nonrelativistic particles and the field bosons) associated with the exact time evolution to the projectors onto the solutions of the Schrödinger–Klein–Gordon equations in trace norm. Furthermore, we derive explicit bounds on the rate of convergence of the one-particle reduced density matrix of the nonrelativistic particles in Sobolev norm."}],"ec_funded":1,"external_id":{"arxiv":["1806.10843"]},"oa_version":"Preprint","day":"27","month":"10","author":[{"orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","full_name":"Leopold, Nikolai K","last_name":"Leopold","first_name":"Nikolai K"},{"last_name":"Pickl","first_name":"Peter","full_name":"Pickl, Peter"}],"date_created":"2018-12-11T11:44:08Z","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","name":"Analysis of quantum many-body systems","call_identifier":"H2020"}],"doi":"10.1007/978-3-030-01602-9_9","intvolume":"       270","type":"conference","_id":"11","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1806.10843"}],"publisher":"Springer"},{"quality_controlled":"1","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","publication_identifier":{"issn":["1530-6984"]},"date_updated":"2026-04-08T14:09:47Z","title":"Single-shot readout of hole spins in Ge","pmid":1,"department":[{"_id":"GeKa"}],"issue":"11","ddc":["530"],"scopus_import":"1","isi":1,"publication":"Nano Letters","citation":{"short":"L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros, Nano Letters 18 (2018) 7141–7145.","chicago":"Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” <i>Nano Letters</i>. American Chemical Society, 2018. <a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">https://doi.org/10.1021/acs.nanolett.8b03217</a>.","mla":"Vukušić, Lada, et al. “Single-Shot Readout of Hole Spins in Ge.” <i>Nano Letters</i>, vol. 18, no. 11, American Chemical Society, 2018, pp. 7141–45, doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">10.1021/acs.nanolett.8b03217</a>.","ista":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. 2018. Single-shot readout of hole spins in Ge. Nano Letters. 18(11), 7141–7145.","ama":"Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot readout of hole spins in Ge. <i>Nano Letters</i>. 2018;18(11):7141-7145. doi:<a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">10.1021/acs.nanolett.8b03217</a>","apa":"Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., &#38; Katsaros, G. (2018). Single-shot readout of hole spins in Ge. <i>Nano Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.nanolett.8b03217\">https://doi.org/10.1021/acs.nanolett.8b03217</a>","ieee":"L. Vukušić, J. Kukucka, H. Watzinger, J. M. Milem, F. Schäffler, and G. Katsaros, “Single-shot readout of hole spins in Ge,” <i>Nano Letters</i>, vol. 18, no. 11. American Chemical Society, pp. 7141–7145, 2018."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"page":"7141 - 7145","pubrep_id":"1065","status":"public","publisher":"American Chemical Society","_id":"23","file":[{"file_id":"5194","checksum":"3e6034a94c6b5335e939145d88bdb371","relation":"main_file","access_level":"open_access","file_size":1361441,"content_type":"application/pdf","file_name":"IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf","date_created":"2018-12-12T10:16:08Z","creator":"system","date_updated":"2020-07-14T12:45:37Z"}],"intvolume":"        18","type":"journal_article","project":[{"_id":"25517E86-B435-11E9-9278-68D0E5697425","name":"Towards Spin qubits and Majorana fermions in Germanium self assembled hut-wires","call_identifier":"FP7","grant_number":"335497"}],"doi":"10.1021/acs.nanolett.8b03217","author":[{"orcid":"0000-0003-2424-8636","id":"31E9F056-F248-11E8-B48F-1D18A9856A87","full_name":"Vukušić, Lada","last_name":"Vukušić","first_name":"Lada"},{"full_name":"Kukucka, Josip","id":"3F5D8856-F248-11E8-B48F-1D18A9856A87","first_name":"Josip","last_name":"Kukucka"},{"full_name":"Watzinger, Hannes","id":"35DF8E50-F248-11E8-B48F-1D18A9856A87","last_name":"Watzinger","first_name":"Hannes"},{"full_name":"Milem, Joshua M","id":"4CDE0A96-F248-11E8-B48F-1D18A9856A87","first_name":"Joshua M","last_name":"Milem"},{"full_name":"Schäffler, Friedrich","first_name":"Friedrich","last_name":"Schäffler"},{"full_name":"Katsaros, Georgios","id":"38DB5788-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8342-202X","first_name":"Georgios","last_name":"Katsaros"}],"date_created":"2018-12-11T11:44:13Z","month":"10","has_accepted_license":"1","day":"25","ec_funded":1,"external_id":{"pmid":["30359041"],"isi":["000451102100064"]},"oa_version":"Published Version","acknowledged_ssus":[{"_id":"M-Shop"},{"_id":"NanoFab"}],"publication_status":"published","abstract":[{"text":"The strong atomistic spin–orbit coupling of holes makes single-shot spin readout measurements difficult because it reduces the spin lifetimes. By integrating the charge sensor into a high bandwidth radio frequency reflectometry setup, we were able to demonstrate single-shot readout of a germanium quantum dot hole spin and measure the spin lifetime. Hole spin relaxation times of about 90 μs at 500 mT are reported, with a total readout visibility of about 70%. By analyzing separately the spin-to-charge conversion and charge readout fidelities, we have obtained insight into the processes limiting the visibilities of hole spins. The analyses suggest that high hole visibilities are feasible at realistic experimental conditions, underlying the potential of hole spins for the realization of viable qubit devices.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:37Z","related_material":{"record":[{"relation":"popular_science","id":"7977"},{"relation":"dissertation_contains","id":"7996","status":"public"},{"relation":"dissertation_contains","status":"public","id":"69"}]},"publist_id":"8032","year":"2018","oa":1,"volume":18,"date_published":"2018-10-25T00:00:00Z"},{"date_updated":"2025-04-14T13:51:04Z","acknowledgement":"This research was supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003; Austrian Science Fund (FWF): S11407-N23(RiSE/SHiNE);and an ERC Start Grant (279307:Graph Games).\r\n","title":"Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives","article_processing_charge":"No","quality_controlled":"1","conference":{"start_date":"2018-07-13","name":"IJCAI: International Joint Conference on Artificial Intelligence","location":"Stockholm, Sweden","end_date":"2018-07-19"},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"status":"public","isi":1,"scopus_import":"1","page":"4692 - 4699","citation":{"short":"K. Chatterjee, A. Elgyütt, P. Novotný, O. Rouillé, in:, IJCAI, 2018, pp. 4692–4699.","chicago":"Chatterjee, Krishnendu, Adrian Elgyütt, Petr Novotný, and Owen Rouillé. “Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives,” 2018:4692–99. IJCAI, 2018. <a href=\"https://doi.org/10.24963/ijcai.2018/652\">https://doi.org/10.24963/ijcai.2018/652</a>.","ista":"Chatterjee K, Elgyütt A, Novotný P, Rouillé O. 2018. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018, 4692–4699.","mla":"Chatterjee, Krishnendu, et al. <i>Expectation Optimization with Probabilistic Guarantees in POMDPs with Discounted-Sum Objectives</i>. Vol. 2018, IJCAI, 2018, pp. 4692–99, doi:<a href=\"https://doi.org/10.24963/ijcai.2018/652\">10.24963/ijcai.2018/652</a>.","apa":"Chatterjee, K., Elgyütt, A., Novotný, P., &#38; Rouillé, O. (2018). Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives (Vol. 2018, pp. 4692–4699). Presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden: IJCAI. <a href=\"https://doi.org/10.24963/ijcai.2018/652\">https://doi.org/10.24963/ijcai.2018/652</a>","ama":"Chatterjee K, Elgyütt A, Novotný P, Rouillé O. Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives. In: Vol 2018. IJCAI; 2018:4692-4699. doi:<a href=\"https://doi.org/10.24963/ijcai.2018/652\">10.24963/ijcai.2018/652</a>","ieee":"K. Chatterjee, A. Elgyütt, P. Novotný, and O. Rouillé, “Expectation optimization with probabilistic guarantees in POMDPs with discounted-sum objectives,” presented at the IJCAI: International Joint Conference on Artificial Intelligence, Stockholm, Sweden, 2018, vol. 2018, pp. 4692–4699."},"department":[{"_id":"KrCh"},{"_id":"ToHe"}],"doi":"10.24963/ijcai.2018/652","project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425"}],"date_created":"2018-12-11T11:44:13Z","author":[{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"id":"4A2E9DBA-F248-11E8-B48F-1D18A9856A87","full_name":"Elgyütt, Adrian","first_name":"Adrian","last_name":"Elgyütt"},{"full_name":"Novotny, Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87","last_name":"Novotny","first_name":"Petr"},{"last_name":"Rouillé","first_name":"Owen","full_name":"Rouillé, Owen"}],"intvolume":"      2018","type":"conference","publisher":"IJCAI","main_file_link":[{"url":"https://arxiv.org/abs/1804.10601","open_access":"1"}],"_id":"24","volume":2018,"date_published":"2018-07-01T00:00:00Z","oa":1,"year":"2018","arxiv":1,"abstract":[{"lang":"eng","text":"Partially-observable Markov decision processes (POMDPs) with discounted-sum payoff are a standard framework to model a wide range of problems related to decision making under uncertainty. Traditionally, the goal has been to obtain policies that optimize the expectation of the discounted-sum payoff. A key drawback of the expectation measure is that even low probability events with extreme payoff can significantly affect the expectation, and thus the obtained policies are not necessarily risk-averse. An alternate approach is to optimize the probability that the payoff is above a certain threshold, which allows obtaining risk-averse policies, but ignores optimization of the expectation. We consider the expectation optimization with probabilistic guarantee (EOPG) problem, where the goal is to optimize the expectation ensuring that the payoff is above a given threshold with at least a specified probability. We present several results on the EOPG problem, including the first algorithm to solve it."}],"publication_status":"published","publist_id":"8031","day":"01","oa_version":"Preprint","ec_funded":1,"external_id":{"arxiv":["1804.10601"],"isi":["000764175404117"]},"month":"07"},{"main_file_link":[{"url":"https://doi.org/10.24963/ijcai.2018/662","open_access":"1"}],"publisher":"IJCAI","_id":"25","doi":"10.24963/ijcai.2018/662","project":[{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF","grant_number":"S 11407_N23"},{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"}],"date_created":"2018-12-11T11:44:13Z","author":[{"full_name":"Horák, Karel","last_name":"Horák","first_name":"Karel"},{"first_name":"Branislav","last_name":"Bošanský","full_name":"Bošanský, Branislav"},{"first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"type":"conference","day":"01","oa_version":"Published Version","external_id":{"isi":["000764175404127"]},"ec_funded":1,"month":"07","volume":"2018-July","date_published":"2018-07-01T00:00:00Z","oa":1,"year":"2018","abstract":[{"text":"Partially observable Markov decision processes (POMDPs) are the standard models for planning under uncertainty with both finite and infinite horizon. Besides the well-known discounted-sum objective, indefinite-horizon objective (aka Goal-POMDPs) is another classical objective for POMDPs. In this case, given a set of target states and a positive cost for each transition, the optimization objective is to minimize the expected total cost until a target state is reached. In the literature, RTDP-Bel or heuristic search value iteration (HSVI) have been used for solving Goal-POMDPs. Neither of these algorithms has theoretical convergence guarantees, and HSVI may even fail to terminate its trials. We give the following contributions: (1) We discuss the challenges introduced in Goal-POMDPs and illustrate how they prevent the original HSVI from converging. (2) We present a novel algorithm inspired by HSVI, termed Goal-HSVI, and show that our algorithm has convergence guarantees. (3) We show that Goal-HSVI outperforms RTDP-Bel on a set of well-known examples.","lang":"eng"}],"publication_status":"published","publist_id":"8030","quality_controlled":"1","language":[{"iso":"eng"}],"conference":{"start_date":"2018-07-13","name":"IJCAI: International Joint Conference on Artificial Intelligence","location":"Stockholm, Sweden","end_date":"2018-07-19"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"∗This work has been supported by Vienna Science and Technology Fund (WWTF) Project ICT15-003, Austrian Science Fund (FWF) NFN Grant No S11407-N23 (RiSE/SHiNE), and ERC Starting grant (279307: Graph Games). This research was sponsored by the Army Research Laboratory and was accomplished under Cooperative Agreement Number W911NF-13-2-0045 (ARL Cyber Security CRA). ","date_updated":"2026-06-18T18:34:17Z","title":"Goal-HSVI: Heuristic search value iteration for goal-POMDPs","article_processing_charge":"No","ddc":["000"],"department":[{"_id":"KrCh"}],"status":"public","isi":1,"scopus_import":"1","page":"4764 - 4770","citation":{"ama":"Horák K, Bošanský B, Chatterjee K. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In: <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>. Vol 2018-July. IJCAI; 2018:4764-4770. doi:<a href=\"https://doi.org/10.24963/ijcai.2018/662\">10.24963/ijcai.2018/662</a>","apa":"Horák, K., Bošanský, B., &#38; Chatterjee, K. (2018). Goal-HSVI: Heuristic search value iteration for goal-POMDPs. In <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i> (Vol. 2018–July, pp. 4764–4770). Stockholm, Sweden: IJCAI. <a href=\"https://doi.org/10.24963/ijcai.2018/662\">https://doi.org/10.24963/ijcai.2018/662</a>","ieee":"K. Horák, B. Bošanský, and K. Chatterjee, “Goal-HSVI: Heuristic search value iteration for goal-POMDPs,” in <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, Stockholm, Sweden, 2018, vol. 2018–July, pp. 4764–4770.","chicago":"Horák, Karel, Branislav Bošanský, and Krishnendu Chatterjee. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” In <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, 2018–July:4764–70. IJCAI, 2018. <a href=\"https://doi.org/10.24963/ijcai.2018/662\">https://doi.org/10.24963/ijcai.2018/662</a>.","mla":"Horák, Karel, et al. “Goal-HSVI: Heuristic Search Value Iteration for Goal-POMDPs.” <i>Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence</i>, vol. 2018–July, IJCAI, 2018, pp. 4764–70, doi:<a href=\"https://doi.org/10.24963/ijcai.2018/662\">10.24963/ijcai.2018/662</a>.","ista":"Horák K, Bošanský B, Chatterjee K. 2018. Goal-HSVI: Heuristic search value iteration for goal-POMDPs. Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence. IJCAI: International Joint Conference on Artificial Intelligence vol. 2018–July, 4764–4770.","short":"K. Horák, B. Bošanský, K. Chatterjee, in:, Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence, IJCAI, 2018, pp. 4764–4770."},"publication":"Proceedings of the Twenty-Seventh International Joint Conference on Artificial Intelligence"},{"month":"06","oa_version":"Preprint","ec_funded":1,"external_id":{"isi":["000457843603087"],"arxiv":["1604.08269"]},"day":"28","abstract":[{"lang":"eng","text":"The accuracy of information retrieval systems is often measured using complex loss functions such as the average precision (AP) or the normalized discounted cumulative gain (NDCG). Given a set of positive and negative samples, the parameters of a retrieval system can be estimated by minimizing these loss functions. However, the non-differentiability and non-decomposability of these loss functions does not allow for simple gradient based optimization algorithms. This issue is generally circumvented by either optimizing a structured hinge-loss upper bound to the loss function or by using asymptotic methods like the direct-loss minimization framework. Yet, the high computational complexity of loss-augmented inference, which is necessary for both the frameworks, prohibits its use in large training data sets. To alleviate this deficiency, we present a novel quicksort flavored algorithm for a large class of non-decomposable loss functions. We provide a complete characterization of the loss functions that are amenable to our algorithm, and show that it includes both AP and NDCG based loss functions. Furthermore, we prove that no comparison based algorithm can improve upon the computational complexity of our approach asymptotically. We demonstrate the effectiveness of our approach in the context of optimizing the structured hinge loss upper bound of AP and NDCG loss for learning models for a variety of vision tasks. We show that our approach provides significantly better results than simpler decomposable loss functions, while requiring a comparable training time."}],"publication_status":"published","arxiv":1,"date_published":"2018-06-28T00:00:00Z","year":"2018","oa":1,"_id":"273","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1604.08269"}],"publisher":"IEEE","type":"conference","date_created":"2018-12-11T11:45:33Z","author":[{"last_name":"Mohapatra","first_name":"Pritish","full_name":"Mohapatra, Pritish"},{"id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87","full_name":"Rolinek, Michal","last_name":"Rolinek","first_name":"Michal"},{"full_name":"Jawahar, C V","first_name":"C V","last_name":"Jawahar"},{"last_name":"Kolmogorov","first_name":"Vladimir","full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"M Pawan","last_name":"Kumar","full_name":"Kumar, M Pawan"}],"doi":"10.1109/cvpr.2018.00389","project":[{"grant_number":"616160","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","_id":"25FBA906-B435-11E9-9278-68D0E5697425"}],"department":[{"_id":"VlKo"}],"page":"3693-3701","citation":{"short":"P. Mohapatra, M. Rolinek, C.V. Jawahar, V. Kolmogorov, M.P. Kumar, in:, 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 3693–3701.","chicago":"Mohapatra, Pritish, Michal Rolinek, C V Jawahar, Vladimir Kolmogorov, and M Pawan Kumar. “Efficient Optimization for Rank-Based Loss Functions.” In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, 3693–3701. IEEE, 2018. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>.","ista":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. 2018. Efficient optimization for rank-based loss functions. 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 3693–3701.","mla":"Mohapatra, Pritish, et al. “Efficient Optimization for Rank-Based Loss Functions.” <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, IEEE, 2018, pp. 3693–701, doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>.","apa":"Mohapatra, P., Rolinek, M., Jawahar, C. V., Kolmogorov, V., &#38; Kumar, M. P. (2018). Efficient optimization for rank-based loss functions. In <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i> (pp. 3693–3701). Salt Lake City, UT, USA: IEEE. <a href=\"https://doi.org/10.1109/cvpr.2018.00389\">https://doi.org/10.1109/cvpr.2018.00389</a>","ama":"Mohapatra P, Rolinek M, Jawahar CV, Kolmogorov V, Kumar MP. Efficient optimization for rank-based loss functions. In: <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>. IEEE; 2018:3693-3701. doi:<a href=\"https://doi.org/10.1109/cvpr.2018.00389\">10.1109/cvpr.2018.00389</a>","ieee":"P. Mohapatra, M. Rolinek, C. V. Jawahar, V. Kolmogorov, and M. P. Kumar, “Efficient optimization for rank-based loss functions,” in <i>2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition</i>, Salt Lake City, UT, USA, 2018, pp. 3693–3701."},"publication":"2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition","isi":1,"scopus_import":"1","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"conference":{"start_date":"2018-06-18","name":"CVPR: Conference on Computer Vision and Pattern Recognition","location":"Salt Lake City, UT, USA","end_date":"2018-06-22"},"quality_controlled":"1","article_processing_charge":"No","title":"Efficient optimization for rank-based loss functions","date_updated":"2024-11-04T13:52:32Z","publication_identifier":{"isbn":["9781538664209"]}},{"status":"public","scopus_import":"1","isi":1,"publication":"Journal of Cell Biology","citation":{"ieee":"M. Brown <i>et al.</i>, “Lymphatic exosomes promote dendritic cell migration along guidance cues,” <i>Journal of Cell Biology</i>, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018.","apa":"Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>","ama":"Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. <i>Journal of Cell Biology</i>. 2018;217(6):2205-2221. doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>","short":"M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221.","ista":"Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221.","mla":"Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:<a href=\"https://doi.org/10.1083/jcb.201612051\">10.1083/jcb.201612051</a>.","chicago":"Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” <i>Journal of Cell Biology</i>. Rockefeller University Press, 2018. <a href=\"https://doi.org/10.1083/jcb.201612051\">https://doi.org/10.1083/jcb.201612051</a>."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"page":"2205 - 2221","issue":"6","corr_author":"1","ddc":["570"],"department":[{"_id":"MiSi"},{"_id":"Bio"}],"pmid":1,"acknowledgement":"M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT).","date_updated":"2025-04-14T13:10:20Z","title":"Lymphatic exosomes promote dendritic cell migration along guidance cues","article_processing_charge":"No","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"year":"2018","oa":1,"volume":217,"date_published":"2018-04-12T00:00:00Z","publication_status":"published","abstract":[{"lang":"eng","text":"Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified &gt; 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments."}],"file_date_updated":"2020-07-14T12:45:45Z","publist_id":"7627","day":"12","ec_funded":1,"external_id":{"isi":["000438077800026"],"pmid":["29650776"]},"oa_version":"Published Version","month":"04","has_accepted_license":"1","project":[{"name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FWF","_id":"25A8E5EA-B435-11E9-9278-68D0E5697425","grant_number":"Y 564-B12"},{"_id":"25A603A2-B435-11E9-9278-68D0E5697425","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","call_identifier":"FP7","grant_number":"281556"}],"doi":"10.1083/jcb.201612051","author":[{"first_name":"Markus","last_name":"Brown","full_name":"Brown, Markus","id":"3DAB9AFC-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Johnson, Louise","first_name":"Louise","last_name":"Johnson"},{"last_name":"Leone","first_name":"Dario","full_name":"Leone, Dario"},{"full_name":"Májek, Peter","last_name":"Májek","first_name":"Peter"},{"orcid":"0000-0001-7829-3518","id":"368EE576-F248-11E8-B48F-1D18A9856A87","full_name":"Vaahtomeri, Kari","last_name":"Vaahtomeri","first_name":"Kari"},{"last_name":"Senfter","first_name":"Daniel","full_name":"Senfter, Daniel"},{"full_name":"Bukosza, Nora","last_name":"Bukosza","first_name":"Nora"},{"full_name":"Schachner, Helga","first_name":"Helga","last_name":"Schachner"},{"full_name":"Asfour, Gabriele","last_name":"Asfour","first_name":"Gabriele"},{"full_name":"Langer, Brigitte","last_name":"Langer","first_name":"Brigitte"},{"orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert"},{"last_name":"Parapatics","first_name":"Katja","full_name":"Parapatics, Katja"},{"full_name":"Hong, Young","first_name":"Young","last_name":"Hong"},{"full_name":"Bennett, Keiryn","first_name":"Keiryn","last_name":"Bennett"},{"full_name":"Kain, Renate","first_name":"Renate","last_name":"Kain"},{"last_name":"Detmar","first_name":"Michael","full_name":"Detmar, Michael"},{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K","last_name":"Sixt"},{"full_name":"Jackson, David","last_name":"Jackson","first_name":"David"},{"full_name":"Kerjaschki, Dontscho","first_name":"Dontscho","last_name":"Kerjaschki"}],"date_created":"2018-12-11T11:45:33Z","type":"journal_article","intvolume":"       217","file":[{"date_updated":"2020-07-14T12:45:45Z","date_created":"2018-12-17T12:50:07Z","file_name":"2018_JournalCellBiology_Brown.pdf","creator":"dernst","checksum":"9c7eba51a35c62da8c13f98120b64df4","relation":"main_file","file_id":"5704","content_type":"application/pdf","access_level":"open_access","file_size":2252043}],"publisher":"Rockefeller University Press","_id":"275"},{"issue":"6","ddc":["570"],"department":[{"_id":"MiSi"}],"status":"public","publication":"PLoS One","citation":{"ieee":"C. Frick <i>et al.</i>, “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” <i>PLoS One</i>, vol. 13, no. 6. Public Library of Science, 2018.","apa":"Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>","ama":"Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. <i>PLoS One</i>. 2018;13(6). doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>","short":"C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018).","ista":"Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330.","mla":"Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:<a href=\"https://doi.org/10.1371/journal.pone.0198330\">10.1371/journal.pone.0198330</a>.","chicago":"Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” <i>PLoS One</i>. Public Library of Science, 2018. <a href=\"https://doi.org/10.1371/journal.pone.0198330\">https://doi.org/10.1371/journal.pone.0198330</a>."},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"scopus_import":"1","isi":1,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1","title":"Nano-scale microfluidics to study 3D chemotaxis at the single cell level","date_updated":"2023-09-13T09:00:15Z","acknowledgement":"This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","article_processing_charge":"No","article_number":"e0198330","external_id":{"isi":["000434384900031"]},"oa_version":"Published Version","day":"07","month":"06","has_accepted_license":"1","oa":1,"year":"2018","date_published":"2018-06-07T00:00:00Z","volume":13,"file_date_updated":"2020-07-14T12:45:45Z","publist_id":"7626","publication_status":"published","article_type":"original","abstract":[{"text":"Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo.","lang":"eng"}],"file":[{"date_updated":"2020-07-14T12:45:45Z","creator":"dernst","date_created":"2018-12-17T14:10:32Z","file_name":"2018_Plos_Frick.pdf","content_type":"application/pdf","access_level":"open_access","file_size":7682167,"checksum":"95fc5dc3938b3ad3b7697d10c83cc143","relation":"main_file","file_id":"5709"}],"_id":"276","publisher":"Public Library of Science","date_created":"2018-12-11T11:45:34Z","author":[{"full_name":"Frick, Corina","last_name":"Frick","first_name":"Corina"},{"full_name":"Dettinger, Philip","last_name":"Dettinger","first_name":"Philip"},{"full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2856-3369","first_name":"Jörg","last_name":"Renkawitz"},{"full_name":"Jauch, Annaïse","first_name":"Annaïse","last_name":"Jauch"},{"last_name":"Berger","first_name":"Christoph","full_name":"Berger, Christoph"},{"full_name":"Recher, Mike","first_name":"Mike","last_name":"Recher"},{"full_name":"Schroeder, Timm","last_name":"Schroeder","first_name":"Timm"},{"full_name":"Mehling, Matthias","first_name":"Matthias","last_name":"Mehling"}],"doi":"10.1371/journal.pone.0198330","intvolume":"        13","type":"journal_article"},{"publication":"Plant Molecular Biology","citation":{"ieee":"L. Dokládal <i>et al.</i>, “An armadillo-domain protein participates in a telomerase interaction network,” <i>Plant Molecular Biology</i>, vol. 97, no. 5. Springer, pp. 407–420, 2018.","ama":"Dokládal L, Benková E, Honys D, et al. An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. 2018;97(5):407-420. doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>","apa":"Dokládal, L., Benková, E., Honys, D., Dupláková, N., Lee, L., Gelvin, S., &#38; Sýkorová, E. (2018). An armadillo-domain protein participates in a telomerase interaction network. <i>Plant Molecular Biology</i>. Springer. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>","short":"L. Dokládal, E. Benková, D. Honys, N. Dupláková, L. Lee, S. Gelvin, E. Sýkorová, Plant Molecular Biology 97 (2018) 407–420.","mla":"Dokládal, Ladislav, et al. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>, vol. 97, no. 5, Springer, 2018, pp. 407–20, doi:<a href=\"https://doi.org/10.1007/s11103-018-0747-4\">10.1007/s11103-018-0747-4</a>.","ista":"Dokládal L, Benková E, Honys D, Dupláková N, Lee L, Gelvin S, Sýkorová E. 2018. An armadillo-domain protein participates in a telomerase interaction network. Plant Molecular Biology. 97(5), 407–420.","chicago":"Dokládal, Ladislav, Eva Benková, David Honys, Nikoleta Dupláková, Lan Lee, Stanton Gelvin, and Eva Sýkorová. “An Armadillo-Domain Protein Participates in a Telomerase Interaction Network.” <i>Plant Molecular Biology</i>. Springer, 2018. <a href=\"https://doi.org/10.1007/s11103-018-0747-4\">https://doi.org/10.1007/s11103-018-0747-4</a>."},"page":"407 - 420","scopus_import":"1","isi":1,"status":"public","department":[{"_id":"EvBe"}],"issue":"5","ddc":["580"],"article_processing_charge":"No","title":"An armadillo-domain protein participates in a telomerase interaction network","date_updated":"2023-09-08T13:21:05Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"quality_controlled":"1","file_date_updated":"2020-07-14T12:45:45Z","publist_id":"7625","article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"Arabidopsis and human ARM protein interact with telomerase. Deregulated mRNA levels of DNA repair and ribosomal protein genes in an Arabidopsis arm mutant suggest non-telomeric ARM function. The human homolog ARMC6 interacts with hTRF2. Abstract: Telomerase maintains telomeres and has proposed non-telomeric functions. We previously identified interaction of the C-terminal domain of Arabidopsis telomerase reverse transcriptase (AtTERT) with an armadillo/β-catenin-like repeat (ARM) containing protein. Here we explore protein–protein interactions of the ARM protein, AtTERT domains, POT1a, TRF-like family and SMH family proteins, and the chromatin remodeling protein CHR19 using bimolecular fluorescence complementation (BiFC), yeast two-hybrid (Y2H) analysis, and co-immunoprecipitation. The ARM protein interacts with both the N- and C-terminal domains of AtTERT in different cellular compartments. ARM interacts with CHR19 and TRF-like I family proteins that also bind AtTERT directly or through interaction with POT1a. The putative human ARM homolog co-precipitates telomerase activity and interacts with hTRF2 protein in vitro. Analysis of Arabidopsis arm mutants shows no obvious changes in telomere length or telomerase activity, suggesting that ARM is not essential for telomere maintenance. The observed interactions with telomerase and Myb-like domain proteins (TRF-like family I) may therefore reflect possible non-telomeric functions. Transcript levels of several DNA repair and ribosomal genes are affected in arm mutants, and ARM, likely in association with other proteins, suppressed expression of XRCC3 and RPSAA promoter constructs in luciferase reporter assays. In conclusion, ARM can participate in non-telomeric functions of telomerase, and can also perform its own telomerase-independent functions."}],"oa":1,"year":"2018","volume":97,"date_published":"2018-06-12T00:00:00Z","month":"06","has_accepted_license":"1","external_id":{"isi":["000438981700009"]},"oa_version":"Submitted Version","day":"12","intvolume":"        97","type":"journal_article","date_created":"2018-12-11T11:45:34Z","author":[{"last_name":"Dokládal","first_name":"Ladislav","full_name":"Dokládal, Ladislav"},{"orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva","last_name":"Benková","first_name":"Eva"},{"first_name":"David","last_name":"Honys","full_name":"Honys, David"},{"full_name":"Dupláková, Nikoleta","first_name":"Nikoleta","last_name":"Dupláková"},{"full_name":"Lee, Lan","first_name":"Lan","last_name":"Lee"},{"first_name":"Stanton","last_name":"Gelvin","full_name":"Gelvin, Stanton"},{"full_name":"Sýkorová, Eva","first_name":"Eva","last_name":"Sýkorová"}],"doi":"10.1007/s11103-018-0747-4","_id":"277","publisher":"Springer","file":[{"date_updated":"2020-07-14T12:45:45Z","creator":"dernst","file_name":"2018_PlantMolecBio_Dokladal.pdf","date_created":"2020-05-14T12:23:08Z","checksum":"451ae47616e6af2533099f596b2a47fb","relation":"main_file","file_id":"7834","content_type":"application/pdf","access_level":"open_access","file_size":1150679}]},{"language":[{"iso":"ger"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","supervisor":[{"first_name":"Brigitte","last_name":"Kromp","full_name":"Kromp, Brigitte"}],"_id":"278","publisher":"Universität Wien","main_file_link":[{"open_access":"1","url":"http://othes.univie.ac.at/51113/"}],"author":[{"first_name":"Márton","last_name":"Villányi","full_name":"Villányi, Márton","id":"3FFCCD3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8126-0426"}],"title":"Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken","date_created":"2018-12-11T11:45:34Z","date_updated":"2026-06-18T18:35:07Z","article_processing_charge":"No","type":"dissertation","oa_version":"Published Version","OA_place":"publisher","day":"06","ddc":["020"],"department":[{"_id":"E-Lib"}],"month":"04","year":"2018","oa":1,"status":"public","date_published":"2018-04-06T00:00:00Z","related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"5577"},{"relation":"dissertation_contains","status":"public","id":"5574"},{"relation":"dissertation_contains","id":"5578","status":"public"},{"relation":"dissertation_contains","status":"public","id":"5579"},{"status":"public","id":"5576","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"5575","status":"public"},{"id":"5582","status":"public","relation":"dissertation_contains"},{"id":"5581","status":"public","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"5580","status":"public"}]},"page":"94","citation":{"apa":"Villányi, M. (2018). <i>Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken</i>. Universität Wien.","ama":"Villányi M. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. 2018.","ieee":"M. Villányi, “Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken,” Universität Wien, 2018.","chicago":"Villányi, Márton. “Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken.” Universität Wien, 2018.","mla":"Villányi, Márton. <i>Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken</i>. Universität Wien, 2018.","ista":"Villányi M. 2018. Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken. Universität Wien.","short":"M. Villányi, Lizenzverträge mit Open-Access-Komponenten an österreichischen Bibliotheken, Universität Wien, 2018."},"publist_id":"7624","publication_status":"published","abstract":[{"lang":"eng","text":"Consortial subscription contracts regulate the digital access to publications between publishers and scientific libraries. However, since a couple of years the tendency towards a freely accessible publishing (Open Access) intensifies. As a consequence of this trend the contractual relationship between licensor and licensee is gradually changing as well: More and more contracts exercise influence on open access publishing. The present study attempts to compare Austrian examples of consortial licence contracts, which include components of open access. It describes the difference between pure subscription contracts and differing innovative deals including open access components. Thereby it becomes obvious that for the evaluation of this licence contracts new methods are needed. An essential new element of such analyses is the evaluation of the open access publication numbers. So this study tries to carry out such publication analyses for Austrian open access deals focusing on quantitative questions: How does the number of publications evolve? How does the open access share change? Publications reports of the publishers and database queries from Scopus form the data basis. The analysis of the data points out that differing approaches of contracts result in highly divergent results: Particular deals can prioritize a saving in costs or else the increase of the open access rate. It is to be assumed that within the following years further numerous open access deals will be negotiated. The finding of this study shall provide guidance."}]},{"department":[{"_id":"FyKo"}],"ddc":["570"],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"citation":{"short":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018).","ista":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67.","mla":"Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>, vol. 19, 67, BioMed Central, 2018, doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>.","chicago":"Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” <i>Genome Biology</i>. BioMed Central, 2018. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>.","ieee":"L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” <i>Genome Biology</i>, vol. 19. BioMed Central, 2018.","ama":"Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. 2018;19. doi:<a href=\"https://doi.org/10.1186/s13059-018-1434-0\">10.1186/s13059-018-1434-0</a>","apa":"Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., &#38; Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. <i>Genome Biology</i>. BioMed Central. <a href=\"https://doi.org/10.1186/s13059-018-1434-0\">https://doi.org/10.1186/s13059-018-1434-0</a>"},"publication":"Genome Biology","isi":1,"scopus_import":"1","status":"public","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","article_processing_charge":"No","article_number":"67","title":"Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome","date_updated":"2025-04-15T08:30:30Z","has_accepted_license":"1","month":"05","oa_version":"Published Version","ec_funded":1,"external_id":{"isi":["000433986200001"]},"day":"31","related_material":{"record":[{"relation":"research_data","status":"public","id":"9811"},{"id":"9812","status":"public","relation":"research_data"}]},"publist_id":"7620","file_date_updated":"2020-07-14T12:45:47Z","abstract":[{"lang":"eng","text":"Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments."}],"publication_status":"published","date_published":"2018-05-31T00:00:00Z","volume":19,"year":"2018","oa":1,"_id":"279","publisher":"BioMed Central","file":[{"date_updated":"2020-07-14T12:45:47Z","creator":"dernst","file_name":"2018_GenomeBiology_Zapata.pdf","date_created":"2018-12-17T14:05:01Z","content_type":"application/pdf","file_size":1414722,"access_level":"open_access","relation":"main_file","checksum":"f3e4922486bd9bf1483271bdbed394a7","file_id":"5708"}],"intvolume":"        19","type":"journal_article","date_created":"2018-12-11T11:45:35Z","author":[{"full_name":"Zapata, Luis","last_name":"Zapata","first_name":"Luis"},{"full_name":"Pich, Oriol","last_name":"Pich","first_name":"Oriol"},{"full_name":"Serrano, Luis","first_name":"Luis","last_name":"Serrano"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"full_name":"Ossowski, Stephan","first_name":"Stephan","last_name":"Ossowski"},{"first_name":"Martin","last_name":"Schaefer","full_name":"Schaefer, Martin"}],"doi":"10.1186/s13059-018-1434-0","project":[{"_id":"26120F5C-B435-11E9-9278-68D0E5697425","name":"Systematic investigation of epistasis in molecular evolution","call_identifier":"FP7","grant_number":"335980"}]},{"title":"KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis","date_updated":"2023-09-13T08:24:17Z","acknowledgement":"We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.).","article_processing_charge":"No","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","status":"public","publication":"Nature Plants","citation":{"chicago":"Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>. Nature Publishing Group, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>.","ista":"Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375.","mla":"Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” <i>Nature Plants</i>, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>.","short":"Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375.","apa":"Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/s41477-018-0160-7\">https://doi.org/10.1038/s41477-018-0160-7</a>","ama":"Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. <i>Nature Plants</i>. 2018;4(6):365-375. doi:<a href=\"https://doi.org/10.1038/s41477-018-0160-7\">10.1038/s41477-018-0160-7</a>","ieee":"Z. Gao <i>et al.</i>, “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” <i>Nature Plants</i>, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018."},"page":"365 - 375","scopus_import":"1","isi":1,"issue":"6","department":[{"_id":"JiFr"}],"author":[{"full_name":"Gao, Zhen","last_name":"Gao","first_name":"Zhen"},{"full_name":"Daneva, Anna","last_name":"Daneva","first_name":"Anna"},{"last_name":"Salanenka","first_name":"Yuliya","full_name":"Salanenka, Yuliya","id":"46DAAE7E-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Matthias","last_name":"Van Durme","full_name":"Van Durme, Matthias"},{"full_name":"Huysmans, Marlies","last_name":"Huysmans","first_name":"Marlies"},{"full_name":"Lin, Zongcheng","last_name":"Lin","first_name":"Zongcheng"},{"full_name":"De Winter, Freya","last_name":"De Winter","first_name":"Freya"},{"full_name":"Vanneste, Steffen","first_name":"Steffen","last_name":"Vanneste"},{"full_name":"Karimi, Mansour","last_name":"Karimi","first_name":"Mansour"},{"full_name":"Van De Velde, Jan","first_name":"Jan","last_name":"Van De Velde"},{"first_name":"Klaas","last_name":"Vandepoele","full_name":"Vandepoele, Klaas"},{"full_name":"Van De Walle, Davy","last_name":"Van De Walle","first_name":"Davy"},{"first_name":"Koen","last_name":"Dewettinck","full_name":"Dewettinck, Koen"},{"full_name":"Lambrecht, Bart","last_name":"Lambrecht","first_name":"Bart"},{"last_name":"Nowack","first_name":"Moritz","full_name":"Nowack, Moritz"}],"date_created":"2018-12-11T11:45:35Z","doi":"10.1038/s41477-018-0160-7","intvolume":"         4","type":"journal_article","_id":"280","publisher":"Nature Publishing Group","year":"2018","date_published":"2018-05-28T00:00:00Z","volume":4,"publist_id":"7619","publication_status":"published","abstract":[{"text":"Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span.","lang":"eng"}],"external_id":{"isi":["000435571000017"]},"oa_version":"None","day":"28","month":"05"},{"quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"article_processing_charge":"No","date_updated":"2026-04-08T13:55:45Z","acknowledgement":"This work was supported by the Biotechnology and Biological Sciences Research Council (J.M.J.P., I.F., and P.S.S.), the Engineering and Physical Sciences Research Council (EPSRC) (A.A.G.), and Austrian Science Fund Grant FWF P28844 (to G.T.).","title":"Distributed and dynamic intracellular organization of extracellular information","pmid":1,"department":[{"_id":"GaTk"}],"issue":"23","scopus_import":"1","isi":1,"publication":"PNAS","page":"6088 - 6093","citation":{"chicago":"Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gašper Tkačik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” <i>PNAS</i>. National Academy of Sciences, 2018. <a href=\"https://doi.org/10.1073/pnas.1716659115\">https://doi.org/10.1073/pnas.1716659115</a>.","ista":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. 2018. Distributed and dynamic intracellular organization of extracellular information. PNAS. 115(23), 6088–6093.","mla":"Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” <i>PNAS</i>, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:<a href=\"https://doi.org/10.1073/pnas.1716659115\">10.1073/pnas.1716659115</a>.","short":"A. Granados, J. Pietsch, S.A. Cepeda Humerez, I. Farquhar, G. Tkačik, P. Swain, PNAS 115 (2018) 6088–6093.","apa":"Granados, A., Pietsch, J., Cepeda Humerez, S. A., Farquhar, I., Tkačik, G., &#38; Swain, P. (2018). Distributed and dynamic intracellular organization of extracellular information. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1716659115\">https://doi.org/10.1073/pnas.1716659115</a>","ama":"Granados A, Pietsch J, Cepeda Humerez SA, Farquhar I, Tkačik G, Swain P. Distributed and dynamic intracellular organization of extracellular information. <i>PNAS</i>. 2018;115(23):6088-6093. doi:<a href=\"https://doi.org/10.1073/pnas.1716659115\">10.1073/pnas.1716659115</a>","ieee":"A. Granados, J. Pietsch, S. A. Cepeda Humerez, I. Farquhar, G. Tkačik, and P. Swain, “Distributed and dynamic intracellular organization of extracellular information,” <i>PNAS</i>, vol. 115, no. 23. National Academy of Sciences, pp. 6088–6093, 2018."},"status":"public","main_file_link":[{"url":"https://www.biorxiv.org/content/early/2017/09/21/192039","open_access":"1"}],"publisher":"National Academy of Sciences","_id":"281","type":"journal_article","intvolume":"       115","project":[{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27"}],"doi":"10.1073/pnas.1716659115","author":[{"full_name":"Granados, Alejandro","first_name":"Alejandro","last_name":"Granados"},{"full_name":"Pietsch, Julian","last_name":"Pietsch","first_name":"Julian"},{"full_name":"Cepeda Humerez, Sarah A","id":"3DEE19A4-F248-11E8-B48F-1D18A9856A87","first_name":"Sarah A","last_name":"Cepeda Humerez"},{"first_name":"Isebail","last_name":"Farquhar","full_name":"Farquhar, Isebail"},{"last_name":"Tkacik","first_name":"Gasper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper"},{"full_name":"Swain, Peter","first_name":"Peter","last_name":"Swain"}],"date_created":"2018-12-11T11:45:35Z","month":"06","day":"05","external_id":{"pmid":["29784812"],"isi":["000434114900071"]},"oa_version":"Preprint","article_type":"original","publication_status":"published","abstract":[{"text":"Although cells respond specifically to environments, how environmental identity is encoded intracellularly is not understood. Here, we study this organization of information in budding yeast by estimating the mutual information between environmental transitions and the dynamics of nuclear translocation for 10 transcription factors. Our method of estimation is general, scalable, and based on decoding from single cells. The dynamics of the transcription factors are necessary to encode the highest amounts of extracellular information, and we show that information is transduced through two channels: Generalists (Msn2/4, Tod6 and Dot6, Maf1, and Sfp1) can encode the nature of multiple stresses, but only if stress is high; specialists (Hog1, Yap1, and Mig1/2) encode one particular stress, but do so more quickly and for a wider range of magnitudes. In particular, Dot6 encodes almost as much information as Msn2, the master regulator of the environmental stress response. Each transcription factor reports differently, and it is only their collective behavior that distinguishes between multiple environmental states. Changes in the dynamics of the localization of transcription factors thus constitute a precise, distributed internal representation of extracellular change. We predict that such multidimensional representations are common in cellular decision-making.","lang":"eng"}],"related_material":{"record":[{"status":"public","id":"6473","relation":"part_of_dissertation"}]},"publist_id":"7618","year":"2018","oa":1,"volume":115,"date_published":"2018-06-05T00:00:00Z"}]