--- OA_place: publisher _id: '6825' 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. " alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Karola full_name: Käfer, Karola id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87 last_name: Käfer citation: ama: Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior. 2019. doi:10.15479/AT:ISTA:6825 apa: Käfer, K. (2019). The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6825 chicago: Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6825. ieee: K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,” Institute of Science and Technology Austria, 2019. ista: Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria. mla: Käfer, Karola. The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6825. short: K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior, Institute of Science and Technology Austria, 2019. corr_author: '1' date_created: 2019-08-21T15:00:57Z date_published: 2019-08-24T00:00:00Z date_updated: 2026-04-08T13:56:14Z day: '24' ddc: - '570' degree_awarded: PhD department: - _id: JoCs - _id: GradSch doi: 10.15479/AT:ISTA:6825 file: - access_level: open_access checksum: 2664420e332a33338568f4f3bfc59287 content_type: application/pdf creator: kkaefer date_created: 2019-09-03T08:07:13Z date_updated: 2020-09-06T22:30:03Z embargo: 2020-09-05 file_id: '6846' file_name: Thesis_Kaefer_PDFA.pdf file_size: 3205202 relation: main_file request_a_copy: 0 - access_level: closed checksum: 9a154eab6f07aa590a3d2651dc0d926a content_type: application/zip creator: kkaefer date_created: 2019-09-03T08:07:17Z date_updated: 2024-04-10T22:30:48Z embargo_to: open_access file_id: '6847' file_name: Thesis_Kaefer.zip file_size: 2506835 relation: source_file file_date_updated: 2024-04-10T22:30:48Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '89' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '5949' relation: part_of_dissertation status: public status: public supervisor: - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 title: The hippocampus and medial prefrontal cortex during flexible behavior type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2019' ... --- _id: '5949' 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. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Karola full_name: Käfer, Karola id: 2DAA49AA-F248-11E8-B48F-1D18A9856A87 last_name: Käfer - first_name: Hugo full_name: Malagon-Vina, Hugo last_name: Malagon-Vina - first_name: Desiree full_name: Dickerson, Desiree id: 444EB89E-F248-11E8-B48F-1D18A9856A87 last_name: Dickerson - first_name: Joseph full_name: O'Neill, Joseph last_name: O'Neill - first_name: Svenja V. full_name: Trossbach, Svenja V. last_name: Trossbach - first_name: Carsten full_name: Korth, Carsten last_name: Korth - first_name: Jozsef L full_name: Csicsvari, Jozsef L id: 3FA14672-F248-11E8-B48F-1D18A9856A87 last_name: Csicsvari orcid: 0000-0002-5193-4036 citation: ama: Käfer K, Malagon-Vina H, Dickerson D, et al. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 2019;29(9):802-816. doi:10.1002/hipo.23076 apa: Käfer, K., Malagon-Vina, H., Dickerson, D., O’Neill, J., Trossbach, S. V., Korth, C., & Csicsvari, J. L. (2019). Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. Wiley. https://doi.org/10.1002/hipo.23076 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.” Hippocampus. Wiley, 2019. https://doi.org/10.1002/hipo.23076. ieee: K. Käfer et al., “Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization,” Hippocampus, vol. 29, no. 9. Wiley, pp. 802–816, 2019. 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.” Hippocampus, vol. 29, no. 9, Wiley, 2019, pp. 802–16, doi:10.1002/hipo.23076. short: K. Käfer, H. Malagon-Vina, D. Dickerson, J. O’Neill, S.V. Trossbach, C. Korth, J.L. Csicsvari, Hippocampus 29 (2019) 802–816. date_created: 2019-02-10T22:59:18Z date_published: 2019-09-01T00:00:00Z date_updated: 2026-07-01T22:31:20Z day: '01' ddc: - '570' department: - _id: JoCs doi: 10.1002/hipo.23076 ec_funded: 1 external_id: isi: - '000480635400003' file: - access_level: open_access checksum: 5e8de271ca04aef92a5de42d6aac4404 content_type: application/pdf creator: dernst date_created: 2019-02-11T10:42:51Z date_updated: 2020-07-14T12:47:13Z file_id: '5950' file_name: 2019_Hippocampus_Kaefer.pdf file_size: 2132893 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 29' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 802-816 project: - _id: 257BBB4C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '607616' name: inter-and intracellular signalling in schizophrenia publication: Hippocampus publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '6825' relation: dissertation_contains status: public scopus_import: '1' status: public title: Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 29 year: '2019' ... --- _id: '6328' abstract: - lang: eng text: During metazoan development, immune surveillance and cancer dissemination, cells migrate in complex three-dimensional microenvironments1,2,3. These spaces are crowded by cells and extracellular matrix, generating mazes with differently sized gaps that are typically smaller than the diameter of the migrating cell4,5. Most mesenchymal and epithelial cells and some—but not all—cancer cells actively generate their migratory path using pericellular tissue proteolysis6. By contrast, amoeboid cells such as leukocytes use non-destructive strategies of locomotion7, raising the question how these extremely fast cells navigate through dense tissues. Here we reveal that leukocytes sample their immediate vicinity for large pore sizes, and are thereby able to choose the path of least resistance. This allows them to circumnavigate local obstacles while effectively following global directional cues such as chemotactic gradients. Pore-size discrimination is facilitated by frontward positioning of the nucleus, which enables the cells to use their bulkiest compartment as a mechanical gauge. Once the nucleus and the closely associated microtubule organizing centre pass the largest pore, cytoplasmic protrusions still lingering in smaller pores are retracted. These retractions are coordinated by dynamic microtubules; when microtubules are disrupted, migrating cells lose coherence and frequently fragment into migratory cytoplasmic pieces. As nuclear positioning in front of the microtubule organizing centre is a typical feature of amoeboid migration, our findings link the fundamental organization of cellular polarity to the strategy of locomotion. acknowledged_ssus: - _id: SSU article_processing_charge: No article_type: letter_note author: - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Aglaja full_name: Kopf, Aglaja id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87 last_name: Kopf orcid: 0000-0002-2187-6656 - first_name: Julian A full_name: Stopp, Julian A id: 489E3F00-F248-11E8-B48F-1D18A9856A87 last_name: Stopp - first_name: Ingrid full_name: de Vries, Ingrid id: 4C7D837E-F248-11E8-B48F-1D18A9856A87 last_name: de Vries - first_name: Meghan K. full_name: Driscoll, Meghan K. last_name: Driscoll - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Erik S. full_name: Welf, Erik S. last_name: Welf - first_name: Gaudenz full_name: Danuser, Gaudenz last_name: Danuser - first_name: Reto full_name: Fiolka, Reto last_name: Fiolka - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: Renkawitz J, Kopf A, Stopp JA, et al. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 2019;568:546-550. doi:10.1038/s41586-019-1087-5 apa: Renkawitz, J., Kopf, A., Stopp, J. A., de Vries, I., Driscoll, M. K., Merrin, J., … Sixt, M. K. (2019). Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1087-5 chicago: Renkawitz, Jörg, Aglaja Kopf, Julian A Stopp, Ingrid de Vries, Meghan K. Driscoll, Jack Merrin, Robert Hauschild, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1087-5. ieee: J. Renkawitz et al., “Nuclear positioning facilitates amoeboid migration along the path of least resistance,” Nature, vol. 568. Springer Nature, pp. 546–550, 2019. ista: Renkawitz J, Kopf A, Stopp JA, de Vries I, Driscoll MK, Merrin J, Hauschild R, Welf ES, Danuser G, Fiolka R, Sixt MK. 2019. Nuclear positioning facilitates amoeboid migration along the path of least resistance. Nature. 568, 546–550. mla: Renkawitz, Jörg, et al. “Nuclear Positioning Facilitates Amoeboid Migration along the Path of Least Resistance.” Nature, vol. 568, Springer Nature, 2019, pp. 546–50, doi:10.1038/s41586-019-1087-5. short: J. Renkawitz, A. Kopf, J.A. Stopp, I. de Vries, M.K. Driscoll, J. Merrin, R. Hauschild, E.S. Welf, G. Danuser, R. Fiolka, M.K. Sixt, Nature 568 (2019) 546–550. date_created: 2019-04-17T06:52:28Z date_published: 2019-04-25T00:00:00Z date_updated: 2026-07-01T22:31:19Z day: '25' department: - _id: MiSi - _id: NanoFab - _id: Bio doi: 10.1038/s41586-019-1087-5 ec_funded: 1 external_id: isi: - '000465594200050' pmid: - '30944468' intvolume: ' 568' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7217284/ month: '04' oa: 1 oa_version: Submitted Version page: 546-550 pmid: 1 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes - _id: 25FE9508-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '724373' name: Cellular Navigation Along Spatial Gradients - _id: 265FAEBA-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W01250-B20 name: Nano-Analytics of Cellular Systems - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25A48D24-B435-11E9-9278-68D0E5697425 grant_number: ALTF 1396-2014 name: Molecular and system level view of immune cell migration publication: Nature publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/leukocytes-use-their-nucleus-as-a-ruler-to-choose-path-of-least-resistance/ record: - id: '14697' relation: dissertation_contains status: public - id: '6891' relation: dissertation_contains status: public scopus_import: '1' status: public title: Nuclear positioning facilitates amoeboid migration along the path of least resistance type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 568 year: '2019' ... --- OA_place: publisher _id: '6947' 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. acknowledged_ssus: - _id: Bio - _id: PreCl - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Frank P full_name: Assen, Frank P id: 3A8E7F24-F248-11E8-B48F-1D18A9856A87 last_name: Assen orcid: 0000-0003-3470-6119 citation: ama: 'Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:10.15479/AT:ISTA:6947' apa: 'Assen, F. P. (2019). Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:6947' chicago: 'Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:6947.' ieee: 'F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019.' 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. Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking. Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:6947.' short: 'F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019.' corr_author: '1' date_created: 2019-10-14T16:54:52Z date_published: 2019-10-09T00:00:00Z date_updated: 2026-06-18T18:47:59Z day: '09' ddc: - '570' degree_awarded: PhD department: - _id: MiSi doi: 10.15479/AT:ISTA:6947 file: - access_level: closed checksum: 53a739752a500f84d0f8ec953cbbd0b6 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: fassen date_created: 2019-11-06T12:30:02Z date_updated: 2020-11-07T23:30:03Z embargo_to: open_access file_id: '6990' file_name: PhDthesis_FrankAssen_revised2.docx file_size: 214172667 relation: source_file - access_level: open_access checksum: 8c156b65d9347bb599623a4b09f15d15 content_type: application/pdf creator: fassen date_created: 2019-11-06T12:30:57Z date_updated: 2020-11-07T23:30:03Z embargo: 2020-11-06 file_id: '6991' file_name: PhDthesis_FrankAssen_revised2.pdf file_size: 83637532 relation: main_file file_date_updated: 2020-11-07T23:30:03Z has_accepted_license: '1' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: '142' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '664' relation: part_of_dissertation status: public - id: '402' relation: part_of_dissertation status: public status: public supervisor: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 title: 'Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking' type: dissertation user_id: ba8df636-2132-11f1-aed0-ed93e2281fdd year: '2019' ... --- _id: '6351' abstract: - lang: eng text: "A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing." acknowledged_ssus: - _id: Bio article_processing_charge: No author: - first_name: Petra full_name: Marhavá, Petra id: 44E59624-F248-11E8-B48F-1D18A9856A87 last_name: Marhavá - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Saiko full_name: Yoshida, Saiko id: 2E46069C-F248-11E8-B48F-1D18A9856A87 last_name: Yoshida orcid: 0000-0001-6111-9353 - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 2019;177(4):957-969.e13. doi:10.1016/j.cell.2019.04.015 apa: Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., & Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. Elsevier. https://doi.org/10.1016/j.cell.2019.04.015 chicago: Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell. Elsevier, 2019. https://doi.org/10.1016/j.cell.2019.04.015. ieee: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” Cell, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019. ista: Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13. mla: Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” Cell, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:10.1016/j.cell.2019.04.015. short: P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13. corr_author: '1' date_created: 2019-04-28T21:59:14Z date_published: 2019-05-02T00:00:00Z date_updated: 2026-07-01T22:31:23Z day: '02' ddc: - '570' department: - _id: JiFr - _id: EvBe doi: 10.1016/j.cell.2019.04.015 ec_funded: 1 external_id: isi: - '000466843000015' pmid: - '31051107' file: - access_level: open_access checksum: 4ceba04a96a74f5092ec3ce2c579a0c7 content_type: application/pdf creator: dernst date_created: 2019-05-13T06:12:45Z date_updated: 2020-07-14T12:47:28Z file_id: '6411' file_name: 2019_Cell_Marhava.pdf file_size: 10272032 relation: main_file file_date_updated: 2020-07-14T12:47:28Z has_accepted_license: '1' intvolume: ' 177' isi: 1 issue: '4' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 957-969.e13 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Cell publication_identifier: eissn: - 1097-4172 issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/ record: - id: '9992' relation: dissertation_contains status: public scopus_import: '1' status: public title: Re-activation of stem cell pathways for pattern restoration in plant wound healing tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 177 year: '2019' ... --- _id: '6943' abstract: - lang: eng text: Plants as sessile organisms are constantly under attack by herbivores, rough environmental situations, or mechanical pressure. These challenges often lead to the induction of wounds or destruction of already specified and developed tissues. Additionally, wounding makes plants vulnerable to invasion by pathogens, which is why wound signalling often triggers specific defence responses. To stay competitive or, eventually, survive under these circumstances, plants need to regenerate efficiently, which in rigid, tissue migration-incompatible plant tissues requires post-embryonic patterning and organogenesis. Now, several studies used laser-assisted single cell ablation in the Arabidopsis root tip as a minimal wounding proxy. Here, we discuss their findings and put them into context of a broader spectrum of wound signalling, pathogen responses and tissue as well as organ regeneration. article_processing_charge: No article_type: original author: - first_name: Lukas full_name: Hörmayer, Lukas id: 2EEE7A2A-F248-11E8-B48F-1D18A9856A87 last_name: Hörmayer orcid: 0000-0001-8295-2926 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Hörmayer L, Friml J. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 2019;52:124-130. doi:10.1016/j.pbi.2019.08.006 apa: Hörmayer, L., & Friml, J. (2019). Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. Elsevier. https://doi.org/10.1016/j.pbi.2019.08.006 chicago: Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology. Elsevier, 2019. https://doi.org/10.1016/j.pbi.2019.08.006. ieee: L. Hörmayer and J. Friml, “Targeted cell ablation-based insights into wound healing and restorative patterning,” Current Opinion in Plant Biology, vol. 52. Elsevier, pp. 124–130, 2019. ista: Hörmayer L, Friml J. 2019. Targeted cell ablation-based insights into wound healing and restorative patterning. Current Opinion in Plant Biology. 52, 124–130. mla: Hörmayer, Lukas, and Jiří Friml. “Targeted Cell Ablation-Based Insights into Wound Healing and Restorative Patterning.” Current Opinion in Plant Biology, vol. 52, Elsevier, 2019, pp. 124–30, doi:10.1016/j.pbi.2019.08.006. short: L. Hörmayer, J. Friml, Current Opinion in Plant Biology 52 (2019) 124–130. corr_author: '1' date_created: 2019-10-14T07:00:24Z date_published: 2019-12-01T00:00:00Z date_updated: 2026-07-01T22:31:23Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.pbi.2019.08.006 ec_funded: 1 external_id: isi: - '000502890600017' pmid: - '31585333' file: - access_level: open_access checksum: d6fd68a6e965f1efe3f0bf2d2070a616 content_type: application/pdf creator: dernst date_created: 2019-10-14T14:48:21Z date_updated: 2020-07-14T12:47:45Z file_id: '6946' file_name: 2019_CurrentOpinionPlant_Hoermayer.pdf file_size: 1659288 relation: main_file file_date_updated: 2020-07-14T12:47:45Z has_accepted_license: '1' intvolume: ' 52' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 124-130 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Current Opinion in Plant Biology publication_identifier: issn: - 1369-5266 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: record: - id: '9992' relation: dissertation_contains status: public scopus_import: '1' status: public title: Targeted cell ablation-based insights into wound healing and restorative patterning tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 52 year: '2019' ... --- _id: '6486' abstract: - lang: eng text: Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow. acknowledged_ssus: - _id: M-Shop article_number: '111105' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Jakob full_name: Kühnen, Jakob id: 3A47AE32-F248-11E8-B48F-1D18A9856A87 last_name: Kühnen orcid: 0000-0003-4312-0179 - first_name: Davide full_name: Scarselli, Davide id: 40315C30-F248-11E8-B48F-1D18A9856A87 last_name: Scarselli orcid: 0000-0001-5227-4271 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 2019;141(11). doi:10.1115/1.4043494 apa: Kühnen, J., Scarselli, D., & Hof, B. (2019). Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. ASME. https://doi.org/10.1115/1.4043494 chicago: Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering. ASME, 2019. https://doi.org/10.1115/1.4043494. ieee: J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means of 3D-printed shaped honeycombs,” Journal of Fluids Engineering, vol. 141, no. 11. ASME, 2019. ista: Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105. mla: Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” Journal of Fluids Engineering, vol. 141, no. 11, 111105, ASME, 2019, doi:10.1115/1.4043494. short: J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019). date_created: 2019-05-26T21:59:13Z date_published: 2019-11-01T00:00:00Z date_updated: 2026-07-01T22:31:24Z day: '01' department: - _id: BjHo doi: 10.1115/1.4043494 ec_funded: 1 external_id: arxiv: - '1809.07625' isi: - '000487748600005' intvolume: ' 141' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.07625 month: '11' oa: 1 oa_version: Preprint project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Journal of Fluids Engineering publication_identifier: eissn: - 1528-901X issn: - 0098-2202 publication_status: published publisher: ASME quality_controlled: '1' related_material: record: - id: '7258' relation: dissertation_contains status: public scopus_import: '1' status: public title: Relaminarization of pipe flow by means of 3D-printed shaped honeycombs type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 141 year: '2019' ... --- _id: '6228' abstract: - lang: eng text: Following the recent observation that turbulent pipe flow can be relaminarised bya relatively simple modification of the mean velocity profile, we here carry out aquantitative experimental investigation of this phenomenon. Our study confirms thata flat velocity profile leads to a collapse of turbulence and in order to achieve theblunted profile shape, we employ a moving pipe segment that is briefly and rapidlyshifted in the streamwise direction. The relaminarisation threshold and the minimumshift length and speeds are determined as a function of Reynolds number. Althoughturbulence is still active after the acceleration phase, the modulated profile possessesa severely decreased lift-up potential as measured by transient growth. As shown,this results in an exponential decay of fluctuations and the flow relaminarises. Whilethis method can be easily applied at low to moderate flow speeds, the minimumstreamwise length over which the acceleration needs to act increases linearly with theReynolds number. article_processing_charge: No arxiv: 1 author: - first_name: Davide full_name: Scarselli, Davide id: 40315C30-F248-11E8-B48F-1D18A9856A87 last_name: Scarselli orcid: 0000-0001-5227-4271 - first_name: Jakob full_name: Kühnen, Jakob id: 3A47AE32-F248-11E8-B48F-1D18A9856A87 last_name: Kühnen orcid: 0000-0003-4312-0179 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 2019;867:934-948. doi:10.1017/jfm.2019.191 apa: Scarselli, D., Kühnen, J., & Hof, B. (2019). Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2019.191 chicago: Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics. Cambridge University Press, 2019. https://doi.org/10.1017/jfm.2019.191. ieee: D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,” Journal of Fluid Mechanics, vol. 867. Cambridge University Press, pp. 934–948, 2019. ista: Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 867, 934–948. mla: Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” Journal of Fluid Mechanics, vol. 867, Cambridge University Press, 2019, pp. 934–48, doi:10.1017/jfm.2019.191. short: D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948. date_created: 2019-04-07T21:59:14Z date_published: 2019-05-25T00:00:00Z date_updated: 2026-07-01T22:31:24Z day: '25' department: - _id: BjHo doi: 10.1017/jfm.2019.191 ec_funded: 1 external_id: arxiv: - '1807.05357' isi: - '000462606100001' intvolume: ' 867' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.05357 month: '05' oa: 1 oa_version: Preprint page: 934-948 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin - _id: 25104D44-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '737549' name: Eliminating turbulence in oil pipelines publication: Journal of Fluid Mechanics publication_identifier: eissn: - 1469-7645 issn: - 0022-1120 publication_status: published publisher: Cambridge University Press quality_controlled: '1' related_material: link: - relation: supplementary_material url: https://doi.org/10.1017/jfm.2019.191 record: - id: '7258' relation: dissertation_contains status: public scopus_import: '1' status: public title: Relaminarising pipe flow by wall movement type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 867 year: '2019' ... --- _id: '10864' abstract: - lang: eng text: We prove that every congruence distributive variety has directed Jónsson terms, and every congruence modular variety has directed Gumm terms. The directed terms we construct witness every case of absorption witnessed by the original Jónsson or Gumm terms. This result is equivalent to a pair of claims about absorption for admissible preorders in congruence distributive and congruence modular varieties, respectively. For finite algebras, these absorption theorems have already seen significant applications, but until now, it was not clear if the theorems hold for general algebras as well. Our method also yields a novel proof of a result by P. Lipparini about the existence of a chain of terms (which we call Pixley terms) in varieties that are at the same time congruence distributive and k-permutable for some k. acknowledgement: The second author was supported by National Science Center grant DEC-2011-/01/B/ST6/01006. article_processing_charge: No arxiv: 1 author: - first_name: Alexandr full_name: Kazda, Alexandr id: 3B32BAA8-F248-11E8-B48F-1D18A9856A87 last_name: Kazda - first_name: Marcin full_name: Kozik, Marcin last_name: Kozik - first_name: Ralph full_name: McKenzie, Ralph last_name: McKenzie - first_name: Matthew full_name: Moore, Matthew last_name: Moore citation: ama: 'Kazda A, Kozik M, McKenzie R, Moore M. Absorption and directed Jónsson terms. In: Czelakowski J, ed. Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. Vol 16. OCTR. Cham: Springer Nature; 2018:203-220. doi:10.1007/978-3-319-74772-9_7' apa: 'Kazda, A., Kozik, M., McKenzie, R., & Moore, M. (2018). Absorption and directed Jónsson terms. In J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science (Vol. 16, pp. 203–220). Cham: Springer Nature. https://doi.org/10.1007/978-3-319-74772-9_7' chicago: 'Kazda, Alexandr, Marcin Kozik, Ralph McKenzie, and Matthew Moore. “Absorption and Directed Jónsson Terms.” In Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, 16:203–20. OCTR. Cham: Springer Nature, 2018. https://doi.org/10.1007/978-3-319-74772-9_7.' ieee: 'A. Kazda, M. Kozik, R. McKenzie, and M. Moore, “Absorption and directed Jónsson terms,” in Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, vol. 16, J. Czelakowski, Ed. Cham: Springer Nature, 2018, pp. 203–220.' ista: 'Kazda A, Kozik M, McKenzie R, Moore M. 2018.Absorption and directed Jónsson terms. In: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science. vol. 16, 203–220.' mla: Kazda, Alexandr, et al. “Absorption and Directed Jónsson Terms.” Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, edited by J Czelakowski, vol. 16, Springer Nature, 2018, pp. 203–20, doi:10.1007/978-3-319-74772-9_7. short: A. Kazda, M. Kozik, R. McKenzie, M. Moore, in:, J. Czelakowski (Ed.), Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science, Springer Nature, Cham, 2018, pp. 203–220. corr_author: '1' date_created: 2022-03-18T10:30:32Z date_published: 2018-03-21T00:00:00Z date_updated: 2024-10-09T21:01:50Z day: '21' department: - _id: VlKo doi: 10.1007/978-3-319-74772-9_7 editor: - first_name: J full_name: Czelakowski, J last_name: Czelakowski external_id: arxiv: - '1502.01072' intvolume: ' 16' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1502.01072 month: '03' oa: 1 oa_version: Preprint page: 203-220 place: Cham publication: Don Pigozzi on Abstract Algebraic Logic, Universal Algebra, and Computer Science publication_identifier: eisbn: - '9783319747729' eissn: - 2211-2766 isbn: - '9783319747712' issn: - 2211-2758 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' series_title: OCTR status: public title: Absorption and directed Jónsson terms type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 16 year: '2018' ... --- _id: '10880' abstract: - lang: eng 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. acknowledgement: This work was supported by JSPS overseas research fellowships (Y.M.) and SENSHIN Medical Research Foundation (K.K.T.). article_processing_charge: No article_type: original author: - first_name: Moriyama full_name: Yuuta, Moriyama id: 4968E7C8-F248-11E8-B48F-1D18A9856A87 last_name: Yuuta orcid: 0000-0002-2853-8051 - first_name: Kazuko full_name: Koshiba-Takeuchi, Kazuko last_name: Koshiba-Takeuchi citation: ama: Yuuta M, Koshiba-Takeuchi K. Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. 2018;17(5):329-338. doi:10.1093/bfgp/ely007 apa: Yuuta, M., & Koshiba-Takeuchi, K. (2018). Significance of whole-genome duplications on the emergence of evolutionary novelties. Briefings in Functional Genomics. Oxford University Press. https://doi.org/10.1093/bfgp/ely007 chicago: Yuuta, Moriyama, and Kazuko Koshiba-Takeuchi. “Significance of Whole-Genome Duplications on the Emergence of Evolutionary Novelties.” Briefings in Functional Genomics. Oxford University Press, 2018. https://doi.org/10.1093/bfgp/ely007. ieee: M. Yuuta and K. Koshiba-Takeuchi, “Significance of whole-genome duplications on the emergence of evolutionary novelties,” Briefings in Functional Genomics, vol. 17, no. 5. Oxford University Press, pp. 329–338, 2018. 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.” Briefings in Functional Genomics, vol. 17, no. 5, Oxford University Press, 2018, pp. 329–38, doi:10.1093/bfgp/ely007. short: M. Yuuta, K. Koshiba-Takeuchi, Briefings in Functional Genomics 17 (2018) 329–338. corr_author: '1' date_created: 2022-03-18T12:40:35Z date_published: 2018-09-01T00:00:00Z date_updated: 2026-06-18T10:44:32Z day: '01' ddc: - '570' department: - _id: CaHe doi: 10.1093/bfgp/ely007 external_id: isi: - '000456054400004' pmid: - '29579140' intvolume: ' 17' isi: 1 issue: '5' keyword: - Genetics - Molecular Biology - Biochemistry - General Medicine language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1093/bfgp/ely007 month: '09' oa: 1 oa_version: Published Version page: 329-338 pmid: 1 publication: Briefings in Functional Genomics publication_identifier: eissn: - 2041-2657 issn: - 2041-2649 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Significance of whole-genome duplications on the emergence of evolutionary novelties type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2018' ... --- _id: '10882' 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.' article_processing_charge: No arxiv: 1 author: - first_name: Jasper full_name: Uijlings, Jasper last_name: Uijlings - first_name: Ksenia full_name: Konyushkova, Ksenia last_name: Konyushkova - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Vittorio full_name: Ferrari, Vittorio last_name: Ferrari citation: ama: 'Uijlings J, Konyushkova K, Lampert C, Ferrari V. Learning intelligent dialogs for bounding box annotation. In: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2018:9175-9184. doi:10.1109/cvpr.2018.00956' apa: 'Uijlings, J., Konyushkova, K., Lampert, C., & Ferrari, V. (2018). Learning intelligent dialogs for bounding box annotation. In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 9175–9184). Salt Lake City, UT, United States: IEEE. https://doi.org/10.1109/cvpr.2018.00956' chicago: Uijlings, Jasper, Ksenia Konyushkova, Christoph Lampert, and Vittorio Ferrari. “Learning Intelligent Dialogs for Bounding Box Annotation.” In 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 9175–84. IEEE, 2018. https://doi.org/10.1109/cvpr.2018.00956. ieee: J. Uijlings, K. Konyushkova, C. Lampert, and V. Ferrari, “Learning intelligent dialogs for bounding box annotation,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Salt Lake City, UT, United States, 2018, pp. 9175–9184. 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.' mla: Uijlings, Jasper, et al. “Learning Intelligent Dialogs for Bounding Box Annotation.” 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2018, pp. 9175–84, doi:10.1109/cvpr.2018.00956. 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. conference: end_date: 2018-06-23 location: Salt Lake City, UT, United States name: 'CVF: Conference on Computer Vision and Pattern Recognition' start_date: 2018-06-18 corr_author: '1' date_created: 2022-03-18T12:45:09Z date_published: 2018-12-17T00:00:00Z date_updated: 2024-10-09T21:02:26Z day: '17' department: - _id: ChLa doi: 10.1109/cvpr.2018.00956 external_id: arxiv: - '1712.08087' isi: - '000457843609036' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1712.08087' month: '12' oa: 1 oa_version: Preprint page: 9175-9184 publication: 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition publication_identifier: eissn: - 2575-7075 isbn: - '9781538664209' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Learning intelligent dialogs for bounding box annotation type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '10883' 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.' 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.' alternative_title: - EPiC Series in Computing article_processing_charge: No arxiv: 1 author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Wolfgang full_name: Dvořák, Wolfgang last_name: Dvořák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Alexander full_name: Svozil, Alexander last_name: Svozil citation: ama: 'Chatterjee K, Dvořák W, Henzinger M, Svozil A. Quasipolynomial set-based symbolic algorithms for parity games. In: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning. Vol 57. EasyChair; 2018:233-253. doi:10.29007/5z5k' apa: 'Chatterjee, K., Dvořák, W., Henzinger, M., & Svozil, A. (2018). Quasipolynomial set-based symbolic algorithms for parity games. In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning (Vol. 57, pp. 233–253). Awassa, Ethiopia: EasyChair. https://doi.org/10.29007/5z5k' chicago: Chatterjee, Krishnendu, Wolfgang Dvořák, Monika Henzinger, and Alexander Svozil. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” In 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, 57:233–53. EasyChair, 2018. https://doi.org/10.29007/5z5k. ieee: K. Chatterjee, W. Dvořák, M. Henzinger, and A. Svozil, “Quasipolynomial set-based symbolic algorithms for parity games,” in 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, Awassa, Ethiopia, 2018, vol. 57, pp. 233–253. 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.' mla: Chatterjee, Krishnendu, et al. “Quasipolynomial Set-Based Symbolic Algorithms for Parity Games.” 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning, vol. 57, EasyChair, 2018, pp. 233–53, doi:10.29007/5z5k. 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. conference: end_date: 2018-11-21 location: Awassa, Ethiopia name: 'LPAR: Logic for Programming, Artificial Intelligence and Reasoning' start_date: 2018-11-17 date_created: 2022-03-18T12:46:32Z date_published: 2018-10-23T00:00:00Z date_updated: 2025-07-10T11:50:02Z day: '23' ddc: - '000' department: - _id: KrCh doi: 10.29007/5z5k ec_funded: 1 external_id: arxiv: - '1909.04983' file: - access_level: open_access checksum: 1229aa8640bd6db610c85decf2265480 content_type: application/pdf creator: dernst date_created: 2022-05-17T07:51:08Z date_updated: 2022-05-17T07:51:08Z file_id: '11392' file_name: 2018_EPiCs_Chatterjee.pdf file_size: 720893 relation: main_file success: 1 file_date_updated: 2022-05-17T07:51:08Z has_accepted_license: '1' intvolume: ' 57' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 233-253 project: - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: 22nd International Conference on Logic for Programming, Artificial Intelligence and Reasoning publication_identifier: issn: - 2398-7340 publication_status: published publisher: EasyChair quality_controlled: '1' scopus_import: '1' status: public title: Quasipolynomial set-based symbolic algorithms for parity games type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 57 year: '2018' ... --- _id: '1092' abstract: - lang: eng text: 'A graphical model encodes conditional independence relations via the Markov properties. For an undirected graph these conditional independence relations can be represented by a simple polytope known as the graph associahedron, which can be constructed as a Minkowski sum of standard simplices. We show that there is an analogous polytope for conditional independence relations coming from a regular Gaussian model, and it can be defined using multiinformation or relative entropy. For directed acyclic graphical models we give a construction of this polytope as a Minkowski sum of matroid polytopes. Finally, we apply this geometric insight to construct a new ordering-based search algorithm for causal inference via directed acyclic graphical models. ' author: - first_name: Fatemeh full_name: Mohammadi, Fatemeh id: 2C29581E-F248-11E8-B48F-1D18A9856A87 last_name: Mohammadi - first_name: Caroline full_name: Uhler, Caroline id: 49ADD78E-F248-11E8-B48F-1D18A9856A87 last_name: Uhler orcid: 0000-0002-7008-0216 - first_name: Charles full_name: Wang, Charles last_name: Wang - first_name: Josephine full_name: Yu, Josephine last_name: Yu citation: ama: Mohammadi F, Uhler C, Wang C, Yu J. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 2018;32(1):64-93. doi:10.1137/16M107894X apa: Mohammadi, F., Uhler, C., Wang, C., & Yu, J. (2018). Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. SIAM. https://doi.org/10.1137/16M107894X chicago: Mohammadi, Fatemeh, Caroline Uhler, Charles Wang, and Josephine Yu. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics. SIAM, 2018. https://doi.org/10.1137/16M107894X. ieee: F. Mohammadi, C. Uhler, C. Wang, and J. Yu, “Generalized permutohedra from probabilistic graphical models,” SIAM Journal on Discrete Mathematics, vol. 32, no. 1. SIAM, pp. 64–93, 2018. ista: Mohammadi F, Uhler C, Wang C, Yu J. 2018. Generalized permutohedra from probabilistic graphical models. SIAM Journal on Discrete Mathematics. 32(1), 64–93. mla: Mohammadi, Fatemeh, et al. “Generalized Permutohedra from Probabilistic Graphical Models.” SIAM Journal on Discrete Mathematics, vol. 32, no. 1, SIAM, 2018, pp. 64–93, doi:10.1137/16M107894X. short: F. Mohammadi, C. Uhler, C. Wang, J. Yu, SIAM Journal on Discrete Mathematics 32 (2018) 64–93. date_created: 2018-12-11T11:50:06Z date_published: 2018-01-01T00:00:00Z date_updated: 2021-01-12T06:48:13Z day: '01' doi: 10.1137/16M107894X extern: '1' intvolume: ' 32' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.01814 month: '01' oa: 1 oa_version: Preprint page: 64-93 publication: SIAM Journal on Discrete Mathematics publication_status: published publisher: SIAM publist_id: '6284' quality_controlled: '1' status: public title: Generalized permutohedra from probabilistic graphical models type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2018' ... --- _id: '11' 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. arxiv: 1 author: - first_name: Nikolai K full_name: Leopold, Nikolai K id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87 last_name: Leopold orcid: 0000-0002-0495-6822 - first_name: Peter full_name: Pickl, Peter last_name: Pickl citation: ama: 'Leopold NK, Pickl P. Mean-field limits of particles in interaction with quantised radiation fields. In: Vol 270. Springer; 2018:185-214. doi:10.1007/978-3-030-01602-9_9' apa: 'Leopold, N. K., & Pickl, P. (2018). Mean-field limits of particles in interaction with quantised radiation fields (Vol. 270, pp. 185–214). Presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany: Springer. https://doi.org/10.1007/978-3-030-01602-9_9' chicago: Leopold, Nikolai K, and Peter Pickl. “Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields,” 270:185–214. Springer, 2018. https://doi.org/10.1007/978-3-030-01602-9_9. ieee: 'N. K. Leopold and P. Pickl, “Mean-field limits of particles in interaction with quantised radiation fields,” presented at the MaLiQS: Macroscopic Limits of Quantum Systems, Munich, Germany, 2018, vol. 270, pp. 185–214.' ista: 'Leopold NK, Pickl P. 2018. Mean-field limits of particles in interaction with quantised radiation fields. MaLiQS: Macroscopic Limits of Quantum Systems vol. 270, 185–214.' mla: Leopold, Nikolai K., and Peter Pickl. Mean-Field Limits of Particles in Interaction with Quantised Radiation Fields. Vol. 270, Springer, 2018, pp. 185–214, doi:10.1007/978-3-030-01602-9_9. short: N.K. Leopold, P. Pickl, in:, Springer, 2018, pp. 185–214. conference: end_date: 2017-04-01 location: Munich, Germany name: 'MaLiQS: Macroscopic Limits of Quantum Systems' start_date: 2017-03-30 date_created: 2018-12-11T11:44:08Z date_published: 2018-10-27T00:00:00Z date_updated: 2021-01-12T06:48:16Z day: '27' department: - _id: RoSe doi: 10.1007/978-3-030-01602-9_9 ec_funded: 1 external_id: arxiv: - '1806.10843' intvolume: ' 270' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.10843 month: '10' oa: 1 oa_version: Preprint page: 185 - 214 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems publication_status: published publisher: Springer publist_id: '8045' quality_controlled: '1' scopus_import: 1 status: public title: Mean-field limits of particles in interaction with quantised radiation fields type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 270 year: '2018' ... --- _id: '11063' abstract: - lang: eng text: The total number of nuclear pore complexes (NPCs) per nucleus varies greatly between different cell types and is known to change during cell differentiation and cell transformation. However, the underlying mechanisms that control how many nuclear transport channels are assembled into a given nuclear envelope remain unclear. Here, we report that depletion of the NPC basket protein Tpr, but not Nup153, dramatically increases the total NPC number in various cell types. This negative regulation of Tpr occurs via a phosphorylation cascade of extracellular signal-regulated kinase (ERK), the central kinase of the mitogen-activated protein kinase (MAPK) pathway. Tpr serves as a scaffold for ERK to phosphorylate the nucleoporin (Nup) Nup153, which is critical for early stages of NPC biogenesis. Our results reveal a critical role of the Nup Tpr in coordinating signal transduction pathways during cell proliferation and the dynamic organization of the nucleus. article_processing_charge: No article_type: original author: - first_name: Asako full_name: McCloskey, Asako last_name: McCloskey - first_name: Arkaitz full_name: Ibarra, Arkaitz last_name: Ibarra - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: McCloskey A, Ibarra A, Hetzer M. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 2018;32(19-20):1321-1331. doi:10.1101/gad.315523.118 apa: McCloskey, A., Ibarra, A., & Hetzer, M. (2018). Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. Cold Spring Harbor Laboratory. https://doi.org/10.1101/gad.315523.118 chicago: McCloskey, Asako, Arkaitz Ibarra, and Martin Hetzer. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development. Cold Spring Harbor Laboratory, 2018. https://doi.org/10.1101/gad.315523.118. ieee: A. McCloskey, A. Ibarra, and M. Hetzer, “Tpr regulates the total number of nuclear pore complexes per cell nucleus,” Genes & Development, vol. 32, no. 19–20. Cold Spring Harbor Laboratory, pp. 1321–1331, 2018. ista: McCloskey A, Ibarra A, Hetzer M. 2018. Tpr regulates the total number of nuclear pore complexes per cell nucleus. Genes & Development. 32(19–20), 1321–1331. mla: McCloskey, Asako, et al. “Tpr Regulates the Total Number of Nuclear Pore Complexes per Cell Nucleus.” Genes & Development, vol. 32, no. 19–20, Cold Spring Harbor Laboratory, 2018, pp. 1321–31, doi:10.1101/gad.315523.118. short: A. McCloskey, A. Ibarra, M. Hetzer, Genes & Development 32 (2018) 1321–1331. date_created: 2022-04-07T07:45:30Z date_published: 2018-09-18T00:00:00Z date_updated: 2024-10-14T11:19:35Z day: '18' doi: 10.1101/gad.315523.118 extern: '1' external_id: pmid: - '30228202' intvolume: ' 32' issue: 19-20 keyword: - Developmental Biology - Genetics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1101/gad.315523.118 month: '09' oa: 1 oa_version: Published Version page: 1321-1331 pmid: 1 publication: Genes & Development publication_identifier: issn: - 0890-9369 - 1549-5477 publication_status: published publisher: Cold Spring Harbor Laboratory quality_controlled: '1' scopus_import: '1' status: public title: Tpr regulates the total number of nuclear pore complexes per cell nucleus type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2018' ... --- _id: '11064' abstract: - lang: eng text: Biomarkers of aging can be used to assess the health of individuals and to study aging and age-related diseases. We generate a large dataset of genome-wide RNA-seq profiles of human dermal fibroblasts from 133 people aged 1 to 94 years old to test whether signatures of aging are encoded within the transcriptome. We develop an ensemble machine learning method that predicts age to a median error of 4 years, outperforming previous methods used to predict age. The ensemble was further validated by testing it on ten progeria patients, and our method is the only one that predicts accelerated aging in these patients. article_number: '221' article_processing_charge: No article_type: original author: - first_name: Jason G. full_name: Fleischer, Jason G. last_name: Fleischer - first_name: Roberta full_name: Schulte, Roberta last_name: Schulte - first_name: Hsiao H. full_name: Tsai, Hsiao H. last_name: Tsai - first_name: Swati full_name: Tyagi, Swati last_name: Tyagi - first_name: Arkaitz full_name: Ibarra, Arkaitz last_name: Ibarra - first_name: Maxim N. full_name: Shokhirev, Maxim N. last_name: Shokhirev - first_name: Ling full_name: Huang, Ling last_name: Huang - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X - first_name: Saket full_name: Navlakha, Saket last_name: Navlakha citation: ama: Fleischer JG, Schulte R, Tsai HH, et al. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 2018;19. doi:10.1186/s13059-018-1599-6 apa: Fleischer, J. G., Schulte, R., Tsai, H. H., Tyagi, S., Ibarra, A., Shokhirev, M. N., … Navlakha, S. (2018). Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1599-6 chicago: Fleischer, Jason G., Roberta Schulte, Hsiao H. Tsai, Swati Tyagi, Arkaitz Ibarra, Maxim N. Shokhirev, Ling Huang, Martin Hetzer, and Saket Navlakha. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1599-6. ieee: J. G. Fleischer et al., “Predicting age from the transcriptome of human dermal fibroblasts,” Genome Biology, vol. 19. BioMed Central, 2018. ista: Fleischer JG, Schulte R, Tsai HH, Tyagi S, Ibarra A, Shokhirev MN, Huang L, Hetzer M, Navlakha S. 2018. Predicting age from the transcriptome of human dermal fibroblasts. Genome Biology. 19, 221. mla: Fleischer, Jason G., et al. “Predicting Age from the Transcriptome of Human Dermal Fibroblasts.” Genome Biology, vol. 19, 221, BioMed Central, 2018, doi:10.1186/s13059-018-1599-6. short: J.G. Fleischer, R. Schulte, H.H. Tsai, S. Tyagi, A. Ibarra, M.N. Shokhirev, L. Huang, M. Hetzer, S. Navlakha, Genome Biology 19 (2018). date_created: 2022-04-07T07:45:40Z date_published: 2018-12-20T00:00:00Z date_updated: 2024-10-14T11:20:00Z day: '20' doi: 10.1186/s13059-018-1599-6 extern: '1' external_id: pmid: - '30567591' intvolume: ' 19' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1186/s13059-018-1599-6 month: '12' oa: 1 oa_version: Published Version pmid: 1 publication: Genome Biology publication_identifier: issn: - 1474-760X publication_status: published publisher: BioMed Central quality_controlled: '1' scopus_import: '1' status: public title: Predicting age from the transcriptome of human dermal fibroblasts type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2018' ... --- _id: '11508' abstract: - lang: eng text: Distant luminous Lyman-α emitters (LAEs) are excellent targets for spectroscopic observations of galaxies in the epoch of reionisation (EoR). We present deep high-resolution (R = 5000) VLT/X-shooter observations, along with an extensive collection of photometric data of COLA1, a proposed double peaked LAE at z = 6.6. We rule out the possibility that COLA1’s emission line is an [OII] doublet at z = 1.475 on the basis of i) the asymmetric red line-profile and flux ratio of the peaks (blue/red=0.31 ± 0.03) and ii) an unphysical [OII]/Hα ratio ([OII]/Hα > 22). We show that COLA1’s observed B-band flux is explained by a faint extended foreground LAE, for which we detect Lyα and [OIII] at z = 2.142. We thus conclude that COLA1 is a real double-peaked LAE at z = 6.593, the first discovered at z > 6. COLA1 is UV luminous (M1500 = −21.6 ± 0.3), has a high equivalent width (EW0,Lyα = 120−40+50 Å) and very compact Lyα emission (r50,Lyα = 0.33−0.04+0.07 kpc). Relatively weak inferred Hβ+[OIII] line-emission from Spitzer/IRAC indicates an extremely low metallicity of Z < 1/20 Z⊙ or reduced strength of nebular lines due to high escape of ionising photons. The small Lyα peak separation of 220 ± 20 km s−1 implies a low HI column density and an ionising photon escape fraction of ≈15 − 30%, providing the first direct evidence that such galaxies contribute actively to the reionisation of the Universe at z > 6. Based on simple estimates, we find that COLA1 could have provided just enough photons to reionise its own ≈0.3 pMpc (2.3 cMpc) bubble, allowing the blue Lyα line to be observed. However, we also discuss alternative scenarios explaining the detected double peaked nature of COLA1. Our results show that future high-resolution observations of statistical samples of double peaked LAEs at z > 5 are a promising probe of the occurrence of ionised regions around galaxies in the EoR. acknowledgement: JM acknowledges the award of a Huygens PhD fellowship from Leiden University. MG acknowledges support from NASA grant NNX17AK58G. APA, PhD::SPACE fellow, acknowledges support from the FCT through the fellowship PD/BD/52706/2014. Based on observations made with ESO Telescopes at the La Silla Paranal Observatory under programme IDs 294.A-5018, 098.A-0819, 099.A-0254 and 0100.A-0213. We are grateful for the excellent data-sets from the COSMOS and UltraVISTA survey teams. This research was supported by the Munich Institute for Astro- and Particle Physics (MIAPP) of the DFG cluster of excellence “Origin and Structure of the Universe”. We thank the referee for their comments that improved the paper. We also thank Christoph Behrens, Len Cowie, Koki Kakiichi, Peter Laursen, Charlotte Mason, Eros Vanzella, Lewis Weinberger and Johannes Zabl for discussions. We have benefited from the public available programming language Python, including the numpy, matplotlib, scipy and astropy packages (Hunter 2007; Astropy Collaboration 2013), the astronomical imaging tools Swarp (Bertin 2010) and ds9 and the Topcat analysis tool (Taylor 2013). article_number: A136 article_processing_charge: No article_type: original arxiv: 1 author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Max full_name: Gronke, Max last_name: Gronke - first_name: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso - first_name: Mauro full_name: Stefanon, Mauro last_name: Stefanon - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering citation: ama: 'Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering H. Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. 2018;619. doi:10.1051/0004-6361/201833528' apa: 'Matthee, J. J., Sobral, D., Gronke, M., Paulino-Afonso, A., Stefanon, M., & Röttgering, H. (2018). Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. EDP Sciences. https://doi.org/10.1051/0004-6361/201833528' chicago: 'Matthee, Jorryt J, David Sobral, Max Gronke, Ana Paulino-Afonso, Mauro Stefanon, and Huub Röttgering. “Confirmation of Double Peaked Lyα Emission at z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the Universe.” Astronomy & Astrophysics. EDP Sciences, 2018. https://doi.org/10.1051/0004-6361/201833528.' ieee: 'J. J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, and H. Röttgering, “Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe,” Astronomy & Astrophysics, vol. 619. EDP Sciences, 2018.' ista: 'Matthee JJ, Sobral D, Gronke M, Paulino-Afonso A, Stefanon M, Röttgering H. 2018. Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe. Astronomy & Astrophysics. 619, A136.' mla: 'Matthee, Jorryt J., et al. “Confirmation of Double Peaked Lyα Emission at z = 6.593: Witnessing a Galaxy Directly Contributing to the Reionisation of the Universe.” Astronomy & Astrophysics, vol. 619, A136, EDP Sciences, 2018, doi:10.1051/0004-6361/201833528.' short: J.J. Matthee, D. Sobral, M. Gronke, A. Paulino-Afonso, M. Stefanon, H. Röttgering, Astronomy & Astrophysics 619 (2018). date_created: 2022-07-06T11:14:23Z date_published: 2018-11-19T00:00:00Z date_updated: 2024-10-14T11:31:36Z day: '19' doi: 10.1051/0004-6361/201833528 extern: '1' external_id: arxiv: - '1805.11621' intvolume: ' 619' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: high-redshift / galaxies: formation / dark ages / reionization / first stars / techniques: spectroscopic / intergalactic medium' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1805.11621 month: '11' oa: 1 oa_version: Published Version publication: Astronomy & Astrophysics publication_identifier: eissn: - 1432-0746 issn: - 0004-6361 publication_status: published publisher: EDP Sciences quality_controlled: '1' scopus_import: '1' status: public title: 'Confirmation of double peaked Lyα emission at z = 6.593: Witnessing a galaxy directly contributing to the reionisation of the universe' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 619 year: '2018' ... --- _id: '11555' abstract: - lang: eng text: We investigate the morphology of the [C II] emission in a sample of ‘normal’ star-forming galaxies at 5 < z < 7.2 in relation to their UV (rest-frame) counterpart. We use new Atacama Large Millimetre/submillimetre Array (ALMA) observations of galaxies at z ∼ 6–7, as well as a careful re-analysis of archival ALMA data. In total 29 galaxies were analysed, 21 of which are detected in [C II]. For several of the latter the [C II] emission breaks into multiple components. Only a fraction of these [C II] components, if any, is associated with the primary UV systems, while the bulk of the [C II] emission is associated either with fainter UV components, or not associated with any UV counterpart at the current limits. By taking into account the presence of all these components, we find that the L[CII]–SFR (star formation rate) relation at early epochs is fully consistent with the local relation, but it has a dispersion of 0.48 ± 0.07 dex, which is about two times larger than observed locally. We also find that the deviation from the local L[CII]–SFR relation has a weak anticorrelation with the EW(Ly α). The morphological analysis also reveals that [C II] emission is generally much more extended than the UV emission. As a consequence, these primordial galaxies are characterized by a [C II] surface brightness generally much lower than expected from the local Σ[CII]−ΣSFR relation. These properties are likely a consequence of a combination of different effects, namely gas metallicity, [C II] emission from obscured star-forming regions, strong variations of the ionization parameter, and circumgalactic gas in accretion or ejected by these primeval galaxies. acknowledgement: "This paper makes use of the following ALMA data:\r\nADS/JAO.ALMA#2012.1.00719.S, ADS/JAO.ALMA#2012.A.00040.S,\r\nADS/JAO.ALMA#2013.A.00433.S, ADS/JAO.ALMA#2011.0.00115.S,\r\nADS/JAO.ALMA#2012.1.00033.S, ADS/JAO.ALMA#2012.1.00523.S,\r\nADS/JAO.ALMA#2013.1.00815.S, ADS/JAO.ALMA#2015.1.00834.S.,\r\nADS/JAO.ALMA#2015.1.01105.S, AND ADS/JAO.ALMA#2016.1.01240.S\r\nwhich can be retrieved from the ALMA data archive:\r\nhttps://almascience.eso.org/ alma-data/archive. ALMA is a partnership of ESO (representing its member states), NSF (USA) and NINS (Japan), together with NRC (Canada) and NSC and ASIAA (Taiwan), in cooperation with the Republic of Chile. The Joint ALMA Observatory is operated by ESO, AUI/NRAO, and NAOJ. We are grateful to G. Jones to for providing his [C II] flux maps. RM and SC acknowledge support by the Science and Technology Facilities Council (STFC). RM acknowledges ERC Advanced Grant 695671 ‘QUENCH’. AF acknowledges support from the ERC Advanced Grant INTERSTELLAR H2020/740120." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: S full_name: Carniani, S last_name: Carniani - first_name: R full_name: Maiolino, R last_name: Maiolino - first_name: R full_name: Amorin, R last_name: Amorin - first_name: L full_name: Pentericci, L last_name: Pentericci - first_name: A full_name: Pallottini, A last_name: Pallottini - first_name: A full_name: Ferrara, A last_name: Ferrara - first_name: C J full_name: Willott, C J last_name: Willott - first_name: R full_name: Smit, R last_name: Smit - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: D full_name: Sobral, D last_name: Sobral - first_name: P full_name: Santini, P last_name: Santini - first_name: M full_name: Castellano, M last_name: Castellano - first_name: S full_name: De Barros, S last_name: De Barros - first_name: A full_name: Fontana, A last_name: Fontana - first_name: A full_name: Grazian, A last_name: Grazian - first_name: L full_name: Guaita, L last_name: Guaita citation: ama: Carniani S, Maiolino R, Amorin R, et al. Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. 2018;478(1):1170-1184. doi:10.1093/mnras/sty1088 apa: Carniani, S., Maiolino, R., Amorin, R., Pentericci, L., Pallottini, A., Ferrara, A., … Guaita, L. (2018). Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty1088 chicago: Carniani, S, R Maiolino, R Amorin, L Pentericci, A Pallottini, A Ferrara, C J Willott, et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at z = 5–7.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty1088. ieee: S. Carniani et al., “Kiloparsec-scale gaseous clumps and star formation at z = 5–7,” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 1. Oxford University Press, pp. 1170–1184, 2018. ista: Carniani S, Maiolino R, Amorin R, Pentericci L, Pallottini A, Ferrara A, Willott CJ, Smit R, Matthee JJ, Sobral D, Santini P, Castellano M, De Barros S, Fontana A, Grazian A, Guaita L. 2018. Kiloparsec-scale gaseous clumps and star formation at z = 5–7. Monthly Notices of the Royal Astronomical Society. 478(1), 1170–1184. mla: Carniani, S., et al. “Kiloparsec-Scale Gaseous Clumps and Star Formation at z = 5–7.” Monthly Notices of the Royal Astronomical Society, vol. 478, no. 1, Oxford University Press, 2018, pp. 1170–84, doi:10.1093/mnras/sty1088. short: S. Carniani, R. Maiolino, R. Amorin, L. Pentericci, A. Pallottini, A. Ferrara, C.J. Willott, R. Smit, J.J. Matthee, D. Sobral, P. Santini, M. Castellano, S. De Barros, A. Fontana, A. Grazian, L. Guaita, Monthly Notices of the Royal Astronomical Society 478 (2018) 1170–1184. date_created: 2022-07-11T08:05:42Z date_published: 2018-07-01T00:00:00Z date_updated: 2022-08-19T06:58:06Z day: '01' doi: 10.1093/mnras/sty1088 extern: '1' external_id: arxiv: - '1712.03985' intvolume: ' 478' issue: '1' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: high-redshift' - 'galaxies: ISM' - 'galaxies: formation' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.03985 month: '07' oa: 1 oa_version: Preprint page: 1170-1184 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: Kiloparsec-scale gaseous clumps and star formation at z = 5–7 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 478 year: '2018' ... --- _id: '11557' abstract: - lang: eng text: Deep narrow-band surveys have revealed a large population of faint Ly α emitters (LAEs) in the distant Universe, but relatively little is known about the most luminous sources (⁠LLyα≳1042.7 erg s−1; LLyα≳L∗Lyα⁠). Here we present the spectroscopic follow-up of 21 luminous LAEs at z ∼ 2–3 found with panoramic narrow-band surveys over five independent extragalactic fields (≈4 × 106 Mpc3 surveyed at z ∼ 2.2 and z ∼ 3.1). We use WHT/ISIS, Keck/DEIMOS, and VLT/X-SHOOTER to study these sources using high ionization UV lines. Luminous LAEs at z ∼ 2–3 have blue UV slopes (⁠β=−2.0+0.3−0.1⁠) and high Ly α escape fractions (⁠50+20−15 per cent) and span five orders of magnitude in UV luminosity (MUV ≈ −19 to −24). Many (70 per cent) show at least one high ionization rest-frame UV line such as C IV, N V, C III], He II or O III], typically blue-shifted by ≈100–200 km s−1 relative to Ly α. Their Ly α profiles reveal a wide variety of shapes, including significant blue-shifted components and widths from 200 to 4000 km s−1. Overall, 60 ± 11 per cent appear to be active galactic nucleus (AGN) dominated, and at LLyα > 1043.3 erg s−1 and/or MUV < −21.5 virtually all LAEs are AGNs with high ionization parameters (log U = 0.6 ± 0.5) and with metallicities of ≈0.5 − 1 Z⊙. Those lacking signatures of AGNs (40 ± 11 per cent) have lower ionization parameters (⁠logU=−3.0+1.6−0.9 and log ξion = 25.4 ± 0.2) and are apparently metal-poor sources likely powered by young, dust-poor ‘maximal’ starbursts. Our results show that luminous LAEs at z ∼ 2–3 are a diverse population and that 2×L∗Lyα and 2×M∗UV mark a sharp transition in the nature of LAEs, from star formation dominated to AGN dominated. acknowledgement: 'We thank the anonymous reviewer for their timely and constructive comments that greatly helped us to improve the manuscript. DS acknowledges financial support from the Netherlands Organization for Scientific research (NWO) through a Veni fellowship and from Lancaster University through an Early Career Internal Grant A100679. JM acknowledges the support of a Huygens PhD fellowship from Leiden University. BD acknowledges financial support from NASA through the Astrophysics Data Analysis Program (ADAP), grant number NNX12AE20G, and the National Science Foundation, grant number 1716907. IRS acknowledges support from the ERC Advanced Grant DUSTYGAL (321334), STFC (ST/P000541/1), and a Royal Society/Wolfson Merit Award. PNB is grateful for support from STFC via grant ST/M001229/1. We thank Anne Verhamme, Kimihiko Nakajima, Ryan Trainor, Sangeeta Malhotra, Max Gronke, James Rhoads, Fang Xia An, Matthew Hayes, Takashi Kojima, Mark Dijkstra, and Anne Jaskot for many helpful and engaging discussions, particularly during the SnowCLAW Ly α workshop. We thank Bruno Ribeiro, Stephane Charlot, and Joseph Caruana for comments on the manuscript. The authors would also like to thank Ingrid Tengs, Meg Singleton, Ali Khostovan, and Sara Perez for participating in part of the observations. We also thank Joao Calhau, Leah Morabito, Sergio Santos, and Aayush Saxena for their assistance with the narrow-band observations which allowed to select some of the sour ces. Based on observations obtained with the William Herschel Telescope, program: W16AN004; the Very Large Telescope, programs: 098.A-0819 & 099.A-0254; and the Keck II telescope, program: C267D. Based on data products from observations made with ESO Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 294.A-5039, 092.A-0786, 093.A-0561, 097.A-0943, 098.A-0819, 099.A-0254 and 179.A-2005. The authors acknowledge the award of service time (SW2014b20) on the WHT. WHT and its service programme are operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. The authors would also like to thank all the extremely helpful observatory staff that have greatly contributed towards our observations, particularly Fiona Riddick, Lilian Dominguez, Florencia Jimenez, and Ian Skillen. We have benefited greatly from the publicly available programming language PYTHON, including the NUMPY & SCIPY (Van Der Walt, Colbert & Varoquaux 2011; Jones et al. 2001), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program (Taylor 2013). This research has made use of the VizieR catalogue access tool, CDS, Strasbourg, France.' article_processing_charge: No article_type: original arxiv: 1 author: - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Behnam full_name: Darvish, Behnam last_name: Darvish - first_name: Ian full_name: Smail, Ian last_name: Smail - first_name: Philip N full_name: Best, Philip N last_name: Best - first_name: Lara full_name: Alegre, Lara last_name: Alegre - first_name: Huub full_name: Röttgering, Huub last_name: Röttgering - first_name: Bahram full_name: Mobasher, Bahram last_name: Mobasher - first_name: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso - first_name: Andra full_name: Stroe, Andra last_name: Stroe - first_name: Iván full_name: Oteo, Iván last_name: Oteo citation: ama: 'Sobral D, Matthee JJ, Darvish B, et al. The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. 2018;477(2):2817-2840. doi:10.1093/mnras/sty782' apa: 'Sobral, D., Matthee, J. J., Darvish, B., Smail, I., Best, P. N., Alegre, L., … Oteo, I. (2018). The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty782' chicago: 'Sobral, David, Jorryt J Matthee, Behnam Darvish, Ian Smail, Philip N Best, Lara Alegre, Huub Röttgering, et al. “The Nature of Luminous Ly α Emitters at z ∼ 2–3: Maximal Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty782.' ieee: 'D. Sobral et al., “The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN,” Monthly Notices of the Royal Astronomical Society, vol. 477, no. 2. Oxford University Press, pp. 2817–2840, 2018.' ista: 'Sobral D, Matthee JJ, Darvish B, Smail I, Best PN, Alegre L, Röttgering H, Mobasher B, Paulino-Afonso A, Stroe A, Oteo I. 2018. The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN. Monthly Notices of the Royal Astronomical Society. 477(2), 2817–2840.' mla: 'Sobral, David, et al. “The Nature of Luminous Ly α Emitters at z ∼ 2–3: Maximal Dust-Poor Starbursts and Highly Ionizing AGN.” Monthly Notices of the Royal Astronomical Society, vol. 477, no. 2, Oxford University Press, 2018, pp. 2817–40, doi:10.1093/mnras/sty782.' short: D. Sobral, J.J. Matthee, B. Darvish, I. Smail, P.N. Best, L. Alegre, H. Röttgering, B. Mobasher, A. Paulino-Afonso, A. Stroe, I. Oteo, Monthly Notices of the Royal Astronomical Society 477 (2018) 2817–2840. date_created: 2022-07-12T07:18:02Z date_published: 2018-06-01T00:00:00Z date_updated: 2022-08-19T07:01:08Z day: '01' doi: 10.1093/mnras/sty782 extern: '1' external_id: arxiv: - '1802.10102' intvolume: ' 477' issue: '2' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: active' - 'galaxies: evolution' - 'galaxies: high-redshift' - 'galaxies: ISM' - 'galaxies: starburst' - 'cosmology: observations' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.10102 month: '06' oa: 1 oa_version: Preprint page: 2817-2840 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'The nature of luminous Ly α emitters at z ∼ 2–3: Maximal dust-poor starbursts and highly ionizing AGN' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 477 year: '2018' ... --- _id: '11558' abstract: - lang: eng text: We present and explore deep narrow- and medium-band data obtained with the Subaru and the Isaac Newton Telescopes in the ∼2 deg2 COSMOS field. We use these data as an extremely wide, low-resolution (R ∼ 20–80) Integral Field Unit survey to slice through the COSMOS field and obtain a large sample of ∼4000 Ly α emitters (LAEs) from z ∼ 2 to 6 in 16 redshift slices (SC4K). We present new Ly α luminosity functions (LFs) covering a comoving volume of ∼108 Mpc3. SC4K extensively complements ultradeep surveys, jointly covering over 4 dex in Ly α luminosity and revealing a global (2.5 < z < 6) synergy LF with α=−1.93+0.12−0.12⁠, log10Φ∗Lyα=−3.45+0.22−0.29 Mpc−3, and log10L∗Lyα=42.93+0.15−0.11 erg s−1. The Schechter component of the Ly α LF reveals a factor ∼5 rise in L∗Lyα and a ∼7 × decline in Φ∗Lyα from z ∼ 2 to 6. The data reveal an extra power-law (or Schechter) component above LLy α ≈ 1043.3 erg s−1 at z ∼ 2.2–3.5 and we show that it is partially driven by X-ray and radio active galactic nucleus (AGN), as their Ly α LF resembles the excess. The power-law component vanishes and/or is below our detection limits above z > 3.5, likely linked with the evolution of the AGN population. The Ly α luminosity density rises by a factor ∼2 from z ∼ 2 to 3 but is then found to be roughly constant (⁠1.1+0.2−0.2×1040 erg s−1 Mpc−3) to z ∼ 6, despite the ∼0.7 dex drop in ultraviolet (UV) luminosity density. The Ly α/UV luminosity density ratio rises from 4 ± 1 per cent to 30 ± 6 per cent from z ∼ 2.2 to 6. Our results imply a rise of a factor of ≈2 in the global ionization efficiency (ξion) and a factor ≈4 ± 1 in the Ly α escape fraction from z ∼ 2 to 6, hinting for evolution in both the typical burstiness/stellar populations and even more so in the typical interstellar medium conditions allowing Ly α photons to escape. acknowledgement: "We thank the anonymous referee for their constructive comments that helped us improve the manuscript. DS acknowledges the hospitality of the IAC and a Severo Ochoa visiting grant. SS and JC acknowledge studentships from the Lancaster University. JM acknowledges a Huygens PhD fellowship from Leiden University. APA acknowledges financial support from the Science and Technology Foundation (FCT, Portugal) through research grants UID/FIS/04434/2013 and fellowship PD/BD/52706/2014. The authors thank Alyssa Drake, Kimihiko Nakajima, Yuichi Harikane, Max Gronke, Irene Shivaei, Helmut Dannerbauer, Huub Rottgering, ¨ Marius Eide, and Masami Ouchi for many engaging and stimulating discussions. We also thank Sara Perez, Alex Bennett, and Tom Rose for their involvement in the early stages of this project. Based on data products from observations made with European Southern Observatory (ESO) Telescopes at the La Silla Paranal Observatory under ESO programme IDs 294.A-5018, 097.A 0943,\r\n098.A-0819, 099.A-0254, and 179.A-2005 and on data products produced by TERAPIX and the Cambridge Astronomy Survey Unit on behalf of the UltraVISTA consortium. Based on observations using the WFC on the 2.5 m INT, as part of programmes 2013AN002, 2013BN008, 2014AC88, 2014AN002, 2014BN006, 2014BC118, and 2016AN001. The INT is operated on the island of La Palma by the Isaac Newton Group in the Spanish Observatorio del Roque de los Muchachos of the Instituto de Astrofisica de Canarias. This work is based in part on data products produced at TERAPIX available at the Canadian Astronomy Data Centre as part of the Canada–France– Hawaii Telescope Legacy Survey (CFHTLS), a collaborative project of NRC and CNRS.\r\nWe are grateful to the CFHTLS, COSMOS-UltraVISTA, and COSMOS survey teams. We are also unmeasurably thankful to the pioneering and continuous work from previous Ly α surveys’ teams. Without these previous Ly α and the wider reach legacy surveys, this research would have been impossible. We also thank the VUDS team for making available spectroscopic redshifts from data obtained with VIMOS at the European Southern Observatory Very Large Telescope, Paranal, Chile, under Large Programme 185.A-0791. Finally, the authors acknowledge the unique value of the publicly available programming language PYTHON, including the NUMPY and SCIPY (Van Der Walt, Colbert & Varoquaux 2011; Jones et al. 2001), MATPLOTLIB (Hunter 2007), ASTROPY (Astropy Collaboration et al. 2013), and the TOPCAT analysis program (Taylor 2005). We publicly release a catalogue with all LAEs used in this paper (SC4K), so it can be freely explored by the community (see five example entries in Table A1)." article_processing_charge: No article_type: original arxiv: 1 author: - first_name: David full_name: Sobral, David last_name: Sobral - first_name: Sérgio full_name: Santos, Sérgio last_name: Santos - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: Ana full_name: Paulino-Afonso, Ana last_name: Paulino-Afonso - first_name: Bruno full_name: Ribeiro, Bruno last_name: Ribeiro - first_name: João full_name: Calhau, João last_name: Calhau - first_name: Ali A full_name: Khostovan, Ali A last_name: Khostovan citation: ama: 'Sobral D, Santos S, Matthee JJ, et al. Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. 2018;476(4):4725-4752. doi:10.1093/mnras/sty378' apa: 'Sobral, D., Santos, S., Matthee, J. J., Paulino-Afonso, A., Ribeiro, B., Calhau, J., & Khostovan, A. A. (2018). Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/sty378' chicago: 'Sobral, David, Sérgio Santos, Jorryt J Matthee, Ana Paulino-Afonso, Bruno Ribeiro, João Calhau, and Ali A Khostovan. “Slicing COSMOS with SC4K: The Evolution of Typical Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2018. https://doi.org/10.1093/mnras/sty378.' ieee: 'D. Sobral et al., “Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6,” Monthly Notices of the Royal Astronomical Society, vol. 476, no. 4. Oxford University Press, pp. 4725–4752, 2018.' ista: 'Sobral D, Santos S, Matthee JJ, Paulino-Afonso A, Ribeiro B, Calhau J, Khostovan AA. 2018. Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6. Monthly Notices of the Royal Astronomical Society. 476(4), 4725–4752.' mla: 'Sobral, David, et al. “Slicing COSMOS with SC4K: The Evolution of Typical Ly α Emitters and the Ly α Escape Fraction from z ∼ 2 to 6.” Monthly Notices of the Royal Astronomical Society, vol. 476, no. 4, Oxford University Press, 2018, pp. 4725–52, doi:10.1093/mnras/sty378.' short: D. Sobral, S. Santos, J.J. Matthee, A. Paulino-Afonso, B. Ribeiro, J. Calhau, A.A. Khostovan, Monthly Notices of the Royal Astronomical Society 476 (2018) 4725–4752. date_created: 2022-07-12T10:41:08Z date_published: 2018-06-01T00:00:00Z date_updated: 2022-08-19T07:04:45Z day: '01' doi: 10.1093/mnras/sty378 extern: '1' external_id: arxiv: - '1712.04451' intvolume: ' 476' issue: '4' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: formation' - 'galaxies: high-redshift' - 'galaxies: luminosity function' - mass function - 'galaxies: statistics' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.04451 month: '06' oa: 1 oa_version: Preprint page: 4725-4752 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'Slicing COSMOS with SC4K: The evolution of typical Ly α emitters and the Ly α escape fraction from z ∼ 2 to 6' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 476 year: '2018' ...