--- _id: '1871' abstract: - lang: eng text: The plant hormone auxin is a key regulator of plant growth and development. Differences in auxin distribution within tissues are mediated by the polar auxin transport machinery, and cellular auxin responses occur depending on changes in cellular auxin levels. Multiple receptor systems at the cell surface and in the interior operate to sense and interpret fluctuations in auxin distribution that occur during plant development. Until now, three proteins or protein complexes that can bind auxin have been identified. SCFTIR1 [a SKP1-cullin-1-F-box complex that contains transport inhibitor response 1 (TIR1) as the F-box protein] and S-phase-kinaseassociated protein 2 (SKP2) localize to the nucleus, whereas auxinbinding protein 1 (ABP1), predominantly associates with the endoplasmic reticulum and cell surface. In this Cell Science at a Glance article, we summarize recent discoveries in the field of auxin transport and signaling that have led to the identification of new components of these pathways, as well as their mutual interaction. acknowledgement: This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP]; European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czech Science Foundation GAČR [grant number GA13-40637S] author: - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Grones P, Friml J. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 2015;128(1):1-7. doi:10.1242/jcs.159418 apa: Grones, P., & Friml, J. (2015). Auxin transporters and binding proteins at a glance. Journal of Cell Science. Company of Biologists. https://doi.org/10.1242/jcs.159418 chicago: Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science. Company of Biologists, 2015. https://doi.org/10.1242/jcs.159418. ieee: P. Grones and J. Friml, “Auxin transporters and binding proteins at a glance,” Journal of Cell Science, vol. 128, no. 1. Company of Biologists, pp. 1–7, 2015. ista: Grones P, Friml J. 2015. Auxin transporters and binding proteins at a glance. Journal of Cell Science. 128(1), 1–7. mla: Grones, Peter, and Jiří Friml. “Auxin Transporters and Binding Proteins at a Glance.” Journal of Cell Science, vol. 128, no. 1, Company of Biologists, 2015, pp. 1–7, doi:10.1242/jcs.159418. short: P. Grones, J. Friml, Journal of Cell Science 128 (2015) 1–7. date_created: 2018-12-11T11:54:28Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:53:45Z day: '01' ddc: - '570' department: - _id: JiFr doi: 10.1242/jcs.159418 file: - access_level: open_access checksum: 24c779f4cd9d549ca6833e26f486be27 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:00Z date_updated: 2020-07-14T12:45:19Z file_id: '4852' file_name: IST-2016-563-v1+1_1.full.pdf file_size: 1688844 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 128' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 1 - 7 publication: Journal of Cell Science publication_status: published publisher: Company of Biologists publist_id: '5225' pubrep_id: '563' quality_controlled: '1' scopus_import: 1 status: public title: Auxin transporters and binding proteins at a glance type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 128 year: '2015' ... --- _id: '1874' abstract: - lang: eng text: 'The hippocampal region, comprising the hippocampal formation and the parahippocampal region, has been one of the most intensively studied parts of the brain for decades. Better understanding of its functional diversity and complexity has led to an increased demand for specificity in experimental procedures and manipulations. In view of the complex 3D structure of the hippocampal region, precisely positioned experimental approaches require a fine-grained architectural description that is available and readable to experimentalists lacking detailed anatomical experience. In this paper, we provide the first cyto- and chemoarchitectural description of the hippocampal formation and parahippocampal region in the rat at high resolution and in the three standard sectional planes: coronal, horizontal and sagittal. The atlas uses a series of adjacent sections stained for neurons and for a number of chemical marker substances, particularly parvalbumin and calbindin. All the borders defined in one plane have been cross-checked against their counterparts in the other two planes. The entire dataset will be made available as a web-based interactive application through the Rodent Brain WorkBench (http://www.rbwb.org) which, together with this paper, provides a unique atlas resource.' author: - first_name: Charlotte full_name: Boccara, Charlotte id: 3FC06552-F248-11E8-B48F-1D18A9856A87 last_name: Boccara orcid: 0000-0001-7237-5109 - first_name: Lisa full_name: Kjønigsen, Lisa last_name: Kjønigsen - first_name: Ingvild full_name: Hammer, Ingvild last_name: Hammer - first_name: Jan full_name: Bjaalie, Jan last_name: Bjaalie - first_name: Trygve full_name: Leergaard, Trygve last_name: Leergaard - first_name: Menno full_name: Witter, Menno last_name: Witter citation: ama: Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 2015;25(7):838-857. doi:10.1002/hipo.22407 apa: Boccara, C. N., Kjønigsen, L., Hammer, I., Bjaalie, J., Leergaard, T., & Witter, M. (2015). A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. Wiley. https://doi.org/10.1002/hipo.22407 chicago: Boccara, Charlotte N., Lisa Kjønigsen, Ingvild Hammer, Jan Bjaalie, Trygve Leergaard, and Menno Witter. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” Hippocampus. Wiley, 2015. https://doi.org/10.1002/hipo.22407. ieee: C. N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, and M. Witter, “A three-plane architectonic atlas of the rat hippocampal region,” Hippocampus, vol. 25, no. 7. Wiley, pp. 838–857, 2015. ista: Boccara CN, Kjønigsen L, Hammer I, Bjaalie J, Leergaard T, Witter M. 2015. A three-plane architectonic atlas of the rat hippocampal region. Hippocampus. 25(7), 838–857. mla: Boccara, Charlotte N., et al. “A Three-Plane Architectonic Atlas of the Rat Hippocampal Region.” Hippocampus, vol. 25, no. 7, Wiley, 2015, pp. 838–57, doi:10.1002/hipo.22407. short: C.N. Boccara, L. Kjønigsen, I. Hammer, J. Bjaalie, T. Leergaard, M. Witter, Hippocampus 25 (2015) 838–857. date_created: 2018-12-11T11:54:29Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:53:46Z day: '01' department: - _id: JoCs doi: 10.1002/hipo.22407 intvolume: ' 25' issue: '7' language: - iso: eng month: '07' oa_version: None page: 838 - 857 publication: Hippocampus publication_status: published publisher: Wiley publist_id: '5222' quality_controlled: '1' scopus_import: 1 status: public title: A three-plane architectonic atlas of the rat hippocampal region type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2015' ... --- _id: '1873' abstract: - lang: eng text: 'We consider partially observable Markov decision processes (POMDPs) with limit-average payoff, where a reward value in the interval [0,1] is associated with every transition, and the payoff of an infinite path is the long-run average of the rewards. We consider two types of path constraints: (i) a quantitative constraint defines the set of paths where the payoff is at least a given threshold λ1ε(0,1]; and (ii) a qualitative constraint which is a special case of the quantitative constraint with λ1=1. We consider the computation of the almost-sure winning set, where the controller needs to ensure that the path constraint is satisfied with probability 1. Our main results for qualitative path constraints are as follows: (i) the problem of deciding the existence of a finite-memory controller is EXPTIME-complete; and (ii) the problem of deciding the existence of an infinite-memory controller is undecidable. For quantitative path constraints we show that the problem of deciding the existence of a finite-memory controller is undecidable. We also present a prototype implementation of our EXPTIME algorithm and experimental results on several examples.' author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik citation: ama: Chatterjee K, Chmelik M. POMDPs under probabilistic semantics. Artificial Intelligence. 2015;221:46-72. doi:10.1016/j.artint.2014.12.009 apa: Chatterjee, K., & Chmelik, M. (2015). POMDPs under probabilistic semantics. Artificial Intelligence. Elsevier. https://doi.org/10.1016/j.artint.2014.12.009 chicago: Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence. Elsevier, 2015. https://doi.org/10.1016/j.artint.2014.12.009. ieee: K. Chatterjee and M. Chmelik, “POMDPs under probabilistic semantics,” Artificial Intelligence, vol. 221. Elsevier, pp. 46–72, 2015. ista: Chatterjee K, Chmelik M. 2015. POMDPs under probabilistic semantics. Artificial Intelligence. 221, 46–72. mla: Chatterjee, Krishnendu, and Martin Chmelik. “POMDPs under Probabilistic Semantics.” Artificial Intelligence, vol. 221, Elsevier, 2015, pp. 46–72, doi:10.1016/j.artint.2014.12.009. short: K. Chatterjee, M. Chmelik, Artificial Intelligence 221 (2015) 46–72. date_created: 2018-12-11T11:54:28Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:53:46Z day: '01' department: - _id: KrCh doi: 10.1016/j.artint.2014.12.009 external_id: arxiv: - '1408.2058' intvolume: ' 221' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1408.2058 month: '04' oa: 1 oa_version: Preprint page: 46 - 72 publication: Artificial Intelligence publication_status: published publisher: Elsevier publist_id: '5224' quality_controlled: '1' scopus_import: 1 status: public title: POMDPs under probabilistic semantics type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 221 year: '2015' ... --- _id: '1879' abstract: - lang: eng text: When electron microscopy (EM) was introduced in the 1930s it gave scientists their first look into the nanoworld of cells. Over the last 80 years EM has vastly increased our understanding of the complex cellular structures that underlie the diverse functions that cells need to maintain life. One drawback that has been difficult to overcome was the inherent lack of volume information, mainly due to the limit on the thickness of sections that could be viewed in a transmission electron microscope (TEM). For many years scientists struggled to achieve three-dimensional (3D) EM using serial section reconstructions, TEM tomography, and scanning EM (SEM) techniques such as freeze-fracture. Although each technique yielded some special information, they required a significant amount of time and specialist expertise to obtain even a very small 3D EM dataset. Almost 20 years ago scientists began to exploit SEMs to image blocks of embedded tissues and perform serial sectioning of these tissues inside the SEM chamber. Using first focused ion beams (FIB) and subsequently robotic ultramicrotomes (serial block-face, SBF-SEM) microscopists were able to collect large volumes of 3D EM information at resolutions that could address many important biological questions, and do so in an efficient manner. We present here some examples of 3D EM taken from the many diverse specimens that have been imaged in our core facility. We propose that the next major step forward will be to efficiently correlate functional information obtained using light microscopy (LM) with 3D EM datasets to more completely investigate the important links between cell structures and their functions. acknowledgement: The Zeiss Merlin with Gatan 3View2XP and Zeiss Auriga were acquired through a CLEM grant from Minister Ingrid Lieten to the VIB Bio-Imaging-Core. Michiel Krols and Saskia Lippens are the recipients of a fellowship from the FWO (Fonds Wetenschappelijk Onderzoek) of Flanders. author: - first_name: A full_name: Kremer, A last_name: Kremer - first_name: Stefaan full_name: Lippens, Stefaan last_name: Lippens - first_name: Sonia full_name: Bartunkova, Sonia last_name: Bartunkova - first_name: Bob full_name: Asselbergh, Bob last_name: Asselbergh - first_name: Cendric full_name: Blanpain, Cendric last_name: Blanpain - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: A full_name: Goossens, A last_name: Goossens - first_name: Matthew full_name: Holt, Matthew last_name: Holt - first_name: Sophie full_name: Janssens, Sophie last_name: Janssens - first_name: Michiel full_name: Krols, Michiel last_name: Krols - first_name: Jean full_name: Larsimont, Jean last_name: Larsimont - first_name: Conor full_name: Mc Guire, Conor last_name: Mc Guire - first_name: Moritz full_name: Nowack, Moritz last_name: Nowack - first_name: Xavier full_name: Saelens, Xavier last_name: Saelens - first_name: Andreas full_name: Schertel, Andreas last_name: Schertel - first_name: B full_name: Schepens, B last_name: Schepens - first_name: M full_name: Slezak, M last_name: Slezak - first_name: Vincent full_name: Timmerman, Vincent last_name: Timmerman - first_name: Clara full_name: Theunis, Clara last_name: Theunis - first_name: Ronald full_name: Van Brempt, Ronald last_name: Van Brempt - first_name: Y full_name: Visser, Y last_name: Visser - first_name: Christophe full_name: Guérin, Christophe last_name: Guérin citation: ama: Kremer A, Lippens S, Bartunkova S, et al. Developing 3D SEM in a broad biological context. Journal of Microscopy. 2015;259(2):80-96. doi:10.1111/jmi.12211 apa: Kremer, A., Lippens, S., Bartunkova, S., Asselbergh, B., Blanpain, C., Fendrych, M., … Guérin, C. (2015). Developing 3D SEM in a broad biological context. Journal of Microscopy. Wiley-Blackwell. https://doi.org/10.1111/jmi.12211 chicago: Kremer, A, Stefaan Lippens, Sonia Bartunkova, Bob Asselbergh, Cendric Blanpain, Matyas Fendrych, A Goossens, et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy. Wiley-Blackwell, 2015. https://doi.org/10.1111/jmi.12211. ieee: A. Kremer et al., “Developing 3D SEM in a broad biological context,” Journal of Microscopy, vol. 259, no. 2. Wiley-Blackwell, pp. 80–96, 2015. ista: Kremer A, Lippens S, Bartunkova S, Asselbergh B, Blanpain C, Fendrych M, Goossens A, Holt M, Janssens S, Krols M, Larsimont J, Mc Guire C, Nowack M, Saelens X, Schertel A, Schepens B, Slezak M, Timmerman V, Theunis C, Van Brempt R, Visser Y, Guérin C. 2015. Developing 3D SEM in a broad biological context. Journal of Microscopy. 259(2), 80–96. mla: Kremer, A., et al. “Developing 3D SEM in a Broad Biological Context.” Journal of Microscopy, vol. 259, no. 2, Wiley-Blackwell, 2015, pp. 80–96, doi:10.1111/jmi.12211. short: A. Kremer, S. Lippens, S. Bartunkova, B. Asselbergh, C. Blanpain, M. Fendrych, A. Goossens, M. Holt, S. Janssens, M. Krols, J. Larsimont, C. Mc Guire, M. Nowack, X. Saelens, A. Schertel, B. Schepens, M. Slezak, V. Timmerman, C. Theunis, R. Van Brempt, Y. Visser, C. Guérin, Journal of Microscopy 259 (2015) 80–96. date_created: 2018-12-11T11:54:30Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:53:48Z day: '01' ddc: - '570' department: - _id: JiFr doi: 10.1111/jmi.12211 file: - access_level: open_access checksum: 3649c5372d1644062d728ea9287e367f content_type: application/pdf creator: system date_created: 2018-12-12T10:11:19Z date_updated: 2020-07-14T12:45:19Z file_id: '4872' file_name: IST-2016-459-v1+1_KREMER_et_al-2015-Journal_of_Microscopy.pdf file_size: 2899898 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 259' issue: '2' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 80 - 96 publication: Journal of Microscopy publication_status: published publisher: Wiley-Blackwell publist_id: '5218' pubrep_id: '459' quality_controlled: '1' scopus_import: 1 status: public title: Developing 3D SEM in a broad biological context 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: 259 year: '2015' ... --- _id: '1880' abstract: - lang: eng text: We investigate the relation between Bose-Einstein condensation (BEC) and superfluidity in the ground state of a one-dimensional model of interacting bosons in a strong random potential. We prove rigorously that in a certain parameter regime the superfluid fraction can be arbitrarily small while complete BEC prevails. In another regime there is both complete BEC and complete superfluidity, despite the strong disorder acknowledgement: Support from the Natural Sciences and Engineering Research Council of Canada NSERC (MK and RS) and from the Austrian Science Fund FWF (JY, under project P 22929-N16) is gratefully acknowledged article_number: '013022' author: - first_name: Martin full_name: Könenberg, Martin last_name: Könenberg - first_name: Thomas full_name: Moser, Thomas id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87 last_name: Moser - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jakob full_name: Yngvason, Jakob last_name: Yngvason citation: ama: Könenberg M, Moser T, Seiringer R, Yngvason J. Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. 2015;17. doi:10.1088/1367-2630/17/1/013022 apa: Könenberg, M., Moser, T., Seiringer, R., & Yngvason, J. (2015). Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/17/1/013022 chicago: Könenberg, Martin, Thomas Moser, Robert Seiringer, and Jakob Yngvason. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New Journal of Physics. IOP Publishing Ltd., 2015. https://doi.org/10.1088/1367-2630/17/1/013022. ieee: M. Könenberg, T. Moser, R. Seiringer, and J. Yngvason, “Superfluid behavior of a Bose-Einstein condensate in a random potential,” New Journal of Physics, vol. 17. IOP Publishing Ltd., 2015. ista: Könenberg M, Moser T, Seiringer R, Yngvason J. 2015. Superfluid behavior of a Bose-Einstein condensate in a random potential. New Journal of Physics. 17, 013022. mla: Könenberg, Martin, et al. “Superfluid Behavior of a Bose-Einstein Condensate in a Random Potential.” New Journal of Physics, vol. 17, 013022, IOP Publishing Ltd., 2015, doi:10.1088/1367-2630/17/1/013022. short: M. Könenberg, T. Moser, R. Seiringer, J. Yngvason, New Journal of Physics 17 (2015). date_created: 2018-12-11T11:54:30Z date_published: 2015-01-15T00:00:00Z date_updated: 2021-01-12T06:53:48Z day: '15' ddc: - '530' department: - _id: RoSe doi: 10.1088/1367-2630/17/1/013022 file: - access_level: open_access checksum: 38fdf2b5ac30445e26a5d613abd84b16 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:44Z date_updated: 2020-07-14T12:45:20Z file_id: '4963' file_name: IST-2016-447-v1+1_document_1_.pdf file_size: 768108 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 17' language: - iso: eng month: '01' oa: 1 oa_version: Published Version project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: New Journal of Physics publication_status: published publisher: IOP Publishing Ltd. publist_id: '5214' pubrep_id: '447' quality_controlled: '1' scopus_import: 1 status: public title: Superfluid behavior of a Bose-Einstein condensate in a random potential 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: 17 year: '2015' ...