[{"publisher":"ACM","article_number":"137","external_id":{"isi":["000340000100104"]},"project":[{"_id":"25636330-B435-11E9-9278-68D0E5697425","name":"Genome-wide Analysis of Root Traits","grant_number":"11-NSF-1070"}],"pubrep_id":"606","abstract":[{"lang":"eng","text":"We present a method for smoothly blending between existing liquid animations. We introduce a semi-automatic method for matching two existing liquid animations, which we use to create new fluid motion that plausibly interpolates the input. Our contributions include a new space-time non-rigid iterative closest point algorithm that incorporates user guidance, a subsampling technique for efficient registration of meshes with millions of vertices, and a fast surface extraction algorithm that produces 3D triangle meshes from a 4D space-time surface. Our technique can be used to instantly create hundreds of new simulations, or to interactively explore complex parameter spaces. Our method is guaranteed to produce output that does not deviate from the input animations, and it generalizes to multiple dimensions. Because our method runs at interactive rates after the initial precomputation step, it has potential applications in games and training simulations."}],"year":"2014","conference":{"start_date":"2014-08-10","name":"SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques","end_date":"2014-08-14","location":"Vancouver, Canada"},"oa":1,"intvolume":"        33","oa_version":"Submitted Version","title":"Blending liquids","publication_status":"published","_id":"2058","publist_id":"4988","doi":"10.1145/2601097.2601126","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","volume":33,"citation":{"chicago":"Raveendran, Karthik, Chris Wojtan, Nils Thuerey, and Greg Türk. “Blending Liquids.” In <i>ACM Transactions on Graphics</i>, Vol. 33. ACM, 2014. <a href=\"https://doi.org/10.1145/2601097.2601126\">https://doi.org/10.1145/2601097.2601126</a>.","mla":"Raveendran, Karthik, et al. “Blending Liquids.” <i>ACM Transactions on Graphics</i>, vol. 33, no. 4, 137, ACM, 2014, doi:<a href=\"https://doi.org/10.1145/2601097.2601126\">10.1145/2601097.2601126</a>.","apa":"Raveendran, K., Wojtan, C., Thuerey, N., &#38; Türk, G. (2014). Blending liquids. In <i>ACM Transactions on Graphics</i> (Vol. 33). Vancouver, Canada: ACM. <a href=\"https://doi.org/10.1145/2601097.2601126\">https://doi.org/10.1145/2601097.2601126</a>","ama":"Raveendran K, Wojtan C, Thuerey N, Türk G. Blending liquids. In: <i>ACM Transactions on Graphics</i>. Vol 33. ACM; 2014. doi:<a href=\"https://doi.org/10.1145/2601097.2601126\">10.1145/2601097.2601126</a>","ieee":"K. Raveendran, C. Wojtan, N. Thuerey, and G. Türk, “Blending liquids,” in <i>ACM Transactions on Graphics</i>, Vancouver, Canada, 2014, vol. 33, no. 4.","ista":"Raveendran K, Wojtan C, Thuerey N, Türk G. 2014. Blending liquids. ACM Transactions on Graphics. SIGGRAPH: International Conference and Exhibition on Computer Graphics and Interactive Techniques vol. 33, 137.","short":"K. Raveendran, C. Wojtan, N. Thuerey, G. Türk, in:, ACM Transactions on Graphics, ACM, 2014."},"quality_controlled":"1","article_processing_charge":"No","file":[{"date_created":"2018-12-12T10:08:27Z","access_level":"open_access","relation":"main_file","file_name":"IST-2016-606-v1+1_BlendingLiquids-Preprint.pdf","date_updated":"2020-07-14T12:45:27Z","creator":"system","checksum":"1752760a2e71e254537f31c0d10d9c6c","content_type":"application/pdf","file_size":8387384,"file_id":"4688"}],"isi":1,"scopus_import":"1","author":[{"full_name":"Raveendran, Karthik","first_name":"Karthik","last_name":"Raveendran"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","first_name":"Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Thuerey, Nils","first_name":"Nils","last_name":"Thuerey"},{"full_name":"Türk, Greg","first_name":"Greg","last_name":"Türk"}],"file_date_updated":"2020-07-14T12:45:27Z","date_created":"2018-12-11T11:55:28Z","language":[{"iso":"eng"}],"day":"01","publication":"ACM Transactions on Graphics","ddc":["000"],"month":"07","date_published":"2014-07-01T00:00:00Z","status":"public","department":[{"_id":"ChWo"}],"has_accepted_license":"1","type":"conference","issue":"4","date_updated":"2025-09-29T11:49:44Z"},{"volume":251,"citation":{"ista":"Dubas E, Moravčíková J, Libantová J, Matušíková I, Benková E, Zur I, Krzewska M. 2014. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. Protoplasma. 251(5), 1077–1087.","short":"E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur, M. Krzewska, Protoplasma 251 (2014) 1077–1087.","ieee":"E. Dubas <i>et al.</i>, “The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos,” <i>Protoplasma</i>, vol. 251, no. 5. Springer, pp. 1077–1087, 2014.","mla":"Dubas, Ewa, et al. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” <i>Protoplasma</i>, vol. 251, no. 5, Springer, 2014, pp. 1077–87, doi:<a href=\"https://doi.org/10.1007/s00709-014-0616-1\">10.1007/s00709-014-0616-1</a>.","apa":"Dubas, E., Moravčíková, J., Libantová, J., Matušíková, I., Benková, E., Zur, I., &#38; Krzewska, M. (2014). The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. <i>Protoplasma</i>. Springer. <a href=\"https://doi.org/10.1007/s00709-014-0616-1\">https://doi.org/10.1007/s00709-014-0616-1</a>","ama":"Dubas E, Moravčíková J, Libantová J, et al. The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos. <i>Protoplasma</i>. 2014;251(5):1077-1087. doi:<a href=\"https://doi.org/10.1007/s00709-014-0616-1\">10.1007/s00709-014-0616-1</a>","chicago":"Dubas, Ewa, Jana Moravčíková, Jana Libantová, Ildikó Matušíková, Eva Benková, Iwona Zur, and Monika Krzewska. “The Influence of Heat Stress on Auxin Distribution in Transgenic B Napus Microspores and Microspore Derived Embryos.” <i>Protoplasma</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00709-014-0616-1\">https://doi.org/10.1007/s00709-014-0616-1</a>."},"quality_controlled":"1","publist_id":"4987","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1007/s00709-014-0616-1","scopus_import":"1","article_processing_charge":"No","file":[{"file_name":"IST-2015-394-v1+1_s00709-014-0616-1.pdf","access_level":"open_access","date_created":"2018-12-12T10:18:31Z","relation":"main_file","file_id":"5353","content_type":"application/pdf","file_size":6377990,"checksum":"d570a6073765118fc0bb83c31d96fa53","creator":"system","date_updated":"2020-07-14T12:45:27Z"}],"isi":1,"author":[{"full_name":"Dubas, Ewa","last_name":"Dubas","first_name":"Ewa"},{"full_name":"Moravčíková, Jana","last_name":"Moravčíková","first_name":"Jana"},{"full_name":"Libantová, Jana","first_name":"Jana","last_name":"Libantová"},{"last_name":"Matušíková","first_name":"Ildikó","full_name":"Matušíková, Ildikó"},{"last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva","orcid":"0000-0002-8510-9739"},{"full_name":"Zur, Iwona","last_name":"Zur","first_name":"Iwona"},{"last_name":"Krzewska","first_name":"Monika","full_name":"Krzewska, Monika"}],"file_date_updated":"2020-07-14T12:45:27Z","language":[{"iso":"eng"}],"day":"20","date_created":"2018-12-11T11:55:29Z","acknowledgement":"The research was supported by the IPP PAS-IPGB SAS bilateral project (“Molecular analysis of auxin distribution in oilseed androgenic embryos”), IPP PAS-FWO VIB bilateral project (“Auxin as signaling molecule in doubled haploid production of rape (B. napus var. oleifera)”), individual national research project 2011/01/D/NZ9/02547, and VEGA 2-0090-14.","department":[{"_id":"EvBe"}],"has_accepted_license":"1","issue":"5","type":"journal_article","date_updated":"2025-09-29T11:49:12Z","publication":"Protoplasma","month":"02","ddc":["580"],"date_published":"2014-02-20T00:00:00Z","page":"1077 - 1087","status":"public","publisher":"Springer","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"external_id":{"isi":["000340480300008"]},"pubrep_id":"394","abstract":[{"text":"Plant embryogenesis is regulated by differential distribution of the plant hormone auxin. However, the cells establishing these gradients during microspore embryogenesis remain to be identified. For the first time, we describe, using the DR5 or DR5rev reporter gene systems, the GFP- and GUS-based auxin biosensors to monitor auxin during Brassica napus androgenesis at cellular resolution in the initial stages. Our study provides evidence that the distribution of auxin changes during embryo development and depends on the temperature-inducible in vitro culture conditions. For this, microspores (mcs) were induced to embryogenesis by heat treatment and then subjected to genetic modification via Agrobacterium tumefaciens. The duration of high temperature treatment had a significant influence on auxin distribution in isolated and in vitro-cultured microspores and on microspore-derived embryo development. In the “mild” heat-treated (1 day at 32 °C) mcs, auxin localized in a polar way already at the uni-nucleate microspore, which was critical for the initiation of embryos with suspensor-like structure. Assuming a mean mcs radius of 20 μm, endogenous auxin content in a single cell corresponded to concentration of 1.01 μM. In mcs subjected to a prolonged heat (5 days at 32 °C), although auxin concentration increased dozen times, auxin polarization was set up at a few-celled pro-embryos without suspensor. Those embryos were enclosed in the outer wall called the exine. The exine rupture was accompanied by the auxin gradient polarization. Relative quantitative estimation of auxin, using time-lapse imaging, revealed that primordia possess up to 1.3-fold higher amounts than those found in the root apices of transgenic MDEs in the presence of exogenous auxin. Our results show, for the first time, which concentration of endogenous auxin coincides with the first cell division and how the high temperature interplays with auxin, by what affects delay early establishing microspore polarity. Moreover, we present how the local auxin accumulation demonstrates the apical–basal axis formation of the androgenic embryo and directs the axiality of the adult haploid plant.","lang":"eng"}],"year":"2014","oa_version":"Published Version","title":"The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos","publication_status":"published","_id":"2059","oa":1,"intvolume":"       251"},{"language":[{"iso":"eng"}],"date_created":"2018-12-11T11:55:29Z","day":"14","author":[{"full_name":"Mazur, Ewa","first_name":"Ewa","last_name":"Mazur"},{"full_name":"Kurczyñska, Ewa","first_name":"Ewa","last_name":"Kurczyñska"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"page":"1125 - 1139","status":"public","publication":"Protoplasma","date_published":"2014-02-14T00:00:00Z","month":"02","date_updated":"2025-09-29T11:48:32Z","department":[{"_id":"JiFr"}],"type":"journal_article","issue":"5","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1007/s00709-014-0620-5","publist_id":"4985","volume":251,"quality_controlled":"1","citation":{"ista":"Mazur E, Kurczyñska E, Friml J. 2014. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 251(5), 1125–1139.","short":"E. Mazur, E. Kurczyñska, J. Friml, Protoplasma 251 (2014) 1125–1139.","ieee":"E. Mazur, E. Kurczyñska, and J. Friml, “Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis,” <i>Protoplasma</i>, vol. 251, no. 5. Springer, pp. 1125–1139, 2014.","mla":"Mazur, Ewa, et al. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” <i>Protoplasma</i>, vol. 251, no. 5, Springer, 2014, pp. 1125–39, doi:<a href=\"https://doi.org/10.1007/s00709-014-0620-5\">10.1007/s00709-014-0620-5</a>.","ama":"Mazur E, Kurczyñska E, Friml J. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. <i>Protoplasma</i>. 2014;251(5):1125-1139. doi:<a href=\"https://doi.org/10.1007/s00709-014-0620-5\">10.1007/s00709-014-0620-5</a>","apa":"Mazur, E., Kurczyñska, E., &#38; Friml, J. (2014). Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. <i>Protoplasma</i>. Springer. <a href=\"https://doi.org/10.1007/s00709-014-0620-5\">https://doi.org/10.1007/s00709-014-0620-5</a>","chicago":"Mazur, Ewa, Ewa Kurczyñska, and Jiří Friml. “Cellular Events during Interfascicular Cambium Ontogenesis in Inflorescence Stems of Arabidopsis.” <i>Protoplasma</i>. Springer, 2014. <a href=\"https://doi.org/10.1007/s00709-014-0620-5\">https://doi.org/10.1007/s00709-014-0620-5</a>."},"isi":1,"article_processing_charge":"No","scopus_import":"1","abstract":[{"text":"Development of cambium and its activity is important for our knowledge of the mechanism of secondary growth. Arabidopsis thaliana emerges as a good model plant for such a kind of study. Thus, this paper reports on cellular events taking place in the interfascicular regions of inflorescence stems of A. thaliana, leading to the development of interfascicular cambium from differentiated interfascicular parenchyma cells (IPC). These events are as follows: appearance of auxin accumulation, PIN1 gene expression, polar PIN1 protein localization in the basal plasma membrane and periclinal divisions. Distribution of auxin was observed to be higher in differentiating into cambium parenchyma cells compared to cells within the pith and cortex. Expression of PIN1 in IPC was always preceded by auxin accumulation. Basal localization of PIN1 was already established in the cells prior to their periclinal division. These cellular events initiated within parenchyma cells adjacent to the vascular bundles and successively extended from that point towards the middle region of the interfascicular area, located between neighboring vascular bundles. The final consequence of which was the closure of the cambial ring within the stem. Changes in the chemical composition of IPC walls were also detected and included changes of pectic epitopes, xyloglucans (XG) and extensins rich in hydroxyproline (HRGPs). In summary, results presented in this paper describe interfascicular cambium ontogenesis in terms of successive cellular events in the interfascicular regions of inflorescence stems of Arabidopsis.","lang":"eng"}],"year":"2014","intvolume":"       251","title":"Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis","_id":"2061","publication_status":"published","oa_version":"None","publisher":"Springer","external_id":{"isi":["000340480300012"]}},{"date_updated":"2025-09-29T11:48:03Z","type":"journal_article","issue":"6196","has_accepted_license":"1","department":[{"_id":"PeJo"}],"status":"public","ddc":["570"],"month":"08","date_published":"2014-08-01T00:00:00Z","publication":"Science","language":[{"iso":"eng"}],"day":"01","date_created":"2018-12-11T11:55:29Z","file_date_updated":"2020-07-14T12:45:27Z","author":[{"full_name":"Hu, Hua","last_name":"Hu","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87","first_name":"Hua"},{"id":"3614E438-F248-11E8-B48F-1D18A9856A87","last_name":"Gan","first_name":"Jian","full_name":"Gan, Jian"},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87"}],"corr_author":"1","scopus_import":"1","isi":1,"file":[{"date_created":"2018-12-12T10:16:00Z","access_level":"open_access","relation":"main_file","file_name":"IST-2017-821-v1+1_1255263JonasPVReviewTextR_Final.pdf","date_updated":"2020-07-14T12:45:27Z","creator":"system","checksum":"a0036a589037d37e86364fa25cc0a82f","file_size":215514,"content_type":"application/pdf","file_id":"5185"},{"access_level":"open_access","date_created":"2018-12-12T10:16:01Z","relation":"main_file","file_name":"IST-2017-821-v1+2_1255263JonasPVReviewFigures_Final.pdf","date_updated":"2020-07-14T12:45:27Z","checksum":"e1f57d2713725449cb898fdcb8ef47b8","creator":"system","file_size":1732723,"content_type":"application/pdf","file_id":"5186"}],"article_processing_charge":"No","citation":{"apa":"Hu, H., Gan, J., &#38; Jonas, P. M. (2014). Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.1255263\">https://doi.org/10.1126/science.1255263</a>","ama":"Hu H, Gan J, Jonas PM. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. <i>Science</i>. 2014;345(6196). doi:<a href=\"https://doi.org/10.1126/science.1255263\">10.1126/science.1255263</a>","mla":"Hu, Hua, et al. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” <i>Science</i>, vol. 345, no. 6196, 1255263, American Association for the Advancement of Science, 2014, doi:<a href=\"https://doi.org/10.1126/science.1255263\">10.1126/science.1255263</a>.","chicago":"Hu, Hua, Jian Gan, and Peter M Jonas. “Fast-Spiking Parvalbumin^+ GABAergic Interneurons: From Cellular Design to Microcircuit Function.” <i>Science</i>. American Association for the Advancement of Science, 2014. <a href=\"https://doi.org/10.1126/science.1255263\">https://doi.org/10.1126/science.1255263</a>.","short":"H. Hu, J. Gan, P.M. Jonas, Science 345 (2014).","ista":"Hu H, Gan J, Jonas PM. 2014. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 345(6196), 1255263.","ieee":"H. Hu, J. Gan, and P. M. Jonas, “Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function,” <i>Science</i>, vol. 345, no. 6196. American Association for the Advancement of Science, 2014."},"quality_controlled":"1","volume":345,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1126/science.1255263","publist_id":"4984","publication_status":"published","_id":"2062","title":"Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function","oa_version":"Submitted Version","intvolume":"       345","ec_funded":1,"oa":1,"year":"2014","abstract":[{"text":"The success story of fast-spiking, parvalbumin-positive (PV+) GABAergic interneurons (GABA, γ-aminobutyric acid) in the mammalian central nervous system is noteworthy. In 1995, the properties of these interneurons were completely unknown. Twenty years later, thanks to the massive use of subcellular patch-clamp techniques, simultaneous multiple-cell recording, optogenetics, in vivo measurements, and computational approaches, our knowledge about PV+ interneurons became more extensive than for several types of pyramidal neurons. These findings have implications beyond the “small world” of basic research on GABAergic cells. For example, the results provide a first proof of principle that neuroscientists might be able to close the gaps between the molecular, cellular, network, and behavioral levels, representing one of the main challenges at the present time. Furthermore, the results may form the basis for PV+ interneurons as therapeutic targets for brain disease in the future. However, much needs to be learned about the basic function of these interneurons before clinical neuroscientists will be able to use PV+ interneurons for therapeutic purposes.","lang":"eng"}],"pubrep_id":"821","project":[{"grant_number":"P24909-B24","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425","name":"Mechanisms of transmitter release at GABAergic synapses"},{"grant_number":"268548","call_identifier":"FP7","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425"}],"external_id":{"isi":["000339651300036"]},"article_number":"1255263","publisher":"American Association for the Advancement of Science"},{"year":"2014","abstract":[{"lang":"eng","text":"We consider Markov decision processes (MDPs) which are a standard model for probabilistic systems.We focus on qualitative properties forMDPs that can express that desired behaviors of the system arise almost-surely (with probability 1) or with positive probability. We introduce a new simulation relation to capture the refinement relation ofMDPs with respect to qualitative properties, and present discrete graph theoretic algorithms with quadratic complexity to compute the simulation relation.We present an automated technique for assume-guarantee style reasoning for compositional analysis ofMDPs with qualitative properties by giving a counterexample guided abstraction-refinement approach to compute our new simulation relation. We have implemented our algorithms and show that the compositional analysis leads to significant improvements."}],"conference":{"end_date":"2014-07-22","name":"CAV: Computer Aided Verification","location":"Vienna, Austria","start_date":"2014-07-18"},"intvolume":"      8559","ec_funded":1,"publication_status":"published","_id":"2063","title":"CEGAR for qualitative analysis of probabilistic systems","oa_version":"None","publisher":"Springer","alternative_title":["LNCS"],"project":[{"name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","grant_number":"P 23499-N23","call_identifier":"FWF"},{"grant_number":"S11407","call_identifier":"FWF","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","grant_number":"S11402-N23","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms"},{"name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307","call_identifier":"FP7"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FP7","grant_number":"267989","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"}],"corr_author":"1","related_material":{"record":[{"relation":"earlier_version","id":"5412","status":"public"},{"status":"public","id":"5413","relation":"earlier_version"},{"relation":"earlier_version","status":"public","id":"5414"},{"status":"public","id":"1155","relation":"dissertation_contains"}]},"date_created":"2018-12-11T11:55:30Z","language":[{"iso":"eng"}],"day":"01","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"last_name":"Chmelik","id":"3624234E-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","full_name":"Chmelik, Martin"},{"full_name":"Daca, Przemyslaw","id":"49351290-F248-11E8-B48F-1D18A9856A87","last_name":"Daca","first_name":"Przemyslaw"}],"status":"public","page":"473 - 490","date_published":"2014-07-01T00:00:00Z","month":"07","date_updated":"2026-04-15T10:02:12Z","type":"conference","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"doi":"10.1007/978-3-319-08867-9_31","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publist_id":"4978","quality_controlled":"1","citation":{"mla":"Chatterjee, Krishnendu, et al. <i>CEGAR for Qualitative Analysis of Probabilistic Systems</i>. Vol. 8559, Springer, 2014, pp. 473–90, doi:<a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">10.1007/978-3-319-08867-9_31</a>.","ama":"Chatterjee K, Chmelik M, Daca P. CEGAR for qualitative analysis of probabilistic systems. In: Vol 8559. Springer; 2014:473-490. doi:<a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">10.1007/978-3-319-08867-9_31</a>","apa":"Chatterjee, K., Chmelik, M., &#38; Daca, P. (2014). CEGAR for qualitative analysis of probabilistic systems (Vol. 8559, pp. 473–490). Presented at the CAV: Computer Aided Verification, Vienna, Austria: Springer. <a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">https://doi.org/10.1007/978-3-319-08867-9_31</a>","chicago":"Chatterjee, Krishnendu, Martin Chmelik, and Przemyslaw Daca. “CEGAR for Qualitative Analysis of Probabilistic Systems,” 8559:473–90. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-08867-9_31\">https://doi.org/10.1007/978-3-319-08867-9_31</a>.","ista":"Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490.","short":"K. Chatterjee, M. Chmelik, P. Daca, in:, Springer, 2014, pp. 473–490.","ieee":"K. Chatterjee, M. Chmelik, and P. Daca, “CEGAR for qualitative analysis of probabilistic systems,” presented at the CAV: Computer Aided Verification, Vienna, Austria, 2014, vol. 8559, pp. 473–490."},"volume":8559,"scopus_import":"1"},{"main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198489/","open_access":"1"}],"year":"2014","abstract":[{"text":"We examined the synaptic structure, quantity, and distribution of α-amino-3-hydroxy-5-methylisoxazole-4-propionic acid (AMPA)- and N-methyl-D-aspartate (NMDA)-type glutamate receptors (AMPARs and NMDARs, respectively) in rat cochlear nuclei by a highly sensitive freeze-fracture replica labeling technique. Four excitatory synapses formed by two distinct inputs, auditory nerve (AN) and parallel fibers (PF), on different cell types were analyzed. These excitatory synapse types included AN synapses on bushy cells (AN-BC synapses) and fusiform cells (AN-FC synapses) and PF synapses on FC (PF-FC synapses) and cartwheel cell spines (PF-CwC synapses). Immunogold labeling revealed differences in synaptic structure as well as AMPAR and NMDAR number and/or density in both AN and PF synapses, indicating a target-dependent organization. The immunogold receptor labeling also identified differences in the synaptic organization of FCs based on AN or PF connections, indicating an input-dependent organization in FCs. Among the four excitatory synapse types, the AN-BC synapses were the smallest and had the most densely packed intramembrane particles (IMPs), whereas the PF-CwC synapses were the largest and had sparsely packed IMPs. All four synapse types showed positive correlations between the IMP-cluster area and the AMPAR number, indicating a common intrasynapse-type relationship for glutamatergic synapses. Immunogold particles for AMPARs were distributed over the entire area of individual AN synapses; PF synapses often showed synaptic areas devoid of labeling. The gold-labeling for NMDARs occurred in a mosaic fashion, with less positive correlations between the IMP-cluster area and the NMDAR number. Our observations reveal target- and input-dependent features in the structure, number, and organization of AMPARs and NMDARs in AN and PF synapses.","lang":"eng"}],"oa_version":"Submitted Version","publication_status":"published","_id":"2064","title":"Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus","intvolume":"       522","oa":1,"publisher":"Wiley-Blackwell","external_id":{"isi":["000343973100005"]},"author":[{"first_name":"Maía","last_name":"Rubio","full_name":"Rubio, Maía"},{"first_name":"Yugo","last_name":"Fukazawa","full_name":"Fukazawa, Yugo"},{"last_name":"Kamasawa","first_name":"Naomi","full_name":"Kamasawa, Naomi"},{"full_name":"Clarkson, Cheryl","first_name":"Cheryl","last_name":"Clarkson"},{"full_name":"Molnár, Elek","last_name":"Molnár","first_name":"Elek"},{"id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","full_name":"Shigemoto, Ryuichi","orcid":"0000-0001-8761-9444"}],"day":"29","date_created":"2018-12-11T11:55:30Z","language":[{"iso":"eng"}],"acknowledgement":"National Institutes of Health (NIH) Grant Number: 1R01DC013048‐0; Biotechnology and Biological Sciences Research Council, UK Grant Number: BB/J015938/1\r\n","type":"journal_article","issue":"18","department":[{"_id":"RySh"}],"date_updated":"2025-09-29T11:47:23Z","month":"07","date_published":"2014-07-29T00:00:00Z","publication":"Journal of Comparative Neurology","status":"public","page":"4023 - 4042","citation":{"short":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, R. Shigemoto, Journal of Comparative Neurology 522 (2014) 4023–4042.","ista":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. 2014. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. Journal of Comparative Neurology. 522(18), 4023–4042.","ieee":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, and R. Shigemoto, “Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus,” <i>Journal of Comparative Neurology</i>, vol. 522, no. 18. Wiley-Blackwell, pp. 4023–4042, 2014.","mla":"Rubio, Maía, et al. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” <i>Journal of Comparative Neurology</i>, vol. 522, no. 18, Wiley-Blackwell, 2014, pp. 4023–42, doi:<a href=\"https://doi.org/10.1002/cne.23654\">10.1002/cne.23654</a>.","apa":"Rubio, M., Fukazawa, Y., Kamasawa, N., Clarkson, C., Molnár, E., &#38; Shigemoto, R. (2014). Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. <i>Journal of Comparative Neurology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/cne.23654\">https://doi.org/10.1002/cne.23654</a>","ama":"Rubio M, Fukazawa Y, Kamasawa N, Clarkson C, Molnár E, Shigemoto R. Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus. <i>Journal of Comparative Neurology</i>. 2014;522(18):4023-4042. doi:<a href=\"https://doi.org/10.1002/cne.23654\">10.1002/cne.23654</a>","chicago":"Rubio, Maía, Yugo Fukazawa, Naomi Kamasawa, Cheryl Clarkson, Elek Molnár, and Ryuichi Shigemoto. “Target- and Input-Dependent Organization of AMPA and NMDA Receptors in Synaptic Connections of the Cochlear Nucleus.” <i>Journal of Comparative Neurology</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/cne.23654\">https://doi.org/10.1002/cne.23654</a>."},"quality_controlled":"1","volume":522,"publist_id":"4974","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1002/cne.23654","scopus_import":"1","article_processing_charge":"No","isi":1},{"alternative_title":["LNCS"],"external_id":{"arxiv":["1305.4519"]},"publication_identifier":{"issn":["0302-9743"]},"publisher":"Springer Nature","oa":1,"intvolume":"      8871","oa_version":"Preprint","title":"Clustered planarity testing revisited","publication_status":"published","_id":"10793","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1305.4519","open_access":"1"}],"OA_type":"green","abstract":[{"text":"The Hanani–Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this classical result to clustered graphs with two disjoint clusters, and show that a straightforward extension of our result to flat clustered graphs with three or more disjoint clusters is not possible.\r\n\r\nWe also give a new and short proof for a related result by Di Battista and Frati based on the matroid intersection algorithm.","lang":"eng"}],"year":"2014","arxiv":1,"article_processing_charge":"No","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1007/978-3-662-45803-7_36","volume":8871,"citation":{"chicago":"Fulek, Radoslav, Jan Kynčl, Igor Malinović, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” In <i>International Symposium on Graph Drawing</i>, 8871:428–36. Cham: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">https://doi.org/10.1007/978-3-662-45803-7_36</a>.","mla":"Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” <i>International Symposium on Graph Drawing</i>, vol. 8871, Springer Nature, 2014, pp. 428–36, doi:<a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">10.1007/978-3-662-45803-7_36</a>.","ama":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. Clustered planarity testing revisited. In: <i>International Symposium on Graph Drawing</i>. Vol 8871. Cham: Springer Nature; 2014:428-436. doi:<a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">10.1007/978-3-662-45803-7_36</a>","apa":"Fulek, R., Kynčl, J., Malinović, I., &#38; Pálvölgyi, D. (2014). Clustered planarity testing revisited. In <i>International Symposium on Graph Drawing</i> (Vol. 8871, pp. 428–436). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-662-45803-7_36\">https://doi.org/10.1007/978-3-662-45803-7_36</a>","ieee":"R. Fulek, J. Kynčl, I. Malinović, and D. Pálvölgyi, “Clustered planarity testing revisited,” in <i>International Symposium on Graph Drawing</i>, 2014, vol. 8871, pp. 428–436.","ista":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. 2014. Clustered planarity testing revisited. International Symposium on Graph Drawing. , LNCS, vol. 8871, 428–436.","short":"R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436."},"quality_controlled":"1","place":"Cham","publication":"International Symposium on Graph Drawing","month":"01","date_published":"2014-01-01T00:00:00Z","page":"428-436","status":"public","department":[{"_id":"UlWa"}],"type":"conference","date_updated":"2025-06-26T07:57:46Z","related_material":{"record":[{"id":"1642","status":"public","relation":"later_version"}]},"OA_place":"repository","author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","first_name":"Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"},{"full_name":"Malinović, Igor","last_name":"Malinović","first_name":"Igor"},{"last_name":"Pálvölgyi","first_name":"Dömötör","full_name":"Pálvölgyi, Dömötör"}],"date_created":"2022-02-25T10:32:14Z","language":[{"iso":"eng"}],"day":"01"},{"editor":[{"first_name":"Eva","last_name":"Zažímalová","full_name":"Zažímalová, Eva"},{"full_name":"Petrášek, Jan","first_name":"Jan","last_name":"Petrášek"},{"first_name":"Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva"}],"scopus_import":"1","article_processing_charge":"No","publication_identifier":{"isbn":["9783709115251"],"eisbn":["9783709115268"]},"quality_controlled":"1","citation":{"apa":"Zažímalová, E., Petrášek, J., &#38; Benková, E. (Eds.). (2014). <i>Auxin and Its Role in Plant Development</i> (1st ed.). Vienna: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">https://doi.org/10.1007/978-3-7091-1526-8</a>","ama":"Zažímalová E, Petrášek J, Benková E, eds. <i>Auxin and Its Role in Plant Development</i>. 1st ed. Vienna: Springer Nature; 2014. doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">10.1007/978-3-7091-1526-8</a>","mla":"Zažímalová, Eva, et al., editors. <i>Auxin and Its Role in Plant Development</i>. 1st ed., Springer Nature, 2014, doi:<a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">10.1007/978-3-7091-1526-8</a>.","chicago":"Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. <i>Auxin and Its Role in Plant Development</i>. 1st ed. Vienna: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-7091-1526-8\">https://doi.org/10.1007/978-3-7091-1526-8</a>.","short":"E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant Development, 1st ed., Springer Nature, Vienna, 2014.","ista":"Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant Development 1st ed., Vienna: Springer Nature, 444p.","ieee":"E. Zažímalová, J. Petrášek, and E. Benková, Eds., <i>Auxin and Its Role in Plant Development</i>, 1st ed. Vienna: Springer Nature, 2014."},"place":"Vienna","publisher":"Springer Nature","doi":"10.1007/978-3-7091-1526-8","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"None","department":[{"_id":"EvBe"}],"type":"book_editor","title":"Auxin and Its Role in Plant Development","date_updated":"2022-03-04T07:38:15Z","_id":"10811","publication_status":"published","date_published":"2014-04-01T00:00:00Z","month":"04","page":"444","status":"public","day":"01","language":[{"iso":"eng"}],"date_created":"2022-03-03T11:52:44Z","edition":"1","abstract":[{"text":"Auxin is an important signaling compound in plants and vital for plant development and growth. The present book, Auxin and its Role in Plant Development, provides the reader with detailed and comprehensive insight into the functioning of the molecule on the whole and specifically in plant development. In the first part, the functioning, metabolism and signaling pathways of auxin in plants are explained, the second part depicts the specific role of auxin in plant development and the third part describes the interaction and functioning of the signaling compound  upon stimuli of the environment. Each chapter is written by international experts in the respective field and designed for scientists and researchers in plant biology, plant development and cell biology to summarize the recent progress in understanding the role of auxin and suggest future perspectives for auxin research.","lang":"eng"}],"year":"2014"},{"scopus_import":"1","article_processing_charge":"No","quality_controlled":"1","citation":{"chicago":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1365/s13291-014-0083-9\">https://doi.org/10.1365/s13291-014-0083-9</a>.","mla":"Seiringer, Robert. “The Excitation Spectrum for Bose Fluids with Weak Interactions.” <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>, vol. 116, Springer Nature, 2014, pp. 21–41, doi:<a href=\"https://doi.org/10.1365/s13291-014-0083-9\">10.1365/s13291-014-0083-9</a>.","ama":"Seiringer R. The excitation spectrum for Bose fluids with weak interactions. <i>Jahresbericht der Deutschen Mathematiker-Vereinigung</i>. 2014;116:21-41. doi:<a href=\"https://doi.org/10.1365/s13291-014-0083-9\">10.1365/s13291-014-0083-9</a>","apa":"Seiringer, R. (2014). The excitation spectrum for Bose fluids with weak interactions. <i>Jahresbericht Der Deutschen Mathematiker-Vereinigung</i>. Springer Nature. <a href=\"https://doi.org/10.1365/s13291-014-0083-9\">https://doi.org/10.1365/s13291-014-0083-9</a>","ieee":"R. Seiringer, “The excitation spectrum for Bose fluids with weak interactions,” <i>Jahresbericht der Deutschen Mathematiker-Vereinigung</i>, vol. 116. Springer Nature, pp. 21–41, 2014.","ista":"Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41.","short":"R. Seiringer, Jahresbericht Der Deutschen Mathematiker-Vereinigung 116 (2014) 21–41."},"volume":116,"doi":"10.1365/s13291-014-0083-9","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2024-10-09T21:01:45Z","type":"journal_article","department":[{"_id":"RoSe"}],"status":"public","page":"21-41","date_published":"2014-03-01T00:00:00Z","month":"03","publication":"Jahresbericht der Deutschen Mathematiker-Vereinigung","date_created":"2022-03-04T07:54:39Z","day":"01","language":[{"iso":"eng"}],"author":[{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"article_type":"original","corr_author":"1","publication_identifier":{"issn":["0012-0456"],"eissn":["1869-7135"]},"publisher":"Springer Nature","_id":"10814","publication_status":"published","title":"The excitation spectrum for Bose fluids with weak interactions","oa_version":"None","intvolume":"       116","year":"2014","keyword":["General Medicine"],"abstract":[{"text":"We review recent progress towards a rigorous understanding of the excitation spectrum of bosonic quantum many-body systems. In particular, we explain how one can rigorously establish the predictions resulting from the Bogoliubov approximation in the mean field limit. The latter predicts that the spectrum is made up of elementary excitations, whose energy behaves linearly in the momentum for small momentum. This property is crucial for the superfluid behavior of the system. We also discuss a list of open problems in this field.","lang":"eng"}]},{"language":[{"iso":"eng"}],"day":"01","date_created":"2022-03-04T08:17:25Z","author":[{"full_name":"Hashimoto, Masakazu","first_name":"Masakazu","last_name":"Hashimoto"},{"full_name":"Morita, Hitoshi","first_name":"Hitoshi","id":"4C6E54C6-F248-11E8-B48F-1D18A9856A87","last_name":"Morita"},{"full_name":"Ueno, Naoto","last_name":"Ueno","first_name":"Naoto"}],"acknowledgement":"The authors thank all the members of the Division of Morphogenesis, National Institute for Basic Biology, for their contributions to the research, their encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical reading of the manuscript. We also thank the Model Animal Research and Spectrography and Bioimaging Facilities, NIBB Core Research Facilities, for technical support. M.H. was supported by a research fellowship from the Japan Society for the Promotion of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan, to N.U.","article_type":"original","date_updated":"2025-09-29T13:21:58Z","department":[{"_id":"CaHe"}],"type":"journal_article","issue":"1","page":"1-7","status":"public","publication":"Congenital Anomalies","month":"02","date_published":"2014-02-01T00:00:00Z","volume":54,"citation":{"ista":"Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7.","short":"M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7.","ieee":"M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of development underlying congenital diseases,” <i>Congenital Anomalies</i>, vol. 54, no. 1. Wiley, pp. 1–7, 2014.","apa":"Hashimoto, M., Morita, H., &#38; Ueno, N. (2014). Molecular and cellular mechanisms of development underlying congenital diseases. <i>Congenital Anomalies</i>. Wiley. <a href=\"https://doi.org/10.1111/cga.12039\">https://doi.org/10.1111/cga.12039</a>","ama":"Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development underlying congenital diseases. <i>Congenital Anomalies</i>. 2014;54(1):1-7. doi:<a href=\"https://doi.org/10.1111/cga.12039\">10.1111/cga.12039</a>","mla":"Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” <i>Congenital Anomalies</i>, vol. 54, no. 1, Wiley, 2014, pp. 1–7, doi:<a href=\"https://doi.org/10.1111/cga.12039\">10.1111/cga.12039</a>.","chicago":"Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” <i>Congenital Anomalies</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/cga.12039\">https://doi.org/10.1111/cga.12039</a>."},"quality_controlled":"1","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1111/cga.12039","scopus_import":"1","isi":1,"article_processing_charge":"No","abstract":[{"lang":"eng","text":"In the last several decades, developmental biology has clarified the molecular mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated that the “tool-kit genes” essential for regulating developmental processes are not only highly conserved among species, but are also used as systems at various times and places in an organism to control distinct developmental events. Therefore, mutations in many of these tool-kit genes may cause congenital diseases involving morphological abnormalities. This link between genes and abnormal morphological phenotypes underscores the importance of understanding how cells behave and contribute to morphogenesis as a result of gene function. Recent improvements in live imaging and in quantitative analyses of cellular dynamics will advance our understanding of the cellular pathogenesis of congenital diseases associated with aberrant morphologies. In these studies, it is critical to select an appropriate model organism for the particular phenomenon of interest."}],"keyword":["Developmental Biology","Embryology","General Medicine","Pediatrics","Perinatology","and Child Health"],"year":"2014","main_file_link":[{"url":"https://doi.org/10.1111/cga.12039","open_access":"1"}],"title":"Molecular and cellular mechanisms of development underlying congenital diseases","publication_status":"published","_id":"10815","oa_version":"None","pmid":1,"oa":1,"intvolume":"        54","publisher":"Wiley","publication_identifier":{"issn":["0914-3505"]},"external_id":{"isi":["000331769200001"],"pmid":["24666178"]}},{"page":"1175-1194","status":"public","publication":"Proceeding of the International Congress of Mathematicans","month":"08","ddc":["500"],"date_published":"2014-08-01T00:00:00Z","date_updated":"2026-06-18T19:30:06Z","department":[{"_id":"RoSe"}],"type":"conference","corr_author":"1","OA_place":"publisher","language":[{"iso":"eng"}],"day":"01","date_created":"2020-06-29T07:59:35Z","author":[{"last_name":"Seiringer","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521"}],"article_processing_charge":"No","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":3,"citation":{"apa":"Seiringer, R. (2014). Structure of the excitation spectrum for many-body quantum systems. In <i>Proceeding of the International Congress of Mathematicans</i> (Vol. 3, pp. 1175–1194). Seoul, South Korea: International Congress of Mathematicians.","ama":"Seiringer R. Structure of the excitation spectrum for many-body quantum systems. In: <i>Proceeding of the International Congress of Mathematicans</i>. Vol 3. International Congress of Mathematicians; 2014:1175-1194.","mla":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” <i>Proceeding of the International Congress of Mathematicans</i>, vol. 3, International Congress of Mathematicians, 2014, pp. 1175–94.","chicago":"Seiringer, Robert. “Structure of the Excitation Spectrum for Many-Body Quantum Systems.” In <i>Proceeding of the International Congress of Mathematicans</i>, 3:1175–94. International Congress of Mathematicians, 2014.","ista":"Seiringer R. 2014. Structure of the excitation spectrum for many-body quantum systems. Proceeding of the International Congress of Mathematicans. ICM: International Congress of Mathematicans vol. 3, 1175–1194.","short":"R. Seiringer, in:, Proceeding of the International Congress of Mathematicans, International Congress of Mathematicians, 2014, pp. 1175–1194.","ieee":"R. Seiringer, “Structure of the excitation spectrum for many-body quantum systems,” in <i>Proceeding of the International Congress of Mathematicans</i>, Seoul, South Korea, 2014, vol. 3, pp. 1175–1194."},"quality_controlled":"1","oa":1,"intvolume":"         3","title":"Structure of the excitation spectrum for many-body quantum systems","publication_status":"published","_id":"8044","oa_version":"Published Version","abstract":[{"text":"Many questions concerning models in quantum mechanics require a detailed analysis of the spectrum of the corresponding Hamiltonian, a linear operator on a suitable Hilbert space. Of particular relevance for an understanding of the low-temperature properties of a system is the structure of the excitation spectrum, which is the part of the spectrum close to the spectral bottom. We present recent progress on this question for bosonic many-body quantum systems with weak two-body interactions. Such system are currently of great interest, due to their experimental realization in ultra-cold atomic gases. We investigate the accuracy of the Bogoliubov approximations, which predicts that the low-energy spectrum is made up of sums of elementary excitations, with linear dispersion law at low momentum. The latter property is crucial for the superfluid behavior the system.","lang":"eng"}],"year":"2014","main_file_link":[{"url":"http://www.icm2014.org/en/vod/proceedings.html","open_access":"1"}],"OA_type":"free access","conference":{"end_date":"2014-08-21","name":"ICM: International Congress of Mathematicans","location":"Seoul, South Korea","start_date":"2014-08-13"},"publication_identifier":{"isbn":["9788961058063"]},"publisher":"International Congress of Mathematicians"},{"publisher":"Elsevier","external_id":{"pmid":["24630728"]},"publication_identifier":{"eissn":["1097-4172"],"issn":["0092-8674"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.cell.2014.01.029"}],"year":"2014","abstract":[{"text":"Dnmt1 epigenetically propagates symmetrical CG methylation in many eukaryotes. Their genomes are typically depleted of CG dinucleotides because of imperfect repair of deaminated methylcytosines. Here, we extensively survey diverse species lacking Dnmt1 and show that, surprisingly, symmetrical CG methylation is nonetheless frequently present and catalyzed by a different DNA methyltransferase family, Dnmt5. Numerous Dnmt5-containing organisms that diverged more than a billion years ago exhibit clustered methylation, specifically in nucleosome linkers. Clustered methylation occurs at unprecedented densities and directly disfavors nucleosomes, contributing to nucleosome positioning between clusters. Dense methylation is enabled by a regime of genomic sequence evolution that enriches CG dinucleotides and drives the highest CG frequencies known. Species with linker methylation have small, transcriptionally active nuclei that approach the physical limits of chromatin compaction. These features constitute a previously unappreciated genome architecture, in which dense methylation influences nucleosome positions, likely facilitating nuclear processes under extreme spatial constraints.","lang":"eng"}],"oa_version":"Published Version","_id":"9458","publication_status":"published","title":"Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes","intvolume":"       156","oa":1,"pmid":1,"citation":{"apa":"Huff, J. T., &#38; Zilberman, D. (2014). Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>","ama":"Huff JT, Zilberman D. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. <i>Cell</i>. 2014;156(6):1286-1297. doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>","mla":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>, vol. 156, no. 6, Elsevier, 2014, pp. 1286–97, doi:<a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">10.1016/j.cell.2014.01.029</a>.","chicago":"Huff, Jason T., and Daniel Zilberman. “Dnmt1-Independent CG Methylation Contributes to Nucleosome Positioning in Diverse Eukaryotes.” <i>Cell</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.cell.2014.01.029\">https://doi.org/10.1016/j.cell.2014.01.029</a>.","ista":"Huff JT, Zilberman D. 2014. Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes. Cell. 156(6), 1286–1297.","short":"J.T. Huff, D. Zilberman, Cell 156 (2014) 1286–1297.","ieee":"J. T. Huff and D. Zilberman, “Dnmt1-independent CG methylation contributes to nucleosome positioning in diverse eukaryotes,” <i>Cell</i>, vol. 156, no. 6. Elsevier, pp. 1286–1297, 2014."},"quality_controlled":"1","volume":156,"extern":"1","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","doi":"10.1016/j.cell.2014.01.029","scopus_import":"1","article_processing_charge":"No","author":[{"last_name":"Huff","first_name":"Jason T.","full_name":"Huff, Jason T."},{"first_name":"Daniel","last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","orcid":"0000-0002-0123-8649","full_name":"Zilberman, Daniel"}],"date_created":"2021-06-04T12:00:16Z","day":"13","language":[{"iso":"eng"}],"article_type":"original","issue":"6","type":"journal_article","department":[{"_id":"DaZi"}],"date_updated":"2021-12-14T08:22:36Z","date_published":"2014-03-13T00:00:00Z","month":"03","publication":"Cell","status":"public","page":"1286-1297"},{"article_type":"original","author":[{"first_name":"Zsuzsanna","last_name":"Mérai","full_name":"Mérai, Zsuzsanna"},{"full_name":"Chumak, Nina","last_name":"Chumak","first_name":"Nina"},{"full_name":"García-Aguilar, Marcelina","first_name":"Marcelina","last_name":"García-Aguilar"},{"last_name":"Hsieh","first_name":"Tzung-Fu","full_name":"Hsieh, Tzung-Fu"},{"full_name":"Nishimura, Toshiro","first_name":"Toshiro","last_name":"Nishimura"},{"first_name":"Vera K.","last_name":"Schoft","full_name":"Schoft, Vera K."},{"full_name":"Bindics, János","first_name":"János","last_name":"Bindics"},{"last_name":"Ślusarz","first_name":"Lucyna","full_name":"Ślusarz, Lucyna"},{"full_name":"Arnoux, Stéphanie","first_name":"Stéphanie","last_name":"Arnoux"},{"first_name":"Susanne","last_name":"Opravil","full_name":"Opravil, Susanne"},{"first_name":"Karl","last_name":"Mechtler","full_name":"Mechtler, Karl"},{"last_name":"Zilberman","id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"},{"full_name":"Fischer, Robert L.","first_name":"Robert L.","last_name":"Fischer"},{"last_name":"Tamaru","first_name":"Hisashi","full_name":"Tamaru, Hisashi"}],"day":"11","date_created":"2021-06-07T07:23:43Z","language":[{"iso":"eng"}],"publication":"Proceedings of the National Academy of Sciences","month":"11","date_published":"2014-11-11T00:00:00Z","page":"16166-16171","status":"public","department":[{"_id":"DaZi"}],"type":"journal_article","issue":"45","date_updated":"2021-12-14T08:23:26Z","extern":"1","doi":"10.1073/pnas.1418564111","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":111,"quality_controlled":"1","citation":{"short":"Z. Mérai, N. Chumak, M. García-Aguilar, T.-F. Hsieh, T. Nishimura, V.K. Schoft, J. Bindics, L. Ślusarz, S. Arnoux, S. Opravil, K. Mechtler, D. Zilberman, R.L. Fischer, H. Tamaru, Proceedings of the National Academy of Sciences 111 (2014) 16166–16171.","ista":"Mérai Z, Chumak N, García-Aguilar M, Hsieh T-F, Nishimura T, Schoft VK, Bindics J, Ślusarz L, Arnoux S, Opravil S, Mechtler K, Zilberman D, Fischer RL, Tamaru H. 2014. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. Proceedings of the National Academy of Sciences. 111(45), 16166–16171.","ieee":"Z. Mérai <i>et al.</i>, “The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45. National Academy of Sciences, pp. 16166–16171, 2014.","mla":"Mérai, Zsuzsanna, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 45, National Academy of Sciences, 2014, pp. 16166–71, doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>.","ama":"Mérai Z, Chumak N, García-Aguilar M, et al. The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(45):16166-16171. doi:<a href=\"https://doi.org/10.1073/pnas.1418564111\">10.1073/pnas.1418564111</a>","apa":"Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, T.-F., Nishimura, T., Schoft, V. K., … Tamaru, H. (2014). The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>","chicago":"Mérai, Zsuzsanna, Nina Chumak, Marcelina García-Aguilar, Tzung-Fu Hsieh, Toshiro Nishimura, Vera K. Schoft, János Bindics, et al. “The AAA-ATPase Molecular Chaperone Cdc48/P97 Disassembles Sumoylated Centromeres, Decondenses Heterochromatin, and Activates Ribosomal RNA Genes.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1418564111\">https://doi.org/10.1073/pnas.1418564111</a>."},"article_processing_charge":"No","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1073/pnas.1418564111","open_access":"1"}],"abstract":[{"lang":"eng","text":"Centromeres mediate chromosome segregation and are defined by the centromere-specific histone H3 variant (CenH3)/centromere protein A (CENP-A). Removal of CenH3 from centromeres is a general property of terminally differentiated cells, and the persistence of CenH3 increases the risk of diseases such as cancer. However, active mechanisms of centromere disassembly are unknown. Nondividing Arabidopsis pollen vegetative cells, which transport engulfed sperm by extended tip growth, undergo loss of CenH3; centromeric heterochromatin decondensation; and bulk activation of silent rRNA genes, accompanied by their translocation into the nucleolus. Here, we show that these processes are blocked by mutations in the evolutionarily conserved AAA-ATPase molecular chaperone, CDC48A, homologous to yeast Cdc48 and human p97 proteins, both of which are implicated in ubiquitin/small ubiquitin-like modifier (SUMO)-targeted protein degradation. We demonstrate that CDC48A physically associates with its heterodimeric cofactor UFD1-NPL4, known to bind ubiquitin and SUMO, as well as with SUMO1-modified CenH3 and mutations in NPL4 phenocopy cdc48a mutations. In WT vegetative cell nuclei, genetically unlinked ribosomal DNA (rDNA) loci are uniquely clustered together within the nucleolus and all major rRNA gene variants, including those rDNA variants silenced in leaves, are transcribed. In cdc48a mutant vegetative cell nuclei, however, these rDNA loci frequently colocalized with condensed centromeric heterochromatin at the external periphery of the nucleolus. Our results indicate that the CDC48ANPL4 complex actively removes sumoylated CenH3 from centromeres and disrupts centromeric heterochromatin to release bulk rRNA genes into the nucleolus for ribosome production, which fuels single nucleus-driven pollen tube growth and is essential for plant reproduction."}],"year":"2014","oa":1,"intvolume":"       111","pmid":1,"oa_version":"Published Version","title":"The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes","publication_status":"published","_id":"9479","publisher":"National Academy of Sciences","external_id":{"pmid":["25344531"]},"publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]}},{"article_type":"review","author":[{"last_name":"Kim","first_name":"M. Yvonne","full_name":"Kim, M. Yvonne"},{"id":"6973db13-dd5f-11ea-814e-b3e5455e9ed1","last_name":"Zilberman","first_name":"Daniel","full_name":"Zilberman, Daniel","orcid":"0000-0002-0123-8649"}],"date_created":"2021-06-07T14:38:09Z","day":"04","language":[{"iso":"eng"}],"publication":"Trends in Plant Science","month":"05","date_published":"2014-05-04T00:00:00Z","page":"320-326","status":"public","department":[{"_id":"DaZi"}],"issue":"5","type":"journal_article","date_updated":"2021-12-14T08:24:48Z","extern":"1","doi":"10.1016/j.tplants.2014.01.014","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","volume":19,"citation":{"ieee":"M. Y. Kim and D. Zilberman, “DNA methylation as a system of plant genomic immunity,” <i>Trends in Plant Science</i>, vol. 19, no. 5. Elsevier, pp. 320–326, 2014.","ista":"Kim MY, Zilberman D. 2014. DNA methylation as a system of plant genomic immunity. Trends in Plant Science. 19(5), 320–326.","short":"M.Y. Kim, D. Zilberman, Trends in Plant Science 19 (2014) 320–326.","chicago":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>.","apa":"Kim, M. Y., &#38; Zilberman, D. (2014). DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">https://doi.org/10.1016/j.tplants.2014.01.014</a>","ama":"Kim MY, Zilberman D. DNA methylation as a system of plant genomic immunity. <i>Trends in Plant Science</i>. 2014;19(5):320-326. doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>","mla":"Kim, M. Yvonne, and Daniel Zilberman. “DNA Methylation as a System of Plant Genomic Immunity.” <i>Trends in Plant Science</i>, vol. 19, no. 5, Elsevier, 2014, pp. 320–26, doi:<a href=\"https://doi.org/10.1016/j.tplants.2014.01.014\">10.1016/j.tplants.2014.01.014</a>."},"quality_controlled":"1","article_processing_charge":"No","scopus_import":"1","abstract":[{"lang":"eng","text":"Transposons are selfish genetic sequences that can increase their copy number and inflict substantial damage on their hosts. To combat these genomic parasites, plants have evolved multiple pathways to identify and silence transposons by methylating their DNA. Plants have also evolved mechanisms to limit the collateral damage from the antitransposon machinery. In this review, we examine recent developments that have elucidated many of the molecular workings of these pathways. We also highlight the evidence that the methylation and demethylation pathways interact, indicating that plants have a highly sophisticated, integrated system of transposon defense that has an important role in the regulation of gene expression."}],"year":"2014","intvolume":"        19","pmid":1,"oa_version":"None","title":"DNA methylation as a system of plant genomic immunity","_id":"9519","publication_status":"published","publisher":"Elsevier","external_id":{"pmid":["24618094 "]},"publication_identifier":{"issn":["1360-1385"],"eissn":["1878-4372"]}},{"citation":{"chicago":"Lovrics, Anna, Yu Gao, Bianka Juhász, István Bock, Helen M. Byrne, András Dinnyés, and Krisztián Kovács. “Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2.” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>.","mla":"Lovrics, Anna, et al. <i>Transition Probability between TF Expression States When Dbx2 Inhibits Nkx2.2</i>. Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>.","apa":"Lovrics, A., Gao, Y., Juhász, B., Bock, I., Byrne, H. M., Dinnyés, A., &#38; Kovács, K. (2014). Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">https://doi.org/10.1371/journal.pone.0111430.s006</a>","ama":"Lovrics A, Gao Y, Juhász B, et al. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2. 2014. doi:<a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>","ieee":"A. Lovrics <i>et al.</i>, “Transition probability between TF expression states when Dbx2 inhibits Nkx2.2.” Public Library of Science, 2014.","short":"A. Lovrics, Y. Gao, B. Juhász, I. Bock, H.M. Byrne, A. Dinnyés, K. Kovács, (2014).","ista":"Lovrics A, Gao Y, Juhász B, Bock I, Byrne HM, Dinnyés A, Kovács K. 2014. Transition probability between TF expression states when Dbx2 inhibits Nkx2.2, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pone.0111430.s006\">10.1371/journal.pone.0111430.s006</a>."},"doi":"10.1371/journal.pone.0111430.s006","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","article_processing_charge":"No","author":[{"first_name":"Anna","last_name":"Lovrics","full_name":"Lovrics, Anna"},{"last_name":"Gao","first_name":"Yu","full_name":"Gao, Yu"},{"full_name":"Juhász, Bianka","last_name":"Juhász","first_name":"Bianka"},{"last_name":"Bock","first_name":"István","full_name":"Bock, István"},{"full_name":"Byrne, Helen M.","last_name":"Byrne","first_name":"Helen M."},{"last_name":"Dinnyés","first_name":"András","full_name":"Dinnyés, András"},{"full_name":"Kovács, Krisztián","id":"2AB5821E-F248-11E8-B48F-1D18A9856A87","last_name":"Kovács","first_name":"Krisztián"}],"date_created":"2021-07-26T14:35:00Z","day":"14","related_material":{"record":[{"id":"2004","status":"public","relation":"used_in_publication"}]},"year":"2014","type":"research_data_reference","oa_version":"Published Version","department":[{"_id":"JoCs"}],"_id":"9722","date_updated":"2025-09-29T12:02:47Z","title":"Transition probability between TF expression states when Dbx2 inhibits Nkx2.2","month":"11","date_published":"2014-11-14T00:00:00Z","status":"public"},{"article_processing_charge":"No","citation":{"ista":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. 2014. Detailed proofs for “The time scale of evolutionary innovation”, Public Library of Science, <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","short":"K. Chatterjee, A. Pavlogiannis, B. Adlam, M. Novak, (2014).","ieee":"K. Chatterjee, A. Pavlogiannis, B. Adlam, and M. Novak, “Detailed proofs for ‘The time scale of evolutionary innovation.’” Public Library of Science, 2014.","apa":"Chatterjee, K., Pavlogiannis, A., Adlam, B., &#38; Novak, M. (2014). Detailed proofs for “The time scale of evolutionary innovation.” Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>","ama":"Chatterjee K, Pavlogiannis A, Adlam B, Novak M. Detailed proofs for “The time scale of evolutionary innovation.” 2014. doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>","mla":"Chatterjee, Krishnendu, et al. <i>Detailed Proofs for “The Time Scale of Evolutionary Innovation.”</i> Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">10.1371/journal.pcbi.1003818.s001</a>.","chicago":"Chatterjee, Krishnendu, Andreas Pavlogiannis, Ben Adlam, and Martin Novak. “Detailed Proofs for ‘The Time Scale of Evolutionary Innovation.’” Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pcbi.1003818.s001\">https://doi.org/10.1371/journal.pcbi.1003818.s001</a>."},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","publisher":"Public Library of Science","doi":"10.1371/journal.pcbi.1003818.s001","oa_version":"Published Version","department":[{"_id":"KrCh"}],"type":"research_data_reference","title":"Detailed proofs for “The time scale of evolutionary innovation”","_id":"9739","date_updated":"2025-09-29T11:53:46Z","date_published":"2014-09-11T00:00:00Z","month":"09","status":"public","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu"},{"orcid":"0000-0002-8943-0722","full_name":"Pavlogiannis, Andreas","first_name":"Andreas","last_name":"Pavlogiannis","id":"49704004-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Adlam, Ben","last_name":"Adlam","first_name":"Ben"},{"last_name":"Novak","first_name":"Martin","full_name":"Novak, Martin"}],"date_created":"2021-07-28T08:13:57Z","day":"11","related_material":{"record":[{"status":"public","id":"2039","relation":"used_in_publication"}]},"year":"2014"},{"status":"public","date_published":"2014-11-13T00:00:00Z","month":"11","oa":1,"date_updated":"2025-09-23T07:55:02Z","_id":"9740","title":"Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host","type":"research_data_reference","department":[{"_id":"SyCr"}],"oa_version":"Published Version","year":"2014","corr_author":"1","abstract":[{"lang":"eng","text":"The fitness effects of symbionts on their hosts can be context-dependent, with usually benign symbionts causing detrimental effects when their hosts are stressed, or typically parasitic symbionts providing protection towards their hosts (e.g. against pathogen infection). Here, we studied the novel association between the invasive garden ant Lasius neglectus and its fungal ectosymbiont Laboulbenia formicarum for potential costs and benefits. We tested ants with different Laboulbenia levels for their survival and immunity under resource limitation and exposure to the obligate killing entomopathogen Metarhizium brunneum. While survival of L. neglectus workers under starvation was significantly decreased with increasing Laboulbenia levels, host survival under Metarhizium exposure increased with higher levels of the ectosymbiont, suggesting a symbiont-mediated anti-pathogen protection, which seems to be driven mechanistically by both improved sanitary behaviours and an upregulated immune system. Ants with high Laboulbenia levels showed significantly longer self-grooming and elevated expression of immune genes relevant for wound repair and antifungal responses (β-1,3-glucan binding protein, Prophenoloxidase), compared with ants carrying low Laboulbenia levels. This suggests that the ectosymbiont Laboulbenia formicarum weakens its ant host by either direct resource exploitation or the costs of an upregulated behavioural and immunological response, which, however, provides a prophylactic protection upon later exposure to pathogens."}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.vm0vc"}],"related_material":{"record":[{"status":"public","id":"1993","relation":"used_in_publication"}]},"date_created":"2021-07-28T08:38:40Z","day":"13","author":[{"first_name":"Matthias","id":"46528076-F248-11E8-B48F-1D18A9856A87","last_name":"Konrad","full_name":"Konrad, Matthias"},{"full_name":"Grasse, Anna V","last_name":"Grasse","id":"406F989C-F248-11E8-B48F-1D18A9856A87","first_name":"Anna V"},{"id":"35A7A418-F248-11E8-B48F-1D18A9856A87","last_name":"Tragust","first_name":"Simon","full_name":"Tragust, Simon"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer"}],"article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.5061/dryad.vm0vc","publisher":"Dryad","citation":{"chicago":"Konrad, Matthias, Anna V Grasse, Simon Tragust, and Sylvia Cremer. “Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>.","ama":"Konrad M, Grasse AV, Tragust S, Cremer S. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>","apa":"Konrad, M., Grasse, A. V., Tragust, S., &#38; Cremer, S. (2014). Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host. Dryad. <a href=\"https://doi.org/10.5061/dryad.vm0vc\">https://doi.org/10.5061/dryad.vm0vc</a>","mla":"Konrad, Matthias, et al. <i>Data from: Anti-Pathogen Protection versus Survival Costs Mediated by an Ectosymbiont in an Ant Host</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","ieee":"M. Konrad, A. V. Grasse, S. Tragust, and S. Cremer, “Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host.” Dryad, 2014.","ista":"Konrad M, Grasse AV, Tragust S, Cremer S. 2014. Data from: Anti-pathogen protection versus survival costs mediated by an ectosymbiont in an ant host, Dryad, <a href=\"https://doi.org/10.5061/dryad.vm0vc\">10.5061/dryad.vm0vc</a>.","short":"M. Konrad, A.V. Grasse, S. Tragust, S. Cremer, (2014)."}},{"date_updated":"2025-09-29T11:46:47Z","_id":"9747","title":"Data from: Role of sex and migration in adaptation to sink environments","type":"research_data_reference","oa_version":"Published Version","department":[{"_id":"CaGu"}],"status":"public","month":"04","date_published":"2014-04-17T00:00:00Z","oa":1,"day":"17","date_created":"2021-07-28T15:32:55Z","author":[{"full_name":"Lagator, Mato","id":"345D25EC-F248-11E8-B48F-1D18A9856A87","last_name":"Lagator","first_name":"Mato"},{"last_name":"Morgan","first_name":"Andrew","full_name":"Morgan, Andrew"},{"full_name":"Neve, Paul","first_name":"Paul","last_name":"Neve"},{"full_name":"Colegrave, Nick","first_name":"Nick","last_name":"Colegrave"}],"year":"2014","abstract":[{"text":"Understanding the effects of sex and migration on adaptation to novel environments remains a key problem in evolutionary biology. Using a single-cell alga Chlamydomonas reinhardtii, we investigated how sex and migration affected rates of evolutionary rescue in a sink environment, and subsequent changes in fitness following evolutionary rescue. We show that sex and migration affect both the rate of evolutionary rescue and subsequent adaptation. However, their combined effects change as the populations adapt to a sink habitat. Both sex and migration independently increased rates of evolutionary rescue, but the effect of sex on subsequent fitness improvements, following initial rescue, changed with migration, as sex was beneficial in the absence of migration but constraining adaptation when combined with migration. These results suggest that sex and migration are beneficial during the initial stages of adaptation, but can become detrimental as the population adapts to its environment.","lang":"eng"}],"related_material":{"record":[{"relation":"used_in_publication","id":"2083","status":"public"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.s42n1"}],"article_processing_charge":"No","citation":{"chicago":"Lagator, Mato, Andrew Morgan, Paul Neve, and Nick Colegrave. “Data from: Role of Sex and Migration in Adaptation to Sink Environments.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>.","mla":"Lagator, Mato, et al. <i>Data from: Role of Sex and Migration in Adaptation to Sink Environments</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>.","ama":"Lagator M, Morgan A, Neve P, Colegrave N. Data from: Role of sex and migration in adaptation to sink environments. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>","apa":"Lagator, M., Morgan, A., Neve, P., &#38; Colegrave, N. (2014). Data from: Role of sex and migration in adaptation to sink environments. Dryad. <a href=\"https://doi.org/10.5061/dryad.s42n1\">https://doi.org/10.5061/dryad.s42n1</a>","ieee":"M. Lagator, A. Morgan, P. Neve, and N. Colegrave, “Data from: Role of sex and migration in adaptation to sink environments.” Dryad, 2014.","short":"M. Lagator, A. Morgan, P. Neve, N. Colegrave, (2014).","ista":"Lagator M, Morgan A, Neve P, Colegrave N. 2014. Data from: Role of sex and migration in adaptation to sink environments, Dryad, <a href=\"https://doi.org/10.5061/dryad.s42n1\">10.5061/dryad.s42n1</a>."},"publisher":"Dryad","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.5061/dryad.s42n1"},{"date_published":"2014-11-07T00:00:00Z","month":"11","oa":1,"status":"public","type":"research_data_reference","department":[{"_id":"GaTk"}],"oa_version":"Published Version","date_updated":"2025-09-29T14:27:23Z","_id":"9752","title":"Data from: Transformation of stimulus correlations by the retina","main_file_link":[{"url":"https://doi.org/10.5061/dryad.246qg","open_access":"1"}],"related_material":{"record":[{"id":"2277","status":"public","relation":"used_in_publication"}]},"year":"2014","abstract":[{"lang":"eng","text":"Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but they were much less correlated than predicted by a non-adapting functional model of retinal response. Meanwhile, responding to stimuli with purely spatial correlations, pairs of ganglion cells showed increased correlations consistent with a static, non-adapting receptive field and nonlinearity. We found that in response to spatio-temporally correlated stimuli, ganglion cells had faster temporal kernels and tended to have stronger surrounds. These properties of individual cells, along with gain changes that opposed changes in effective contrast at the ganglion cell input, largely explained the pattern of pairwise correlations across stimuli where receptive field measurements were possible."}],"author":[{"last_name":"Simmons","first_name":"Kristina","full_name":"Simmons, Kristina"},{"full_name":"Prentice, Jason","last_name":"Prentice","first_name":"Jason"},{"full_name":"Tkačik, Gašper","orcid":"0000-0002-6699-1455","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gašper"},{"last_name":"Homann","first_name":"Jan","full_name":"Homann, Jan"},{"last_name":"Yee","first_name":"Heather","full_name":"Yee, Heather"},{"full_name":"Palmer, Stephanie","first_name":"Stephanie","last_name":"Palmer"},{"last_name":"Nelson","first_name":"Philip","full_name":"Nelson, Philip"},{"first_name":"Vijay","last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay"}],"day":"07","date_created":"2021-07-30T08:13:52Z","article_processing_charge":"No","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","doi":"10.5061/dryad.246qg","publisher":"Dryad","citation":{"ieee":"K. Simmons <i>et al.</i>, “Data from: Transformation of stimulus correlations by the retina.” Dryad, 2014.","ista":"Simmons K, Prentice J, Tkačik G, Homann J, Yee H, Palmer S, Nelson P, Balasubramanian V. 2014. Data from: Transformation of stimulus correlations by the retina, Dryad, <a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","short":"K. Simmons, J. Prentice, G. Tkačik, J. Homann, H. Yee, S. Palmer, P. Nelson, V. Balasubramanian, (2014).","chicago":"Simmons, Kristina, Jason Prentice, Gašper Tkačik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.” Dryad, 2014. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>.","mla":"Simmons, Kristina, et al. <i>Data from: Transformation of Stimulus Correlations by the Retina</i>. Dryad, 2014, doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>.","apa":"Simmons, K., Prentice, J., Tkačik, G., Homann, J., Yee, H., Palmer, S., … Balasubramanian, V. (2014). Data from: Transformation of stimulus correlations by the retina. Dryad. <a href=\"https://doi.org/10.5061/dryad.246qg\">https://doi.org/10.5061/dryad.246qg</a>","ama":"Simmons K, Prentice J, Tkačik G, et al. Data from: Transformation of stimulus correlations by the retina. 2014. doi:<a href=\"https://doi.org/10.5061/dryad.246qg\">10.5061/dryad.246qg</a>"}},{"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","orcid":"0000-0002-9823-6833"}],"language":[{"iso":"eng"}],"date_created":"2019-09-06T09:22:33Z","day":"01","related_material":{"link":[{"url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=356106","relation":"other","description":"available as eBook via catalog IST BookList"},{"relation":"other","description":"available via catalog IST BookList","url":"https://koha.app.ist.ac.at/cgi-bin/koha/opac-detail.pl?biblionumber=373842"}]},"edition":"1","abstract":[{"lang":"eng","text":"This monograph presents a short course in computational geometry and topology. In the first part the book covers Voronoi diagrams and Delaunay triangulations, then it presents the theory of alpha complexes which play a crucial role in biology. The central part of the book is the homology theory and their computation, including the theory of persistence which is indispensable for applications, e.g. shape reconstruction. The target audience comprises researchers and practitioners in mathematics, biology, neuroscience and computer science, but the book may also be beneficial to graduate students of these fields."}],"year":"2014","department":[{"_id":"HeEd"}],"oa_version":"None","type":"book","title":"A Short Course in Computational Geometry and Topology","publication_status":"published","_id":"6853","date_updated":"2022-03-04T07:47:54Z","date_published":"2014-01-01T00:00:00Z","month":"01","page":"IX, 110","status":"public","quality_controlled":"1","citation":{"chicago":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. SpringerBriefs in Applied Sciences and Technology. Cham: Springer Nature, 2014. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>.","mla":"Edelsbrunner, Herbert. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed., Springer Nature, 2014, doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>.","ama":"Edelsbrunner H. <i>A Short Course in Computational Geometry and Topology</i>. 1st ed. Cham: Springer Nature; 2014. doi:<a href=\"https://doi.org/10.1007/978-3-319-05957-0\">10.1007/978-3-319-05957-0</a>","apa":"Edelsbrunner, H. (2014). <i>A Short Course in Computational Geometry and Topology</i> (1st ed.). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-319-05957-0\">https://doi.org/10.1007/978-3-319-05957-0</a>","ieee":"H. Edelsbrunner, <i>A Short Course in Computational Geometry and Topology</i>, 1st ed. Cham: Springer Nature, 2014.","short":"H. Edelsbrunner, A Short Course in Computational Geometry and Topology, 1st ed., Springer Nature, Cham, 2014.","ista":"Edelsbrunner H. 2014. A Short Course in Computational Geometry and Topology 1st ed., Cham: Springer Nature, IX, 110p."},"place":"Cham","series_title":"SpringerBriefs in Applied Sciences and Technology","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Springer Nature","doi":"10.1007/978-3-319-05957-0","scopus_import":"1","alternative_title":["SpringerBriefs in Applied Sciences and Technology"],"article_processing_charge":"No","publication_identifier":{"isbn":["9-783-3190-5956-3"],"issn":["2191-530X"],"eisbn":["9-783-3190-5957-0"],"eissn":["2191-5318"]}}]