[{"scopus_import":"1","external_id":{"isi":["000340480300008"]},"date_updated":"2025-09-29T11:49:12Z","doi":"10.1007/s00709-014-0616-1","publisher":"Springer","volume":251,"citation":{"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>.","short":"E. Dubas, J. Moravčíková, J. Libantová, I. Matušíková, E. Benková, I. Zur, M. Krzewska, Protoplasma 251 (2014) 1077–1087.","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>","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.","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>.","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.","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>"},"year":"2014","department":[{"_id":"EvBe"}],"author":[{"last_name":"Dubas","first_name":"Ewa","full_name":"Dubas, Ewa"},{"last_name":"Moravčíková","first_name":"Jana","full_name":"Moravčíková, Jana"},{"last_name":"Libantová","full_name":"Libantová, Jana","first_name":"Jana"},{"first_name":"Ildikó","full_name":"Matušíková, Ildikó","last_name":"Matušíková"},{"first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Iwona","full_name":"Zur, Iwona","last_name":"Zur"},{"last_name":"Krzewska","full_name":"Krzewska, Monika","first_name":"Monika"}],"publication":"Protoplasma","fulldoi":"https://doi.org/10.1007/s00709-014-0616-1","file":[{"checksum":"d570a6073765118fc0bb83c31d96fa53","content_type":"application/pdf","relation":"main_file","file_id":"5353","date_updated":"2020-07-14T12:45:27Z","creator":"system","access_level":"open_access","file_size":6377990,"file_name":"IST-2015-394-v1+1_s00709-014-0616-1.pdf","date_created":"2018-12-12T10:18:31Z"}],"page":"1077 - 1087","title":"The influence of heat stress on auxin distribution in transgenic B napus microspores and microspore derived embryos","ddc":["580"],"pubrep_id":"394","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.","issue":"5","file_date_updated":"2020-07-14T12:45:27Z","date_published":"2014-02-20T00:00:00Z","publication_status":"published","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"}],"status":"public","has_accepted_license":"1","isi":1,"article_processing_charge":"No","oa_version":"Published Version","language":[{"iso":"eng"}],"publist_id":"4987","oa":1,"quality_controlled":"1","type":"journal_article","_id":"2059","day":"20","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:55:29Z","intvolume":"       251","month":"02","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"}},{"oa_version":"None","abstract":[{"lang":"eng","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."}],"publication_status":"published","status":"public","date_published":"2014-02-14T00:00:00Z","article_processing_charge":"No","isi":1,"publist_id":"4985","language":[{"iso":"eng"}],"quality_controlled":"1","day":"14","_id":"2061","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2018-12-11T11:55:29Z","month":"02","intvolume":"       251","scopus_import":"1","doi":"10.1007/s00709-014-0620-5","date_updated":"2025-09-29T11:48:32Z","external_id":{"isi":["000340480300012"]},"volume":251,"publisher":"Springer","department":[{"_id":"JiFr"}],"year":"2014","citation":{"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>.","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>","short":"E. Mazur, E. Kurczyñska, J. Friml, Protoplasma 251 (2014) 1125–1139.","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>.","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>","ista":"Mazur E, Kurczyñska E, Friml J. 2014. Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis. Protoplasma. 251(5), 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."},"title":"Cellular events during interfascicular cambium ontogenesis in inflorescence stems of Arabidopsis","page":"1125 - 1139","author":[{"full_name":"Mazur, Ewa","first_name":"Ewa","last_name":"Mazur"},{"full_name":"Kurczyñska, Ewa","first_name":"Ewa","last_name":"Kurczyñska"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří"}],"publication":"Protoplasma","fulldoi":"https://doi.org/10.1007/s00709-014-0620-5","issue":"5"},{"ec_funded":1,"scopus_import":"1","external_id":{"isi":["000339651300036"]},"doi":"10.1126/science.1255263","date_updated":"2025-09-29T11:48:03Z","publisher":"American Association for the Advancement of Science","volume":345,"year":"2014","citation":{"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>.","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>","short":"H. Hu, J. Gan, P.M. Jonas, Science 345 (2014).","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>.","ista":"Hu H, Gan J, Jonas PM. 2014. Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function. Science. 345(6196), 1255263.","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>","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."},"department":[{"_id":"PeJo"}],"publication":"Science","author":[{"first_name":"Hua","full_name":"Hu, Hua","last_name":"Hu","id":"4AC0145C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Gan","id":"3614E438-F248-11E8-B48F-1D18A9856A87","full_name":"Gan, Jian","first_name":"Jian"},{"first_name":"Peter M","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"fulldoi":"https://doi.org/10.1126/science.1255263","project":[{"name":"Mechanisms of transmitter release at GABAergic synapses","grant_number":"P24909-B24","call_identifier":"FWF","_id":"25C26B1E-B435-11E9-9278-68D0E5697425"},{"grant_number":"268548","name":"Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons","_id":"25C0F108-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"file":[{"access_level":"open_access","checksum":"a0036a589037d37e86364fa25cc0a82f","content_type":"application/pdf","file_id":"5185","relation":"main_file","date_updated":"2020-07-14T12:45:27Z","creator":"system","date_created":"2018-12-12T10:16:00Z","file_name":"IST-2017-821-v1+1_1255263JonasPVReviewTextR_Final.pdf","file_size":215514},{"file_size":1732723,"file_name":"IST-2017-821-v1+2_1255263JonasPVReviewFigures_Final.pdf","date_created":"2018-12-12T10:16:01Z","content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:45:27Z","relation":"main_file","file_id":"5186","checksum":"e1f57d2713725449cb898fdcb8ef47b8","access_level":"open_access"}],"title":"Fast-spiking parvalbumin^+ GABAergic interneurons: From cellular design to microcircuit function","ddc":["570"],"pubrep_id":"821","issue":"6196","file_date_updated":"2020-07-14T12:45:27Z","date_published":"2014-08-01T00:00:00Z","has_accepted_license":"1","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"}],"status":"public","publication_status":"published","isi":1,"article_processing_charge":"No","oa_version":"Submitted Version","article_number":"1255263","language":[{"iso":"eng"}],"publist_id":"4984","oa":1,"corr_author":"1","quality_controlled":"1","type":"journal_article","_id":"2062","day":"01","date_created":"2018-12-11T11:55:29Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","intvolume":"       345","month":"08"},{"ec_funded":1,"scopus_import":"1","doi":"10.1007/978-3-319-08867-9_31","date_updated":"2026-04-15T10:02:12Z","publisher":"Springer","volume":8559,"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>.","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>","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.","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>.","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>","ista":"Chatterjee K, Chmelik M, Daca P. 2014. CEGAR for qualitative analysis of probabilistic systems. CAV: Computer Aided Verification, LNCS, vol. 8559, 473–490."},"year":"2014","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"full_name":"Chmelik, Martin","first_name":"Martin","id":"3624234E-F248-11E8-B48F-1D18A9856A87","last_name":"Chmelik"},{"last_name":"Daca","id":"49351290-F248-11E8-B48F-1D18A9856A87","first_name":"Przemyslaw","full_name":"Daca, Przemyslaw"}],"fulldoi":"https://doi.org/10.1007/978-3-319-08867-9_31","conference":{"end_date":"2014-07-22","name":"CAV: Computer Aided Verification","start_date":"2014-07-18","location":"Vienna, Austria"},"project":[{"grant_number":"P 23499-N23","name":"Modern Graph Algorithmic Techniques in Formal Verification","_id":"2584A770-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"S11407","name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","name":"Moderne Concurrency Paradigms","grant_number":"S11402-N23"},{"name":"Quantitative Graph Games: Theory and Applications","grant_number":"279307","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425"},{"name":"Microsoft Research Faculty Fellowship","_id":"2587B514-B435-11E9-9278-68D0E5697425"},{"grant_number":"267989","name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}],"page":"473 - 490","title":"CEGAR for qualitative analysis of probabilistic systems","related_material":{"record":[{"relation":"earlier_version","id":"5412","status":"public"},{"id":"5413","status":"public","relation":"earlier_version"},{"id":"5414","status":"public","relation":"earlier_version"},{"relation":"dissertation_contains","status":"public","id":"1155"}]},"date_published":"2014-07-01T00:00:00Z","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."}],"status":"public","publication_status":"published","oa_version":"None","alternative_title":["LNCS"],"language":[{"iso":"eng"}],"publist_id":"4978","corr_author":"1","quality_controlled":"1","type":"conference","_id":"2063","day":"01","date_created":"2018-12-11T11:55:30Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"      8559","month":"07"},{"publist_id":"4974","language":[{"iso":"eng"}],"oa_version":"Submitted Version","abstract":[{"lang":"eng","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."}],"status":"public","publication_status":"published","date_published":"2014-07-29T00:00:00Z","article_processing_charge":"No","isi":1,"date_created":"2018-12-11T11:55:30Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","month":"07","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4198489/","open_access":"1"}],"intvolume":"       522","quality_controlled":"1","_id":"2064","day":"29","type":"journal_article","oa":1,"publisher":"Wiley-Blackwell","volume":522,"department":[{"_id":"RySh"}],"year":"2014","citation":{"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>.","short":"M. Rubio, Y. Fukazawa, N. Kamasawa, C. Clarkson, E. Molnár, R. Shigemoto, Journal of Comparative Neurology 522 (2014) 4023–4042.","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>","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.","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>.","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>","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."},"scopus_import":"1","doi":"10.1002/cne.23654","date_updated":"2025-09-29T11:47:23Z","external_id":{"isi":["000343973100005"]},"acknowledgement":"National Institutes of Health (NIH) Grant Number: 1R01DC013048‐0; Biotechnology and Biological Sciences Research Council, UK Grant Number: BB/J015938/1\r\n","issue":"18","title":"Target- and input-dependent organization of AMPA and NMDA receptors in synaptic connections of the cochlear nucleus","page":"4023 - 4042","author":[{"first_name":"Maía","full_name":"Rubio, Maía","last_name":"Rubio"},{"full_name":"Fukazawa, Yugo","first_name":"Yugo","last_name":"Fukazawa"},{"last_name":"Kamasawa","first_name":"Naomi","full_name":"Kamasawa, Naomi"},{"first_name":"Cheryl","full_name":"Clarkson, Cheryl","last_name":"Clarkson"},{"last_name":"Molnár","first_name":"Elek","full_name":"Molnár, Elek"},{"full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","orcid":"0000-0001-8761-9444","last_name":"Shigemoto","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"}],"publication":"Journal of Comparative Neurology","fulldoi":"https://doi.org/10.1002/cne.23654"},{"publist_id":"4958","article_type":"original","language":[{"iso":"eng"}],"article_number":"96","article_processing_charge":"No","status":"public","abstract":[{"lang":"eng","text":"Spinning tops and yo-yos have long fascinated cultures around the world with their unexpected, graceful motions that seemingly elude gravity. We present an algorithm to generate designs for spinning objects by optimizing rotational dynamics properties. As input, the user provides a solid 3D model and a desired axis of rotation. Our approach then modifies the mass distribution such that the principal directions of the moment of inertia align with the target rotation frame. We augment the model by creating voids inside its volume, with interior fill represented by an adaptive multi-resolution vox-elization. The discrete voxel fill values are optimized using a continuous, nonlinear formulation. Further, we optimize for rotational stability by maximizing the dominant principal moment. We extend our technique to incorporate deformation and multiple materials for cases where internal voids alone are insufficient. Our method is well-suited for a variety of 3D printed models, ranging from characters to abstract shapes. We demonstrate tops and yo-yos that spin surprisingly stably despite their asymmetric appearance. "}],"publication_status":"published","date_published":"2014-07-01T00:00:00Z","extern":"1","oa_version":"None","month":"07","intvolume":"        33","date_created":"2018-12-11T11:55:35Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"2080","type":"journal_article","day":"01","quality_controlled":"1","citation":{"mla":"Bächer, Moritz, et al. “Spin-It: Optimizing Moment of Inertia for Spinnable Objects.” <i>ACM Transactions on Graphics</i>, vol. 33, no. 4, 96, ACM, 2014, doi:<a href=\"https://doi.org/10.1145/2601097.2601157\">10.1145/2601097.2601157</a>.","short":"M. Bächer, E. Whiting, B. Bickel, O. Sorkine Hornung, ACM Transactions on Graphics 33 (2014).","apa":"Bächer, M., Whiting, E., Bickel, B., &#38; Sorkine Hornung, O. (2014). Spin-It: Optimizing moment of inertia for spinnable objects. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/2601097.2601157\">https://doi.org/10.1145/2601097.2601157</a>","ieee":"M. Bächer, E. Whiting, B. Bickel, and O. Sorkine Hornung, “Spin-It: Optimizing moment of inertia for spinnable objects,” <i>ACM Transactions on Graphics</i>, vol. 33, no. 4. ACM, 2014.","chicago":"Bächer, Moritz, Emily Whiting, Bernd Bickel, and Olga Sorkine Hornung. “Spin-It: Optimizing Moment of Inertia for Spinnable Objects.” <i>ACM Transactions on Graphics</i>. ACM, 2014. <a href=\"https://doi.org/10.1145/2601097.2601157\">https://doi.org/10.1145/2601097.2601157</a>.","ista":"Bächer M, Whiting E, Bickel B, Sorkine Hornung O. 2014. Spin-It: Optimizing moment of inertia for spinnable objects. ACM Transactions on Graphics. 33(4), 96.","ama":"Bächer M, Whiting E, Bickel B, Sorkine Hornung O. Spin-It: Optimizing moment of inertia for spinnable objects. <i>ACM Transactions on Graphics</i>. 2014;33(4). doi:<a href=\"https://doi.org/10.1145/2601097.2601157\">10.1145/2601097.2601157</a>"},"year":"2014","volume":33,"publisher":"ACM","doi":"10.1145/2601097.2601157","date_updated":"2025-08-05T14:20:24Z","scopus_import":"1","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"related_material":{"record":[{"id":"452","status":"public","relation":"later_version"}]},"issue":"4","acknowledgement":"This project was supported in part by the ERC Starting Grant iModel (StG-2012-306877). Emily Whiting is supported by the ETH Zurich / Marie Curie COFUND Postdoctoral Fellowship.","fulldoi":"https://doi.org/10.1145/2601097.2601157","author":[{"first_name":"Moritz","full_name":"Bächer, Moritz","last_name":"Bächer"},{"last_name":"Whiting","first_name":"Emily","full_name":"Whiting, Emily"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd","last_name":"Bickel","id":"49876194-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sorkine Hornung, Olga","first_name":"Olga","last_name":"Sorkine Hornung"}],"publication":"ACM Transactions on Graphics","title":"Spin-It: Optimizing moment of inertia for spinnable objects"},{"issue":"4","acknowledgement":"This work was partly funded by the NCCR Co-Me of the Swiss NSF.","intvolume":"        33","month":"07","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2018-12-11T11:55:36Z","day":"01","_id":"2081","type":"conference","title":"Designing inflatable structures","conference":{"name":"SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques"},"fulldoi":"https://doi.org/10.1145/2601097.2601166","author":[{"last_name":"Skouras","full_name":"Skouras, Mélina","first_name":"Mélina"},{"last_name":"Thomaszewski","first_name":"Bernhard","full_name":"Thomaszewski, Bernhard"},{"full_name":"Kaufmann, Peter","first_name":"Peter","last_name":"Kaufmann"},{"first_name":"Akash","full_name":"Garg, Akash","last_name":"Garg"},{"id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","first_name":"Bernd"},{"last_name":"Grinspun","full_name":"Grinspun, Eitan","first_name":"Eitan"},{"first_name":"Markus","full_name":"Gross, Markus","last_name":"Gross"}],"language":[{"iso":"eng"}],"publist_id":"4957","article_number":"63","citation":{"mla":"Skouras, Mélina, et al. <i>Designing Inflatable Structures</i>. Vol. 33, no. 4, 63, ACM, 2014, doi:<a href=\"https://doi.org/10.1145/2601097.2601166\">10.1145/2601097.2601166</a>.","apa":"Skouras, M., Thomaszewski, B., Kaufmann, P., Garg, A., Bickel, B., Grinspun, E., &#38; Gross, M. (2014). Designing inflatable structures (Vol. 33). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM. <a href=\"https://doi.org/10.1145/2601097.2601166\">https://doi.org/10.1145/2601097.2601166</a>","short":"M. Skouras, B. Thomaszewski, P. Kaufmann, A. Garg, B. Bickel, E. Grinspun, M. Gross, in:, ACM, 2014.","chicago":"Skouras, Mélina, Bernhard Thomaszewski, Peter Kaufmann, Akash Garg, Bernd Bickel, Eitan Grinspun, and Markus Gross. “Designing Inflatable Structures,” Vol. 33. ACM, 2014. <a href=\"https://doi.org/10.1145/2601097.2601166\">https://doi.org/10.1145/2601097.2601166</a>.","ama":"Skouras M, Thomaszewski B, Kaufmann P, et al. Designing inflatable structures. In: Vol 33. ACM; 2014. doi:<a href=\"https://doi.org/10.1145/2601097.2601166\">10.1145/2601097.2601166</a>","ista":"Skouras M, Thomaszewski B, Kaufmann P, Garg A, Bickel B, Grinspun E, Gross M. 2014. Designing inflatable structures. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 33, 63.","ieee":"M. Skouras <i>et al.</i>, “Designing inflatable structures,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, 2014, vol. 33, no. 4."},"year":"2014","volume":33,"publisher":"ACM","extern":"1","doi":"10.1145/2601097.2601166","date_updated":"2021-01-12T06:55:11Z","oa_version":"None","date_published":"2014-07-01T00:00:00Z","publication_status":"published","status":"public","abstract":[{"text":"We propose an interactive, optimization-in-the-loop tool for designing inflatable structures. Given a target shape, the user draws a network of seams defining desired segment boundaries in 3D. Our method computes optimally-shaped flat panels for the segments, such that the inflated structure is as close as possible to the target while satisfying the desired seam positions. Our approach is underpinned by physics-based pattern optimization, accurate coarse-scale simulation using tension field theory, and a specialized constraint-optimization method. Our system is fast enough to warrant interactive exploration of different seam layouts, including internal connections, and their effects on the inflated shape. We demonstrate the resulting design process on a varied set of simulation examples, some of which we have fabricated, demonstrating excellent agreement with the design intent.","lang":"eng"}]},{"arxiv":1,"intvolume":"       111","month":"12","main_file_link":[{"url":"https://www.pnas.org/content/111/50/17869","open_access":"1"}],"keyword":["multidisciplinary"],"date_created":"2021-11-29T13:09:53Z","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"10382","type":"journal_article","day":"01","quality_controlled":"1","oa":1,"language":[{"iso":"eng"}],"article_type":"original","extern":"1","oa_version":"Published Version","article_processing_charge":"No","date_published":"2014-12-01T00:00:00Z","publication_status":"published","status":"public","abstract":[{"text":"Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory.","lang":"eng"}],"issue":"50","acknowledgement":"We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758.","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"page":"17869-17874","title":"Crucial role of nonspecific interactions in amyloid nucleation","fulldoi":"https://doi.org/10.1073/pnas.1410159111","author":[{"id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","orcid":"0000-0002-7854-2139","first_name":"Anđela","full_name":"Šarić, Anđela"},{"full_name":"Chebaro, Yassmine C.","first_name":"Yassmine C.","last_name":"Chebaro"},{"first_name":"Tuomas P. J.","full_name":"Knowles, Tuomas P. J.","last_name":"Knowles"},{"last_name":"Frenkel","full_name":"Frenkel, Daan","first_name":"Daan"}],"publication":"Proceedings of the National Academy of Sciences","citation":{"apa":"Šarić, A., Chebaro, Y. C., Knowles, T. P. J., &#38; Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>","short":"A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874.","mla":"Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>.","ama":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. <i>Proceedings of the National Academy of Sciences</i>. 2014;111(50):17869-17874. doi:<a href=\"https://doi.org/10.1073/pnas.1410159111\">10.1073/pnas.1410159111</a>","ista":"Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874.","chicago":"Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” <i>Proceedings of the National Academy of Sciences</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1410159111\">https://doi.org/10.1073/pnas.1410159111</a>.","ieee":"A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” <i>Proceedings of the National Academy of Sciences</i>, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014."},"year":"2014","publisher":"National Academy of Sciences","volume":111,"external_id":{"pmid":["25453085"],"arxiv":["1412.0897"]},"pmid":1,"date_updated":"2021-11-29T13:29:05Z","doi":"10.1073/pnas.1410159111","scopus_import":"1"},{"_id":"10383","type":"journal_article","day":"06","quality_controlled":"1","oa":1,"arxiv":1,"intvolume":"        89","month":"05","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1310.0826"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_created":"2021-11-29T13:10:33Z","extern":"1","oa_version":"Preprint","article_processing_charge":"No","date_published":"2014-05-06T00:00:00Z","status":"public","abstract":[{"text":"We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles.","lang":"eng"}],"publication_status":"published","language":[{"iso":"eng"}],"article_type":"original","article_number":"052303","title":"Anomalous thermomechanical properties of a self-propelled colloidal fluid","fulldoi":"https://doi.org/10.1103/physreve.89.052303","author":[{"last_name":"Mallory","first_name":"S. A.","full_name":"Mallory, S. A."},{"first_name":"Anđela","orcid":"0000-0002-7854-2139","full_name":"Šarić, Anđela","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić"},{"last_name":"Valeriani","full_name":"Valeriani, C.","first_name":"C."},{"last_name":"Cacciuto","first_name":"A.","full_name":"Cacciuto, A."}],"publication":"Physical Review E","issue":"5","publication_identifier":{"eissn":["1550-2376"],"issn":["1539-3755"]},"external_id":{"pmid":["25353796"],"arxiv":["1310.0826"]},"pmid":1,"date_updated":"2021-11-29T13:29:01Z","doi":"10.1103/physreve.89.052303","scopus_import":"1","year":"2014","citation":{"ieee":"S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical properties of a self-propelled colloidal fluid,” <i>Physical Review E</i>, vol. 89, no. 5. American Physical Society, 2014.","chicago":"Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.89.052303\">https://doi.org/10.1103/physreve.89.052303</a>.","ista":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303.","ama":"Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. <i>Physical Review E</i>. 2014;89(5). doi:<a href=\"https://doi.org/10.1103/physreve.89.052303\">10.1103/physreve.89.052303</a>","mla":"Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” <i>Physical Review E</i>, vol. 89, no. 5, 052303, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.89.052303\">10.1103/physreve.89.052303</a>.","apa":"Mallory, S. A., Šarić, A., Valeriani, C., &#38; Cacciuto, A. (2014). Anomalous thermomechanical properties of a self-propelled colloidal fluid. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.89.052303\">https://doi.org/10.1103/physreve.89.052303</a>","short":"S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014)."},"volume":89,"publisher":"American Physical Society"},{"_id":"10793","type":"conference","day":"01","quality_controlled":"1","oa":1,"OA_type":"green","arxiv":1,"month":"01","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.1305.4519","open_access":"1"}],"intvolume":"      8871","date_created":"2022-02-25T10:32:14Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","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."}],"status":"public","date_published":"2014-01-01T00:00:00Z","language":[{"iso":"eng"}],"alternative_title":["LNCS"],"title":"Clustered planarity testing revisited","page":"428-436","fulldoi":"https://doi.org/10.1007/978-3-662-45803-7_36","publication":"International Symposium on Graph Drawing","author":[{"full_name":"Fulek, Radoslav","first_name":"Radoslav","orcid":"0000-0001-8485-1774","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kynčl, Jan","first_name":"Jan","last_name":"Kynčl"},{"last_name":"Malinović","first_name":"Igor","full_name":"Malinović, Igor"},{"last_name":"Pálvölgyi","first_name":"Dömötör","full_name":"Pálvölgyi, Dömötör"}],"place":"Cham","publication_identifier":{"issn":["0302-9743"]},"related_material":{"record":[{"relation":"later_version","id":"1642","status":"public"}]},"date_updated":"2025-06-26T07:57:46Z","doi":"10.1007/978-3-662-45803-7_36","external_id":{"arxiv":["1305.4519"]},"scopus_import":"1","OA_place":"repository","department":[{"_id":"UlWa"}],"citation":{"ista":"Fulek R, Kynčl J, Malinović I, Pálvölgyi D. 2014. Clustered planarity testing revisited. International Symposium on Graph Drawing. , LNCS, vol. 8871, 428–436.","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>","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>.","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.","short":"R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436.","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>","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>."},"year":"2014","publisher":"Springer Nature","volume":8871},{"citation":{"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>","ista":"Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant Development 1st ed., Vienna: Springer Nature, 444p.","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>.","ieee":"E. Zažímalová, J. Petrášek, and E. Benková, Eds., <i>Auxin and Its Role in Plant Development</i>, 1st ed. Vienna: Springer Nature, 2014.","short":"E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant Development, 1st ed., Springer Nature, Vienna, 2014.","apa":"Zažímalová, E., Petrášek, J., &#38; Benková, E. (Eds.). (2014). <i>Auxin and Its Role in Plant Development</i> (1st ed.). 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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."}],"status":"public","publication_status":"published","date_updated":"2022-03-04T07:38:15Z","doi":"10.1007/978-3-7091-1526-8","oa_version":"None","scopus_import":"1","month":"04","publication_identifier":{"eisbn":["9783709115268"],"isbn":["9783709115251"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2022-03-03T11:52:44Z","place":"Vienna","fulldoi":"https://doi.org/10.1007/978-3-7091-1526-8","edition":"1","_id":"10811","type":"book_editor","day":"01","quality_controlled":"1","page":"444","title":"Auxin and Its Role in Plant Development"},{"publication_identifier":{"issn":["0012-0456"],"eissn":["1869-7135"]},"title":"The excitation spectrum for Bose fluids with weak interactions","page":"21-41","fulldoi":"https://doi.org/10.1365/s13291-014-0083-9","publication":"Jahresbericht der Deutschen Mathematiker-Vereinigung","author":[{"full_name":"Seiringer, Robert","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer"}],"department":[{"_id":"RoSe"}],"year":"2014","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>.","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>","ista":"Seiringer R. 2014. The excitation spectrum for Bose fluids with weak interactions. Jahresbericht der Deutschen Mathematiker-Vereinigung. 116, 21–41.","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.","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>.","short":"R. Seiringer, Jahresbericht Der Deutschen Mathematiker-Vereinigung 116 (2014) 21–41.","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>"},"publisher":"Springer Nature","volume":116,"doi":"10.1365/s13291-014-0083-9","date_updated":"2024-10-09T21:01:45Z","scopus_import":"1","month":"03","intvolume":"       116","date_created":"2022-03-04T07:54:39Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","keyword":["General Medicine"],"day":"01","_id":"10814","type":"journal_article","quality_controlled":"1","corr_author":"1","article_type":"original","language":[{"iso":"eng"}],"oa_version":"None","article_processing_charge":"No","status":"public","abstract":[{"lang":"eng","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."}],"publication_status":"published","date_published":"2014-03-01T00:00:00Z"},{"publication_status":"published","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."}],"status":"public","date_published":"2014-02-01T00:00:00Z","article_processing_charge":"No","isi":1,"oa_version":"None","language":[{"iso":"eng"}],"article_type":"original","oa":1,"quality_controlled":"1","_id":"10815","day":"01","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","date_created":"2022-03-04T08:17:25Z","keyword":["Developmental Biology","Embryology","General Medicine","Pediatrics","Perinatology","and Child Health"],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1111/cga.12039"}],"month":"02","intvolume":"        54","scopus_import":"1","doi":"10.1111/cga.12039","date_updated":"2025-09-29T13:21:58Z","external_id":{"isi":["000331769200001"],"pmid":["24666178"]},"pmid":1,"publisher":"Wiley","volume":54,"department":[{"_id":"CaHe"}],"year":"2014","citation":{"ieee":"M. Hashimoto, H. Morita, and N. 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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>.","short":"M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7.","apa":"Hashimoto, M., Morita, H., &#38; Ueno, N. (2014). Molecular and cellular mechanisms of development underlying congenital diseases. <i>Congenital Anomalies</i>. 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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.","issue":"1"},{"intvolume":"         9","month":"12","date_created":"2020-03-21T16:08:18Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"oa":1,"day":"11","_id":"7598","type":"journal_article","quality_controlled":"1","article_type":"original","language":[{"iso":"eng"}],"article_processing_charge":"No","date_published":"2014-12-11T00:00:00Z","status":"public","publication_status":"published","has_accepted_license":"1","extern":"1","oa_version":"Published Version","publication_identifier":{"issn":["2211-1247"]},"issue":"5","file_date_updated":"2020-07-14T12:48:01Z","ddc":["580"],"fulldoi":"https://doi.org/10.1016/j.celrep.2014.10.047","file":[{"file_size":2755808,"file_name":"2014_CellPress_Tan.pdf","date_created":"2020-03-23T12:23:40Z","checksum":"23c30de4ac98ce9879fc054121517626","content_type":"application/pdf","creator":"dernst","relation":"main_file","date_updated":"2020-07-14T12:48:01Z","file_id":"7613","access_level":"open_access"}],"author":[{"full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","first_name":"Shutang","id":"2DE75584-F248-11E8-B48F-1D18A9856A87","last_name":"Tan"},{"full_name":"Xue, Hong-Wei","first_name":"Hong-Wei","last_name":"Xue"}],"publication":"Cell Reports","page":"1692-1702","title":"Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5","citation":{"short":"S. Tan, H.-W. Xue, Cell Reports 9 (2014) 1692–1702.","apa":"Tan, S., &#38; Xue, H.-W. (2014). Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2014.10.047\">https://doi.org/10.1016/j.celrep.2014.10.047</a>","mla":"Tan, Shutang, and Hong-Wei Xue. “Casein Kinase 1 Regulates Ethylene Synthesis by Phosphorylating and Promoting the Turnover of ACS5.” <i>Cell Reports</i>, vol. 9, no. 5, Elsevier, 2014, pp. 1692–702, doi:<a href=\"https://doi.org/10.1016/j.celrep.2014.10.047\">10.1016/j.celrep.2014.10.047</a>.","ieee":"S. Tan and H.-W. Xue, “Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5,” <i>Cell Reports</i>, vol. 9, no. 5. Elsevier, pp. 1692–1702, 2014.","ama":"Tan S, Xue H-W. Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5. <i>Cell Reports</i>. 2014;9(5):1692-1702. doi:<a href=\"https://doi.org/10.1016/j.celrep.2014.10.047\">10.1016/j.celrep.2014.10.047</a>","ista":"Tan S, Xue H-W. 2014. Casein kinase 1 regulates ethylene synthesis by phosphorylating and promoting the turnover of ACS5. Cell Reports. 9(5), 1692–1702.","chicago":"Tan, Shutang, and Hong-Wei Xue. “Casein Kinase 1 Regulates Ethylene Synthesis by Phosphorylating and Promoting the Turnover of ACS5.” <i>Cell Reports</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.celrep.2014.10.047\">https://doi.org/10.1016/j.celrep.2014.10.047</a>."},"year":"2014","volume":9,"publisher":"Elsevier","doi":"10.1016/j.celrep.2014.10.047","date_updated":"2021-01-12T08:14:24Z"},{"volume":28,"publisher":"Elsevier","citation":{"short":"L.B. Sweeney, D.B. Kelley, Current Opinion in Neurobiology 28 (2014) 34–41.","apa":"Sweeney, L. B., &#38; Kelley, D. B. (2014). Harnessing vocal patterns for social communication. <i>Current Opinion in Neurobiology</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.conb.2014.06.006\">https://doi.org/10.1016/j.conb.2014.06.006</a>","mla":"Sweeney, Lora B., and Darcy B. Kelley. “Harnessing Vocal Patterns for Social Communication.” <i>Current Opinion in Neurobiology</i>, vol. 28, no. 10, Elsevier, 2014, pp. 34–41, doi:<a href=\"https://doi.org/10.1016/j.conb.2014.06.006\">10.1016/j.conb.2014.06.006</a>.","ama":"Sweeney LB, Kelley DB. Harnessing vocal patterns for social communication. <i>Current Opinion in Neurobiology</i>. 2014;28(10):34-41. doi:<a href=\"https://doi.org/10.1016/j.conb.2014.06.006\">10.1016/j.conb.2014.06.006</a>","ista":"Sweeney LB, Kelley DB. 2014. Harnessing vocal patterns for social communication. Current Opinion in Neurobiology. 28(10), 34–41.","chicago":"Sweeney, Lora B., and Darcy B Kelley. “Harnessing Vocal Patterns for Social Communication.” <i>Current Opinion in Neurobiology</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.conb.2014.06.006\">https://doi.org/10.1016/j.conb.2014.06.006</a>.","ieee":"L. B. Sweeney and D. B. Kelley, “Harnessing vocal patterns for social communication,” <i>Current Opinion in Neurobiology</i>, vol. 28, no. 10. 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Understanding the genetic architecture of phenotype across environments will require statistical tests that can describe both changes in genetic variance and covariance across environments. This chapter outlines the theoretical framework for the processes of sexual selection in the wild, identifying key parameters in wild systems, and highlighting the potential effects of the environment. It describes the proposed approaches for the estimation of these key parameters in a quantitative genetic framework within naturally occurring pedigreed populations. The chapter provides a worked example for a range of analysis methods. It aims to provide an overview of the analytical methods that can be used to model GEIs for traits involved in sexual selection in naturally occurring pedigreed populations.","lang":"eng"}],"publication_status":"published","date_published":"2014-08-29T00:00:00Z","article_processing_charge":"No","oa_version":"None","extern":"1","date_updated":"2021-01-12T08:15:13Z","doi":"10.1002/9781118912591.ch6","publisher":"Wiley","editor":[{"first_name":"John","full_name":"Hunt, John","last_name":"Hunt"},{"full_name":"Hosken, David","first_name":"David","last_name":"Hosken"}],"year":"2014","citation":{"apa":"Robinson, M. R., &#38; Qvarnström, A. (2014). Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations. In J. Hunt &#38; D. Hosken (Eds.), <i>Genotype-by-Environment Interactions and Sexual Selection</i> (pp. 137–168). Chichester, UK: Wiley. <a href=\"https://doi.org/10.1002/9781118912591.ch6\">https://doi.org/10.1002/9781118912591.ch6</a>","short":"M.R. Robinson, A. Qvarnström, in:, J. Hunt, D. Hosken (Eds.), Genotype-by-Environment Interactions and Sexual Selection, Wiley, Chichester, UK, 2014, pp. 137–168.","mla":"Robinson, Matthew Richard, and Anna Qvarnström. “Influence of the Environment on the Genetic Architecture of Traits Involved in Sexual Selection within Wild Populations.” <i>Genotype-by-Environment Interactions and Sexual Selection</i>, edited by John Hunt and David Hosken, Wiley, 2014, pp. 137–68, doi:<a href=\"https://doi.org/10.1002/9781118912591.ch6\">10.1002/9781118912591.ch6</a>.","ieee":"M. R. Robinson and A. Qvarnström, “Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations,” in <i>Genotype-by-Environment Interactions and Sexual Selection</i>, J. Hunt and D. Hosken, Eds. Chichester, UK: Wiley, 2014, pp. 137–168.","ama":"Robinson MR, Qvarnström A. Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations. In: Hunt J, Hosken D, eds. <i>Genotype-by-Environment Interactions and Sexual Selection</i>. Chichester, UK: Wiley; 2014:137-168. doi:<a href=\"https://doi.org/10.1002/9781118912591.ch6\">10.1002/9781118912591.ch6</a>","ista":"Robinson MR, Qvarnström A. 2014.Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations. In: Genotype-by-Environment Interactions and Sexual Selection. , 137–168.","chicago":"Robinson, Matthew Richard, and Anna Qvarnström. “Influence of the Environment on the Genetic Architecture of Traits Involved in Sexual Selection within Wild Populations.” In <i>Genotype-by-Environment Interactions and Sexual Selection</i>, edited by John Hunt and David Hosken, 137–68. Chichester, UK: Wiley, 2014. <a href=\"https://doi.org/10.1002/9781118912591.ch6\">https://doi.org/10.1002/9781118912591.ch6</a>."},"language":[{"iso":"eng"}],"author":[{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"last_name":"Qvarnström","first_name":"Anna","full_name":"Qvarnström, Anna"}],"publication":"Genotype-by-Environment Interactions and Sexual Selection","fulldoi":"https://doi.org/10.1002/9781118912591.ch6","title":"Influence of the environment on the genetic architecture of traits involved in sexual selection within wild populations","page":"137-168","quality_controlled":"1","type":"book_chapter","_id":"7743","day":"29","date_created":"2020-04-30T10:58:39Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","publication_identifier":{"isbn":["9780470671795"],"eisbn":["9781118912591"]},"place":"Chichester, UK"},{"citation":{"apa":"Robinson, M. R., Wray, N. R., &#38; Visscher, P. M. (2014). Explaining additional genetic variation in complex traits. <i>Trends in Genetics</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">https://doi.org/10.1016/j.tig.2014.02.003</a>","short":"M.R. Robinson, N.R. Wray, P.M. Visscher, Trends in Genetics 30 (2014) 124–132.","mla":"Robinson, Matthew Richard, et al. “Explaining Additional Genetic Variation in Complex Traits.” <i>Trends in Genetics</i>, vol. 30, no. 4, Elsevier, 2014, pp. 124–32, doi:<a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">10.1016/j.tig.2014.02.003</a>.","ama":"Robinson MR, Wray NR, Visscher PM. Explaining additional genetic variation in complex traits. <i>Trends in Genetics</i>. 2014;30(4):124-132. doi:<a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">10.1016/j.tig.2014.02.003</a>","ista":"Robinson MR, Wray NR, Visscher PM. 2014. Explaining additional genetic variation in complex traits. Trends in Genetics. 30(4), 124–132.","chicago":"Robinson, Matthew Richard, Naomi R. Wray, and Peter M. Visscher. “Explaining Additional Genetic Variation in Complex Traits.” <i>Trends in Genetics</i>. Elsevier, 2014. <a href=\"https://doi.org/10.1016/j.tig.2014.02.003\">https://doi.org/10.1016/j.tig.2014.02.003</a>.","ieee":"M. R. Robinson, N. R. Wray, and P. M. Visscher, “Explaining additional genetic variation in complex traits,” <i>Trends in Genetics</i>, vol. 30, no. 4. Elsevier, pp. 124–132, 2014."},"year":"2014","publisher":"Elsevier","volume":30,"language":[{"iso":"eng"}],"article_type":"original","article_processing_charge":"No","date_published":"2014-04-01T00:00:00Z","publication_status":"published","status":"public","extern":"1","doi":"10.1016/j.tig.2014.02.003","date_updated":"2021-01-12T08:15:14Z","oa_version":"None","intvolume":"        30","publication_identifier":{"issn":["0168-9525"]},"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-30T10:58:58Z","issue":"4","fulldoi":"https://doi.org/10.1016/j.tig.2014.02.003","publication":"Trends in Genetics","author":[{"first_name":"Matthew Richard","orcid":"0000-0001-8982-8813","full_name":"Robinson, Matthew Richard","last_name":"Robinson","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"last_name":"Wray","full_name":"Wray, Naomi R.","first_name":"Naomi R."},{"last_name":"Visscher","first_name":"Peter M.","full_name":"Visscher, Peter M."}],"day":"01","_id":"7744","type":"journal_article","page":"124-132","quality_controlled":"1","title":"Explaining additional genetic variation in complex traits"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-30T11:41:54Z","publication_identifier":{"issn":["1539-3755","1550-2376"]},"month":"12","intvolume":"        90","issue":"6","publication":"Physical Review E","author":[{"last_name":"Lohr","full_name":"Lohr, Matthew A.","first_name":"Matthew A."},{"full_name":"Still, Tim","first_name":"Tim","last_name":"Still"},{"last_name":"Ganti","full_name":"Ganti, Raman","first_name":"Raman"},{"last_name":"Gratale","first_name":"Matthew D.","full_name":"Gratale, Matthew D."},{"first_name":"Zoey S.","full_name":"Davidson, Zoey S.","last_name":"Davidson"},{"first_name":"Kevin B.","full_name":"Aptowicz, Kevin B.","last_name":"Aptowicz"},{"last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","full_name":"Goodrich, Carl Peter","first_name":"Carl Peter","orcid":"0000-0002-1307-5074"},{"full_name":"Sussman, Daniel M.","first_name":"Daniel M.","last_name":"Sussman"},{"last_name":"Yodh","first_name":"A. G.","full_name":"Yodh, A. G."}],"fulldoi":"https://doi.org/10.1103/physreve.90.062305","title":"Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings","quality_controlled":"1","_id":"7768","type":"journal_article","day":"05","volume":90,"publisher":"American Physical Society","year":"2014","citation":{"ieee":"M. A. Lohr <i>et al.</i>, “Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings,” <i>Physical Review E</i>, vol. 90, no. 6. American Physical Society, 2014.","chicago":"Lohr, Matthew A., Tim Still, Raman Ganti, Matthew D. Gratale, Zoey S. Davidson, Kevin B. Aptowicz, Carl Peter Goodrich, Daniel M. Sussman, and A. G. Yodh. “Vibrational and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.90.062305\">https://doi.org/10.1103/physreve.90.062305</a>.","ista":"Lohr MA, Still T, Ganti R, Gratale MD, Davidson ZS, Aptowicz KB, Goodrich CP, Sussman DM, Yodh AG. 2014. Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. Physical Review E. 90(6), 062305.","ama":"Lohr MA, Still T, Ganti R, et al. Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. <i>Physical Review E</i>. 2014;90(6). doi:<a href=\"https://doi.org/10.1103/physreve.90.062305\">10.1103/physreve.90.062305</a>","mla":"Lohr, Matthew A., et al. “Vibrational and Structural Signatures of the Crossover between Dense Glassy and Sparse Gel-like Attractive Colloidal Packings.” <i>Physical Review E</i>, vol. 90, no. 6, 062305, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.90.062305\">10.1103/physreve.90.062305</a>.","short":"M.A. Lohr, T. Still, R. Ganti, M.D. Gratale, Z.S. Davidson, K.B. Aptowicz, C.P. Goodrich, D.M. Sussman, A.G. Yodh, Physical Review E 90 (2014).","apa":"Lohr, M. A., Still, T., Ganti, R., Gratale, M. D., Davidson, Z. S., Aptowicz, K. B., … Yodh, A. G. (2014). Vibrational and structural signatures of the crossover between dense glassy and sparse gel-like attractive colloidal packings. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.90.062305\">https://doi.org/10.1103/physreve.90.062305</a>"},"article_number":"062305","language":[{"iso":"eng"}],"article_type":"original","publication_status":"published","abstract":[{"lang":"eng","text":"We investigate the vibrational modes of quasi-two-dimensional disordered colloidal packings of hard colloidal spheres with short-range attractions as a function of packing fraction. Certain properties of the vibrational density of states (vDOS) are shown to correlate with the density and structure of the samples (i.e., in sparsely versus densely packed samples). Specifically, a crossover from dense glassy to sparse gel-like states is suggested by an excess of phonon modes at low frequency and by a variation in the slope of the vDOS with frequency at low frequency. This change in phonon mode distribution is demonstrated to arise largely from localized vibrations that involve individual and/or small clusters of particles with few local bonds. Conventional order parameters and void statistics did not exhibit obvious gel-glass signatures as a function of volume fraction. These mode behaviors and accompanying structural insights offer a potentially new set of indicators for identification of glass-gel transitions and for assignment of gel-like versus glass-like character to a disordered solid material."}],"status":"public","date_published":"2014-12-05T00:00:00Z","article_processing_charge":"No","oa_version":"None","doi":"10.1103/physreve.90.062305","date_updated":"2021-01-12T08:15:24Z","extern":"1"},{"year":"2014","citation":{"short":"C.P. Goodrich, S. Dagois-Bohy, B.P. Tighe, M. van Hecke, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014).","apa":"Goodrich, C. P., Dagois-Bohy, S., Tighe, B. P., van Hecke, M., Liu, A. J., &#38; Nagel, S. R. (2014). Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.90.022138\">https://doi.org/10.1103/physreve.90.022138</a>","mla":"Goodrich, Carl Peter, et al. “Jamming in Finite Systems: Stability, Anisotropy, Fluctuations, and Scaling.” <i>Physical Review E</i>, vol. 90, no. 2, 022138, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.90.022138\">10.1103/physreve.90.022138</a>.","ama":"Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. <i>Physical Review E</i>. 2014;90(2). doi:<a href=\"https://doi.org/10.1103/physreve.90.022138\">10.1103/physreve.90.022138</a>","ista":"Goodrich CP, Dagois-Bohy S, Tighe BP, van Hecke M, Liu AJ, Nagel SR. 2014. Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling. Physical Review E. 90(2), 022138.","chicago":"Goodrich, Carl Peter, Simon Dagois-Bohy, Brian P. Tighe, Martin van Hecke, Andrea J. Liu, and Sidney R. Nagel. “Jamming in Finite Systems: Stability, Anisotropy, Fluctuations, and Scaling.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.90.022138\">https://doi.org/10.1103/physreve.90.022138</a>.","ieee":"C. P. Goodrich, S. Dagois-Bohy, B. P. Tighe, M. van Hecke, A. J. Liu, and S. R. Nagel, “Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling,” <i>Physical Review E</i>, vol. 90, no. 2. American Physical Society, 2014."},"publisher":"American Physical Society","volume":90,"language":[{"iso":"eng"}],"article_type":"original","article_number":"022138","article_processing_charge":"No","date_published":"2014-08-27T00:00:00Z","publication_status":"published","status":"public","abstract":[{"text":"Athermal packings of soft repulsive spheres exhibit a sharp jamming transition in the thermodynamic limit. Upon further compression, various structural and mechanical properties display clean power-law behavior over many decades in pressure. As with any phase transition, the rounding of such behavior in finite systems close to the transition plays an important role in understanding the nature of the transition itself. The situation for jamming is surprisingly rich: the assumption that jammed packings are isotropic is only strictly true in the large-size limit, and finite-size has a profound effect on the very meaning of jamming. Here, we provide a comprehensive numerical study of finite-size effects in sphere packings above the jamming transition, focusing on stability as well as the scaling of the contact number and the elastic response.","lang":"eng"}],"extern":"1","date_updated":"2021-01-12T08:15:24Z","doi":"10.1103/physreve.90.022138","oa_version":"None","intvolume":"        90","publication_identifier":{"issn":["1539-3755","1550-2376"]},"month":"08","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-30T11:42:09Z","issue":"2","fulldoi":"https://doi.org/10.1103/physreve.90.022138","author":[{"id":"EB352CD2-F68A-11E9-89C5-A432E6697425","last_name":"Goodrich","full_name":"Goodrich, Carl Peter","orcid":"0000-0002-1307-5074","first_name":"Carl Peter"},{"full_name":"Dagois-Bohy, Simon","first_name":"Simon","last_name":"Dagois-Bohy"},{"full_name":"Tighe, Brian P.","first_name":"Brian P.","last_name":"Tighe"},{"last_name":"van Hecke","first_name":"Martin","full_name":"van Hecke, Martin"},{"full_name":"Liu, Andrea J.","first_name":"Andrea J.","last_name":"Liu"},{"first_name":"Sidney R.","full_name":"Nagel, Sidney R.","last_name":"Nagel"}],"publication":"Physical Review E","_id":"7769","type":"journal_article","day":"27","quality_controlled":"1","title":"Jamming in finite systems: Stability, anisotropy, fluctuations, and scaling"},{"article_number":"022201","language":[{"iso":"eng"}],"article_type":"original","volume":90,"publisher":"American Physical Society","year":"2014","citation":{"mla":"Goodrich, Carl Peter, et al. “Contact Nonlinearities and Linear Response in Jammed Particulate Packings.” <i>Physical Review E</i>, vol. 90, no. 2, 022201, American Physical Society, 2014, doi:<a href=\"https://doi.org/10.1103/physreve.90.022201\">10.1103/physreve.90.022201</a>.","apa":"Goodrich, C. P., Liu, A. J., &#38; Nagel, S. R. (2014). Contact nonlinearities and linear response in jammed particulate packings. <i>Physical Review E</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physreve.90.022201\">https://doi.org/10.1103/physreve.90.022201</a>","short":"C.P. Goodrich, A.J. Liu, S.R. Nagel, Physical Review E 90 (2014).","chicago":"Goodrich, Carl Peter, Andrea J. Liu, and Sidney R. Nagel. “Contact Nonlinearities and Linear Response in Jammed Particulate Packings.” <i>Physical Review E</i>. American Physical Society, 2014. <a href=\"https://doi.org/10.1103/physreve.90.022201\">https://doi.org/10.1103/physreve.90.022201</a>.","ama":"Goodrich CP, Liu AJ, Nagel SR. Contact nonlinearities and linear response in jammed particulate packings. <i>Physical Review E</i>. 2014;90(2). doi:<a href=\"https://doi.org/10.1103/physreve.90.022201\">10.1103/physreve.90.022201</a>","ista":"Goodrich CP, Liu AJ, Nagel SR. 2014. Contact nonlinearities and linear response in jammed particulate packings. Physical Review E. 90(2), 022201.","ieee":"C. P. Goodrich, A. J. Liu, and S. R. Nagel, “Contact nonlinearities and linear response in jammed particulate packings,” <i>Physical Review E</i>, vol. 90, no. 2. American Physical Society, 2014."},"oa_version":"None","date_updated":"2021-01-12T08:15:25Z","extern":"1","doi":"10.1103/physreve.90.022201","status":"public","abstract":[{"text":"Packings of frictionless athermal particles that interact only when they overlap experience a jamming transition as a function of packing density. Such packings provide the foundation for the theory of jamming. This theory rests on the observation that, despite the multitude of disordered configurations, the mechanical response to linear order depends only on the distance to the transition. We investigate the validity and utility of such measurements that invoke the harmonic approximation and show that, despite particles coming in and out of contact, there is a well-defined linear regime in the thermodynamic limit.","lang":"eng"}],"publication_status":"published","date_published":"2014-08-04T00:00:00Z","article_processing_charge":"No","issue":"2","date_created":"2020-04-30T11:42:24Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["1539-3755","1550-2376"]},"month":"08","intvolume":"        90","title":"Contact nonlinearities and linear response in jammed particulate packings","quality_controlled":"1","day":"04","_id":"7770","type":"journal_article","author":[{"last_name":"Goodrich","id":"EB352CD2-F68A-11E9-89C5-A432E6697425","orcid":"0000-0002-1307-5074","first_name":"Carl Peter","full_name":"Goodrich, Carl Peter"},{"last_name":"Liu","first_name":"Andrea J.","full_name":"Liu, Andrea J."},{"last_name":"Nagel","first_name":"Sidney R.","full_name":"Nagel, Sidney R."}],"publication":"Physical Review E","fulldoi":"https://doi.org/10.1103/physreve.90.022201"}]