[{"type":"journal_article","abstract":[{"lang":"eng","text":"G-protein-coupled receptors (GPCRs) form the largest receptor family, relay environmental stimuli to changes in cell behavior and represent prime drug targets. Many GPCRs are classified as orphan receptors because of the limited knowledge on their ligands and coupling to cellular signaling machineries. Here, we engineer a library of 63 chimeric receptors that contain the signaling domains of human orphan and understudied GPCRs functionally linked to the light-sensing domain of rhodopsin. Upon stimulation with visible light, we identify activation of canonical cell signaling pathways, including cAMP-, Ca2+-, MAPK/ERK-, and Rho-dependent pathways, downstream of the engineered receptors. For the human pseudogene GPR33, we resurrect a signaling function that supports its hypothesized role as a pathogen entry site. These results demonstrate that substituting unknown chemical activators with a light switch can reveal information about protein function and provide an optically controlled protein library for exploring the physiology and therapeutic potential of understudied GPCRs."}],"issue":"1","title":"Optical functionalization of human class A orphan G-protein-coupled receptors","ddc":["570"],"status":"public","intvolume":" 9","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5984","file":[{"file_name":"2018_Springer_Morri.pdf","access_level":"open_access","file_size":1349914,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"5985","date_created":"2019-02-14T10:58:29Z","date_updated":"2020-07-14T12:47:14Z","checksum":"8325fcc194264af4749e662a73bf66b5"}],"oa_version":"Published Version","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","publication":"Nature Communications","citation":{"ama":"Morri M, Sanchez-Romero I, Tichy A-M, et al. Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. 2018;9(1). doi:10.1038/s41467-018-04342-1","ista":"Morri M, Sanchez-Romero I, Tichy A-M, Kainrath S, Gerrard EJ, Hirschfeld P, Schwarz J, Janovjak HL. 2018. Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. 9(1), 1950.","apa":"Morri, M., Sanchez-Romero, I., Tichy, A.-M., Kainrath, S., Gerrard, E. J., Hirschfeld, P., … Janovjak, H. L. (2018). Optical functionalization of human class A orphan G-protein-coupled receptors. Nature Communications. Springer Nature. https://doi.org/10.1038/s41467-018-04342-1","ieee":"M. Morri et al., “Optical functionalization of human class A orphan G-protein-coupled receptors,” Nature Communications, vol. 9, no. 1. Springer Nature, 2018.","mla":"Morri, Maurizio, et al. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.” Nature Communications, vol. 9, no. 1, 1950, Springer Nature, 2018, doi:10.1038/s41467-018-04342-1.","short":"M. Morri, I. Sanchez-Romero, A.-M. Tichy, S. Kainrath, E.J. Gerrard, P. Hirschfeld, J. Schwarz, H.L. Janovjak, Nature Communications 9 (2018).","chicago":"Morri, Maurizio, Inmaculada Sanchez-Romero, Alexandra-Madelaine Tichy, Stephanie Kainrath, Elliot J. Gerrard, Priscila Hirschfeld, Jan Schwarz, and Harald L Janovjak. “Optical Functionalization of Human Class A Orphan G-Protein-Coupled Receptors.” Nature Communications. Springer Nature, 2018. https://doi.org/10.1038/s41467-018-04342-1."},"date_published":"2018-12-01T00:00:00Z","article_number":"1950","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2020-07-14T12:47:14Z","ec_funded":1,"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HaJa"},{"_id":"CaGu"},{"_id":"MiSi"}],"year":"2018","date_updated":"2023-09-19T14:29:32Z","date_created":"2019-02-14T10:50:24Z","volume":9,"author":[{"full_name":"Morri, Maurizio","first_name":"Maurizio","last_name":"Morri","id":"4863116E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sanchez-Romero, Inmaculada","id":"3D9C5D30-F248-11E8-B48F-1D18A9856A87","first_name":"Inmaculada","last_name":"Sanchez-Romero"},{"id":"29D8BB2C-F248-11E8-B48F-1D18A9856A87","last_name":"Tichy","first_name":"Alexandra-Madelaine","full_name":"Tichy, Alexandra-Madelaine"},{"full_name":"Kainrath, Stephanie","last_name":"Kainrath","first_name":"Stephanie","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Elliot J.","last_name":"Gerrard","full_name":"Gerrard, Elliot J."},{"full_name":"Hirschfeld, Priscila","id":"435ACB3A-F248-11E8-B48F-1D18A9856A87","first_name":"Priscila","last_name":"Hirschfeld"},{"first_name":"Jan","last_name":"Schwarz","id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","full_name":"Schwarz, Jan"},{"last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L"}],"month":"12","publication_identifier":{"issn":["2041-1723"]},"isi":1,"quality_controlled":"1","project":[{"_id":"25548C20-B435-11E9-9278-68D0E5697425","grant_number":"303564","call_identifier":"FP7","name":"Microbial Ion Channels for Synthetic Neurobiology"},{"_id":"255A6082-B435-11E9-9278-68D0E5697425","grant_number":"W1232-B24","call_identifier":"FWF","name":"Molecular Drug Targets"}],"external_id":{"isi":["000432280000006"]},"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1038/s41467-018-04342-1"},{"publication_identifier":{"issn":["0730-0301"]},"month":"11","project":[{"name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767"},{"call_identifier":"H2020","name":"Soft-bodied intelligence for Manipulation","grant_number":"645599","_id":"25082902-B435-11E9-9278-68D0E5697425"},{"name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000455953100064"]},"language":[{"iso":"eng"}],"doi":"10.1145/3272127.3275076","article_number":"241","ec_funded":1,"file_date_updated":"2020-07-14T12:47:14Z","publisher":"Association for Computing Machinery (ACM)","department":[{"_id":"BeBi"}],"publication_status":"published","year":"2018","volume":37,"date_created":"2019-02-13T13:12:53Z","date_updated":"2023-09-19T14:25:30Z","author":[{"full_name":"Malomo, Luigi","first_name":"Luigi","last_name":"Malomo"},{"full_name":"Perez Rodriguez, Jesus","id":"2DC83906-F248-11E8-B48F-1D18A9856A87","last_name":"Perez Rodriguez","first_name":"Jesus"},{"full_name":"Iarussi, Emmanuel","first_name":"Emmanuel","last_name":"Iarussi","id":"33F19F16-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Pietroni, Nico","last_name":"Pietroni","first_name":"Nico"},{"full_name":"Miguel, Eder","last_name":"Miguel","first_name":"Eder"},{"full_name":"Cignoni, Paolo","last_name":"Cignoni","first_name":"Paolo"},{"full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","id":"49876194-F248-11E8-B48F-1D18A9856A87","last_name":"Bickel","first_name":"Bernd"}],"scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"01","article_type":"original","citation":{"short":"L. Malomo, J. Perez Rodriguez, E. Iarussi, N. Pietroni, E. Miguel, P. Cignoni, B. Bickel, ACM Transactions on Graphics 37 (2018).","mla":"Malomo, Luigi, et al. “FlexMaps: Computational Design of Flat Flexible Shells for Shaping 3D Objects.” ACM Transactions on Graphics, vol. 37, no. 6, 241, Association for Computing Machinery (ACM), 2018, doi:10.1145/3272127.3275076.","chicago":"Malomo, Luigi, Jesus Perez Rodriguez, Emmanuel Iarussi, Nico Pietroni, Eder Miguel, Paolo Cignoni, and Bernd Bickel. “FlexMaps: Computational Design of Flat Flexible Shells for Shaping 3D Objects.” ACM Transactions on Graphics. Association for Computing Machinery (ACM), 2018. https://doi.org/10.1145/3272127.3275076.","ama":"Malomo L, Perez Rodriguez J, Iarussi E, et al. FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. 2018;37(6). doi:10.1145/3272127.3275076","apa":"Malomo, L., Perez Rodriguez, J., Iarussi, E., Pietroni, N., Miguel, E., Cignoni, P., & Bickel, B. (2018). FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. Association for Computing Machinery (ACM). https://doi.org/10.1145/3272127.3275076","ieee":"L. Malomo et al., “FlexMaps: Computational design of flat flexible shells for shaping 3D objects,” ACM Transactions on Graphics, vol. 37, no. 6. Association for Computing Machinery (ACM), 2018.","ista":"Malomo L, Perez Rodriguez J, Iarussi E, Pietroni N, Miguel E, Cignoni P, Bickel B. 2018. FlexMaps: Computational design of flat flexible shells for shaping 3D objects. ACM Transactions on Graphics. 37(6), 241."},"publication":"ACM Transactions on Graphics","date_published":"2018-11-01T00:00:00Z","type":"journal_article","issue":"6","abstract":[{"text":"We propose FlexMaps, a novel framework for fabricating smooth shapes out of flat, flexible panels with tailored mechanical properties. We start by mapping the 3D surface onto a 2D domain as in traditional UV mapping to design a set of deformable flat panels called FlexMaps. For these panels, we design and obtain specific mechanical properties such that, once they are assembled, the static equilibrium configuration matches the desired 3D shape. FlexMaps can be fabricated from an almost rigid material, such as wood or plastic, and are made flexible in a controlled way by using computationally designed spiraling microstructures.","lang":"eng"}],"intvolume":" 37","title":"FlexMaps: Computational design of flat flexible shells for shaping 3D objects","ddc":["000"],"status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5976","file":[{"relation":"main_file","file_id":"6901","checksum":"d0529a41c78b37ab8840685579fb33b4","date_created":"2019-09-23T12:48:52Z","date_updated":"2020-07-14T12:47:14Z","access_level":"open_access","file_name":"flexmaps_author_version.pdf","content_type":"application/pdf","file_size":100109811,"creator":"bbickel"}],"oa_version":"Published Version","pubrep_id":"1068"},{"issue":"22","abstract":[{"text":"We study a quantum impurity possessing both translational and internal rotational degrees of freedom interacting with a bosonic bath. Such a system corresponds to a “rotating polaron,” which can be used to model, e.g., a rotating molecule immersed in an ultracold Bose gas or superfluid helium. We derive the Hamiltonian of the rotating polaron and study its spectrum in the weak- and strong-coupling regimes using a combination of variational, diagrammatic, and mean-field approaches. We reveal how the coupling between linear and angular momenta affects stable quasiparticle states, and demonstrate that internal rotation leads to an enhanced self-localization in the translational degrees of freedom.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 98","status":"public","title":"Theory of the rotating polaron: Spectrum and self-localization","_id":"5983","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","article_processing_charge":"No","day":"12","scopus_import":"1","date_published":"2018-12-12T00:00:00Z","citation":{"ista":"Yakaboylu E, Midya B, Deuchert A, Leopold NK, Lemeshko M. 2018. Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. 98(22), 224506.","apa":"Yakaboylu, E., Midya, B., Deuchert, A., Leopold, N. K., & Lemeshko, M. (2018). Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.98.224506","ieee":"E. Yakaboylu, B. Midya, A. Deuchert, N. K. Leopold, and M. Lemeshko, “Theory of the rotating polaron: Spectrum and self-localization,” Physical Review B, vol. 98, no. 22. American Physical Society, 2018.","ama":"Yakaboylu E, Midya B, Deuchert A, Leopold NK, Lemeshko M. Theory of the rotating polaron: Spectrum and self-localization. Physical Review B. 2018;98(22). doi:10.1103/physrevb.98.224506","chicago":"Yakaboylu, Enderalp, Bikashkali Midya, Andreas Deuchert, Nikolai K Leopold, and Mikhail Lemeshko. “Theory of the Rotating Polaron: Spectrum and Self-Localization.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/physrevb.98.224506.","mla":"Yakaboylu, Enderalp, et al. “Theory of the Rotating Polaron: Spectrum and Self-Localization.” Physical Review B, vol. 98, no. 22, 224506, American Physical Society, 2018, doi:10.1103/physrevb.98.224506.","short":"E. Yakaboylu, B. Midya, A. Deuchert, N.K. Leopold, M. Lemeshko, Physical Review B 98 (2018)."},"publication":"Physical Review B","ec_funded":1,"article_number":"224506","volume":98,"date_created":"2019-02-14T10:37:09Z","date_updated":"2023-09-19T14:29:03Z","author":[{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5973-0874","first_name":"Enderalp","last_name":"Yakaboylu"},{"full_name":"Midya, Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","first_name":"Bikashkali","last_name":"Midya"},{"last_name":"Deuchert","first_name":"Andreas","orcid":"0000-0003-3146-6746","id":"4DA65CD0-F248-11E8-B48F-1D18A9856A87","full_name":"Deuchert, Andreas"},{"full_name":"Leopold, Nikolai K","last_name":"Leopold","first_name":"Nikolai K","orcid":"0000-0002-0495-6822","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lemeshko","first_name":"Mikhail","orcid":"0000-0002-6990-7802","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail"}],"department":[{"_id":"MiLe"},{"_id":"RoSe"}],"publisher":"American Physical Society","publication_status":"published","year":"2018","publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"month":"12","language":[{"iso":"eng"}],"doi":"10.1103/physrevb.98.224506","project":[{"call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734"},{"name":"Analysis of quantum many-body systems","call_identifier":"H2020","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","isi":1,"external_id":{"arxiv":["1809.01204"],"isi":["000452992700008"]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.01204"}],"oa":1},{"oa_version":"Submitted Version","intvolume":" 57","status":"public","title":"Tin diselenide molecular precursor for solution-processable thermoelectric materials","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5982","issue":"52","abstract":[{"lang":"eng","text":"In the present work, we detail a fast and simple solution-based method to synthesize hexagonal SnSe2 nanoplates (NPLs) and their use to produce crystallographically textured SnSe2 nanomaterials. We also demonstrate that the same strategy can be used to produce orthorhombic SnSe nanostructures and nanomaterials. NPLs are grown through a screw dislocation-driven mechanism. This mechanism typically results in pyramidal structures, but we demonstrate here that the growth from multiple dislocations results in flower-like structures. Crystallographically textured SnSe2 bulk nanomaterials obtained from the hot pressing of these SnSe2 structures display highly anisotropic charge and heat transport properties and thermoelectric (TE) figures of merit limited by relatively low electrical conductivities. To improve this parameter, SnSe2 NPLs are blended here with metal nanoparticles. The electrical conductivities of the blends are significantly improved with respect to bare SnSe2 NPLs, what translates into a three-fold increase of the TE Figure of merit, reaching unprecedented ZT values up to 0.65."}],"type":"journal_article","date_published":"2018-12-21T00:00:00Z","page":"17063-17068","article_type":"original","citation":{"chicago":"Zhang, Yu, Yu Liu, Khak Ho Lim, Congcong Xing, Mengyao Li, Ting Zhang, Pengyi Tang, et al. “Tin Diselenide Molecular Precursor for Solution-Processable Thermoelectric Materials.” Angewandte Chemie International Edition. Wiley, 2018. https://doi.org/10.1002/anie.201809847.","short":"Y. Zhang, Y. Liu, K.H. Lim, C. Xing, M. Li, T. Zhang, P. Tang, J. Arbiol, J. Llorca, K.M. Ng, M. Ibáñez, P. Guardia, M. Prato, D. Cadavid, A. Cabot, Angewandte Chemie International Edition 57 (2018) 17063–17068.","mla":"Zhang, Yu, et al. “Tin Diselenide Molecular Precursor for Solution-Processable Thermoelectric Materials.” Angewandte Chemie International Edition, vol. 57, no. 52, Wiley, 2018, pp. 17063–68, doi:10.1002/anie.201809847.","apa":"Zhang, Y., Liu, Y., Lim, K. H., Xing, C., Li, M., Zhang, T., … Cabot, A. (2018). Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.201809847","ieee":"Y. Zhang et al., “Tin diselenide molecular precursor for solution-processable thermoelectric materials,” Angewandte Chemie International Edition, vol. 57, no. 52. Wiley, pp. 17063–17068, 2018.","ista":"Zhang Y, Liu Y, Lim KH, Xing C, Li M, Zhang T, Tang P, Arbiol J, Llorca J, Ng KM, Ibáñez M, Guardia P, Prato M, Cadavid D, Cabot A. 2018. Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. 57(52), 17063–17068.","ama":"Zhang Y, Liu Y, Lim KH, et al. Tin diselenide molecular precursor for solution-processable thermoelectric materials. Angewandte Chemie International Edition. 2018;57(52):17063-17068. doi:10.1002/anie.201809847"},"publication":"Angewandte Chemie International Edition","article_processing_charge":"No","day":"21","scopus_import":"1","volume":57,"date_updated":"2023-09-19T14:28:31Z","date_created":"2019-02-14T10:23:27Z","author":[{"last_name":"Zhang","first_name":"Yu","full_name":"Zhang, Yu"},{"full_name":"Liu, Yu","last_name":"Liu","first_name":"Yu"},{"full_name":"Lim, Khak Ho","last_name":"Lim","first_name":"Khak Ho"},{"full_name":"Xing, Congcong","last_name":"Xing","first_name":"Congcong"},{"full_name":"Li, Mengyao","last_name":"Li","first_name":"Mengyao"},{"full_name":"Zhang, Ting","last_name":"Zhang","first_name":"Ting"},{"full_name":"Tang, Pengyi","last_name":"Tang","first_name":"Pengyi"},{"first_name":"Jordi","last_name":"Arbiol","full_name":"Arbiol, Jordi"},{"full_name":"Llorca, Jordi","last_name":"Llorca","first_name":"Jordi"},{"first_name":"Ka Ming","last_name":"Ng","full_name":"Ng, Ka Ming"},{"full_name":"Ibáñez, Maria","last_name":"Ibáñez","first_name":"Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Guardia","first_name":"Pablo","full_name":"Guardia, Pablo"},{"full_name":"Prato, Mirko","last_name":"Prato","first_name":"Mirko"},{"first_name":"Doris","last_name":"Cadavid","full_name":"Cadavid, Doris"},{"last_name":"Cabot","first_name":"Andreu","full_name":"Cabot, Andreu"}],"publisher":"Wiley","department":[{"_id":"MaIb"}],"publication_status":"published","year":"2018","language":[{"iso":"eng"}],"doi":"10.1002/anie.201809847","quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://upcommons.upc.edu/bitstream/2117/130444/1/Zhang%20preprint.pdf","open_access":"1"}],"external_id":{"isi":["000454575500020"]},"publication_identifier":{"issn":["1433-7851"]},"month":"12"},{"article_processing_charge":"No","month":"02","day":"01","scopus_import":"1","date_published":"2018-02-01T00:00:00Z","conference":{"name":"AAAI: Conference on Artificial Intelligence","end_date":"2018-02-07","start_date":"2018-02-02","location":"New Orleans, LU, United States"},"language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2004.06370"}],"external_id":{"arxiv":["2004.06370"],"isi":["000485488906082"]},"citation":{"ama":"Haller S, Swoboda P, Savchynskyy B. Exact MAP-inference by confining combinatorial search with LP relaxation. In: Proceedings of the 32st AAAI Conference on Artificial Intelligence. AAAI Press; 2018:6581-6588.","ista":"Haller S, Swoboda P, Savchynskyy B. 2018. Exact MAP-inference by confining combinatorial search with LP relaxation. Proceedings of the 32st AAAI Conference on Artificial Intelligence. AAAI: Conference on Artificial Intelligence, 6581–6588.","ieee":"S. Haller, P. Swoboda, and B. Savchynskyy, “Exact MAP-inference by confining combinatorial search with LP relaxation,” in Proceedings of the 32st AAAI Conference on Artificial Intelligence, New Orleans, LU, United States, 2018, pp. 6581–6588.","apa":"Haller, S., Swoboda, P., & Savchynskyy, B. (2018). Exact MAP-inference by confining combinatorial search with LP relaxation. In Proceedings of the 32st AAAI Conference on Artificial Intelligence (pp. 6581–6588). New Orleans, LU, United States: AAAI Press.","mla":"Haller, Stefan, et al. “Exact MAP-Inference by Confining Combinatorial Search with LP Relaxation.” Proceedings of the 32st AAAI Conference on Artificial Intelligence, AAAI Press, 2018, pp. 6581–88.","short":"S. Haller, P. Swoboda, B. Savchynskyy, in:, Proceedings of the 32st AAAI Conference on Artificial Intelligence, AAAI Press, 2018, pp. 6581–6588.","chicago":"Haller, Stefan, Paul Swoboda, and Bogdan Savchynskyy. “Exact MAP-Inference by Confining Combinatorial Search with LP Relaxation.” In Proceedings of the 32st AAAI Conference on Artificial Intelligence, 6581–88. AAAI Press, 2018."},"oa":1,"publication":"Proceedings of the 32st AAAI Conference on Artificial Intelligence","page":"6581-6588","isi":1,"quality_controlled":"1","abstract":[{"text":"We consider the MAP-inference problem for graphical models,which is a valued constraint satisfaction problem defined onreal numbers with a natural summation operation. We proposea family of relaxations (different from the famous Sherali-Adams hierarchy), which naturally define lower bounds for itsoptimum. This family always contains a tight relaxation andwe give an algorithm able to find it and therefore, solve theinitial non-relaxed NP-hard problem.The relaxations we consider decompose the original probleminto two non-overlapping parts: an easy LP-tight part and adifficult one. For the latter part a combinatorial solver must beused. As we show in our experiments, in a number of applica-tions the second, difficult part constitutes only a small fractionof the whole problem. This property allows to significantlyreduce the computational time of the combinatorial solver andtherefore solve problems which were out of reach before.","lang":"eng"}],"type":"conference","author":[{"full_name":"Haller, Stefan","first_name":"Stefan","last_name":"Haller"},{"id":"446560C6-F248-11E8-B48F-1D18A9856A87","first_name":"Paul","last_name":"Swoboda","full_name":"Swoboda, Paul"},{"full_name":"Savchynskyy, Bogdan","first_name":"Bogdan","last_name":"Savchynskyy"}],"oa_version":"Preprint","date_created":"2019-02-13T13:32:48Z","date_updated":"2023-09-19T14:26:52Z","_id":"5978","year":"2018","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"VlKo"}],"publisher":"AAAI Press","publication_status":"published","title":"Exact MAP-inference by confining combinatorial search with LP relaxation","status":"public"},{"scopus_import":"1","day":"02","article_processing_charge":"No","publication":"Advanced Materials","citation":{"ama":"Ridderbos J, Brauns M, Shen J, et al. Josephson effect in a few-hole quantum dot. Advanced Materials. 2018;30(44). doi:10.1002/adma.201802257","apa":"Ridderbos, J., Brauns, M., Shen, J., de Vries, F. K., Li, A., Bakkers, E. P. A. M., … Zwanenburg, F. A. (2018). Josephson effect in a few-hole quantum dot. Advanced Materials. Wiley. https://doi.org/10.1002/adma.201802257","ieee":"J. Ridderbos et al., “Josephson effect in a few-hole quantum dot,” Advanced Materials, vol. 30, no. 44. Wiley, 2018.","ista":"Ridderbos J, Brauns M, Shen J, de Vries FK, Li A, Bakkers EPAM, Brinkman A, Zwanenburg FA. 2018. Josephson effect in a few-hole quantum dot. Advanced Materials. 30(44), 1802257.","short":"J. Ridderbos, M. Brauns, J. Shen, F.K. de Vries, A. Li, E.P.A.M. Bakkers, A. Brinkman, F.A. Zwanenburg, Advanced Materials 30 (2018).","mla":"Ridderbos, Joost, et al. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials, vol. 30, no. 44, 1802257, Wiley, 2018, doi:10.1002/adma.201802257.","chicago":"Ridderbos, Joost, Matthias Brauns, Jie Shen, Folkert K. de Vries, Ang Li, Erik P. A. M. Bakkers, Alexander Brinkman, and Floris A. Zwanenburg. “Josephson Effect in a Few-Hole Quantum Dot.” Advanced Materials. Wiley, 2018. https://doi.org/10.1002/adma.201802257."},"date_published":"2018-11-02T00:00:00Z","type":"journal_article","abstract":[{"text":"A Ge–Si core–shell nanowire is used to realize a Josephson field‐effect transistor with highly transparent contacts to superconducting leads. By changing the electric field, access to two distinct regimes, not combined before in a single device, is gained: in the accumulation mode the device is highly transparent and the supercurrent is carried by multiple subbands, while near depletion, the supercurrent is carried by single‐particle levels of a strongly coupled quantum dot operating in the few‐hole regime. These results establish Ge–Si nanowires as an important platform for hybrid superconductor–semiconductor physics and Majorana fermions.","lang":"eng"}],"issue":"44","title":"Josephson effect in a few-hole quantum dot","status":"public","intvolume":" 30","_id":"5990","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Preprint","month":"11","publication_identifier":{"issn":["0935-9648"]},"quality_controlled":"1","isi":1,"external_id":{"isi":["000450232800015"],"arxiv":["1809.08487"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1809.08487"}],"language":[{"iso":"eng"}],"doi":"10.1002/adma.201802257","article_number":"1802257","publication_status":"published","department":[{"_id":"GeKa"}],"publisher":"Wiley","year":"2018","date_updated":"2023-09-19T14:29:58Z","date_created":"2019-02-14T12:14:26Z","volume":30,"author":[{"last_name":"Ridderbos","first_name":"Joost","full_name":"Ridderbos, Joost"},{"first_name":"Matthias","last_name":"Brauns","id":"33F94E3C-F248-11E8-B48F-1D18A9856A87","full_name":"Brauns, Matthias"},{"last_name":"Shen","first_name":"Jie","full_name":"Shen, Jie"},{"last_name":"de Vries","first_name":"Folkert K.","full_name":"de Vries, Folkert K."},{"first_name":"Ang","last_name":"Li","full_name":"Li, Ang"},{"full_name":"Bakkers, Erik P. A. M.","last_name":"Bakkers","first_name":"Erik P. A. M."},{"first_name":"Alexander","last_name":"Brinkman","full_name":"Brinkman, Alexander"},{"full_name":"Zwanenburg, Floris A.","first_name":"Floris A.","last_name":"Zwanenburg"}]},{"volume":14,"date_created":"2019-02-14T13:07:45Z","date_updated":"2023-09-19T14:31:43Z","author":[{"full_name":"Velicky, Philipp","last_name":"Velicky","first_name":"Philipp","orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Gudrun","last_name":"Meinhardt","full_name":"Meinhardt, Gudrun"},{"last_name":"Plessl","first_name":"Kerstin","full_name":"Plessl, Kerstin"},{"full_name":"Vondra, Sigrid","first_name":"Sigrid","last_name":"Vondra"},{"full_name":"Weiss, Tamara","first_name":"Tamara","last_name":"Weiss"},{"first_name":"Peter","last_name":"Haslinger","full_name":"Haslinger, Peter"},{"full_name":"Lendl, Thomas","last_name":"Lendl","first_name":"Thomas"},{"first_name":"Karin","last_name":"Aumayr","full_name":"Aumayr, Karin"},{"full_name":"Mairhofer, Mario","last_name":"Mairhofer","first_name":"Mario"},{"full_name":"Zhu, Xiaowei","first_name":"Xiaowei","last_name":"Zhu"},{"full_name":"Schütz, Birgit","first_name":"Birgit","last_name":"Schütz"},{"full_name":"Hannibal, Roberta L.","last_name":"Hannibal","first_name":"Roberta L."},{"full_name":"Lindau, Robert","first_name":"Robert","last_name":"Lindau"},{"full_name":"Weil, Beatrix","first_name":"Beatrix","last_name":"Weil"},{"full_name":"Ernerudh, Jan","last_name":"Ernerudh","first_name":"Jan"},{"last_name":"Neesen","first_name":"Jürgen","full_name":"Neesen, Jürgen"},{"last_name":"Egger","first_name":"Gerda","full_name":"Egger, Gerda"},{"full_name":"Mikula, Mario","last_name":"Mikula","first_name":"Mario"},{"full_name":"Röhrl, Clemens","first_name":"Clemens","last_name":"Röhrl"},{"full_name":"Urban, Alexander E.","first_name":"Alexander E.","last_name":"Urban"},{"first_name":"Julie","last_name":"Baker","full_name":"Baker, Julie"},{"first_name":"Martin","last_name":"Knöfler","full_name":"Knöfler, Martin"},{"full_name":"Pollheimer, Jürgen","first_name":"Jürgen","last_name":"Pollheimer"}],"publisher":"Public Library of Science","department":[{"_id":"JoDa"}],"publication_status":"published","year":"2018","file_date_updated":"2020-07-14T12:47:15Z","article_number":"e1007698","language":[{"iso":"eng"}],"doi":"10.1371/journal.pgen.1007698","isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000449328500025"]},"oa":1,"publication_identifier":{"issn":["1553-7404"]},"month":"10","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"6000","date_created":"2019-02-14T13:14:35Z","date_updated":"2020-07-14T12:47:15Z","checksum":"34aa9a5972f61889c19f18be8ee787a0","file_name":"2018_PLOS_Velicky.pdf","access_level":"open_access","content_type":"application/pdf","file_size":4592947,"creator":"kschuh"}],"intvolume":" 14","ddc":["570"],"title":"Genome amplification and cellular senescence are hallmarks of human placenta development","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","_id":"5998","issue":"10","abstract":[{"lang":"eng","text":"Genome amplification and cellular senescence are commonly associated with pathological processes. While physiological roles for polyploidization and senescence have been described in mouse development, controversy exists over their significance in humans. Here, we describe tetraploidization and senescence as phenomena of normal human placenta development. During pregnancy, placental extravillous trophoblasts (EVTs) invade the pregnant endometrium, termed decidua, to establish an adapted microenvironment required for the developing embryo. This process is critically dependent on continuous cell proliferation and differentiation, which is thought to follow the classical model of cell cycle arrest prior to terminal differentiation. Strikingly, flow cytometry and DNAseq revealed that EVT formation is accompanied with a genome-wide polyploidization, independent of mitotic cycles. DNA replication in these cells was analysed by a fluorescent cell-cycle indicator reporter system, cell cycle marker expression and EdU incorporation. Upon invasion into the decidua, EVTs widely lose their replicative potential and enter a senescent state characterized by high senescence-associated (SA) β-galactosidase activity, induction of a SA secretory phenotype as well as typical metabolic alterations. Furthermore, we show that the shift from endocycle-dependent genome amplification to growth arrest is disturbed in androgenic complete hydatidiform moles (CHM), a hyperplastic pregnancy disorder associated with increased risk of developing choriocarinoma. Senescence is decreased in CHM-EVTs, accompanied by exacerbated endoreduplication and hyperploidy. We propose induction of cellular senescence as a ploidy-limiting mechanism during normal human placentation and unravel a link between excessive polyploidization and reduced senescence in CHM."}],"type":"journal_article","date_published":"2018-10-12T00:00:00Z","citation":{"short":"P. Velicky, G. Meinhardt, K. Plessl, S. Vondra, T. Weiss, P. Haslinger, T. Lendl, K. Aumayr, M. Mairhofer, X. Zhu, B. Schütz, R.L. Hannibal, R. Lindau, B. Weil, J. Ernerudh, J. Neesen, G. Egger, M. Mikula, C. Röhrl, A.E. Urban, J. Baker, M. Knöfler, J. Pollheimer, PLOS Genetics 14 (2018).","mla":"Velicky, Philipp, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics, vol. 14, no. 10, e1007698, Public Library of Science, 2018, doi:10.1371/journal.pgen.1007698.","chicago":"Velicky, Philipp, Gudrun Meinhardt, Kerstin Plessl, Sigrid Vondra, Tamara Weiss, Peter Haslinger, Thomas Lendl, et al. “Genome Amplification and Cellular Senescence Are Hallmarks of Human Placenta Development.” PLOS Genetics. Public Library of Science, 2018. https://doi.org/10.1371/journal.pgen.1007698.","ama":"Velicky P, Meinhardt G, Plessl K, et al. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 2018;14(10). doi:10.1371/journal.pgen.1007698","ieee":"P. Velicky et al., “Genome amplification and cellular senescence are hallmarks of human placenta development,” PLOS Genetics, vol. 14, no. 10. Public Library of Science, 2018.","apa":"Velicky, P., Meinhardt, G., Plessl, K., Vondra, S., Weiss, T., Haslinger, P., … Pollheimer, J. (2018). Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1007698","ista":"Velicky P, Meinhardt G, Plessl K, Vondra S, Weiss T, Haslinger P, Lendl T, Aumayr K, Mairhofer M, Zhu X, Schütz B, Hannibal RL, Lindau R, Weil B, Ernerudh J, Neesen J, Egger G, Mikula M, Röhrl C, Urban AE, Baker J, Knöfler M, Pollheimer J. 2018. Genome amplification and cellular senescence are hallmarks of human placenta development. PLOS Genetics. 14(10), e1007698."},"publication":"PLOS Genetics","has_accepted_license":"1","article_processing_charge":"No","day":"12","scopus_import":"1"},{"month":"11","publication_identifier":{"issn":["1367-4803","1460-2059"]},"quality_controlled":"1","isi":1,"project":[{"call_identifier":"FP7","name":"Systematic investigation of epistasis in molecular evolution","grant_number":"335980","_id":"26120F5C-B435-11E9-9278-68D0E5697425"}],"oa":1,"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)"},"external_id":{"isi":["000450038900008"],"pmid":["29722803"]},"language":[{"iso":"eng"}],"doi":"10.1093/bioinformatics/bty340","license":"https://creativecommons.org/licenses/by-nc/4.0/","file_date_updated":"2020-07-14T12:47:15Z","ec_funded":1,"publication_status":"published","department":[{"_id":"FyKo"}],"publisher":"Oxford University Press ","year":"2018","pmid":1,"date_created":"2019-02-14T12:48:00Z","date_updated":"2023-09-19T14:31:13Z","volume":34,"author":[{"last_name":"Usmanova","first_name":"Dinara R","full_name":"Usmanova, Dinara R"},{"full_name":"Bogatyreva, Natalya S","last_name":"Bogatyreva","first_name":"Natalya S"},{"full_name":"Ariño Bernad, Joan","last_name":"Ariño Bernad","first_name":"Joan"},{"first_name":"Aleksandra A","last_name":"Eremina","full_name":"Eremina, Aleksandra A"},{"full_name":"Gorshkova, Anastasiya A","last_name":"Gorshkova","first_name":"Anastasiya A"},{"full_name":"Kanevskiy, German M","last_name":"Kanevskiy","first_name":"German M"},{"last_name":"Lonishin","first_name":"Lyubov R","full_name":"Lonishin, Lyubov R"},{"last_name":"Meister","first_name":"Alexander V","full_name":"Meister, Alexander V"},{"full_name":"Yakupova, Alisa G","last_name":"Yakupova","first_name":"Alisa G"},{"id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"full_name":"Ivankov, Dmitry","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry","last_name":"Ivankov"}],"scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1","page":"3653-3658","publication":"Bioinformatics","citation":{"chicago":"Usmanova, Dinara R, Natalya S Bogatyreva, Joan Ariño Bernad, Aleksandra A Eremina, Anastasiya A Gorshkova, German M Kanevskiy, Lyubov R Lonishin, et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics. Oxford University Press , 2018. https://doi.org/10.1093/bioinformatics/bty340.","short":"D.R. Usmanova, N.S. Bogatyreva, J. Ariño Bernad, A.A. Eremina, A.A. Gorshkova, G.M. Kanevskiy, L.R. Lonishin, A.V. Meister, A.G. Yakupova, F. Kondrashov, D. Ivankov, Bioinformatics 34 (2018) 3653–3658.","mla":"Usmanova, Dinara R., et al. “Self-Consistency Test Reveals Systematic Bias in Programs for Prediction Change of Stability upon Mutation.” Bioinformatics, vol. 34, no. 21, Oxford University Press , 2018, pp. 3653–58, doi:10.1093/bioinformatics/bty340.","ieee":"D. R. Usmanova et al., “Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation,” Bioinformatics, vol. 34, no. 21. Oxford University Press , pp. 3653–3658, 2018.","apa":"Usmanova, D. R., Bogatyreva, N. S., Ariño Bernad, J., Eremina, A. A., Gorshkova, A. A., Kanevskiy, G. M., … Ivankov, D. (2018). Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. Oxford University Press . https://doi.org/10.1093/bioinformatics/bty340","ista":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, Eremina AA, Gorshkova AA, Kanevskiy GM, Lonishin LR, Meister AV, Yakupova AG, Kondrashov F, Ivankov D. 2018. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 34(21), 3653–3658.","ama":"Usmanova DR, Bogatyreva NS, Ariño Bernad J, et al. Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation. Bioinformatics. 2018;34(21):3653-3658. doi:10.1093/bioinformatics/bty340"},"date_published":"2018-11-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Motivation\r\nComputational prediction of the effect of mutations on protein stability is used by researchers in many fields. The utility of the prediction methods is affected by their accuracy and bias. Bias, a systematic shift of the predicted change of stability, has been noted as an issue for several methods, but has not been investigated systematically. Presence of the bias may lead to misleading results especially when exploring the effects of combination of different mutations.\r\n\r\nResults\r\nHere we use a protocol to measure the bias as a function of the number of introduced mutations. It is based on a self-consistency test of the reciprocity the effect of a mutation. An advantage of the used approach is that it relies solely on crystal structures without experimentally measured stability values. We applied the protocol to four popular algorithms predicting change of protein stability upon mutation, FoldX, Eris, Rosetta and I-Mutant, and found an inherent bias. For one program, FoldX, we manage to substantially reduce the bias using additional relaxation by Modeller. Authors using algorithms for predicting effects of mutations should be aware of the bias described here."}],"issue":"21","status":"public","ddc":["570"],"title":"Self-consistency test reveals systematic bias in programs for prediction change of stability upon mutation","intvolume":" 34","_id":"5995","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":291969,"creator":"kschuh","file_name":"2018_Oxford_Usmanova.pdf","access_level":"open_access","date_created":"2019-02-14T13:00:55Z","date_updated":"2020-07-14T12:47:15Z","checksum":"7e0495153f44211479674601d7f6ee03","relation":"main_file","file_id":"5997"}]},{"scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"01","page":"2674-2686","citation":{"chicago":"Dolati, Setareh, Frieda Kage, Jan Mueller, Mathias Müsken, Marieluise Kirchner, Gunnar Dittmar, Michael K Sixt, Klemens Rottner, and Martin Falcke. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell. American Society for Cell Biology , 2018. https://doi.org/10.1091/mbc.e18-02-0082.","short":"S. Dolati, F. Kage, J. Mueller, M. Müsken, M. Kirchner, G. Dittmar, M.K. Sixt, K. Rottner, M. Falcke, Molecular Biology of the Cell 29 (2018) 2674–2686.","mla":"Dolati, Setareh, et al. “On the Relation between Filament Density, Force Generation, and Protrusion Rate in Mesenchymal Cell Motility.” Molecular Biology of the Cell, vol. 29, no. 22, American Society for Cell Biology , 2018, pp. 2674–86, doi:10.1091/mbc.e18-02-0082.","apa":"Dolati, S., Kage, F., Mueller, J., Müsken, M., Kirchner, M., Dittmar, G., … Falcke, M. (2018). On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. American Society for Cell Biology . https://doi.org/10.1091/mbc.e18-02-0082","ieee":"S. Dolati et al., “On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility,” Molecular Biology of the Cell, vol. 29, no. 22. American Society for Cell Biology , pp. 2674–2686, 2018.","ista":"Dolati S, Kage F, Mueller J, Müsken M, Kirchner M, Dittmar G, Sixt MK, Rottner K, Falcke M. 2018. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 29(22), 2674–2686.","ama":"Dolati S, Kage F, Mueller J, et al. On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility. Molecular Biology of the Cell. 2018;29(22):2674-2686. doi:10.1091/mbc.e18-02-0082"},"publication":"Molecular Biology of the Cell","date_published":"2018-11-01T00:00:00Z","type":"journal_article","issue":"22","abstract":[{"text":"Lamellipodia are flat membrane protrusions formed during mesenchymal motion. Polymerization at the leading edge assembles the actin filament network and generates protrusion force. How this force is supported by the network and how the assembly rate is shared between protrusion and network retrograde flow determines the protrusion rate. We use mathematical modeling to understand experiments changing the F-actin density in lamellipodia of B16-F1 melanoma cells by modulation of Arp2/3 complex activity or knockout of the formins FMNL2 and FMNL3. Cells respond to a reduction of density with a decrease of protrusion velocity, an increase in the ratio of force to filament number, but constant network assembly rate. The relation between protrusion force and tension gradient in the F-actin network and the density dependency of friction, elasticity, and viscosity of the network explain the experimental observations. The formins act as filament nucleators and elongators with differential rates. Modulation of their activity suggests an effect on network assembly rate. Contrary to these expectations, the effect of changes in elongator composition is much weaker than the consequences of the density change. We conclude that the force acting on the leading edge membrane is the force required to drive F-actin network retrograde flow.","lang":"eng"}],"intvolume":" 29","status":"public","ddc":["570"],"title":"On the relation between filament density, force generation, and protrusion rate in mesenchymal cell motility","_id":"5992","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","oa_version":"Published Version","file":[{"checksum":"e98465b4416b3e804c47f40086932af2","date_updated":"2020-07-14T12:47:15Z","date_created":"2019-02-14T12:34:29Z","relation":"main_file","file_id":"5994","file_size":6668971,"content_type":"application/pdf","creator":"kschuh","access_level":"open_access","file_name":"2018_ASCB_Dolati.pdf"}],"publication_identifier":{"eissn":["1939-4586"]},"month":"11","isi":1,"quality_controlled":"1","external_id":{"pmid":["30156465"],"isi":["000455641000011"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1091/mbc.e18-02-0082","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","file_date_updated":"2020-07-14T12:47:15Z","department":[{"_id":"MiSi"}],"publisher":"American Society for Cell Biology ","publication_status":"published","pmid":1,"year":"2018","volume":29,"date_created":"2019-02-14T12:25:47Z","date_updated":"2023-09-19T14:30:23Z","author":[{"last_name":"Dolati","first_name":"Setareh","full_name":"Dolati, Setareh"},{"first_name":"Frieda","last_name":"Kage","full_name":"Kage, Frieda"},{"last_name":"Mueller","first_name":"Jan","full_name":"Mueller, Jan"},{"first_name":"Mathias","last_name":"Müsken","full_name":"Müsken, Mathias"},{"first_name":"Marieluise","last_name":"Kirchner","full_name":"Kirchner, Marieluise"},{"last_name":"Dittmar","first_name":"Gunnar","full_name":"Dittmar, Gunnar"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"},{"first_name":"Klemens","last_name":"Rottner","full_name":"Rottner, Klemens"},{"last_name":"Falcke","first_name":"Martin","full_name":"Falcke, Martin"}]},{"scopus_import":"1","day":"07","article_processing_charge":"No","publication":"Proceedings of the National Academy of Sciences","citation":{"ista":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, Fernandez P, López-Jury L, González-Cabrera C, Karten HJ, Luksch H, Marín GJ. 2018. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 115(32), E7615–E7623.","ieee":"F. Garrido-Charad et al., ““Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network,” Proceedings of the National Academy of Sciences, vol. 115, no. 32. National Academy of Sciences, pp. E7615–E7623, 2018.","apa":"Garrido-Charad, F., Vega Zuniga, T. A., Gutiérrez-Ibáñez, C., Fernandez, P., López-Jury, L., González-Cabrera, C., … Marín, G. J. (2018). “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1804517115","ama":"Garrido-Charad F, Vega Zuniga TA, Gutiérrez-Ibáñez C, et al. “Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network. Proceedings of the National Academy of Sciences. 2018;115(32):E7615-E7623. doi:10.1073/pnas.1804517115","chicago":"Garrido-Charad, Florencia, Tomas A Vega Zuniga, Cristián Gutiérrez-Ibáñez, Pedro Fernandez, Luciana López-Jury, Cristian González-Cabrera, Harvey J. Karten, Harald Luksch, and Gonzalo J. Marín. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1804517115.","mla":"Garrido-Charad, Florencia, et al. ““Shepherd’s Crook” Neurons Drive and Synchronize the Enhancing and Suppressive Mechanisms of the Midbrain Stimulus Selection Network.” Proceedings of the National Academy of Sciences, vol. 115, no. 32, National Academy of Sciences, 2018, pp. E7615–23, doi:10.1073/pnas.1804517115.","short":"F. Garrido-Charad, T.A. Vega Zuniga, C. Gutiérrez-Ibáñez, P. Fernandez, L. López-Jury, C. González-Cabrera, H.J. Karten, H. Luksch, G.J. Marín, Proceedings of the National Academy of Sciences 115 (2018) E7615–E7623."},"page":"E7615-E7623","date_published":"2018-08-07T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"The optic tectum (TeO), or superior colliculus, is a multisensory midbrain center that organizes spatially orienting responses to relevant stimuli. To define the stimulus with the highest priority at each moment, a network of reciprocal connections between the TeO and the isthmi promotes competition between concurrent tectal inputs. In the avian midbrain, the neurons mediating enhancement and suppression of tectal inputs are located in separate isthmic nuclei, facilitating the analysis of the neural processes that mediate competition. A specific subset of radial neurons in the intermediate tectal layers relay retinal inputs to the isthmi, but at present it is unclear whether separate neurons innervate individual nuclei or a single neural type sends a common input to several of them. In this study, we used in vitro neural tracing and cell-filling experiments in chickens to show that single neurons innervate, via axon collaterals, the three nuclei that comprise the isthmotectal network. This demonstrates that the input signals representing the strength of the incoming stimuli are simultaneously relayed to the mechanisms promoting both enhancement and suppression of the input signals. By performing in vivo recordings in anesthetized chicks, we also show that this common input generates synchrony between both antagonistic mechanisms, demonstrating that activity enhancement and suppression are closely coordinated. From a computational point of view, these results suggest that these tectal neurons constitute integrative nodes that combine inputs from different sources to drive in parallel several concurrent neural processes, each performing complementary functions within the network through different firing patterns and connectivity."}],"issue":"32","_id":"6010","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public","title":"“Shepherd’s crook” neurons drive and synchronize the enhancing and suppressive mechanisms of the midbrain stimulus selection network","intvolume":" 115","oa_version":"Submitted Version","month":"08","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30026198"}],"external_id":{"isi":["000440982000020"],"pmid":["30026198"]},"oa":1,"isi":1,"quality_controlled":"1","doi":"10.1073/pnas.1804517115","language":[{"iso":"eng"}],"year":"2018","pmid":1,"publication_status":"published","publisher":"National Academy of Sciences","department":[{"_id":"MaJö"}],"author":[{"first_name":"Florencia","last_name":"Garrido-Charad","full_name":"Garrido-Charad, Florencia"},{"last_name":"Vega Zuniga","first_name":"Tomas A","id":"2E7C4E78-F248-11E8-B48F-1D18A9856A87","full_name":"Vega Zuniga, Tomas A"},{"last_name":"Gutiérrez-Ibáñez","first_name":"Cristián","full_name":"Gutiérrez-Ibáñez, Cristián"},{"full_name":"Fernandez, Pedro","first_name":"Pedro","last_name":"Fernandez"},{"last_name":"López-Jury","first_name":"Luciana","full_name":"López-Jury, Luciana"},{"full_name":"González-Cabrera, Cristian","last_name":"González-Cabrera","first_name":"Cristian"},{"full_name":"Karten, Harvey J.","last_name":"Karten","first_name":"Harvey J."},{"full_name":"Luksch, Harald","last_name":"Luksch","first_name":"Harald"},{"full_name":"Marín, Gonzalo J.","first_name":"Gonzalo J.","last_name":"Marín"}],"date_created":"2019-02-14T14:33:34Z","date_updated":"2023-09-19T14:35:36Z","volume":115}]