[{"department":[{"_id":"JiFr"}],"publist_id":"5248","language":[{"iso":"eng"}],"publisher":"Cell Press","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Sassi, Massimiliano","first_name":"Massimiliano","last_name":"Sassi"},{"full_name":"Ali, Olivier","last_name":"Ali","first_name":"Olivier"},{"full_name":"Boudon, Frédéric","first_name":"Frédéric","last_name":"Boudon"},{"full_name":"Cloarec, Gladys","first_name":"Gladys","last_name":"Cloarec"},{"last_name":"Abad","first_name":"Ursula","full_name":"Abad, Ursula"},{"full_name":"Cellier, Coralie","first_name":"Coralie","last_name":"Cellier"},{"last_name":"Chen","first_name":"Xu","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","full_name":"Chen, Xu"},{"full_name":"Gilles, Benjamin","first_name":"Benjamin","last_name":"Gilles"},{"full_name":"Milani, Pascale","last_name":"Milani","first_name":"Pascale"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"},{"last_name":"Vernoux","first_name":"Teva","full_name":"Vernoux, Teva"},{"last_name":"Godin","first_name":"Christophe","full_name":"Godin, Christophe"},{"last_name":"Hamant","first_name":"Olivier","full_name":"Hamant, Olivier"},{"full_name":"Traas, Jan","last_name":"Traas","first_name":"Jan"}],"title":"An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis","publication_status":"published","citation":{"mla":"Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” <i>Current Biology</i>, vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:<a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">10.1016/j.cub.2014.08.036</a>.","apa":"Sassi, M., Ali, O., Boudon, F., Cloarec, G., Abad, U., Cellier, C., … Traas, J. (2014). An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. <i>Current Biology</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">https://doi.org/10.1016/j.cub.2014.08.036</a>","chicago":"Sassi, Massimiliano, Olivier Ali, Frédéric Boudon, Gladys Cloarec, Ursula Abad, Coralie Cellier, Xu Chen, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” <i>Current Biology</i>. Cell Press, 2014. <a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">https://doi.org/10.1016/j.cub.2014.08.036</a>.","ista":"Sassi M, Ali O, Boudon F, Cloarec G, Abad U, Cellier C, Chen X, Gilles B, Milani P, Friml J, Vernoux T, Godin C, Hamant O, Traas J. 2014. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. Current Biology. 24(19), 2335–2342.","short":"M. Sassi, O. Ali, F. Boudon, G. Cloarec, U. Abad, C. Cellier, X. Chen, B. Gilles, P. Milani, J. Friml, T. Vernoux, C. Godin, O. Hamant, J. Traas, Current Biology 24 (2014) 2335–2342.","ieee":"M. Sassi <i>et al.</i>, “An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis,” <i>Current Biology</i>, vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014.","ama":"Sassi M, Ali O, Boudon F, et al. An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis. <i>Current Biology</i>. 2014;24(19):2335-2342. doi:<a href=\"https://doi.org/10.1016/j.cub.2014.08.036\">10.1016/j.cub.2014.08.036</a>"},"scopus_import":1,"abstract":[{"lang":"eng","text":"To control morphogenesis, molecular regulatory networks have to interfere with the mechanical properties of the individual cells of developing organs and tissues, but how this is achieved is not well known. We study this issue here in the shoot meristem of higher plants, a group of undifferentiated cells where complex changes in growth rates and directions lead to the continuous formation of new organs [1, 2]. Here, we show that the plant hormone auxin plays an important role in this process via a dual, local effect on the extracellular matrix, the cell wall, which determines cell shape. Our study reveals that auxin not only causes a limited reduction in wall stiffness but also directly interferes with wall anisotropy via the regulation of cortical microtubule dynamics. We further show that to induce growth isotropy and organ outgrowth, auxin somehow interferes with the cortical microtubule-ordering activity of a network of proteins, including AUXIN BINDING PROTEIN 1 and KATANIN 1. Numerical simulations further indicate that the induced isotropy is sufficient to amplify the effects of the relatively minor changes in wall stiffness to promote organogenesis and the establishment of new growth axes in a robust manner."}],"type":"journal_article","_id":"1852","quality_controlled":"1","page":"2335 - 2342","year":"2014","date_published":"2014-10-06T00:00:00Z","intvolume":"        24","month":"10","acknowledgement":"This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ","date_updated":"2021-01-12T06:53:37Z","oa":1,"issue":"19","publication":"Current Biology","doi":"10.1016/j.cub.2014.08.036","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-01074821"}],"oa_version":"Submitted Version","volume":24,"date_created":"2018-12-11T11:54:22Z","status":"public","day":"06"},{"oa_version":"None","publication_status":"published","doi":"10.1109/IOT.2014.7030120","date_created":"2018-12-11T11:54:22Z","_id":"1853","day":"03","status":"public","quality_controlled":"1","citation":{"apa":"Jha, S., Tripakis, S., Seshia, S., &#38; Chatterjee, K. (2014). Game theoretic secure localization in wireless sensor networks (pp. 85–90). Presented at the IOT: Internet of Things, Cambridge, USA: IEEE. <a href=\"https://doi.org/10.1109/IOT.2014.7030120\">https://doi.org/10.1109/IOT.2014.7030120</a>","mla":"Jha, Susmit, et al. <i>Game Theoretic Secure Localization in Wireless Sensor Networks</i>. IEEE, 2014, pp. 85–90, doi:<a href=\"https://doi.org/10.1109/IOT.2014.7030120\">10.1109/IOT.2014.7030120</a>.","ista":"Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization in wireless sensor networks. IOT: Internet of Things, 85–90.","short":"S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90.","ieee":"S. Jha, S. Tripakis, S. Seshia, and K. Chatterjee, “Game theoretic secure localization in wireless sensor networks,” presented at the IOT: Internet of Things, Cambridge, USA, 2014, pp. 85–90.","ama":"Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization in wireless sensor networks. In: IEEE; 2014:85-90. doi:<a href=\"https://doi.org/10.1109/IOT.2014.7030120\">10.1109/IOT.2014.7030120</a>","chicago":"Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee. “Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE, 2014. <a href=\"https://doi.org/10.1109/IOT.2014.7030120\">https://doi.org/10.1109/IOT.2014.7030120</a>."},"abstract":[{"lang":"eng","text":"Wireless sensor networks (WSNs) composed of low-power, low-cost sensor nodes are expected to form the backbone of future intelligent networks for a broad range of civil, industrial and military applications. These sensor nodes are often deployed through random spreading, and function in dynamic environments. Many applications of WSNs such as pollution tracking, forest fire detection, and military surveillance require knowledge of the location of constituent nodes. But the use of technologies such as GPS on all nodes is prohibitive due to power and cost constraints. So, the sensor nodes need to autonomously determine their locations. Most localization techniques use anchor nodes with known locations to determine the position of remaining nodes. Localization techniques have two conflicting requirements. On one hand, an ideal localization technique should be computationally simple and on the other hand, it must be resistant to attacks that compromise anchor nodes. In this paper, we propose a computationally light-weight game theoretic secure localization technique and demonstrate its effectiveness in comparison to existing techniques."}],"type":"conference","language":[{"iso":"eng"}],"year":"2014","page":"85 - 90","publist_id":"5247","department":[{"_id":"KrCh"}],"conference":{"end_date":"2014-10-08","start_date":"2014-10-06","name":"IOT: Internet of Things","location":"Cambridge, USA"},"date_updated":"2021-01-12T06:53:38Z","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Susmit","last_name":"Jha","full_name":"Jha, Susmit"},{"full_name":"Tripakis, Stavros","first_name":"Stavros","last_name":"Tripakis"},{"full_name":"Seshia, Sanjit","last_name":"Seshia","first_name":"Sanjit"},{"id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"}],"title":"Game theoretic secure localization in wireless sensor networks","date_published":"2014-02-03T00:00:00Z","month":"02","publisher":"IEEE"},{"language":[{"iso":"eng"}],"pubrep_id":"574","publist_id":"5246","department":[{"_id":"ChWo"}],"file":[{"checksum":"91946bfc509c77f5fd3151a3ff2b2c8f","relation":"main_file","access_level":"open_access","file_id":"5182","content_type":"application/pdf","file_size":24817484,"creator":"system","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:15:58Z","file_name":"IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Partial shape matching using transformation parameter similarity","author":[{"full_name":"Guerrero, Paul","first_name":"Paul","last_name":"Guerrero"},{"full_name":"Auzinger, Thomas","id":"4718F954-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas","orcid":"0000-0002-1546-3265","last_name":"Auzinger"},{"last_name":"Wimmer","first_name":"Michael","full_name":"Wimmer, Michael"},{"full_name":"Jeschke, Stefan","last_name":"Jeschke","first_name":"Stefan","id":"44D6411A-F248-11E8-B48F-1D18A9856A87"}],"has_accepted_license":"1","publisher":"Wiley","publication_status":"published","_id":"1854","quality_controlled":"1","citation":{"ama":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation parameter similarity. <i>Computer Graphics Forum</i>. 2014;34(1):239-252. doi:<a href=\"https://doi.org/10.1111/cgf.12509\">10.1111/cgf.12509</a>","short":"P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 34 (2014) 239–252.","ista":"Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252.","ieee":"P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching using transformation parameter similarity,” <i>Computer Graphics Forum</i>, vol. 34, no. 1. Wiley, pp. 239–252, 2014.","chicago":"Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial Shape Matching Using Transformation Parameter Similarity.” <i>Computer Graphics Forum</i>. Wiley, 2014. <a href=\"https://doi.org/10.1111/cgf.12509\">https://doi.org/10.1111/cgf.12509</a>.","apa":"Guerrero, P., Auzinger, T., Wimmer, M., &#38; Jeschke, S. (2014). Partial shape matching using transformation parameter similarity. <i>Computer Graphics Forum</i>. Wiley. <a href=\"https://doi.org/10.1111/cgf.12509\">https://doi.org/10.1111/cgf.12509</a>","mla":"Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter Similarity.” <i>Computer Graphics Forum</i>, vol. 34, no. 1, Wiley, 2014, pp. 239–52, doi:<a href=\"https://doi.org/10.1111/cgf.12509\">10.1111/cgf.12509</a>."},"file_date_updated":"2020-07-14T12:45:19Z","type":"journal_article","scopus_import":1,"abstract":[{"text":"In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching. In this paper, we present a method for non-rigid, partial shape matching in vector graphics. Given a user-specified query region in a 2D shape, similar regions are found, even if they are non-linearly distorted. Furthermore, a non-linear mapping is established between the query regions and these matches, which allows the automatic transfer of editing operations such as texturing. This is achieved by a two-step approach. First, pointwise correspondences between the query region and the whole shape are established. The transformation parameters of these correspondences are registered in an appropriate transformation space. For transformations between similar regions, these parameters form surfaces in transformation space, which are extracted in the second step of our method. The extracted regions may be related to the query region by a non-rigid transform, enabling non-rigid shape matching.","lang":"eng"}],"year":"2014","page":"239 - 252","date_updated":"2021-01-12T06:53:38Z","issue":"1","oa":1,"month":"11","intvolume":"        34","date_published":"2014-11-05T00:00:00Z","oa_version":"Submitted Version","doi":"10.1111/cgf.12509","publication":"Computer Graphics Forum","date_created":"2018-12-11T11:54:22Z","ddc":["000"],"day":"05","status":"public","volume":34},{"project":[{"_id":"25716A02-B435-11E9-9278-68D0E5697425","name":"Polarity and subcellular dynamics in plants","call_identifier":"FP7","grant_number":"282300"}],"publication_status":"published","citation":{"apa":"Chen, X., Grandont, L., Li, H., Hauschild, R., Paque, S., Abuzeineh, A., … Friml, J. (2014). Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. <i>Nature</i>. Nature Publishing Group. <a href=\"https://doi.org/10.1038/nature13889\">https://doi.org/10.1038/nature13889</a>","mla":"Chen, Xu, et al. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” <i>Nature</i>, vol. 516, no. 729, Nature Publishing Group, 2014, pp. 90–93, doi:<a href=\"https://doi.org/10.1038/nature13889\">10.1038/nature13889</a>.","ama":"Chen X, Grandont L, Li H, et al. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. <i>Nature</i>. 2014;516(729):90-93. doi:<a href=\"https://doi.org/10.1038/nature13889\">10.1038/nature13889</a>","short":"X. Chen, L. Grandont, H. Li, R. Hauschild, S. Paque, A. Abuzeineh, H. Rakusova, E. Benková, C. Perrot Rechenmann, J. Friml, Nature 516 (2014) 90–93.","ieee":"X. Chen <i>et al.</i>, “Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules,” <i>Nature</i>, vol. 516, no. 729. Nature Publishing Group, pp. 90–93, 2014.","ista":"Chen X, Grandont L, Li H, Hauschild R, Paque S, Abuzeineh A, Rakusova H, Benková E, Perrot Rechenmann C, Friml J. 2014. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 516(729), 90–93.","chicago":"Chen, Xu, Laurie Grandont, Hongjiang Li, Robert Hauschild, Sébastien Paque, Anas Abuzeineh, Hana Rakusova, Eva Benková, Catherine Perrot Rechenmann, and Jiří Friml. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” <i>Nature</i>. Nature Publishing Group, 2014. <a href=\"https://doi.org/10.1038/nature13889\">https://doi.org/10.1038/nature13889</a>."},"publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"abstract":[{"text":"The prominent and evolutionarily ancient role of the plant hormone auxin is the regulation of cell expansion. Cell expansion requires ordered arrangement of the cytoskeleton but molecular mechanisms underlying its regulation by signalling molecules including auxin are unknown. Here we show in the model plant Arabidopsis thaliana that in elongating cells exogenous application of auxin or redistribution of endogenous auxin induces very rapid microtubule re-orientation from transverse to longitudinal, coherent with the inhibition of cell expansion. This fast auxin effect requires auxin binding protein 1 (ABP1) and involves a contribution of downstream signalling components such as ROP6 GTPase, ROP-interactive protein RIC1 and the microtubule-severing protein katanin. These components are required for rapid auxin-and ABP1-mediated re-orientation of microtubules to regulate cell elongation in roots and dark-grown hypocotyls as well as asymmetric growth during gravitropic responses.","lang":"eng"}],"scopus_import":"1","type":"journal_article","_id":"1862","quality_controlled":"1","article_processing_charge":"No","publist_id":"5237","department":[{"_id":"JiFr"},{"_id":"Bio"},{"_id":"EvBe"}],"language":[{"iso":"eng"}],"article_type":"original","publisher":"Nature Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Chen, Xu","last_name":"Chen","id":"4E5ADCAA-F248-11E8-B48F-1D18A9856A87","first_name":"Xu"},{"first_name":"Laurie","last_name":"Grandont","full_name":"Grandont, Laurie"},{"full_name":"Li, Hongjiang","last_name":"Li","orcid":"0000-0001-5039-9660","id":"33CA54A6-F248-11E8-B48F-1D18A9856A87","first_name":"Hongjiang"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","orcid":"0000-0001-9843-3522","first_name":"Robert","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Sébastien","last_name":"Paque","full_name":"Paque, Sébastien"},{"full_name":"Abuzeineh, Anas","last_name":"Abuzeineh","first_name":"Anas"},{"full_name":"Rakusova, Hana","id":"4CAAA450-78D2-11EA-8E57-B40A396E08BA","first_name":"Hana","last_name":"Rakusova"},{"orcid":"0000-0002-8510-9739","last_name":"Benková","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","full_name":"Benková, Eva"},{"full_name":"Perrot Rechenmann, Catherine","last_name":"Perrot Rechenmann","first_name":"Catherine"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"}],"title":"Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules","publication":"Nature","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/","open_access":"1"}],"doi":"10.1038/nature13889","oa_version":"Submitted Version","ec_funded":1,"volume":516,"pmid":1,"date_created":"2018-12-11T11:54:25Z","status":"public","day":"04","external_id":{"pmid":["25409144"]},"page":"90 - 93","year":"2014","date_published":"2014-12-04T00:00:00Z","intvolume":"       516","month":"12","acknowledgement":"We thank R. Dixit for performing complementary experiments, D. W. Ehrhardt and T. Hashimoto for providing the seeds of TUB6–RFP and EB1b–GFP respectively, E. Zazimalova, J. Petrasek and M. Fendrych for discussing the manuscript and J. Leung for text optimization. This work was supported by the European Research Council (project ERC-2011-StG-20101109-PSDP, to J.F.), ANR blanc AuxiWall project (ANR-11-BSV5-0007, to C.P.-R. and L.G.) and the Agency for Innovation by Science and Technology (IWT) (to H.R.). This work benefited from the facilities and expertise of the Imagif Cell Biology platform (http://www.imagif.cnrs.fr), which is supported by the Conseil Général de l’Essonne.","date_updated":"2025-05-07T11:12:31Z","oa":1,"issue":"729"},{"project":[{"grant_number":"267989","call_identifier":"FP7","_id":"25EE3708-B435-11E9-9278-68D0E5697425","name":"Quantitative Reactive Modeling"},{"name":"Game Theory","_id":"25863FF4-B435-11E9-9278-68D0E5697425","grant_number":"S11407","call_identifier":"FWF"}],"publication_status":"published","editor":[{"full_name":"Yahav, Eran","last_name":"Yahav","first_name":"Eran"}],"_id":"1869","quality_controlled":"1","citation":{"chicago":"Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” In <i>HVC 2014</i>, edited by Eran Yahav, 8855:68–74. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-13338-6_6\">https://doi.org/10.1007/978-3-319-13338-6_6</a>.","short":"G. Hofferek, A. Gupta, in:, E. Yahav (Ed.), HVC 2014, Springer, 2014, pp. 68–74.","ista":"Hofferek G, Gupta A. 2014. Suraq - a controller synthesis tool using uninterpreted functions. HVC 2014. HVC: Haifa Verification Conference, LNCS, vol. 8855, 68–74.","ieee":"G. Hofferek and A. Gupta, “Suraq - a controller synthesis tool using uninterpreted functions,” in <i>HVC 2014</i>, Haifa, Israel, 2014, vol. 8855, pp. 68–74.","ama":"Hofferek G, Gupta A. Suraq - a controller synthesis tool using uninterpreted functions. In: Yahav E, ed. <i>HVC 2014</i>. Vol 8855. Springer; 2014:68-74. doi:<a href=\"https://doi.org/10.1007/978-3-319-13338-6_6\">10.1007/978-3-319-13338-6_6</a>","mla":"Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” <i>HVC 2014</i>, edited by Eran Yahav, vol. 8855, Springer, 2014, pp. 68–74, doi:<a href=\"https://doi.org/10.1007/978-3-319-13338-6_6\">10.1007/978-3-319-13338-6_6</a>.","apa":"Hofferek, G., &#38; Gupta, A. (2014). Suraq - a controller synthesis tool using uninterpreted functions. In E. Yahav (Ed.), <i>HVC 2014</i> (Vol. 8855, pp. 68–74). Haifa, Israel: Springer. <a href=\"https://doi.org/10.1007/978-3-319-13338-6_6\">https://doi.org/10.1007/978-3-319-13338-6_6</a>"},"type":"conference","abstract":[{"lang":"eng","text":"Boolean controllers for systems with complex datapaths are often very difficult to implement correctly, in particular when concurrency is involved. Yet, in many instances it is easy to formally specify correctness. For example, the specification for the controller of a pipelined processor only has to state that the pipelined processor gives the same results as a non-pipelined reference design. This makes such controllers a good target for automated synthesis. However, an efficient abstraction for the complex datapath elements is needed, as a bit-precise description is often infeasible. We present Suraq, the first controller synthesis tool which uses uninterpreted functions for the abstraction. Quantified firstorder formulas (with specific quantifier structure) serve as the specification language from which Suraq synthesizes Boolean controllers. Suraq transforms the specification into an unsatisfiable SMT formula, and uses Craig interpolation to compute its results. Using Suraq, we were able to synthesize a controller (consisting of two Boolean signals) for a five-stage pipelined DLX processor in roughly one hour and 15 minutes."}],"language":[{"iso":"eng"}],"department":[{"_id":"ToHe"}],"publist_id":"5228","author":[{"full_name":"Hofferek, Georg","last_name":"Hofferek","first_name":"Georg"},{"full_name":"Gupta, Ashutosh","last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87"}],"title":"Suraq - a controller synthesis tool using uninterpreted functions","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","publisher":"Springer","ec_funded":1,"oa_version":"None","doi":"10.1007/978-3-319-13338-6_6","publication":"HVC 2014","date_created":"2018-12-11T11:54:27Z","status":"public","day":"01","volume":8855,"year":"2014","page":"68 - 74","conference":{"location":"Haifa, Israel","name":"HVC: Haifa Verification Conference","end_date":"2014-11-20","start_date":"2014-11-18"},"date_updated":"2021-01-12T06:53:44Z","month":"01","intvolume":"      8855","date_published":"2014-01-01T00:00:00Z","alternative_title":["LNCS"],"acknowledgement":"The work presented in this paper was supported in part by the European Research Council (ERC) under grant agreement QUAINT (I774-N23)"},{"date_updated":"2021-01-12T06:53:45Z","oa":1,"intvolume":"        29","month":"12","alternative_title":["LIPIcs"],"date_published":"2014-12-01T00:00:00Z","year":"2014","page":"431 - 443","conference":{"start_date":"2014-12-15","end_date":"2014-12-17","name":"FSTTCS: Foundations of Software Technology and Theoretical Computer Science","location":"Delhi, India"},"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:54:27Z","ddc":["004"],"status":"public","day":"01","volume":29,"oa_version":"Published Version","doi":"10.4230/LIPIcs.FSTTCS.2014.431","publication":"Leibniz International Proceedings in Informatics, LIPIcs","file":[{"content_type":"application/pdf","file_id":"4734","creator":"system","file_size":562151,"relation":"main_file","access_level":"open_access","checksum":"7b1aff1710a8bffb7080ec07f62d9a17","file_name":"IST-2017-804-v1+1_37.pdf","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:09:11Z"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000−0002−2985−7724","last_name":"Henzinger"},{"last_name":"Otop","first_name":"Jan","id":"2FC5DA74-F248-11E8-B48F-1D18A9856A87","full_name":"Otop, Jan"},{"full_name":"Samanta, Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87","first_name":"Roopsha","last_name":"Samanta"}],"title":"Lipschitz robustness of finite-state transducers","has_accepted_license":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","language":[{"iso":"eng"}],"pubrep_id":"804","department":[{"_id":"ToHe"}],"publist_id":"5227","_id":"1870","quality_controlled":"1","citation":{"apa":"Henzinger, T. A., Otop, J., &#38; Samanta, R. (2014). Lipschitz robustness of finite-state transducers. In <i>Leibniz International Proceedings in Informatics, LIPIcs</i> (Vol. 29, pp. 431–443). Delhi, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431</a>","mla":"Henzinger, Thomas A., et al. “Lipschitz Robustness of Finite-State Transducers.” <i>Leibniz International Proceedings in Informatics, LIPIcs</i>, vol. 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–43, doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">10.4230/LIPIcs.FSTTCS.2014.431</a>.","ista":"Henzinger TA, Otop J, Samanta R. 2014. Lipschitz robustness of finite-state transducers. Leibniz International Proceedings in Informatics, LIPIcs. FSTTCS: Foundations of Software Technology and Theoretical Computer Science, LIPIcs, vol. 29, 431–443.","ieee":"T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of finite-state transducers,” in <i>Leibniz International Proceedings in Informatics, LIPIcs</i>, Delhi, India, 2014, vol. 29, pp. 431–443.","short":"T.A. Henzinger, J. Otop, R. Samanta, in:, Leibniz International Proceedings in Informatics, LIPIcs, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–443.","ama":"Henzinger TA, Otop J, Samanta R. Lipschitz robustness of finite-state transducers. In: <i>Leibniz International Proceedings in Informatics, LIPIcs</i>. Vol 29. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:431-443. doi:<a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">10.4230/LIPIcs.FSTTCS.2014.431</a>","chicago":"Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Finite-State Transducers.” In <i>Leibniz International Proceedings in Informatics, LIPIcs</i>, 29:431–43. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. <a href=\"https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431\">https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431</a>."},"type":"conference","file_date_updated":"2020-07-14T12:45:19Z","abstract":[{"text":"We investigate the problem of checking if a finite-state transducer is robust to uncertainty in its input. Our notion of robustness is based on the analytic notion of Lipschitz continuity - a transducer is K-(Lipschitz) robust if the perturbation in its output is at most K times the perturbation in its input. We quantify input and output perturbation using similarity functions. We show that K-robustness is undecidable even for deterministic transducers. We identify a class of functional transducers, which admits a polynomial time automata-theoretic decision procedure for K-robustness. This class includes Mealy machines and functional letter-to-letter transducers. We also study K-robustness of nondeterministic transducers. Since a nondeterministic transducer generates a set of output words for each input word, we quantify output perturbation using setsimilarity functions. We show that K-robustness of nondeterministic transducers is undecidable, even for letter-to-letter transducers. We identify a class of set-similarity functions which admit decidable K-robustness of letter-to-letter transducers.","lang":"eng"}],"publication_status":"published"},{"conference":{"end_date":"2014-11-07","start_date":"2014-11-03","name":"ATVA: Automated Technology for Verification and Analysis","location":"Sydney, Australia"},"page":"185 - 200","year":"2014","acknowledgement":"This research was supported in part by the Austrian National Research Network RiSE (S11410-N23).","month":"01","intvolume":"      8837","alternative_title":["LNCS"],"date_published":"2014-01-01T00:00:00Z","oa":1,"date_updated":"2021-01-12T06:53:45Z","doi":"10.1007/978-3-319-11936-6_14","publication":"ATVA 2014","oa_version":"Submitted Version","ec_funded":1,"volume":8837,"status":"public","day":"01","date_created":"2018-12-11T11:54:28Z","ddc":["000"],"publist_id":"5226","department":[{"_id":"ToHe"}],"pubrep_id":"641","language":[{"iso":"eng"}],"publisher":"Springer","has_accepted_license":"1","file":[{"checksum":"af4bd3fc1f4c93075e4dc5cbf625fe7b","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"4801","file_size":244294,"creator":"system","date_created":"2018-12-12T10:10:15Z","date_updated":"2020-07-14T12:45:19Z","file_name":"IST-2016-641-v1+1_atva2014.pdf"}],"title":"Extensional crisis and proving identity","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Gupta","first_name":"Ashutosh","id":"335E5684-F248-11E8-B48F-1D18A9856A87","full_name":"Gupta, Ashutosh"},{"last_name":"Kovács","first_name":"Laura","full_name":"Kovács, Laura"},{"full_name":"Kragl, Bernhard","first_name":"Bernhard","id":"320FC952-F248-11E8-B48F-1D18A9856A87","last_name":"Kragl","orcid":"0000-0001-7745-9117"},{"full_name":"Voronkov, Andrei","first_name":"Andrei","last_name":"Voronkov"}],"publication_status":"published","project":[{"name":"Quantitative Reactive Modeling","_id":"25EE3708-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"267989"},{"name":"Moderne Concurrency Paradigms","_id":"25F5A88A-B435-11E9-9278-68D0E5697425","grant_number":"S11402-N23","call_identifier":"FWF"}],"type":"conference","file_date_updated":"2020-07-14T12:45:19Z","abstract":[{"lang":"eng","text":"Extensionality axioms are common when reasoning about data collections, such as arrays and functions in program analysis, or sets in mathematics. An extensionality axiom asserts that two collections are equal if they consist of the same elements at the same indices. Using extensionality is often required to show that two collections are equal. A typical example is the set theory theorem (∀x)(∀y)x∪y = y ∪x. Interestingly, while humans have no problem with proving such set identities using extensionality, they are very hard for superposition theorem provers because of the calculi they use. In this paper we show how addition of a new inference rule, called extensionality resolution, allows first-order theorem provers to easily solve problems no modern first-order theorem prover can solve. We illustrate this by running the VAMPIRE theorem prover with extensionality resolution on a number of set theory and array problems. Extensionality resolution helps VAMPIRE to solve problems from the TPTP library of first-order problems that were never solved before by any prover."}],"scopus_import":1,"citation":{"mla":"Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” <i>ATVA 2014</i>, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 185–200, doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">10.1007/978-3-319-11936-6_14</a>.","apa":"Gupta, A., Kovács, L., Kragl, B., &#38; Voronkov, A. (2014). Extensional crisis and proving identity. In F. Cassez &#38; J.-F. Raskin (Eds.), <i>ATVA 2014</i> (Vol. 8837, pp. 185–200). Sydney, Australia: Springer. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">https://doi.org/10.1007/978-3-319-11936-6_14</a>","chicago":"Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional Crisis and Proving Identity.” In <i>ATVA 2014</i>, edited by Franck Cassez and Jean-François Raskin, 8837:185–200. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">https://doi.org/10.1007/978-3-319-11936-6_14</a>.","ama":"Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity. In: Cassez F, Raskin J-F, eds. <i>ATVA 2014</i>. Vol 8837. Springer; 2014:185-200. doi:<a href=\"https://doi.org/10.1007/978-3-319-11936-6_14\">10.1007/978-3-319-11936-6_14</a>","short":"A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, F. Cassez, J.-F. Raskin (Eds.), ATVA 2014, Springer, 2014, pp. 185–200.","ieee":"A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving identity,” in <i>ATVA 2014</i>, Sydney, Australia, 2014, vol. 8837, pp. 185–200.","ista":"Gupta A, Kovács L, Kragl B, Voronkov A. 2014. Extensional crisis and proving identity. ATVA 2014. ATVA: Automated Technology for Verification and Analysis, LNCS, vol. 8837, 185–200."},"quality_controlled":"1","editor":[{"first_name":"Franck","last_name":"Cassez","full_name":"Cassez, Franck"},{"full_name":"Raskin, Jean-François","last_name":"Raskin","first_name":"Jean-François"}],"_id":"1872"},{"scopus_import":1,"abstract":[{"text":"We present a formal framework for repairing infinite-state, imperative, sequential programs, with (possibly recursive) procedures and multiple assertions; the framework can generate repaired programs by modifying the original erroneous program in multiple program locations, and can ensure the readability of the repaired program using user-defined expression templates; the framework also generates a set of inductive assertions that serve as a proof of correctness of the repaired program. As a step toward integrating programmer intent and intuition in automated program repair, we present a cost-aware formulation - given a cost function associated with permissible statement modifications, the goal is to ensure that the total program modification cost does not exceed a given repair budget. As part of our predicate abstractionbased solution framework, we present a sound and complete algorithm for repair of Boolean programs. We have developed a prototype tool based on SMT solving and used it successfully to repair diverse errors in benchmark C programs.","lang":"eng"}],"file_date_updated":"2020-07-14T12:45:19Z","type":"conference","citation":{"ista":"Samanta R, Olivo O, Allen E. 2014. Cost-aware automatic program repair. SAS: Static Analysis Symposium, LNCS, vol. 8723, 268–284.","short":"R. Samanta, O. Olivo, E. Allen, in:, M. Müller-Olm, H. Seidl (Eds.), Springer, 2014, pp. 268–284.","ieee":"R. Samanta, O. Olivo, and E. Allen, “Cost-aware automatic program repair,” presented at the SAS: Static Analysis Symposium, Munich, Germany, 2014, vol. 8723, pp. 268–284.","ama":"Samanta R, Olivo O, Allen E. Cost-aware automatic program repair. In: Müller-Olm M, Seidl H, eds. Vol 8723. Springer; 2014:268-284. doi:<a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">10.1007/978-3-319-10936-7_17</a>","chicago":"Samanta, Roopsha, Oswaldo Olivo, and Emerson Allen. “Cost-Aware Automatic Program Repair.” edited by Markus Müller-Olm and Helmut Seidl, 8723:268–84. Springer, 2014. <a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">https://doi.org/10.1007/978-3-319-10936-7_17</a>.","apa":"Samanta, R., Olivo, O., &#38; Allen, E. (2014). Cost-aware automatic program repair. In M. Müller-Olm &#38; H. Seidl (Eds.) (Vol. 8723, pp. 268–284). Presented at the SAS: Static Analysis Symposium, Munich, Germany: Springer. <a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">https://doi.org/10.1007/978-3-319-10936-7_17</a>","mla":"Samanta, Roopsha, et al. <i>Cost-Aware Automatic Program Repair</i>. Edited by Markus Müller-Olm and Helmut Seidl, vol. 8723, Springer, 2014, pp. 268–84, doi:<a href=\"https://doi.org/10.1007/978-3-319-10936-7_17\">10.1007/978-3-319-10936-7_17</a>."},"quality_controlled":"1","_id":"1875","editor":[{"last_name":"Müller-Olm","first_name":"Markus","full_name":"Müller-Olm, Markus"},{"full_name":"Seidl, Helmut","first_name":"Helmut","last_name":"Seidl"}],"publication_status":"published","publisher":"Springer","has_accepted_license":"1","author":[{"full_name":"Samanta, Roopsha","last_name":"Samanta","first_name":"Roopsha","id":"3D2AAC08-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Olivo, Oswaldo","first_name":"Oswaldo","last_name":"Olivo"},{"full_name":"Allen, Emerson","last_name":"Allen","first_name":"Emerson"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","title":"Cost-aware automatic program repair","file":[{"file_id":"4650","content_type":"application/pdf","file_size":409485,"creator":"system","checksum":"78ec4ea1bdecc676cd3e8cad35c6182c","relation":"main_file","access_level":"open_access","file_name":"IST-2014-313-v1+1_SOE.SAS14.pdf","date_updated":"2020-07-14T12:45:19Z","date_created":"2018-12-12T10:07:51Z"}],"department":[{"_id":"ToHe"}],"publist_id":"5221","pubrep_id":"313","language":[{"iso":"eng"}],"volume":8723,"status":"public","day":"01","ddc":["000","005"],"date_created":"2018-12-11T11:54:29Z","doi":"10.1007/978-3-319-10936-7_17","oa_version":"Submitted Version","alternative_title":["LNCS"],"date_published":"2014-09-01T00:00:00Z","month":"09","intvolume":"      8723","oa":1,"date_updated":"2021-01-12T06:53:46Z","conference":{"location":"Munich, Germany","name":"SAS: Static Analysis Symposium","end_date":"2014-09-14","start_date":"2014-09-11"},"page":"268 - 284","year":"2014"},{"day":"01","status":"public","date_created":"2018-12-11T11:54:29Z","volume":14,"oa_version":"Submitted Version","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1211.7053"}],"doi":"10.17323/1609-4514-2014-14-3-491-504","publication":"Moscow Mathematical Journal","issue":"3","oa":1,"date_updated":"2022-03-03T11:47:09Z","intvolume":"        14","month":"07","date_published":"2014-07-01T00:00:00Z","year":"2014","external_id":{"arxiv":["1211.7053"]},"page":"491 - 504","quality_controlled":"1","_id":"1876","type":"journal_article","abstract":[{"text":"We study densities of functionals over uniformly bounded triangulations of a Delaunay set of vertices, and prove that the minimum is attained for the Delaunay triangulation if this is the case for finite sets.","lang":"eng"}],"arxiv":1,"scopus_import":"1","publication_identifier":{"issn":["16093321"]},"citation":{"mla":"Dolbilin, Nikolai, et al. “Functionals on Triangulations of Delaunay Sets.” <i>Moscow Mathematical Journal</i>, vol. 14, no. 3, Independent University of Moscow, 2014, pp. 491–504, doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">10.17323/1609-4514-2014-14-3-491-504</a>.","apa":"Dolbilin, N., Edelsbrunner, H., Glazyrin, A., &#38; Musin, O. (2014). Functionals on triangulations of delaunay sets. <i>Moscow Mathematical Journal</i>. Independent University of Moscow. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">https://doi.org/10.17323/1609-4514-2014-14-3-491-504</a>","chicago":"Dolbilin, Nikolai, Herbert Edelsbrunner, Alexey Glazyrin, and Oleg Musin. “Functionals on Triangulations of Delaunay Sets.” <i>Moscow Mathematical Journal</i>. Independent University of Moscow, 2014. <a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">https://doi.org/10.17323/1609-4514-2014-14-3-491-504</a>.","ama":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. Functionals on triangulations of delaunay sets. <i>Moscow Mathematical Journal</i>. 2014;14(3):491-504. doi:<a href=\"https://doi.org/10.17323/1609-4514-2014-14-3-491-504\">10.17323/1609-4514-2014-14-3-491-504</a>","short":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, O. Musin, Moscow Mathematical Journal 14 (2014) 491–504.","ieee":"N. Dolbilin, H. Edelsbrunner, A. Glazyrin, and O. Musin, “Functionals on triangulations of delaunay sets,” <i>Moscow Mathematical Journal</i>, vol. 14, no. 3. Independent University of Moscow, pp. 491–504, 2014.","ista":"Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. 2014. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 14(3), 491–504."},"publication_status":"published","author":[{"full_name":"Dolbilin, Nikolai","first_name":"Nikolai","last_name":"Dolbilin"},{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","last_name":"Edelsbrunner"},{"full_name":"Glazyrin, Alexey","last_name":"Glazyrin","first_name":"Alexey"},{"last_name":"Musin","first_name":"Oleg","full_name":"Musin, Oleg"}],"title":"Functionals on triangulations of delaunay sets","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Independent University of Moscow","article_type":"original","language":[{"iso":"eng"}],"department":[{"_id":"HeEd"}],"publist_id":"5220","article_processing_charge":"No"},{"date_created":"2018-12-11T11:54:30Z","_id":"1877","day":"23","quality_controlled":"1","status":"public","citation":{"ama":"Sixt MK, Vaahtomeri K. Physiology: Relax and come in. <i>Nature</i>. 2014;514(7523):441-442. doi:<a href=\"https://doi.org/10.1038/514441a\">10.1038/514441a</a>","ieee":"M. K. Sixt and K. Vaahtomeri, “Physiology: Relax and come in,” <i>Nature</i>, vol. 514, no. 7523. Springer Nature, pp. 441–442, 2014.","short":"M.K. Sixt, K. Vaahtomeri, Nature 514 (2014) 441–442.","ista":"Sixt MK, Vaahtomeri K. 2014. Physiology: Relax and come in. Nature. 514(7523), 441–442.","chicago":"Sixt, Michael K, and Kari Vaahtomeri. “Physiology: Relax and Come In.” <i>Nature</i>. Springer Nature, 2014. <a href=\"https://doi.org/10.1038/514441a\">https://doi.org/10.1038/514441a</a>.","apa":"Sixt, M. K., &#38; Vaahtomeri, K. (2014). Physiology: Relax and come in. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/514441a\">https://doi.org/10.1038/514441a</a>","mla":"Sixt, Michael K., and Kari Vaahtomeri. “Physiology: Relax and Come In.” <i>Nature</i>, vol. 514, no. 7523, Springer Nature, 2014, pp. 441–42, doi:<a href=\"https://doi.org/10.1038/514441a\">10.1038/514441a</a>."},"volume":514,"type":"journal_article","abstract":[{"lang":"eng","text":"During inflammation, lymph nodes swell with an influx of immune cells. New findings identify a signalling pathway that induces relaxation in the contractile cells that give structure to these organs."}],"scopus_import":1,"oa_version":"None","doi":"10.1038/514441a","publication_status":"published","publication":"Nature","date_updated":"2021-01-12T06:53:47Z","issue":"7523","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Physiology: Relax and come in","author":[{"orcid":"0000-0002-6620-9179","last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K","full_name":"Sixt, Michael K"},{"id":"368EE576-F248-11E8-B48F-1D18A9856A87","first_name":"Kari","last_name":"Vaahtomeri","orcid":"0000-0001-7829-3518","full_name":"Vaahtomeri, Kari"}],"intvolume":"       514","month":"10","date_published":"2014-10-23T00:00:00Z","publisher":"Springer Nature","language":[{"iso":"eng"}],"year":"2014","article_type":"letter_note","page":"441 - 442","publist_id":"5219","department":[{"_id":"MiSi"}]},{"oa_version":"None","main_file_link":[{"url":"http://www.bloodjournal.org/content/124/21/1952?sso-checked=true"}],"publication_status":"published","publication":"Blood","date_created":"2018-12-11T11:54:32Z","_id":"1884","status":"public","day":"04","citation":{"chicago":"Landau, Dan, Chip Stewart, Johannes Reiter, Michael Lawrence, Carrie Sougnez, Jennifer Brown, Armando Lopez Guillermo, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” <i>Blood</i>. American Society of Hematology, 2014.","ieee":"D. Landau <i>et al.</i>, “Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples,” <i>Blood</i>, vol. 124, no. 21. American Society of Hematology, pp. 1952–1952, 2014.","short":"D. Landau, C. Stewart, J. Reiter, M. Lawrence, C. Sougnez, J. Brown, A. Lopez Guillermo, S. Gabriel, E. Lander, D. Neuberg, C. López Otín, E. Campo, G. Getz, C. Wu, Blood 124 (2014) 1952–1952.","ista":"Landau D, Stewart C, Reiter J, Lawrence M, Sougnez C, Brown J, Lopez Guillermo A, Gabriel S, Lander E, Neuberg D, López Otín C, Campo E, Getz G, Wu C. 2014. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. Blood. 124(21), 1952–1952.","ama":"Landau D, Stewart C, Reiter J, et al. Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. <i>Blood</i>. 2014;124(21):1952-1952.","mla":"Landau, Dan, et al. “Novel Putative Driver Gene Mutations in Chronic Lymphocytic Leukemia (CLL): Results from a Combined Analysis of Whole Exome Sequencing of 262 Primary CLL Aamples.” <i>Blood</i>, vol. 124, no. 21, American Society of Hematology, 2014, pp. 1952–1952.","apa":"Landau, D., Stewart, C., Reiter, J., Lawrence, M., Sougnez, C., Brown, J., … Wu, C. (2014). Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples. <i>Blood</i>. American Society of Hematology."},"volume":124,"type":"journal_article","abstract":[{"lang":"eng","text":"Unbiased high-throughput massively parallel sequencing methods have transformed the process of discovery of novel putative driver gene mutations in cancer. In chronic lymphocytic leukemia (CLL), these methods have yielded several unexpected findings, including the driver genes SF3B1, NOTCH1 and POT1. Recent analysis, utilizing down-sampling of existing datasets, has shown that the discovery process of putative drivers is far from complete across cancer. In CLL, while driver gene mutations affecting >10% of patients were efficiently discovered with previously published CLL cohorts of up to 160 samples subjected to whole exome sequencing (WES), this sample size has only 0.78 power to detect drivers affecting 5% of patients, and only 0.12 power for drivers affecting 2% of patients. These calculations emphasize the need to apply unbiased WES to larger patient cohorts."}],"language":[{"iso":"eng"}],"year":"2014","page":"1952 - 1952","department":[{"_id":"KrCh"}],"publist_id":"5211","date_updated":"2021-01-12T06:53:50Z","issue":"21","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Landau","first_name":"Dan","full_name":"Landau, Dan"},{"full_name":"Stewart, Chip","last_name":"Stewart","first_name":"Chip"},{"full_name":"Reiter, Johannes","last_name":"Reiter","orcid":"0000-0002-0170-7353","first_name":"Johannes","id":"4A918E98-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lawrence, Michael","first_name":"Michael","last_name":"Lawrence"},{"first_name":"Carrie","last_name":"Sougnez","full_name":"Sougnez, Carrie"},{"full_name":"Brown, Jennifer","first_name":"Jennifer","last_name":"Brown"},{"first_name":"Armando","last_name":"Lopez Guillermo","full_name":"Lopez Guillermo, Armando"},{"full_name":"Gabriel, Stacey","last_name":"Gabriel","first_name":"Stacey"},{"full_name":"Lander, Eric","first_name":"Eric","last_name":"Lander"},{"first_name":"Donna","last_name":"Neuberg","full_name":"Neuberg, Donna"},{"full_name":"López Otín, Carlos","first_name":"Carlos","last_name":"López Otín"},{"full_name":"Campo, Elias","first_name":"Elias","last_name":"Campo"},{"full_name":"Getz, Gad","first_name":"Gad","last_name":"Getz"},{"full_name":"Wu, Catherine","last_name":"Wu","first_name":"Catherine"}],"title":"Novel putative driver gene mutations in chronic lymphocytic leukemia (CLL): results from a combined analysis of whole exome sequencing of 262 primary CLL aamples","intvolume":"       124","month":"12","date_published":"2014-12-04T00:00:00Z","publisher":"American Society of Hematology"},{"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:54:32Z","ddc":["570"],"day":"14","status":"public","oa_version":"Published Version","publication":"eLife","doi":"10.7554/eLife.03722","date_updated":"2021-01-12T06:53:50Z","oa":1,"issue":"November","date_published":"2014-11-14T00:00:00Z","month":"11","article_number":"e03722","year":"2014","_id":"1886","quality_controlled":"1","citation":{"mla":"Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” <i>ELife</i>, no. November, e03722, eLife Sciences Publications, 2014, doi:<a href=\"https://doi.org/10.7554/eLife.03722\">10.7554/eLife.03722</a>.","apa":"Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., &#38; Tkačik, G. (2014). Variance predicts salience in central sensory processing. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.03722\">https://doi.org/10.7554/eLife.03722</a>","chicago":"Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” <i>ELife</i>. eLife Sciences Publications, 2014. <a href=\"https://doi.org/10.7554/eLife.03722\">https://doi.org/10.7554/eLife.03722</a>.","ama":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. Variance predicts salience in central sensory processing. <i>eLife</i>. 2014;(November). doi:<a href=\"https://doi.org/10.7554/eLife.03722\">10.7554/eLife.03722</a>","ieee":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” <i>eLife</i>, no. November. eLife Sciences Publications, 2014.","short":"A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014).","ista":"Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. 2014. Variance predicts salience in central sensory processing. eLife. (November), e03722."},"scopus_import":1,"abstract":[{"lang":"eng","text":"Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime—when sampling limitations constrain performance—efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability."}],"file_date_updated":"2020-07-14T12:45:20Z","type":"journal_article","project":[{"name":"Sensitivity to higher-order statistics in natural scenes","_id":"254D1A94-B435-11E9-9278-68D0E5697425","grant_number":"P 25651-N26","call_identifier":"FWF"}],"publication_status":"published","title":"Variance predicts salience in central sensory processing","author":[{"last_name":"Hermundstad","first_name":"Ann","full_name":"Hermundstad, Ann"},{"first_name":"John","last_name":"Briguglio","full_name":"Briguglio, John"},{"first_name":"Mary","last_name":"Conte","full_name":"Conte, Mary"},{"full_name":"Victor, Jonathan","last_name":"Victor","first_name":"Jonathan"},{"first_name":"Vijay","last_name":"Balasubramanian","full_name":"Balasubramanian, Vijay"},{"full_name":"Tkacik, Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"IST-2016-420-v1+1_e03722.full.pdf","date_updated":"2020-07-14T12:45:20Z","date_created":"2018-12-12T10:12:04Z","creator":"system","file_size":5117086,"file_id":"4922","content_type":"application/pdf","access_level":"open_access","checksum":"766ac8999ac6e3364f10065a06024b8f","relation":"main_file"}],"has_accepted_license":"1","publisher":"eLife Sciences Publications","language":[{"iso":"eng"}],"pubrep_id":"420","publist_id":"5209","department":[{"_id":"GaTk"}]},{"oa_version":"Published Version","main_file_link":[{"url":"https://www.dzg-ev.de/wp-content/uploads/2019/05/zoologie2014.pdf","open_access":"1"}],"publication_status":"published","publication":"Zoologie","_id":"1887","date_created":"2018-12-11T11:54:33Z","quality_controlled":"1","day":"01","status":"public","citation":{"chicago":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” <i>Zoologie</i>. Deutsche Zoologische Gesellschaft, 2014.","ista":"Cremer S. 2014. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. Zoologie., 23–30.","short":"S. Cremer, Zoologie (2014) 23–30.","ieee":"S. Cremer, “Gemeinsame Krankheitsabwehr in Ameisengesellschaften,” <i>Zoologie</i>. Deutsche Zoologische Gesellschaft, pp. 23–30, 2014.","ama":"Cremer S. Gemeinsame Krankheitsabwehr in Ameisengesellschaften. <i>Zoologie</i>. 2014:23-30.","mla":"Cremer, Sylvia. “Gemeinsame Krankheitsabwehr in Ameisengesellschaften.” <i>Zoologie</i>, Deutsche Zoologische Gesellschaft, 2014, pp. 23–30.","apa":"Cremer, S. (2014). Gemeinsame Krankheitsabwehr in Ameisengesellschaften. <i>Zoologie</i>. Deutsche Zoologische Gesellschaft."},"type":"journal_article","language":[{"iso":"eng"}],"year":"2014","article_type":"original","page":"23 - 30","article_processing_charge":"No","publist_id":"5208","department":[{"_id":"SyCr"}],"date_updated":"2023-10-17T07:54:57Z","author":[{"full_name":"Cremer, Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","last_name":"Cremer","orcid":"0000-0002-2193-3868"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"title":"Gemeinsame Krankheitsabwehr in Ameisengesellschaften","month":"01","date_published":"2014-01-01T00:00:00Z","publisher":"Deutsche Zoologische Gesellschaft"},{"date_updated":"2023-10-17T12:28:45Z","title":"Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Cremer, Sylvia","first_name":"Sylvia","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","last_name":"Cremer"}],"month":"01","intvolume":"        43","date_published":"2014-01-01T00:00:00Z","alternative_title":["Rundgespräche der Kommission für Ökologie"],"publisher":"Verlag Dr. Friedrich Pfeil","language":[{"iso":"eng"}],"year":"2014","article_processing_charge":"No","page":"65 - 72","department":[{"_id":"SyCr"}],"publist_id":"5207","_id":"1888","date_created":"2018-12-11T11:54:33Z","day":"01","status":"public","quality_controlled":"1","publication_identifier":{"issn":["2366-2875"]},"citation":{"short":"S. Cremer, in:, Soziale Insekten in Einer Sich Wandelnden Welt, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.","ieee":"S. Cremer, “Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften,” in <i>Soziale Insekten in einer sich wandelnden Welt</i>, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72.","ista":"Cremer S. 2014.Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften. In: Soziale Insekten in einer sich wandelnden Welt. Rundgespräche der Kommission für Ökologie, vol. 43, 65–72.","ama":"Cremer S. Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften. In: <i>Soziale Insekten in Einer Sich Wandelnden Welt</i>. Vol 43. Verlag Dr. Friedrich Pfeil; 2014:65-72.","chicago":"Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene Wehrt  Bayerische Akademie Der Wissenschaften.” In <i>Soziale Insekten in Einer Sich Wandelnden Welt</i>, 43:65–72. Verlag Dr. Friedrich Pfeil, 2014.","apa":"Cremer, S. (2014). Soziale Immunität: Wie sich der Staat gegen Pathogene wehrt  Bayerische Akademie der Wissenschaften. In <i>Soziale Insekten in einer sich wandelnden Welt</i> (Vol. 43, pp. 65–72). Verlag Dr. Friedrich Pfeil.","mla":"Cremer, Sylvia. “Soziale Immunität: Wie Sich Der Staat Gegen Pathogene Wehrt  Bayerische Akademie Der Wissenschaften.” <i>Soziale Insekten in Einer Sich Wandelnden Welt</i>, vol. 43, Verlag Dr. Friedrich Pfeil, 2014, pp. 65–72."},"volume":43,"type":"book_chapter","abstract":[{"lang":"ger","text":"Im Rahmen meiner Arbeit mit der kollektiven Krankheitsabwehr in Ameisengesellschaften interessiert mich vor allem, wie sich die Kolonien als Ganzes gegen Krankheiten wehren können. Warum ist dieses Thema der Krankheitsdynamik in Gruppen so wichtig? Ein Vergleich von solitär lebenden Individuen mit Individuen, die in sozialen Gruppen zusammenleben, zeigt die Kosten und die Vorteile des Gruppenlebens: Einerseits haben Individuen in sozialen Gruppen aufgrund der hohen Dichte, in der die Tiere zusammenleben, den hohen Interaktionsraten, die sie miteinander haben, und der engen Verwandtschaft, die sie verbindet, ein höheres Ansteckungsrisiko. Andererseits kann die individuelle Krankheitsabwehr durch die kollektive Abwehr in den Gruppen ergänzt werden."}],"oa_version":"None","publication_status":"published","publication":"Soziale Insekten in einer sich wandelnden Welt"},{"doi":"10.1142/S0129055X14500123","main_file_link":[{"url":"http://arxiv.org/abs/1305.5135","open_access":"1"}],"publication":"Reviews in Mathematical Physics","oa_version":"Submitted Version","volume":26,"date_created":"2018-12-11T11:54:33Z","day":"01","status":"public","external_id":{"arxiv":["1305.5135"]},"year":"2014","month":"08","intvolume":"        26","date_published":"2014-08-01T00:00:00Z","acknowledgement":"We would like to thank Max Lein and Andreas Deuchert for valuable suggestions and remarks. Partial financial support by the NSERC (R.S.) is gratefully acknowledged.","article_number":"1450012","date_updated":"2022-06-07T09:03:09Z","issue":"7","oa":1,"publication_status":"published","citation":{"short":"G. Bräunlich, C. Hainzl, R. Seiringer, Reviews in Mathematical Physics 26 (2014).","ista":"Bräunlich G, Hainzl C, Seiringer R. 2014. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 26(7), 1450012.","ieee":"G. Bräunlich, C. Hainzl, and R. Seiringer, “Translation-invariant quasi-free states for fermionic systems and the BCS approximation,” <i>Reviews in Mathematical Physics</i>, vol. 26, no. 7. World Scientific Publishing, 2014.","ama":"Bräunlich G, Hainzl C, Seiringer R. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. <i>Reviews in Mathematical Physics</i>. 2014;26(7). doi:<a href=\"https://doi.org/10.1142/S0129055X14500123\">10.1142/S0129055X14500123</a>","chicago":"Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” <i>Reviews in Mathematical Physics</i>. World Scientific Publishing, 2014. <a href=\"https://doi.org/10.1142/S0129055X14500123\">https://doi.org/10.1142/S0129055X14500123</a>.","apa":"Bräunlich, G., Hainzl, C., &#38; Seiringer, R. (2014). Translation-invariant quasi-free states for fermionic systems and the BCS approximation. <i>Reviews in Mathematical Physics</i>. World Scientific Publishing. <a href=\"https://doi.org/10.1142/S0129055X14500123\">https://doi.org/10.1142/S0129055X14500123</a>","mla":"Bräunlich, Gerhard, et al. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” <i>Reviews in Mathematical Physics</i>, vol. 26, no. 7, 1450012, World Scientific Publishing, 2014, doi:<a href=\"https://doi.org/10.1142/S0129055X14500123\">10.1142/S0129055X14500123</a>."},"type":"journal_article","abstract":[{"text":"We study translation-invariant quasi-free states for a system of fermions with two-particle interactions. The associated energy functional is similar to the BCS functional but also includes direct and exchange energies. We show that for suitable short-range interactions, these latter terms only lead to a renormalization of the chemical potential, with the usual properties of the BCS functional left unchanged. Our analysis thus represents a rigorous justification of part of the BCS approximation. We give bounds on the critical temperature below which the system displays superfluidity.","lang":"eng"}],"arxiv":1,"scopus_import":"1","_id":"1889","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"RoSe"}],"publist_id":"5206","language":[{"iso":"eng"}],"article_type":"original","publisher":"World Scientific Publishing","title":"Translation-invariant quasi-free states for fermionic systems and the BCS approximation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Bräunlich, Gerhard","first_name":"Gerhard","last_name":"Bräunlich"},{"full_name":"Hainzl, Christian","first_name":"Christian","last_name":"Hainzl"},{"last_name":"Seiringer","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","full_name":"Seiringer, Robert"}]},{"volume":51,"day":"11","status":"public","tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:54:34Z","ddc":["000"],"doi":"10.1111/psyp.12062","publication":"Psychophysiology","oa_version":"Published Version","acknowledgement":"Funded by Austrian Science Fund (FWF) Grant Number: P 22189-B18; European Union within the 6th Framework Programme Grant Number: 517590; State government of Styria Grant Number: PN 4055","month":"02","intvolume":"        51","date_published":"2014-02-11T00:00:00Z","issue":"4","oa":1,"date_updated":"2021-01-12T06:53:52Z","page":"385 - 395","year":"2014","file_date_updated":"2020-07-14T12:45:20Z","type":"journal_article","scopus_import":1,"abstract":[{"lang":"eng","text":"To search for a target in a complex environment is an everyday behavior that ends with finding the target. When we search for two identical targets, however, we must continue the search after finding the first target and memorize its location. We used fixation-related potentials to investigate the neural correlates of different stages of the search, that is, before and after finding the first target. Having found the first target influenced subsequent distractor processing. Compared to distractor fixations before the first target fixation, a negative shift was observed for three subsequent distractor fixations. These results suggest that processing a target in continued search modulates the brain's response, either transiently by reflecting temporary working memory processes or permanently by reflecting working memory retention."}],"citation":{"ama":"Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. <i>Psychophysiology</i>. 2014;51(4):385-395. doi:<a href=\"https://doi.org/10.1111/psyp.12062\">10.1111/psyp.12062</a>","short":"C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, A. Ischebeck, Psychophysiology 51 (2014) 385–395.","ieee":"C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, and A. Ischebeck, “Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection,” <i>Psychophysiology</i>, vol. 51, no. 4. Wiley-Blackwell, pp. 385–395, 2014.","ista":"Körner C, Braunstein V, Stangl M, Schlögl A, Neuper C, Ischebeck A. 2014. Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. Psychophysiology. 51(4), 385–395.","chicago":"Körner, Christof, Verena Braunstein, Matthias Stangl, Alois Schlögl, Christa Neuper, and Anja Ischebeck. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” <i>Psychophysiology</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1111/psyp.12062\">https://doi.org/10.1111/psyp.12062</a>.","apa":"Körner, C., Braunstein, V., Stangl, M., Schlögl, A., Neuper, C., &#38; Ischebeck, A. (2014). Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection. <i>Psychophysiology</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1111/psyp.12062\">https://doi.org/10.1111/psyp.12062</a>","mla":"Körner, Christof, et al. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” <i>Psychophysiology</i>, vol. 51, no. 4, Wiley-Blackwell, 2014, pp. 385–95, doi:<a href=\"https://doi.org/10.1111/psyp.12062\">10.1111/psyp.12062</a>."},"_id":"1890","publication_status":"published","publisher":"Wiley-Blackwell","has_accepted_license":"1","file":[{"date_created":"2018-12-12T10:16:44Z","date_updated":"2020-07-14T12:45:20Z","file_name":"IST-2016-442-v1+1_K-rner_et_al-2014-Psychophysiology.pdf","access_level":"open_access","relation":"main_file","checksum":"4255b6185e774acce1d99f8e195c564d","file_id":"5233","content_type":"application/pdf","creator":"system","file_size":543243}],"author":[{"full_name":"Körner, Christof","first_name":"Christof","last_name":"Körner"},{"last_name":"Braunstein","first_name":"Verena","full_name":"Braunstein, Verena"},{"first_name":"Matthias","last_name":"Stangl","full_name":"Stangl, Matthias"},{"full_name":"Schlögl, Alois","id":"45BF87EE-F248-11E8-B48F-1D18A9856A87","first_name":"Alois","orcid":"0000-0002-5621-8100","last_name":"Schlögl"},{"full_name":"Neuper, Christa","first_name":"Christa","last_name":"Neuper"},{"full_name":"Ischebeck, Anja","first_name":"Anja","last_name":"Ischebeck"}],"title":"Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ScienComp"},{"_id":"PeJo"}],"publist_id":"5205","pubrep_id":"442","language":[{"iso":"eng"}]},{"publication":"Proteins: Structure, Function and Bioinformatics","publication_status":"published","doi":"10.1002/prot.24436","oa_version":"None","abstract":[{"lang":"eng","text":"We provide theoretical tests of a novel experimental technique to determine mechanostability of proteins based on stretching a mechanically protected protein by single-molecule force spectroscopy. This technique involves stretching a homogeneous or heterogeneous chain of reference proteins (single-molecule markers) in which one of them acts as host to the guest protein under study. The guest protein is grafted into the host through genetic engineering. It is expected that unraveling of the host precedes the unraveling of the guest removing ambiguities in the reading of the force-extension patterns of the guest protein. We study examples of such systems within a coarse-grained structure-based model. We consider systems with various ratios of mechanostability for the host and guest molecules and compare them to experimental results involving cohesin I as the guest molecule. For a comparison, we also study the force-displacement patterns in proteins that are linked in a serial fashion. We find that the mechanostability of the guest is similar to that of the isolated or serially linked protein. We also demonstrate that the ideal configuration of this strategy would be one in which the host is much more mechanostable than the single-molecule markers. We finally show that it is troublesome to use the highly stable cystine knot proteins as a host to graft a guest in stretching studies because this would involve a cleaving procedure."}],"scopus_import":1,"type":"journal_article","volume":82,"citation":{"mla":"Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:<a href=\"https://doi.org/10.1002/prot.24436\">10.1002/prot.24436</a>.","apa":"Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez, M., &#38; Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy in protein nanomechanics. <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley-Blackwell. <a href=\"https://doi.org/10.1002/prot.24436\">https://doi.org/10.1002/prot.24436</a>","chicago":"Chwastyk, Mateusz, Albert Galera Prat, Mateusz K Sikora, Àngel Gómez Sicilia, Mariano Carrión Vázquez, and Marek Cieplak. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” <i>Proteins: Structure, Function and Bioinformatics</i>. Wiley-Blackwell, 2014. <a href=\"https://doi.org/10.1002/prot.24436\">https://doi.org/10.1002/prot.24436</a>.","ama":"Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. Theoretical tests of the mechanical protection strategy in protein nanomechanics. <i>Proteins: Structure, Function and Bioinformatics</i>. 2014;82(5):717-726. doi:<a href=\"https://doi.org/10.1002/prot.24436\">10.1002/prot.24436</a>","ieee":"M. Chwastyk, A. Galera Prat, M. K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, and M. Cieplak, “Theoretical tests of the mechanical protection strategy in protein nanomechanics,” <i>Proteins: Structure, Function and Bioinformatics</i>, vol. 82, no. 5. Wiley-Blackwell, pp. 717–726, 2014.","short":"M. Chwastyk, A. Galera Prat, M.K. Sikora, À. Gómez Sicilia, M. Carrión Vázquez, M. Cieplak, Proteins: Structure, Function and Bioinformatics 82 (2014) 717–726.","ista":"Chwastyk M, Galera Prat A, Sikora MK, Gómez Sicilia À, Carrión Vázquez M, Cieplak M. 2014. Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. 82(5), 717–726."},"status":"public","day":"01","_id":"1891","date_created":"2018-12-11T11:54:34Z","department":[{"_id":"CaHe"}],"publist_id":"5204","page":"717 - 726","year":"2014","language":[{"iso":"eng"}],"publisher":"Wiley-Blackwell","acknowledgement":"Grant Nr. 2011/01/N/ST3/02475","date_published":"2014-05-01T00:00:00Z","month":"05","intvolume":"        82","author":[{"last_name":"Chwastyk","first_name":"Mateusz","full_name":"Chwastyk, Mateusz"},{"last_name":"Galera Prat","first_name":"Albert","full_name":"Galera Prat, Albert"},{"full_name":"Sikora, Mateusz K","last_name":"Sikora","first_name":"Mateusz K","id":"2F74BCDE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Gómez Sicilia, Àngel","first_name":"Àngel","last_name":"Gómez Sicilia"},{"last_name":"Carrión Vázquez","first_name":"Mariano","full_name":"Carrión Vázquez, Mariano"},{"first_name":"Marek","last_name":"Cieplak","full_name":"Cieplak, Marek"}],"title":"Theoretical tests of the mechanical protection strategy in protein nanomechanics","user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","issue":"5","date_updated":"2021-01-12T06:53:52Z"},{"doi":"10.1098/rspb.2014.0253","main_file_link":[{"open_access":"1","url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211437/"}],"publication":"Proceedings of the Royal Society of London Series B Biological Sciences","oa_version":"Submitted Version","pmid":1,"volume":281,"date_created":"2018-12-11T11:54:34Z","status":"public","day":"07","external_id":{"pmid":["25232141"]},"year":"2014","intvolume":"       281","month":"11","date_published":"2014-11-07T00:00:00Z","article_number":"20140253","acknowledgement":"This research was supported by grants of the Swiss National Science Foundation to M.T.\r\nWe thank Tetsu Sato for providing field samples, Olivier Goffinet for field assistance, Dolores Schütz for vital help in the field and with the manuscript, David Lank, Barbara Taborsky, Suzanne Alonzo and two anonymous referees for comments on earlier manuscript versions, and the Fisheries Department, Ministry of Agriculture and Livestock of Zambia, for permission and support.","date_updated":"2022-06-07T09:12:32Z","issue":"1794","oa":1,"publication_status":"published","citation":{"apa":"Ocana, S., Meidl, P., Bonfils, D., &#38; Taborsky, M. (2014). Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society. <a href=\"https://doi.org/10.1098/rspb.2014.0253\">https://doi.org/10.1098/rspb.2014.0253</a>","mla":"Ocana, Sabine, et al. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 281, no. 1794, 20140253, The Royal Society, 2014, doi:<a href=\"https://doi.org/10.1098/rspb.2014.0253\">10.1098/rspb.2014.0253</a>.","ama":"Ocana S, Meidl P, Bonfils D, Taborsky M. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. 2014;281(1794). doi:<a href=\"https://doi.org/10.1098/rspb.2014.0253\">10.1098/rspb.2014.0253</a>","short":"S. Ocana, P. Meidl, D. Bonfils, M. Taborsky, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014).","ista":"Ocana S, Meidl P, Bonfils D, Taborsky M. 2014. Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids. Proceedings of the Royal Society of London Series B Biological Sciences. 281(1794), 20140253.","ieee":"S. Ocana, P. Meidl, D. Bonfils, and M. Taborsky, “Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids,” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>, vol. 281, no. 1794. The Royal Society, 2014.","chicago":"Ocana, Sabine, Patrick Meidl, Danielle Bonfils, and Michael Taborsky. “Y-Linked Mendelian Inheritance of Giant and Dwarf Male Morphs in Shell-Brooding Cichlids.” <i>Proceedings of the Royal Society of London Series B Biological Sciences</i>. The Royal Society, 2014. <a href=\"https://doi.org/10.1098/rspb.2014.0253\">https://doi.org/10.1098/rspb.2014.0253</a>."},"type":"journal_article","scopus_import":"1","abstract":[{"text":"Behavioural variation among conspecifics is typically contingent on individual state or environmental conditions. Sex-specific genetic polymorphisms are enigmatic because they lack conditionality, and genes causing adaptive trait variation in one sex may reduce Darwinian fitness in the other. One way to avoid such genetic antagonism is to control sex-specific traits by inheritance via sex chromosomes. Here, controlled laboratory crossings suggest that in snail-brooding cichlid fish a single locus, two-allele polymorphism located on a sex-linked chromosome of heterogametic males generates an extreme reproductive dimorphism. Both natural and sexual selection are responsible for exceptionally large body size of bourgeois males, creating a niche for a miniature male phenotype to evolve. This extreme intrasexual dimorphism results from selection on opposite size thresholds caused by a single ecological factor, empty snail shells used as breeding substrate. Paternity analyses reveal that in the field parasitic dwarf males sire the majority of offspring in direct sperm competition with large nest owners exceeding their size more than 40 times. Apparently, use of empty snail shells as breeding substrate and single locus sex-linked inheritance of growth are the major ecological and genetic mechanisms responsible for the extreme intrasexual diversity observed in Lamprologus callipterus.","lang":"eng"}],"_id":"1892","quality_controlled":"1","article_processing_charge":"No","department":[{"_id":"CampIT"}],"publist_id":"5203","language":[{"iso":"eng"}],"article_type":"original","publisher":"The Royal Society","title":"Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Ocana","first_name":"Sabine","full_name":"Ocana, Sabine"},{"first_name":"Patrick","id":"4709BCE6-F248-11E8-B48F-1D18A9856A87","last_name":"Meidl","full_name":"Meidl, Patrick"},{"first_name":"Danielle","last_name":"Bonfils","full_name":"Bonfils, Danielle"},{"first_name":"Michael","last_name":"Taborsky","full_name":"Taborsky, Michael"}]},{"acknowledgement":"This work was supported by grants from the Research Foundation-Flanders (Odysseus).","date_published":"2014-02-18T00:00:00Z","intvolume":"       111","month":"02","oa":1,"issue":"7","date_updated":"2021-01-12T06:53:53Z","page":"2818 - 2823","year":"2014","volume":111,"day":"18","status":"public","date_created":"2018-12-11T11:54:34Z","publication":"PNAS","main_file_link":[{"url":"http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/","open_access":"1"}],"doi":"10.1073/pnas.1324264111","oa_version":"Submitted Version","ec_funded":1,"publisher":"National Academy of Sciences","author":[{"last_name":"Nováková","id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","full_name":"Nováková, Petra"},{"full_name":"Hirsch, Sibylle","first_name":"Sibylle","last_name":"Hirsch"},{"last_name":"Feraru","first_name":"Elena","full_name":"Feraru, Elena"},{"first_name":"Ricardo","last_name":"Tejos","full_name":"Tejos, Ricardo"},{"full_name":"Van Wijk, Ringo","first_name":"Ringo","last_name":"Van Wijk"},{"full_name":"Viaene, Tom","first_name":"Tom","last_name":"Viaene"},{"full_name":"Heilmann, Mareike","first_name":"Mareike","last_name":"Heilmann"},{"first_name":"Jennifer","last_name":"Lerche","full_name":"Lerche, Jennifer"},{"full_name":"De Rycke, Riet","last_name":"De Rycke","first_name":"Riet"},{"full_name":"Feraru, Mugurel","first_name":"Mugurel","last_name":"Feraru"},{"full_name":"Grones, Peter","first_name":"Peter","id":"399876EC-F248-11E8-B48F-1D18A9856A87","last_name":"Grones"},{"first_name":"Marc","last_name":"Van Montagu","full_name":"Van Montagu, Marc"},{"last_name":"Heilmann","first_name":"Ingo","full_name":"Heilmann, Ingo"},{"full_name":"Munnik, Teun","first_name":"Teun","last_name":"Munnik"},{"last_name":"Friml","orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jirí","full_name":"Friml, Jirí"}],"title":"SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"JiFr"}],"publist_id":"5202","language":[{"iso":"eng"}],"scopus_import":1,"abstract":[{"text":"Phosphatidylinositol (PtdIns) is a structural phospholipid that can be phosphorylated into various lipid signaling molecules, designated polyphosphoinositides (PPIs). The reversible phosphorylation of PPIs on the 3, 4, or 5 position of inositol is performed by a set of organelle-specific kinases and phosphatases, and the characteristic head groups make these molecules ideal for regulating biological processes in time and space. In yeast and mammals, PtdIns3P and PtdIns(3,5)P2 play crucial roles in trafficking toward the lytic compartments, whereas the role in plants is not yet fully understood. Here we identified the role of a land plant-specific subgroup of PPI phosphatases, the suppressor of actin 2 (SAC2) to SAC5, during vacuolar trafficking and morphogenesis in Arabidopsis thaliana. SAC2-SAC5 localize to the tonoplast along with PtdIns3P, the presumable product of their activity. In SAC gain- and loss-of-function mutants, the levels of PtdIns monophosphates and bisphosphates were changed, with opposite effects on the morphology of storage and lytic vacuoles, and the trafficking toward the vacuoles was defective. Moreover, multiple sac knockout mutants had an increased number of smaller storage and lytic vacuoles, whereas extralarge vacuoles were observed in the overexpression lines, correlating with various growth and developmental defects. The fragmented vacuolar phenotype of sac mutants could be mimicked by treating wild-type seedlings with PtdIns(3,5)P2, corroborating that this PPI is important for vacuole morphology. Taken together, these results provide evidence that PPIs, together with their metabolic enzymes SAC2-SAC5, are crucial for vacuolar trafficking and for vacuolar morphology and function in plants.","lang":"eng"}],"type":"journal_article","citation":{"chicago":"Marhavá, Petra, Sibylle Hirsch, Elena Feraru, Ricardo Tejos, Ringo Van Wijk, Tom Viaene, Mareike Heilmann, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” <i>PNAS</i>. National Academy of Sciences, 2014. <a href=\"https://doi.org/10.1073/pnas.1324264111\">https://doi.org/10.1073/pnas.1324264111</a>.","ieee":"P. Marhavá <i>et al.</i>, “SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis,” <i>PNAS</i>, vol. 111, no. 7. National Academy of Sciences, pp. 2818–2823, 2014.","short":"P. Marhavá, S. Hirsch, E. Feraru, R. Tejos, R. Van Wijk, T. Viaene, M. Heilmann, J. Lerche, R. De Rycke, M. Feraru, P. Grones, M. Van Montagu, I. Heilmann, T. Munnik, J. Friml, PNAS 111 (2014) 2818–2823.","ista":"Marhavá P, Hirsch S, Feraru E, Tejos R, Van Wijk R, Viaene T, Heilmann M, Lerche J, De Rycke R, Feraru M, Grones P, Van Montagu M, Heilmann I, Munnik T, Friml J. 2014. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 111(7), 2818–2823.","ama":"Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. <i>PNAS</i>. 2014;111(7):2818-2823. doi:<a href=\"https://doi.org/10.1073/pnas.1324264111\">10.1073/pnas.1324264111</a>","mla":"Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” <i>PNAS</i>, vol. 111, no. 7, National Academy of Sciences, 2014, pp. 2818–23, doi:<a href=\"https://doi.org/10.1073/pnas.1324264111\">10.1073/pnas.1324264111</a>.","apa":"Marhavá, P., Hirsch, S., Feraru, E., Tejos, R., Van Wijk, R., Viaene, T., … Friml, J. (2014). SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1324264111\">https://doi.org/10.1073/pnas.1324264111</a>"},"_id":"1893","publication_status":"published","project":[{"name":"Polarity and subcellular dynamics in plants","_id":"25716A02-B435-11E9-9278-68D0E5697425","grant_number":"282300","call_identifier":"FP7"}]},{"year":"2014","intvolume":"         9","month":"09","date_published":"2014-09-02T00:00:00Z","article_number":"e106247","date_updated":"2021-01-12T06:53:54Z","issue":"9","oa":1,"doi":"10.1371/journal.pone.0106247","publication":"PLoS One","oa_version":"Published Version","volume":9,"tmp":{"image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"date_created":"2018-12-11T11:54:35Z","ddc":["570"],"day":"02","status":"public","publist_id":"5201","department":[{"_id":"CaGu"}],"language":[{"iso":"eng"}],"pubrep_id":"438","has_accepted_license":"1","publisher":"Public Library of Science","file":[{"file_id":"5205","content_type":"application/pdf","file_size":4248801,"creator":"system","relation":"main_file","checksum":"7d02c3da7f72b82bb5d7932d80c3251f","access_level":"open_access","file_name":"IST-2016-438-v1+1_journal.pone.0106247.pdf","date_created":"2018-12-12T10:16:19Z","date_updated":"2020-07-14T12:45:20Z"}],"user_id":"4435EBFC-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Grabowska, Anna","last_name":"Grabowska","first_name":"Anna"},{"last_name":"Wywiał","first_name":"Ewa","full_name":"Wywiał, Ewa"},{"last_name":"Dunin Horkawicz","first_name":"Stanislaw","full_name":"Dunin Horkawicz, Stanislaw"},{"last_name":"Łasica","first_name":"Anna","full_name":"Łasica, Anna"},{"full_name":"Wösten, Marc","last_name":"Wösten","first_name":"Marc"},{"last_name":"Nagy-Staron","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87","first_name":"Anna A","full_name":"Nagy-Staron, Anna A"},{"last_name":"Godlewska","first_name":"Renata","full_name":"Godlewska, Renata"},{"full_name":"Bocian Ostrzycka, Katarzyna","first_name":"Katarzyna","last_name":"Bocian Ostrzycka"},{"last_name":"Pieńkowska","first_name":"Katarzyna","full_name":"Pieńkowska, Katarzyna"},{"full_name":"Łaniewski, Paweł","first_name":"Paweł","last_name":"Łaniewski"},{"last_name":"Bujnicki","first_name":"Janusz","full_name":"Bujnicki, Janusz"},{"full_name":"Van Putten, Jos","last_name":"Van Putten","first_name":"Jos"},{"full_name":"Jagusztyn Krynicka, Elzbieta","first_name":"Elzbieta","last_name":"Jagusztyn Krynicka"}],"title":"Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA","publication_status":"published","citation":{"chicago":"Grabowska, Anna, Ewa Wywiał, Stanislaw Dunin Horkawicz, Anna Łasica, Marc Wösten, Anna A Nagy-Staron, Renata Godlewska, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” <i>PLoS One</i>. Public Library of Science, 2014. <a href=\"https://doi.org/10.1371/journal.pone.0106247\">https://doi.org/10.1371/journal.pone.0106247</a>.","ista":"Grabowska A, Wywiał E, Dunin Horkawicz S, Łasica A, Wösten M, Nagy-Staron AA, Godlewska R, Bocian Ostrzycka K, Pieńkowska K, Łaniewski P, Bujnicki J, Van Putten J, Jagusztyn Krynicka E. 2014. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. PLoS One. 9(9), e106247.","short":"A. Grabowska, E. Wywiał, S. Dunin Horkawicz, A. Łasica, M. Wösten, A.A. Nagy-Staron, R. Godlewska, K. Bocian Ostrzycka, K. Pieńkowska, P. Łaniewski, J. Bujnicki, J. Van Putten, E. Jagusztyn Krynicka, PLoS One 9 (2014).","ieee":"A. Grabowska <i>et al.</i>, “Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” <i>PLoS One</i>, vol. 9, no. 9. Public Library of Science, 2014.","ama":"Grabowska A, Wywiał E, Dunin Horkawicz S, et al. Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. <i>PLoS One</i>. 2014;9(9). doi:<a href=\"https://doi.org/10.1371/journal.pone.0106247\">10.1371/journal.pone.0106247</a>","mla":"Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” <i>PLoS One</i>, vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:<a href=\"https://doi.org/10.1371/journal.pone.0106247\">10.1371/journal.pone.0106247</a>.","apa":"Grabowska, A., Wywiał, E., Dunin Horkawicz, S., Łasica, A., Wösten, M., Nagy-Staron, A. A., … Jagusztyn Krynicka, E. (2014). Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA. <i>PLoS One</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pone.0106247\">https://doi.org/10.1371/journal.pone.0106247</a>"},"file_date_updated":"2020-07-14T12:45:20Z","type":"journal_article","scopus_import":1,"abstract":[{"text":"Background: Bacterial Dsb enzymes are involved in the oxidative folding of many proteins, through the formation of disulfide bonds between their cysteine residues. The Dsb protein network has been well characterized in cells of the model microorganism Escherichia coli. To gain insight into the functioning of the Dsb system in epsilon-Proteobacteria, where it plays an important role in the colonization process, we studied two homologs of the main Escherichia coli Dsb oxidase (EcDsbA) that are present in the cells of the enteric pathogen Campylobacter jejuni, the most frequently reported bacterial cause of human enteritis in the world. Methods and Results: Phylogenetic analysis suggests the horizontal transfer of the epsilon-Proteobacterial DsbAs from a common ancestor to gamma-Proteobacteria, which then gave rise to the DsbL lineage. Phenotype and enzymatic assays suggest that the two C. jejuni DsbAs play different roles in bacterial cells and have divergent substrate spectra. CjDsbA1 is essential for the motility and autoagglutination phenotypes, while CjDsbA2 has no impact on those processes. CjDsbA1 plays a critical role in the oxidative folding that ensures the activity of alkaline phosphatase CjPhoX, whereas CjDsbA2 is crucial for the activity of arylsulfotransferase CjAstA, encoded within the dsbA2-dsbB-astA operon. Conclusions: Our results show that CjDsbA1 is the primary thiol-oxidoreductase affecting life processes associated with bacterial spread and host colonization, as well as ensuring the oxidative folding of particular protein substrates. In contrast, CjDsbA2 activity does not affect the same processes and so far its oxidative folding activity has been demonstrated for one substrate, arylsulfotransferase CjAstA. The results suggest the cooperation between CjDsbA2 and CjDsbB. In the case of the CjDsbA1, this cooperation is not exclusive and there is probably another protein to be identified in C. jejuni cells that acts to re-oxidize CjDsbA1. Altogether the data presented here constitute the considerable insight to the Epsilonproteobacterial Dsb systems, which have been poorly understood so far.","lang":"eng"}],"_id":"1894","quality_controlled":"1"}]