--- _id: '1058' abstract: - lang: eng text: Diffraction-unlimited far-field super-resolution fluorescence (nanoscopy) methods typically rely on transiently transferring fluorophores between two states, whereby this transfer is usually laid out as a switch. However, depending on whether this is induced in a spatially controlled manner using a pattern of light (coordinate-targeted) or stochastically on a single-molecule basis, specific requirements on the fluorophores are imposed. Therefore, the fluorophores are usually utilized just for one class of methods only. In this study we demonstrate that the reversibly switchable fluorescent protein Dreiklang enables live-cell recordings in both spatially controlled and stochastic modes. We show that the Dreiklang chromophore entails three different light-induced switching mechanisms, namely a reversible photochemical one, off-switching by stimulated emission, and a reversible transfer to a long-lived dark state from the S1 state, all of which can be utilized to overcome the diffraction barrier. We also find that for the single-molecule- based stochastic GSDIM approach (ground-state depletion followed by individual molecule return), Dreiklang provides a larger number of on-off localization events as compared to its progenitor Citrine. Altogether, Dreiklang is a versatile probe for essentially all popular forms of live-cell fluorescence nanoscopy. article_processing_charge: No author: - first_name: Nickels full_name: Jensen, Nickels last_name: Jensen - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Katrin full_name: Willig, Katrin last_name: Willig - first_name: Flavie full_name: Lavoie Cardinal, Flavie last_name: Lavoie Cardinal - first_name: Tanja full_name: Brakemann, Tanja last_name: Brakemann - first_name: Stefan full_name: Hell, Stefan last_name: Hell - first_name: Stefan full_name: Jakobs, Stefan last_name: Jakobs citation: ama: Jensen N, Danzl JG, Willig K, et al. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 2014;15(4):756-762. doi:10.1002/cphc.201301034 apa: Jensen, N., Danzl, J. G., Willig, K., Lavoie Cardinal, F., Brakemann, T., Hell, S., & Jakobs, S. (2014). Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. Wiley-Blackwell. https://doi.org/10.1002/cphc.201301034 chicago: Jensen, Nickels, Johann G Danzl, Katrin Willig, Flavie Lavoie Cardinal, Tanja Brakemann, Stefan Hell, and Stefan Jakobs. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem. Wiley-Blackwell, 2014. https://doi.org/10.1002/cphc.201301034. ieee: N. Jensen et al., “Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang,” ChemPhysChem, vol. 15, no. 4. Wiley-Blackwell, pp. 756–762, 2014. ista: Jensen N, Danzl JG, Willig K, Lavoie Cardinal F, Brakemann T, Hell S, Jakobs S. 2014. Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang. ChemPhysChem. 15(4), 756–762. mla: Jensen, Nickels, et al. “Coordinate-Targeted and Coordinate-Stochastic Super-Resolution Microscopy with the Reversibly Switchable Fluorescent Protein Dreiklang.” ChemPhysChem, vol. 15, no. 4, Wiley-Blackwell, 2014, pp. 756–62, doi:10.1002/cphc.201301034. short: N. Jensen, J.G. Danzl, K. Willig, F. Lavoie Cardinal, T. Brakemann, S. Hell, S. Jakobs, ChemPhysChem 15 (2014) 756–762. date_created: 2018-12-11T11:49:55Z date_published: 2014-03-17T00:00:00Z date_updated: 2021-01-12T06:47:58Z day: '17' doi: 10.1002/cphc.201301034 extern: '1' intvolume: ' 15' issue: '4' language: - iso: eng month: '03' oa_version: None page: 756 - 762 publication: ChemPhysChem publication_status: published publisher: Wiley-Blackwell publist_id: '6332' status: public title: Coordinate-targeted and coordinate-stochastic super-resolution microscopy with the reversibly switchable fluorescent protein dreiklang type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2014' ... --- _id: '10815' abstract: - lang: eng text: In the last several decades, developmental biology has clarified the molecular mechanisms of embryogenesis and organogenesis. In particular, it has demonstrated that the “tool-kit genes” essential for regulating developmental processes are not only highly conserved among species, but are also used as systems at various times and places in an organism to control distinct developmental events. Therefore, mutations in many of these tool-kit genes may cause congenital diseases involving morphological abnormalities. This link between genes and abnormal morphological phenotypes underscores the importance of understanding how cells behave and contribute to morphogenesis as a result of gene function. Recent improvements in live imaging and in quantitative analyses of cellular dynamics will advance our understanding of the cellular pathogenesis of congenital diseases associated with aberrant morphologies. In these studies, it is critical to select an appropriate model organism for the particular phenomenon of interest. acknowledgement: The authors thank all the members of the Division of Morphogenesis, National Institute for Basic Biology, for their contributions to the research, their encouragement, and helpful discussions, particularly Dr M. Suzuki for his critical reading of the manuscript. We also thank the Model Animal Research and Spectrography and Bioimaging Facilities, NIBB Core Research Facilities, for technical support. M.H. was supported by a research fellowship from the Japan Society for the Promotion of Science (JSPS). Our work introduced in this review was supported by a Grant-in-Aid for Scientific Research on Innovative Areas from the Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan, to N.U. article_processing_charge: No article_type: original author: - first_name: Masakazu full_name: Hashimoto, Masakazu last_name: Hashimoto - first_name: Hitoshi full_name: Morita, Hitoshi id: 4C6E54C6-F248-11E8-B48F-1D18A9856A87 last_name: Morita - first_name: Naoto full_name: Ueno, Naoto last_name: Ueno citation: ama: Hashimoto M, Morita H, Ueno N. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 2014;54(1):1-7. doi:10.1111/cga.12039 apa: Hashimoto, M., Morita, H., & Ueno, N. (2014). Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. Wiley. https://doi.org/10.1111/cga.12039 chicago: Hashimoto, Masakazu, Hitoshi Morita, and Naoto Ueno. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies. Wiley, 2014. https://doi.org/10.1111/cga.12039. ieee: M. Hashimoto, H. Morita, and N. Ueno, “Molecular and cellular mechanisms of development underlying congenital diseases,” Congenital Anomalies, vol. 54, no. 1. Wiley, pp. 1–7, 2014. ista: Hashimoto M, Morita H, Ueno N. 2014. Molecular and cellular mechanisms of development underlying congenital diseases. Congenital Anomalies. 54(1), 1–7. mla: Hashimoto, Masakazu, et al. “Molecular and Cellular Mechanisms of Development Underlying Congenital Diseases.” Congenital Anomalies, vol. 54, no. 1, Wiley, 2014, pp. 1–7, doi:10.1111/cga.12039. short: M. Hashimoto, H. Morita, N. Ueno, Congenital Anomalies 54 (2014) 1–7. date_created: 2022-03-04T08:17:25Z date_published: 2014-02-01T00:00:00Z date_updated: 2022-03-04T08:26:05Z day: '01' department: - _id: CaHe doi: 10.1111/cga.12039 external_id: pmid: - '24666178' intvolume: ' 54' issue: '1' keyword: - Developmental Biology - Embryology - General Medicine - Pediatrics - Perinatology - and Child Health language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1111/cga.12039 month: '02' oa: 1 oa_version: None page: 1-7 pmid: 1 publication: Congenital Anomalies publication_identifier: issn: - 0914-3505 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Molecular and cellular mechanisms of development underlying congenital diseases type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2014' ... --- _id: '10811' abstract: - lang: eng text: Auxin is an important signaling compound in plants and vital for plant development and growth. The present book, Auxin and its Role in Plant Development, provides the reader with detailed and comprehensive insight into the functioning of the molecule on the whole and specifically in plant development. In the first part, the functioning, metabolism and signaling pathways of auxin in plants are explained, the second part depicts the specific role of auxin in plant development and the third part describes the interaction and functioning of the signaling compound upon stimuli of the environment. Each chapter is written by international experts in the respective field and designed for scientists and researchers in plant biology, plant development and cell biology to summarize the recent progress in understanding the role of auxin and suggest future perspectives for auxin research. article_processing_charge: No citation: ama: 'Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. 1st ed. Vienna: Springer Nature; 2014. doi:10.1007/978-3-7091-1526-8' apa: 'Zažímalová, E., Petrášek, J., & Benková, E. (Eds.). (2014). Auxin and Its Role in Plant Development (1st ed.). Vienna: Springer Nature. https://doi.org/10.1007/978-3-7091-1526-8' chicago: 'Zažímalová, Eva, Jan Petrášek, and Eva Benková, eds. Auxin and Its Role in Plant Development. 1st ed. Vienna: Springer Nature, 2014. https://doi.org/10.1007/978-3-7091-1526-8.' ieee: 'E. Zažímalová, J. Petrášek, and E. Benková, Eds., Auxin and Its Role in Plant Development, 1st ed. Vienna: Springer Nature, 2014.' ista: 'Zažímalová E, Petrášek J, Benková E eds. 2014. Auxin and Its Role in Plant Development 1st ed., Vienna: Springer Nature, 444p.' mla: Zažímalová, Eva, et al., editors. Auxin and Its Role in Plant Development. 1st ed., Springer Nature, 2014, doi:10.1007/978-3-7091-1526-8. short: E. Zažímalová, J. Petrášek, E. Benková, eds., Auxin and Its Role in Plant Development, 1st ed., Springer Nature, Vienna, 2014. date_created: 2022-03-03T11:52:44Z date_published: 2014-04-01T00:00:00Z date_updated: 2022-03-04T07:38:15Z day: '01' department: - _id: EvBe doi: 10.1007/978-3-7091-1526-8 edition: '1' editor: - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 language: - iso: eng month: '04' oa_version: None page: '444' place: Vienna publication_identifier: eisbn: - '9783709115268' isbn: - '9783709115251' publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Auxin and Its Role in Plant Development type: book_editor user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '10884' abstract: - lang: eng text: "We revisit the parameterized model checking problem for token-passing systems and specifications in indexed CTL  ∗ \\X. Emerson and Namjoshi (1995, 2003) have shown that parameterized model checking of indexed CTL  ∗ \\X in uni-directional token rings can be reduced to checking rings up to some cutoff size. Clarke et al. (2004) have shown a similar result for general topologies and indexed LTL \\X, provided processes cannot choose the directions for sending or receiving the token.\r\nWe unify and substantially extend these results by systematically exploring fragments of indexed CTL  ∗ \\X with respect to general topologies. For each fragment we establish whether a cutoff exists, and for some concrete topologies, such as rings, cliques and stars, we infer small cutoffs. Finally, we show that the problem becomes undecidable, and thus no cutoffs exist, if processes are allowed to choose the directions in which they send or from which they receive the token." acknowledgement: "This work was supported by the Austrian Science Fund through grant P23499-N23\r\nand through the RiSE network (S11403, S11405, S11406, S11407-N23); ERC Starting Grant (279307: Graph Games); Vienna Science and Technology Fund (WWTF)\r\ngrants PROSEED, ICT12-059, and VRG11-005." alternative_title: - LNCS article_processing_charge: No author: - first_name: Benjamin full_name: Aminof, Benjamin id: 4A55BD00-F248-11E8-B48F-1D18A9856A87 last_name: Aminof - first_name: Swen full_name: Jacobs, Swen last_name: Jacobs - first_name: Ayrat full_name: Khalimov, Ayrat last_name: Khalimov - first_name: Sasha full_name: Rubin, Sasha id: 2EC51194-F248-11E8-B48F-1D18A9856A87 last_name: Rubin citation: ama: 'Aminof B, Jacobs S, Khalimov A, Rubin S. Parameterized model checking of token-passing systems. In: Verification, Model Checking, and Abstract Interpretation. Vol 8318. Springer Nature; 2014:262-281. doi:10.1007/978-3-642-54013-4_15' apa: 'Aminof, B., Jacobs, S., Khalimov, A., & Rubin, S. (2014). Parameterized model checking of token-passing systems. In Verification, Model Checking, and Abstract Interpretation (Vol. 8318, pp. 262–281). San Diego, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-642-54013-4_15' chicago: Aminof, Benjamin, Swen Jacobs, Ayrat Khalimov, and Sasha Rubin. “Parameterized Model Checking of Token-Passing Systems.” In Verification, Model Checking, and Abstract Interpretation, 8318:262–81. Springer Nature, 2014. https://doi.org/10.1007/978-3-642-54013-4_15. ieee: B. Aminof, S. Jacobs, A. Khalimov, and S. Rubin, “Parameterized model checking of token-passing systems,” in Verification, Model Checking, and Abstract Interpretation, San Diego, CA, United States, 2014, vol. 8318, pp. 262–281. ista: 'Aminof B, Jacobs S, Khalimov A, Rubin S. 2014. Parameterized model checking of token-passing systems. Verification, Model Checking, and Abstract Interpretation. VMCAI: Verifcation, Model Checking, and Abstract Interpretation, LNCS, vol. 8318, 262–281.' mla: Aminof, Benjamin, et al. “Parameterized Model Checking of Token-Passing Systems.” Verification, Model Checking, and Abstract Interpretation, vol. 8318, Springer Nature, 2014, pp. 262–81, doi:10.1007/978-3-642-54013-4_15. short: B. Aminof, S. Jacobs, A. Khalimov, S. Rubin, in:, Verification, Model Checking, and Abstract Interpretation, Springer Nature, 2014, pp. 262–281. conference: end_date: 2014-01-21 location: San Diego, CA, United States name: 'VMCAI: Verifcation, Model Checking, and Abstract Interpretation' start_date: 2014-01-19 date_created: 2022-03-18T13:01:22Z date_published: 2014-01-30T00:00:00Z date_updated: 2022-05-17T08:36:01Z day: '30' department: - _id: KrCh doi: 10.1007/978-3-642-54013-4_15 ec_funded: 1 external_id: arxiv: - '1311.4425' intvolume: ' 8318' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.1311.4425' month: '01' oa: 1 oa_version: Preprint page: 262-281 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: Verification, Model Checking, and Abstract Interpretation publication_identifier: eisbn: - '9783642540134' eissn: - 1611-3349 isbn: - '9783642540127' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Parameterized model checking of token-passing systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8318 year: '2014' ... --- _id: '10893' abstract: - lang: eng text: Saddle periodic orbits are an essential and stable part of the topological skeleton of a 3D vector field. Nevertheless, there is currently no efficient algorithm to robustly extract these features. In this chapter, we present a novel technique to extract saddle periodic orbits. Exploiting the analytic properties of such an orbit, we propose a scalar measure based on the finite-time Lyapunov exponent (FTLE) that indicates its presence. Using persistent homology, we can then extract the robust cycles of this field. These cycles thereby represent the saddle periodic orbits of the given vector field. We discuss the different existing FTLE approximation schemes regarding their applicability to this specific problem and propose an adapted version of FTLE called Normalized Velocity Separation. Finally, we evaluate our method using simple analytic vector field data. acknowledgement: First, we thank the reviewers of this paper for their ideas and critical comments. In addition, we thank Ronny Peikert and Filip Sadlo for a fruitful discussions. This research is supported by the European Commission under the TOPOSYS project FP7-ICT-318493-STREP, the European Social Fund (ESF App. No. 100098251), and the European Science Foundation under the ACAT Research Network Program. article_processing_charge: No author: - first_name: Jens full_name: Kasten, Jens last_name: Kasten - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus - first_name: Wieland full_name: Reich, Wieland last_name: Reich - first_name: Gerik full_name: Scheuermann, Gerik last_name: Scheuermann citation: ama: 'Kasten J, Reininghaus J, Reich W, Scheuermann G. Toward the extraction of saddle periodic orbits. In: Bremer P-T, Hotz I, Pascucci V, Peikert R, eds. Topological Methods in Data Analysis and Visualization III . Vol 1. Mathematics and Visualization. Cham: Springer; 2014:55-69. doi:10.1007/978-3-319-04099-8_4' apa: 'Kasten, J., Reininghaus, J., Reich, W., & Scheuermann, G. (2014). Toward the extraction of saddle periodic orbits. In P.-T. Bremer, I. Hotz, V. Pascucci, & R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III (Vol. 1, pp. 55–69). Cham: Springer. https://doi.org/10.1007/978-3-319-04099-8_4' chicago: 'Kasten, Jens, Jan Reininghaus, Wieland Reich, and Gerik Scheuermann. “Toward the Extraction of Saddle Periodic Orbits.” In Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer, Ingrid Hotz, Valerio Pascucci, and Ronald Peikert, 1:55–69. Mathematics and Visualization. Cham: Springer, 2014. https://doi.org/10.1007/978-3-319-04099-8_4.' ieee: 'J. Kasten, J. Reininghaus, W. Reich, and G. Scheuermann, “Toward the extraction of saddle periodic orbits,” in Topological Methods in Data Analysis and Visualization III , vol. 1, P.-T. Bremer, I. Hotz, V. Pascucci, and R. Peikert, Eds. Cham: Springer, 2014, pp. 55–69.' ista: 'Kasten J, Reininghaus J, Reich W, Scheuermann G. 2014.Toward the extraction of saddle periodic orbits. In: Topological Methods in Data Analysis and Visualization III . vol. 1, 55–69.' mla: Kasten, Jens, et al. “Toward the Extraction of Saddle Periodic Orbits.” Topological Methods in Data Analysis and Visualization III , edited by Peer-Timo Bremer et al., vol. 1, Springer, 2014, pp. 55–69, doi:10.1007/978-3-319-04099-8_4. short: J. Kasten, J. Reininghaus, W. Reich, G. Scheuermann, in:, P.-T. Bremer, I. Hotz, V. Pascucci, R. Peikert (Eds.), Topological Methods in Data Analysis and Visualization III , Springer, Cham, 2014, pp. 55–69. date_created: 2022-03-21T07:11:23Z date_published: 2014-03-19T00:00:00Z date_updated: 2022-06-21T12:01:47Z day: '19' department: - _id: HeEd doi: 10.1007/978-3-319-04099-8_4 ec_funded: 1 editor: - first_name: Peer-Timo full_name: Bremer, Peer-Timo last_name: Bremer - first_name: Ingrid full_name: Hotz, Ingrid last_name: Hotz - first_name: Valerio full_name: Pascucci, Valerio last_name: Pascucci - first_name: Ronald full_name: Peikert, Ronald last_name: Peikert intvolume: ' 1' language: - iso: eng month: '03' oa_version: None page: 55-69 place: Cham project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: 'Topological Methods in Data Analysis and Visualization III ' publication_identifier: eisbn: - '9783319040998' eissn: - 2197-666X isbn: - '9783319040981' issn: - 1612-3786 publication_status: published publisher: Springer quality_controlled: '1' scopus_import: '1' series_title: Mathematics and Visualization status: public title: Toward the extraction of saddle periodic orbits type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 1 year: '2014' ... --- _id: '11080' abstract: - lang: eng text: The spindle assembly checkpoint prevents separation of sister chromatids until each kinetochore is attached to the mitotic spindle. Rodriguez-Bravo et al. report that the nuclear pore complex scaffolds spindle assembly checkpoint signaling in interphase, providing a store of inhibitory signals that limits the speed of the subsequent mitosis. article_processing_charge: No article_type: original author: - first_name: Abigail full_name: Buchwalter, Abigail last_name: Buchwalter - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Buchwalter A, Hetzer M. Nuclear pores set the speed limit for mitosis. Cell. 2014;156(5):868-869. doi:10.1016/j.cell.2014.02.004 apa: Buchwalter, A., & Hetzer, M. (2014). Nuclear pores set the speed limit for mitosis. Cell. Elsevier. https://doi.org/10.1016/j.cell.2014.02.004 chicago: Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit for Mitosis.” Cell. Elsevier, 2014. https://doi.org/10.1016/j.cell.2014.02.004. ieee: A. Buchwalter and M. Hetzer, “Nuclear pores set the speed limit for mitosis,” Cell, vol. 156, no. 5. Elsevier, pp. 868–869, 2014. ista: Buchwalter A, Hetzer M. 2014. Nuclear pores set the speed limit for mitosis. Cell. 156(5), 868–869. mla: Buchwalter, Abigail, and Martin Hetzer. “Nuclear Pores Set the Speed Limit for Mitosis.” Cell, vol. 156, no. 5, Elsevier, 2014, pp. 868–69, doi:10.1016/j.cell.2014.02.004. short: A. Buchwalter, M. Hetzer, Cell 156 (2014) 868–869. date_created: 2022-04-07T07:50:04Z date_published: 2014-02-27T00:00:00Z date_updated: 2022-07-18T08:44:33Z day: '27' doi: 10.1016/j.cell.2014.02.004 extern: '1' external_id: pmid: - '24581486' intvolume: ' 156' issue: '5' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cell.2014.02.004 month: '02' oa: 1 oa_version: Published Version page: 868-869 pmid: 1 publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Nuclear pores set the speed limit for mitosis type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 156 year: '2014' ... --- _id: '11082' abstract: - lang: eng text: The nuclear pore complex (NPC) plays a critical role in gene expression by mediating import of transcription regulators into the nucleus and export of RNA transcripts to the cytoplasm. Emerging evidence suggests that in addition to mediating transport, a subset of nucleoporins (Nups) engage in transcriptional activation and elongation at genomic loci that are not associated with NPCs. The underlying mechanism and regulation of Nup mobility on and off nuclear pores remain unclear. Here we show that Nup50 is a mobile Nup with a pronounced presence both at the NPC and in the nucleoplasm that can move between these different localizations. Strikingly, the dynamic behavior of Nup50 in both locations is dependent on active transcription by RNA polymerase II and requires the N-terminal half of the protein, which contains importin α– and Nup153-binding domains. However, Nup50 dynamics are independent of importin α, Nup153, and Nup98, even though the latter two proteins also exhibit transcription-dependent mobility. Of interest, depletion of Nup50 from C2C12 myoblasts does not affect cell proliferation but inhibits differentiation into myotubes. Taken together, our results suggest a transport-independent role for Nup50 in chromatin biology that occurs away from the NPC. article_processing_charge: No article_type: original author: - first_name: Abigail L. full_name: Buchwalter, Abigail L. last_name: Buchwalter - first_name: Yun full_name: Liang, Yun last_name: Liang - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Buchwalter AL, Liang Y, Hetzer M. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. 2014;25(16):2472-2484. doi:10.1091/mbc.e14-04-0865 apa: Buchwalter, A. L., Liang, Y., & Hetzer, M. (2014). Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. American Society for Cell Biology. https://doi.org/10.1091/mbc.e14-04-0865 chicago: Buchwalter, Abigail L., Yun Liang, and Martin Hetzer. “Nup50 Is Required for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell. American Society for Cell Biology, 2014. https://doi.org/10.1091/mbc.e14-04-0865. ieee: A. L. Buchwalter, Y. Liang, and M. Hetzer, “Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics,” Molecular Biology of the Cell, vol. 25, no. 16. American Society for Cell Biology, pp. 2472–2484, 2014. ista: Buchwalter AL, Liang Y, Hetzer M. 2014. Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics. Molecular Biology of the Cell. 25(16), 2472–2484. mla: Buchwalter, Abigail L., et al. “Nup50 Is Required for Cell Differentiation and Exhibits Transcription-Dependent Dynamics.” Molecular Biology of the Cell, vol. 25, no. 16, American Society for Cell Biology, 2014, pp. 2472–84, doi:10.1091/mbc.e14-04-0865. short: A.L. Buchwalter, Y. Liang, M. Hetzer, Molecular Biology of the Cell 25 (2014) 2472–2484. date_created: 2022-04-07T07:50:24Z date_published: 2014-08-15T00:00:00Z date_updated: 2022-07-18T08:45:20Z day: '15' doi: 10.1091/mbc.e14-04-0865 extern: '1' intvolume: ' 25' issue: '16' keyword: - Cell Biology - Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1091/mbc.e14-04-0865 month: '08' oa: 1 oa_version: Published Version page: 2472-2484 publication: Molecular Biology of the Cell publication_identifier: issn: - 1059-1524 - 1939-4586 publication_status: published publisher: American Society for Cell Biology quality_controlled: '1' scopus_import: '1' status: public title: Nup50 is required for cell differentiation and exhibits transcription-dependent dynamics type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 25 year: '2014' ... --- _id: '11081' abstract: - lang: eng text: In eukaryotic cells the nuclear genome is enclosed by the nuclear envelope (NE). In metazoans, the NE breaks down in mitosis and it has been assumed that the physical barrier separating nucleoplasm and cytoplasm remains intact during the rest of the cell cycle and cell differentiation. However, recent studies suggest that nonmitotic NE remodeling plays a critical role in development, virus infection, laminopathies, and cancer. Although the mechanisms underlying these NE restructuring events are currently being defined, one common theme is activation of protein kinase C family members in the interphase nucleus to disrupt the nuclear lamina, demonstrating the importance of the lamina in maintaining nuclear integrity. article_processing_charge: No article_type: review author: - first_name: Emily full_name: Hatch, Emily last_name: Hatch - first_name: Martin W full_name: HETZER, Martin W id: 86c0d31b-b4eb-11ec-ac5a-eae7b2e135ed last_name: HETZER orcid: 0000-0002-2111-992X citation: ama: Hatch E, Hetzer M. Breaching the nuclear envelope in development and disease. Journal of Cell Biology. 2014;205(2):133-141. doi:10.1083/jcb.201402003 apa: Hatch, E., & Hetzer, M. (2014). Breaching the nuclear envelope in development and disease. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201402003 chicago: Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development and Disease.” Journal of Cell Biology. Rockefeller University Press, 2014. https://doi.org/10.1083/jcb.201402003. ieee: E. Hatch and M. Hetzer, “Breaching the nuclear envelope in development and disease,” Journal of Cell Biology, vol. 205, no. 2. Rockefeller University Press, pp. 133–141, 2014. ista: Hatch E, Hetzer M. 2014. Breaching the nuclear envelope in development and disease. Journal of Cell Biology. 205(2), 133–141. mla: Hatch, Emily, and Martin Hetzer. “Breaching the Nuclear Envelope in Development and Disease.” Journal of Cell Biology, vol. 205, no. 2, Rockefeller University Press, 2014, pp. 133–41, doi:10.1083/jcb.201402003. short: E. Hatch, M. Hetzer, Journal of Cell Biology 205 (2014) 133–141. date_created: 2022-04-07T07:50:13Z date_published: 2014-04-21T00:00:00Z date_updated: 2022-07-18T08:45:09Z day: '21' doi: 10.1083/jcb.201402003 extern: '1' external_id: pmid: - '24751535' intvolume: ' 205' issue: '2' keyword: - Cell Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1083/jcb.201402003 month: '04' oa: 1 oa_version: Published Version page: 133-141 pmid: 1 publication: Journal of Cell Biology publication_identifier: issn: - 1540-8140 - 0021-9525 publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: Breaching the nuclear envelope in development and disease type: journal_article user_id: 72615eeb-f1f3-11ec-aa25-d4573ddc34fd volume: 205 year: '2014' ... --- _id: '11583' abstract: - lang: eng text: 'Candidate galaxies at redshifts of z ∼ 10 are now being found in extremely deep surveys, probing very small areas. As a consequence, candidates are very faint, making spectroscopic confirmation practically impossible. In order to overcome such limitations, we have undertaken the CF-HiZELS survey, which is a large-area, medium-depth near-infrared narrow-band survey targeted at z = 8.8 Lyman α (Lyα) emitters (LAEs) and covering 10 deg2 in part of the SSA22 field with the Canada–France–Hawaii Telescope (CFHT). We surveyed a comoving volume of 4.7 × 106 Mpc3 to a Lyα luminosity limit of 6.3 × 1043舁erg舁s−1. We look for Lyα candidates by applying the following criteria: (i) clear emission-line source, (ii) no optical detections (ugriz from CFHTLS), (iii) no visible detection in the optical stack (ugriz > 27), (iv) visually checked reliable NBJ and J detections and (v) J − K ≤ 0. We compute photometric redshifts and remove a significant amount of dusty lower redshift line-emitters at z ∼ 1.4 or 2.2. A total of 13 Lyα candidates were found, of which two are marked as strong candidates, but the majority have very weak constraints on their spectral energy distributions. Using follow-up observations with SINFONI/VLT, we are able to exclude the most robust candidates as LAEs. We put a strong constraint on the Lyα luminosity function at z ∼ 9 and make realistic predictions for ongoing and future surveys. Our results show that surveys for the highest redshift LAEs are susceptible of multiple contaminations and that spectroscopic follow-up is absolutely necessary.' acknowledgement: We thank the anonymous referee for the comments and suggestions which improved both the quality and clarity of this work. DS acknowledges financial support from the Netherlands Organisation for Scientific Research (NWO) through a Veni fellowship. IRS acknowledges support from STFC (ST/I001573/1), a Leverhulme Fellowship, the ERC Advanced Investigator programme DUSTYGAL 321334 and a Royal Society/Wolfson Merit Award. PNB acknowledges support from the Leverhulme Trust. JWK acknowledges the support from the Creative Research Initiative Program, no. 2008- 0060544, of the National Research Foundation of Korea (NRF) funded by the Korean government (MSIP). JPUF and BMJ acknowledge support from the ERC-StG grant EGGS-278202. The Dark Cosmology Centre is funded by the Danish National Research Foundation. This work is based in part on data obtained as part of the UKIRT Infrared Deep Sky Survey. Based on observations obtained with MegaPrime/MegaCam, a joint project of CFHT and CEA/IRFU, at the Canada–France–Hawaii Telescope (CFHT) which is operated by the National Research Council (NRC) of Canada, the Institut National des Science de l’Univers of the Centre National de la Recherche Scientifique (CNRS) of France and the University of Hawaii. This work is based in part on data products produced at Terapix available at the Canadian Astronomy Data Centre as part of the Canada-France-Hawaii Telescope Legacy Survey, a collaborative project of NRC and CNRS. This work was only possible due to OPTICON/FP7 and the access that it granted to the CFHT telescope. The authors also wish to acknowledge the CFHTLS and UKIDSS surveys for their excellent legacy and complementary value – without such high-quality data sets, this research would not have been possible. article_processing_charge: No article_type: original author: - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X - first_name: David full_name: Sobral, David last_name: Sobral - first_name: A. M. full_name: Swinbank, A. M. last_name: Swinbank - first_name: Ian full_name: Smail, Ian last_name: Smail - first_name: P. N. full_name: Best, P. N. last_name: Best - first_name: Jae-Woo full_name: Kim, Jae-Woo last_name: Kim - first_name: Marijn full_name: Franx, Marijn last_name: Franx - first_name: Bo full_name: Milvang-Jensen, Bo last_name: Milvang-Jensen - first_name: Johan full_name: Fynbo, Johan last_name: Fynbo citation: ama: 'Matthee JJ, Sobral D, Swinbank AM, et al. A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. 2014;440(3):2375-2387. doi:10.1093/mnras/stu392' apa: 'Matthee, J. J., Sobral, D., Swinbank, A. M., Smail, I., Best, P. N., Kim, J.-W., … Fynbo, J. (2014). A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stu392' chicago: 'Matthee, Jorryt J, David Sobral, A. M. Swinbank, Ian Smail, P. N. Best, Jae-Woo Kim, Marijn Franx, Bo Milvang-Jensen, and Johan Fynbo. “A 10 Deg2 Lyman α Survey at Z=8.8 with Spectroscopic Follow-up: Strong Constraints on the Luminosity Function and Implications for Other Surveys.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2014. https://doi.org/10.1093/mnras/stu392.' ieee: 'J. J. Matthee et al., “A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys,” Monthly Notices of the Royal Astronomical Society, vol. 440, no. 3. Oxford University Press, pp. 2375–2387, 2014.' ista: 'Matthee JJ, Sobral D, Swinbank AM, Smail I, Best PN, Kim J-W, Franx M, Milvang-Jensen B, Fynbo J. 2014. A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys. Monthly Notices of the Royal Astronomical Society. 440(3), 2375–2387.' mla: 'Matthee, Jorryt J., et al. “A 10 Deg2 Lyman α Survey at Z=8.8 with Spectroscopic Follow-up: Strong Constraints on the Luminosity Function and Implications for Other Surveys.” Monthly Notices of the Royal Astronomical Society, vol. 440, no. 3, Oxford University Press, 2014, pp. 2375–87, doi:10.1093/mnras/stu392.' short: J.J. Matthee, D. Sobral, A.M. Swinbank, I. Smail, P.N. Best, J.-W. Kim, M. Franx, B. Milvang-Jensen, J. Fynbo, Monthly Notices of the Royal Astronomical Society 440 (2014) 2375–2387. date_created: 2022-07-14T12:33:24Z date_published: 2014-05-21T00:00:00Z date_updated: 2022-08-19T08:30:30Z day: '21' doi: 10.1093/mnras/stu392 extern: '1' external_id: arxiv: - '1402.6697' intvolume: ' 440' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: evolution' - 'galaxies: high-redshift' - 'cosmology: observations' - dark ages - reionization - first stars language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1402.6697 month: '05' oa: 1 oa_version: Preprint page: 2375-2387 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: 'A 10 deg2 Lyman α survey at z=8.8 with spectroscopic follow-up: Strong constraints on the luminosity function and implications for other surveys' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 440 year: '2014' ... --- _id: '11582' abstract: - lang: eng text: We have observed a sample of typical z ∼ 1 star-forming galaxies, selected from the HiZELS survey, with the new K-band Multi-Object Spectrograph (KMOS) near-infrared, multi-integral field unit instrument on the Very Large Telescope (VLT), in order to obtain their dynamics and metallicity gradients. The majority of our galaxies have a metallicity gradient consistent with being flat or negative (i.e. higher metallicity cores than outskirts). Intriguingly, we find a trend between metallicity gradient and specific star formation rate (sSFR), such that galaxies with a high sSFR tend to have relatively metal poor centres, a result which is strengthened when combined with data sets from the literature. This result appears to explain the discrepancies reported between different high-redshift studies and varying claims for evolution. From a galaxy evolution perspective, the trend we see would mean that a galaxy's sSFR is governed by the amount of metal-poor gas that can be funnelled into its core, triggered either by merging or through efficient accretion. In fact, merging may play a significant role as it is the starburst galaxies at all epochs, which have the more positive metallicity gradients. Our results may help to explain the origin of the fundamental metallicity relation, in which galaxies at a fixed mass are observed to have lower metallicities at higher star formation rates, especially if the metallicity is measured in an aperture encompassing only the central regions of the galaxy. Finally, we note that this study demonstrates the power of KMOS as an efficient instrument for large-scale resolved galaxy surveys. acknowledgement: First, we acknowledge the referee for their comments, which have improved the clarity of this paper. JPS and IRS acknowledge support from STFC (ST/I001573/1). IRS also acknowledges support from the ERC Advanced Investigator programme DUSTYGAL and a Royal Society/Wolfson Merit Award. DS acknowledges financial support from NWO through a Veni fellowship and from FCT through the award of an FCT-IF starting grant. PNB acknowledges STFC for financial support. article_processing_charge: No article_type: original author: - first_name: John P. full_name: Stott, John P. last_name: Stott - first_name: David full_name: Sobral, David last_name: Sobral - first_name: A. M. full_name: Swinbank, A. M. last_name: Swinbank - first_name: Ian full_name: Smail, Ian last_name: Smail - first_name: Richard full_name: Bower, Richard last_name: Bower - first_name: Philip N. full_name: Best, Philip N. last_name: Best - first_name: Ray M. full_name: Sharples, Ray M. last_name: Sharples - first_name: James E. full_name: Geach, James E. last_name: Geach - first_name: Jorryt J full_name: Matthee, Jorryt J id: 7439a258-f3c0-11ec-9501-9df22fe06720 last_name: Matthee orcid: 0000-0003-2871-127X citation: ama: Stott JP, Sobral D, Swinbank AM, et al. A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. 2014;443(3):2695-2704. doi:10.1093/mnras/stu1343 apa: Stott, J. P., Sobral, D., Swinbank, A. M., Smail, I., Bower, R., Best, P. N., … Matthee, J. J. (2014). A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. Oxford University Press. https://doi.org/10.1093/mnras/stu1343 chicago: Stott, John P., David Sobral, A. M. Swinbank, Ian Smail, Richard Bower, Philip N. Best, Ray M. Sharples, James E. Geach, and Jorryt J Matthee. “A Relationship between Specific Star Formation Rate and Metallicity Gradient within z ∼ 1 Galaxies from KMOS-HiZELS.” Monthly Notices of the Royal Astronomical Society. Oxford University Press, 2014. https://doi.org/10.1093/mnras/stu1343. ieee: J. P. Stott et al., “A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS,” Monthly Notices of the Royal Astronomical Society, vol. 443, no. 3. Oxford University Press, pp. 2695–2704, 2014. ista: Stott JP, Sobral D, Swinbank AM, Smail I, Bower R, Best PN, Sharples RM, Geach JE, Matthee JJ. 2014. A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS. Monthly Notices of the Royal Astronomical Society. 443(3), 2695–2704. mla: Stott, John P., et al. “A Relationship between Specific Star Formation Rate and Metallicity Gradient within z ∼ 1 Galaxies from KMOS-HiZELS.” Monthly Notices of the Royal Astronomical Society, vol. 443, no. 3, Oxford University Press, 2014, pp. 2695–704, doi:10.1093/mnras/stu1343. short: J.P. Stott, D. Sobral, A.M. Swinbank, I. Smail, R. Bower, P.N. Best, R.M. Sharples, J.E. Geach, J.J. Matthee, Monthly Notices of the Royal Astronomical Society 443 (2014) 2695–2704. date_created: 2022-07-14T12:16:10Z date_published: 2014-09-21T00:00:00Z date_updated: 2022-08-19T08:27:25Z day: '21' doi: 10.1093/mnras/stu1343 extern: '1' external_id: arxiv: - '1407.1047' intvolume: ' 443' issue: '3' keyword: - Space and Planetary Science - Astronomy and Astrophysics - 'galaxies: abundances' - 'galaxies: evolution' - 'galaxies: kinematics and dynamics' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1407.1047 month: '09' oa: 1 oa_version: Preprint page: 2695-2704 publication: Monthly Notices of the Royal Astronomical Society publication_identifier: eissn: - 1365-2966 issn: - 0035-8711 publication_status: published publisher: Oxford University Press quality_controlled: '1' scopus_import: '1' status: public title: A relationship between specific star formation rate and metallicity gradient within z ∼ 1 galaxies from KMOS-HiZELS type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 443 year: '2014' ... --- _id: '11750' abstract: - lang: eng text: We report on the magnetic properties of a hot-pressed FeSb 2 sample. We find a significant increase in the magnetic susceptibility in our sample when compared with the values previously reported for the polycrystalline sample. The pronounced Curie tail at low temperature corresponds to 0.2% of Fe 2+ impurities per mole. In the intrinsic conductivity region, the susceptibility due to free carriers shows thermally activated behavior and is consistent with the data reported for single crystal FeSb 2 . Based on our data and analysis, while the enhanced magnetic susceptibility in our sample comes mainly from a small amount of unreacted Fe, the contribution from the enhanced carrier density due to lattice and strain defects arising from the ball milling process is also significant. Existence of an unreacted Fe phase is evidenced by small coercivity values of ~100 observed at 50 and 300 K. article_number: '6675864' article_processing_charge: No article_type: original author: - first_name: Mani full_name: Pokharel, Mani last_name: Pokharel - first_name: Huaizhou full_name: Zhao, Huaizhou last_name: Zhao - first_name: Kimberly A full_name: Modic, Kimberly A id: 13C26AC0-EB69-11E9-87C6-5F3BE6697425 last_name: Modic orcid: 0000-0001-9760-3147 - first_name: Zhifeng full_name: Ren, Zhifeng last_name: Ren - first_name: Cyril full_name: Opeil, Cyril last_name: Opeil citation: ama: Pokharel M, Zhao H, Modic KA, Ren Z, Opeil C. Magnetic properties of hot-pressed FeSb2. IEEE Transactions on Magnetics. 2014;50(5). doi:10.1109/TMAG.2013.2292607 apa: Pokharel, M., Zhao, H., Modic, K. A., Ren, Z., & Opeil, C. (2014). Magnetic properties of hot-pressed FeSb2. IEEE Transactions on Magnetics. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TMAG.2013.2292607 chicago: Pokharel, Mani, Huaizhou Zhao, Kimberly A Modic, Zhifeng Ren, and Cyril Opeil. “Magnetic Properties of Hot-Pressed FeSb2.” IEEE Transactions on Magnetics. Institute of Electrical and Electronics Engineers, 2014. https://doi.org/10.1109/TMAG.2013.2292607. ieee: M. Pokharel, H. Zhao, K. A. Modic, Z. Ren, and C. Opeil, “Magnetic properties of hot-pressed FeSb2,” IEEE Transactions on Magnetics, vol. 50, no. 5. Institute of Electrical and Electronics Engineers, 2014. ista: Pokharel M, Zhao H, Modic KA, Ren Z, Opeil C. 2014. Magnetic properties of hot-pressed FeSb2. IEEE Transactions on Magnetics. 50(5), 6675864. mla: Pokharel, Mani, et al. “Magnetic Properties of Hot-Pressed FeSb2.” IEEE Transactions on Magnetics, vol. 50, no. 5, 6675864, Institute of Electrical and Electronics Engineers, 2014, doi:10.1109/TMAG.2013.2292607. short: M. Pokharel, H. Zhao, K.A. Modic, Z. Ren, C. Opeil, IEEE Transactions on Magnetics 50 (2014). date_created: 2022-08-08T08:26:02Z date_published: 2014-05-01T00:00:00Z date_updated: 2022-08-11T09:51:22Z day: '01' doi: 10.1109/TMAG.2013.2292607 extern: '1' intvolume: ' 50' issue: '5' language: - iso: eng month: '05' oa_version: None publication: IEEE Transactions on Magnetics publication_identifier: eissn: - 1941-0069 issn: - 0018-9464 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Magnetic properties of hot-pressed FeSb2 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 50 year: '2014' ... --- _id: '11789' abstract: - lang: eng text: "We study a weighted online bipartite matching problem: G(V 1, V 2, E) is a weighted bipartite graph where V 1 is known beforehand and the vertices of V 2 arrive online. The goal is to match vertices of V 2 as they arrive to vertices in V 1, so as to maximize the sum of weights of edges in the matching. If assignments to V 1 cannot be changed, no bounded competitive ratio is achievable. We study the weighted online matching problem with free disposal, where vertices in V 1 can be assigned multiple times, but only get credit for the maximum weight edge assigned to them over the course of the algorithm. For this problem, the greedy algorithm is 0.5-competitive and determining whether a better competitive ratio is achievable is a well known open problem.\r\n\r\nWe identify an interesting special case where the edge weights are decomposable as the product of two factors, one corresponding to each end point of the edge. This is analogous to the well studied related machines model in the scheduling literature, although the objective functions are different. For this case of decomposable edge weights, we design a 0.5664 competitive randomized algorithm in complete bipartite graphs. We show that such instances with decomposable weights are non-trivial by establishing upper bounds of 0.618 for deterministic and 0.8 for randomized algorithms.\r\n\r\nA tight competitive ratio of 1 − 1/e ≈ 0.632 was known previously for both the 0-1 case as well as the case where edge weights depend on the offline vertices only, but for these cases, reassignments cannot change the quality of the solution. Beating 0.5 for weighted matching where reassignments are necessary has been a significant challenge. We thus give the first online algorithm with competitive ratio strictly better than 0.5 for a non-trivial case of weighted matching with free disposal." alternative_title: - LNCS article_processing_charge: No author: - first_name: Moses full_name: Charikar, Moses last_name: Charikar - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Huy L. full_name: Nguyễn, Huy L. last_name: Nguyễn citation: ama: 'Charikar M, Henzinger MH, Nguyễn HL. Online bipartite matching with decomposable weights. In: 22nd Annual European Symposium on Algorithms. Vol 8737. Springer Nature; 2014:260-271. doi:10.1007/978-3-662-44777-2_22' apa: 'Charikar, M., Henzinger, M. H., & Nguyễn, H. L. (2014). Online bipartite matching with decomposable weights. In 22nd Annual European Symposium on Algorithms (Vol. 8737, pp. 260–271). Wroclaw, Poland: Springer Nature. https://doi.org/10.1007/978-3-662-44777-2_22' chicago: Charikar, Moses, Monika H Henzinger, and Huy L. Nguyễn. “Online Bipartite Matching with Decomposable Weights.” In 22nd Annual European Symposium on Algorithms, 8737:260–71. Springer Nature, 2014. https://doi.org/10.1007/978-3-662-44777-2_22. ieee: M. Charikar, M. H. Henzinger, and H. L. Nguyễn, “Online bipartite matching with decomposable weights,” in 22nd Annual European Symposium on Algorithms, Wroclaw, Poland, 2014, vol. 8737, pp. 260–271. ista: 'Charikar M, Henzinger MH, Nguyễn HL. 2014. Online bipartite matching with decomposable weights. 22nd Annual European Symposium on Algorithms. ESA: Annual European Symposium on Algorithms, LNCS, vol. 8737, 260–271.' mla: Charikar, Moses, et al. “Online Bipartite Matching with Decomposable Weights.” 22nd Annual European Symposium on Algorithms, vol. 8737, Springer Nature, 2014, pp. 260–71, doi:10.1007/978-3-662-44777-2_22. short: M. Charikar, M.H. Henzinger, H.L. Nguyễn, in:, 22nd Annual European Symposium on Algorithms, Springer Nature, 2014, pp. 260–271. conference: end_date: 2014-09-10 location: Wroclaw, Poland name: 'ESA: Annual European Symposium on Algorithms' start_date: 2014-09-08 date_created: 2022-08-11T10:41:47Z date_published: 2014-09-01T00:00:00Z date_updated: 2023-02-13T11:16:24Z day: '01' doi: 10.1007/978-3-662-44777-2_22 extern: '1' external_id: arxiv: - '1409.2139' intvolume: ' 8737' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1409.2139 month: '09' oa: 1 oa_version: Preprint page: 260 - 271 publication: 22nd Annual European Symposium on Algorithms publication_identifier: isbn: - 978-366244776-5 issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Online bipartite matching with decomposable weights type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8737 year: '2014' ... --- _id: '11790' abstract: - lang: eng text: "Assume a seller wants to sell a digital product in a social network where a buyer’s valuation of the item has positive network externalities from her neighbors that already have the item. The goal of the seller is to maximize his revenue. Previous work on this problem [7] studies the case where clients are offered the item in sequence and have to pay personalized prices. This is highly infeasible in large scale networks such as the Facebook graph: (1) Offering items to the clients one after the other consumes a large amount of time, and (2) price-discrimination of clients could appear unfair to them and result in negative client reaction or could conflict with legal requirements.\r\n\r\nWe study a setting dealing with these issues. Specifically, the item is offered in parallel to multiple clients at the same time and at the same price. This is called a round. We show that with O(logn) rounds, where n is the number of clients, a constant factor of the revenue with price discrimination can be achieved and that this is not possible with o(logn) rounds. Moreover we show that it is APX-hard to maximize the revenue and we give constant factor approximation algorithms for various further settings of limited price discrimination." alternative_title: - LNCS article_processing_charge: No author: - first_name: Luděk full_name: Cigler, Luděk last_name: Cigler - first_name: Wolfgang full_name: Dvořák, Wolfgang last_name: Dvořák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Martin full_name: Starnberger, Martin last_name: Starnberger citation: ama: 'Cigler L, Dvořák W, Henzinger MH, Starnberger M. Limiting price discrimination when selling products with positive network externalities. In: 10th International Conference of Web and Internet Economics. Vol 8877. Springer Nature; 2014:44-57. doi:10.1007/978-3-319-13129-0_4' apa: 'Cigler, L., Dvořák, W., Henzinger, M. H., & Starnberger, M. (2014). Limiting price discrimination when selling products with positive network externalities. In 10th International Conference of Web and Internet Economics (Vol. 8877, pp. 44–57). Beijing, China: Springer Nature. https://doi.org/10.1007/978-3-319-13129-0_4' chicago: Cigler, Luděk, Wolfgang Dvořák, Monika H Henzinger, and Martin Starnberger. “Limiting Price Discrimination When Selling Products with Positive Network Externalities.” In 10th International Conference of Web and Internet Economics, 8877:44–57. Springer Nature, 2014. https://doi.org/10.1007/978-3-319-13129-0_4. ieee: L. Cigler, W. Dvořák, M. H. Henzinger, and M. Starnberger, “Limiting price discrimination when selling products with positive network externalities,” in 10th International Conference of Web and Internet Economics, Beijing, China, 2014, vol. 8877, pp. 44–57. ista: 'Cigler L, Dvořák W, Henzinger MH, Starnberger M. 2014. Limiting price discrimination when selling products with positive network externalities. 10th International Conference of Web and Internet Economics. WINE: International Conference on Web and Internet Economics, LNCS, vol. 8877, 44–57.' mla: Cigler, Luděk, et al. “Limiting Price Discrimination When Selling Products with Positive Network Externalities.” 10th International Conference of Web and Internet Economics, vol. 8877, Springer Nature, 2014, pp. 44–57, doi:10.1007/978-3-319-13129-0_4. short: L. Cigler, W. Dvořák, M.H. Henzinger, M. Starnberger, in:, 10th International Conference of Web and Internet Economics, Springer Nature, 2014, pp. 44–57. conference: end_date: 2014-12-17 location: Beijing, China name: 'WINE: International Conference on Web and Internet Economics' start_date: 2014-12-14 date_created: 2022-08-11T10:58:44Z date_published: 2014-12-01T00:00:00Z date_updated: 2023-02-13T11:18:30Z day: '01' doi: 10.1007/978-3-319-13129-0_4 extern: '1' intvolume: ' 8877' language: - iso: eng month: '12' oa_version: None page: 44 - 57 publication: 10th International Conference of Web and Internet Economics publication_identifier: issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Limiting price discrimination when selling products with positive network externalities type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8877 year: '2014' ... --- _id: '118' abstract: - lang: eng text: While the penetration of objects into granular media is well-studied, there is little understanding of how objects settle in gravities, geff, different from that of Earth - a scenario potentially relevant to the geomorphology of planets and asteroids and also to their exploration using man-made devices. By conducting experiments in an accelerating frame, we explore geff ranging from 0.4 g to 1.2 g. Surprisingly, we find that the rest depth is independent of geff and also that the time required for the object to come to rest scales like geff-1/2. With discrete element modeling simulations, we reproduce the experimental results and extend the range of geff to objects as small as asteroids and as large as Jupiter. Our results shed light on the initial stage of sedimentation into dry granular media across a range of celestial bodies and also have implications for the design of man-made, extraterrestrial vehicles and structures. Key Points The settling depth in granular media is independent of gravity The settling time scales like g-1/2 Layering driven by granular sedimentation should be similar. acknowledgement: 'The Spanish MINECO project FIS2011-26675, the PIUNA program (U. Navarra), and the Project 29942WL (Fonds de Solidarité Prioritaire France-Cuba) have partially supported this research. ' author: - first_name: Ernesto full_name: Altshuler, Ernesto last_name: Altshuler - first_name: H full_name: Torres, H last_name: Torres - first_name: A full_name: González_Pita, A last_name: González_Pita - first_name: Colina G full_name: Sánchez, Colina G last_name: Sánchez - first_name: Carlos full_name: Pérez Penichet, Carlos last_name: Pérez Penichet - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Rauól full_name: Hidalgo, Rauól last_name: Hidalgo citation: ama: Altshuler E, Torres H, González_Pita A, et al. Settling into dry granular media in different gravities. Geophysical Research Letters. 2014;41(9):3032-3037. doi:10.1002/2014GL059229 apa: Altshuler, E., Torres, H., González_Pita, A., Sánchez, C. G., Pérez Penichet, C., Waitukaitis, S. R., & Hidalgo, R. (2014). Settling into dry granular media in different gravities. Geophysical Research Letters. Wiley-Blackwell. https://doi.org/10.1002/2014GL059229 chicago: Altshuler, Ernesto, H Torres, A González_Pita, Colina G Sánchez, Carlos Pérez Penichet, Scott R Waitukaitis, and Rauól Hidalgo. “Settling into Dry Granular Media in Different Gravities.” Geophysical Research Letters. Wiley-Blackwell, 2014. https://doi.org/10.1002/2014GL059229. ieee: E. Altshuler et al., “Settling into dry granular media in different gravities,” Geophysical Research Letters, vol. 41, no. 9. Wiley-Blackwell, pp. 3032–3037, 2014. ista: Altshuler E, Torres H, González_Pita A, Sánchez CG, Pérez Penichet C, Waitukaitis SR, Hidalgo R. 2014. Settling into dry granular media in different gravities. Geophysical Research Letters. 41(9), 3032–3037. mla: Altshuler, Ernesto, et al. “Settling into Dry Granular Media in Different Gravities.” Geophysical Research Letters, vol. 41, no. 9, Wiley-Blackwell, 2014, pp. 3032–37, doi:10.1002/2014GL059229. short: E. Altshuler, H. Torres, A. González_Pita, C.G. Sánchez, C. Pérez Penichet, S.R. Waitukaitis, R. Hidalgo, Geophysical Research Letters 41 (2014) 3032–3037. date_created: 2018-12-11T11:44:43Z date_published: 2014-05-16T00:00:00Z date_updated: 2021-01-12T06:48:53Z day: '16' doi: 10.1002/2014GL059229 extern: '1' intvolume: ' 41' issue: '9' language: - iso: eng month: '05' oa_version: None page: 3032 - 3037 publication: Geophysical Research Letters publication_status: published publisher: Wiley-Blackwell publist_id: '7936' quality_controlled: '1' status: public title: Settling into dry granular media in different gravities type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 41 year: '2014' ... --- _id: '11855' abstract: - lang: eng text: 'The decremental single-source shortest paths (SSSP) problem concerns maintaining the distances between a given source node s to every node in an n-node m-edge graph G undergoing edge deletions. While its static counterpart can be easily solved in near-linear time, this decremental problem is much more challenging even in the undirected unweighted case. In this case, the classic O(mn) total update time of Even and Shiloach (JACM 1981) has been the fastest known algorithm for three decades. With the loss of a (1 + ε)-approximation factor, the running time was recently improved to O(n 2+o(1) ) by Bernstein and Roditty (SODA 2011), and more recently to O(n 1.8+o(1) + m 1+o(1) ) by Henzinger, Krinninger, and Nanongkai (SODA 2014). In this paper, we finally bring the running time of this case down to near-linear: We give a (1 + ε)-approximation algorithm with O(m 1+o(1) ) total update time, thus obtaining near-linear time. Moreover, we obtain O(m 1+o(1) log W) time for the weighted case, where the edge weights are integers from 1 to W. The only prior work on weighted graphs in o(mn log W) time is the O(mn 0.986 log W)-time algorithm by Henzinger, Krinninger, and Nanongkai (STOC 2014) which works for the general weighted directed case. In contrast to the previous results which rely on maintaining a sparse emulator, our algorithm relies on maintaining a so-called sparse (d, ε)-hop set introduced by Cohen (JACM 2000) in the PRAM literature. A (d, ε)-hop set of a graph G = (V, E) is a set E'' of weighted edges such that the distance between any pair of nodes in G can be (1 + ε)-approximated by their d-hop distance (given by a path containing at most d edges) on G''=(V, E∪E''). Our algorithm can maintain an (n o(1) , ε)-hop set of near-linear size in near-linear time under edge deletions. It is the first of its kind to the best of our knowledge. To maintain the distances on this hop set, we develop a monotone bounded-hop Even-Shiloach tree. It results from extending and combining the monotone Even-Shiloach tree of Henzinger, Krinninger, and Nanongkai (FOCS 2013) with the bounded-hop SSSP technique of Bernstein (STOC 2013). These two new tools might be of independent interest.' article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Henzinger MH, Krinninger S, Nanongkai D. Decremental single-source shortest paths on undirected graphs in near-linear total update time. In: 55th Annual Symposium on Foundations of Computer Science. Institute of Electrical and Electronics Engineers; 2014:146-155. doi:10.1109/focs.2014.24' apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Decremental single-source shortest paths on undirected graphs in near-linear total update time. In 55th Annual Symposium on Foundations of Computer Science (pp. 146–155). Philadelphia, PA, United States: Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/focs.2014.24' chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” In 55th Annual Symposium on Foundations of Computer Science, 146–55. Institute of Electrical and Electronics Engineers, 2014. https://doi.org/10.1109/focs.2014.24. ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Decremental single-source shortest paths on undirected graphs in near-linear total update time,” in 55th Annual Symposium on Foundations of Computer Science, Philadelphia, PA, United States, 2014, pp. 146–155. ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2014. Decremental single-source shortest paths on undirected graphs in near-linear total update time. 55th Annual Symposium on Foundations of Computer Science. FOCS: Annual Symposium on Foundations of Computer Science, 146–155.' mla: Henzinger, Monika H., et al. “Decremental Single-Source Shortest Paths on Undirected Graphs in near-Linear Total Update Time.” 55th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2014, pp. 146–55, doi:10.1109/focs.2014.24. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 55th Annual Symposium on Foundations of Computer Science, Institute of Electrical and Electronics Engineers, 2014, pp. 146–155. conference: end_date: 2014-10-21 location: Philadelphia, PA, United States name: 'FOCS: Annual Symposium on Foundations of Computer Science' start_date: 2014-10-18 date_created: 2022-08-16T08:14:33Z date_published: 2014-10-01T00:00:00Z date_updated: 2023-02-21T16:27:34Z day: '01' doi: 10.1109/focs.2014.24 extern: '1' external_id: arxiv: - '1402.0054' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1402.0054 month: '10' oa: 1 oa_version: Preprint page: 146-155 publication: 55th Annual Symposium on Foundations of Computer Science publication_identifier: eisbn: - 978-1-4799-6517-5 issn: - 0272-5428 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' related_material: record: - id: '11768' relation: later_version status: public scopus_import: '1' status: public title: Decremental single-source shortest paths on undirected graphs in near-linear total update time type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '11870' abstract: - lang: eng text: "We consider dynamic algorithms for maintaining Single-Source Reachability (SSR) and approximate Single-Source Shortest Paths (SSSP) on n-node m-edge directed graphs under edge deletions (decremental algorithms). The previous fastest algorithm for SSR and SSSP goes back three decades to Even and Shiloach (JACM 1981); it has O(1) query time and O(mn) total update time (i.e., linear amortized update time if all edges are deleted). This algorithm serves as a building block for several other dynamic algorithms. The question whether its total update time can be improved is a major, long standing, open problem.\r\n\r\nIn this paper, we answer this question affirmatively. We obtain a randomized algorithm which, in a simplified form, achieves an Õ(mn0.984) expected total update time for SSR and (1 + ε)-approximate SSSP, where Õ(·) hides poly log n. We also extend our algorithm to achieve roughly the same running time for Strongly Connected Components (SCC), improving the algorithm of Roditty and Zwick (FOCS 2002), and an algorithm that improves the Õ (mn log W)-time algorithm of Bernstein (STOC 2013) for approximating SSSP on weighted directed graphs, where the edge weights are integers from 1 to W. All our algorithms have constant query time in the worst case." article_number: 674 - 683 article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Henzinger MH, Krinninger S, Nanongkai D. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In: 46th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2014. doi:10.1145/2591796.2591869' apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. In 46th Annual ACM Symposium on Theory of Computing. New York, NY, United States: Association for Computing Machinery. https://doi.org/10.1145/2591796.2591869' chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” In 46th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery, 2014. https://doi.org/10.1145/2591796.2591869. ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs,” in 46th Annual ACM Symposium on Theory of Computing, New York, NY, United States, 2014. ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2014. Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs. 46th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 674–683.' mla: Henzinger, Monika H., et al. “Sublinear-Time Decremental Algorithms for Single-Source Reachability and Shortest Paths on Directed Graphs.” 46th Annual ACM Symposium on Theory of Computing, 674–683, Association for Computing Machinery, 2014, doi:10.1145/2591796.2591869. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 46th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2014. conference: end_date: 2014-06-03 location: New York, NY, United States name: 'STOC: Symposium on Theory of Computing' start_date: 2014-05-31 date_created: 2022-08-16T09:41:57Z date_published: 2014-05-01T00:00:00Z date_updated: 2023-02-17T11:18:52Z day: '01' doi: 10.1145/2591796.2591869 extern: '1' external_id: arxiv: - '1504.07959' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1504.07959 month: '05' oa: 1 oa_version: Preprint publication: 46th Annual ACM Symposium on Theory of Computing publication_identifier: isbn: - 978-145032710-7 issn: - 0737-8017 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: Sublinear-time decremental algorithms for single-source reachability and shortest paths on directed graphs type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '11876' abstract: - lang: eng text: "We study dynamic (1 + ∊)-approximation algorithms for the single-source shortest paths problem in an unweighted undirected n-node m-edge graph under edge deletions. The fastest algorithm for this problem is an algorithm with O(n2+o(1)) total update time and constant query time by Bernstein and Roditty (SODA 2011). In this paper, we improve the total update time to O(n1.8+o(1) + m1+o(1)) while keeping the query time constant. This running time is essentially tight when m = Ω(n1.8) since we need Ω(m) time even in the static setting. For smaller values of m, the running time of our algorithm is subquadratic, and is the first that breaks through the quadratic time barrier.\r\n\r\nIn obtaining this result, we develop a fast algorithm for what we call center cover data structure. We also make non-trivial extensions to our previous techniques called lazy-update and monotone Even-Shiloach trees (ICALP 2013 and FOCS 2013). As by-products of our new techniques, we obtain two new results for the decremental all-pairs shortest-paths problem. Our first result is the first approximation algorithm whose total update time is faster than Õ(mn) for all values of m. Our second result is a new trade-off between the total update time and the additive approximation guarantee." article_processing_charge: No author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Danupon full_name: Nanongkai, Danupon last_name: Nanongkai citation: ama: 'Henzinger MH, Krinninger S, Nanongkai D. A subquadratic-time algorithm for decremental single-source shortest paths. In: 25th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:1053-1072. doi:10.1137/1.9781611973402.79' apa: 'Henzinger, M. H., Krinninger, S., & Nanongkai, D. (2014). A subquadratic-time algorithm for decremental single-source shortest paths. In 25th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 1053–1072). Portland, OR, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973402.79' chicago: Henzinger, Monika H, Sebastian Krinninger, and Danupon Nanongkai. “A Subquadratic-Time Algorithm for Decremental Single-Source Shortest Paths.” In 25th Annual ACM-SIAM Symposium on Discrete Algorithms, 1053–72. Society for Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973402.79. ieee: M. H. Henzinger, S. Krinninger, and D. Nanongkai, “A subquadratic-time algorithm for decremental single-source shortest paths,” in 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Portland, OR, United States, 2014, pp. 1053–1072. ista: 'Henzinger MH, Krinninger S, Nanongkai D. 2014. A subquadratic-time algorithm for decremental single-source shortest paths. 25th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 1053–1072.' mla: Henzinger, Monika H., et al. “A Subquadratic-Time Algorithm for Decremental Single-Source Shortest Paths.” 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 1053–72, doi:10.1137/1.9781611973402.79. short: M.H. Henzinger, S. Krinninger, D. Nanongkai, in:, 25th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 1053–1072. conference: end_date: 2014-01-07 location: Portland, OR, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2014-01-05 date_created: 2022-08-16T12:58:31Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-17T11:58:42Z day: '01' doi: 10.1137/1.9781611973402.79 extern: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1137/1.9781611973402.79 month: '01' oa: 1 oa_version: Published Version page: 1053-1072 publication: 25th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - 978-1-61197-340-2 isbn: - 978-1-61197-338-9 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' scopus_import: '1' status: public title: A subquadratic-time algorithm for decremental single-source shortest paths type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '11875' abstract: - lang: eng text: We present the first deterministic data structures for maintaining approximate minimum vertex cover and maximum matching in a fully dynamic graph in time per update. In particular, for minimum vertex cover we provide deterministic data structures for maintaining a (2 + ε) approximation in O(log n/ε2) amortized time per update. For maximum matching, we show how to maintain a (3 + e) approximation in O(m1/3/ε2) amortized time per update, and a (4 + ε) approximation in O(m1/3/ε2) worst-case time per update. Our data structure for fully dynamic minimum vertex cover is essentially near-optimal and settles an open problem by Onak and Rubinfeld [13]. article_processing_charge: No author: - first_name: Sayan full_name: Bhattacharya, Sayan last_name: Bhattacharya - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Giuseppe F. full_name: Italiano, Giuseppe F. last_name: Italiano citation: ama: 'Bhattacharya S, Henzinger MH, Italiano GF. Deterministic fully dynamic data structures for vertex cover and matching. In: 26th Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2014:785-804. doi:10.1137/1.9781611973730.54' apa: 'Bhattacharya, S., Henzinger, M. H., & Italiano, G. F. (2014). Deterministic fully dynamic data structures for vertex cover and matching. In 26th Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 785–804). San Diego, CA, United States: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611973730.54' chicago: Bhattacharya, Sayan, Monika H Henzinger, and Giuseppe F. Italiano. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” In 26th Annual ACM-SIAM Symposium on Discrete Algorithms, 785–804. Society for Industrial and Applied Mathematics, 2014. https://doi.org/10.1137/1.9781611973730.54. ieee: S. Bhattacharya, M. H. Henzinger, and G. F. Italiano, “Deterministic fully dynamic data structures for vertex cover and matching,” in 26th Annual ACM-SIAM Symposium on Discrete Algorithms, San Diego, CA, United States, 2014, pp. 785–804. ista: 'Bhattacharya S, Henzinger MH, Italiano GF. 2014. Deterministic fully dynamic data structures for vertex cover and matching. 26th Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 785–804.' mla: Bhattacharya, Sayan, et al. “Deterministic Fully Dynamic Data Structures for Vertex Cover and Matching.” 26th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 785–804, doi:10.1137/1.9781611973730.54. short: S. Bhattacharya, M.H. Henzinger, G.F. Italiano, in:, 26th Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2014, pp. 785–804. conference: end_date: 2015-01-06 location: San Diego, CA, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2015-01-04 date_created: 2022-08-16T12:36:42Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-21T16:32:06Z day: '01' doi: 10.1137/1.9781611973730.54 extern: '1' external_id: arxiv: - '1412.1318' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1412.1318 month: '01' oa: 1 oa_version: Preprint page: 785-804 publication: 26th Annual ACM-SIAM Symposium on Discrete Algorithms publication_identifier: eisbn: - 978-1-61197-373-0 isbn: - 978-1-61197-374-7 publication_status: published publisher: Society for Industrial and Applied Mathematics quality_controlled: '1' related_material: record: - id: '11890' relation: later_version status: public scopus_import: '1' status: public title: Deterministic fully dynamic data structures for vertex cover and matching type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '119' abstract: - lang: eng text: Observations of flowing granular matter have suggested that same-material tribocharging depends on particle size, typically rendering large grains positive and small ones negative. Models assuming the transfer of trapped electrons can account for this trend, but have not been validated. Tracking individual grains in an electric field, we show quantitatively that charge is transferred based on size between materially identical grains. However, the surface density of trapped electrons, measured independently by thermoluminescence techniques, is orders of magnitude too small to account for the scale of charge transferred. This reveals that trapped electrons are not a necessary ingredient for same-material tribocharging. acknowledgement: This work was supported by the NSF through DMR-1309611. Access to the shared experimental facilities provided by the NSF-supported Chicago MRSEC (DMR-0820054) is gratefully acknowledged. S. L. F. and J. L. P. acknowledge funding from UIC NSF Grants No. 0850830 and No. 0602308. S. R. W. acknowledges support from a University of Chicago Millikan Fellowship and from Mrs. Joan Winstein through the Winstein Prize for Instrumentation. article_number: '218001' author: - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 - first_name: Victor full_name: Lee, Victor last_name: Lee - first_name: James full_name: Pierson, James last_name: Pierson - first_name: Steven full_name: Forman, Steven last_name: Forman - first_name: Heinrich full_name: Jaeger, Heinrich last_name: Jaeger citation: ama: Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. 2014;112(21). doi:10.1103/PhysRevLett.112.218001 apa: Waitukaitis, S. R., Lee, V., Pierson, J., Forman, S., & Jaeger, H. (2014). Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.112.218001 chicago: Waitukaitis, Scott R, Victor Lee, James Pierson, Steven Forman, and Heinrich Jaeger. “Size-Dependent Same-Material Tribocharging in Insulating Grains.” APS Physics, Physical Review Letters. American Physical Society, 2014. https://doi.org/10.1103/PhysRevLett.112.218001. ieee: S. R. Waitukaitis, V. Lee, J. Pierson, S. Forman, and H. Jaeger, “Size-dependent same-material tribocharging in insulating grains,” APS Physics, Physical Review Letters, vol. 112, no. 21. American Physical Society, 2014. ista: Waitukaitis SR, Lee V, Pierson J, Forman S, Jaeger H. 2014. Size-dependent same-material tribocharging in insulating grains. APS Physics, Physical Review Letters. 112(21), 218001. mla: Waitukaitis, Scott R., et al. “Size-Dependent Same-Material Tribocharging in Insulating Grains.” APS Physics, Physical Review Letters, vol. 112, no. 21, 218001, American Physical Society, 2014, doi:10.1103/PhysRevLett.112.218001. short: S.R. Waitukaitis, V. Lee, J. Pierson, S. Forman, H. Jaeger, APS Physics, Physical Review Letters 112 (2014). date_created: 2018-12-11T11:44:44Z date_published: 2014-05-30T00:00:00Z date_updated: 2021-01-12T06:48:58Z day: '30' doi: 10.1103/PhysRevLett.112.218001 extern: '1' external_id: arxiv: - '1309.2578' intvolume: ' 112' issue: '21' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1309.2578 month: '05' oa: 1 oa_version: Submitted Version publication: APS Physics, Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7935' quality_controlled: '1' status: public title: Size-dependent same-material tribocharging in insulating grains type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2014' ... --- _id: '11968' abstract: - lang: eng text: 'Membrane phospholipids typically contain fatty acids (FAs) of 16 and 18 carbon atoms. This particular chain length is evolutionarily highly conserved and presumably provides maximum stability and dynamic properties to biological membranes in response to nutritional or environmental cues. Here, we show that the relative proportion of C16 versus C18 FAs is regulated by the activity of acetyl-CoA carboxylase (Acc1), the first and rate-limiting enzyme of FA de novo synthesis. Acc1 activity is attenuated by AMPK/Snf1-dependent phosphorylation, which is required to maintain an appropriate acyl-chain length distribution. Moreover, we find that the transcriptional repressor Opi1 preferentially binds to C16 over C18 phosphatidic acid (PA) species: thus, C16-chain containing PA sequesters Opi1 more effectively to the ER, enabling AMPK/Snf1 control of PA acyl-chain length to determine the degree of derepression of Opi1 target genes. These findings reveal an unexpected regulatory link between the major energy-sensing kinase, membrane lipid composition, and transcription.' article_processing_charge: No article_type: original author: - first_name: Harald F. full_name: Hofbauer, Harald F. last_name: Hofbauer - first_name: Florian H. full_name: Schopf, Florian H. last_name: Schopf - first_name: Hannes full_name: Schleifer, Hannes last_name: Schleifer - first_name: Oskar L. full_name: Knittelfelder, Oskar L. last_name: Knittelfelder - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Gerald N. full_name: Rechberger, Gerald N. last_name: Rechberger - first_name: Heimo full_name: Wolinski, Heimo last_name: Wolinski - first_name: Maria L. full_name: Gaspar, Maria L. last_name: Gaspar - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe - first_name: Johannes full_name: Stadlmann, Johannes last_name: Stadlmann - first_name: Karl full_name: Mechtler, Karl last_name: Mechtler - first_name: Alexandra full_name: Zenz, Alexandra last_name: Zenz - first_name: Karl full_name: Lohner, Karl last_name: Lohner - first_name: Oksana full_name: Tehlivets, Oksana last_name: Tehlivets - first_name: Susan A. full_name: Henry, Susan A. last_name: Henry - first_name: Sepp D. full_name: Kohlwein, Sepp D. last_name: Kohlwein citation: ama: Hofbauer HF, Schopf FH, Schleifer H, et al. Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. 2014;29(6):P729-739. doi:10.1016/j.devcel.2014.04.025 apa: Hofbauer, H. F., Schopf, F. H., Schleifer, H., Knittelfelder, O. L., Pieber, B., Rechberger, G. N., … Kohlwein, S. D. (2014). Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2014.04.025 chicago: Hofbauer, Harald F., Florian H. Schopf, Hannes Schleifer, Oskar L. Knittelfelder, Bartholomäus Pieber, Gerald N. Rechberger, Heimo Wolinski, et al. “Regulation of Gene Expression through a Transcriptional Repressor That Senses Acyl-Chain Length in Membrane Phospholipids.” Developmental Cell. Elsevier, 2014. https://doi.org/10.1016/j.devcel.2014.04.025. ieee: H. F. Hofbauer et al., “Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids,” Developmental Cell, vol. 29, no. 6. Elsevier, pp. P729-739, 2014. ista: Hofbauer HF, Schopf FH, Schleifer H, Knittelfelder OL, Pieber B, Rechberger GN, Wolinski H, Gaspar ML, Kappe CO, Stadlmann J, Mechtler K, Zenz A, Lohner K, Tehlivets O, Henry SA, Kohlwein SD. 2014. Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids. Developmental Cell. 29(6), P729-739. mla: Hofbauer, Harald F., et al. “Regulation of Gene Expression through a Transcriptional Repressor That Senses Acyl-Chain Length in Membrane Phospholipids.” Developmental Cell, vol. 29, no. 6, Elsevier, 2014, pp. P729-739, doi:10.1016/j.devcel.2014.04.025. short: H.F. Hofbauer, F.H. Schopf, H. Schleifer, O.L. Knittelfelder, B. Pieber, G.N. Rechberger, H. Wolinski, M.L. Gaspar, C.O. Kappe, J. Stadlmann, K. Mechtler, A. Zenz, K. Lohner, O. Tehlivets, S.A. Henry, S.D. Kohlwein, Developmental Cell 29 (2014) P729-739. date_created: 2022-08-25T08:42:42Z date_published: 2014-06-23T00:00:00Z date_updated: 2023-02-21T10:09:45Z day: '23' doi: 10.1016/j.devcel.2014.04.025 extern: '1' external_id: pmid: - '24960695' intvolume: ' 29' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.devcel.2014.04.025 month: '06' oa: 1 oa_version: Published Version page: P729-739 pmid: 1 publication: Developmental Cell publication_identifier: eissn: - 1878-1551 issn: - 1534-5807 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2014' ... --- _id: '11967' abstract: - lang: eng text: An experimentally easy to perform method for the generation of alumina-supported Fe3O4 nanoparticles [(6±1) nm size, 0.67 wt %]and the use of this material in hydrazine-mediated heterogeneously catalyzed reductions of nitroarenes to anilines under batch and continuous-flow conditions is presented. The bench-stable, reusable nano-Fe3O4@Al2O3 catalyst can selectively reduce functionalized nitroarenes at 1 mol % catalyst loading by using a 20 mol % excess of hydrazine hydrate in an elevated temperature regime (150 °C, reaction time 2–6 min in batch). For continuous-flow processing, the catalyst material is packed into dedicated cartridges and used in a commercially available high-temperature/-pressure flow device. In continuous mode, reaction times can be reduced to less than 1 min at 150 °C (30 bar back pressure) in a highly intensified process. The nano-Fe3O4@Al2O3 catalyst demonstrated stable reduction of nitrobenzene (0.5 M in MeOH) for more than 10 h on stream at a productivity of 30 mmol h−1 (0.72 mol per day). Importantly, virtually no leaching of the catalytically active material could be observed by inductively coupled plasma MS monitoring. article_processing_charge: No article_type: original author: - first_name: Mojtaba Mirhosseini full_name: Moghaddam, Mojtaba Mirhosseini last_name: Moghaddam - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Toma full_name: Glasnov, Toma last_name: Glasnov - first_name: C. Oliver full_name: Kappe, C. Oliver last_name: Kappe citation: ama: Moghaddam MM, Pieber B, Glasnov T, Kappe CO. Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. 2014;7(11):3122-3131. doi:10.1002/cssc.201402455 apa: Moghaddam, M. M., Pieber, B., Glasnov, T., & Kappe, C. O. (2014). Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. Wiley. https://doi.org/10.1002/cssc.201402455 chicago: Moghaddam, Mojtaba Mirhosseini, Bartholomäus Pieber, Toma Glasnov, and C. Oliver Kappe. “Immobilized Iron Oxide Nanoparticles as Stable and Reusable Catalysts for Hydrazine-Mediated Nitro Reductions in Continuous Flow.” ChemSusChem. Wiley, 2014. https://doi.org/10.1002/cssc.201402455. ieee: M. M. Moghaddam, B. Pieber, T. Glasnov, and C. O. Kappe, “Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow,” ChemSusChem, vol. 7, no. 11. Wiley, pp. 3122–3131, 2014. ista: Moghaddam MM, Pieber B, Glasnov T, Kappe CO. 2014. Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow. ChemSusChem. 7(11), 3122–3131. mla: Moghaddam, Mojtaba Mirhosseini, et al. “Immobilized Iron Oxide Nanoparticles as Stable and Reusable Catalysts for Hydrazine-Mediated Nitro Reductions in Continuous Flow.” ChemSusChem, vol. 7, no. 11, Wiley, 2014, pp. 3122–31, doi:10.1002/cssc.201402455. short: M.M. Moghaddam, B. Pieber, T. Glasnov, C.O. Kappe, ChemSusChem 7 (2014) 3122–3131. date_created: 2022-08-25T08:36:54Z date_published: 2014-11-01T00:00:00Z date_updated: 2023-02-21T10:09:42Z day: '01' doi: 10.1002/cssc.201402455 extern: '1' external_id: pmid: - '25209099' intvolume: ' 7' issue: '11' language: - iso: eng month: '11' oa_version: None page: 3122-3131 pmid: 1 publication: ChemSusChem publication_identifier: eissn: - 1864-564X issn: - 1864-5631 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Immobilized iron oxide nanoparticles as stable and reusable catalysts for hydrazine-mediated nitro reductions in continuous flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2014' ... --- _id: '11987' abstract: - lang: eng text: A method for the direct lithiation of terminal alkynes and heterocycles with subsequent carboxylation in a continuous flow format was developed. This method provides carboxylic acids at ambient conditions within less than five seconds with only little excess of the organometallic base and CO2. article_number: '13430' article_processing_charge: No article_type: letter_note author: - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X - first_name: Toma full_name: Glasnov, Toma last_name: Glasnov - first_name: C. O. full_name: Kappe, C. O. last_name: Kappe citation: ama: 'Pieber B, Glasnov T, Kappe CO. Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. 2014;4(26). doi:10.1039/c4ra01442a' apa: 'Pieber, B., Glasnov, T., & Kappe, C. O. (2014). Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. Royal Society of Chemistry. https://doi.org/10.1039/c4ra01442a' chicago: 'Pieber, Bartholomäus, Toma Glasnov, and C. O. Kappe. “Flash Carboxylation: Fast Lithiation–Carboxylation Sequence at Room Temperature in Continuous Flow.” RSC Advances. Royal Society of Chemistry, 2014. https://doi.org/10.1039/c4ra01442a.' ieee: 'B. Pieber, T. Glasnov, and C. O. Kappe, “Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow,” RSC Advances, vol. 4, no. 26. Royal Society of Chemistry, 2014.' ista: 'Pieber B, Glasnov T, Kappe CO. 2014. Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow. RSC Advances. 4(26), 13430.' mla: 'Pieber, Bartholomäus, et al. “Flash Carboxylation: Fast Lithiation–Carboxylation Sequence at Room Temperature in Continuous Flow.” RSC Advances, vol. 4, no. 26, 13430, Royal Society of Chemistry, 2014, doi:10.1039/c4ra01442a.' short: B. Pieber, T. Glasnov, C.O. Kappe, RSC Advances 4 (2014). date_created: 2022-08-25T11:48:19Z date_published: 2014-03-03T00:00:00Z date_updated: 2023-02-21T10:10:31Z day: '03' doi: 10.1039/c4ra01442a extern: '1' intvolume: ' 4' issue: '26' language: - iso: eng month: '03' oa_version: None publication: RSC Advances publication_identifier: eissn: - 2046-2069 publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: 'Flash carboxylation: Fast lithiation–carboxylation sequence at room temperature in continuous flow' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2014' ... --- _id: '1309' abstract: - lang: eng text: We show that weak solutions of the Derrida-Lebowitz-Speer-Spohn (DLSS) equation display infinite speed of support propagation. We apply our method to the case of the quantum drift-diffusion equation which augments the DLSS equation with a drift term and possibly a second-order diffusion term. The proof is accomplished using weighted entropy estimates, Hardy's inequality and a family of singular weight functions to derive a differential inequality; the differential inequality shows exponential growth of the weighted entropy, with the growth constant blowing up very fast as the singularity of the weight becomes sharper. To the best of our knowledge, this is the first example of a nonnegativity-preserving higher-order parabolic equation displaying infinite speed of support propagation. author: - first_name: Julian L full_name: Julian Fischer id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: Fischer JL. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 2014;21(1):27-50. doi:10.1007/s00030-013-0235-0 apa: Fischer, J. L. (2014). Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. Birkhäuser. https://doi.org/10.1007/s00030-013-0235-0 chicago: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications. Birkhäuser, 2014. https://doi.org/10.1007/s00030-013-0235-0. ieee: J. L. Fischer, “Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models,” Nonlinear Differential Equations and Applications, vol. 21, no. 1. Birkhäuser, pp. 27–50, 2014. ista: Fischer JL. 2014. Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models. Nonlinear Differential Equations and Applications. 21(1), 27–50. mla: Fischer, Julian L. “Infinite Speed of Support Propagation for the Derrida-Lebowitz-Speer-Spohn Equation and Quantum Drift-Diffusion Models.” Nonlinear Differential Equations and Applications, vol. 21, no. 1, Birkhäuser, 2014, pp. 27–50, doi:10.1007/s00030-013-0235-0. short: J.L. Fischer, Nonlinear Differential Equations and Applications 21 (2014) 27–50. date_created: 2018-12-11T11:51:17Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:49:47Z day: '01' doi: 10.1007/s00030-013-0235-0 extern: 1 intvolume: ' 21' issue: '1' month: '01' page: 27 - 50 publication: Nonlinear Differential Equations and Applications publication_status: published publisher: Birkhäuser publist_id: '5960' quality_controlled: 0 status: public title: Infinite speed of support propagation for the Derrida-Lebowitz-Speer-Spohn equation and quantum drift-diffusion models type: journal_article volume: 21 year: '2014' ... --- _id: '1312' abstract: - lang: eng text: We derive upper bounds on the waiting time of solutions to the thin-film equation in the regime of weak slippage n ∈ [2, 32\11). In particular, we give sufficient conditions on the initial data for instantaneous forward motion of the free boundary. For n ∈ (2, 32\11), our estimates are sharp, for n = 2, they are sharp up to a logarithmic correction term. Note that the case n = 2 corresponds-with a grain of salt-to the assumption of the Navier slip condition at the fluid-solid interface. We also obtain results in the regime of strong slippage n ∈ (1,2); however, in this regime we expect them not to be optimal. Our method is based on weighted backward entropy estimates, Hardy's inequality and singular weight functions; we deduce a differential inequality which would enforce blowup of the weighted entropy if the contact line were to remain stationary for too long. author: - first_name: Julian L full_name: Julian Fischer id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: 'Fischer JL. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 2014;211(3):771-818. doi:10.1007/s00205-013-0690-0' apa: 'Fischer, J. L. (2014). Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. Springer. https://doi.org/10.1007/s00205-013-0690-0' chicago: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis. Springer, 2014. https://doi.org/10.1007/s00205-013-0690-0.' ieee: 'J. L. Fischer, “Upper bounds on waiting times for the Thin-film equation: The case of weak slippage,” Archive for Rational Mechanics and Analysis, vol. 211, no. 3. Springer, pp. 771–818, 2014.' ista: 'Fischer JL. 2014. Upper bounds on waiting times for the Thin-film equation: The case of weak slippage. Archive for Rational Mechanics and Analysis. 211(3), 771–818.' mla: 'Fischer, Julian L. “Upper Bounds on Waiting Times for the Thin-Film Equation: The Case of Weak Slippage.” Archive for Rational Mechanics and Analysis, vol. 211, no. 3, Springer, 2014, pp. 771–818, doi:10.1007/s00205-013-0690-0.' short: J.L. Fischer, Archive for Rational Mechanics and Analysis 211 (2014) 771–818. date_created: 2018-12-11T11:51:18Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:49:48Z day: '01' doi: 10.1007/s00205-013-0690-0 extern: 1 intvolume: ' 211' issue: '3' month: '01' page: 771 - 818 publication: Archive for Rational Mechanics and Analysis publication_status: published publisher: Springer publist_id: '5959' quality_controlled: 0 status: public title: 'Upper bounds on waiting times for the Thin-film equation: The case of weak slippage' type: journal_article volume: 211 year: '2014' ... --- _id: '1375' abstract: - lang: eng text: 'We consider directed graphs where each edge is labeled with an integer weight and study the fundamental algorithmic question of computing the value of a cycle with minimum mean weight. Our contributions are twofold: (1) First we show that the algorithmic question is reducible to the problem of a logarithmic number of min-plus matrix multiplications of n×n-matrices, where n is the number of vertices of the graph. (2) Second, when the weights are nonnegative, we present the first (1+ε)-approximation algorithm for the problem and the running time of our algorithm is Õ(nωlog3(nW/ε)/ε),1 where O(nω) is the time required for the classic n×n-matrix multiplication and W is the maximum value of the weights. With an additional O(log(nW/ε)) factor in space a cycle with approximately optimal weight can be computed within the same time bound.' article_processing_charge: No article_type: original author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Sebastian full_name: Krinninger, Sebastian last_name: Krinninger - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer - first_name: Michael full_name: Raskin, Michael last_name: Raskin citation: ama: Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. Approximating the minimum cycle mean. Theoretical Computer Science. 2014;547(C):104-116. doi:10.1016/j.tcs.2014.06.031 apa: Chatterjee, K., Henzinger, M. H., Krinninger, S., Loitzenbauer, V., & Raskin, M. (2014). Approximating the minimum cycle mean. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2014.06.031 chicago: Chatterjee, Krishnendu, Monika H Henzinger, Sebastian Krinninger, Veronika Loitzenbauer, and Michael Raskin. “Approximating the Minimum Cycle Mean.” Theoretical Computer Science. Elsevier, 2014. https://doi.org/10.1016/j.tcs.2014.06.031. ieee: K. Chatterjee, M. H. Henzinger, S. Krinninger, V. Loitzenbauer, and M. Raskin, “Approximating the minimum cycle mean,” Theoretical Computer Science, vol. 547, no. C. Elsevier, pp. 104–116, 2014. ista: Chatterjee K, Henzinger MH, Krinninger S, Loitzenbauer V, Raskin M. 2014. Approximating the minimum cycle mean. Theoretical Computer Science. 547(C), 104–116. mla: Chatterjee, Krishnendu, et al. “Approximating the Minimum Cycle Mean.” Theoretical Computer Science, vol. 547, no. C, Elsevier, 2014, pp. 104–16, doi:10.1016/j.tcs.2014.06.031. short: K. Chatterjee, M.H. Henzinger, S. Krinninger, V. Loitzenbauer, M. Raskin, Theoretical Computer Science 547 (2014) 104–116. date_created: 2018-12-11T11:51:40Z date_published: 2014-08-28T00:00:00Z date_updated: 2022-09-09T11:50:58Z day: '28' department: - _id: KrCh doi: 10.1016/j.tcs.2014.06.031 ec_funded: 1 external_id: arxiv: - '1307.4473' intvolume: ' 547' issue: C language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.4473 month: '08' oa: 1 oa_version: Preprint page: 104 - 116 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '5836' quality_controlled: '1' scopus_import: '1' status: public title: Approximating the minimum cycle mean type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 547 year: '2014' ... --- _id: '1392' abstract: - lang: eng text: Fault-tolerant distributed algorithms play an important role in ensuring the reliability of many software applications. In this paper we consider distributed algorithms whose computations are organized in rounds. To verify the correctness of such algorithms, we reason about (i) properties (such as invariants) of the state, (ii) the transitions controlled by the algorithm, and (iii) the communication graph. We introduce a logic that addresses these points, and contains set comprehensions with cardinality constraints, function symbols to describe the local states of each process, and a limited form of quantifier alternation to express the verification conditions. We show its use in automating the verification of consensus algorithms. In particular, we give a semi-decision procedure for the unsatisfiability problem of the logic and identify a decidable fragment. We successfully applied our framework to verify the correctness of a variety of consensus algorithms tolerant to both benign faults (message loss, process crashes) and value faults (message corruption). acknowledgement: Supported by the Vienna Science and Technology Fund (WWTF) through grant PROSEED. alternative_title: - LNCS author: - first_name: Cezara full_name: Dragoi, Cezara id: 2B2B5ED0-F248-11E8-B48F-1D18A9856A87 last_name: Dragoi - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Helmut full_name: Veith, Helmut last_name: Veith - first_name: Josef full_name: Widder, Josef last_name: Widder - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: 'Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. A logic-based framework for verifying consensus algorithms. In: Vol 8318. Springer; 2014:161-181. doi:10.1007/978-3-642-54013-4_10' apa: 'Dragoi, C., Henzinger, T. A., Veith, H., Widder, J., & Zufferey, D. (2014). A logic-based framework for verifying consensus algorithms (Vol. 8318, pp. 161–181). Presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA: Springer. https://doi.org/10.1007/978-3-642-54013-4_10' chicago: Dragoi, Cezara, Thomas A Henzinger, Helmut Veith, Josef Widder, and Damien Zufferey. “A Logic-Based Framework for Verifying Consensus Algorithms,” 8318:161–81. Springer, 2014. https://doi.org/10.1007/978-3-642-54013-4_10. ieee: 'C. Dragoi, T. A. Henzinger, H. Veith, J. Widder, and D. Zufferey, “A logic-based framework for verifying consensus algorithms,” presented at the VMCAI: Verification, Model Checking and Abstract Interpretation, San Diego, USA, 2014, vol. 8318, pp. 161–181.' ista: 'Dragoi C, Henzinger TA, Veith H, Widder J, Zufferey D. 2014. A logic-based framework for verifying consensus algorithms. VMCAI: Verification, Model Checking and Abstract Interpretation, LNCS, vol. 8318, 161–181.' mla: Dragoi, Cezara, et al. A Logic-Based Framework for Verifying Consensus Algorithms. Vol. 8318, Springer, 2014, pp. 161–81, doi:10.1007/978-3-642-54013-4_10. short: C. Dragoi, T.A. Henzinger, H. Veith, J. Widder, D. Zufferey, in:, Springer, 2014, pp. 161–181. conference: end_date: 2014-01-21 location: San Diego, USA name: 'VMCAI: Verification, Model Checking and Abstract Interpretation' start_date: 2014-01-19 date_created: 2018-12-11T11:51:45Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:50:22Z day: '01' ddc: - '000' - '005' department: - _id: ToHe doi: 10.1007/978-3-642-54013-4_10 ec_funded: 1 file: - access_level: open_access checksum: bffa33d39be77df0da39defe97eabf84 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:06Z date_updated: 2020-07-14T12:44:48Z file_id: '4859' file_name: IST-2014-179-v1+1_vmcai14.pdf file_size: 444138 relation: main_file file_date_updated: 2020-07-14T12:44:48Z has_accepted_license: '1' intvolume: ' 8318' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 161 - 181 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication_status: published publisher: Springer publist_id: '5817' pubrep_id: '179' quality_controlled: '1' scopus_import: 1 status: public title: A logic-based framework for verifying consensus algorithms type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8318 year: '2014' ... --- _id: '1393' abstract: - lang: eng text: 'Probabilistic programs are usual functional or imperative programs with two added constructs: (1) the ability to draw values at random from distributions, and (2) the ability to condition values of variables in a program via observations. Models from diverse application areas such as computer vision, coding theory, cryptographic protocols, biology and reliability analysis can be written as probabilistic programs. Probabilistic inference is the problem of computing an explicit representation of the probability distribution implicitly specified by a probabilistic program. Depending on the application, the desired output from inference may vary-we may want to estimate the expected value of some function f with respect to the distribution, or the mode of the distribution, or simply a set of samples drawn from the distribution. In this paper, we describe connections this research area called \Probabilistic Programming" has with programming languages and software engineering, and this includes language design, and the static and dynamic analysis of programs. We survey current state of the art and speculate on promising directions for future research.' article_processing_charge: No author: - first_name: Andrew full_name: Gordon, Andrew last_name: Gordon - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Aditya full_name: Nori, Aditya last_name: Nori - first_name: Sriram full_name: Rajamani, Sriram last_name: Rajamani citation: ama: 'Gordon A, Henzinger TA, Nori A, Rajamani S. Probabilistic programming. In: Proceedings of the on Future of Software Engineering. ACM; 2014:167-181. doi:10.1145/2593882.2593900' apa: 'Gordon, A., Henzinger, T. A., Nori, A., & Rajamani, S. (2014). Probabilistic programming. In Proceedings of the on Future of Software Engineering (pp. 167–181). Hyderabad, India: ACM. https://doi.org/10.1145/2593882.2593900' chicago: Gordon, Andrew, Thomas A Henzinger, Aditya Nori, and Sriram Rajamani. “Probabilistic Programming.” In Proceedings of the on Future of Software Engineering, 167–81. ACM, 2014. https://doi.org/10.1145/2593882.2593900. ieee: A. Gordon, T. A. Henzinger, A. Nori, and S. Rajamani, “Probabilistic programming,” in Proceedings of the on Future of Software Engineering, Hyderabad, India, 2014, pp. 167–181. ista: 'Gordon A, Henzinger TA, Nori A, Rajamani S. 2014. Probabilistic programming. Proceedings of the on Future of Software Engineering. FOSE: Future of Software Engineering, 167–181.' mla: Gordon, Andrew, et al. “Probabilistic Programming.” Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–81, doi:10.1145/2593882.2593900. short: A. Gordon, T.A. Henzinger, A. Nori, S. Rajamani, in:, Proceedings of the on Future of Software Engineering, ACM, 2014, pp. 167–181. conference: end_date: 2014-06-07 location: Hyderabad, India name: 'FOSE: Future of Software Engineering' start_date: 2014-05-31 date_created: 2018-12-11T11:51:45Z date_published: 2014-05-31T00:00:00Z date_updated: 2021-01-12T06:50:22Z day: '31' department: - _id: ToHe doi: 10.1145/2593882.2593900 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/2593882.2593900 month: '05' oa: 1 oa_version: Published Version page: 167 - 181 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Proceedings of the on Future of Software Engineering publication_status: published publisher: ACM publist_id: '5816' quality_controlled: '1' scopus_import: 1 status: public title: Probabilistic programming type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1404' abstract: - lang: eng text: "The co-evolution of hosts and pathogens is characterized by continuous adaptations of both parties. Pathogens of social insects need to adapt towards disease defences at two levels: 1) individual immunity of each colony member consisting of behavioural defence strategies as well as humoral and cellular immune responses and 2) social immunity that is collectively performed by all group members comprising behavioural, physiological and organisational defence strategies.\r\n\r\nTo disentangle the selection pressure on pathogens by the collective versus individual level of disease defence in social insects, we performed an evolution experiment using the Argentine Ant, Linepithema humile, as a host and a mixture of the general insect pathogenic fungus Metarhizium spp. (6 strains) as a pathogen. We allowed pathogen evolution over 10 serial host passages to two different evolution host treatments: (1) only individual host immunity in a single host treatment, and (2) simultaneously acting individual and social immunity in a social host treatment, in which an exposed ant was accompanied by two untreated nestmates.\r\n\r\nBefore starting the pathogen evolution experiment, the 6 Metarhizium spp. strains were characterised concerning conidiospore size killing rates in singly and socially reared ants, their competitiveness under coinfecting conditions and their influence on ant behaviour. We analysed how the ancestral atrain mixture changed in conidiospere size, killing rate and strain composition dependent on host treatment (single or social hosts) during 10 passages and found that killing rate and conidiospere size of the pathogen increased under both evolution regimes, but different depending on host treatment.\r\n\r\nTesting the evolved strain mixtures that evolved under either the single or social host treatment under both single and social current rearing conditions in a full factorial design experiment revealed that the additional collective defences in insect societies add new selection pressure for their coevolving pathogens that compromise their ability to adapt to its host at the group level. To our knowledge, this is the first study directly measuring the influence of social immunity on pathogen evolution." acknowledgement: This work was funded by the DFG and the ERC. alternative_title: - IST Austria Thesis author: - first_name: Miriam full_name: Stock, Miriam id: 42462816-F248-11E8-B48F-1D18A9856A87 last_name: Stock citation: ama: Stock M. Evolution of a fungal pathogen towards individual versus social immunity in ants. 2014. apa: Stock, M. (2014). Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria. chicago: Stock, Miriam. “Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants.” IST Austria, 2014. ieee: M. Stock, “Evolution of a fungal pathogen towards individual versus social immunity in ants,” IST Austria, 2014. ista: Stock M. 2014. Evolution of a fungal pathogen towards individual versus social immunity in ants. IST Austria. mla: Stock, Miriam. Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants. IST Austria, 2014. short: M. Stock, Evolution of a Fungal Pathogen towards Individual versus Social Immunity in Ants, IST Austria, 2014. date_created: 2018-12-11T11:51:49Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:50:30Z day: '01' department: - _id: SyCr language: - iso: eng month: '04' oa_version: None page: '101' publication_status: published publisher: IST Austria publist_id: '5803' status: public supervisor: - first_name: Sylvia M full_name: Cremer, Sylvia M id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 title: Evolution of a fungal pathogen towards individual versus social immunity in ants type: dissertation user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1516' abstract: - lang: eng text: "We present a rigorous derivation of the BCS gap equation for superfluid fermionic gases with point interactions. Our starting point is the BCS energy functional, whose minimizer we investigate in the limit when the range of the interaction potential goes to zero.\r\n" article_processing_charge: No author: - first_name: Gerhard full_name: Bräunlich, Gerhard last_name: Bräunlich - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Bräunlich G, Hainzl C, Seiringer R. On the BCS gap equation for superfluid fermionic gases. In: Proceedings of the QMath12 Conference. World Scientific Publishing; 2014:127-137. doi:10.1142/9789814618144_0007' apa: 'Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). On the BCS gap equation for superfluid fermionic gases. In Proceedings of the QMath12 Conference (pp. 127–137). Berlin, Germany: World Scientific Publishing. https://doi.org/10.1142/9789814618144_0007' chicago: Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “On the BCS Gap Equation for Superfluid Fermionic Gases.” In Proceedings of the QMath12 Conference, 127–37. World Scientific Publishing, 2014. https://doi.org/10.1142/9789814618144_0007. ieee: G. Bräunlich, C. Hainzl, and R. Seiringer, “On the BCS gap equation for superfluid fermionic gases,” in Proceedings of the QMath12 Conference, Berlin, Germany, 2014, pp. 127–137. ista: 'Bräunlich G, Hainzl C, Seiringer R. 2014. On the BCS gap equation for superfluid fermionic gases. Proceedings of the QMath12 Conference. QMath: Mathematical Results in Quantum Physics, 127–137.' mla: Bräunlich, Gerhard, et al. “On the BCS Gap Equation for Superfluid Fermionic Gases.” Proceedings of the QMath12 Conference, World Scientific Publishing, 2014, pp. 127–37, doi:10.1142/9789814618144_0007. short: G. Bräunlich, C. Hainzl, R. Seiringer, in:, Proceedings of the QMath12 Conference, World Scientific Publishing, 2014, pp. 127–137. conference: end_date: 2013-09-13 location: Berlin, Germany name: 'QMath: Mathematical Results in Quantum Physics' start_date: 2013-09-10 date_created: 2018-12-11T11:52:28Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:51:19Z day: '01' department: - _id: RoSe doi: 10.1142/9789814618144_0007 external_id: arxiv: - '1403.2563' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1403.2563 month: '01' oa: 1 oa_version: Preprint page: 127 - 137 publication: Proceedings of the QMath12 Conference publication_status: published publisher: World Scientific Publishing publist_id: '5661' quality_controlled: '1' status: public title: On the BCS gap equation for superfluid fermionic gases type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1629' abstract: - lang: eng text: We propose a method for propagating edit operations in 2D vector graphics, based on geometric relationship functions. These functions quantify the geometric relationship of a point to a polygon, such as the distance to the boundary or the direction to the closest corner vertex. The level sets of the relationship functions describe points with the same relationship to a polygon. For a given query point, we first determine a set of relationships to local features, construct all level sets for these relationships, and accumulate them. The maxima of the resulting distribution are points with similar geometric relationships. We show extensions to handle mirror symmetries, and discuss the use of relationship functions as local coordinate systems. Our method can be applied, for example, to interactive floorplan editing, and it is especially useful for large layouts, where individual edits would be cumbersome. We demonstrate populating 2D layouts with tens to hundreds of objects by propagating relatively few edit operations. article_number: '15' author: - first_name: Paul full_name: Guerrero, Paul last_name: Guerrero - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Michael full_name: Wimmer, Michael last_name: Wimmer - first_name: Peter full_name: Wonka, Peter last_name: Wonka citation: ama: Guerrero P, Jeschke S, Wimmer M, Wonka P. Edit propagation using geometric relationship functions. ACM Transactions on Graphics. 2014;33(2). doi:10.1145/2591010 apa: Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2014). Edit propagation using geometric relationship functions. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/2591010 chicago: Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Edit Propagation Using Geometric Relationship Functions.” ACM Transactions on Graphics. ACM, 2014. https://doi.org/10.1145/2591010. ieee: P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Edit propagation using geometric relationship functions,” ACM Transactions on Graphics, vol. 33, no. 2. ACM, 2014. ista: Guerrero P, Jeschke S, Wimmer M, Wonka P. 2014. Edit propagation using geometric relationship functions. ACM Transactions on Graphics. 33(2), 15. mla: Guerrero, Paul, et al. “Edit Propagation Using Geometric Relationship Functions.” ACM Transactions on Graphics, vol. 33, no. 2, 15, ACM, 2014, doi:10.1145/2591010. short: P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, ACM Transactions on Graphics 33 (2014). date_created: 2018-12-11T11:53:08Z date_published: 2014-03-01T00:00:00Z date_updated: 2021-01-12T06:52:06Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1145/2591010 file: - access_level: open_access checksum: 7f91e588a4e888610313b98271e6418e content_type: application/pdf creator: system date_created: 2018-12-12T10:11:22Z date_updated: 2020-07-14T12:45:07Z file_id: '4876' file_name: IST-2016-577-v1+1_2014.TOG.Paul.EditingPropagation.final.pdf file_size: 9832561 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 33' issue: '2' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version publication: ACM Transactions on Graphics publication_status: published publisher: ACM publist_id: '5526' pubrep_id: '577' quality_controlled: '1' status: public title: Edit propagation using geometric relationship functions type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2014' ... --- _id: '10793' abstract: - lang: eng text: "The Hanani–Tutte theorem is a classical result proved for the first time in the 1930s that characterizes planar graphs as graphs that admit a drawing in the plane in which every pair of edges not sharing a vertex cross an even number of times. We generalize this classical result to clustered graphs with two disjoint clusters, and show that a straightforward extension of our result to flat clustered graphs with three or more disjoint clusters is not possible.\r\n\r\nWe also give a new and short proof for a related result by Di Battista and Frati based on the matroid intersection algorithm." alternative_title: - LNCS article_processing_charge: No author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Jan full_name: Kynčl, Jan last_name: Kynčl - first_name: Igor full_name: Malinović, Igor last_name: Malinović - first_name: Dömötör full_name: Pálvölgyi, Dömötör last_name: Pálvölgyi citation: ama: 'Fulek R, Kynčl J, Malinović I, Pálvölgyi D. Clustered planarity testing revisited. In: International Symposium on Graph Drawing. Vol 8871. Cham: Springer Nature; 2014:428-436. doi:10.1007/978-3-662-45803-7_36' apa: 'Fulek, R., Kynčl, J., Malinović, I., & Pálvölgyi, D. (2014). Clustered planarity testing revisited. In International Symposium on Graph Drawing (Vol. 8871, pp. 428–436). Cham: Springer Nature. https://doi.org/10.1007/978-3-662-45803-7_36' chicago: 'Fulek, Radoslav, Jan Kynčl, Igor Malinović, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” In International Symposium on Graph Drawing, 8871:428–36. Cham: Springer Nature, 2014. https://doi.org/10.1007/978-3-662-45803-7_36.' ieee: R. Fulek, J. Kynčl, I. Malinović, and D. Pálvölgyi, “Clustered planarity testing revisited,” in International Symposium on Graph Drawing, 2014, vol. 8871, pp. 428–436. ista: Fulek R, Kynčl J, Malinović I, Pálvölgyi D. 2014. Clustered planarity testing revisited. International Symposium on Graph Drawing. , LNCS, vol. 8871, 428–436. mla: Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” International Symposium on Graph Drawing, vol. 8871, Springer Nature, 2014, pp. 428–36, doi:10.1007/978-3-662-45803-7_36. short: R. Fulek, J. Kynčl, I. Malinović, D. Pálvölgyi, in:, International Symposium on Graph Drawing, Springer Nature, Cham, 2014, pp. 428–436. date_created: 2022-02-25T10:32:14Z date_published: 2014-01-01T00:00:00Z date_updated: 2023-02-23T10:08:04Z day: '01' department: - _id: UlWa doi: 10.1007/978-3-662-45803-7_36 external_id: arxiv: - '1305.4519' intvolume: ' 8871' language: - iso: eng month: '01' oa_version: Preprint page: 428-436 place: Cham publication: International Symposium on Graph Drawing publication_identifier: issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '1642' relation: later_version status: public scopus_import: '1' status: public title: Clustered planarity testing revisited type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 8871 year: '2014' ... --- _id: '1643' abstract: - lang: eng text: We extend the notion of verifiable random functions (VRF) to constrained VRFs, which generalize the concept of constrained pseudorandom functions, put forward by Boneh and Waters (Asiacrypt’13), and independently by Kiayias et al. (CCS’13) and Boyle et al. (PKC’14), who call them delegatable PRFs and functional PRFs, respectively. In a standard VRF the secret key sk allows one to evaluate a pseudorandom function at any point of its domain; in addition, it enables computation of a non-interactive proof that the function value was computed correctly. In a constrained VRF from the key sk one can derive constrained keys skS for subsets S of the domain, which allow computation of function values and proofs only at points in S. After formally defining constrained VRFs, we derive instantiations from the multilinear-maps-based constrained PRFs by Boneh and Waters, yielding a VRF with constrained keys for any set that can be decided by a polynomial-size circuit. Our VRFs have the same function values as the Boneh-Waters PRFs and are proved secure under the same hardness assumption, showing that verifiability comes at no cost. Constrained (functional) VRFs were stated as an open problem by Boyle et al. alternative_title: - LNCS author: - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer citation: ama: 'Fuchsbauer G. Constrained Verifiable Random Functions . In: Abdalla M, De Prisco R, eds. SCN 2014. Vol 8642. Springer; 2014:95-114. doi:10.1007/978-3-319-10879-7_7' apa: 'Fuchsbauer, G. (2014). Constrained Verifiable Random Functions . In M. Abdalla & R. De Prisco (Eds.), SCN 2014 (Vol. 8642, pp. 95–114). Amalfi, Italy: Springer. https://doi.org/10.1007/978-3-319-10879-7_7' chicago: Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” In SCN 2014, edited by Michel Abdalla and Roberto De Prisco, 8642:95–114. Springer, 2014. https://doi.org/10.1007/978-3-319-10879-7_7. ieee: G. Fuchsbauer, “Constrained Verifiable Random Functions ,” in SCN 2014, Amalfi, Italy, 2014, vol. 8642, pp. 95–114. ista: 'Fuchsbauer G. 2014. Constrained Verifiable Random Functions . SCN 2014. SCN: Security and Cryptography for Networks, LNCS, vol. 8642, 95–114.' mla: Fuchsbauer, Georg. “Constrained Verifiable Random Functions .” SCN 2014, edited by Michel Abdalla and Roberto De Prisco, vol. 8642, Springer, 2014, pp. 95–114, doi:10.1007/978-3-319-10879-7_7. short: G. Fuchsbauer, in:, M. Abdalla, R. De Prisco (Eds.), SCN 2014, Springer, 2014, pp. 95–114. conference: end_date: 2014-09-05 location: Amalfi, Italy name: 'SCN: Security and Cryptography for Networks' start_date: 2014-09-03 date_created: 2018-12-11T11:53:13Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:52:12Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-319-10879-7_7 ec_funded: 1 editor: - first_name: Michel full_name: Abdalla, Michel last_name: Abdalla - first_name: Roberto full_name: De Prisco, Roberto last_name: De Prisco intvolume: ' 8642' language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2014/537 month: '01' oa: 1 oa_version: Submitted Version page: 95 - 114 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: SCN 2014 publication_status: published publisher: Springer publist_id: '5509' scopus_import: 1 status: public title: 'Constrained Verifiable Random Functions ' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8642 year: '2014' ... --- _id: '1702' abstract: - lang: eng text: In this paper we present INTERHORN, a solver for recursion-free Horn clauses. The main application domain of INTERHORN lies in solving interpolation problems arising in software verification. We show how a range of interpolation problems, including path, transition, nested, state/transition and well-founded interpolation can be handled directly by INTERHORN. By detailing these interpolation problems and their Horn clause representations, we hope to encourage the emergence of a common back-end interpolation interface useful for diverse verification tools. alternative_title: - EPTCS author: - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Corneliu full_name: Popeea, Corneliu last_name: Popeea - first_name: Andrey full_name: Rybalchenko, Andrey last_name: Rybalchenko citation: ama: 'Gupta A, Popeea C, Rybalchenko A. Generalised interpolation by solving recursion free-horn clauses. In: Electronic Proceedings in Theoretical Computer Science, EPTCS. Vol 169. Open Publishing; 2014:31-38. doi:10.4204/EPTCS.169.5' apa: 'Gupta, A., Popeea, C., & Rybalchenko, A. (2014). Generalised interpolation by solving recursion free-horn clauses. In Electronic Proceedings in Theoretical Computer Science, EPTCS (Vol. 169, pp. 31–38). Vienna, Austria: Open Publishing. https://doi.org/10.4204/EPTCS.169.5' chicago: Gupta, Ashutosh, Corneliu Popeea, and Andrey Rybalchenko. “Generalised Interpolation by Solving Recursion Free-Horn Clauses.” In Electronic Proceedings in Theoretical Computer Science, EPTCS, 169:31–38. Open Publishing, 2014. https://doi.org/10.4204/EPTCS.169.5. ieee: A. Gupta, C. Popeea, and A. Rybalchenko, “Generalised interpolation by solving recursion free-horn clauses,” in Electronic Proceedings in Theoretical Computer Science, EPTCS, Vienna, Austria, 2014, vol. 169, pp. 31–38. ista: 'Gupta A, Popeea C, Rybalchenko A. 2014. Generalised interpolation by solving recursion free-horn clauses. Electronic Proceedings in Theoretical Computer Science, EPTCS. HCVS: Horn Clauses for Verification and Synthesis, EPTCS, vol. 169, 31–38.' mla: Gupta, Ashutosh, et al. “Generalised Interpolation by Solving Recursion Free-Horn Clauses.” Electronic Proceedings in Theoretical Computer Science, EPTCS, vol. 169, Open Publishing, 2014, pp. 31–38, doi:10.4204/EPTCS.169.5. short: A. Gupta, C. Popeea, A. Rybalchenko, in:, Electronic Proceedings in Theoretical Computer Science, EPTCS, Open Publishing, 2014, pp. 31–38. conference: end_date: 2014-07-17 location: Vienna, Austria name: 'HCVS: Horn Clauses for Verification and Synthesis' start_date: 2014-07-17 date_created: 2018-12-11T11:53:33Z date_published: 2014-12-02T00:00:00Z date_updated: 2021-01-12T06:52:38Z day: '02' department: - _id: ToHe doi: 10.4204/EPTCS.169.5 intvolume: ' 169' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1303.7378v2 month: '12' oa: 1 oa_version: Submitted Version page: 31 - 38 publication: Electronic Proceedings in Theoretical Computer Science, EPTCS publication_status: published publisher: Open Publishing publist_id: '5435' quality_controlled: '1' status: public title: Generalised interpolation by solving recursion free-horn clauses type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 169 year: '2014' ... --- _id: '1708' abstract: - lang: eng text: It has been long argued that, because of inherent ambiguity and noise, the brain needs to represent uncertainty in the form of probability distributions. The neural encoding of such distributions remains however highly controversial. Here we present a novel circuit model for representing multidimensional real-valued distributions using a spike based spatio-temporal code. Our model combines the computational advantages of the currently competing models for probabilistic codes and exhibits realistic neural responses along a variety of classic measures. Furthermore, the model highlights the challenges associated with interpreting neural activity in relation to behavioral uncertainty and points to alternative population-level approaches for the experimental validation of distributed representations. author: - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin - first_name: Sophie full_name: Denève, Sophie last_name: Denève citation: ama: 'Savin C, Denève S. Spatio-temporal representations of uncertainty in spiking neural networks. In: Vol 3. Neural Information Processing Systems; 2014:2024-2032.' apa: 'Savin, C., & Denève, S. (2014). Spatio-temporal representations of uncertainty in spiking neural networks (Vol. 3, pp. 2024–2032). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.' chicago: Savin, Cristina, and Sophie Denève. “Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks,” 3:2024–32. Neural Information Processing Systems, 2014. ieee: 'C. Savin and S. Denève, “Spatio-temporal representations of uncertainty in spiking neural networks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2014, vol. 3, no. January, pp. 2024–2032.' ista: 'Savin C, Denève S. 2014. Spatio-temporal representations of uncertainty in spiking neural networks. NIPS: Neural Information Processing Systems vol. 3, 2024–2032.' mla: Savin, Cristina, and Sophie Denève. Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks. Vol. 3, no. January, Neural Information Processing Systems, 2014, pp. 2024–32. short: C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp. 2024–2032. conference: end_date: 2014-12-13 location: Montreal, Canada name: 'NIPS: Neural Information Processing Systems' start_date: 2014-12-08 date_created: 2018-12-11T11:53:35Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:52:40Z day: '01' department: - _id: GaTk intvolume: ' 3' issue: January language: - iso: eng main_file_link: - url: http://papers.nips.cc/paper/5343-spatio-temporal-representations-of-uncertainty-in-spiking-neural-networks.pdf month: '01' oa_version: None page: 2024 - 2032 publication_status: published publisher: Neural Information Processing Systems publist_id: '5427' quality_controlled: '1' scopus_import: 1 status: public title: Spatio-temporal representations of uncertainty in spiking neural networks type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2014' ... --- _id: '1761' abstract: - lang: eng text: Metal silicides formed by means of thermal annealing processes are employed as contact materials in microelectronics. Control of the structure of silicide/silicon interfaces becomes a critical issue when the characteristic size of the device is reduced below a few tens of nanometers. Here, we report on silicide clustering occurring within the channel of PtSi/Si/PtSi Schottky-barrier transistors. This phenomenon is investigated through atomistic simulations and low-temperature resonant-tunneling spectroscopy. Our results provide evidence for the segregation of a PtSi cluster with a diameter of a few nanometers from the silicide contact. The cluster acts as a metallic quantum dot giving rise to distinct signatures of quantum transport through its discrete energy states. acknowledgement: This work was supported by the Agence Nationale de la Recherche and by the EU through the ERC Starting Grant HybridNano author: - first_name: Massimo full_name: Mongillo, Massimo last_name: Mongillo - first_name: Panayotis full_name: Spathis, Panayotis N last_name: Spathis - first_name: Georgios full_name: Georgios Katsaros id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros - first_name: Silvano full_name: De Franceschi, Silvano last_name: De Franceschi - first_name: Pascal full_name: Gentile, Pascal last_name: Gentile - first_name: Riccardo full_name: Rurali, Riccardo last_name: Rurali - first_name: Xavier full_name: Cartoixà, Xavier last_name: Cartoixà citation: ama: Mongillo M, Spathis P, Katsaros G, et al. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 2014;3(4). doi:10.1103/PhysRevX.3.041025 apa: Mongillo, M., Spathis, P., Katsaros, G., De Franceschi, S., Gentile, P., Rurali, R., & Cartoixà, X. (2014). PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. American Physical Society. https://doi.org/10.1103/PhysRevX.3.041025 chicago: Mongillo, Massimo, Panayotis Spathis, Georgios Katsaros, Silvano De Franceschi, Pascal Gentile, Riccardo Rurali, and Xavier Cartoixà. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X. American Physical Society, 2014. https://doi.org/10.1103/PhysRevX.3.041025. ieee: M. Mongillo et al., “PtSi clustering in silicon probed by transport spectroscopy,” Physical Review X, vol. 3, no. 4. American Physical Society, 2014. ista: Mongillo M, Spathis P, Katsaros G, De Franceschi S, Gentile P, Rurali R, Cartoixà X. 2014. PtSi clustering in silicon probed by transport spectroscopy. Physical Review X. 3(4). mla: Mongillo, Massimo, et al. “PtSi Clustering in Silicon Probed by Transport Spectroscopy.” Physical Review X, vol. 3, no. 4, American Physical Society, 2014, doi:10.1103/PhysRevX.3.041025. short: M. Mongillo, P. Spathis, G. Katsaros, S. De Franceschi, P. Gentile, R. Rurali, X. Cartoixà, Physical Review X 3 (2014). date_created: 2018-12-11T11:53:52Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:53:02Z day: '01' doi: 10.1103/PhysRevX.3.041025 extern: 1 intvolume: ' 3' issue: '4' main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.5413 month: '01' oa: 1 publication: Physical Review X publication_status: published publisher: American Physical Society publist_id: '5363' quality_controlled: 0 status: public title: PtSi clustering in silicon probed by transport spectroscopy type: journal_article volume: 3 year: '2014' ... --- _id: '1791' abstract: - lang: eng text: Acute gene inactivation using short hairpin RNA (shRNA, knockdown) in developing brain is a powerful technique to study genetic function; however, discrepancies between knockdown and knockout murine phenotypes have left unanswered questions. For example, doublecortin (Dcx) knockdown but not knockout shows a neocortical neuronal migration phenotype. Here we report that in utero electroporation of shRNA, but not siRNA or miRNA, to Dcx demonstrates a migration phenotype in Dcx knockouts akin to the effect in wild-type mice, suggestingshRNA-mediated off-target toxicity. This effect wasnot limited to Dcx, as it was observed in Dclk1 knockouts, as well as with a fraction of scrambled shRNAs, suggesting a sequence-dependent but not sequence-specific effect. Profiling RNAs from electroporated cells showed a defect in endogenous let7 miRNA levels, and disruption of let7 or Dicer recapitulated the migration defect. The results suggest that shRNA-mediated knockdown can produce untoward migration effects by altering endogenous miRNA pathways. acknowledgement: This work was supported by the National Institutes of Health R01NS41537. G.K. was supported by an EMBO Long Term Fellowship, S.L.B. by the A.P. Giannini Fellowship, and A.G.F. by the Brain Behavior Research Foundation author: - first_name: Seungtae full_name: Baek, SeungTae last_name: Baek - first_name: Géraldine full_name: Kerjan, Géraldine last_name: Kerjan - first_name: Stephanie full_name: Bielas, Stephanie L last_name: Bielas - first_name: Jieun full_name: Lee, Jieun last_name: Lee - first_name: Ali full_name: Fenstermaker, Ali G last_name: Fenstermaker - first_name: Gaia full_name: Gaia Novarino id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Joseph full_name: Gleeson, Joseph G last_name: Gleeson citation: ama: Baek S, Kerjan G, Bielas S, et al. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 2014;82(6):1255-1262. doi:10.1016/j.neuron.2014.04.036 apa: Baek, S., Kerjan, G., Bielas, S., Lee, J., Fenstermaker, A., Novarino, G., & Gleeson, J. (2014). Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.04.036 chicago: Baek, Seungtae, Géraldine Kerjan, Stephanie Bielas, Jieun Lee, Ali Fenstermaker, Gaia Novarino, and Joseph Gleeson. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.04.036. ieee: S. Baek et al., “Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation,” Neuron, vol. 82, no. 6. Elsevier, pp. 1255–1262, 2014. ista: Baek S, Kerjan G, Bielas S, Lee J, Fenstermaker A, Novarino G, Gleeson J. 2014. Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation. Neuron. 82(6), 1255–1262. mla: Baek, Seungtae, et al. “Off-Target Effect of Doublecortin Family ShRNA on Neuronal Migration Associated with Endogenous MicroRNA Dysregulation.” Neuron, vol. 82, no. 6, Elsevier, 2014, pp. 1255–62, doi:10.1016/j.neuron.2014.04.036. short: S. Baek, G. Kerjan, S. Bielas, J. Lee, A. Fenstermaker, G. Novarino, J. Gleeson, Neuron 82 (2014) 1255–1262. date_created: 2018-12-11T11:54:01Z date_published: 2014-06-18T00:00:00Z date_updated: 2021-01-12T06:53:13Z day: '18' doi: 10.1016/j.neuron.2014.04.036 extern: 1 intvolume: ' 82' issue: '6' month: '06' page: 1255 - 1262 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5322' quality_controlled: 0 status: public title: Off-target effect of doublecortin family shRNA on neuronal migration associated with endogenous MicroRNA dysregulation type: journal_article volume: 82 year: '2014' ... --- _id: '1806' abstract: - lang: eng text: The generation of asymmetry, at both cellular and tissue level, is one of the most essential capabilities of all eukaryotic organisms. It mediates basically all multicellular development ranging from embryogenesis and de novo organ formation till responses to various environmental stimuli. In plants, the awe-inspiring number of such processes is regulated by phytohormone auxin and its directional, cell-to-cell transport. The mediators of this transport, PIN auxin transporters, are asymmetrically localized at the plasma membrane, and this polar localization determines the directionality of intercellular auxin flow. Thus, auxin transport contributes crucially to the generation of local auxin gradients or maxima, which instruct given cell to change its developmental program. Here, we introduce and discuss the molecular components and cellular mechanisms regulating the generation and maintenance of cellular PIN polarity, as the general hallmarks of cell polarity in plants. author: - first_name: Pawel full_name: Baster, Pawel id: 3028BD74-F248-11E8-B48F-1D18A9856A87 last_name: Baster - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Baster P, Friml J. Auxin on the road navigated by cellular PIN polarity. In: Zažímalová E, Petrášek J, Benková E, eds. Auxin and Its Role in Plant Development. Springer; 2014:143-170. doi:10.1007/978-3-7091-1526-8_8' apa: Baster, P., & Friml, J. (2014). Auxin on the road navigated by cellular PIN polarity. In E. Zažímalová, J. Petrášek, & E. Benková (Eds.), Auxin and Its Role in Plant Development (pp. 143–170). Springer. https://doi.org/10.1007/978-3-7091-1526-8_8 chicago: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” In Auxin and Its Role in Plant Development, edited by Eva Zažímalová, Jan Petrášek, and Eva Benková, 143–70. Springer, 2014. https://doi.org/10.1007/978-3-7091-1526-8_8. ieee: P. Baster and J. Friml, “Auxin on the road navigated by cellular PIN polarity,” in Auxin and Its Role in Plant Development, E. Zažímalová, J. Petrášek, and E. Benková, Eds. Springer, 2014, pp. 143–170. ista: 'Baster P, Friml J. 2014.Auxin on the road navigated by cellular PIN polarity. In: Auxin and Its Role in Plant Development. , 143–170.' mla: Baster, Pawel, and Jiří Friml. “Auxin on the Road Navigated by Cellular PIN Polarity.” Auxin and Its Role in Plant Development, edited by Eva Zažímalová et al., Springer, 2014, pp. 143–70, doi:10.1007/978-3-7091-1526-8_8. short: P. Baster, J. Friml, in:, E. Zažímalová, J. Petrášek, E. Benková (Eds.), Auxin and Its Role in Plant Development, Springer, 2014, pp. 143–170. date_created: 2018-12-11T11:54:07Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:53:19Z day: '01' department: - _id: JiFr doi: 10.1007/978-3-7091-1526-8_8 editor: - first_name: Eva full_name: Zažímalová, Eva last_name: Zažímalová - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 language: - iso: eng month: '04' oa_version: None page: 143 - 170 publication: Auxin and Its Role in Plant Development publication_status: published publisher: Springer publist_id: '5304' quality_controlled: '1' scopus_import: 1 status: public title: Auxin on the road navigated by cellular PIN polarity type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1816' abstract: - lang: eng text: Watermarking techniques for vector graphics dislocate vertices in order to embed imperceptible, yet detectable, statistical features into the input data. The embedding process may result in a change of the topology of the input data, e.g., by introducing self-intersections, which is undesirable or even disastrous for many applications. In this paper we present a watermarking framework for two-dimensional vector graphics that employs conventional watermarking techniques but still provides the guarantee that the topology of the input data is preserved. The geometric part of this framework computes so-called maximum perturbation regions (MPR) of vertices. We propose two efficient algorithms to compute MPRs based on Voronoi diagrams and constrained triangulations. Furthermore, we present two algorithms to conditionally correct the watermarked data in order to increase the watermark embedding capacity and still guarantee topological correctness. While we focus on the watermarking of input formed by straight-line segments, one of our approaches can also be extended to circular arcs. We conclude the paper by demonstrating and analyzing the applicability of our framework in conjunction with two well-known watermarking techniques. acknowledgement: 'Work by Martin Held and Stefan Huber was supported by Austrian Science Fund (FWF): L367-N15 and P25816-N15.' author: - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Peter full_name: Meerwald, Peter last_name: Meerwald - first_name: Roland full_name: Kwitt, Roland last_name: Kwitt citation: ama: Huber S, Held M, Meerwald P, Kwitt R. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 2014;24(1):61-86. doi:10.1142/S0218195914500034 apa: Huber, S., Held, M., Meerwald, P., & Kwitt, R. (2014). Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. World Scientific Publishing. https://doi.org/10.1142/S0218195914500034 chicago: Huber, Stefan, Martin Held, Peter Meerwald, and Roland Kwitt. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications. World Scientific Publishing, 2014. https://doi.org/10.1142/S0218195914500034. ieee: S. Huber, M. Held, P. Meerwald, and R. Kwitt, “Topology-preserving watermarking of vector graphics,” International Journal of Computational Geometry and Applications, vol. 24, no. 1. World Scientific Publishing, pp. 61–86, 2014. ista: Huber S, Held M, Meerwald P, Kwitt R. 2014. Topology-preserving watermarking of vector graphics. International Journal of Computational Geometry and Applications. 24(1), 61–86. mla: Huber, Stefan, et al. “Topology-Preserving Watermarking of Vector Graphics.” International Journal of Computational Geometry and Applications, vol. 24, no. 1, World Scientific Publishing, 2014, pp. 61–86, doi:10.1142/S0218195914500034. short: S. Huber, M. Held, P. Meerwald, R. Kwitt, International Journal of Computational Geometry and Applications 24 (2014) 61–86. date_created: 2018-12-11T11:54:10Z date_published: 2014-03-16T00:00:00Z date_updated: 2021-01-12T06:53:23Z day: '16' ddc: - '000' department: - _id: HeEd doi: 10.1142/S0218195914500034 file: - access_level: open_access checksum: be45c133ab4d43351260e21beaa8f4b1 content_type: application/pdf creator: system date_created: 2018-12-12T10:08:43Z date_updated: 2020-07-14T12:45:17Z file_id: '4704' file_name: IST-2016-443-v1+1_S0218195914500034.pdf file_size: 991734 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 24' issue: '1' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 61 - 86 publication: International Journal of Computational Geometry and Applications publication_status: published publisher: World Scientific Publishing publist_id: '5290' pubrep_id: '443' quality_controlled: '1' scopus_import: 1 status: public title: Topology-preserving watermarking of vector graphics tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2014' ... --- _id: '1821' abstract: - lang: eng text: We review recent progress towards a rigorous understanding of the Bogoliubov approximation for bosonic quantum many-body systems. We focus, in particular, on the excitation spectrum of a Bose gas in the mean-field (Hartree) limit. A list of open problems will be discussed at the end. article_number: '1.4881536' author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Seiringer R. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4881536 apa: Seiringer, R. (2014). Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4881536 chicago: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4881536. ieee: R. Seiringer, “Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014. ista: Seiringer R. 2014. Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation. Journal of Mathematical Physics. 55(7), 1.4881536. mla: Seiringer, Robert. “Bose Gases, Bose-Einstein Condensation, and the Bogoliubov Approximation.” Journal of Mathematical Physics, vol. 55, no. 7, 1.4881536, American Institute of Physics, 2014, doi:10.1063/1.4881536. short: R. Seiringer, Journal of Mathematical Physics 55 (2014). date_created: 2018-12-11T11:54:11Z date_published: 2014-06-26T00:00:00Z date_updated: 2021-01-12T06:53:25Z day: '26' ddc: - '510' - '530' department: - _id: RoSe doi: 10.1063/1.4881536 file: - access_level: open_access checksum: ed0efc93c10f1341155f0316af617b82 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:49Z date_updated: 2020-07-14T12:45:17Z file_id: '5172' file_name: IST-2016-532-v1+1_J._Mathematical_Phys._2014_Seiringer.pdf file_size: 269171 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 55' issue: '7' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: Journal of Mathematical Physics publication_status: published publisher: American Institute of Physics publist_id: '5285' pubrep_id: '532' quality_controlled: '1' scopus_import: 1 status: public title: Bose gases, Bose-Einstein condensation, and the Bogoliubov approximation type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2014' ... --- _id: '1822' article_number: '075101' author: - first_name: Vojkan full_name: Jakšić, Vojkan last_name: Jakšić - first_name: Claude full_name: Pillet, Claude last_name: Pillet - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Jakšić V, Pillet C, Seiringer R. Introduction. Journal of Mathematical Physics. 2014;55(7). doi:10.1063/1.4884877 apa: Jakšić, V., Pillet, C., & Seiringer, R. (2014). Introduction. Journal of Mathematical Physics. American Institute of Physics. https://doi.org/10.1063/1.4884877 chicago: Jakšić, Vojkan, Claude Pillet, and Robert Seiringer. “Introduction.” Journal of Mathematical Physics. American Institute of Physics, 2014. https://doi.org/10.1063/1.4884877. ieee: V. Jakšić, C. Pillet, and R. Seiringer, “Introduction,” Journal of Mathematical Physics, vol. 55, no. 7. American Institute of Physics, 2014. ista: Jakšić V, Pillet C, Seiringer R. 2014. Introduction. Journal of Mathematical Physics. 55(7), 075101. mla: Jakšić, Vojkan, et al. “Introduction.” Journal of Mathematical Physics, vol. 55, no. 7, 075101, American Institute of Physics, 2014, doi:10.1063/1.4884877. short: V. Jakšić, C. Pillet, R. Seiringer, Journal of Mathematical Physics 55 (2014). date_created: 2018-12-11T11:54:12Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T06:53:25Z day: '01' department: - _id: RoSe doi: 10.1063/1.4884877 intvolume: ' 55' issue: '7' language: - iso: eng month: '07' oa_version: None publication: Journal of Mathematical Physics publication_status: published publisher: American Institute of Physics publist_id: '5284' quality_controlled: '1' scopus_import: 1 status: public title: Introduction type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 55 year: '2014' ... --- _id: '1829' abstract: - lang: eng text: Hitting and batting tasks, such as tennis forehands, ping-pong strokes, or baseball batting, depend on predictions where the ball can be intercepted and how it can properly be returned to the opponent. These predictions get more accurate over time, hence the behaviors need to be continuously modified. As a result, movement templates with a learned global shape need to be adapted during the execution so that the racket reaches a target position and velocity that will return the ball over to the other side of the net or court. It requires altering learned movements to hit a varying target with the necessary velocity at a specific instant in time. Such a task cannot be incorporated straightforwardly in most movement representations suitable for learning. For example, the standard formulation of the dynamical system based motor primitives (introduced by Ijspeert et al (2002b)) does not satisfy this property despite their flexibility which has allowed learning tasks ranging from locomotion to kendama. In order to fulfill this requirement, we reformulate the Ijspeert framework to incorporate the possibility of specifying a desired hitting point and a desired hitting velocity while maintaining all advantages of the original formulation.We show that the proposed movement template formulation works well in two scenarios, i.e., for hitting a ball on a string with a table tennis racket at a specified velocity and for returning balls launched by a ball gun successfully over the net using forehand movements. alternative_title: - Springer Tracts in Advanced Robotics author: - first_name: Katharina full_name: Muelling, Katharina last_name: Muelling - first_name: Oliver full_name: Kroemer, Oliver last_name: Kroemer - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf citation: ama: 'Muelling K, Kroemer O, Lampert C, Schölkopf B. Movement templates for learning of hitting and batting. In: Kober J, Peters J, eds. Learning Motor Skills. Vol 97. From Algorithms to Robot Experiments. Springer; 2014:69-82. doi:10.1007/978-3-319-03194-1_3' apa: Muelling, K., Kroemer, O., Lampert, C., & Schölkopf, B. (2014). Movement templates for learning of hitting and batting. In J. Kober & J. Peters (Eds.), Learning Motor Skills (Vol. 97, pp. 69–82). Springer. https://doi.org/10.1007/978-3-319-03194-1_3 chicago: Muelling, Katharina, Oliver Kroemer, Christoph Lampert, and Bernhard Schölkopf. “Movement Templates for Learning of Hitting and Batting.” In Learning Motor Skills, edited by Jens Kober and Jan Peters, 97:69–82. From Algorithms to Robot Experiments. Springer, 2014. https://doi.org/10.1007/978-3-319-03194-1_3. ieee: K. Muelling, O. Kroemer, C. Lampert, and B. Schölkopf, “Movement templates for learning of hitting and batting,” in Learning Motor Skills, vol. 97, J. Kober and J. Peters, Eds. Springer, 2014, pp. 69–82. ista: 'Muelling K, Kroemer O, Lampert C, Schölkopf B. 2014.Movement templates for learning of hitting and batting. In: Learning Motor Skills. Springer Tracts in Advanced Robotics, vol. 97, 69–82.' mla: Muelling, Katharina, et al. “Movement Templates for Learning of Hitting and Batting.” Learning Motor Skills, edited by Jens Kober and Jan Peters, vol. 97, Springer, 2014, pp. 69–82, doi:10.1007/978-3-319-03194-1_3. short: K. Muelling, O. Kroemer, C. Lampert, B. Schölkopf, in:, J. Kober, J. Peters (Eds.), Learning Motor Skills, Springer, 2014, pp. 69–82. date_created: 2018-12-11T11:54:14Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:53:28Z day: '01' department: - _id: ChLa doi: 10.1007/978-3-319-03194-1_3 editor: - first_name: Jens full_name: Kober, Jens last_name: Kober - first_name: Jan full_name: Peters, Jan last_name: Peters intvolume: ' 97' language: - iso: eng month: '01' oa_version: None page: 69 - 82 publication: Learning Motor Skills publication_status: published publisher: Springer publist_id: '5274' quality_controlled: '1' scopus_import: 1 series_title: From Algorithms to Robot Experiments status: public title: Movement templates for learning of hitting and batting type: book_chapter user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 97 year: '2014' ... --- _id: '1844' abstract: - lang: eng text: 'Local protein interactions ("molecular context" effects) dictate amino acid replacements and can be described in terms of site-specific, energetic preferences for any different amino acid. It has been recently debated whether these preferences remain approximately constant during evolution or whether, due to coevolution of sites, they change strongly. Such research highlights an unresolved and fundamental issue with far-reaching implications for phylogenetic analysis and molecular evolution modeling. Here, we take advantage of the recent availability of phenotypically supported laboratory resurrections of Precambrian thioredoxins and β-lactamases to experimentally address the change of site-specific amino acid preferences over long geological timescales. Extensive mutational analyses support the notion that evolutionary adjustment to a new amino acid may occur, but to a large extent this is insufficient to erase the primitive preference for amino acid replacements. Generally, site-specific amino acid preferences appear to remain conserved throughout evolutionary history despite local sequence divergence. We show such preference conservation to be readily understandable in molecular terms and we provide crystallographic evidence for an intriguing structural-switch mechanism: Energetic preference for an ancestral amino acid in a modern protein can be linked to reorganization upon mutation to the ancestral local structure around the mutated site. Finally, we point out that site-specific preference conservation naturally leads to one plausible evolutionary explanation for the existence of intragenic global suppressor mutations.' author: - first_name: Valeria full_name: Risso, Valeria last_name: Risso - first_name: Fadia full_name: Manssour Triedo, Fadia last_name: Manssour Triedo - first_name: Asuncion full_name: Delgado Delgado, Asuncion last_name: Delgado Delgado - first_name: Rocio full_name: Arco, Rocio last_name: Arco - first_name: Alicia full_name: Barroso Deljesús, Alicia last_name: Barroso Deljesús - first_name: Álvaro full_name: Inglés Prieto, Álvaro id: 2A9DB292-F248-11E8-B48F-1D18A9856A87 last_name: Inglés Prieto orcid: 0000-0002-5409-8571 - first_name: Raquel full_name: Godoy Ruiz, Raquel last_name: Godoy Ruiz - first_name: Josè full_name: Gavira, Josè last_name: Gavira - first_name: Eric full_name: Gaucher, Eric last_name: Gaucher - first_name: Beatriz full_name: Ibarra Molero, Beatriz last_name: Ibarra Molero - first_name: Jose full_name: Sánchez Ruiz, Jose last_name: Sánchez Ruiz citation: ama: Risso V, Manssour Triedo F, Delgado Delgado A, et al. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 2014;32(2):440-455. doi:10.1093/molbev/msu312 apa: Risso, V., Manssour Triedo, F., Delgado Delgado, A., Arco, R., Barroso Deljesús, A., Inglés Prieto, Á., … Sánchez Ruiz, J. (2014). Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msu312 chicago: Risso, Valeria, Fadia Manssour Triedo, Asuncion Delgado Delgado, Rocio Arco, Alicia Barroso Deljesús, Álvaro Inglés Prieto, Raquel Godoy Ruiz, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/msu312. ieee: V. Risso et al., “Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history,” Molecular Biology and Evolution, vol. 32, no. 2. Oxford University Press, pp. 440–455, 2014. ista: Risso V, Manssour Triedo F, Delgado Delgado A, Arco R, Barroso Deljesús A, Inglés Prieto Á, Godoy Ruiz R, Gavira J, Gaucher E, Ibarra Molero B, Sánchez Ruiz J. 2014. Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history. Molecular Biology and Evolution. 32(2), 440–455. mla: Risso, Valeria, et al. “Mutational Studies on Resurrected Ancestral Proteins Reveal Conservation of Site-Specific Amino Acid Preferences throughout Evolutionary History.” Molecular Biology and Evolution, vol. 32, no. 2, Oxford University Press, 2014, pp. 440–55, doi:10.1093/molbev/msu312. short: V. Risso, F. Manssour Triedo, A. Delgado Delgado, R. Arco, A. Barroso Deljesús, Á. Inglés Prieto, R. Godoy Ruiz, J. Gavira, E. Gaucher, B. Ibarra Molero, J. Sánchez Ruiz, Molecular Biology and Evolution 32 (2014) 440–455. date_created: 2018-12-11T11:54:19Z date_published: 2014-11-12T00:00:00Z date_updated: 2021-01-12T06:53:34Z day: '12' ddc: - '571' department: - _id: HaJa doi: 10.1093/molbev/msu312 file: - access_level: open_access checksum: 06215318e66be8f3e0c33abb07e9d3da content_type: application/pdf creator: system date_created: 2018-12-12T10:16:56Z date_updated: 2020-07-14T12:45:19Z file_id: '5247' file_name: IST-2016-430-v1+1_Mol_Biol_Evol-2015-Risso-440-55.pdf file_size: 1545246 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 32' issue: '2' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '11' oa: 1 oa_version: Published Version page: 440 - 455 publication: Molecular Biology and Evolution publication_status: published publisher: Oxford University Press publist_id: '5257' pubrep_id: '430' quality_controlled: '1' scopus_import: 1 status: public title: Mutational studies on resurrected ancestral proteins reveal conservation of site-specific amino acid preferences throughout evolutionary history tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 32 year: '2014' ... --- _id: '1842' abstract: - lang: eng text: We prove polynomial upper bounds of geometric Ramsey numbers of pathwidth-2 outerplanar triangulations in both convex and general cases. We also prove that the geometric Ramsey numbers of the ladder graph on 2n vertices are bounded by O(n3) and O(n10), in the convex and general case, respectively. We then apply similar methods to prove an (Formula presented.) upper bound on the Ramsey number of a path with n ordered vertices. acknowledgement: Marek Krčál was supported by the ERC Advanced Grant No. 267165. author: - first_name: Josef full_name: Cibulka, Josef last_name: Cibulka - first_name: Pu full_name: Gao, Pu last_name: Gao - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál - first_name: Tomáš full_name: Valla, Tomáš last_name: Valla - first_name: Pavel full_name: Valtr, Pavel last_name: Valtr citation: ama: Cibulka J, Gao P, Krcál M, Valla T, Valtr P. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 2014;53(1):64-79. doi:10.1007/s00454-014-9646-x apa: Cibulka, J., Gao, P., Krcál, M., Valla, T., & Valtr, P. (2014). On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-014-9646-x chicago: Cibulka, Josef, Pu Gao, Marek Krcál, Tomáš Valla, and Pavel Valtr. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-014-9646-x. ieee: J. Cibulka, P. Gao, M. Krcál, T. Valla, and P. Valtr, “On the geometric ramsey number of outerplanar graphs,” Discrete & Computational Geometry, vol. 53, no. 1. Springer, pp. 64–79, 2014. ista: Cibulka J, Gao P, Krcál M, Valla T, Valtr P. 2014. On the geometric ramsey number of outerplanar graphs. Discrete & Computational Geometry. 53(1), 64–79. mla: Cibulka, Josef, et al. “On the Geometric Ramsey Number of Outerplanar Graphs.” Discrete & Computational Geometry, vol. 53, no. 1, Springer, 2014, pp. 64–79, doi:10.1007/s00454-014-9646-x. short: J. Cibulka, P. Gao, M. Krcál, T. Valla, P. Valtr, Discrete & Computational Geometry 53 (2014) 64–79. date_created: 2018-12-11T11:54:18Z date_published: 2014-11-14T00:00:00Z date_updated: 2021-01-12T06:53:33Z day: '14' department: - _id: UlWa - _id: HeEd doi: 10.1007/s00454-014-9646-x intvolume: ' 53' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1310.7004 month: '11' oa: 1 oa_version: Submitted Version page: 64 - 79 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '5260' scopus_import: 1 status: public title: On the geometric ramsey number of outerplanar graphs type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2014' ... --- _id: '1854' abstract: - lang: eng 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. author: - first_name: Paul full_name: Guerrero, Paul last_name: Guerrero - first_name: Thomas full_name: Auzinger, Thomas id: 4718F954-F248-11E8-B48F-1D18A9856A87 last_name: Auzinger orcid: 0000-0002-1546-3265 - first_name: Michael full_name: Wimmer, Michael last_name: Wimmer - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke citation: ama: Guerrero P, Auzinger T, Wimmer M, Jeschke S. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 2014;34(1):239-252. doi:10.1111/cgf.12509 apa: Guerrero, P., Auzinger, T., Wimmer, M., & Jeschke, S. (2014). Partial shape matching using transformation parameter similarity. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12509 chicago: Guerrero, Paul, Thomas Auzinger, Michael Wimmer, and Stefan Jeschke. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum. Wiley, 2014. https://doi.org/10.1111/cgf.12509. ieee: P. Guerrero, T. Auzinger, M. Wimmer, and S. Jeschke, “Partial shape matching using transformation parameter similarity,” Computer Graphics Forum, vol. 34, no. 1. Wiley, pp. 239–252, 2014. ista: Guerrero P, Auzinger T, Wimmer M, Jeschke S. 2014. Partial shape matching using transformation parameter similarity. Computer Graphics Forum. 34(1), 239–252. mla: Guerrero, Paul, et al. “Partial Shape Matching Using Transformation Parameter Similarity.” Computer Graphics Forum, vol. 34, no. 1, Wiley, 2014, pp. 239–52, doi:10.1111/cgf.12509. short: P. Guerrero, T. Auzinger, M. Wimmer, S. Jeschke, Computer Graphics Forum 34 (2014) 239–252. date_created: 2018-12-11T11:54:22Z date_published: 2014-11-05T00:00:00Z date_updated: 2021-01-12T06:53:38Z day: '05' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.12509 file: - access_level: open_access checksum: 91946bfc509c77f5fd3151a3ff2b2c8f content_type: application/pdf creator: system date_created: 2018-12-12T10:15:58Z date_updated: 2020-07-14T12:45:19Z file_id: '5182' file_name: IST-2016-574-v1+1_Guerrero-2014-TPS-paper.pdf file_size: 24817484 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 34' issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 239 - 252 publication: Computer Graphics Forum publication_status: published publisher: Wiley publist_id: '5246' pubrep_id: '574' quality_controlled: '1' scopus_import: 1 status: public title: Partial shape matching using transformation parameter similarity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2014' ... --- _id: '1852' 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. acknowledgement: 'This work was funded by grants from EraSysBio+ (iSAM) and ERC (Morphodynamics). ' author: - first_name: Massimiliano full_name: Sassi, Massimiliano last_name: Sassi - first_name: Olivier full_name: Ali, Olivier last_name: Ali - first_name: Frédéric full_name: Boudon, Frédéric last_name: Boudon - first_name: Gladys full_name: Cloarec, Gladys last_name: Cloarec - first_name: Ursula full_name: Abad, Ursula last_name: Abad - first_name: Coralie full_name: Cellier, Coralie last_name: Cellier - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Benjamin full_name: Gilles, Benjamin last_name: Gilles - first_name: Pascale full_name: Milani, Pascale last_name: Milani - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Teva full_name: Vernoux, Teva last_name: Vernoux - first_name: Christophe full_name: Godin, Christophe last_name: Godin - first_name: Olivier full_name: Hamant, Olivier last_name: Hamant - first_name: Jan full_name: Traas, Jan last_name: Traas citation: 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. Current Biology. 2014;24(19):2335-2342. doi:10.1016/j.cub.2014.08.036 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. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.08.036 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.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.08.036. ieee: M. Sassi et al., “An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis,” Current Biology, vol. 24, no. 19. Cell Press, pp. 2335–2342, 2014. 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. mla: Sassi, Massimiliano, et al. “An Auxin-Mediated Shift toward Growth Isotropy Promotes Organ Formation at the Shoot Meristem in Arabidopsis.” Current Biology, vol. 24, no. 19, Cell Press, 2014, pp. 2335–42, doi:10.1016/j.cub.2014.08.036. 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. date_created: 2018-12-11T11:54:22Z date_published: 2014-10-06T00:00:00Z date_updated: 2021-01-12T06:53:37Z day: '06' department: - _id: JiFr doi: 10.1016/j.cub.2014.08.036 intvolume: ' 24' issue: '19' language: - iso: eng main_file_link: - open_access: '1' url: https://hal.archives-ouvertes.fr/hal-01074821 month: '10' oa: 1 oa_version: Submitted Version page: 2335 - 2342 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '5248' quality_controlled: '1' scopus_import: 1 status: public title: An auxin-mediated shift toward growth isotropy promotes organ formation at the shoot meristem in Arabidopsis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2014' ... --- _id: '1853' 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. author: - first_name: Susmit full_name: Jha, Susmit last_name: Jha - first_name: Stavros full_name: Tripakis, Stavros last_name: Tripakis - first_name: Sanjit full_name: Seshia, Sanjit last_name: Seshia - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Jha S, Tripakis S, Seshia S, Chatterjee K. Game theoretic secure localization in wireless sensor networks. In: IEEE; 2014:85-90. doi:10.1109/IOT.2014.7030120' apa: 'Jha, S., Tripakis, S., Seshia, S., & Chatterjee, K. (2014). Game theoretic secure localization in wireless sensor networks (pp. 85–90). Presented at the IOT: Internet of Things, Cambridge, USA: IEEE. https://doi.org/10.1109/IOT.2014.7030120' chicago: Jha, Susmit, Stavros Tripakis, Sanjit Seshia, and Krishnendu Chatterjee. “Game Theoretic Secure Localization in Wireless Sensor Networks,” 85–90. IEEE, 2014. https://doi.org/10.1109/IOT.2014.7030120. 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.' ista: 'Jha S, Tripakis S, Seshia S, Chatterjee K. 2014. Game theoretic secure localization in wireless sensor networks. IOT: Internet of Things, 85–90.' mla: Jha, Susmit, et al. Game Theoretic Secure Localization in Wireless Sensor Networks. IEEE, 2014, pp. 85–90, doi:10.1109/IOT.2014.7030120. short: S. Jha, S. Tripakis, S. Seshia, K. Chatterjee, in:, IEEE, 2014, pp. 85–90. conference: end_date: 2014-10-08 location: Cambridge, USA name: 'IOT: Internet of Things' start_date: 2014-10-06 date_created: 2018-12-11T11:54:22Z date_published: 2014-02-03T00:00:00Z date_updated: 2021-01-12T06:53:38Z day: '03' department: - _id: KrCh doi: 10.1109/IOT.2014.7030120 language: - iso: eng month: '02' oa_version: None page: 85 - 90 publication_status: published publisher: IEEE publist_id: '5247' quality_controlled: '1' status: public title: Game theoretic secure localization in wireless sensor networks type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1862' abstract: - lang: eng 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. 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. article_processing_charge: No article_type: original author: - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Laurie full_name: Grandont, Laurie last_name: Grandont - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Sébastien full_name: Paque, Sébastien last_name: Paque - first_name: Anas full_name: Abuzeineh, Anas last_name: Abuzeineh - first_name: Hana full_name: Rakusova, Hana id: 4CAAA450-78D2-11EA-8E57-B40A396E08BA last_name: Rakusova - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Catherine full_name: Perrot Rechenmann, Catherine last_name: Perrot Rechenmann - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Chen X, Grandont L, Li H, et al. Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules. Nature. 2014;516(729):90-93. doi:10.1038/nature13889 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. Nature. Nature Publishing Group. https://doi.org/10.1038/nature13889 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.” Nature. Nature Publishing Group, 2014. https://doi.org/10.1038/nature13889. ieee: X. Chen et al., “Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules,” Nature, 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. mla: Chen, Xu, et al. “Inhibition of Cell Expansion by Rapid ABP1-Mediated Auxin Effect on Microtubules.” Nature, vol. 516, no. 729, Nature Publishing Group, 2014, pp. 90–93, doi:10.1038/nature13889. 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. date_created: 2018-12-11T11:54:25Z date_published: 2014-12-04T00:00:00Z date_updated: 2022-05-23T08:26:44Z day: '04' department: - _id: JiFr - _id: Bio - _id: EvBe doi: 10.1038/nature13889 ec_funded: 1 external_id: pmid: - '25409144' intvolume: ' 516' issue: '729' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4257754/ month: '12' oa: 1 oa_version: Submitted Version page: 90 - 93 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Nature Publishing Group publist_id: '5237' quality_controlled: '1' scopus_import: '1' status: public title: Inhibition of cell expansion by rapid ABP1-mediated auxin effect on microtubules type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 516 year: '2014' ... --- _id: '1869' 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. acknowledgement: The work presented in this paper was supported in part by the European Research Council (ERC) under grant agreement QUAINT (I774-N23) alternative_title: - LNCS author: - first_name: Georg full_name: Hofferek, Georg last_name: Hofferek - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta citation: ama: 'Hofferek G, Gupta A. Suraq - a controller synthesis tool using uninterpreted functions. In: Yahav E, ed. HVC 2014. Vol 8855. Springer; 2014:68-74. doi:10.1007/978-3-319-13338-6_6' apa: 'Hofferek, G., & Gupta, A. (2014). Suraq - a controller synthesis tool using uninterpreted functions. In E. Yahav (Ed.), HVC 2014 (Vol. 8855, pp. 68–74). Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-13338-6_6' chicago: Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” In HVC 2014, edited by Eran Yahav, 8855:68–74. Springer, 2014. https://doi.org/10.1007/978-3-319-13338-6_6. ieee: G. Hofferek and A. Gupta, “Suraq - a controller synthesis tool using uninterpreted functions,” in HVC 2014, Haifa, Israel, 2014, vol. 8855, 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.' mla: Hofferek, Georg, and Ashutosh Gupta. “Suraq - a Controller Synthesis Tool Using Uninterpreted Functions.” HVC 2014, edited by Eran Yahav, vol. 8855, Springer, 2014, pp. 68–74, doi:10.1007/978-3-319-13338-6_6. short: G. Hofferek, A. Gupta, in:, E. Yahav (Ed.), HVC 2014, Springer, 2014, pp. 68–74. conference: end_date: 2014-11-20 location: Haifa, Israel name: 'HVC: Haifa Verification Conference' start_date: 2014-11-18 date_created: 2018-12-11T11:54:27Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:53:44Z day: '01' department: - _id: ToHe doi: 10.1007/978-3-319-13338-6_6 ec_funded: 1 editor: - first_name: Eran full_name: Yahav, Eran last_name: Yahav intvolume: ' 8855' language: - iso: eng month: '01' oa_version: None page: 68 - 74 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25863FF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11407 name: Game Theory publication: HVC 2014 publication_status: published publisher: Springer publist_id: '5228' quality_controlled: '1' status: public title: Suraq - a controller synthesis tool using uninterpreted functions type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8855 year: '2014' ... --- _id: '1872' 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. acknowledgement: This research was supported in part by the Austrian National Research Network RiSE (S11410-N23). alternative_title: - LNCS author: - first_name: Ashutosh full_name: Gupta, Ashutosh id: 335E5684-F248-11E8-B48F-1D18A9856A87 last_name: Gupta - first_name: Laura full_name: Kovács, Laura last_name: Kovács - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Andrei full_name: Voronkov, Andrei last_name: Voronkov citation: ama: 'Gupta A, Kovács L, Kragl B, Voronkov A. Extensional crisis and proving identity. In: Cassez F, Raskin J-F, eds. ATVA 2014. Vol 8837. Springer; 2014:185-200. doi:10.1007/978-3-319-11936-6_14' apa: 'Gupta, A., Kovács, L., Kragl, B., & Voronkov, A. (2014). Extensional crisis and proving identity. In F. Cassez & J.-F. Raskin (Eds.), ATVA 2014 (Vol. 8837, pp. 185–200). Sydney, Australia: Springer. https://doi.org/10.1007/978-3-319-11936-6_14' chicago: Gupta, Ashutosh, Laura Kovács, Bernhard Kragl, and Andrei Voronkov. “Extensional Crisis and Proving Identity.” In ATVA 2014, edited by Franck Cassez and Jean-François Raskin, 8837:185–200. Springer, 2014. https://doi.org/10.1007/978-3-319-11936-6_14. ieee: A. Gupta, L. Kovács, B. Kragl, and A. Voronkov, “Extensional crisis and proving identity,” in ATVA 2014, 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.' mla: Gupta, Ashutosh, et al. “Extensional Crisis and Proving Identity.” ATVA 2014, edited by Franck Cassez and Jean-François Raskin, vol. 8837, Springer, 2014, pp. 185–200, doi:10.1007/978-3-319-11936-6_14. short: A. Gupta, L. Kovács, B. Kragl, A. Voronkov, in:, F. Cassez, J.-F. Raskin (Eds.), ATVA 2014, Springer, 2014, pp. 185–200. conference: end_date: 2014-11-07 location: Sydney, Australia name: 'ATVA: Automated Technology for Verification and Analysis' start_date: 2014-11-03 date_created: 2018-12-11T11:54:28Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:53:45Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-11936-6_14 ec_funded: 1 editor: - first_name: Franck full_name: Cassez, Franck last_name: Cassez - first_name: Jean-François full_name: Raskin, Jean-François last_name: Raskin file: - access_level: open_access checksum: af4bd3fc1f4c93075e4dc5cbf625fe7b content_type: application/pdf creator: system date_created: 2018-12-12T10:10:15Z date_updated: 2020-07-14T12:45:19Z file_id: '4801' file_name: IST-2016-641-v1+1_atva2014.pdf file_size: 244294 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 8837' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version page: 185 - 200 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication: ATVA 2014 publication_status: published publisher: Springer publist_id: '5226' pubrep_id: '641' quality_controlled: '1' scopus_import: 1 status: public title: Extensional crisis and proving identity type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8837 year: '2014' ... --- _id: '1870' abstract: - lang: eng 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. alternative_title: - LIPIcs author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop - first_name: Roopsha full_name: Samanta, Roopsha id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87 last_name: Samanta citation: ama: 'Henzinger TA, Otop J, Samanta R. Lipschitz robustness of finite-state transducers. In: Leibniz International Proceedings in Informatics, LIPIcs. Vol 29. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2014:431-443. doi:10.4230/LIPIcs.FSTTCS.2014.431' apa: 'Henzinger, T. A., Otop, J., & Samanta, R. (2014). Lipschitz robustness of finite-state transducers. In Leibniz International Proceedings in Informatics, LIPIcs (Vol. 29, pp. 431–443). Delhi, India: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431' chicago: Henzinger, Thomas A, Jan Otop, and Roopsha Samanta. “Lipschitz Robustness of Finite-State Transducers.” In Leibniz International Proceedings in Informatics, LIPIcs, 29:431–43. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014. https://doi.org/10.4230/LIPIcs.FSTTCS.2014.431. ieee: T. A. Henzinger, J. Otop, and R. Samanta, “Lipschitz robustness of finite-state transducers,” in Leibniz International Proceedings in Informatics, LIPIcs, Delhi, India, 2014, vol. 29, pp. 431–443. 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.' mla: Henzinger, Thomas A., et al. “Lipschitz Robustness of Finite-State Transducers.” Leibniz International Proceedings in Informatics, LIPIcs, vol. 29, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2014, pp. 431–43, doi:10.4230/LIPIcs.FSTTCS.2014.431. 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. conference: end_date: 2014-12-17 location: Delhi, India name: 'FSTTCS: Foundations of Software Technology and Theoretical Computer Science' start_date: 2014-12-15 date_created: 2018-12-11T11:54:27Z date_published: 2014-12-01T00:00:00Z date_updated: 2021-01-12T06:53:45Z day: '01' ddc: - '004' department: - _id: ToHe doi: 10.4230/LIPIcs.FSTTCS.2014.431 file: - access_level: open_access checksum: 7b1aff1710a8bffb7080ec07f62d9a17 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:11Z date_updated: 2020-07-14T12:45:19Z file_id: '4734' file_name: IST-2017-804-v1+1_37.pdf file_size: 562151 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 29' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 431 - 443 publication: Leibniz International Proceedings in Informatics, LIPIcs publication_status: published publisher: Schloss Dagstuhl - Leibniz-Zentrum für Informatik publist_id: '5227' pubrep_id: '804' quality_controlled: '1' status: public title: Lipschitz robustness of finite-state transducers tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2014' ... --- _id: '1875' abstract: - lang: eng 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. alternative_title: - LNCS author: - first_name: Roopsha full_name: Samanta, Roopsha id: 3D2AAC08-F248-11E8-B48F-1D18A9856A87 last_name: Samanta - first_name: Oswaldo full_name: Olivo, Oswaldo last_name: Olivo - first_name: Emerson full_name: Allen, Emerson last_name: Allen citation: 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:10.1007/978-3-319-10936-7_17' apa: 'Samanta, R., Olivo, O., & Allen, E. (2014). Cost-aware automatic program repair. In M. Müller-Olm & H. Seidl (Eds.) (Vol. 8723, pp. 268–284). Presented at the SAS: Static Analysis Symposium, Munich, Germany: Springer. https://doi.org/10.1007/978-3-319-10936-7_17' 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. https://doi.org/10.1007/978-3-319-10936-7_17. 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.' ista: 'Samanta R, Olivo O, Allen E. 2014. Cost-aware automatic program repair. SAS: Static Analysis Symposium, LNCS, vol. 8723, 268–284.' mla: Samanta, Roopsha, et al. Cost-Aware Automatic Program Repair. Edited by Markus Müller-Olm and Helmut Seidl, vol. 8723, Springer, 2014, pp. 268–84, doi:10.1007/978-3-319-10936-7_17. short: R. Samanta, O. Olivo, E. Allen, in:, M. Müller-Olm, H. Seidl (Eds.), Springer, 2014, pp. 268–284. conference: end_date: 2014-09-14 location: Munich, Germany name: 'SAS: Static Analysis Symposium' start_date: 2014-09-11 date_created: 2018-12-11T11:54:29Z date_published: 2014-09-01T00:00:00Z date_updated: 2021-01-12T06:53:46Z day: '01' ddc: - '000' - '005' department: - _id: ToHe doi: 10.1007/978-3-319-10936-7_17 editor: - first_name: Markus full_name: Müller-Olm, Markus last_name: Müller-Olm - first_name: Helmut full_name: Seidl, Helmut last_name: Seidl file: - access_level: open_access checksum: 78ec4ea1bdecc676cd3e8cad35c6182c content_type: application/pdf creator: system date_created: 2018-12-12T10:07:51Z date_updated: 2020-07-14T12:45:19Z file_id: '4650' file_name: IST-2014-313-v1+1_SOE.SAS14.pdf file_size: 409485 relation: main_file file_date_updated: 2020-07-14T12:45:19Z has_accepted_license: '1' intvolume: ' 8723' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 268 - 284 publication_status: published publisher: Springer publist_id: '5221' pubrep_id: '313' quality_controlled: '1' scopus_import: 1 status: public title: Cost-aware automatic program repair type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8723 year: '2014' ... --- _id: '1876' abstract: - lang: eng 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. article_processing_charge: No article_type: original author: - first_name: Nikolai full_name: Dolbilin, Nikolai last_name: Dolbilin - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Alexey full_name: Glazyrin, Alexey last_name: Glazyrin - first_name: Oleg full_name: Musin, Oleg last_name: Musin citation: ama: Dolbilin N, Edelsbrunner H, Glazyrin A, Musin O. Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. 2014;14(3):491-504. doi:10.17323/1609-4514-2014-14-3-491-504 apa: Dolbilin, N., Edelsbrunner, H., Glazyrin, A., & Musin, O. (2014). Functionals on triangulations of delaunay sets. Moscow Mathematical Journal. Independent University of Moscow. https://doi.org/10.17323/1609-4514-2014-14-3-491-504 chicago: Dolbilin, Nikolai, Herbert Edelsbrunner, Alexey Glazyrin, and Oleg Musin. “Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal. Independent University of Moscow, 2014. https://doi.org/10.17323/1609-4514-2014-14-3-491-504. ieee: N. Dolbilin, H. Edelsbrunner, A. Glazyrin, and O. Musin, “Functionals on triangulations of delaunay sets,” Moscow Mathematical Journal, 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. mla: Dolbilin, Nikolai, et al. “Functionals on Triangulations of Delaunay Sets.” Moscow Mathematical Journal, vol. 14, no. 3, Independent University of Moscow, 2014, pp. 491–504, doi:10.17323/1609-4514-2014-14-3-491-504. short: N. Dolbilin, H. Edelsbrunner, A. Glazyrin, O. Musin, Moscow Mathematical Journal 14 (2014) 491–504. date_created: 2018-12-11T11:54:29Z date_published: 2014-07-01T00:00:00Z date_updated: 2022-03-03T11:47:09Z day: '01' department: - _id: HeEd doi: 10.17323/1609-4514-2014-14-3-491-504 external_id: arxiv: - '1211.7053' intvolume: ' 14' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1211.7053 month: '07' oa: 1 oa_version: Submitted Version page: 491 - 504 publication: Moscow Mathematical Journal publication_identifier: issn: - '16093321' publication_status: published publisher: Independent University of Moscow publist_id: '5220' quality_controlled: '1' scopus_import: '1' status: public title: Functionals on triangulations of delaunay sets type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14 year: '2014' ... --- _id: '1877' 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. article_type: letter_note author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Kari full_name: Vaahtomeri, Kari id: 368EE576-F248-11E8-B48F-1D18A9856A87 last_name: Vaahtomeri orcid: 0000-0001-7829-3518 citation: ama: 'Sixt MK, Vaahtomeri K. Physiology: Relax and come in. Nature. 2014;514(7523):441-442. doi:10.1038/514441a' apa: 'Sixt, M. K., & Vaahtomeri, K. (2014). Physiology: Relax and come in. Nature. Springer Nature. https://doi.org/10.1038/514441a' chicago: 'Sixt, Michael K, and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature. Springer Nature, 2014. https://doi.org/10.1038/514441a.' ieee: 'M. K. Sixt and K. Vaahtomeri, “Physiology: Relax and come in,” Nature, vol. 514, no. 7523. Springer Nature, pp. 441–442, 2014.' ista: 'Sixt MK, Vaahtomeri K. 2014. Physiology: Relax and come in. Nature. 514(7523), 441–442.' mla: 'Sixt, Michael K., and Kari Vaahtomeri. “Physiology: Relax and Come In.” Nature, vol. 514, no. 7523, Springer Nature, 2014, pp. 441–42, doi:10.1038/514441a.' short: M.K. Sixt, K. Vaahtomeri, Nature 514 (2014) 441–442. date_created: 2018-12-11T11:54:30Z date_published: 2014-10-23T00:00:00Z date_updated: 2021-01-12T06:53:47Z day: '23' department: - _id: MiSi doi: 10.1038/514441a intvolume: ' 514' issue: '7523' language: - iso: eng month: '10' oa_version: None page: 441 - 442 publication: Nature publication_status: published publisher: Springer Nature publist_id: '5219' quality_controlled: '1' scopus_import: 1 status: public title: 'Physiology: Relax and come in' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 514 year: '2014' ... --- _id: '1886' 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.' article_number: e03722 author: - first_name: Ann full_name: Hermundstad, Ann last_name: Hermundstad - first_name: John full_name: Briguglio, John last_name: Briguglio - first_name: Mary full_name: Conte, Mary last_name: Conte - first_name: Jonathan full_name: Victor, Jonathan last_name: Victor - first_name: Vijay full_name: Balasubramanian, Vijay last_name: Balasubramanian - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. Variance predicts salience in central sensory processing. eLife. 2014;(November). doi:10.7554/eLife.03722 apa: Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., & Tkačik, G. (2014). Variance predicts salience in central sensory processing. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.03722 chicago: Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.03722. ieee: A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” eLife, no. November. eLife Sciences Publications, 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. mla: Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722. short: A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014). date_created: 2018-12-11T11:54:32Z date_published: 2014-11-14T00:00:00Z date_updated: 2021-01-12T06:53:50Z day: '14' ddc: - '570' department: - _id: GaTk doi: 10.7554/eLife.03722 file: - access_level: open_access checksum: 766ac8999ac6e3364f10065a06024b8f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:04Z date_updated: 2020-07-14T12:45:20Z file_id: '4922' file_name: IST-2016-420-v1+1_e03722.full.pdf file_size: 5117086 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' issue: November language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '5209' pubrep_id: '420' quality_controlled: '1' scopus_import: 1 status: public title: Variance predicts salience in central sensory processing tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1890' 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. 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' author: - first_name: Christof full_name: Körner, Christof last_name: Körner - first_name: Verena full_name: Braunstein, Verena last_name: Braunstein - first_name: Matthias full_name: Stangl, Matthias last_name: Stangl - first_name: Alois full_name: Schlögl, Alois id: 45BF87EE-F248-11E8-B48F-1D18A9856A87 last_name: Schlögl orcid: 0000-0002-5621-8100 - first_name: Christa full_name: Neuper, Christa last_name: Neuper - first_name: Anja full_name: Ischebeck, Anja last_name: Ischebeck 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. Psychophysiology. 2014;51(4):385-395. doi:10.1111/psyp.12062' apa: '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. Wiley-Blackwell. https://doi.org/10.1111/psyp.12062' 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.” Psychophysiology. Wiley-Blackwell, 2014. https://doi.org/10.1111/psyp.12062.' 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,” Psychophysiology, 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.' mla: 'Körner, Christof, et al. “Sequential Effects in Continued Visual Search: Using Fixation-Related Potentials to Compare Distractor Processing before and after Target Detection.” Psychophysiology, vol. 51, no. 4, Wiley-Blackwell, 2014, pp. 385–95, doi:10.1111/psyp.12062.' short: C. Körner, V. Braunstein, M. Stangl, A. Schlögl, C. Neuper, A. Ischebeck, Psychophysiology 51 (2014) 385–395. date_created: 2018-12-11T11:54:34Z date_published: 2014-02-11T00:00:00Z date_updated: 2021-01-12T06:53:52Z day: '11' ddc: - '000' department: - _id: ScienComp - _id: PeJo doi: 10.1111/psyp.12062 file: - access_level: open_access checksum: 4255b6185e774acce1d99f8e195c564d content_type: application/pdf creator: system date_created: 2018-12-12T10:16:44Z date_updated: 2020-07-14T12:45:20Z file_id: '5233' file_name: IST-2016-442-v1+1_K-rner_et_al-2014-Psychophysiology.pdf file_size: 543243 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 51' issue: '4' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 385 - 395 publication: Psychophysiology publication_status: published publisher: Wiley-Blackwell publist_id: '5205' pubrep_id: '442' scopus_import: 1 status: public title: 'Sequential effects in continued visual search: Using fixation-related potentials to compare distractor processing before and after target detection' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2014' ... --- _id: '1892' abstract: - lang: eng 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. 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." article_number: '20140253' article_processing_charge: No article_type: original author: - first_name: Sabine full_name: Ocana, Sabine last_name: Ocana - first_name: Patrick full_name: Meidl, Patrick id: 4709BCE6-F248-11E8-B48F-1D18A9856A87 last_name: Meidl - first_name: Danielle full_name: Bonfils, Danielle last_name: Bonfils - first_name: Michael full_name: Taborsky, Michael last_name: Taborsky citation: ama: Ocana S, Meidl P, Bonfils D, Taborsky M. 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. 2014;281(1794). doi:10.1098/rspb.2014.0253 apa: 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. The Royal Society. https://doi.org/10.1098/rspb.2014.0253 chicago: Ocana, Sabine, Patrick Meidl, Danielle Bonfils, and Michael Taborsky. “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. The Royal Society, 2014. https://doi.org/10.1098/rspb.2014.0253. ieee: S. Ocana, P. Meidl, D. Bonfils, and M. Taborsky, “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, vol. 281, no. 1794. The Royal Society, 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. mla: Ocana, Sabine, et al. “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, vol. 281, no. 1794, 20140253, The Royal Society, 2014, doi:10.1098/rspb.2014.0253. short: S. Ocana, P. Meidl, D. Bonfils, M. Taborsky, Proceedings of the Royal Society of London Series B Biological Sciences 281 (2014). date_created: 2018-12-11T11:54:34Z date_published: 2014-11-07T00:00:00Z date_updated: 2022-06-07T09:12:32Z day: '07' department: - _id: CampIT doi: 10.1098/rspb.2014.0253 external_id: pmid: - '25232141' intvolume: ' 281' issue: '1794' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4211437/ month: '11' oa: 1 oa_version: Submitted Version pmid: 1 publication: Proceedings of the Royal Society of London Series B Biological Sciences publication_status: published publisher: The Royal Society publist_id: '5203' quality_controlled: '1' scopus_import: '1' status: public title: Y-linked Mendelian inheritance of giant and dwarf male morphs in shell-brooding cichlids type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 281 year: '2014' ... --- _id: '1891' 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. acknowledgement: Grant Nr. 2011/01/N/ST3/02475 author: - first_name: Mateusz full_name: Chwastyk, Mateusz last_name: Chwastyk - first_name: Albert full_name: Galera Prat, Albert last_name: Galera Prat - first_name: Mateusz K full_name: Sikora, Mateusz K id: 2F74BCDE-F248-11E8-B48F-1D18A9856A87 last_name: Sikora - first_name: Àngel full_name: Gómez Sicilia, Àngel last_name: Gómez Sicilia - first_name: Mariano full_name: Carrión Vázquez, Mariano last_name: Carrión Vázquez - first_name: Marek full_name: Cieplak, Marek last_name: Cieplak citation: 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. Proteins: Structure, Function and Bioinformatics. 2014;82(5):717-726. doi:10.1002/prot.24436' apa: 'Chwastyk, M., Galera Prat, A., Sikora, M. K., Gómez Sicilia, À., Carrión Vázquez, M., & Cieplak, M. (2014). Theoretical tests of the mechanical protection strategy in protein nanomechanics. Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell. https://doi.org/10.1002/prot.24436' 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.” Proteins: Structure, Function and Bioinformatics. Wiley-Blackwell, 2014. https://doi.org/10.1002/prot.24436.' 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,” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5. Wiley-Blackwell, pp. 717–726, 2014.' 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.' mla: 'Chwastyk, Mateusz, et al. “Theoretical Tests of the Mechanical Protection Strategy in Protein Nanomechanics.” Proteins: Structure, Function and Bioinformatics, vol. 82, no. 5, Wiley-Blackwell, 2014, pp. 717–26, doi:10.1002/prot.24436.' 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.' date_created: 2018-12-11T11:54:34Z date_published: 2014-05-01T00:00:00Z date_updated: 2021-01-12T06:53:52Z day: '01' department: - _id: CaHe doi: 10.1002/prot.24436 intvolume: ' 82' issue: '5' language: - iso: eng month: '05' oa_version: None page: 717 - 726 publication: 'Proteins: Structure, Function and Bioinformatics' publication_status: published publisher: Wiley-Blackwell publist_id: '5204' scopus_import: 1 status: public title: Theoretical tests of the mechanical protection strategy in protein nanomechanics type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2014' ... --- _id: '1884' 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. author: - first_name: Dan full_name: Landau, Dan last_name: Landau - first_name: Chip full_name: Stewart, Chip last_name: Stewart - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Michael full_name: Lawrence, Michael last_name: Lawrence - first_name: Carrie full_name: Sougnez, Carrie last_name: Sougnez - first_name: Jennifer full_name: Brown, Jennifer last_name: Brown - first_name: Armando full_name: Lopez Guillermo, Armando last_name: Lopez Guillermo - first_name: Stacey full_name: Gabriel, Stacey last_name: Gabriel - first_name: Eric full_name: Lander, Eric last_name: Lander - first_name: Donna full_name: Neuberg, Donna last_name: Neuberg - first_name: Carlos full_name: López Otín, Carlos last_name: López Otín - first_name: Elias full_name: Campo, Elias last_name: Campo - first_name: Gad full_name: Getz, Gad last_name: Getz - first_name: Catherine full_name: Wu, Catherine last_name: Wu citation: 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. Blood. 2014;124(21):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. Blood. American Society of Hematology.' 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.” Blood. American Society of Hematology, 2014.' ieee: 'D. Landau 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,” Blood, vol. 124, no. 21. American Society of Hematology, pp. 1952–1952, 2014.' 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.' 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.” Blood, vol. 124, no. 21, American Society of Hematology, 2014, pp. 1952–1952.' 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. date_created: 2018-12-11T11:54:32Z date_published: 2014-12-04T00:00:00Z date_updated: 2021-01-12T06:53:50Z day: '04' department: - _id: KrCh intvolume: ' 124' issue: '21' language: - iso: eng main_file_link: - url: http://www.bloodjournal.org/content/124/21/1952?sso-checked=true month: '12' oa_version: None page: 1952 - 1952 publication: Blood publication_status: published publisher: American Society of Hematology publist_id: '5211' status: public 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' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 124 year: '2014' ... --- _id: '1889' abstract: - lang: eng 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. 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' article_processing_charge: No article_type: original author: - first_name: Gerhard full_name: Bräunlich, Gerhard last_name: Bräunlich - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Bräunlich G, Hainzl C, Seiringer R. Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. 2014;26(7). doi:10.1142/S0129055X14500123 apa: Bräunlich, G., Hainzl, C., & Seiringer, R. (2014). Translation-invariant quasi-free states for fermionic systems and the BCS approximation. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X14500123 chicago: Bräunlich, Gerhard, Christian Hainzl, and Robert Seiringer. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X14500123. ieee: G. Bräunlich, C. Hainzl, and R. Seiringer, “Translation-invariant quasi-free states for fermionic systems and the BCS approximation,” Reviews in Mathematical Physics, vol. 26, no. 7. World Scientific Publishing, 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. mla: Bräunlich, Gerhard, et al. “Translation-Invariant Quasi-Free States for Fermionic Systems and the BCS Approximation.” Reviews in Mathematical Physics, vol. 26, no. 7, 1450012, World Scientific Publishing, 2014, doi:10.1142/S0129055X14500123. short: G. Bräunlich, C. Hainzl, R. Seiringer, Reviews in Mathematical Physics 26 (2014). date_created: 2018-12-11T11:54:33Z date_published: 2014-08-01T00:00:00Z date_updated: 2022-06-07T09:03:09Z day: '01' department: - _id: RoSe doi: 10.1142/S0129055X14500123 external_id: arxiv: - '1305.5135' intvolume: ' 26' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1305.5135 month: '08' oa: 1 oa_version: Submitted Version publication: Reviews in Mathematical Physics publication_status: published publisher: World Scientific Publishing publist_id: '5206' quality_controlled: '1' scopus_import: '1' status: public title: Translation-invariant quasi-free states for fermionic systems and the BCS approximation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2014' ... --- _id: '1894' abstract: - lang: eng 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.' article_number: e106247 author: - first_name: Anna full_name: Grabowska, Anna last_name: Grabowska - first_name: Ewa full_name: Wywiał, Ewa last_name: Wywiał - first_name: Stanislaw full_name: Dunin Horkawicz, Stanislaw last_name: Dunin Horkawicz - first_name: Anna full_name: Łasica, Anna last_name: Łasica - first_name: Marc full_name: Wösten, Marc last_name: Wösten - first_name: Anna A full_name: Nagy-Staron, Anna A id: 3ABC5BA6-F248-11E8-B48F-1D18A9856A87 last_name: Nagy-Staron - first_name: Renata full_name: Godlewska, Renata last_name: Godlewska - first_name: Katarzyna full_name: Bocian Ostrzycka, Katarzyna last_name: Bocian Ostrzycka - first_name: Katarzyna full_name: Pieńkowska, Katarzyna last_name: Pieńkowska - first_name: Paweł full_name: Łaniewski, Paweł last_name: Łaniewski - first_name: Janusz full_name: Bujnicki, Janusz last_name: Bujnicki - first_name: Jos full_name: Van Putten, Jos last_name: Van Putten - first_name: Elzbieta full_name: Jagusztyn Krynicka, Elzbieta last_name: Jagusztyn Krynicka citation: 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. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0106247 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. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0106247 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.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0106247. ieee: A. Grabowska et al., “Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014. 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. mla: Grabowska, Anna, et al. “Functional and Bioinformatics Analysis of Two Campylobacter Jejuni Homologs of the Thiol-Disulfide Oxidoreductase, DsbA.” PLoS One, vol. 9, no. 9, e106247, Public Library of Science, 2014, doi:10.1371/journal.pone.0106247. 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). date_created: 2018-12-11T11:54:35Z date_published: 2014-09-02T00:00:00Z date_updated: 2021-01-12T06:53:54Z day: '02' ddc: - '570' department: - _id: CaGu doi: 10.1371/journal.pone.0106247 file: - access_level: open_access checksum: 7d02c3da7f72b82bb5d7932d80c3251f content_type: application/pdf creator: system date_created: 2018-12-12T10:16:19Z date_updated: 2020-07-14T12:45:20Z file_id: '5205' file_name: IST-2016-438-v1+1_journal.pone.0106247.pdf file_size: 4248801 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 9' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '5201' pubrep_id: '438' quality_controlled: '1' scopus_import: 1 status: public title: Functional and bioinformatics analysis of two Campylobacter jejuni homologs of the thiol-disulfide oxidoreductase, DsbA tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '1895' abstract: - lang: eng text: Major histocompatibility complex class I (MHCI) molecules were recently identified as novel regulators of synaptic plasticity. These molecules are expressed in various brain areas, especially in regions undergoing activity-dependent synaptic plasticity, but their role in the nucleus accumbens (NAc) is unknown. In this study, we investigated the effects of genetic disruption of MHCI function, through deletion of β2-microblobulin, which causes lack of cell surface expression of MHCI. First, we confirmed that MHCI molecules are expressed in the NAc core in wild-type mice. Second, we performed electrophysiological recordings with NAc core slices from wild-type and β2-microglobulin knock-out mice lacking cell surface expression of MHCI. We found that low frequency stimulation induced long-term depression in wild-type but not knock-out mice, whereas high frequency stimulation induced long-term potentiation in both genotypes, with a larger magnitude in knock-out mice. Furthermore, we demonstrated that knock-out mice showed more persistent behavioral sensitization to cocaine, which is a NAc-related behavior. Using this model, we analyzed the density of total AMPA receptors and their subunits GluR1 and GluR2 in the NAc core, by SDS-digested freeze-fracture replica labeling. After repeated cocaine exposure, the density of GluR1 was increased, but there was no change in total AMPA receptors and GluR2 levels in wildtype mice. In contrast, following repeated cocaine exposure, increased densities of total AMPA receptors, GluR1 and GluR2 were observed in knock-out mice. These results indicate that functional deficiency of MHCI enhances synaptic potentiation, induced by electrical and pharmacological stimulation. acknowledgement: This work was supported in part by a Grant-in-Aid for Scientific Research on Innovative Areas (Comprehensive Brain Science Network) and (B) 17330153, from the Ministry of Education, Culture, Sports, Science and Technology of Japan. article_number: e107099 author: - first_name: Mitsuhiro full_name: Edamura, Mitsuhiro last_name: Edamura - first_name: Gen full_name: Murakami, Gen last_name: Murakami - first_name: Hongrui full_name: Meng, Hongrui last_name: Meng - first_name: Makoto full_name: Itakura, Makoto last_name: Itakura - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Atsuo full_name: Fukuda, Atsuo last_name: Fukuda - first_name: Daiichiro full_name: Nakahara, Daiichiro last_name: Nakahara citation: ama: Edamura M, Murakami G, Meng H, et al. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 2014;9(9). doi:10.1371/journal.pone.0107099 apa: Edamura, M., Murakami, G., Meng, H., Itakura, M., Shigemoto, R., Fukuda, A., & Nakahara, D. (2014). Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0107099 chicago: Edamura, Mitsuhiro, Gen Murakami, Hongrui Meng, Makoto Itakura, Ryuichi Shigemoto, Atsuo Fukuda, and Daiichiro Nakahara. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One. Public Library of Science, 2014. https://doi.org/10.1371/journal.pone.0107099. ieee: M. Edamura et al., “Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice,” PLoS One, vol. 9, no. 9. Public Library of Science, 2014. ista: Edamura M, Murakami G, Meng H, Itakura M, Shigemoto R, Fukuda A, Nakahara D. 2014. Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice. PLoS One. 9(9), e107099. mla: Edamura, Mitsuhiro, et al. “Functional Deficiency of MHC Class i Enhances LTP and Abolishes LTD in the Nucleus Accumbens of Mice.” PLoS One, vol. 9, no. 9, e107099, Public Library of Science, 2014, doi:10.1371/journal.pone.0107099. short: M. Edamura, G. Murakami, H. Meng, M. Itakura, R. Shigemoto, A. Fukuda, D. Nakahara, PLoS One 9 (2014). date_created: 2018-12-11T11:54:35Z date_published: 2014-09-30T00:00:00Z date_updated: 2021-01-12T06:53:54Z day: '30' ddc: - '570' department: - _id: RySh doi: 10.1371/journal.pone.0107099 file: - access_level: open_access checksum: 1f3be936be93114596d61ba44cacee69 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:01Z date_updated: 2020-07-14T12:45:20Z file_id: '4724' file_name: IST-2016-439-v1+1_journal.pone.0107099.pdf file_size: 6262085 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 9' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '5200' pubrep_id: '439' scopus_import: 1 status: public title: Functional deficiency of MHC class i enhances LTP and abolishes LTD in the nucleus accumbens of mice tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2014' ... --- _id: '1893' abstract: - lang: eng 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. acknowledgement: This work was supported by grants from the Research Foundation-Flanders (Odysseus). author: - first_name: Petra full_name: Nováková, Petra id: 44E59624-F248-11E8-B48F-1D18A9856A87 last_name: Nováková - first_name: Sibylle full_name: Hirsch, Sibylle last_name: Hirsch - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Ringo full_name: Van Wijk, Ringo last_name: Van Wijk - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Mareike full_name: Heilmann, Mareike last_name: Heilmann - first_name: Jennifer full_name: Lerche, Jennifer last_name: Lerche - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Mugurel full_name: Feraru, Mugurel last_name: Feraru - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Marc full_name: Van Montagu, Marc last_name: Van Montagu - first_name: Ingo full_name: Heilmann, Ingo last_name: Heilmann - first_name: Teun full_name: Munnik, Teun last_name: Munnik - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Marhavá P, Hirsch S, Feraru E, et al. SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis. PNAS. 2014;111(7):2818-2823. doi:10.1073/pnas.1324264111 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. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1324264111 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.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1324264111. ieee: P. Marhavá et al., “SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis,” PNAS, vol. 111, no. 7. National Academy of Sciences, pp. 2818–2823, 2014. 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. mla: Marhavá, Petra, et al. “SAC Phosphoinositide Phosphatases at the Tonoplast Mediate Vacuolar Function in Arabidopsis.” PNAS, vol. 111, no. 7, National Academy of Sciences, 2014, pp. 2818–23, doi:10.1073/pnas.1324264111. 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. date_created: 2018-12-11T11:54:34Z date_published: 2014-02-18T00:00:00Z date_updated: 2021-01-12T06:53:53Z day: '18' department: - _id: JiFr doi: 10.1073/pnas.1324264111 ec_funded: 1 intvolume: ' 111' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3932866/ month: '02' oa: 1 oa_version: Submitted Version page: 2818 - 2823 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5202' scopus_import: 1 status: public title: SAC phosphoinositide phosphatases at the tonoplast mediate vacuolar function in Arabidopsis type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '1896' abstract: - lang: eng text: 'Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.' acknowledgement: The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.). article_number: '032701' article_processing_charge: No author: - first_name: Richard full_name: Kollár, Richard last_name: Kollár - first_name: Katarína full_name: Bod'ová, Katarína id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bod'ová orcid: 0000-0002-7214-0171 - first_name: Jozef full_name: Nosek, Jozef last_name: Nosek - first_name: Ľubomír full_name: Tomáška, Ľubomír last_name: Tomáška citation: ama: Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701 apa: Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701 chicago: Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.032701. ieee: R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014. ista: Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701. mla: Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701. short: R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014). date_created: 2018-12-11T11:54:35Z date_published: 2014-03-04T00:00:00Z date_updated: 2022-08-01T10:50:10Z day: '04' department: - _id: NiBa - _id: GaTk doi: 10.1103/PhysRevE.89.032701 intvolume: ' 89' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.0430 month: '03' oa: 1 oa_version: Submitted Version publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '5198' scopus_import: '1' status: public title: Mathematical model of alternative mechanism of telomere length maintenance type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2014' ... --- _id: '1897' abstract: - lang: eng text: GNOM is one of the most characterized membrane trafficking regulators in plants, with crucial roles in development. GNOM encodes an ARF-guanine nucleotide exchange factor (ARF-GEF) that activates small GTPases of the ARF (ADP ribosylation factor) class to mediate vesicle budding at endomembranes. The crucial role of GNOM in recycling of PIN auxin transporters and other proteins to the plasma membrane was identified in studies using the ARF-GEF inhibitor brefeldin A (BFA). GNOM, the most prominent regulator of recycling in plants, has been proposed to act and localize at so far elusive recycling endosomes. Here, we report the GNOM localization in context of its cellular function in Arabidopsis thaliana. State-of-the-art imaging, pharmacological interference, and ultrastructure analysis show that GNOM predominantly localizes to Golgi apparatus. Super-resolution confocal live imaging microscopy identified GNOM and its closest homolog GNOM-like 1 at distinct subdomains on Golgi cisternae. Short-term BFA treatment stabilizes GNOM at the Golgi apparatus, whereas prolonged exposures results in GNOM translocation to trans-Golgi network (TGN)/early endosomes (EEs). Malformed TGN/EE in gnom mutants suggests a role for GNOM in maintaining TGN/EE function. Our results redefine the subcellular action of GNOM and reevaluate the identity and function of recycling endosomes in plants. acknowledgement: This work was supported by the Odysseus Program of the Research Foundation-Flanders (J.F.). author: - first_name: Satoshi full_name: Naramoto, Satoshi last_name: Naramoto - first_name: Marisa full_name: Otegui, Marisa last_name: Otegui - first_name: Natsumaro full_name: Kutsuna, Natsumaro last_name: Kutsuna - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Tomoko full_name: Dainobu, Tomoko last_name: Dainobu - first_name: Michael full_name: Karampelias, Michael last_name: Karampelias - first_name: Masaru full_name: Fujimoto, Masaru last_name: Fujimoto - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Daisuke full_name: Miki, Daisuke last_name: Miki - first_name: Hiroo full_name: Fukuda, Hiroo last_name: Fukuda - first_name: Akihiko full_name: Nakano, Akihiko last_name: Nakano - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Naramoto S, Otegui M, Kutsuna N, et al. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 2014;26(7):3062-3076. doi:10.1105/tpc.114.125880 apa: Naramoto, S., Otegui, M., Kutsuna, N., De Rycke, R., Dainobu, T., Karampelias, M., … Friml, J. (2014). Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.125880 chicago: Naramoto, Satoshi, Marisa Otegui, Natsumaro Kutsuna, Riet De Rycke, Tomoko Dainobu, Michael Karampelias, Masaru Fujimoto, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.125880. ieee: S. Naramoto et al., “Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis,” Plant Cell, vol. 26, no. 7. American Society of Plant Biologists, pp. 3062–3076, 2014. ista: Naramoto S, Otegui M, Kutsuna N, De Rycke R, Dainobu T, Karampelias M, Fujimoto M, Feraru E, Miki D, Fukuda H, Nakano A, Friml J. 2014. Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis. Plant Cell. 26(7), 3062–3076. mla: Naramoto, Satoshi, et al. “Insights into the Localization and Function of the Membrane Trafficking Regulator GNOM ARF-GEF at the Golgi Apparatus in Arabidopsis.” Plant Cell, vol. 26, no. 7, American Society of Plant Biologists, 2014, pp. 3062–76, doi:10.1105/tpc.114.125880. short: S. Naramoto, M. Otegui, N. Kutsuna, R. De Rycke, T. Dainobu, M. Karampelias, M. Fujimoto, E. Feraru, D. Miki, H. Fukuda, A. Nakano, J. Friml, Plant Cell 26 (2014) 3062–3076. date_created: 2018-12-11T11:54:36Z date_published: 2014-07-01T00:00:00Z date_updated: 2021-01-12T06:53:55Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.114.125880 intvolume: ' 26' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4145132/ month: '07' oa: 1 oa_version: Submitted Version page: 3062 - 3076 publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '5199' scopus_import: 1 status: public title: Insights into the localization and function of the membrane trafficking regulator GNOM ARF-GEF at the Golgi apparatus in Arabidopsis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2014' ... --- _id: '1899' abstract: - lang: eng text: Asymmetric cell divisions allow stem cells to balance proliferation and differentiation. During embryogenesis, murine epidermis expands rapidly from a single layer of unspecified basal layer progenitors to a stratified, differentiated epithelium. Morphogenesis involves perpendicular (asymmetric) divisions and the spindle orientation protein LGN, but little is known about how the apical localization of LGN is regulated. Here, we combine conventional genetics and lentiviral-mediated in vivo RNAi to explore the functions of the LGN-interacting proteins Par3, mInsc and Gα i3. Whereas loss of each gene alone leads to randomized division angles, combined loss of Gnai3 and mInsc causes a phenotype of mostly planar divisions, akin to loss of LGN. These findings lend experimental support for the hitherto untested model that Par3-mInsc and Gα i3 act cooperatively to polarize LGN and promote perpendicular divisions. Finally, we uncover a developmental switch between delamination-driven early stratification and spindle-orientation-dependent differentiation that occurs around E15, revealing a two-step mechanism underlying epidermal maturation. article_processing_charge: No article_type: original author: - first_name: Scott full_name: Williams, Scott last_name: Williams - first_name: Lyndsay full_name: Ratliff, Lyndsay last_name: Ratliff - first_name: Maria P full_name: Postiglione, Maria P id: 2C67902A-F248-11E8-B48F-1D18A9856A87 last_name: Postiglione - first_name: Juergen full_name: Knoblich, Juergen last_name: Knoblich - first_name: Elaine full_name: Fuchs, Elaine last_name: Fuchs citation: ama: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 2014;16(8):758-769. doi:10.1038/ncb3001 apa: Williams, S., Ratliff, L., Postiglione, M. P., Knoblich, J., & Fuchs, E. (2014). Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb3001 chicago: Williams, Scott, Lyndsay Ratliff, Maria P Postiglione, Juergen Knoblich, and Elaine Fuchs. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb3001. ieee: S. Williams, L. Ratliff, M. P. Postiglione, J. Knoblich, and E. Fuchs, “Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN,” Nature Cell Biology, vol. 16, no. 8. Nature Publishing Group, pp. 758–769, 2014. ista: Williams S, Ratliff L, Postiglione MP, Knoblich J, Fuchs E. 2014. Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN. Nature Cell Biology. 16(8), 758–769. mla: Williams, Scott, et al. “Par3-MInsc and Gα I3 Cooperate to Promote Oriented Epidermal Cell Divisions through LGN.” Nature Cell Biology, vol. 16, no. 8, Nature Publishing Group, 2014, pp. 758–69, doi:10.1038/ncb3001. short: S. Williams, L. Ratliff, M.P. Postiglione, J. Knoblich, E. Fuchs, Nature Cell Biology 16 (2014) 758–769. date_created: 2018-12-11T11:54:36Z date_published: 2014-07-13T00:00:00Z date_updated: 2021-01-12T06:53:55Z day: '13' department: - _id: SiHi doi: 10.1038/ncb3001 external_id: pmid: - '25016959' intvolume: ' 16' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4159251/ month: '07' oa: 1 oa_version: Submitted Version page: 758 - 769 pmid: 1 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '5196' quality_controlled: '1' scopus_import: 1 status: public title: Par3-mInsc and Gα i3 cooperate to promote oriented epidermal cell divisions through LGN type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2014' ... --- _id: '1898' abstract: - lang: eng text: Fast synaptic transmission is important for rapid information processing. To explore the maximal rate of neuronal signaling and to analyze the presynaptic mechanisms, we focused on the input layer of the cerebellar cortex, where exceptionally high action potential (AP) frequencies have been reported invivo. With paired recordings between presynaptic cerebellar mossy fiber boutons and postsynaptic granule cells, we demonstrate reliable neurotransmission upto ~1 kHz. Presynaptic APs are ultrafast, with ~100μs half-duration. Both Kv1 and Kv3 potassium channels mediate the fast repolarization, rapidly inactivating sodium channels ensure metabolic efficiency, and little AP broadening occurs during bursts of up to 1.5 kHz. Presynaptic Cav2.1 (P/Q-type) calcium channels open efficiently during ultrafast APs. Furthermore, a subset of synaptic vesicles is tightly coupled to Ca2+ channels, and vesicles are rapidly recruited to the release site. These data reveal mechanisms of presynaptic AP generation and transmitter release underlying neuronal kHz signaling. author: - first_name: Andreas full_name: Ritzau Jost, Andreas last_name: Ritzau Jost - first_name: Igor full_name: Delvendahl, Igor last_name: Delvendahl - first_name: Annika full_name: Rings, Annika last_name: Rings - first_name: Niklas full_name: Byczkowicz, Niklas last_name: Byczkowicz - first_name: Harumi full_name: Harada, Harumi id: 2E55CDF2-F248-11E8-B48F-1D18A9856A87 last_name: Harada orcid: 0000-0001-7429-7896 - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Johannes full_name: Hirrlinger, Johannes last_name: Hirrlinger - first_name: Jens full_name: Eilers, Jens last_name: Eilers - first_name: Stefan full_name: Hallermann, Stefan last_name: Hallermann citation: ama: Ritzau Jost A, Delvendahl I, Rings A, et al. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 2014;84(1):152-163. doi:10.1016/j.neuron.2014.08.036 apa: Ritzau Jost, A., Delvendahl, I., Rings, A., Byczkowicz, N., Harada, H., Shigemoto, R., … Hallermann, S. (2014). Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2014.08.036 chicago: Ritzau Jost, Andreas, Igor Delvendahl, Annika Rings, Niklas Byczkowicz, Harumi Harada, Ryuichi Shigemoto, Johannes Hirrlinger, Jens Eilers, and Stefan Hallermann. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron. Elsevier, 2014. https://doi.org/10.1016/j.neuron.2014.08.036. ieee: A. Ritzau Jost et al., “Ultrafast action potentials mediate kilohertz signaling at a central synapse,” Neuron, vol. 84, no. 1. Elsevier, pp. 152–163, 2014. ista: Ritzau Jost A, Delvendahl I, Rings A, Byczkowicz N, Harada H, Shigemoto R, Hirrlinger J, Eilers J, Hallermann S. 2014. Ultrafast action potentials mediate kilohertz signaling at a central synapse. Neuron. 84(1), 152–163. mla: Ritzau Jost, Andreas, et al. “Ultrafast Action Potentials Mediate Kilohertz Signaling at a Central Synapse.” Neuron, vol. 84, no. 1, Elsevier, 2014, pp. 152–63, doi:10.1016/j.neuron.2014.08.036. short: A. Ritzau Jost, I. Delvendahl, A. Rings, N. Byczkowicz, H. Harada, R. Shigemoto, J. Hirrlinger, J. Eilers, S. Hallermann, Neuron 84 (2014) 152–163. date_created: 2018-12-11T11:54:36Z date_published: 2014-10-01T00:00:00Z date_updated: 2021-01-12T06:53:55Z day: '01' department: - _id: RySh doi: 10.1016/j.neuron.2014.08.036 intvolume: ' 84' issue: '1' language: - iso: eng month: '10' oa_version: None page: 152 - 163 publication: Neuron publication_status: published publisher: Elsevier publist_id: '5197' quality_controlled: '1' scopus_import: 1 status: public title: Ultrafast action potentials mediate kilohertz signaling at a central synapse type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 84 year: '2014' ... --- _id: '1906' abstract: - lang: eng text: In this paper, we introduce a novel scene representation for the visualization of large-scale point clouds accompanied by a set of high-resolution photographs. Many real-world applications deal with very densely sampled point-cloud data, which are augmented with photographs that often reveal lighting variations and inaccuracies in registration. Consequently, the high-quality representation of the captured data, i.e., both point clouds and photographs together, is a challenging and time-consuming task. We propose a two-phase approach, in which the first (preprocessing) phase generates multiple overlapping surface patches and handles the problem of seamless texture generation locally for each patch. The second phase stitches these patches at render-time to produce a high-quality visualization of the data. As a result of the proposed localization of the global texturing problem, our algorithm is more than an order of magnitude faster than equivalent mesh-based texturing techniques. Furthermore, since our preprocessing phase requires only a minor fraction of the whole data set at once, we provide maximum flexibility when dealing with growing data sets. acknowledgement: This research was supported by the Austrian Research Promotion Agency (FFG) project REPLICATE (no. 835948), the EU FP7 project HARVEST4D (no. 323567). author: - first_name: Murat full_name: Arikan, Murat last_name: Arikan - first_name: Reinhold full_name: Preiner, Reinhold last_name: Preiner - first_name: Claus full_name: Scheiblauer, Claus last_name: Scheiblauer - first_name: Stefan full_name: Jeschke, Stefan id: 44D6411A-F248-11E8-B48F-1D18A9856A87 last_name: Jeschke - first_name: Michael full_name: Wimmer, Michael last_name: Wimmer citation: ama: Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 2014;20(9):1280-1292. doi:10.1109/TVCG.2014.2312011 apa: Arikan, M., Preiner, R., Scheiblauer, C., Jeschke, S., & Wimmer, M. (2014). Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2312011 chicago: Arikan, Murat, Reinhold Preiner, Claus Scheiblauer, Stefan Jeschke, and Michael Wimmer. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2312011. ieee: M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, and M. Wimmer, “Large-scale point-cloud visualization through localized textured surface reconstruction,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9. IEEE, pp. 1280–1292, 2014. ista: Arikan M, Preiner R, Scheiblauer C, Jeschke S, Wimmer M. 2014. Large-scale point-cloud visualization through localized textured surface reconstruction. IEEE Transactions on Visualization and Computer Graphics. 20(9), 1280–1292. mla: Arikan, Murat, et al. “Large-Scale Point-Cloud Visualization through Localized Textured Surface Reconstruction.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 9, IEEE, 2014, pp. 1280–92, doi:10.1109/TVCG.2014.2312011. short: M. Arikan, R. Preiner, C. Scheiblauer, S. Jeschke, M. Wimmer, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 1280–1292. date_created: 2018-12-11T11:54:39Z date_published: 2014-09-09T00:00:00Z date_updated: 2021-01-12T06:53:59Z day: '09' ddc: - '000' department: - _id: ChWo doi: 10.1109/TVCG.2014.2312011 file: - access_level: open_access checksum: 5bf58942d2eb20adf03c7f9ea2e68124 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:41Z date_updated: 2020-07-14T12:45:20Z file_id: '5297' file_name: IST-2016-573-v1+1_arikan-2014-pcvis-draft.pdf file_size: 13594598 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 20' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 1280 - 1292 project: - _id: 25357BD2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 24352-N23 name: 'Deep Pictures: Creating Visual and Haptic Vector Images' publication: IEEE Transactions on Visualization and Computer Graphics publication_status: published publisher: IEEE publist_id: '5189' pubrep_id: '573' scopus_import: 1 status: public title: Large-scale point-cloud visualization through localized textured surface reconstruction type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2014' ... --- _id: '1905' abstract: - lang: eng text: The unprecedented polymorphism in the major histocompatibility complex (MHC) genes is thought to be maintained by balancing selection from parasites. However, do parasites also drive divergence at MHC loci between host populations, or do the effects of balancing selection maintain similarities among populations? We examined MHC variation in populations of the livebearing fish Poecilia mexicana and characterized their parasite communities. Poecilia mexicana populations in the Cueva del Azufre system are locally adapted to darkness and the presence of toxic hydrogen sulphide, representing highly divergent ecotypes or incipient species. Parasite communities differed significantly across populations, and populations with higher parasite loads had higher levels of diversity at class II MHC genes. However, despite different parasite communities, marked divergence in adaptive traits and in neutral genetic markers, we found MHC alleles to be remarkably similar among host populations. Our findings indicate that balancing selection from parasites maintains immunogenetic diversity of hosts, but this process does not promote MHC divergence in this system. On the contrary, we suggest that balancing selection on immunogenetic loci may outweigh divergent selection causing divergence, thereby hindering host divergence and speciation. Our findings support the hypothesis that balancing selection maintains MHC similarities among lineages during and after speciation (trans-species evolution). acknowledgement: This study was funded by grants from the National Science Foundation (NSF) to MT (IOS-1121832) and IS (DEB-0743406) and from the German Science Foundation (DFG; PL 470/1-2) and ‘LOEWE − Landesoffensive zur Entwicklung wissenschaftlich-ökonomischer Exzellenz’ of Hesse's Ministry of Higher Education, Research, and the Arts, to MP. article_processing_charge: No article_type: original author: - first_name: Michael full_name: Tobler, Michael last_name: Tobler - first_name: Martin full_name: Plath, Martin last_name: Plath - first_name: Rüdiger full_name: Riesch, Rüdiger last_name: Riesch - first_name: Ingo full_name: Schlupp, Ingo last_name: Schlupp - first_name: Anna V full_name: Grasse, Anna V id: 406F989C-F248-11E8-B48F-1D18A9856A87 last_name: Grasse - first_name: Gopi full_name: Munimanda, Gopi last_name: Munimanda - first_name: C full_name: Setzer, C last_name: Setzer - first_name: Dustin full_name: Penn, Dustin last_name: Penn - first_name: Yoshan full_name: Moodley, Yoshan last_name: Moodley citation: ama: Tobler M, Plath M, Riesch R, et al. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 2014;27(5):960-974. doi:10.1111/jeb.12370 apa: Tobler, M., Plath, M., Riesch, R., Schlupp, I., Grasse, A. V., Munimanda, G., … Moodley, Y. (2014). Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. Wiley. https://doi.org/10.1111/jeb.12370 chicago: Tobler, Michael, Martin Plath, Rüdiger Riesch, Ingo Schlupp, Anna V Grasse, Gopi Munimanda, C Setzer, Dustin Penn, and Yoshan Moodley. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology. Wiley, 2014. https://doi.org/10.1111/jeb.12370. ieee: M. Tobler et al., “Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations,” Journal of Evolutionary Biology, vol. 27, no. 5. Wiley, pp. 960–974, 2014. ista: Tobler M, Plath M, Riesch R, Schlupp I, Grasse AV, Munimanda G, Setzer C, Penn D, Moodley Y. 2014. Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations. Journal of Evolutionary Biology. 27(5), 960–974. mla: Tobler, Michael, et al. “Selection from Parasites Favours Immunogenetic Diversity but Not Divergence among Locally Adapted Host Populations.” Journal of Evolutionary Biology, vol. 27, no. 5, Wiley, 2014, pp. 960–74, doi:10.1111/jeb.12370. short: M. Tobler, M. Plath, R. Riesch, I. Schlupp, A.V. Grasse, G. Munimanda, C. Setzer, D. Penn, Y. Moodley, Journal of Evolutionary Biology 27 (2014) 960–974. date_created: 2018-12-11T11:54:38Z date_published: 2014-04-12T00:00:00Z date_updated: 2022-06-07T09:22:20Z day: '12' department: - _id: SyCr doi: 10.1111/jeb.12370 external_id: pmid: - '24725091' intvolume: ' 27' issue: '5' language: - iso: eng month: '04' oa_version: None page: 960 - 974 pmid: 1 publication: Journal of Evolutionary Biology publication_identifier: eissn: - 1420-9101 issn: - 1010-061X publication_status: published publisher: Wiley publist_id: '5190' quality_controlled: '1' scopus_import: '1' status: public title: Selection from parasites favours immunogenetic diversity but not divergence among locally adapted host populations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2014' ... --- _id: '1902' abstract: - lang: eng text: In the 1960s-1980s, determination of bacterial growth rates was an important tool in microbial genetics, biochemistry, molecular biology, and microbial physiology. The exciting technical developments of the 1990s and the 2000s eclipsed that tool; as a result, many investigators today lack experience with growth rate measurements. Recently, investigators in a number of areas have started to use measurements of bacterial growth rates for a variety of purposes. Those measurements have been greatly facilitated by the availability of microwell plate readers that permit the simultaneous measurements on up to 384 different cultures. Only the exponential (logarithmic) portions of the resulting growth curves are useful for determining growth rates, and manual determination of that portion and calculation of growth rates can be tedious for high-throughput purposes. Here, we introduce the program GrowthRates that uses plate reader output files to automatically determine the exponential portion of the curve and to automatically calculate the growth rate, the maximum culture density, and the duration of the growth lag phase. GrowthRates is freely available for Macintosh, Windows, and Linux.We discuss the effects of culture volume, the classical bacterial growth curve, and the differences between determinations in rich media and minimal (mineral salts) media. This protocol covers calibration of the plate reader, growth of culture inocula for both rich and minimal media, and experimental setup. As a guide to reliability, we report typical day-to-day variation in growth rates and variation within experiments with respect to position of wells within the plates. article_processing_charge: No article_type: original author: - first_name: Barry full_name: Hall, Barry last_name: Hall - first_name: Hande full_name: Acar, Hande id: 2DDF136A-F248-11E8-B48F-1D18A9856A87 last_name: Acar orcid: 0000-0003-1986-9753 - first_name: Anna full_name: Nandipati, Anna last_name: Nandipati - first_name: Miriam full_name: Barlow, Miriam last_name: Barlow citation: ama: Hall B, Acar H, Nandipati A, Barlow M. Growth rates made easy. Molecular Biology and Evolution. 2014;31(1):232-238. doi:10.1093/molbev/mst187 apa: Hall, B., Acar, H., Nandipati, A., & Barlow, M. (2014). Growth rates made easy. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/mst187 chicago: Hall, Barry, Hande Acar, Anna Nandipati, and Miriam Barlow. “Growth Rates Made Easy.” Molecular Biology and Evolution. Oxford University Press, 2014. https://doi.org/10.1093/molbev/mst187. ieee: B. Hall, H. Acar, A. Nandipati, and M. Barlow, “Growth rates made easy,” Molecular Biology and Evolution, vol. 31, no. 1. Oxford University Press, pp. 232–238, 2014. ista: Hall B, Acar H, Nandipati A, Barlow M. 2014. Growth rates made easy. Molecular Biology and Evolution. 31(1), 232–238. mla: Hall, Barry, et al. “Growth Rates Made Easy.” Molecular Biology and Evolution, vol. 31, no. 1, Oxford University Press, 2014, pp. 232–38, doi:10.1093/molbev/mst187. short: B. Hall, H. Acar, A. Nandipati, M. Barlow, Molecular Biology and Evolution 31 (2014) 232–238. date_created: 2018-12-11T11:54:37Z date_published: 2014-01-01T00:00:00Z date_updated: 2022-06-07T11:08:13Z day: '01' department: - _id: JoBo doi: 10.1093/molbev/mst187 external_id: pmid: - '24170494' intvolume: ' 31' issue: '1' language: - iso: eng month: '01' oa_version: None page: 232 - 238 pmid: 1 publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: Oxford University Press publist_id: '5193' quality_controlled: '1' scopus_import: '1' status: public title: Growth rates made easy type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 31 year: '2014' ... --- _id: '1901' abstract: - lang: eng text: In plants, the patterning of stem cell-enriched meristems requires a graded auxin response maximum that emerges from the concerted action of polar auxin transport, auxin biosynthesis, auxin metabolism, and cellular auxin response machinery. However, mechanisms underlying this auxin response maximum-mediated root stem cell maintenance are not fully understood. Here, we present unexpected evidence that WUSCHEL-RELATED HOMEOBOX 5 (WOX5) transcription factor modulates expression of auxin biosynthetic genes in the quiescent center (QC) of the root and thus provides a robust mechanism for the maintenance of auxin response maximum in the root tip. This WOX5 action is balanced through the activity of indole-3-acetic acid 17 (IAA17) auxin response repressor. Our combined genetic, cell biology, and computational modeling studies revealed a previously uncharacterized feedback loop linking WOX5-mediated auxin production to IAA17-dependent repression of auxin responses. This WOX5-IAA17 feedback circuit further assures the maintenance of auxin response maximum in the root tip and thereby contributes to the maintenance of distal stem cell (DSC) populations. Our experimental studies and in silico computer simulations both demonstrate that the WOX5-IAA17 feedback circuit is essential for the maintenance of auxin gradient in the root tip and the auxin-mediated root DSC differentiation. acknowledgement: "This work was supported by funding from the projects CZ.1.07/2.3.00/20.0043 and CZ.1.05/1.1.00/02.0068 (to CEITEC, Central European Institute of Technology) and the Odysseus program of the Research Foundation-Flanders to J.F\r\n" author: - first_name: Huiyu full_name: Tian, Huiyu last_name: Tian - first_name: Krzysztof T full_name: Wabnik, Krzysztof T last_name: Wabnik - first_name: Tiantian full_name: Niu, Tiantian last_name: Niu - first_name: Hongjiang full_name: Li, Hongjiang last_name: Li - first_name: Qianqian full_name: Yu, Qianqian last_name: Yu - first_name: Stephan full_name: Pollmann, Stephan last_name: Pollmann - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Willy full_name: Govaerts, Willy last_name: Govaerts - first_name: Jakub full_name: Rolčík, Jakub last_name: Rolčík - first_name: Markus full_name: Geisler, Markus last_name: Geisler - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Zhaojun full_name: Ding, Zhaojun last_name: Ding citation: ama: Tian H, Wabnik KT, Niu T, et al. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 2014;7(2):277-289. doi:10.1093/mp/sst118 apa: Tian, H., Wabnik, K. T., Niu, T., Li, H., Yu, Q., Pollmann, S., … Ding, Z. (2014). WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. Oxford University Press. https://doi.org/10.1093/mp/sst118 chicago: Tian, Huiyu, Krzysztof T Wabnik, Tiantian Niu, Hongjiang Li, Qianqian Yu, Stephan Pollmann, Steffen Vanneste, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant. Oxford University Press, 2014. https://doi.org/10.1093/mp/sst118. ieee: H. Tian et al., “WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis,” Molecular Plant, vol. 7, no. 2. Oxford University Press, pp. 277–289, 2014. ista: Tian H, Wabnik KT, Niu T, Li H, Yu Q, Pollmann S, Vanneste S, Govaerts W, Rolčík J, Geisler M, Friml J, Ding Z. 2014. WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis. Molecular Plant. 7(2), 277–289. mla: Tian, Huiyu, et al. “WOX5-IAA17 Feedback Circuit-Mediated Cellular Auxin Response Is Crucial for the Patterning of Root Stem Cell Niches in Arabidopsis.” Molecular Plant, vol. 7, no. 2, Oxford University Press, 2014, pp. 277–89, doi:10.1093/mp/sst118. short: H. Tian, K.T. Wabnik, T. Niu, H. Li, Q. Yu, S. Pollmann, S. Vanneste, W. Govaerts, J. Rolčík, M. Geisler, J. Friml, Z. Ding, Molecular Plant 7 (2014) 277–289. date_created: 2018-12-11T11:54:37Z date_published: 2014-02-01T00:00:00Z date_updated: 2021-01-12T06:53:57Z day: '01' department: - _id: JiFr doi: 10.1093/mp/sst118 intvolume: ' 7' issue: '2' language: - iso: eng month: '02' oa_version: None page: 277 - 289 publication: Molecular Plant publication_status: published publisher: Oxford University Press publist_id: '5194' scopus_import: 1 status: public title: WOX5-IAA17 feedback circuit-mediated cellular auxin response is crucial for the patterning of root stem cell niches in arabidopsis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2014' ... --- _id: '1904' abstract: - lang: eng text: We prove a Strichartz inequality for a system of orthonormal functions, with an optimal behavior of the constant in the limit of a large number of functions. The estimate generalizes the usual Strichartz inequality, in the same fashion as the Lieb-Thirring inequality generalizes the Sobolev inequality. As an application, we consider the Schrödinger equation with a time-dependent potential and we show the existence of the wave operator in Schatten spaces. author: - first_name: Rupert full_name: Frank, Rupert last_name: Frank - first_name: Mathieu full_name: Lewin, Mathieu last_name: Lewin - first_name: Élliott full_name: Lieb, Élliott last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Frank R, Lewin M, Lieb É, Seiringer R. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 2014;16(7):1507-1526. doi:10.4171/JEMS/467 apa: Frank, R., Lewin, M., Lieb, É., & Seiringer, R. (2014). Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. European Mathematical Society. https://doi.org/10.4171/JEMS/467 chicago: Frank, Rupert, Mathieu Lewin, Élliott Lieb, and Robert Seiringer. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society. European Mathematical Society, 2014. https://doi.org/10.4171/JEMS/467. ieee: R. Frank, M. Lewin, É. Lieb, and R. Seiringer, “Strichartz inequality for orthonormal functions,” Journal of the European Mathematical Society, vol. 16, no. 7. European Mathematical Society, pp. 1507–1526, 2014. ista: Frank R, Lewin M, Lieb É, Seiringer R. 2014. Strichartz inequality for orthonormal functions. Journal of the European Mathematical Society. 16(7), 1507–1526. mla: Frank, Rupert, et al. “Strichartz Inequality for Orthonormal Functions.” Journal of the European Mathematical Society, vol. 16, no. 7, European Mathematical Society, 2014, pp. 1507–26, doi:10.4171/JEMS/467. short: R. Frank, M. Lewin, É. Lieb, R. Seiringer, Journal of the European Mathematical Society 16 (2014) 1507–1526. date_created: 2018-12-11T11:54:38Z date_published: 2014-08-23T00:00:00Z date_updated: 2021-01-12T06:53:58Z day: '23' department: - _id: RoSe doi: 10.4171/JEMS/467 intvolume: ' 16' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1306.1309 month: '08' oa: 1 oa_version: Submitted Version page: 1507 - 1526 project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: Journal of the European Mathematical Society publication_status: published publisher: European Mathematical Society publist_id: '5191' quality_controlled: '1' scopus_import: 1 status: public title: Strichartz inequality for orthonormal functions type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2014' ... --- _id: '1900' abstract: - lang: eng text: Epithelial cell layers need to be tightly regulated to maintain their integrity and correct function. Cell integration into epithelial sheets is now shown to depend on the N-WASP-regulated stabilization of cortical F-actin, which generates distinct patterns of apical-lateral contractility at E-cadherin-based cell-cell junctions. author: - first_name: Martin full_name: Behrndt, Martin id: 3ECECA3A-F248-11E8-B48F-1D18A9856A87 last_name: Behrndt - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Behrndt M, Heisenberg C-PJ. Lateral junction dynamics lead the way out. Nature Cell Biology. 2014;16(2):127-129. doi:10.1038/ncb2913 apa: Behrndt, M., & Heisenberg, C.-P. J. (2014). Lateral junction dynamics lead the way out. Nature Cell Biology. Nature Publishing Group. https://doi.org/10.1038/ncb2913 chicago: Behrndt, Martin, and Carl-Philipp J Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology. Nature Publishing Group, 2014. https://doi.org/10.1038/ncb2913. ieee: M. Behrndt and C.-P. J. Heisenberg, “Lateral junction dynamics lead the way out,” Nature Cell Biology, vol. 16, no. 2. Nature Publishing Group, pp. 127–129, 2014. ista: Behrndt M, Heisenberg C-PJ. 2014. Lateral junction dynamics lead the way out. Nature Cell Biology. 16(2), 127–129. mla: Behrndt, Martin, and Carl-Philipp J. Heisenberg. “Lateral Junction Dynamics Lead the Way Out.” Nature Cell Biology, vol. 16, no. 2, Nature Publishing Group, 2014, pp. 127–29, doi:10.1038/ncb2913. short: M. Behrndt, C.-P.J. Heisenberg, Nature Cell Biology 16 (2014) 127–129. date_created: 2018-12-11T11:54:37Z date_published: 2014-01-31T00:00:00Z date_updated: 2021-01-12T06:53:56Z day: '31' department: - _id: CaHe doi: 10.1038/ncb2913 intvolume: ' 16' issue: '2' language: - iso: eng month: '01' oa_version: None page: 127 - 129 publication: Nature Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '5195' quality_controlled: '1' scopus_import: 1 status: public title: Lateral junction dynamics lead the way out type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2014' ... --- _id: '1909' abstract: - lang: eng text: 'Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.' acknowledgement: 'Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1' author: - first_name: Thomas full_name: Ezard, Thomas last_name: Ezard - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Rebecca full_name: Hoyle, Rebecca last_name: Hoyle citation: ama: Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207 apa: Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207 chicago: Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207. ieee: T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014. ista: Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701. mla: Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207. short: T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701. date_created: 2018-12-11T11:54:40Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:54:00Z day: '01' ddc: - '570' department: - _id: NiBa - _id: GaTk doi: 10.1111/1365-2435.12207 file: - access_level: open_access checksum: 3cbe8623174709a8ceec2103246f8fe0 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:45Z date_updated: 2020-07-14T12:45:20Z file_id: '5167' file_name: IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf file_size: 536154 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 28' issue: '3' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 693 - 701 publication: Functional Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '5186' pubrep_id: '419' scopus_import: 1 status: public title: The fitness costs of adaptation via phenotypic plasticity and maternal effects tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2014' ... --- _id: '1910' abstract: - lang: eng text: angerhans cells (LCs) are a unique subset of dendritic cells (DCs) that express epithelial adhesion molecules, allowing them to form contacts with epithelial cells and reside in epidermal/epithelial tissues. The dynamic regulation of epithelial adhesion plays a decisive role in the life cycle of LCs. It controls whether LCs remain immature and sessile within the epidermis or mature and egress to initiate immune responses. So far, the molecular machinery regulating epithelial adhesion molecules during LC maturation remains elusive. Here, we generated pure populations of immature human LCs in vitro to systematically probe for gene-expression changes during LC maturation. LCs down-regulate a set of epithelial genes including E-cadherin, while they upregulate the mesenchymal marker N-cadherin known to facilitate cell migration. In addition, N-cadherin is constitutively expressed by monocyte-derived DCs known to exhibit characteristics of both inflammatory-type and interstitial/dermal DCs. Moreover, the transcription factors ZEB1 and ZEB2 (ZEB is zinc-finger E-box-binding homeobox) are upregulated in migratory LCs. ZEB1 and ZEB2 have been shown to induce epithelial-to-mesenchymal transition (EMT) and invasive behavior in cancer cells undergoing metastasis. Our results provide the first hint that the molecular EMT machinery might facilitate LC mobilization. Moreover, our study suggests that N-cadherin plays a role during DC migration. acknowledgement: 'FWF. Grant Number: P22058-B20' author: - first_name: Sabine full_name: Konradi, Sabine last_name: Konradi - first_name: Nighat full_name: Yasmin, Nighat last_name: Yasmin - first_name: Denise full_name: Haslwanter, Denise last_name: Haslwanter - first_name: Michele full_name: Weber, Michele id: 3A3FC708-F248-11E8-B48F-1D18A9856A87 last_name: Weber - first_name: Bernd full_name: Gesslbauer, Bernd last_name: Gesslbauer - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Herbert full_name: Strobl, Herbert last_name: Strobl citation: ama: Konradi S, Yasmin N, Haslwanter D, et al. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 2014;44(2):553-560. doi:10.1002/eji.201343681 apa: Konradi, S., Yasmin, N., Haslwanter, D., Weber, M., Gesslbauer, B., Sixt, M. K., & Strobl, H. (2014). Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. Wiley-Blackwell. https://doi.org/10.1002/eji.201343681 chicago: Konradi, Sabine, Nighat Yasmin, Denise Haslwanter, Michele Weber, Bernd Gesslbauer, Michael K Sixt, and Herbert Strobl. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology. Wiley-Blackwell, 2014. https://doi.org/10.1002/eji.201343681. ieee: S. Konradi et al., “Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2,” European Journal of Immunology, vol. 44, no. 2. Wiley-Blackwell, pp. 553–560, 2014. ista: Konradi S, Yasmin N, Haslwanter D, Weber M, Gesslbauer B, Sixt MK, Strobl H. 2014. Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2. European Journal of Immunology. 44(2), 553–560. mla: Konradi, Sabine, et al. “Langerhans Cell Maturation Is Accompanied by Induction of N-Cadherin and the Transcriptional Regulators of Epithelial-Mesenchymal Transition ZEB1/2.” European Journal of Immunology, vol. 44, no. 2, Wiley-Blackwell, 2014, pp. 553–60, doi:10.1002/eji.201343681. short: S. Konradi, N. Yasmin, D. Haslwanter, M. Weber, B. Gesslbauer, M.K. Sixt, H. Strobl, European Journal of Immunology 44 (2014) 553–560. date_created: 2018-12-11T11:54:40Z date_published: 2014-02-01T00:00:00Z date_updated: 2021-01-12T06:54:01Z day: '01' department: - _id: MiSi doi: 10.1002/eji.201343681 intvolume: ' 44' issue: '2' language: - iso: eng month: '02' oa_version: None page: 553 - 560 publication: European Journal of Immunology publication_status: published publisher: Wiley-Blackwell publist_id: '5185' scopus_import: 1 status: public title: Langerhans cell maturation is accompanied by induction of N-cadherin and the transcriptional regulators of epithelial-mesenchymal transition ZEB1/2 type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 44 year: '2014' ... --- _id: '1907' abstract: - lang: eng text: 'Most cryptographic security proofs require showing that two systems are indistinguishable. A central tool in such proofs is that of a game, where winning the game means provoking a certain condition, and it is shown that the two systems considered cannot be distinguished unless this condition is provoked. Upper bounding the probability of winning such a game, i.e., provoking this condition, for an arbitrary strategy is usually hard, except in the special case where the best strategy for winning such a game is known to be non-adaptive. A sufficient criterion for ensuring the optimality of non-adaptive strategies is that of conditional equivalence to a system, a notion introduced in [1]. In this paper, we show that this criterion is not necessary to ensure the optimality of non-adaptive strategies by giving two results of independent interest: 1) the optimality of non-adaptive strategies is not preserved under parallel composition; 2) in contrast, conditional equivalence is preserved under parallel composition.' article_number: '6875125' author: - first_name: Grégory full_name: Demay, Grégory last_name: Demay - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Ueli full_name: Maurer, Ueli last_name: Maurer - first_name: Björn full_name: Tackmann, Björn last_name: Tackmann citation: ama: 'Demay G, Gazi P, Maurer U, Tackmann B. Optimality of non-adaptive strategies: The case of parallel games. In: IEEE International Symposium on Information Theory. IEEE; 2014. doi:10.1109/ISIT.2014.6875125' apa: 'Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2014). Optimality of non-adaptive strategies: The case of parallel games. In IEEE International Symposium on Information Theory. Honolulu, USA: IEEE. https://doi.org/10.1109/ISIT.2014.6875125' chicago: 'Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” In IEEE International Symposium on Information Theory. IEEE, 2014. https://doi.org/10.1109/ISIT.2014.6875125.' ieee: 'G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Optimality of non-adaptive strategies: The case of parallel games,” in IEEE International Symposium on Information Theory, Honolulu, USA, 2014.' ista: 'Demay G, Gazi P, Maurer U, Tackmann B. 2014. Optimality of non-adaptive strategies: The case of parallel games. IEEE International Symposium on Information Theory. IEEE International Symposium on Information Theory Proceedings, 6875125.' mla: 'Demay, Grégory, et al. “Optimality of Non-Adaptive Strategies: The Case of Parallel Games.” IEEE International Symposium on Information Theory, 6875125, IEEE, 2014, doi:10.1109/ISIT.2014.6875125.' short: G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, IEEE International Symposium on Information Theory, IEEE, 2014. conference: end_date: 2014-07-04 location: Honolulu, USA name: IEEE International Symposium on Information Theory Proceedings start_date: 2014-06-29 date_created: 2018-12-11T11:54:39Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:53:59Z day: '01' department: - _id: KrPi doi: 10.1109/ISIT.2014.6875125 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2014/299 month: '01' oa: 1 oa_version: Submitted Version publication: IEEE International Symposium on Information Theory publication_status: published publisher: IEEE publist_id: '5188' quality_controlled: '1' scopus_import: 1 status: public title: 'Optimality of non-adaptive strategies: The case of parallel games' type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1908' abstract: - lang: eng text: In large populations, multiple beneficial mutations may be simultaneously spreading. In asexual populations, these mutations must either arise on the same background or compete against each other. In sexual populations, recombination can bring together beneficial alleles from different backgrounds, but tightly linked alleles may still greatly interfere with each other. We show for well-mixed populations that when this interference is strong, the genome can be seen as consisting of many effectively asexual stretches linked together. The rate at which beneficial alleles fix is thus roughly proportional to the rate of recombination and depends only logarithmically on the mutation supply and the strength of selection. Our scaling arguments also allow us to predict, with reasonable accuracy, the fitness distribution of fixed mutations when the mutational effect sizes are broad. We focus on the regime in which crossovers occur more frequently than beneficial mutations, as is likely to be the case for many natural populations. author: - first_name: Daniel full_name: Weissman, Daniel id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Oskar full_name: Hallatschek, Oskar last_name: Hallatschek citation: ama: Weissman D, Hallatschek O. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 2014;196(4):1167-1183. doi:10.1534/genetics.113.160705 apa: Weissman, D., & Hallatschek, O. (2014). The rate of adaptation in large sexual populations with linear chromosomes. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.113.160705 chicago: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics. Genetics Society of America, 2014. https://doi.org/10.1534/genetics.113.160705. ieee: D. Weissman and O. Hallatschek, “The rate of adaptation in large sexual populations with linear chromosomes,” Genetics, vol. 196, no. 4. Genetics Society of America, pp. 1167–1183, 2014. ista: Weissman D, Hallatschek O. 2014. The rate of adaptation in large sexual populations with linear chromosomes. Genetics. 196(4), 1167–1183. mla: Weissman, Daniel, and Oskar Hallatschek. “The Rate of Adaptation in Large Sexual Populations with Linear Chromosomes.” Genetics, vol. 196, no. 4, Genetics Society of America, 2014, pp. 1167–83, doi:10.1534/genetics.113.160705. short: D. Weissman, O. Hallatschek, Genetics 196 (2014) 1167–1183. date_created: 2018-12-11T11:54:39Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:53:59Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.113.160705 ec_funded: 1 intvolume: ' 196' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.0737 month: '04' oa: 1 oa_version: Submitted Version page: 1167 - 1183 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5187' quality_controlled: '1' scopus_import: 1 status: public title: The rate of adaptation in large sexual populations with linear chromosomes type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 196 year: '2014' ... --- _id: '1911' abstract: - lang: eng text: The topological Tverberg theorem has been generalized in several directions by setting extra restrictions on the Tverberg partitions. Restricted Tverberg partitions, defined by the idea that certain points cannot be in the same part, are encoded with graphs. When two points are adjacent in the graph, they are not in the same part. If the restrictions are too harsh, then the topological Tverberg theorem fails. The colored Tverberg theorem corresponds to graphs constructed as disjoint unions of small complete graphs. Hell studied the case of paths and cycles. In graph theory these partitions are usually viewed as graph colorings. As explored by Aharoni, Haxell, Meshulam and others there are fundamental connections between several notions of graph colorings and topological combinatorics. For ordinary graph colorings it is enough to require that the number of colors q satisfy q>Δ, where Δ is the maximal degree of the graph. It was proven by the first author using equivariant topology that if q>Δ 2 then the topological Tverberg theorem still works. It is conjectured that q>KΔ is also enough for some constant K, and in this paper we prove a fixed-parameter version of that conjecture. The required topological connectivity results are proven with shellability, which also strengthens some previous partial results where the topological connectivity was proven with the nerve lemma. acknowledgement: Patrik Norén gratefully acknowledges support from the Wallenberg foundation author: - first_name: Alexander full_name: Engström, Alexander last_name: Engström - first_name: Patrik full_name: Noren, Patrik id: 46870C74-F248-11E8-B48F-1D18A9856A87 last_name: Noren citation: ama: Engström A, Noren P. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 2014;51(1):207-220. doi:10.1007/s00454-013-9556-3 apa: Engström, A., & Noren, P. (2014). Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-013-9556-3 chicago: Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry. Springer, 2014. https://doi.org/10.1007/s00454-013-9556-3. ieee: A. Engström and P. Noren, “Tverberg’s Theorem and Graph Coloring,” Discrete & Computational Geometry, vol. 51, no. 1. Springer, pp. 207–220, 2014. ista: Engström A, Noren P. 2014. Tverberg’s Theorem and Graph Coloring. Discrete & Computational Geometry. 51(1), 207–220. mla: Engström, Alexander, and Patrik Noren. “Tverberg’s Theorem and Graph Coloring.” Discrete & Computational Geometry, vol. 51, no. 1, Springer, 2014, pp. 207–20, doi:10.1007/s00454-013-9556-3. short: A. Engström, P. Noren, Discrete & Computational Geometry 51 (2014) 207–220. date_created: 2018-12-11T11:54:40Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:01Z day: '01' department: - _id: CaUh doi: 10.1007/s00454-013-9556-3 intvolume: ' 51' issue: '1' language: - iso: eng month: '01' oa_version: None page: 207 - 220 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '5183' scopus_import: 1 status: public title: Tverberg's Theorem and Graph Coloring type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2014' ... --- _id: '1916' abstract: - lang: eng text: Hereditary spastic paraplegias (HSPs) are neurodegenerative motor neuron diseases characterized by progressive age-dependent loss of corticospinal motor tract function. Although the genetic basis is partly understood, only a fraction of cases can receive a genetic diagnosis, and a global view of HSP is lacking. By using whole-exome sequencing in combination with network analysis, we identified 18 previously unknown putative HSP genes and validated nearly all of these genes functionally or genetically. The pathways highlighted by these mutations link HSP to cellular transport, nucleotide metabolism, and synapse and axon development. Network analysis revealed a host of further candidate genes, of which three were mutated in our cohort. Our analysis links HSP to other neurodegenerative disorders and can facilitate gene discovery and mechanistic understanding of disease. acknowledgement: Supported by the Deutsche Forschungsgemeinschaft (G.N.) article_processing_charge: No article_type: original author: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Ali full_name: Fenstermaker, Ali last_name: Fenstermaker - first_name: Maha full_name: Zaki, Maha last_name: Zaki - first_name: Matan full_name: Hofree, Matan last_name: Hofree - first_name: Jennifer full_name: Silhavy, Jennifer last_name: Silhavy - first_name: Andrew full_name: Heiberg, Andrew last_name: Heiberg - first_name: Mostafa full_name: Abdellateef, Mostafa last_name: Abdellateef - first_name: Başak full_name: Rosti, Başak last_name: Rosti - first_name: Eric full_name: Scott, Eric last_name: Scott - first_name: Lobna full_name: Mansour, Lobna last_name: Mansour - first_name: Amira full_name: Masri, Amira last_name: Masri - first_name: Hülya full_name: Kayserili, Hülya last_name: Kayserili - first_name: Jumana full_name: Al Aama, Jumana last_name: Al Aama - first_name: Ghada full_name: Abdel Salam, Ghada last_name: Abdel Salam - first_name: Ariana full_name: Karminejad, Ariana last_name: Karminejad - first_name: Majdi full_name: Kara, Majdi last_name: Kara - first_name: Bülent full_name: Kara, Bülent last_name: Kara - first_name: Bita full_name: Bozorgmehri, Bita last_name: Bozorgmehri - first_name: Tawfeg full_name: Ben Omran, Tawfeg last_name: Ben Omran - first_name: Faezeh full_name: Mojahedi, Faezeh last_name: Mojahedi - first_name: Iman full_name: Mahmoud, Iman last_name: Mahmoud - first_name: Naïma full_name: Bouslam, Naïma last_name: Bouslam - first_name: Ahmed full_name: Bouhouche, Ahmed last_name: Bouhouche - first_name: Ali full_name: Benomar, Ali last_name: Benomar - first_name: Sylvain full_name: Hanein, Sylvain last_name: Hanein - first_name: Laure full_name: Raymond, Laure last_name: Raymond - first_name: Sylvie full_name: Forlani, Sylvie last_name: Forlani - first_name: Massimo full_name: Mascaro, Massimo last_name: Mascaro - first_name: Laila full_name: Selim, Laila last_name: Selim - first_name: Nabil full_name: Shehata, Nabil last_name: Shehata - first_name: Nasir full_name: Al Allawi, Nasir last_name: Al Allawi - first_name: Parayil full_name: Bindu, Parayil last_name: Bindu - first_name: Matloob full_name: Azam, Matloob last_name: Azam - first_name: Murat full_name: Günel, Murat last_name: Günel - first_name: Ahmet full_name: Caglayan, Ahmet last_name: Caglayan - first_name: Kaya full_name: Bilgüvar, Kaya last_name: Bilgüvar - first_name: Aslihan full_name: Tolun, Aslihan last_name: Tolun - first_name: Mahmoud full_name: Issa, Mahmoud last_name: Issa - first_name: Jana full_name: Schroth, Jana last_name: Schroth - first_name: Emily full_name: Spencer, Emily last_name: Spencer - first_name: Rasim full_name: Rosti, Rasim last_name: Rosti - first_name: Naiara full_name: Akizu, Naiara last_name: Akizu - first_name: Keith full_name: Vaux, Keith last_name: Vaux - first_name: Anide full_name: Johansen, Anide last_name: Johansen - first_name: Alice full_name: Koh, Alice last_name: Koh - first_name: Hisham full_name: Megahed, Hisham last_name: Megahed - first_name: Alexandra full_name: Dürr, Alexandra last_name: Dürr - first_name: Alexis full_name: Brice, Alexis last_name: Brice - first_name: Giovanni full_name: Stévanin, Giovanni last_name: Stévanin - first_name: Stacy full_name: Gabriel, Stacy last_name: Gabriel - first_name: Trey full_name: Ideker, Trey last_name: Ideker - first_name: Joseph full_name: Gleeson, Joseph last_name: Gleeson citation: ama: Novarino G, Fenstermaker A, Zaki M, et al. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 2014;343(6170):506-511. doi:10.1126/science.1247363 apa: Novarino, G., Fenstermaker, A., Zaki, M., Hofree, M., Silhavy, J., Heiberg, A., … Gleeson, J. (2014). Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1247363 chicago: Novarino, Gaia, Ali Fenstermaker, Maha Zaki, Matan Hofree, Jennifer Silhavy, Andrew Heiberg, Mostafa Abdellateef, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1247363. ieee: G. Novarino et al., “Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders,” Science, vol. 343, no. 6170. American Association for the Advancement of Science, pp. 506–511, 2014. ista: Novarino G, Fenstermaker A, Zaki M, Hofree M, Silhavy J, Heiberg A, Abdellateef M, Rosti B, Scott E, Mansour L, Masri A, Kayserili H, Al Aama J, Abdel Salam G, Karminejad A, Kara M, Kara B, Bozorgmehri B, Ben Omran T, Mojahedi F, Mahmoud I, Bouslam N, Bouhouche A, Benomar A, Hanein S, Raymond L, Forlani S, Mascaro M, Selim L, Shehata N, Al Allawi N, Bindu P, Azam M, Günel M, Caglayan A, Bilgüvar K, Tolun A, Issa M, Schroth J, Spencer E, Rosti R, Akizu N, Vaux K, Johansen A, Koh A, Megahed H, Dürr A, Brice A, Stévanin G, Gabriel S, Ideker T, Gleeson J. 2014. Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders. Science. 343(6170), 506–511. mla: Novarino, Gaia, et al. “Exome Sequencing Links Corticospinal Motor Neuron Disease to Common Neurodegenerative Disorders.” Science, vol. 343, no. 6170, American Association for the Advancement of Science, 2014, pp. 506–11, doi:10.1126/science.1247363. short: G. Novarino, A. Fenstermaker, M. Zaki, M. Hofree, J. Silhavy, A. Heiberg, M. Abdellateef, B. Rosti, E. Scott, L. Mansour, A. Masri, H. Kayserili, J. Al Aama, G. Abdel Salam, A. Karminejad, M. Kara, B. Kara, B. Bozorgmehri, T. Ben Omran, F. Mojahedi, I. Mahmoud, N. Bouslam, A. Bouhouche, A. Benomar, S. Hanein, L. Raymond, S. Forlani, M. Mascaro, L. Selim, N. Shehata, N. Al Allawi, P. Bindu, M. Azam, M. Günel, A. Caglayan, K. Bilgüvar, A. Tolun, M. Issa, J. Schroth, E. Spencer, R. Rosti, N. Akizu, K. Vaux, A. Johansen, A. Koh, H. Megahed, A. Dürr, A. Brice, G. Stévanin, S. Gabriel, T. Ideker, J. Gleeson, Science 343 (2014) 506–511. date_created: 2018-12-11T11:54:42Z date_published: 2014-01-31T00:00:00Z date_updated: 2021-01-12T06:54:03Z day: '31' department: - _id: GaNo doi: 10.1126/science.1247363 external_id: pmid: - '24482476' intvolume: ' 343' issue: '6170' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157572/ month: '01' oa: 1 oa_version: Submitted Version page: 506 - 511 pmid: 1 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5178' quality_controlled: '1' scopus_import: 1 status: public title: Exome sequencing links corticospinal motor neuron disease to common neurodegenerative disorders type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 343 year: '2014' ... --- _id: '1917' abstract: - lang: eng text: Auxin-binding protein 1 (ABP1) was discovered nearly 40 years ago and was shown to be essential for plant development and morphogenesis, but its mode of action remains unclear. Here, we report that the plasma membrane-localized transmembrane kinase (TMK) receptor-like kinases interact with ABP1 and transduce auxin signal to activate plasma membrane-associated ROPs [Rho-like guanosine triphosphatases (GTPase) from plants], leading to changes in the cytoskeleton and the shape of leaf pavement cells in Arabidopsis. The interaction between ABP1 and TMK at the cell surface is induced by auxin and requires ABP1 sensing of auxin. These findings show that TMK proteins and ABP1 form a cell surface auxin perception complex that activates ROP signaling pathways, regulating nontranscriptional cytoplasmic responses and associated fundamental processes. acknowledgement: Supported by the intramural research program of the National Institute of Arthritis and Musculoskeletal and Skin Diseases and by its Laboratory Animal Care and Use Section and Flow Cytometry Group, Office of Science and Technology article_processing_charge: No article_type: original author: - first_name: Tongda full_name: Xu, Tongda last_name: Xu - first_name: Ning full_name: Dai, Ning last_name: Dai - first_name: Jisheng full_name: Chen, Jisheng last_name: Chen - first_name: Shingo full_name: Nagawa, Shingo last_name: Nagawa - first_name: Min full_name: Cao, Min last_name: Cao - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Zimin full_name: Zhou, Zimin last_name: Zhou - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Riet full_name: De Rycke, Riet last_name: De Rycke - first_name: Hana full_name: Rakusová, Hana last_name: Rakusová - first_name: Wen full_name: Wang, Wen last_name: Wang - first_name: Alan full_name: Jones, Alan last_name: Jones - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Sara full_name: Patterson, Sara last_name: Patterson - first_name: Anthony full_name: Bleecker, Anthony last_name: Bleecker - first_name: Zhenbiao full_name: Yang, Zhenbiao last_name: Yang citation: ama: Xu T, Dai N, Chen J, et al. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 2014;343(6174):1025-1028. doi:10.1126/science.1245125 apa: Xu, T., Dai, N., Chen, J., Nagawa, S., Cao, M., Li, H., … Yang, Z. (2014). Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.1245125 chicago: Xu, Tongda, Ning Dai, Jisheng Chen, Shingo Nagawa, Min Cao, Hongjiang Li, Zimin Zhou, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science. American Association for the Advancement of Science, 2014. https://doi.org/10.1126/science.1245125. ieee: T. Xu et al., “Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling,” Science, vol. 343, no. 6174. American Association for the Advancement of Science, pp. 1025–1028, 2014. ista: Xu T, Dai N, Chen J, Nagawa S, Cao M, Li H, Zhou Z, Chen X, De Rycke R, Rakusová H, Wang W, Jones A, Friml J, Patterson S, Bleecker A, Yang Z. 2014. Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling. Science. 343(6174), 1025–1028. mla: Xu, Tongda, et al. “Cell Surface ABP1-TMK Auxin Sensing Complex Activates ROP GTPase Signaling.” Science, vol. 343, no. 6174, American Association for the Advancement of Science, 2014, pp. 1025–28, doi:10.1126/science.1245125. short: T. Xu, N. Dai, J. Chen, S. Nagawa, M. Cao, H. Li, Z. Zhou, X. Chen, R. De Rycke, H. Rakusová, W. Wang, A. Jones, J. Friml, S. Patterson, A. Bleecker, Z. Yang, Science 343 (2014) 1025–1028. date_created: 2018-12-11T11:54:42Z date_published: 2014-02-28T00:00:00Z date_updated: 2021-01-12T06:54:03Z day: '28' department: - _id: JiFr doi: 10.1126/science.1245125 external_id: pmid: - '24578577' intvolume: ' 343' issue: '6174' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166562/ month: '02' oa: 1 oa_version: Submitted Version page: 1025 - 1028 pmid: 1 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5177' quality_controlled: '1' scopus_import: 1 status: public title: Cell surface ABP1-TMK auxin sensing complex activates ROP GTPase signaling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 343 year: '2014' ... --- _id: '1920' abstract: - lang: eng text: Cerebellar motor learning is suggested to be caused by long-term plasticity of excitatory parallel fiber-Purkinje cell (PF-PC) synapses associated with changes in the number of synaptic AMPA-type glutamate receptors (AMPARs). However, whether the AMPARs decrease or increase in individual PF-PC synapses occurs in physiological motor learning and accounts for memory that lasts over days remains elusive. We combined quantitative SDS-digested freeze-fracture replica labeling for AMPAR and physical dissector electron microscopy with a simple model of cerebellar motor learning, adaptation of horizontal optokinetic response (HOKR) in mouse. After 1-h training of HOKR, short-term adaptation (STA) was accompanied with transient decrease in AMPARs by 28% in target PF-PC synapses. STA was well correlated with AMPAR decrease in individual animals and both STA and AMPAR decrease recovered to basal levels within 24 h. Surprisingly, long-termadaptation (LTA) after five consecutive daily trainings of 1-h HOKR did not alter the number of AMPARs in PF-PC synapses but caused gradual and persistent synapse elimination by 45%, with corresponding PC spine loss by the fifth training day. Furthermore, recovery of LTA after 2 wk was well correlated with increase of PF-PC synapses to the control level. Our findings indicate that the AMPARs decrease in PF-PC synapses and the elimination of these synapses are in vivo engrams in short- and long-term motor learning, respectively, showing a unique type of synaptic plasticity that may contribute to memory consolidation. acknowledgement: This work was supported by Solution-Oriented Research for Science and Technology from the Japan Science and Technology Agency; Ministry of Education, Culture, Sports, Science and Technology of Japan Grant 16300114 (to R.S.). author: - first_name: Wen full_name: Wang, Wen last_name: Wang - first_name: Kazuhiko full_name: Nakadate, Kazuhiko last_name: Nakadate - first_name: Miwako full_name: Masugi Tokita, Miwako last_name: Masugi Tokita - first_name: Fumihiro full_name: Shutoh, Fumihiro last_name: Shutoh - first_name: Wajeeha full_name: Aziz, Wajeeha last_name: Aziz - first_name: Etsuko full_name: Tarusawa, Etsuko last_name: Tarusawa - first_name: Andrea full_name: Lörincz, Andrea last_name: Lörincz - first_name: Elek full_name: Molnár, Elek last_name: Molnár - first_name: Sebnem full_name: Kesaf, Sebnem id: 401AB46C-F248-11E8-B48F-1D18A9856A87 last_name: Kesaf - first_name: Yunqing full_name: Li, Yunqing last_name: Li - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Soichi full_name: Nagao, Soichi last_name: Nagao - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Wang W, Nakadate K, Masugi Tokita M, et al. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 2014;111(1):E188-E193. doi:10.1073/pnas.1315541111 apa: Wang, W., Nakadate, K., Masugi Tokita, M., Shutoh, F., Aziz, W., Tarusawa, E., … Shigemoto, R. (2014). Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1315541111 chicago: Wang, Wen, Kazuhiko Nakadate, Miwako Masugi Tokita, Fumihiro Shutoh, Wajeeha Aziz, Etsuko Tarusawa, Andrea Lörincz, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1315541111. ieee: W. Wang et al., “Distinct cerebellar engrams in short-term and long-term motor learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E188–E193, 2014. ista: Wang W, Nakadate K, Masugi Tokita M, Shutoh F, Aziz W, Tarusawa E, Lörincz A, Molnár E, Kesaf S, Li Y, Fukazawa Y, Nagao S, Shigemoto R. 2014. Distinct cerebellar engrams in short-term and long-term motor learning. PNAS. 111(1), E188–E193. mla: Wang, Wen, et al. “Distinct Cerebellar Engrams in Short-Term and Long-Term Motor Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E188–93, doi:10.1073/pnas.1315541111. short: W. Wang, K. Nakadate, M. Masugi Tokita, F. Shutoh, W. Aziz, E. Tarusawa, A. Lörincz, E. Molnár, S. Kesaf, Y. Li, Y. Fukazawa, S. Nagao, R. Shigemoto, PNAS 111 (2014) E188–E193. date_created: 2018-12-11T11:54:43Z date_published: 2014-01-07T00:00:00Z date_updated: 2021-01-12T06:54:05Z day: '07' department: - _id: RySh doi: 10.1073/pnas.1315541111 intvolume: ' 111' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890858/ month: '01' oa: 1 oa_version: Submitted Version page: E188 - E193 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5174' scopus_import: 1 status: public title: Distinct cerebellar engrams in short-term and long-term motor learning type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '1915' abstract: - lang: eng text: ROPs (Rho of plants) belong to a large family of plant-specific Rho-like small GTPases that function as essential molecular switches to control diverse cellular processes including cytoskeleton organization, cell polarization, cytokinesis, cell differentiation and vesicle trafficking. Although the machineries of vesicle trafficking and cell polarity in plants have been individually well addressed, how ROPs co-ordinate those processes is still largely unclear. Recent progress has been made towards an understanding of the coordination of ROP signalling and trafficking of PIN (PINFORMED) transporters for the plant hormone auxin in both root and leaf pavement cells. PIN transporters constantly shuttle between the endosomal compartments and the polar plasma membrane domains, therefore the modulation of PIN-dependent auxin transport between cells is a main developmental output of ROP-regulated vesicle trafficking. The present review focuses on these cellular mechanisms, especially the integration of ROP-based vesicle trafficking and plant cell polarity. acknowledgement: This work was supported by the European Research Council [project ERC-2011-StG-20101109-PSDP], Central European Institute of Technology (CEITEC) [grant number CZ.1.05/1.1.00/02.0068], European Social Fund [grant number CZ.1.07/2.3.00/20.0043] and the Czec article_processing_charge: No article_type: original author: - first_name: Xu full_name: Chen, Xu id: 4E5ADCAA-F248-11E8-B48F-1D18A9856A87 last_name: Chen - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Chen X, Friml J. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 2014;42(1):212-218. doi:10.1042/BST20130269 apa: Chen, X., & Friml, J. (2014). Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. Portland Press. https://doi.org/10.1042/BST20130269 chicago: Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions. Portland Press, 2014. https://doi.org/10.1042/BST20130269. ieee: X. Chen and J. Friml, “Rho-GTPase-regulated vesicle trafficking in plant cell polarity,” Biochemical Society Transactions, vol. 42, no. 1. Portland Press, pp. 212–218, 2014. ista: Chen X, Friml J. 2014. Rho-GTPase-regulated vesicle trafficking in plant cell polarity. Biochemical Society Transactions. 42(1), 212–218. mla: Chen, Xu, and Jiří Friml. “Rho-GTPase-Regulated Vesicle Trafficking in Plant Cell Polarity.” Biochemical Society Transactions, vol. 42, no. 1, Portland Press, 2014, pp. 212–18, doi:10.1042/BST20130269. short: X. Chen, J. Friml, Biochemical Society Transactions 42 (2014) 212–218. date_created: 2018-12-11T11:54:41Z date_published: 2014-02-01T00:00:00Z date_updated: 2022-06-07T11:20:56Z day: '01' department: - _id: JiFr doi: 10.1042/BST20130269 ec_funded: 1 external_id: pmid: - '24450654' intvolume: ' 42' issue: '1' language: - iso: eng month: '02' oa_version: None page: 212 - 218 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Biochemical Society Transactions publication_identifier: eissn: - 1470-8752 issn: - 0300-5127 publication_status: published publisher: Portland Press publist_id: '5179' quality_controlled: '1' scopus_import: '1' status: public title: Rho-GTPase-regulated vesicle trafficking in plant cell polarity type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2014' ... --- _id: '1919' abstract: - lang: eng text: Long-lasting memories are formed when the stimulus is temporally distributed (spacing effect). However, the synaptic mechanisms underlying this robust phenomenon and the precise time course of the synaptic modifications that occur during learning remain unclear. Here we examined the adaptation of horizontal optokinetic response in mice that underwent 1 h of massed and spaced training at varying intervals. Despite similar acquisition by all training protocols, 1 h of spacing produced the highest memory retention at 24 h, which lasted for 1 mo. The distinct kinetics of memory are strongly correlated with the reduction of floccular parallel fiber-Purkinje cell synapses but not with AMPA receptor (AMPAR) number and synapse size. After the spaced training, we observed 25%, 23%, and 12% reduction in AMPAR density, synapse size, and synapse number, respectively. Four hours after the spaced training, half of the synapses and Purkinje cell spines had been eliminated, whereas AMPAR density and synapse size were recovered in remaining synapses. Surprisingly, massed training also produced long-term memory and halving of synapses; however, this occurred slowly over days, and the memory lasted for only 1 wk. This distinct kinetics of structural plasticity may serve as a basis for unique temporal profiles in the formation and decay of memory with or without intervals. acknowledgement: his work was supported by Solution Oriented Research for Science and Technology (R.S.), Core Research for Evolutional Science and Technology, Japan Science and Technology Agency (Y.F.), and Grants-in-Aid for Scientific Research on Priority Areas-Molecular Brain Sciences 16300114 (to R.S.) and 18022043 (to Y.F.). author: - first_name: Wajeeha full_name: Aziz, Wajeeha last_name: Aziz - first_name: Wen full_name: Wang, Wen last_name: Wang - first_name: Sebnem full_name: Kesaf, Sebnem id: 401AB46C-F248-11E8-B48F-1D18A9856A87 last_name: Kesaf - first_name: Alsayed full_name: Mohamed, Alsayed last_name: Mohamed - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 citation: ama: Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 2014;111(1):E194-E202. doi:10.1073/pnas.1303317110 apa: Aziz, W., Wang, W., Kesaf, S., Mohamed, A., Fukazawa, Y., & Shigemoto, R. (2014). Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1303317110 chicago: Aziz, Wajeeha, Wen Wang, Sebnem Kesaf, Alsayed Mohamed, Yugo Fukazawa, and Ryuichi Shigemoto. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1303317110. ieee: W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, and R. Shigemoto, “Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning,” PNAS, vol. 111, no. 1. National Academy of Sciences, pp. E194–E202, 2014. ista: Aziz W, Wang W, Kesaf S, Mohamed A, Fukazawa Y, Shigemoto R. 2014. Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning. PNAS. 111(1), E194–E202. mla: Aziz, Wajeeha, et al. “Distinct Kinetics of Synaptic Structural Plasticity, Memory Formation, and Memory Decay in Massed and Spaced Learning.” PNAS, vol. 111, no. 1, National Academy of Sciences, 2014, pp. E194–202, doi:10.1073/pnas.1303317110. short: W. Aziz, W. Wang, S. Kesaf, A. Mohamed, Y. Fukazawa, R. Shigemoto, PNAS 111 (2014) E194–E202. date_created: 2018-12-11T11:54:43Z date_published: 2014-01-07T00:00:00Z date_updated: 2021-01-12T06:54:04Z day: '07' department: - _id: RySh doi: 10.1073/pnas.1303317110 intvolume: ' 111' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3890840/ month: '01' oa: 1 oa_version: Submitted Version page: E194 - E202 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5175' scopus_import: 1 status: public title: Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 111 year: '2014' ... --- _id: '1918' abstract: - lang: eng text: As the nuclear charge Z is continuously decreased an N-electron atom undergoes a binding-unbinding transition. We investigate whether the electrons remain bound and whether the radius of the system stays finite as the critical value Zc is approached. Existence of a ground state at Zc is shown under the condition Zc < N-K, where K is the maximal number of electrons that can be removed at Zc without changing the energy. article_number: '1350021' author: - first_name: Jacopo full_name: Bellazzini, Jacopo last_name: Bellazzini - first_name: Rupert full_name: Frank, Rupert last_name: Frank - first_name: Élliott full_name: Lieb, Élliott last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Bellazzini J, Frank R, Lieb É, Seiringer R. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 2014;26(1). doi:10.1142/S0129055X13500219 apa: Bellazzini, J., Frank, R., Lieb, É., & Seiringer, R. (2014). Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X13500219 chicago: Bellazzini, Jacopo, Rupert Frank, Élliott Lieb, and Robert Seiringer. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics. World Scientific Publishing, 2014. https://doi.org/10.1142/S0129055X13500219. ieee: J. Bellazzini, R. Frank, É. Lieb, and R. Seiringer, “Existence of ground states for negative ions at the binding threshold,” Reviews in Mathematical Physics, vol. 26, no. 1. World Scientific Publishing, 2014. ista: Bellazzini J, Frank R, Lieb É, Seiringer R. 2014. Existence of ground states for negative ions at the binding threshold. Reviews in Mathematical Physics. 26(1), 1350021. mla: Bellazzini, Jacopo, et al. “Existence of Ground States for Negative Ions at the Binding Threshold.” Reviews in Mathematical Physics, vol. 26, no. 1, 1350021, World Scientific Publishing, 2014, doi:10.1142/S0129055X13500219. short: J. Bellazzini, R. Frank, É. Lieb, R. Seiringer, Reviews in Mathematical Physics 26 (2014). date_created: 2018-12-11T11:54:42Z date_published: 2014-02-01T00:00:00Z date_updated: 2021-01-12T06:54:04Z day: '01' department: - _id: RoSe doi: 10.1142/S0129055X13500219 intvolume: ' 26' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1301.5370 month: '02' oa: 1 oa_version: Submitted Version project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: Reviews in Mathematical Physics publication_status: published publisher: World Scientific Publishing publist_id: '5176' quality_controlled: '1' scopus_import: 1 status: public title: Existence of ground states for negative ions at the binding threshold type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2014' ... --- _id: '1914' abstract: - lang: eng text: Targeting membrane proteins for degradation requires the sequential action of ESCRT sub-complexes ESCRT-0 to ESCRT-III. Although this machinery is generally conserved among kingdoms, plants lack the essential ESCRT-0 components. A new report closes this gap by identifying a novel protein family that substitutes for ESCRT-0 function in plants. author: - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Sauer M, Friml J. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 2014;24(1):R27-R29. doi:10.1016/j.cub.2013.11.019' apa: 'Sauer, M., & Friml, J. (2014). Plant biology: Gatekeepers of the road to protein perdition. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2013.11.019' chicago: 'Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2013.11.019.' ieee: 'M. Sauer and J. Friml, “Plant biology: Gatekeepers of the road to protein perdition,” Current Biology, vol. 24, no. 1. Cell Press, pp. R27–R29, 2014.' ista: 'Sauer M, Friml J. 2014. Plant biology: Gatekeepers of the road to protein perdition. Current Biology. 24(1), R27–R29.' mla: 'Sauer, Michael, and Jiří Friml. “Plant Biology: Gatekeepers of the Road to Protein Perdition.” Current Biology, vol. 24, no. 1, Cell Press, 2014, pp. R27–29, doi:10.1016/j.cub.2013.11.019.' short: M. Sauer, J. Friml, Current Biology 24 (2014) R27–R29. date_created: 2018-12-11T11:54:41Z date_published: 2014-01-06T00:00:00Z date_updated: 2021-01-12T06:54:02Z day: '06' department: - _id: JiFr doi: 10.1016/j.cub.2013.11.019 intvolume: ' 24' issue: '1' language: - iso: eng month: '01' oa_version: None page: R27 - R29 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '5180' quality_controlled: '1' scopus_import: 1 status: public title: 'Plant biology: Gatekeepers of the road to protein perdition' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2014' ... --- _id: '1925' abstract: - lang: eng text: In the past decade carbon nanotubes (CNTs) have been widely studied as a potential drug-delivery system, especially with functionality for cellular targeting. Yet, little is known about the actual process of docking to cell receptors and transport dynamics after internalization. Here we performed single-particle studies of folic acid (FA) mediated CNT binding to human carcinoma cells and their transport inside the cytosol. In particular, we employed molecular recognition force spectroscopy, an atomic force microscopy based method, to visualize and quantify docking of FA functionalized CNTs to FA binding receptors in terms of binding probability and binding force. We then traced individual fluorescently labeled, FA functionalized CNTs after specific uptake, and created a dynamic 'roadmap' that clearly showed trajectories of directed diffusion and areas of nanotube confinement in the cytosol. Our results demonstrate the potential of a single-molecule approach for investigation of drug-delivery vehicles and their targeting capacity. acknowledgement: "This work was supported by EC grant Marie Curie RTN-CT-2006-035616, CARBIO 'Carbon nanotubes for biomedical applications' and Austrian FFG grant mnt-era.net 823980, 'IntelliTip'.\r\n" article_number: '125704' article_processing_charge: No article_type: original author: - first_name: Constanze full_name: Lamprecht, Constanze last_name: Lamprecht - first_name: Birgit full_name: Plochberger, Birgit last_name: Plochberger - first_name: Verena full_name: Ruprecht, Verena id: 4D71A03A-F248-11E8-B48F-1D18A9856A87 last_name: Ruprecht orcid: 0000-0003-4088-8633 - first_name: Stefan full_name: Wieser, Stefan id: 355AA5A0-F248-11E8-B48F-1D18A9856A87 last_name: Wieser orcid: 0000-0002-2670-2217 - first_name: Christian full_name: Rankl, Christian last_name: Rankl - first_name: Elena full_name: Heister, Elena last_name: Heister - first_name: Barbara full_name: Unterauer, Barbara last_name: Unterauer - first_name: Mario full_name: Brameshuber, Mario last_name: Brameshuber - first_name: Jürgen full_name: Danzberger, Jürgen last_name: Danzberger - first_name: Petar full_name: Lukanov, Petar last_name: Lukanov - first_name: Emmanuel full_name: Flahaut, Emmanuel last_name: Flahaut - first_name: Gerhard full_name: Schütz, Gerhard last_name: Schütz - first_name: Peter full_name: Hinterdorfer, Peter last_name: Hinterdorfer - first_name: Andreas full_name: Ebner, Andreas last_name: Ebner citation: ama: Lamprecht C, Plochberger B, Ruprecht V, et al. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 2014;25(12). doi:10.1088/0957-4484/25/12/125704 apa: Lamprecht, C., Plochberger, B., Ruprecht, V., Wieser, S., Rankl, C., Heister, E., … Ebner, A. (2014). A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. IOP Publishing. https://doi.org/10.1088/0957-4484/25/12/125704 chicago: Lamprecht, Constanze, Birgit Plochberger, Verena Ruprecht, Stefan Wieser, Christian Rankl, Elena Heister, Barbara Unterauer, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology. IOP Publishing, 2014. https://doi.org/10.1088/0957-4484/25/12/125704. ieee: C. Lamprecht et al., “A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes,” Nanotechnology, vol. 25, no. 12. IOP Publishing, 2014. ista: Lamprecht C, Plochberger B, Ruprecht V, Wieser S, Rankl C, Heister E, Unterauer B, Brameshuber M, Danzberger J, Lukanov P, Flahaut E, Schütz G, Hinterdorfer P, Ebner A. 2014. A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes. Nanotechnology. 25(12), 125704. mla: Lamprecht, Constanze, et al. “A Single-Molecule Approach to Explore Binding Uptake and Transport of Cancer Cell Targeting Nanotubes.” Nanotechnology, vol. 25, no. 12, 125704, IOP Publishing, 2014, doi:10.1088/0957-4484/25/12/125704. short: C. Lamprecht, B. Plochberger, V. Ruprecht, S. Wieser, C. Rankl, E. Heister, B. Unterauer, M. Brameshuber, J. Danzberger, P. Lukanov, E. Flahaut, G. Schütz, P. Hinterdorfer, A. Ebner, Nanotechnology 25 (2014). date_created: 2018-12-11T11:54:45Z date_published: 2014-03-28T00:00:00Z date_updated: 2021-01-12T06:54:07Z day: '28' ddc: - '570' department: - _id: CaHe - _id: MiSi doi: 10.1088/0957-4484/25/12/125704 file: - access_level: open_access checksum: df4e03d225a19179e7790f6d87a12332 content_type: application/pdf creator: dernst date_created: 2020-05-15T09:21:19Z date_updated: 2020-07-14T12:45:21Z file_id: '7856' file_name: 2014_Nanotechnology_Lamprecht.pdf file_size: 3804152 relation: main_file file_date_updated: 2020-07-14T12:45:21Z has_accepted_license: '1' intvolume: ' 25' issue: '12' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version publication: Nanotechnology publication_status: published publisher: IOP Publishing publist_id: '5169' scopus_import: 1 status: public title: A single-molecule approach to explore binding uptake and transport of cancer cell targeting nanotubes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2014' ... --- _id: '1923' abstract: - lang: eng text: We derive the equations for a thin, axisymmetric elastic shell subjected to an internal active stress giving rise to active tension and moments within the shell. We discuss the stability of a cylindrical elastic shell and its response to a localized change in internal active stress. This description is relevant to describe the cellular actomyosin cortex, a thin shell at the cell surface behaving elastically at a short timescale and subjected to active internal forces arising from myosin molecular motor activity. We show that the recent observations of cell deformation following detachment of adherent cells (Maître J-L et al 2012 Science 338 253-6) are well accounted for by this mechanical description. The actin cortex elastic and bending moduli can be obtained from a quantitative analysis of cell shapes observed in these experiments. Our approach thus provides a non-invasive, imaging-based method for the extraction of cellular physical parameters. article_number: '065005' author: - first_name: Hélène full_name: Berthoumieux, Hélène last_name: Berthoumieux - first_name: Jean-Léon full_name: Maître, Jean-Léon id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87 last_name: Maître orcid: 0000-0002-3688-1474 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: Ewa full_name: Paluch, Ewa last_name: Paluch - first_name: Frank full_name: Julicher, Frank last_name: Julicher - first_name: Guillaume full_name: Salbreux, Guillaume last_name: Salbreux citation: ama: Berthoumieux H, Maître J-L, Heisenberg C-PJ, Paluch E, Julicher F, Salbreux G. Active elastic thin shell theory for cellular deformations. New Journal of Physics. 2014;16. doi:10.1088/1367-2630/16/6/065005 apa: Berthoumieux, H., Maître, J.-L., Heisenberg, C.-P. J., Paluch, E., Julicher, F., & Salbreux, G. (2014). Active elastic thin shell theory for cellular deformations. New Journal of Physics. IOP Publishing Ltd. https://doi.org/10.1088/1367-2630/16/6/065005 chicago: Berthoumieux, Hélène, Jean-Léon Maître, Carl-Philipp J Heisenberg, Ewa Paluch, Frank Julicher, and Guillaume Salbreux. “Active Elastic Thin Shell Theory for Cellular Deformations.” New Journal of Physics. IOP Publishing Ltd., 2014. https://doi.org/10.1088/1367-2630/16/6/065005. ieee: H. Berthoumieux, J.-L. Maître, C.-P. J. Heisenberg, E. Paluch, F. Julicher, and G. Salbreux, “Active elastic thin shell theory for cellular deformations,” New Journal of Physics, vol. 16. IOP Publishing Ltd., 2014. ista: Berthoumieux H, Maître J-L, Heisenberg C-PJ, Paluch E, Julicher F, Salbreux G. 2014. Active elastic thin shell theory for cellular deformations. New Journal of Physics. 16, 065005. mla: Berthoumieux, Hélène, et al. “Active Elastic Thin Shell Theory for Cellular Deformations.” New Journal of Physics, vol. 16, 065005, IOP Publishing Ltd., 2014, doi:10.1088/1367-2630/16/6/065005. short: H. Berthoumieux, J.-L. Maître, C.-P.J. Heisenberg, E. Paluch, F. Julicher, G. Salbreux, New Journal of Physics 16 (2014). date_created: 2018-12-11T11:54:44Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:54:06Z day: '01' ddc: - '570' department: - _id: CaHe doi: 10.1088/1367-2630/16/6/065005 file: - access_level: open_access checksum: 8dbe81ec656bf1264d8889bda9b2b985 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:16Z date_updated: 2020-07-14T12:45:21Z file_id: '5202' file_name: IST-2016-429-v1+1_document.pdf file_size: 941387 relation: main_file file_date_updated: 2020-07-14T12:45:21Z has_accepted_license: '1' intvolume: ' 16' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: New Journal of Physics publication_status: published publisher: IOP Publishing Ltd. publist_id: '5171' pubrep_id: '429' quality_controlled: '1' scopus_import: 1 status: public title: Active elastic thin shell theory for cellular deformations tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2014' ... --- _id: '1921' abstract: - lang: eng text: Cell polarity manifested by asymmetric distribution of cargoes, such as receptors and transporters, within the plasma membrane (PM) is crucial for essential functions in multicellular organisms. In plants, cell polarity (re)establishment is intimately linked to patterning processes. Despite the importance of cell polarity, its underlying mechanisms are still largely unknown, including the definition and distinctiveness of the polar domains within the PM. Here, we show in Arabidopsis thaliana that the signaling membrane components, the phosphoinositides phosphatidylinositol 4-phosphate (PtdIns4P) and phosphatidylinositol 4, 5-bisphosphate [PtdIns(4, 5)P2] as well as PtdIns4P 5-kinases mediating their interconversion, are specifically enriched at apical and basal polar plasma membrane domains. The PtdIns4P 5-kinases PIP5K1 and PIP5K2 are redundantly required for polar localization of specifically apical and basal cargoes, such as PIN-FORMED transporters for the plant hormone auxin. As a consequence of the polarity defects, instructive auxin gradients as well as embryonic and postembryonic patterning are severely compromised. Furthermore, auxin itself regulates PIP5K transcription and PtdIns4P and PtdIns(4, 5)P2 levels, in particular their association with polar PM domains. Our results provide insight into the polar domain-delineating mechanisms in plant cells that depend on apical and basal distribution of membrane lipids and are essential for embryonic and postembryonic patterning. acknowledgement: This work was supported by grants from the Odysseus program of the Research Foundation-Flanders (to J.F.). author: - first_name: Ricardo full_name: Tejos, Ricardo last_name: Tejos - first_name: Michael full_name: Sauer, Michael last_name: Sauer - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: 'MiriamPalacios ' full_name: 'Palacios-Gomez, MiriamPalacios ' last_name: Palacios-Gomez - first_name: Hongjiang full_name: Li, Hongjiang id: 33CA54A6-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0001-5039-9660 - first_name: Mareike full_name: Heilmann, Mareike last_name: Heilmann - first_name: Ringo full_name: Van Wijk, Ringo last_name: Van Wijk - first_name: Joop full_name: Vermeer, Joop last_name: Vermeer - first_name: Ingo full_name: Heilmann, Ingo last_name: Heilmann - first_name: Teun full_name: Munnik, Teun last_name: Munnik - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Tejos R, Sauer M, Vanneste S, et al. Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. 2014;26(5):2114-2128. doi:10.1105/tpc.114.126185 apa: Tejos, R., Sauer, M., Vanneste, S., Palacios-Gomez, M., Li, H., Heilmann, M., … Friml, J. (2014). Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. American Society of Plant Biologists. https://doi.org/10.1105/tpc.114.126185 chicago: Tejos, Ricardo, Michael Sauer, Steffen Vanneste, MiriamPalacios Palacios-Gomez, Hongjiang Li, Mareike Heilmann, Ringo Van Wijk, et al. “Bipolar Plasma Membrane Distribution of Phosphoinositides and Their Requirement for Auxin-Mediated Cell Polarity and Patterning in Arabidopsis.” Plant Cell. American Society of Plant Biologists, 2014. https://doi.org/10.1105/tpc.114.126185. ieee: R. Tejos et al., “Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis,” Plant Cell, vol. 26, no. 5. American Society of Plant Biologists, pp. 2114–2128, 2014. ista: Tejos R, Sauer M, Vanneste S, Palacios-Gomez M, Li H, Heilmann M, Van Wijk R, Vermeer J, Heilmann I, Munnik T, Friml J. 2014. Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis. Plant Cell. 26(5), 2114–2128. mla: Tejos, Ricardo, et al. “Bipolar Plasma Membrane Distribution of Phosphoinositides and Their Requirement for Auxin-Mediated Cell Polarity and Patterning in Arabidopsis.” Plant Cell, vol. 26, no. 5, American Society of Plant Biologists, 2014, pp. 2114–28, doi:10.1105/tpc.114.126185. short: R. Tejos, M. Sauer, S. Vanneste, M. Palacios-Gomez, H. Li, M. Heilmann, R. Van Wijk, J. Vermeer, I. Heilmann, T. Munnik, J. Friml, Plant Cell 26 (2014) 2114–2128. date_created: 2018-12-11T11:54:43Z date_published: 2014-05-01T00:00:00Z date_updated: 2021-01-12T06:54:05Z day: '01' department: - _id: JiFr doi: 10.1105/tpc.114.126185 ec_funded: 1 intvolume: ' 26' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079372/ month: '05' oa: 1 oa_version: Submitted Version page: 2114 - 2128 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Plant Cell publication_status: published publisher: American Society of Plant Biologists publist_id: '5173' scopus_import: 1 status: public title: Bipolar plasma membrane distribution of phosphoinositides and their requirement for auxin-mediated cell polarity and patterning in Arabidopsis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2014' ... --- _id: '1922' abstract: - lang: eng text: Germination of Arabidopsis seeds in darkness induces apical hook development, based on a tightly regulated differential growth coordinated by a multiple hormone cross-talk. Here, we endeavoured to clarify the function of brassinosteroids (BRs) and cross-talk with ethylene in hook development. An automated infrared imaging system was developed to study the kinetics of hook development in etiolated Arabidopsis seedlings. To ascertain the photomorphogenic control of hook opening, the system was equipped with an automatic light dimmer. We demonstrate that ethylene and BRs are indispensable for hook formation and maintenance. Ethylene regulation of hook formation functions partly through BRs, with BR feedback inhibition of ethylene action. Conversely, BR-mediated extension of hook maintenance functions partly through ethylene. Furthermore, we revealed that a short light pulse is sufficient to induce rapid hook opening. Our dynamic infrared imaging system allows high-resolution, kinetic imaging of up to 112 seedlings in a single experimental run. At this high throughput, it is ideally suited to rapidly gain insight in pathway networks. We demonstrate that BRs and ethylene cooperatively regulate apical hook development in a phase-dependent manner. Furthermore, we show that light is a predominant regulator of hook opening, inhibiting ethylene- and BR-mediated postponement of hook opening. acknowledgement: 'Funded by Ghent University; Research Foundation Flanders Grant Number: G065613N European Research Council Grant Number: CZ.1.07/2.3.00/20.0043' author: - first_name: Dajo full_name: Smet, Dajo last_name: Smet - first_name: Petra full_name: Žádníková, Petra last_name: Žádníková - first_name: Filip full_name: Vandenbussche, Filip last_name: Vandenbussche - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Dominique full_name: Van Der Straeten, Dominique last_name: Van Der Straeten citation: ama: 'Smet D, Žádníková P, Vandenbussche F, Benková E, Van Der Straeten D. Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. 2014;202(4):1398-1411. doi:10.1111/nph.12751' apa: 'Smet, D., Žádníková, P., Vandenbussche, F., Benková, E., & Van Der Straeten, D. (2014). Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. Wiley-Blackwell. https://doi.org/10.1111/nph.12751' chicago: 'Smet, Dajo, Petra Žádníková, Filip Vandenbussche, Eva Benková, and Dominique Van Der Straeten. “Dynamic Infrared Imaging Analysis of Apical Hook Development in Arabidopsis: The Case of Brassinosteroids.” New Phytologist. Wiley-Blackwell, 2014. https://doi.org/10.1111/nph.12751.' ieee: 'D. Smet, P. Žádníková, F. Vandenbussche, E. Benková, and D. Van Der Straeten, “Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids,” New Phytologist, vol. 202, no. 4. Wiley-Blackwell, pp. 1398–1411, 2014.' ista: 'Smet D, Žádníková P, Vandenbussche F, Benková E, Van Der Straeten D. 2014. Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids. New Phytologist. 202(4), 1398–1411.' mla: 'Smet, Dajo, et al. “Dynamic Infrared Imaging Analysis of Apical Hook Development in Arabidopsis: The Case of Brassinosteroids.” New Phytologist, vol. 202, no. 4, Wiley-Blackwell, 2014, pp. 1398–411, doi:10.1111/nph.12751.' short: D. Smet, P. Žádníková, F. Vandenbussche, E. Benková, D. Van Der Straeten, New Phytologist 202 (2014) 1398–1411. date_created: 2018-12-11T11:54:44Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:54:05Z day: '01' department: - _id: EvBe doi: 10.1111/nph.12751 ec_funded: 1 intvolume: ' 202' issue: '4' language: - iso: eng month: '06' oa_version: None page: 1398 - 1411 project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: New Phytologist publication_status: published publisher: Wiley-Blackwell publist_id: '5172' scopus_import: 1 status: public title: 'Dynamic infrared imaging analysis of apical hook development in Arabidopsis: The case of brassinosteroids' type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2014' ... --- _id: '1927' abstract: - lang: eng text: Constrained pseudorandom functions have recently been introduced independently by Boneh and Waters (Asiacrypt’13), Kiayias et al. (CCS’13), and Boyle et al. (PKC’14). In a standard pseudorandom function (PRF) a key k is used to evaluate the PRF on all inputs in the domain. Constrained PRFs additionally offer the functionality to delegate “constrained” keys kS which allow to evaluate the PRF only on a subset S of the domain. The three above-mentioned papers all show that the classical GGM construction (J.ACM’86) of a PRF from a pseudorandom generator (PRG) directly yields a constrained PRF where one can compute constrained keys to evaluate the PRF on all inputs with a given prefix. This constrained PRF has already found many interesting applications. Unfortunately, the existing security proofs only show selective security (by a reduction to the security of the underlying PRG). To achieve full security, one has to use complexity leveraging, which loses an exponential factor 2N in security, where N is the input length. The first contribution of this paper is a new reduction that only loses a quasipolynomial factor qlog N, where q is the number of adversarial queries. For this we develop a new proof technique which constructs a distinguisher by interleaving simple guessing steps and hybrid arguments a small number of times. This approach might be of interest also in other contexts where currently the only technique to achieve full security is complexity leveraging. Our second contribution is concerned with another constrained PRF, due to Boneh and Waters, which allows for constrained keys for the more general class of bit-fixing functions. Their security proof also suffers from a 2N loss, which we show is inherent. We construct a meta-reduction which shows that any “simple” reduction of full security from a noninteractive hardness assumption must incur an exponential security loss. acknowledgement: We are grateful to Mihir Bellare for his feedback on earlier versions of this paper. We are indebted to Vanishree Rao for her generous assistance in preparing this proceedings version. author: - first_name: Georg full_name: Georg Fuchsbauer id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Momchil full_name: Konstantinov, Momchil last_name: Konstantinov - first_name: Krzysztof Z full_name: Krzysztof Pietrzak id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Vanishree full_name: Rao, Vanishree last_name: Rao citation: ama: 'Fuchsbauer G, Konstantinov M, Pietrzak KZ, Rao V. Adaptive security of constrained PRFs. In: Vol 8874. Springer; 2014:173-192. doi:10.1145/2591796.2591825' apa: Fuchsbauer, G., Konstantinov, M., Pietrzak, K. Z., & Rao, V. (2014). Adaptive security of constrained PRFs (Vol. 8874, pp. 173–192). Presented at the Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), Springer. https://doi.org/10.1145/2591796.2591825 chicago: Fuchsbauer, Georg, Momchil Konstantinov, Krzysztof Z Pietrzak, and Vanishree Rao. “Adaptive Security of Constrained PRFs,” 8874:173–92. Springer, 2014. https://doi.org/10.1145/2591796.2591825. ieee: G. Fuchsbauer, M. Konstantinov, K. Z. Pietrzak, and V. Rao, “Adaptive security of constrained PRFs,” presented at the Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics), 2014, vol. 8874, pp. 173–192. ista: Fuchsbauer G, Konstantinov M, Pietrzak KZ, Rao V. 2014. Adaptive security of constrained PRFs. Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) vol. 8874, 173–192. mla: Fuchsbauer, Georg, et al. Adaptive Security of Constrained PRFs. Vol. 8874, Springer, 2014, pp. 173–92, doi:10.1145/2591796.2591825. short: G. Fuchsbauer, M. Konstantinov, K.Z. Pietrzak, V. Rao, in:, Springer, 2014, pp. 173–192. conference: name: Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) date_created: 2018-12-11T11:54:45Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:54:08Z day: '01' doi: 10.1145/2591796.2591825 extern: 1 intvolume: ' 8874' main_file_link: - open_access: '1' url: http://eprint.iacr.org/2014/416 month: '01' oa: 1 page: 173 - 192 publication_status: published publisher: Springer publist_id: '5167' quality_controlled: 0 status: public title: Adaptive security of constrained PRFs type: conference volume: 8874 year: '2014' ... --- _id: '1926' abstract: - lang: eng text: We consider cross products of finite graphs with a class of trees that have arbitrarily but finitely long line segments, such as the Fibonacci tree. Such cross products are called tree-strips. We prove that for small disorder random Schrödinger operators on such tree-strips have purely absolutely continuous spectrum in a certain set. article_processing_charge: No article_type: original author: - first_name: Christian full_name: Sadel, Christian id: 4760E9F8-F248-11E8-B48F-1D18A9856A87 last_name: Sadel orcid: 0000-0001-8255-3968 citation: ama: Sadel C. Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. 2014;17(3-4):409-440. doi:10.1007/s11040-014-9163-4 apa: Sadel, C. (2014). Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-014-9163-4 chicago: Sadel, Christian. “Absolutely Continuous Spectrum for Random Schrödinger Operators on the Fibonacci and Similar Tree-Strips.” Mathematical Physics, Analysis and Geometry. Springer, 2014. https://doi.org/10.1007/s11040-014-9163-4. ieee: C. Sadel, “Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips,” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4. Springer, pp. 409–440, 2014. ista: Sadel C. 2014. Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips. Mathematical Physics, Analysis and Geometry. 17(3–4), 409–440. mla: Sadel, Christian. “Absolutely Continuous Spectrum for Random Schrödinger Operators on the Fibonacci and Similar Tree-Strips.” Mathematical Physics, Analysis and Geometry, vol. 17, no. 3–4, Springer, 2014, pp. 409–40, doi:10.1007/s11040-014-9163-4. short: C. Sadel, Mathematical Physics, Analysis and Geometry 17 (2014) 409–440. date_created: 2018-12-11T11:54:45Z date_published: 2014-12-17T00:00:00Z date_updated: 2021-01-12T06:54:07Z day: '17' department: - _id: LaEr doi: 10.1007/s11040-014-9163-4 ec_funded: 1 external_id: arxiv: - '1304.3862' intvolume: ' 17' issue: 3-4 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1304.3862 month: '12' oa: 1 oa_version: Preprint page: 409 - 440 project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Mathematical Physics, Analysis and Geometry publication_status: published publisher: Springer publist_id: '5168' quality_controlled: '1' scopus_import: 1 status: public title: Absolutely continuous spectrum for random Schrödinger operators on the Fibonacci and similar Tree-strips type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2014' ... --- _id: '1924' abstract: - lang: eng text: Stomata are two-celled valves that control epidermal pores whose spacing optimizes shoot-atmosphere gas exchange. They develop from protodermal cells after unequal divisions followed by an equal division and differentiation. The concentration of the hormone auxin, a master plant developmental regulator, is tightly controlled in time and space, but its role, if any, in stomatal formation is obscure. Here dynamic changes of auxin activity during stomatal development are monitored using auxin input (DII-VENUS) and output (DR5:VENUS) markers by time-lapse imaging. A decrease in auxin levels in the smaller daughter cell after unequal division presages the acquisition of a guard mother cell fate whose equal division produces the two guard cells. Thus, stomatal patterning requires auxin pathway control of stem cell compartment size, as well as auxin depletion that triggers a developmental switch from unequal to equal division. article_number: '3090' author: - first_name: Jie full_name: Le, Jie last_name: Le - first_name: Xuguang full_name: Liu, Xuguang last_name: Liu - first_name: Kezhen full_name: Yang, Kezhen last_name: Yang - first_name: Xiaolan full_name: Chen, Xiaolan last_name: Chen - first_name: Lingling full_name: Zhu, Lingling last_name: Zhu - first_name: Hongzhe full_name: Wang, Hongzhe last_name: Wang - first_name: Ming full_name: Wang, Ming last_name: Wang - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Miyo full_name: Morita, Miyo last_name: Morita - first_name: Masao full_name: Tasaka, Masao last_name: Tasaka - first_name: Zhaojun full_name: Ding, Zhaojun last_name: Ding - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Fred full_name: Sack, Fred last_name: Sack citation: ama: Le J, Liu X, Yang K, et al. Auxin transport and activity regulate stomatal patterning and development. Nature Communications. 2014;5. doi:10.1038/ncomms4090 apa: Le, J., Liu, X., Yang, K., Chen, X., Zhu, L., Wang, H., … Sack, F. (2014). Auxin transport and activity regulate stomatal patterning and development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms4090 chicago: Le, Jie, Xuguang Liu, Kezhen Yang, Xiaolan Chen, Lingling Zhu, Hongzhe Wang, Ming Wang, et al. “Auxin Transport and Activity Regulate Stomatal Patterning and Development.” Nature Communications. Nature Publishing Group, 2014. https://doi.org/10.1038/ncomms4090. ieee: J. Le et al., “Auxin transport and activity regulate stomatal patterning and development,” Nature Communications, vol. 5. Nature Publishing Group, 2014. ista: Le J, Liu X, Yang K, Chen X, Zhu L, Wang H, Wang M, Vanneste S, Morita M, Tasaka M, Ding Z, Friml J, Beeckman T, Sack F. 2014. Auxin transport and activity regulate stomatal patterning and development. Nature Communications. 5, 3090. mla: Le, Jie, et al. “Auxin Transport and Activity Regulate Stomatal Patterning and Development.” Nature Communications, vol. 5, 3090, Nature Publishing Group, 2014, doi:10.1038/ncomms4090. short: J. Le, X. Liu, K. Yang, X. Chen, L. Zhu, H. Wang, M. Wang, S. Vanneste, M. Morita, M. Tasaka, Z. Ding, J. Friml, T. Beeckman, F. Sack, Nature Communications 5 (2014). date_created: 2018-12-11T11:54:44Z date_published: 2014-01-27T00:00:00Z date_updated: 2021-01-12T06:54:06Z day: '27' department: - _id: JiFr doi: 10.1038/ncomms4090 intvolume: ' 5' language: - iso: eng month: '01' oa_version: None publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5170' quality_controlled: '1' scopus_import: 1 status: public title: Auxin transport and activity regulate stomatal patterning and development type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2014' ... --- _id: '1928' abstract: - lang: eng text: In infectious disease epidemiology the basic reproductive ratio, R0, is defined as the average number of new infections caused by a single infected individual in a fully susceptible population. Many models describing competition for hosts between non-interacting pathogen strains in an infinite population lead to the conclusion that selection favors invasion of new strains if and only if they have higher R0 values than the resident. Here we demonstrate that this picture fails in finite populations. Using a simple stochastic SIS model, we show that in general there is no analogous optimization principle. We find that successive invasions may in some cases lead to strains that infect a smaller fraction of the host population, and that mutually invasible pathogen strains exist. In the limit of weak selection we demonstrate that an optimization principle does exist, although it differs from R0 maximization. For strains with very large R0, we derive an expression for this local fitness function and use it to establish a lower bound for the error caused by neglecting stochastic effects. Furthermore, we apply this weak selection limit to investigate the selection dynamics in the presence of a trade-off between the virulence and the transmission rate of a pathogen. acknowledgement: J.H. received support from the Zdenek Bakala Foundation and the Mobility Fund of Charles University in Prague. author: - first_name: Jan full_name: Humplik, Jan id: 2E9627A8-F248-11E8-B48F-1D18A9856A87 last_name: Humplik - first_name: Alison full_name: Hill, Alison last_name: Hill - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Humplik J, Hill A, Nowak M. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 2014;360:149-162. doi:10.1016/j.jtbi.2014.06.039 apa: Humplik, J., Hill, A., & Nowak, M. (2014). Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2014.06.039 chicago: Humplik, Jan, Alison Hill, and Martin Nowak. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology. Elsevier, 2014. https://doi.org/10.1016/j.jtbi.2014.06.039. ieee: J. Humplik, A. Hill, and M. Nowak, “Evolutionary dynamics of infectious diseases in finite populations,” Journal of Theoretical Biology, vol. 360. Elsevier, pp. 149–162, 2014. ista: Humplik J, Hill A, Nowak M. 2014. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 360, 149–162. mla: Humplik, Jan, et al. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology, vol. 360, Elsevier, 2014, pp. 149–62, doi:10.1016/j.jtbi.2014.06.039. short: J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162. date_created: 2018-12-11T11:54:46Z date_published: 2014-11-07T00:00:00Z date_updated: 2021-01-12T06:54:08Z day: '07' department: - _id: GaTk doi: 10.1016/j.jtbi.2014.06.039 intvolume: ' 360' language: - iso: eng month: '11' oa_version: None page: 149 - 162 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '5166' scopus_import: 1 status: public title: Evolutionary dynamics of infectious diseases in finite populations type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 360 year: '2014' ... --- _id: '1929' abstract: - lang: eng text: We propose an algorithm for the generalization of cartographic objects that can be used to represent maps on different scales. acknowledgement: We would like to offer our special thanks to students of the Department of Mathematics of Demidov Yaroslavl State University A. A. Gorokhov and V. N. Knyazev for participation in developing the program and assistance in preparation of test data. This work was supported by grant 11.G34.31.0053 from the government of the Russian Federation. article_processing_charge: No article_type: original author: - first_name: V V full_name: Alexeev, V V last_name: Alexeev - first_name: V G full_name: Bogaevskaya, V G last_name: Bogaevskaya - first_name: M M full_name: Preobrazhenskaya, M M last_name: Preobrazhenskaya - first_name: A Y full_name: Ukhalov, A Y last_name: Ukhalov - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Olga full_name: Yakimova, Olga last_name: Yakimova citation: ama: Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner H, Yakimova O. An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. 2014;203(6):754-760. doi:10.1007/s10958-014-2165-8 apa: Alexeev, V. V., Bogaevskaya, V. G., Preobrazhenskaya, M. M., Ukhalov, A. Y., Edelsbrunner, H., & Yakimova, O. (2014). An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. Springer. https://doi.org/10.1007/s10958-014-2165-8 chicago: Alexeev, V V, V G Bogaevskaya, M M Preobrazhenskaya, A Y Ukhalov, Herbert Edelsbrunner, and Olga Yakimova. “An Algorithm for Cartographic Generalization That Preserves Global Topology.” Journal of Mathematical Sciences. Springer, 2014. https://doi.org/10.1007/s10958-014-2165-8. ieee: V. V. Alexeev, V. G. Bogaevskaya, M. M. Preobrazhenskaya, A. Y. Ukhalov, H. Edelsbrunner, and O. Yakimova, “An algorithm for cartographic generalization that preserves global topology,” Journal of Mathematical Sciences, vol. 203, no. 6. Springer, pp. 754–760, 2014. ista: Alexeev VV, Bogaevskaya VG, Preobrazhenskaya MM, Ukhalov AY, Edelsbrunner H, Yakimova O. 2014. An algorithm for cartographic generalization that preserves global topology. Journal of Mathematical Sciences. 203(6), 754–760. mla: Alexeev, V. V., et al. “An Algorithm for Cartographic Generalization That Preserves Global Topology.” Journal of Mathematical Sciences, vol. 203, no. 6, Springer, 2014, pp. 754–60, doi:10.1007/s10958-014-2165-8. short: V.V. Alexeev, V.G. Bogaevskaya, M.M. Preobrazhenskaya, A.Y. Ukhalov, H. Edelsbrunner, O. Yakimova, Journal of Mathematical Sciences 203 (2014) 754–760. date_created: 2018-12-11T11:54:46Z date_published: 2014-11-16T00:00:00Z date_updated: 2022-05-24T10:39:06Z day: '16' department: - _id: HeEd doi: 10.1007/s10958-014-2165-8 intvolume: ' 203' issue: '6' language: - iso: eng month: '11' oa_version: None page: 754 - 760 publication: Journal of Mathematical Sciences publication_identifier: eissn: - 1573-8795 issn: - 1072-3374 publication_status: published publisher: Springer publist_id: '5165' quality_controlled: '1' scopus_import: '1' status: public title: An algorithm for cartographic generalization that preserves global topology type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 203 year: '2014' ... --- _id: '1935' abstract: - lang: eng text: 'We consider Ising models in d = 2 and d = 3 dimensions with nearest neighbor ferromagnetic and long-range antiferromagnetic interactions, the latter decaying as (distance)-p, p > 2d, at large distances. If the strength J of the ferromagnetic interaction is larger than a critical value J c, then the ground state is homogeneous. It has been conjectured that when J is smaller than but close to J c, the ground state is periodic and striped, with stripes of constant width h = h(J), and h → ∞ as J → Jc -. (In d = 3 stripes mean slabs, not columns.) Here we rigorously prove that, if we normalize the energy in such a way that the energy of the homogeneous state is zero, then the ratio e 0(J)/e S(J) tends to 1 as J → Jc -, with e S(J) being the energy per site of the optimal periodic striped/slabbed state and e 0(J) the actual ground state energy per site of the system. Our proof comes with explicit bounds on the difference e 0(J)-e S(J) at small but positive J c-J, and also shows that in this parameter range the ground state is striped/slabbed in a certain sense: namely, if one looks at a randomly chosen window, of suitable size ℓ (very large compared to the optimal stripe size h(J)), one finds a striped/slabbed state with high probability.' acknowledgement: "2014 by the authors. This paper may be reproduced, in its entirety, for non-commercial purposes.\r\n\r\nThe research leading to these results has received funding from the European Research\r\nCouncil under the European Union’s Seventh Framework Programme ERC Starting Grant CoMBoS (Grant Agreement No. 239694; A.G. and R.S.), the U.S. National Science Foundation (Grant PHY 0965859; E.H.L.), the Simons Foundation (Grant # 230207; E.H.L) and the NSERC (R.S.). The work is part of a project started in collaboration with Joel Lebowitz, whom we thank for many useful discussions and for his constant encouragement." article_processing_charge: No article_type: original author: - first_name: Alessandro full_name: Giuliani, Alessandro last_name: Giuliani - first_name: Élliott full_name: Lieb, Élliott last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Giuliani A, Lieb É, Seiringer R. Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. 2014;331:333-350. doi:10.1007/s00220-014-1923-2 apa: Giuliani, A., Lieb, É., & Seiringer, R. (2014). Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-014-1923-2 chicago: Giuliani, Alessandro, Élliott Lieb, and Robert Seiringer. “Formation of Stripes and Slabs near the Ferromagnetic Transition.” Communications in Mathematical Physics. Springer, 2014. https://doi.org/10.1007/s00220-014-1923-2. ieee: A. Giuliani, É. Lieb, and R. Seiringer, “Formation of stripes and slabs near the ferromagnetic transition,” Communications in Mathematical Physics, vol. 331. Springer, pp. 333–350, 2014. ista: Giuliani A, Lieb É, Seiringer R. 2014. Formation of stripes and slabs near the ferromagnetic transition. Communications in Mathematical Physics. 331, 333–350. mla: Giuliani, Alessandro, et al. “Formation of Stripes and Slabs near the Ferromagnetic Transition.” Communications in Mathematical Physics, vol. 331, Springer, 2014, pp. 333–50, doi:10.1007/s00220-014-1923-2. short: A. Giuliani, É. Lieb, R. Seiringer, Communications in Mathematical Physics 331 (2014) 333–350. date_created: 2018-12-11T11:54:48Z date_published: 2014-10-01T00:00:00Z date_updated: 2022-05-24T08:32:50Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00220-014-1923-2 external_id: arxiv: - '1304.6344' file: - access_level: open_access checksum: c8423271cd1e1ba9e44c47af75efe7b6 content_type: application/pdf creator: dernst date_created: 2022-05-24T08:30:40Z date_updated: 2022-05-24T08:30:40Z file_id: '11409' file_name: 2014_CommMathPhysics_Giuliani.pdf file_size: 334064 relation: main_file success: 1 file_date_updated: 2022-05-24T08:30:40Z has_accepted_license: '1' intvolume: ' 331' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 333 - 350 publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: published publisher: Springer publist_id: '5159' quality_controlled: '1' scopus_import: '1' status: public title: Formation of stripes and slabs near the ferromagnetic transition type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 331 year: '2014' ... --- _id: '1936' abstract: - lang: eng text: 'The social intelligence hypothesis states that the need to cope with complexities of social life has driven the evolution of advanced cognitive abilities. It is usually invoked in the context of challenges arising from complex intragroup structures, hierarchies, and alliances. However, a fundamental aspect of group living remains largely unexplored as a driving force in cognitive evolution: the competition between individuals searching for resources (producers) and conspecifics that parasitize their findings (scroungers). In populations of social foragers, abilities that enable scroungers to steal by outsmarting producers, and those allowing producers to prevent theft by outsmarting scroungers, are likely to be beneficial and may fuel a cognitive arms race. Using analytical theory and agent-based simulations, we present a general model for such a race that is driven by the producer-scrounger game and show that the race''s plausibility is dramatically affected by the nature of the evolving abilities. If scrounging and scrounging avoidance rely on separate, strategy-specific cognitive abilities, arms races are short-lived and have a limited effect on cognition. However, general cognitive abilities that facilitate both scrounging and scrounging avoidance undergo stable, long-lasting arms races. Thus, ubiquitous foraging interactions may lead to the evolution of general cognitive abilities in social animals, without the requirement of complex intragroup structures.' author: - first_name: Michal full_name: Arbilly, Michal last_name: Arbilly - first_name: Daniel full_name: Weissman, Daniel id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Marcus full_name: Feldman, Marcus last_name: Feldman - first_name: Uri full_name: Grodzinski, Uri last_name: Grodzinski citation: ama: Arbilly M, Weissman D, Feldman M, Grodzinski U. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 2014;25(3):487-495. doi:10.1093/beheco/aru002 apa: Arbilly, M., Weissman, D., Feldman, M., & Grodzinski, U. (2014). An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. Oxford University Press. https://doi.org/10.1093/beheco/aru002 chicago: Arbilly, Michal, Daniel Weissman, Marcus Feldman, and Uri Grodzinski. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology. Oxford University Press, 2014. https://doi.org/10.1093/beheco/aru002. ieee: M. Arbilly, D. Weissman, M. Feldman, and U. Grodzinski, “An arms race between producers and scroungers can drive the evolution of social cognition,” Behavioral Ecology, vol. 25, no. 3. Oxford University Press, pp. 487–495, 2014. ista: Arbilly M, Weissman D, Feldman M, Grodzinski U. 2014. An arms race between producers and scroungers can drive the evolution of social cognition. Behavioral Ecology. 25(3), 487–495. mla: Arbilly, Michal, et al. “An Arms Race between Producers and Scroungers Can Drive the Evolution of Social Cognition.” Behavioral Ecology, vol. 25, no. 3, Oxford University Press, 2014, pp. 487–95, doi:10.1093/beheco/aru002. short: M. Arbilly, D. Weissman, M. Feldman, U. Grodzinski, Behavioral Ecology 25 (2014) 487–495. date_created: 2018-12-11T11:54:48Z date_published: 2014-02-13T00:00:00Z date_updated: 2021-01-12T06:54:11Z day: '13' department: - _id: NiBa doi: 10.1093/beheco/aru002 ec_funded: 1 intvolume: ' 25' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4014306/ month: '02' oa: 1 oa_version: Submitted Version page: 487 - 495 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Behavioral Ecology publication_status: published publisher: Oxford University Press publist_id: '5157' quality_controlled: '1' scopus_import: 1 status: public title: An arms race between producers and scroungers can drive the evolution of social cognition type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2014' ... --- _id: '1934' abstract: - lang: eng text: The plant hormones auxin and cytokinin mutually coordinate their activities to control various aspects of development [1-9], and their crosstalk occurs at multiple levels [10, 11]. Cytokinin-mediated modulation of auxin transport provides an efficient means to regulate auxin distribution in plant organs. Here, we demonstrate that cytokinin does not merely control the overall auxin flow capacity, but might also act as a polarizing cue and control the auxin stream directionality during plant organogenesis. Cytokinin enhances the PIN-FORMED1 (PIN1) auxin transporter depletion at specific polar domains, thus rearranging the cellular PIN polarities and directly regulating the auxin flow direction. This selective cytokinin sensitivity correlates with the PIN protein phosphorylation degree. PIN1 phosphomimicking mutations, as well as enhanced phosphorylation in plants with modulated activities of PIN-specific kinases and phosphatases, desensitize PIN1 to cytokinin. Our results reveal conceptually novel, cytokinin-driven polarization mechanism that operates in developmental processes involving rapid auxin stream redirection, such as lateral root organogenesis, in which a gradual PIN polarity switch defines the growth axis of the newly formed organ. author: - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Jérôme full_name: Duclercq, Jérôme last_name: Duclercq - first_name: Benjamin full_name: Weller, Benjamin last_name: Weller - first_name: Elena full_name: Feraru, Elena last_name: Feraru - first_name: Agnieszka full_name: Bielach, Agnieszka last_name: Bielach - first_name: Remko full_name: Offringa, Remko last_name: Offringa - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Claus full_name: Schwechheimer, Claus last_name: Schwechheimer - first_name: Angus full_name: Murphy, Angus last_name: Murphy - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Marhavý P, Duclercq J, Weller B, et al. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. 2014;24(9):1031-1037. doi:10.1016/j.cub.2014.04.002 apa: Marhavý, P., Duclercq, J., Weller, B., Feraru, E., Bielach, A., Offringa, R., … Benková, E. (2014). Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2014.04.002 chicago: Marhavý, Peter, Jérôme Duclercq, Benjamin Weller, Elena Feraru, Agnieszka Bielach, Remko Offringa, Jiří Friml, Claus Schwechheimer, Angus Murphy, and Eva Benková. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during Lateral Root Organogenesis.” Current Biology. Cell Press, 2014. https://doi.org/10.1016/j.cub.2014.04.002. ieee: P. Marhavý et al., “Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis,” Current Biology, vol. 24, no. 9. Cell Press, pp. 1031–1037, 2014. ista: Marhavý P, Duclercq J, Weller B, Feraru E, Bielach A, Offringa R, Friml J, Schwechheimer C, Murphy A, Benková E. 2014. Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis. Current Biology. 24(9), 1031–1037. mla: Marhavý, Peter, et al. “Cytokinin Controls Polarity of PIN1-Dependent Auxin Transport during Lateral Root Organogenesis.” Current Biology, vol. 24, no. 9, Cell Press, 2014, pp. 1031–37, doi:10.1016/j.cub.2014.04.002. short: P. Marhavý, J. Duclercq, B. Weller, E. Feraru, A. Bielach, R. Offringa, J. Friml, C. Schwechheimer, A. Murphy, E. Benková, Current Biology 24 (2014) 1031–1037. date_created: 2018-12-11T11:54:48Z date_published: 2014-05-05T00:00:00Z date_updated: 2021-01-12T06:54:10Z day: '05' department: - _id: EvBe - _id: JiFr doi: 10.1016/j.cub.2014.04.002 ec_funded: 1 intvolume: ' 24' issue: '9' language: - iso: eng month: '05' oa_version: None page: 1031 - 1037 project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: Current Biology publication_status: published publisher: Cell Press publist_id: '5160' quality_controlled: '1' scopus_import: 1 status: public title: Cytokinin controls polarity of PIN1-dependent Auxin transport during lateral root organogenesis type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2014' ... --- _id: '1932' abstract: - lang: eng text: The existence of complex (multiple-step) genetic adaptations that are "irreducible" (i.e., all partial combinations are less fit than the original genotype) is one of the longest standing problems in evolutionary biology. In standard genetics parlance, these adaptations require the crossing of a wide adaptive valley of deleterious intermediate stages. Here, we demonstrate, using a simple model, that evolution can cross wide valleys to produce "irreducibly complex" adaptations by making use of previously cryptic mutations. When revealed by an evolutionary capacitor, previously cryptic mutants have higher initial frequencies than do new mutations, bringing them closer to a valley-crossing saddle in allele frequency space. Moreover, simple combinatorics implies an enormous number of candidate combinations exist within available cryptic genetic variation. We model the dynamics of crossing of a wide adaptive valley after a capacitance event using both numerical simulations and analytical approximations. Although individual valley crossing events become less likely as valleys widen, by taking the combinatorics of genotype space into account, we see that revealing cryptic variation can cause the frequent evolution of complex adaptations. acknowledgement: "Funded by National Institutes of Health. Grant Numbers: R01GM076041, R01GM104040 \r\n\r\nSimons Foundation\r\n\r\n" author: - first_name: Meredith full_name: Trotter, Meredith last_name: Trotter - first_name: Daniel full_name: Weissman, Daniel id: 2D0CE020-F248-11E8-B48F-1D18A9856A87 last_name: Weissman - first_name: Grant full_name: Peterson, Grant last_name: Peterson - first_name: Kayla full_name: Peck, Kayla last_name: Peck - first_name: Joanna full_name: Masel, Joanna last_name: Masel citation: ama: Trotter M, Weissman D, Peterson G, Peck K, Masel J. Cryptic genetic variation can make &quot;irreducible complexity&quot; a common mode of adaptation in sexual populations. Evolution. 2014;68(12):3357-3367. doi:10.1111/evo.12517 apa: Trotter, M., Weissman, D., Peterson, G., Peck, K., & Masel, J. (2014). Cryptic genetic variation can make &quot;irreducible complexity&quot; a common mode of adaptation in sexual populations. Evolution. Wiley-Blackwell. https://doi.org/10.1111/evo.12517 chicago: Trotter, Meredith, Daniel Weissman, Grant Peterson, Kayla Peck, and Joanna Masel. “Cryptic Genetic Variation Can Make &quot;Irreducible Complexity&quot; a Common Mode of Adaptation in Sexual Populations.” Evolution. Wiley-Blackwell, 2014. https://doi.org/10.1111/evo.12517. ieee: M. Trotter, D. Weissman, G. Peterson, K. Peck, and J. Masel, “Cryptic genetic variation can make &quot;irreducible complexity&quot; a common mode of adaptation in sexual populations,” Evolution, vol. 68, no. 12. Wiley-Blackwell, pp. 3357–3367, 2014. ista: Trotter M, Weissman D, Peterson G, Peck K, Masel J. 2014. Cryptic genetic variation can make &quot;irreducible complexity&quot; a common mode of adaptation in sexual populations. Evolution. 68(12), 3357–3367. mla: Trotter, Meredith, et al. “Cryptic Genetic Variation Can Make &quot;Irreducible Complexity&quot; a Common Mode of Adaptation in Sexual Populations.” Evolution, vol. 68, no. 12, Wiley-Blackwell, 2014, pp. 3357–67, doi:10.1111/evo.12517. short: M. Trotter, D. Weissman, G. Peterson, K. Peck, J. Masel, Evolution 68 (2014) 3357–3367. date_created: 2018-12-11T11:54:47Z date_published: 2014-12-01T00:00:00Z date_updated: 2021-01-12T06:54:10Z day: '01' department: - _id: NiBa doi: 10.1111/evo.12517 ec_funded: 1 intvolume: ' 68' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1310.6077 month: '12' oa: 1 oa_version: Submitted Version page: 3357 - 3367 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Evolution publication_status: published publisher: Wiley-Blackwell publist_id: '5162' quality_controlled: '1' scopus_import: 1 status: public title: Cryptic genetic variation can make "irreducible complexity" a common mode of adaptation in sexual populations type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 68 year: '2014' ... --- _id: '1930' abstract: - lang: eng text: (Figure Presented) Data acquisition, numerical inaccuracies, and sampling often introduce noise in measurements and simulations. Removing this noise is often necessary for efficient analysis and visualization of this data, yet many denoising techniques change the minima and maxima of a scalar field. For example, the extrema can appear or disappear, spatially move, and change their value. This can lead to wrong interpretations of the data, e.g., when the maximum temperature over an area is falsely reported being a few degrees cooler because the denoising method is unaware of these features. Recently, a topological denoising technique based on a global energy optimization was proposed, which allows the topology-controlled denoising of 2D scalar fields. While this method preserves the minima and maxima, it is constrained by the size of the data. We extend this work to large 2D data and medium-sized 3D data by introducing a novel domain decomposition approach. It allows processing small patches of the domain independently while still avoiding the introduction of new critical points. Furthermore, we propose an iterative refinement of the solution, which decreases the optimization energy compared to the previous approach and therefore gives smoother results that are closer to the input. We illustrate our technique on synthetic and real-world 2D and 3D data sets that highlight potential applications. acknowledgement: RTRA Digiteoproject; ERC grant; SNF award; Intel Doctoral Fellowship; MPC-VCC author: - first_name: David full_name: Günther, David last_name: Günther - first_name: Alec full_name: Jacobson, Alec last_name: Jacobson - first_name: Jan full_name: Reininghaus, Jan id: 4505473A-F248-11E8-B48F-1D18A9856A87 last_name: Reininghaus - first_name: Hans full_name: Seidel, Hans last_name: Seidel - first_name: Olga full_name: Sorkine Hornung, Olga last_name: Sorkine Hornung - first_name: Tino full_name: Weinkauf, Tino last_name: Weinkauf citation: ama: Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf T. Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. 2014;20(12):2585-2594. doi:10.1109/TVCG.2014.2346432 apa: Günther, D., Jacobson, A., Reininghaus, J., Seidel, H., Sorkine Hornung, O., & Weinkauf, T. (2014). Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. IEEE. https://doi.org/10.1109/TVCG.2014.2346432 chicago: Günther, David, Alec Jacobson, Jan Reininghaus, Hans Seidel, Olga Sorkine Hornung, and Tino Weinkauf. “Fast and Memory-Efficient Topological Denoising of 2D and 3D Scalar Fields.” IEEE Transactions on Visualization and Computer Graphics. IEEE, 2014. https://doi.org/10.1109/TVCG.2014.2346432. ieee: D. Günther, A. Jacobson, J. Reininghaus, H. Seidel, O. Sorkine Hornung, and T. Weinkauf, “Fast and memory-efficient topological denoising of 2D and 3D scalar fields,” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 12. IEEE, pp. 2585–2594, 2014. ista: Günther D, Jacobson A, Reininghaus J, Seidel H, Sorkine Hornung O, Weinkauf T. 2014. Fast and memory-efficient topological denoising of 2D and 3D scalar fields. IEEE Transactions on Visualization and Computer Graphics. 20(12), 2585–2594. mla: Günther, David, et al. “Fast and Memory-Efficient Topological Denoising of 2D and 3D Scalar Fields.” IEEE Transactions on Visualization and Computer Graphics, vol. 20, no. 12, IEEE, 2014, pp. 2585–94, doi:10.1109/TVCG.2014.2346432. short: D. Günther, A. Jacobson, J. Reininghaus, H. Seidel, O. Sorkine Hornung, T. Weinkauf, IEEE Transactions on Visualization and Computer Graphics 20 (2014) 2585–2594. date_created: 2018-12-11T11:54:46Z date_published: 2014-12-31T00:00:00Z date_updated: 2021-01-12T06:54:09Z day: '31' department: - _id: HeEd doi: 10.1109/TVCG.2014.2346432 intvolume: ' 20' issue: '12' language: - iso: eng month: '12' oa_version: None page: 2585 - 2594 publication: IEEE Transactions on Visualization and Computer Graphics publication_status: published publisher: IEEE publist_id: '5164' quality_controlled: '1' scopus_import: 1 status: public title: Fast and memory-efficient topological denoising of 2D and 3D scalar fields type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 20 year: '2014' ... --- _id: '1933' abstract: - lang: eng text: The development of the vertebrate brain requires an exquisite balance between proliferation and differentiation of neural progenitors. Notch signaling plays a pivotal role in regulating this balance, yet the interaction between signaling and receiving cells remains poorly understood. We have found that numerous nascent neurons and/or intermediate neurogenic progenitors expressing the ligand of Notch retain apical endfeet transiently at the ventricular lumen that form adherens junctions (AJs) with the endfeet of progenitors. Forced detachment of the apical endfeet of those differentiating cells by disrupting AJs resulted in precocious neurogenesis that was preceded by the downregulation of Notch signaling. Both Notch1 and its ligand Dll1 are distributed around AJs in the apical endfeet, and these proteins physically interact with ZO-1, a constituent of the AJ. Furthermore, live imaging of a fluorescently tagged Notch1 demonstrated its trafficking from the apical endfoot to the nucleus upon cleavage. Our results identified the apical endfoot as the central site of active Notch signaling to securely prohibit inappropriate differentiation of neural progenitors. author: - first_name: Jun full_name: Hatakeyama, Jun last_name: Hatakeyama - first_name: Yoshio full_name: Wakamatsu, Yoshio last_name: Wakamatsu - first_name: Akira full_name: Nagafuchi, Akira last_name: Nagafuchi - first_name: Ryoichiro full_name: Kageyama, Ryoichiro last_name: Kageyama - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Kenji full_name: Shimamura, Kenji last_name: Shimamura citation: ama: Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura K. Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. Development. 2014;141(8):1671-1682. doi:10.1242/dev.102988 apa: Hatakeyama, J., Wakamatsu, Y., Nagafuchi, A., Kageyama, R., Shigemoto, R., & Shimamura, K. (2014). Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. Development. Company of Biologists. https://doi.org/10.1242/dev.102988 chicago: Hatakeyama, Jun, Yoshio Wakamatsu, Akira Nagafuchi, Ryoichiro Kageyama, Ryuichi Shigemoto, and Kenji Shimamura. “Cadherin-Based Adhesions in the Apical Endfoot Are Required for Active Notch Signaling to Control Neurogenesis in Vertebrates.” Development. Company of Biologists, 2014. https://doi.org/10.1242/dev.102988. ieee: J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, and K. Shimamura, “Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates,” Development, vol. 141, no. 8. Company of Biologists, pp. 1671–1682, 2014. ista: Hatakeyama J, Wakamatsu Y, Nagafuchi A, Kageyama R, Shigemoto R, Shimamura K. 2014. Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates. Development. 141(8), 1671–1682. mla: Hatakeyama, Jun, et al. “Cadherin-Based Adhesions in the Apical Endfoot Are Required for Active Notch Signaling to Control Neurogenesis in Vertebrates.” Development, vol. 141, no. 8, Company of Biologists, 2014, pp. 1671–82, doi:10.1242/dev.102988. short: J. Hatakeyama, Y. Wakamatsu, A. Nagafuchi, R. Kageyama, R. Shigemoto, K. Shimamura, Development 141 (2014) 1671–1682. date_created: 2018-12-11T11:54:47Z date_published: 2014-04-01T00:00:00Z date_updated: 2021-01-12T06:54:10Z day: '01' department: - _id: RySh doi: 10.1242/dev.102988 intvolume: ' 141' issue: '8' language: - iso: eng month: '04' oa_version: None page: 1671 - 1682 publication: Development publication_status: published publisher: Company of Biologists publist_id: '5161' quality_controlled: '1' scopus_import: 1 status: public title: Cadherin-based adhesions in the apical endfoot are required for active Notch signaling to control neurogenesis in vertebrates type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 141 year: '2014' ... --- _id: '1931' abstract: - lang: eng text: A wealth of experimental evidence suggests that working memory circuits preferentially represent information that is behaviorally relevant. Still, we are missing a mechanistic account of how these representations come about. Here we provide a simple explanation for a range of experimental findings, in light of prefrontal circuits adapting to task constraints by reward-dependent learning. In particular, we model a neural network shaped by reward-modulated spike-timing dependent plasticity (r-STDP) and homeostatic plasticity (intrinsic excitability and synaptic scaling). We show that the experimentally-observed neural representations naturally emerge in an initially unstructured circuit as it learns to solve several working memory tasks. These results point to a critical, and previously unappreciated, role for reward-dependent learning in shaping prefrontal cortex activity. acknowledgement: Supported in part by EC MEXT project PLICON and the LOEWE-Program “Neuronal Coordination Research Focus Frankfurt” (NeFF). Jochen Triesch was supported by the Quandt foundation. article_number: '57' author: - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin - first_name: Jochen full_name: Triesch, Jochen last_name: Triesch citation: ama: Savin C, Triesch J. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 2014;8(MAY). doi:10.3389/fncom.2014.00057 apa: Savin, C., & Triesch, J. (2014). Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2014.00057 chicago: Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncom.2014.00057. ieee: C. Savin and J. Triesch, “Emergence of task-dependent representations in working memory circuits,” Frontiers in Computational Neuroscience, vol. 8, no. MAY. Frontiers Research Foundation, 2014. ista: Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57. mla: Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience, vol. 8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:10.3389/fncom.2014.00057. short: C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014). date_created: 2018-12-11T11:54:46Z date_published: 2014-05-28T00:00:00Z date_updated: 2021-01-12T06:54:09Z day: '28' department: - _id: GaTk doi: 10.3389/fncom.2014.00057 intvolume: ' 8' issue: MAY language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/ month: '05' oa: 1 oa_version: Submitted Version publication: Frontiers in Computational Neuroscience publication_status: published publisher: Frontiers Research Foundation publist_id: '5163' quality_controlled: '1' scopus_import: 1 status: public title: Emergence of task-dependent representations in working memory circuits type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2014' ...