--- _id: '15160' abstract: - lang: eng text: The circadian clock orchestrates global changes in transcriptional regulation on a daily basis via the bHLH-PAS transcription factor CLOCK:BMAL1. Pathways driven by other bHLH-PAS transcription factors have a homologous repressor that modulates activity on a tissue-specific basis, but none have been identified for CLOCK:BMAL1. We show here that the cancer/testis antigen PASD1 fulfills this role to suppress circadian rhythms. PASD1 is evolutionarily related to CLOCK and interacts with the CLOCK:BMAL1 complex to repress transcriptional activation. Expression of PASD1 is restricted to germline tissues in healthy individuals but can be induced in cells of somatic origin upon oncogenic transformation. Reducing PASD1 in human cancer cells significantly increases the amplitude of transcriptional oscillations to generate more robust circadian rhythms. Our results describe a function for a germline-specific protein in regulation of the circadian clock and provide a molecular link from oncogenic transformation to suppression of circadian rhythms. article_processing_charge: No article_type: original author: - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Stacy L. full_name: Harvey, Stacy L. last_name: Harvey - first_name: Patrick J. full_name: Sammons, Patrick J. last_name: Sammons - first_name: Amanda P. full_name: Anderson, Amanda P. last_name: Anderson - first_name: Hema M. full_name: Kopalle, Hema M. last_name: Kopalle - first_name: Alison H. full_name: Banham, Alison H. last_name: Banham - first_name: Carrie L. full_name: Partch, Carrie L. last_name: Partch citation: ama: Michael AK, Harvey SL, Sammons PJ, et al. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 2015;58(5):743-754. doi:10.1016/j.molcel.2015.03.031 apa: Michael, A. K., Harvey, S. L., Sammons, P. J., Anderson, A. P., Kopalle, H. M., Banham, A. H., & Partch, C. L. (2015). Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. Elsevier. https://doi.org/10.1016/j.molcel.2015.03.031 chicago: Michael, Alicia K., Stacy L. Harvey, Patrick J. Sammons, Amanda P. Anderson, Hema M. Kopalle, Alison H. Banham, and Carrie L. Partch. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell. Elsevier, 2015. https://doi.org/10.1016/j.molcel.2015.03.031. ieee: A. K. Michael et al., “Cancer/Testis antigen PASD1 silences the circadian clock,” Molecular Cell, vol. 58, no. 5. Elsevier, pp. 743–754, 2015. ista: Michael AK, Harvey SL, Sammons PJ, Anderson AP, Kopalle HM, Banham AH, Partch CL. 2015. Cancer/Testis antigen PASD1 silences the circadian clock. Molecular Cell. 58(5), 743–754. mla: Michael, Alicia K., et al. “Cancer/Testis Antigen PASD1 Silences the Circadian Clock.” Molecular Cell, vol. 58, no. 5, Elsevier, 2015, pp. 743–54, doi:10.1016/j.molcel.2015.03.031. short: A.K. Michael, S.L. Harvey, P.J. Sammons, A.P. Anderson, H.M. Kopalle, A.H. Banham, C.L. Partch, Molecular Cell 58 (2015) 743–754. date_created: 2024-03-21T07:58:08Z date_published: 2015-06-04T00:00:00Z date_updated: 2024-03-25T11:52:26Z day: '04' doi: 10.1016/j.molcel.2015.03.031 extern: '1' intvolume: ' 58' issue: '5' keyword: - Cell Biology - Molecular Biology language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.molcel.2015.03.031 month: '06' oa: 1 oa_version: Published Version page: 743-754 publication: Molecular Cell publication_identifier: issn: - 1097-2765 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Cancer/Testis antigen PASD1 silences the circadian clock type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 58 year: '2015' ... --- _id: '15159' abstract: - lang: eng text: It is widely recognized that BMAL1 is an essential subunit of the primary transcription factor that drives rhythmic circadian transcription in the nucleus. In a surprising turn, Lipton et al. now show that BMAL1 rhythmically interacts with translational machinery in the cytosol to stimulate protein synthesis in response to mTOR signaling. article_processing_charge: No article_type: original author: - first_name: Alicia Kathleen full_name: Michael, Alicia Kathleen id: 6437c950-2a03-11ee-914d-d6476dd7b75c last_name: Michael - first_name: Hande full_name: Asimgil, Hande last_name: Asimgil - first_name: Carrie L. full_name: Partch, Carrie L. last_name: Partch citation: ama: Michael AK, Asimgil H, Partch CL. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 2015;40(9):489-490. doi:10.1016/j.tibs.2015.07.006 apa: Michael, A. K., Asimgil, H., & Partch, C. L. (2015). Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. Elsevier. https://doi.org/10.1016/j.tibs.2015.07.006 chicago: Michael, Alicia K., Hande Asimgil, and Carrie L. Partch. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences. Elsevier, 2015. https://doi.org/10.1016/j.tibs.2015.07.006. ieee: A. K. Michael, H. Asimgil, and C. L. Partch, “Cytosolic BMAL1 moonlights as a translation factor,” Trends in Biochemical Sciences, vol. 40, no. 9. Elsevier, pp. 489–490, 2015. ista: Michael AK, Asimgil H, Partch CL. 2015. Cytosolic BMAL1 moonlights as a translation factor. Trends in Biochemical Sciences. 40(9), 489–490. mla: Michael, Alicia K., et al. “Cytosolic BMAL1 Moonlights as a Translation Factor.” Trends in Biochemical Sciences, vol. 40, no. 9, Elsevier, 2015, pp. 489–90, doi:10.1016/j.tibs.2015.07.006. short: A.K. Michael, H. Asimgil, C.L. Partch, Trends in Biochemical Sciences 40 (2015) 489–490. date_created: 2024-03-21T07:57:44Z date_published: 2015-09-01T00:00:00Z date_updated: 2024-03-25T11:53:58Z day: '01' doi: 10.1016/j.tibs.2015.07.006 extern: '1' intvolume: ' 40' issue: '9' keyword: - Molecular Biology - Biochemistry language: - iso: eng month: '09' oa_version: None page: 489-490 publication: Trends in Biochemical Sciences publication_identifier: issn: - 0968-0004 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Cytosolic BMAL1 moonlights as a translation factor type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 40 year: '2015' ... --- _id: '1619' abstract: - lang: eng text: The emergence of drug resistant pathogens is a serious public health problem. It is a long-standing goal to predict rates of resistance evolution and design optimal treatment strategies accordingly. To this end, it is crucial to reveal the underlying causes of drug-specific differences in the evolutionary dynamics leading to resistance. However, it remains largely unknown why the rates of resistance evolution via spontaneous mutations and the diversity of mutational paths vary substantially between drugs. Here we comprehensively quantify the distribution of fitness effects (DFE) of mutations, a key determinant of evolutionary dynamics, in the presence of eight antibiotics representing the main modes of action. Using precise high-throughput fitness measurements for genome-wide Escherichia coli gene deletion strains, we find that the width of the DFE varies dramatically between antibiotics and, contrary to conventional wisdom, for some drugs the DFE width is lower than in the absence of stress. We show that this previously underappreciated divergence in DFE width among antibiotics is largely caused by their distinct drug-specific dose-response characteristics. Unlike the DFE, the magnitude of the changes in tolerated drug concentration resulting from genome-wide mutations is similar for most drugs but exceptionally small for the antibiotic nitrofurantoin, i.e., mutations generally have considerably smaller resistance effects for nitrofurantoin than for other drugs. A population genetics model predicts that resistance evolution for drugs with this property is severely limited and confined to reproducible mutational paths. We tested this prediction in laboratory evolution experiments using the “morbidostat”, a device for evolving bacteria in well-controlled drug environments. Nitrofurantoin resistance indeed evolved extremely slowly via reproducible mutations—an almost paradoxical behavior since this drug causes DNA damage and increases the mutation rate. Overall, we identified novel quantitative characteristics of the evolutionary landscape that provide the conceptual foundation for predicting the dynamics of drug resistance evolution. article_number: e1002299 author: - first_name: Guillaume full_name: Chevereau, Guillaume id: 424D78A0-F248-11E8-B48F-1D18A9856A87 last_name: Chevereau - first_name: Marta full_name: Dravecka, Marta id: 4342E402-F248-11E8-B48F-1D18A9856A87 last_name: Dravecka orcid: 0000-0002-2519-8004 - first_name: Tugce full_name: Batur, Tugce last_name: Batur - first_name: Aysegul full_name: Guvenek, Aysegul last_name: Guvenek - first_name: Dilay full_name: Ayhan, Dilay last_name: Ayhan - first_name: Erdal full_name: Toprak, Erdal last_name: Toprak - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Chevereau G, Lukacisinova M, Batur T, et al. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 2015;13(11). doi:10.1371/journal.pbio.1002299 apa: Chevereau, G., Lukacisinova, M., Batur, T., Guvenek, A., Ayhan, D., Toprak, E., & Bollenbach, M. T. (2015). Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.1002299 chicago: Chevereau, Guillaume, Marta Lukacisinova, Tugce Batur, Aysegul Guvenek, Dilay Ayhan, Erdal Toprak, and Mark Tobias Bollenbach. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pbio.1002299. ieee: G. Chevereau et al., “Quantifying the determinants of evolutionary dynamics leading to drug resistance,” PLoS Biology, vol. 13, no. 11. Public Library of Science, 2015. ista: Chevereau G, Lukacisinova M, Batur T, Guvenek A, Ayhan D, Toprak E, Bollenbach MT. 2015. Quantifying the determinants of evolutionary dynamics leading to drug resistance. PLoS Biology. 13(11), e1002299. mla: Chevereau, Guillaume, et al. “Quantifying the Determinants of Evolutionary Dynamics Leading to Drug Resistance.” PLoS Biology, vol. 13, no. 11, e1002299, Public Library of Science, 2015, doi:10.1371/journal.pbio.1002299. short: G. Chevereau, M. Lukacisinova, T. Batur, A. Guvenek, D. Ayhan, E. Toprak, M.T. Bollenbach, PLoS Biology 13 (2015). date_created: 2018-12-11T11:53:04Z date_published: 2015-11-18T00:00:00Z date_updated: 2024-03-27T23:30:28Z day: '18' ddc: - '570' department: - _id: ToBo doi: 10.1371/journal.pbio.1002299 ec_funded: 1 file: - access_level: open_access checksum: 0e82e3279f50b15c6c170c042627802b content_type: application/pdf creator: system date_created: 2018-12-12T10:09:00Z date_updated: 2020-07-14T12:45:07Z file_id: '4723' file_name: IST-2016-468-v1+1_journal.pbio.1002299.pdf file_size: 1387760 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 13' issue: '11' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '11' oa: 1 oa_version: Published Version project: - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25E83C2C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '303507' name: Optimality principles in responses to antibiotics publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '5547' pubrep_id: '468' quality_controlled: '1' related_material: record: - id: '9711' relation: research_data status: public - id: '9765' relation: research_data status: public - id: '6263' relation: dissertation_contains status: public scopus_import: 1 status: public title: Quantifying the determinants of evolutionary dynamics leading to drug resistance 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2015' ... --- _id: '10382' abstract: - lang: eng text: 'Protein oligomers have been implicated as toxic agents in a wide range of amyloid-related diseases. However, it has remained unsolved whether the oligomers are a necessary step in the formation of amyloid fibrils or just a dangerous byproduct. Analogously, it has not been resolved if the amyloid nucleation process is a classical one-step nucleation process or a two-step process involving prenucleation clusters. We use coarse-grained computer simulations to study the effect of nonspecific attractions between peptides on the primary nucleation process underlying amyloid fibrillization. We find that, for peptides that do not attract, the classical one-step nucleation mechanism is possible but only at nonphysiologically high peptide concentrations. At low peptide concentrations, which mimic the physiologically relevant regime, attractive interpeptide interactions are essential for fibril formation. Nucleation then inevitably takes place through a two-step mechanism involving prefibrillar oligomers. We show that oligomers not only help peptides meet each other but also, create an environment that facilitates the conversion of monomers into the β-sheet–rich form characteristic of fibrils. Nucleation typically does not proceed through the most prevalent oligomers but through an oligomer size that is only observed in rare fluctuations, which is why such aggregates might be hard to capture experimentally. Finally, we find that the nucleation of amyloid fibrils cannot be described by classical nucleation theory: in the two-step mechanism, the critical nucleus size increases with increases in both concentration and interpeptide interactions, which is in direct contrast with predictions from classical nucleation theory.' acknowledgement: We thank Michele Vendruscolo, Iskra Staneva, and William M. Jacobs, for helpful discussions. A.Š. acknowledges support from the Human Frontier Science Program and Emmanuel College. Y.C.C. and D.F. are supported by Engineering and Physical Sciences Research Council Programme Grant EP/I001352/1. T.P.J.K. acknowledges the Frances and Augustus Newman Foundation, the European Research Council, and the Biotechnology and Biological Sciences Research Council. D.F. acknowledges European Research Council Advanced Grant 227758. article_processing_charge: No article_type: original author: - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Yassmine C. full_name: Chebaro, Yassmine C. last_name: Chebaro - first_name: Tuomas P. J. full_name: Knowles, Tuomas P. J. last_name: Knowles - first_name: Daan full_name: Frenkel, Daan last_name: Frenkel citation: ama: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 2014;111(50):17869-17874. doi:10.1073/pnas.1410159111 apa: Šarić, A., Chebaro, Y. C., Knowles, T. P. J., & Frenkel, D. (2014). Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. National Academy of Sciences. https://doi.org/10.1073/pnas.1410159111 chicago: Šarić, Anđela, Yassmine C. Chebaro, Tuomas P. J. Knowles, and Daan Frenkel. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences. National Academy of Sciences, 2014. https://doi.org/10.1073/pnas.1410159111. ieee: A. Šarić, Y. C. Chebaro, T. P. J. Knowles, and D. Frenkel, “Crucial role of nonspecific interactions in amyloid nucleation,” Proceedings of the National Academy of Sciences, vol. 111, no. 50. National Academy of Sciences, pp. 17869–17874, 2014. ista: Šarić A, Chebaro YC, Knowles TPJ, Frenkel D. 2014. Crucial role of nonspecific interactions in amyloid nucleation. Proceedings of the National Academy of Sciences. 111(50), 17869–17874. mla: Šarić, Anđela, et al. “Crucial Role of Nonspecific Interactions in Amyloid Nucleation.” Proceedings of the National Academy of Sciences, vol. 111, no. 50, National Academy of Sciences, 2014, pp. 17869–74, doi:10.1073/pnas.1410159111. short: A. Šarić, Y.C. Chebaro, T.P.J. Knowles, D. Frenkel, Proceedings of the National Academy of Sciences 111 (2014) 17869–17874. date_created: 2021-11-29T13:09:53Z date_published: 2014-12-01T00:00:00Z date_updated: 2021-11-29T13:29:05Z day: '01' doi: 10.1073/pnas.1410159111 extern: '1' external_id: arxiv: - '1412.0897' pmid: - '25453085' intvolume: ' 111' issue: '50' keyword: - multidisciplinary language: - iso: eng main_file_link: - open_access: '1' url: https://www.pnas.org/content/111/50/17869 month: '12' oa: 1 oa_version: Published Version page: 17869-17874 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: eissn: - 1091-6490 issn: - 0027-8424 publication_status: published publisher: National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Crucial role of nonspecific interactions in amyloid nucleation type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 111 year: '2014' ... --- _id: '10383' abstract: - lang: eng text: We use numerical simulations to compute the equation of state of a suspension of spherical self-propelled nanoparticles in two and three dimensions. We study in detail the effect of excluded volume interactions and confinement as a function of the system's temperature, concentration, and strength of the propulsion. We find a striking nonmonotonic dependence of the pressure on the temperature and provide simple scaling arguments to predict and explain the occurrence of such anomalous behavior. We explicitly show how our results have important implications for the effective forces on passive components suspended in a bath of active particles. article_number: '052303' article_processing_charge: No article_type: original author: - first_name: S. A. full_name: Mallory, S. A. last_name: Mallory - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: C. full_name: Valeriani, C. last_name: Valeriani - first_name: A. full_name: Cacciuto, A. last_name: Cacciuto citation: ama: Mallory SA, Šarić A, Valeriani C, Cacciuto A. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 2014;89(5). doi:10.1103/physreve.89.052303 apa: Mallory, S. A., Šarić, A., Valeriani, C., & Cacciuto, A. (2014). Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. American Physical Society. https://doi.org/10.1103/physreve.89.052303 chicago: Mallory, S. A., Anđela Šarić, C. Valeriani, and A. Cacciuto. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E. American Physical Society, 2014. https://doi.org/10.1103/physreve.89.052303. ieee: S. A. Mallory, A. Šarić, C. Valeriani, and A. Cacciuto, “Anomalous thermomechanical properties of a self-propelled colloidal fluid,” Physical Review E, vol. 89, no. 5. American Physical Society, 2014. ista: Mallory SA, Šarić A, Valeriani C, Cacciuto A. 2014. Anomalous thermomechanical properties of a self-propelled colloidal fluid. Physical Review E. 89(5), 052303. mla: Mallory, S. A., et al. “Anomalous Thermomechanical Properties of a Self-Propelled Colloidal Fluid.” Physical Review E, vol. 89, no. 5, 052303, American Physical Society, 2014, doi:10.1103/physreve.89.052303. short: S.A. Mallory, A. Šarić, C. Valeriani, A. Cacciuto, Physical Review E 89 (2014). date_created: 2021-11-29T13:10:33Z date_published: 2014-05-06T00:00:00Z date_updated: 2021-11-29T13:29:01Z day: '06' doi: 10.1103/physreve.89.052303 extern: '1' external_id: arxiv: - '1310.0826' pmid: - '25353796' intvolume: ' 89' issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1310.0826 month: '05' oa: 1 oa_version: Preprint pmid: 1 publication: Physical Review E publication_identifier: eissn: - 1550-2376 issn: - 1539-3755 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Anomalous thermomechanical properties of a self-propelled colloidal fluid type: journal_article user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 89 year: '2014' ... --- _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' ...