--- _id: '1574' abstract: - lang: eng text: Multiple plant developmental processes, such as lateral root development, depend on auxin distribution patterns that are in part generated by the PIN-formed family of auxin-efflux transporters. Here we propose that AUXIN RESPONSE FACTOR7 (ARF7) and the ARF7-regulated FOUR LIPS/MYB124 (FLP) transcription factors jointly form a coherent feed-forward motif that mediates the auxin-responsive PIN3 transcription in planta to steer the early steps of lateral root formation. This regulatory mechanism might endow the PIN3 circuitry with a temporal 'memory' of auxin stimuli, potentially maintaining and enhancing the robustness of the auxin flux directionality during lateral root development. The cooperative action between canonical auxin signalling and other transcription factors might constitute a general mechanism by which transcriptional auxin-sensitivity can be regulated at a tissue-specific level. acknowledgement: 'of the European Research Council (project ERC-2011-StG-20101109-PSDP) (to J.F.), a FEBS long-term fellowship (to P.M.) ' article_number: '8821' author: - first_name: Qian full_name: Chen, Qian last_name: Chen - first_name: Yang full_name: Liu, Yang last_name: Liu - first_name: Steven full_name: Maere, Steven last_name: Maere - first_name: Eunkyoung full_name: Lee, Eunkyoung last_name: Lee - first_name: Gert full_name: Van Isterdael, Gert last_name: Van Isterdael - first_name: Zidian full_name: Xie, Zidian last_name: Xie - first_name: Wei full_name: Xuan, Wei last_name: Xuan - first_name: Jessica full_name: Lucas, Jessica last_name: Lucas - first_name: Valya full_name: Vassileva, Valya last_name: Vassileva - first_name: Saeko full_name: Kitakura, Saeko last_name: Kitakura - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Niko full_name: Geldner, Niko last_name: Geldner - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 - first_name: Jie full_name: Le, Jie last_name: Le - first_name: Hidehiro full_name: Fukaki, Hidehiro last_name: Fukaki - first_name: Erich full_name: Grotewold, Erich last_name: Grotewold - first_name: Chuanyou full_name: Li, Chuanyou last_name: Li - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Fred full_name: Sack, Fred last_name: Sack - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste citation: ama: Chen Q, Liu Y, Maere S, et al. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 2015;6. doi:10.1038/ncomms9821 apa: Chen, Q., Liu, Y., Maere, S., Lee, E., Van Isterdael, G., Xie, Z., … Vanneste, S. (2015). A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9821 chicago: Chen, Qian, Yang Liu, Steven Maere, Eunkyoung Lee, Gert Van Isterdael, Zidian Xie, Wei Xuan, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9821. ieee: Q. Chen et al., “A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Chen Q, Liu Y, Maere S, Lee E, Van Isterdael G, Xie Z, Xuan W, Lucas J, Vassileva V, Kitakura S, Marhavý P, Wabnik KT, Geldner N, Benková E, Le J, Fukaki H, Grotewold E, Li C, Friml J, Sack F, Beeckman T, Vanneste S. 2015. A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development. Nature Communications. 6, 8821. mla: Chen, Qian, et al. “A Coherent Transcriptional Feed-Forward Motif Model for Mediating Auxin-Sensitive PIN3 Expression during Lateral Root Development.” Nature Communications, vol. 6, 8821, Nature Publishing Group, 2015, doi:10.1038/ncomms9821. short: Q. Chen, Y. Liu, S. Maere, E. Lee, G. Van Isterdael, Z. Xie, W. Xuan, J. Lucas, V. Vassileva, S. Kitakura, P. Marhavý, K.T. Wabnik, N. Geldner, E. Benková, J. Le, H. Fukaki, E. Grotewold, C. Li, J. Friml, F. Sack, T. Beeckman, S. Vanneste, Nature Communications 6 (2015). date_created: 2018-12-11T11:52:48Z date_published: 2015-11-18T00:00:00Z date_updated: 2021-01-12T06:51:42Z day: '18' ddc: - '580' department: - _id: EvBe - _id: JiFr doi: 10.1038/ncomms9821 file: - access_level: open_access checksum: 8ff5c108899b548806e1cb7a302fe76d content_type: application/pdf creator: system date_created: 2018-12-12T10:14:32Z date_updated: 2020-07-14T12:45:02Z file_id: '5085' file_name: IST-2016-477-v1+1_ncomms9821.pdf file_size: 1701815 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5597' pubrep_id: '477' quality_controlled: '1' scopus_import: 1 status: public title: A coherent transcriptional feed-forward motif model for mediating auxin-sensitive PIN3 expression during lateral root development 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: 6 year: '2015' ... --- _id: '1575' abstract: - lang: eng text: The immune response relies on the migration of leukocytes and on their ability to stop in precise anatomical locations to fulfil their task. How leukocyte migration and function are coordinated is unknown. Here we show that in immature dendritic cells, which patrol their environment by engulfing extracellular material, cell migration and antigen capture are antagonistic. This antagonism results from transient enrichment of myosin IIA at the cell front, which disrupts the back-to-front gradient of the motor protein, slowing down locomotion but promoting antigen capture. We further highlight that myosin IIA enrichment at the cell front requires the MHC class II-associated invariant chain (Ii). Thus, by controlling myosin IIA localization, Ii imposes on dendritic cells an intermittent antigen capture behaviour that might facilitate environment patrolling. We propose that the requirement for myosin II in both cell migration and specific cell functions may provide a general mechanism for their coordination in time and space. acknowledgement: M.C. and M.L.H. were supported by fellowships from the Fondation pour la Recherche Médicale and the Association pour la Recherche contre le Cancer, respectively. This work was funded by grants from the City of Paris and the European Research Council to A.-M.L.-D. (Strapacemi 243103), the Association Nationale pour la Recherche (ANR-09-PIRI-0027-PCVI) and the InnaBiosanté foundation (Micemico) to A.-M.L.-D., M.P. and R.V., and the DCBIOL Labex from the French Government (ANR-10-IDEX-0001-02-PSL* and ANR-11-LABX-0043). The super-resolution SIM microscope was funded through an ERC Advanced Investigator Grant (250367) to Edith Heard (CNRS UMR3215/Inserm U934, Institut Curie). article_number: '7526' author: - first_name: Mélanie full_name: Chabaud, Mélanie last_name: Chabaud - first_name: Mélina full_name: Heuzé, Mélina last_name: Heuzé - first_name: Marine full_name: Bretou, Marine last_name: Bretou - first_name: Pablo full_name: Vargas, Pablo last_name: Vargas - first_name: Paolo full_name: Maiuri, Paolo last_name: Maiuri - first_name: Paola full_name: Solanes, Paola last_name: Solanes - first_name: Mathieu full_name: Maurin, Mathieu last_name: Maurin - first_name: Emmanuel full_name: Terriac, Emmanuel last_name: Terriac - first_name: Maël full_name: Le Berre, Maël last_name: Le Berre - first_name: Danielle full_name: Lankar, Danielle last_name: Lankar - first_name: Tristan full_name: Piolot, Tristan last_name: Piolot - first_name: Robert full_name: Adelstein, Robert last_name: Adelstein - first_name: Yingfan full_name: Zhang, Yingfan last_name: Zhang - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Jordan full_name: Jacobelli, Jordan last_name: Jacobelli - first_name: Olivier full_name: Bénichou, Olivier last_name: Bénichou - first_name: Raphaël full_name: Voituriez, Raphaël last_name: Voituriez - first_name: Matthieu full_name: Piel, Matthieu last_name: Piel - first_name: Ana full_name: Lennon Duménil, Ana last_name: Lennon Duménil citation: ama: Chabaud M, Heuzé M, Bretou M, et al. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 2015;6. doi:10.1038/ncomms8526 apa: Chabaud, M., Heuzé, M., Bretou, M., Vargas, P., Maiuri, P., Solanes, P., … Lennon Duménil, A. (2015). Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms8526 chicago: Chabaud, Mélanie, Mélina Heuzé, Marine Bretou, Pablo Vargas, Paolo Maiuri, Paola Solanes, Mathieu Maurin, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms8526. ieee: M. Chabaud et al., “Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Chabaud M, Heuzé M, Bretou M, Vargas P, Maiuri P, Solanes P, Maurin M, Terriac E, Le Berre M, Lankar D, Piolot T, Adelstein R, Zhang Y, Sixt MK, Jacobelli J, Bénichou O, Voituriez R, Piel M, Lennon Duménil A. 2015. Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells. Nature Communications. 6, 7526. mla: Chabaud, Mélanie, et al. “Cell Migration and Antigen Capture Are Antagonistic Processes Coupled by Myosin II in Dendritic Cells.” Nature Communications, vol. 6, 7526, Nature Publishing Group, 2015, doi:10.1038/ncomms8526. short: M. Chabaud, M. Heuzé, M. Bretou, P. Vargas, P. Maiuri, P. Solanes, M. Maurin, E. Terriac, M. Le Berre, D. Lankar, T. Piolot, R. Adelstein, Y. Zhang, M.K. Sixt, J. Jacobelli, O. Bénichou, R. Voituriez, M. Piel, A. Lennon Duménil, Nature Communications 6 (2015). date_created: 2018-12-11T11:52:48Z date_published: 2015-06-25T00:00:00Z date_updated: 2021-01-12T06:51:42Z day: '25' ddc: - '570' department: - _id: MiSi doi: 10.1038/ncomms8526 file: - access_level: open_access checksum: bae12e86be2adb28253f890b8bba8315 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:58Z date_updated: 2020-07-14T12:45:02Z file_id: '4915' file_name: IST-2016-476-v1+1_ncomms8526.pdf file_size: 4530215 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5596' pubrep_id: '476' quality_controlled: '1' scopus_import: 1 status: public title: Cell migration and antigen capture are antagonistic processes coupled by myosin II in dendritic cells 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: 6 year: '2015' ... --- _id: '1569' abstract: - lang: eng text: Spatial regulation of the plant hormone indole-3-acetic acid (IAA, or auxin) is essential for plant development. Auxin gradient establishment is mediated by polarly localized auxin transporters, including PIN-FORMED (PIN) proteins. Their localization and abundance at the plasma membrane are tightly regulated by endomembrane machinery, especially the endocytic and recycling pathways mediated by the ADP ribosylation factor guanine nucleotide exchange factor (ARF-GEF) GNOM. We assessed the role of the early secretory pathway in establishing PIN1 polarity in Arabidopsis thaliana by pharmacological and genetic approaches. We identified the compound endosidin 8 (ES8), which selectively interferes with PIN1 basal polarity without altering the polarity of apical proteins. ES8 alters the auxin distribution pattern in the root and induces a strong developmental phenotype, including reduced root length. The ARF-GEF- defective mutants gnom-like 1 ( gnl1-1) and gnom ( van7) are significantly resistant to ES8. The compound does not affect recycling or vacuolar trafficking of PIN1 but leads to its intracellular accumulation, resulting in loss of PIN1 basal polarity at the plasma membrane. Our data confirm a role for GNOM in endoplasmic reticulum (ER) - Golgi trafficking and reveal that a GNL1/GNOM-mediated early secretory pathway selectively regulates PIN1 basal polarity establishment in a manner essential for normal plant development. acknowledgement: 'This work was supported by Vetenskapsrådet and Vinnova (Verket för Innovationssystemet) (S.M.D., T.V., M.Ł., and S.R.), Knut och Alice Wallenbergs Stiftelse (S.M.D., A.R., and C.V.), Kempestiftelserna (A.H. and Q.M.), Carl Tryggers Stiftelse för Vetenskaplig Forskning (Q.M.), European Research Council Grant ERC-2011-StG-20101109-PSDP (to J.F.), US Department of Energy Grant DE-FG02-02ER15295 (to N.V.R.), and National Science Foundation Grant MCB-0817916 (to N.V.R. and G.R.H.). ' author: - first_name: Siamsa full_name: Doyle, Siamsa last_name: Doyle - first_name: Ash full_name: Haegera, Ash last_name: Haegera - first_name: Thomas full_name: Vain, Thomas last_name: Vain - first_name: Adeline full_name: Rigala, Adeline last_name: Rigala - first_name: Corrado full_name: Viotti, Corrado last_name: Viotti - first_name: Małgorzata full_name: Łangowskaa, Małgorzata last_name: Łangowskaa - first_name: Qian full_name: Maa, Qian last_name: Maa - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Natasha full_name: Raikhel, Natasha last_name: Raikhel - first_name: Glenn full_name: Hickse, Glenn last_name: Hickse - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert citation: ama: Doyle S, Haegera A, Vain T, et al. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 2015;112(7):E806-E815. doi:10.1073/pnas.1424856112 apa: Doyle, S., Haegera, A., Vain, T., Rigala, A., Viotti, C., Łangowskaa, M., … Robert, S. (2015). An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1424856112 chicago: Doyle, Siamsa, Ash Haegera, Thomas Vain, Adeline Rigala, Corrado Viotti, Małgorzata Łangowskaa, Qian Maa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1424856112. ieee: S. Doyle et al., “An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana,” PNAS, vol. 112, no. 7. National Academy of Sciences, pp. E806–E815, 2015. ista: Doyle S, Haegera A, Vain T, Rigala A, Viotti C, Łangowskaa M, Maa Q, Friml J, Raikhel N, Hickse G, Robert S. 2015. An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana. PNAS. 112(7), E806–E815. mla: Doyle, Siamsa, et al. “An Early Secretory Pathway Mediated by Gnom-like 1 and Gnom Is Essential for Basal Polarity Establishment in Arabidopsis Thaliana.” PNAS, vol. 112, no. 7, National Academy of Sciences, 2015, pp. E806–15, doi:10.1073/pnas.1424856112. short: S. Doyle, A. Haegera, T. Vain, A. Rigala, C. Viotti, M. Łangowskaa, Q. Maa, J. Friml, N. Raikhel, G. Hickse, S. Robert, PNAS 112 (2015) E806–E815. date_created: 2018-12-11T11:52:46Z date_published: 2015-02-17T00:00:00Z date_updated: 2021-01-12T06:51:39Z day: '17' department: - _id: JiFr doi: 10.1073/pnas.1424856112 ec_funded: 1 intvolume: ' 112' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4343110/ month: '02' oa: 1 oa_version: Published Version page: E806 - E815 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5602' quality_controlled: '1' scopus_import: 1 status: public title: An early secretory pathway mediated by gnom-like 1 and gnom is essential for basal polarity establishment in Arabidopsis thaliana type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1570' abstract: - lang: eng text: Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution. author: - first_name: Ralf full_name: Der, Ralf last_name: Der - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius citation: ama: Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 2015;112(45):E6224-E6232. doi:10.1073/pnas.1508400112 apa: Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1508400112 chicago: Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1508400112. ieee: R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015. ista: Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232. mla: Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS, vol. 112, no. 45, National Academy of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112. short: R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232. date_created: 2018-12-11T11:52:47Z date_published: 2015-11-10T00:00:00Z date_updated: 2021-01-12T06:51:40Z day: '10' department: - _id: ChLa - _id: GaTk doi: 10.1073/pnas.1508400112 ec_funded: 1 external_id: pmid: - '26504200' intvolume: ' 112' issue: '45' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/ month: '11' oa: 1 oa_version: Submitted Version page: E6224 - E6232 pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5601' quality_controlled: '1' scopus_import: 1 status: public title: Novel plasticity rule can explain the development of sensorimotor intelligence type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1571' abstract: - lang: eng text: Epistatic interactions can frustrate and shape evolutionary change. Indeed, phenotypes may fail to evolve when essential mutations are only accessible through positive selection if they are fixed simultaneously. How environmental variability affects such constraints is poorly understood. Here, we studied genetic constraints in fixed and fluctuating environments using the Escherichia coli lac operon as a model system for genotype-environment interactions. We found that, in different fixed environments, all trajectories that were reconstructed by applying point mutations within the transcription factor-operator interface became trapped at suboptima, where no additional improvements were possible. Paradoxically, repeated switching between these same environments allows unconstrained adaptation by continuous improvements. This evolutionary mode is explained by pervasive cross-environmental tradeoffs that reposition the peaks in such a way that trapped genotypes can repeatedly climb ascending slopes and hence, escape adaptive stasis. Using a Markov approach, we developed a mathematical framework to quantify the landscape-crossing rates and show that this ratchet-like adaptive mechanism is robust in a wide spectrum of fluctuating environments. Overall, this study shows that genetic constraints can be overcome by environmental change and that crossenvironmental tradeoffs do not necessarily impede but also, can facilitate adaptive evolution. Because tradeoffs and environmental variability are ubiquitous in nature, we speculate this evolutionary mode to be of general relevance. acknowledgement: This work is part of the research program of the Foundation for Fundamental Research on Matter, which is part of the Netherlands Organization for Scientific Research (NWO). M.G.J.d.V. was (partially) funded by NWO Earth and Life Sciences (ALW), project 863.14.015. We thank D. M. Weinreich, J. A. G. M. de Visser, T. Paixão, J. Polechová, T. Friedlander, and A. E. Mayo for reading and commenting on earlier versions of the manuscript and B. Houchmandzadeh, O. Rivoire, and M. Hemery for discussions and suggestions on the Markov computation. Furthermore, we thank F. J. Poelwijk for sharing plasmid pCascade5 and pRD007 and Y. Yokobayashi for sharing plasmid pINV-110. We also thank the anonymous reviewers for remarks on the initial version of the manuscript. author: - first_name: Marjon full_name: De Vos, Marjon id: 3111FFAC-F248-11E8-B48F-1D18A9856A87 last_name: De Vos - first_name: Alexandre full_name: Dawid, Alexandre last_name: Dawid - first_name: Vanda full_name: Šunderlíková, Vanda last_name: Šunderlíková - first_name: Sander full_name: Tans, Sander last_name: Tans citation: ama: de Vos M, Dawid A, Šunderlíková V, Tans S. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 2015;112(48):14906-14911. doi:10.1073/pnas.1510282112 apa: de Vos, M., Dawid, A., Šunderlíková, V., & Tans, S. (2015). Breaking evolutionary constraint with a tradeoff ratchet. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1510282112 chicago: Vos, Marjon de, Alexandre Dawid, Vanda Šunderlíková, and Sander Tans. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1510282112. ieee: M. de Vos, A. Dawid, V. Šunderlíková, and S. Tans, “Breaking evolutionary constraint with a tradeoff ratchet,” PNAS, vol. 112, no. 48. National Academy of Sciences, pp. 14906–14911, 2015. ista: de Vos M, Dawid A, Šunderlíková V, Tans S. 2015. Breaking evolutionary constraint with a tradeoff ratchet. PNAS. 112(48), 14906–14911. mla: de Vos, Marjon, et al. “Breaking Evolutionary Constraint with a Tradeoff Ratchet.” PNAS, vol. 112, no. 48, National Academy of Sciences, 2015, pp. 14906–11, doi:10.1073/pnas.1510282112. short: M. de Vos, A. Dawid, V. Šunderlíková, S. Tans, PNAS 112 (2015) 14906–14911. date_created: 2018-12-11T11:52:47Z date_published: 2015-12-01T00:00:00Z date_updated: 2021-01-12T06:51:40Z day: '01' department: - _id: ToBo doi: 10.1073/pnas.1510282112 intvolume: ' 112' issue: '48' language: - iso: eng month: '12' oa_version: None page: 14906 - 14911 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5600' quality_controlled: '1' scopus_import: 1 status: public title: Breaking evolutionary constraint with a tradeoff ratchet type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1572' abstract: - lang: eng text: "We consider the quantum ferromagnetic Heisenberg model in three dimensions, for all spins S ≥ 1/2. We rigorously prove the validity of the spin-wave approximation for the excitation spectrum, at the level of the first non-trivial contribution to the free energy at low temperatures. Our proof comes with explicit, constructive upper and lower bounds on the error term. It uses in an essential way the bosonic formulation of the model in terms of the Holstein-Primakoff representation. In this language, the model describes interacting bosons with a hard-core on-site repulsion and a nearest-neighbor attraction. This attractive interaction makes the lower bound on the free energy particularly tricky: the key idea there is to prove a differential inequality for the two-particle density, which is thereby shown to be smaller than the probability density of a suitably weighted two-particle random process on the lattice.\r\n" author: - first_name: Michele full_name: Correggi, Michele last_name: Correggi - first_name: Alessandro full_name: Giuliani, Alessandro last_name: Giuliani - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Correggi M, Giuliani A, Seiringer R. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 2015;339(1):279-307. doi:10.1007/s00220-015-2402-0 apa: Correggi, M., Giuliani, A., & Seiringer, R. (2015). Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. Springer. https://doi.org/10.1007/s00220-015-2402-0 chicago: Correggi, Michele, Alessandro Giuliani, and Robert Seiringer. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s00220-015-2402-0. ieee: M. Correggi, A. Giuliani, and R. Seiringer, “Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet,” Communications in Mathematical Physics, vol. 339, no. 1. Springer, pp. 279–307, 2015. ista: Correggi M, Giuliani A, Seiringer R. 2015. Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet. Communications in Mathematical Physics. 339(1), 279–307. mla: Correggi, Michele, et al. “Validity of the Spin-Wave Approximation for the Free Energy of the Heisenberg Ferromagnet.” Communications in Mathematical Physics, vol. 339, no. 1, Springer, 2015, pp. 279–307, doi:10.1007/s00220-015-2402-0. short: M. Correggi, A. Giuliani, R. Seiringer, Communications in Mathematical Physics 339 (2015) 279–307. date_created: 2018-12-11T11:52:47Z date_published: 2015-06-23T00:00:00Z date_updated: 2021-01-12T06:51:41Z day: '23' department: - _id: RoSe doi: 10.1007/s00220-015-2402-0 intvolume: ' 339' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1312.7873 month: '06' oa: 1 oa_version: Preprint page: 279 - 307 publication: Communications in Mathematical Physics publication_status: published publisher: Springer publist_id: '5599' quality_controlled: '1' scopus_import: 1 status: public title: Validity of the spin-wave approximation for the free energy of the Heisenberg ferromagnet type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 339 year: '2015' ... --- _id: '1573' abstract: - lang: eng text: We present a new, simpler proof of the unconditional uniqueness of solutions to the cubic Gross-Pitaevskii hierarchy in ℝ3. One of the main tools in our analysis is the quantum de Finetti theorem. Our uniqueness result is equivalent to the one established in the celebrated works of Erdos, Schlein, and Yau. author: - first_name: Thomas full_name: Chen, Thomas last_name: Chen - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Nataša full_name: Pavlović, Nataša last_name: Pavlović - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Chen T, Hainzl C, Pavlović N, Seiringer R. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 2015;68(10):1845-1884. doi:10.1002/cpa.21552 apa: Chen, T., Hainzl, C., Pavlović, N., & Seiringer, R. (2015). Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. Wiley. https://doi.org/10.1002/cpa.21552 chicago: Chen, Thomas, Christian Hainzl, Nataša Pavlović, and Robert Seiringer. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics. Wiley, 2015. https://doi.org/10.1002/cpa.21552. ieee: T. Chen, C. Hainzl, N. Pavlović, and R. Seiringer, “Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti,” Communications on Pure and Applied Mathematics, vol. 68, no. 10. Wiley, pp. 1845–1884, 2015. ista: Chen T, Hainzl C, Pavlović N, Seiringer R. 2015. Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti. Communications on Pure and Applied Mathematics. 68(10), 1845–1884. mla: Chen, Thomas, et al. “Unconditional Uniqueness for the Cubic Gross Pitaevskii Hierarchy via Quantum de Finetti.” Communications on Pure and Applied Mathematics, vol. 68, no. 10, Wiley, 2015, pp. 1845–84, doi:10.1002/cpa.21552. short: T. Chen, C. Hainzl, N. Pavlović, R. Seiringer, Communications on Pure and Applied Mathematics 68 (2015) 1845–1884. date_created: 2018-12-11T11:52:48Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:51:41Z day: '01' department: - _id: RoSe doi: 10.1002/cpa.21552 intvolume: ' 68' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1307.3168 month: '10' oa: 1 oa_version: Preprint page: 1845 - 1884 project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication: Communications on Pure and Applied Mathematics publication_status: published publisher: Wiley publist_id: '5598' quality_controlled: '1' scopus_import: 1 status: public title: Unconditional uniqueness for the cubic gross pitaevskii hierarchy via quantum de finetti type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 68 year: '2015' ... --- _id: '1580' abstract: - lang: eng text: Synapsins (Syns) are an evolutionarily conserved family of presynaptic proteins crucial for the fine-tuning of synaptic function. A large amount of experimental evidences has shown that Syns are involved in the development of epileptic phenotypes and several mutations in Syn genes have been associated with epilepsy in humans and animal models. Syn mutations induce alterations in circuitry and neurotransmitter release, differentially affecting excitatory and inhibitory synapses, thus causing an excitation/inhibition imbalance in network excitability toward hyperexcitability that may be a determinant with regard to the development of epilepsy. Another approach to investigate epileptogenic mechanisms is to understand how silencing Syn affects the cellular behavior of single neurons and is associated with the hyperexcitable phenotypes observed in epilepsy. Here, we examined the functional effects of antisense-RNA inhibition of Syn expression on individually identified and isolated serotonergic cells of the Helix land snail. We found that Helix synapsin silencing increases cell excitability characterized by a slightly depolarized resting membrane potential, decreases the rheobase, reduces the threshold for action potential (AP) firing and increases the mean and instantaneous firing rates, with respect to control cells. The observed increase of Ca2+ and BK currents in Syn-silenced cells seems to be related to changes in the shape of the AP waveform. These currents sustain the faster spiking in Syn-deficient cells by increasing the after hyperpolarization and limiting the Na+ and Ca2+ channel inactivation during repetitive firing. This in turn speeds up the depolarization phase by reaching the AP threshold faster. Our results provide evidence that Syn silencing increases intrinsic cell excitability associated with increased Ca2+ and Ca2+-dependent BK currents in the absence of excitatory or inhibitory inputs. article_processing_charge: No article_type: original author: - first_name: Oscar full_name: Brenes, Oscar last_name: Brenes - first_name: David H full_name: Vandael, David H id: 3AE48E0A-F248-11E8-B48F-1D18A9856A87 last_name: Vandael orcid: 0000-0001-7577-1676 - first_name: Emilio full_name: Carbone, Emilio last_name: Carbone - first_name: Pier full_name: Montarolo, Pier last_name: Montarolo - first_name: Mirella full_name: Ghirardi, Mirella last_name: Ghirardi citation: ama: Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 2015;311:430-443. doi:10.1016/j.neuroscience.2015.10.046 apa: Brenes, O., Vandael, D. H., Carbone, E., Montarolo, P., & Ghirardi, M. (2015). Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. Elsevier. https://doi.org/10.1016/j.neuroscience.2015.10.046 chicago: Brenes, Oscar, David H Vandael, Emilio Carbone, Pier Montarolo, and Mirella Ghirardi. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience. Elsevier, 2015. https://doi.org/10.1016/j.neuroscience.2015.10.046. ieee: O. Brenes, D. H. Vandael, E. Carbone, P. Montarolo, and M. Ghirardi, “Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons,” Neuroscience, vol. 311. Elsevier, pp. 430–443, 2015. ista: Brenes O, Vandael DH, Carbone E, Montarolo P, Ghirardi M. 2015. Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons. Neuroscience. 311, 430–443. mla: Brenes, Oscar, et al. “Knock-down of Synapsin Alters Cell Excitability and Action Potential Waveform by Potentiating BK and Voltage Gated Ca2 Currents in Helix Serotonergic Neurons.” Neuroscience, vol. 311, Elsevier, 2015, pp. 430–43, doi:10.1016/j.neuroscience.2015.10.046. short: O. Brenes, D.H. Vandael, E. Carbone, P. Montarolo, M. Ghirardi, Neuroscience 311 (2015) 430–443. date_created: 2018-12-11T11:52:50Z date_published: 2015-12-17T00:00:00Z date_updated: 2021-01-12T06:51:44Z day: '17' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.neuroscience.2015.10.046 file: - access_level: open_access checksum: af2c4c994718c7be417eba0dc746aac9 content_type: application/pdf creator: dernst date_created: 2020-05-15T06:50:20Z date_updated: 2020-07-14T12:45:02Z file_id: '7849' file_name: 2015_Neuroscience_Brenes.pdf file_size: 5563015 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 311' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version page: 430 - 443 publication: Neuroscience publication_status: published publisher: Elsevier publist_id: '5591' quality_controlled: '1' scopus_import: 1 status: public title: Knock-down of synapsin alters cell excitability and action potential waveform by potentiating BK and voltage gated Ca2 currents in Helix serotonergic neurons tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 311 year: '2015' ... --- _id: '1577' abstract: - lang: eng text: Contrary to the pattern seen in mammalian sex chromosomes, where most Y-linked genes have X-linked homologs, the Drosophila X and Y chromosomes appear to be unrelated. Most of the Y-linked genes have autosomal paralogs, so autosome-to-Y transposition must be the main source of Drosophila Y-linked genes. Here we show how these genes were acquired. We found a previously unidentified gene (flagrante delicto Y, FDY) that originated from a recent duplication of the autosomal gene vig2 to the Y chromosome of Drosophila melanogaster. Four contiguous genes were duplicated along with vig2, but they became pseudogenes through the accumulation of deletions and transposable element insertions, whereas FDY remained functional, acquired testis-specific expression, and now accounts for ∼20% of the vig2-like mRNA in testis. FDY is absent in the closest relatives of D. melanogaster, and DNA sequence divergence indicates that the duplication to the Y chromosome occurred ∼2 million years ago. Thus, FDY provides a snapshot of the early stages of the establishment of a Y-linked gene and demonstrates how the Drosophila Y has been accumulating autosomal genes. acknowledgement: "This work was supported by grants from Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq), FAPERJ, and CAPES (to A.B.C.), and National Institutes of Health Grant R01 GM64590 (to A.G.C. and A.B.C.).\r\nWe thank M. Vibranovski, C. Bergman, and the Berkeley Drosophila Genome Project for access to unpublished data; M. Vibranovski, R. Hoskins, S. Celniker, C. Kennedy, J. Carlson, S. Galasinski, B. Wakimoto, J. Yasuhara, G. Sutton, M. Kuhner, J. Felsenstein, and C. Santos for help in various steps of the work; and B. Bitner-Mathe, R. Ventura, the members of the A.B.C. and A.G.C. laboratories, and two reviewers for many valuable comments on the manuscript." article_processing_charge: No article_type: original author: - first_name: Antonio full_name: Carvalho, Antonio last_name: Carvalho - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 - first_name: Claudia full_name: Russo, Claudia last_name: Russo - first_name: Bonnielin full_name: Swenor, Bonnielin last_name: Swenor - first_name: Andrew full_name: Clark, Andrew last_name: Clark citation: ama: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 2015;112(40):12450-12455. doi:10.1073/pnas.1516543112 apa: Carvalho, A., Vicoso, B., Russo, C., Swenor, B., & Clark, A. (2015). Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1516543112 chicago: Carvalho, Antonio, Beatriz Vicoso, Claudia Russo, Bonnielin Swenor, and Andrew Clark. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1516543112. ieee: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, and A. Clark, “Birth of a new gene on the Y chromosome of Drosophila melanogaster,” PNAS, vol. 112, no. 40. National Academy of Sciences, pp. 12450–12455, 2015. ista: Carvalho A, Vicoso B, Russo C, Swenor B, Clark A. 2015. Birth of a new gene on the Y chromosome of Drosophila melanogaster. PNAS. 112(40), 12450–12455. mla: Carvalho, Antonio, et al. “Birth of a New Gene on the Y Chromosome of Drosophila Melanogaster.” PNAS, vol. 112, no. 40, National Academy of Sciences, 2015, pp. 12450–55, doi:10.1073/pnas.1516543112. short: A. Carvalho, B. Vicoso, C. Russo, B. Swenor, A. Clark, PNAS 112 (2015) 12450–12455. date_created: 2018-12-11T11:52:49Z date_published: 2015-10-06T00:00:00Z date_updated: 2021-01-12T06:51:43Z day: '06' department: - _id: BeVi doi: 10.1073/pnas.1516543112 external_id: pmid: - '26385968' intvolume: ' 112' issue: '40' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4603513/ month: '10' oa: 1 oa_version: Published Version page: 12450 - 12455 pmid: 1 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5594' quality_controlled: '1' scopus_import: 1 status: public title: Birth of a new gene on the Y chromosome of Drosophila melanogaster type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1579' abstract: - lang: eng text: We show that the Galois group of any Schubert problem involving lines in projective space contains the alternating group. This constitutes the largest family of enumerative problems whose Galois groups have been largely determined. Using a criterion of Vakil and a special position argument due to Schubert, our result follows from a particular inequality among Kostka numbers of two-rowed tableaux. In most cases, a combinatorial injection proves the inequality. For the remaining cases, we use the Weyl integral formulas to obtain an integral formula for these Kostka numbers. This rewrites the inequality as an integral, which we estimate to establish the inequality. acknowledgement: "This research was supported in part by NSF grant DMS-915211 and the Institut Mittag-Leffler.\r\n" article_processing_charge: No author: - first_name: Christopher full_name: Brooks, Christopher last_name: Brooks - first_name: Abraham full_name: Martin Del Campo Sanchez, Abraham id: 4CF47F6A-F248-11E8-B48F-1D18A9856A87 last_name: Martin Del Campo Sanchez - first_name: Frank full_name: Sottile, Frank last_name: Sottile citation: ama: Brooks C, Martin del Campo Sanchez A, Sottile F. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 2015;367(6):4183-4206. doi:10.1090/S0002-9947-2014-06192-8 apa: Brooks, C., Martin del Campo Sanchez, A., & Sottile, F. (2015). Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. American Mathematical Society. https://doi.org/10.1090/S0002-9947-2014-06192-8 chicago: Brooks, Christopher, Abraham Martin del Campo Sanchez, and Frank Sottile. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society. American Mathematical Society, 2015. https://doi.org/10.1090/S0002-9947-2014-06192-8. ieee: C. Brooks, A. Martin del Campo Sanchez, and F. Sottile, “Galois groups of Schubert problems of lines are at least alternating,” Transactions of the American Mathematical Society, vol. 367, no. 6. American Mathematical Society, pp. 4183–4206, 2015. ista: Brooks C, Martin del Campo Sanchez A, Sottile F. 2015. Galois groups of Schubert problems of lines are at least alternating. Transactions of the American Mathematical Society. 367(6), 4183–4206. mla: Brooks, Christopher, et al. “Galois Groups of Schubert Problems of Lines Are at Least Alternating.” Transactions of the American Mathematical Society, vol. 367, no. 6, American Mathematical Society, 2015, pp. 4183–206, doi:10.1090/S0002-9947-2014-06192-8. short: C. Brooks, A. Martin del Campo Sanchez, F. Sottile, Transactions of the American Mathematical Society 367 (2015) 4183–4206. date_created: 2018-12-11T11:52:50Z date_published: 2015-06-01T00:00:00Z date_updated: 2021-01-12T06:51:43Z day: '01' department: - _id: CaUh doi: 10.1090/S0002-9947-2014-06192-8 intvolume: ' 367' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1207.4280 month: '06' oa: 1 oa_version: Preprint page: 4183 - 4206 publication: Transactions of the American Mathematical Society publication_status: published publisher: American Mathematical Society publist_id: '5592' quality_controlled: '1' scopus_import: 1 status: public title: Galois groups of Schubert problems of lines are at least alternating type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 367 year: '2015' ... --- _id: '1578' abstract: - lang: eng text: We prove that the dual of the digital Voronoi diagram constructed by flooding the plane from the data points gives a geometrically and topologically correct dual triangulation. This provides the proof of correctness for recently developed GPU algorithms that outperform traditional CPU algorithms for constructing two-dimensional Delaunay triangulations. acknowledgement: "The research of the second author is partially supported by NSF under grant DBI-0820624 and by DARPA under grants HR011-05-1-0057 and HR0011-09-006\r\n" author: - first_name: Thanhtung full_name: Cao, Thanhtung last_name: Cao - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Tiowseng full_name: Tan, Tiowseng last_name: Tan citation: ama: Cao T, Edelsbrunner H, Tan T. Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. 2015;48(7):507-519. doi:10.1016/j.comgeo.2015.04.001 apa: Cao, T., Edelsbrunner, H., & Tan, T. (2015). Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. Elsevier. https://doi.org/10.1016/j.comgeo.2015.04.001 chicago: Cao, Thanhtung, Herbert Edelsbrunner, and Tiowseng Tan. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.04.001. ieee: T. Cao, H. Edelsbrunner, and T. Tan, “Triangulations from topologically correct digital Voronoi diagrams,” Computational Geometry, vol. 48, no. 7. Elsevier, pp. 507–519, 2015. ista: Cao T, Edelsbrunner H, Tan T. 2015. Triangulations from topologically correct digital Voronoi diagrams. Computational Geometry. 48(7), 507–519. mla: Cao, Thanhtung, et al. “Triangulations from Topologically Correct Digital Voronoi Diagrams.” Computational Geometry, vol. 48, no. 7, Elsevier, 2015, pp. 507–19, doi:10.1016/j.comgeo.2015.04.001. short: T. Cao, H. Edelsbrunner, T. Tan, Computational Geometry 48 (2015) 507–519. date_created: 2018-12-11T11:52:49Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:51:43Z day: '01' department: - _id: HeEd doi: 10.1016/j.comgeo.2015.04.001 intvolume: ' 48' issue: '7' language: - iso: eng month: '08' oa_version: None page: 507 - 519 publication: Computational Geometry publication_status: published publisher: Elsevier publist_id: '5593' quality_controlled: '1' scopus_import: 1 status: public title: Triangulations from topologically correct digital Voronoi diagrams type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 48 year: '2015' ... --- _id: '1581' abstract: - lang: eng text: In animal embryos, morphogen gradients determine tissue patterning and morphogenesis. Shyer et al. provide evidence that, during vertebrate gut formation, tissue folding generates graded activity of signals required for subsequent steps of gut growth and differentiation, thereby revealing an intriguing link between tissue morphogenesis and morphogen gradient formation. article_processing_charge: No author: - first_name: Mark Tobias full_name: Bollenbach, Mark Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Bollenbach MT, Heisenberg C-PJ. Gradients are shaping up. Cell. 2015;161(3):431-432. doi:10.1016/j.cell.2015.04.009 apa: Bollenbach, M. T., & Heisenberg, C.-P. J. (2015). Gradients are shaping up. Cell. Cell Press. https://doi.org/10.1016/j.cell.2015.04.009 chicago: Bollenbach, Mark Tobias, and Carl-Philipp J Heisenberg. “Gradients Are Shaping Up.” Cell. Cell Press, 2015. https://doi.org/10.1016/j.cell.2015.04.009. ieee: M. T. Bollenbach and C.-P. J. Heisenberg, “Gradients are shaping up,” Cell, vol. 161, no. 3. Cell Press, pp. 431–432, 2015. ista: Bollenbach MT, Heisenberg C-PJ. 2015. Gradients are shaping up. Cell. 161(3), 431–432. mla: Bollenbach, Mark Tobias, and Carl-Philipp J. Heisenberg. “Gradients Are Shaping Up.” Cell, vol. 161, no. 3, Cell Press, 2015, pp. 431–32, doi:10.1016/j.cell.2015.04.009. short: M.T. Bollenbach, C.-P.J. Heisenberg, Cell 161 (2015) 431–432. date_created: 2018-12-11T11:52:50Z date_published: 2015-04-23T00:00:00Z date_updated: 2022-08-25T13:56:10Z day: '23' department: - _id: ToBo - _id: CaHe doi: 10.1016/j.cell.2015.04.009 intvolume: ' 161' issue: '3' language: - iso: eng month: '04' oa_version: None page: 431 - 432 publication: Cell publication_status: published publisher: Cell Press publist_id: '5590' quality_controlled: '1' scopus_import: '1' status: public title: Gradients are shaping up type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 161 year: '2015' ... --- _id: '1589' abstract: - lang: eng text: We investigate the dynamics of ferrofluidic wavy vortex flows in the counter-rotating Taylor-Couette system, with a focus on wavy flows with a mixture of the dominant azimuthal modes. Without external magnetic field flows are stable and pro-grade with respect to the rotation of the inner cylinder. More complex behaviors can arise when an axial or a transverse magnetic field is applied. Depending on the direction and strength of the field, multi-stable wavy states and bifurcations can occur. We uncover the phenomenon of flow pattern reversal as the strength of the magnetic field is increased through a critical value. In between the regimes of pro-grade and retrograde flow rotations, standing waves with zero angular velocities can emerge. A striking finding is that, under a transverse magnetic field, a second reversal in the flow pattern direction can occur, where the flow pattern evolves into pro-grade rotation again from a retrograde state. Flow reversal is relevant to intriguing phenomena in nature such as geomagnetic reversal. Our results suggest that, in ferrofluids, flow pattern reversal can be induced by varying a magnetic field in a controlled manner, which can be realized in laboratory experiments with potential applications in the development of modern fluid devices. article_number: '18589' article_type: original author: - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 - first_name: Younghae full_name: Do, Younghae last_name: Do - first_name: Ying full_name: Lai, Ying last_name: Lai citation: ama: Altmeyer S, Do Y, Lai Y. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 2015;5. doi:10.1038/srep18589 apa: Altmeyer, S., Do, Y., & Lai, Y. (2015). Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep18589 chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep18589. ieee: S. Altmeyer, Y. Do, and Y. Lai, “Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system,” Scientific Reports, vol. 5. Nature Publishing Group, 2015. ista: Altmeyer S, Do Y, Lai Y. 2015. Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system. Scientific Reports. 5, 18589. mla: Altmeyer, Sebastian, et al. “Magnetic Field Induced Flow Pattern Reversal in a Ferrofluidic Taylor-Couette System.” Scientific Reports, vol. 5, 18589, Nature Publishing Group, 2015, doi:10.1038/srep18589. short: S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015). date_created: 2018-12-11T11:52:53Z date_published: 2015-12-21T00:00:00Z date_updated: 2021-01-12T06:51:48Z day: '21' ddc: - '530' - '540' department: - _id: BjHo doi: 10.1038/srep18589 file: - access_level: open_access checksum: 927e151674347661ce36eae2818dafdc content_type: application/pdf creator: system date_created: 2018-12-12T10:13:49Z date_updated: 2020-07-14T12:45:03Z file_id: '5036' file_name: IST-2016-472-v1+1_srep18589.pdf file_size: 2771236 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '5582' pubrep_id: '472' quality_controlled: '1' scopus_import: 1 status: public title: Magnetic field induced flow pattern reversal in a ferrofluidic Taylor-Couette system 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: 5 year: '2015' ... --- _id: '1584' abstract: - lang: eng text: We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights. author: - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Dominik full_name: Kaaser, Dominik last_name: Kaaser - first_name: Peter full_name: Palfrader, Peter last_name: Palfrader citation: ama: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 2015;48(5):429-442. doi:10.1016/j.comgeo.2015.01.004' apa: 'Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2015.01.004' chicago: 'Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2015.01.004.' ieee: 'T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Reprint of: Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 5. Elsevier, pp. 429–442, 2015.' ista: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Reprint of: Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(5), 429–442.' mla: 'Biedl, Therese, et al. “Reprint of: Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 5, Elsevier, 2015, pp. 429–42, doi:10.1016/j.comgeo.2015.01.004.' short: 'T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 429–442.' date_created: 2018-12-11T11:52:51Z date_published: 2015-07-01T00:00:00Z date_updated: 2023-02-23T10:05:22Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1016/j.comgeo.2015.01.004 file: - access_level: open_access checksum: 5b33719a86f7f4c8e5dc62c1b6893f49 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:36Z date_updated: 2020-07-14T12:45:03Z file_id: '5292' file_name: IST-2016-475-v1+1_1-s2.0-S092577211500005X-main.pdf file_size: 508379 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 48' issue: '5' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 429 - 442 publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '5587' pubrep_id: '475' quality_controlled: '1' related_material: record: - id: '1582' relation: other status: public scopus_import: 1 status: public title: 'Reprint of: Weighted straight skeletons in the plane' 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: 48 year: '2015' ... --- _id: '1582' abstract: - lang: eng text: We investigate weighted straight skeletons from a geometric, graph-theoretical, and combinatorial point of view. We start with a thorough definition and shed light on some ambiguity issues in the procedural definition. We investigate the geometry, combinatorics, and topology of faces and the roof model, and we discuss in which cases a weighted straight skeleton is connected. Finally, we show that the weighted straight skeleton of even a simple polygon may be non-planar and may contain cycles, and we discuss under which restrictions on the weights and/or the input polygon the weighted straight skeleton still behaves similar to its unweighted counterpart. In particular, we obtain a non-procedural description and a linear-time construction algorithm for the straight skeleton of strictly convex polygons with arbitrary weights. author: - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Dominik full_name: Kaaser, Dominik last_name: Kaaser - first_name: Peter full_name: Palfrader, Peter last_name: Palfrader citation: ama: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 2015;48(2):120-133. doi:10.1016/j.comgeo.2014.08.006' apa: 'Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2014.08.006' chicago: 'Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications. Elsevier, 2015. https://doi.org/10.1016/j.comgeo.2014.08.006.' ieee: 'T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “Weighted straight skeletons in the plane,” Computational Geometry: Theory and Applications, vol. 48, no. 2. Elsevier, pp. 120–133, 2015.' ista: 'Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. Weighted straight skeletons in the plane. Computational Geometry: Theory and Applications. 48(2), 120–133.' mla: 'Biedl, Therese, et al. “Weighted Straight Skeletons in the Plane.” Computational Geometry: Theory and Applications, vol. 48, no. 2, Elsevier, 2015, pp. 120–33, doi:10.1016/j.comgeo.2014.08.006.' short: 'T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Computational Geometry: Theory and Applications 48 (2015) 120–133.' date_created: 2018-12-11T11:52:51Z date_published: 2015-02-01T00:00:00Z date_updated: 2023-02-23T10:05:27Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1016/j.comgeo.2014.08.006 file: - access_level: open_access checksum: c1ef67f6ec925e12f73a96b8fe285ab4 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:28Z date_updated: 2020-07-14T12:45:02Z file_id: '5215' file_name: IST-2016-474-v1+1_1-s2.0-S0925772114000807-main.pdf file_size: 505987 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 48' issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 120 - 133 publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '5589' pubrep_id: '474' quality_controlled: '1' related_material: record: - id: '1584' relation: other status: public scopus_import: 1 status: public title: Weighted straight skeletons in the plane 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: 48 year: '2015' ... --- _id: '1583' abstract: - lang: eng text: We study the characteristics of straight skeletons of monotone polygonal chains and use them to devise an algorithm for computing positively weighted straight skeletons of monotone polygons. Our algorithm runs in O(nlogn) time and O(n) space, where n denotes the number of vertices of the polygon. author: - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Dominik full_name: Kaaser, Dominik last_name: Kaaser - first_name: Peter full_name: Palfrader, Peter last_name: Palfrader citation: ama: Biedl T, Held M, Huber S, Kaaser D, Palfrader P. A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 2015;115(2):243-247. doi:10.1016/j.ipl.2014.09.021 apa: Biedl, T., Held, M., Huber, S., Kaaser, D., & Palfrader, P. (2015). A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. Elsevier. https://doi.org/10.1016/j.ipl.2014.09.021 chicago: Biedl, Therese, Martin Held, Stefan Huber, Dominik Kaaser, and Peter Palfrader. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters. Elsevier, 2015. https://doi.org/10.1016/j.ipl.2014.09.021. ieee: T. Biedl, M. Held, S. Huber, D. Kaaser, and P. Palfrader, “A simple algorithm for computing positively weighted straight skeletons of monotone polygons,” Information Processing Letters, vol. 115, no. 2. Elsevier, pp. 243–247, 2015. ista: Biedl T, Held M, Huber S, Kaaser D, Palfrader P. 2015. A simple algorithm for computing positively weighted straight skeletons of monotone polygons. Information Processing Letters. 115(2), 243–247. mla: Biedl, Therese, et al. “A Simple Algorithm for Computing Positively Weighted Straight Skeletons of Monotone Polygons.” Information Processing Letters, vol. 115, no. 2, Elsevier, 2015, pp. 243–47, doi:10.1016/j.ipl.2014.09.021. short: T. Biedl, M. Held, S. Huber, D. Kaaser, P. Palfrader, Information Processing Letters 115 (2015) 243–247. date_created: 2018-12-11T11:52:51Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:51:45Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1016/j.ipl.2014.09.021 file: - access_level: open_access checksum: 2779a648610c9b5c86d0b51a62816d23 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:45Z date_updated: 2020-07-14T12:45:03Z file_id: '5367' file_name: IST-2016-473-v1+1_1-s2.0-S0020019014001987-main.pdf file_size: 270137 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 115' issue: '2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version page: 243 - 247 publication: Information Processing Letters publication_status: published publisher: Elsevier publist_id: '5588' pubrep_id: '473' quality_controlled: '1' scopus_import: 1 status: public title: A simple algorithm for computing positively weighted straight skeletons of monotone polygons 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: 115 year: '2015' ... --- _id: '1587' abstract: - lang: eng text: We investigate the quantum interference shifts between energetically close states, where the state structure is observed by laser spectroscopy. We report a compact and analytical expression that models the quantum interference induced shift for any admixture of circular polarization of the incident laser and angle of observation. An experimental scenario free of quantum interference can thus be predicted with this formula. Although this study is exemplified here for muonic deuterium, it can be applied to any other laser spectroscopy measurement of ns-n′p frequencies of a nonrelativistic atomic system, via an ns→n′p→n′′s scheme. article_number: '062506' article_processing_charge: No article_type: original author: - first_name: Pedro full_name: Amaro, Pedro last_name: Amaro - first_name: Filippo full_name: Fratini, Filippo last_name: Fratini - first_name: Laleh full_name: Safari, Laleh id: 3C325E5E-F248-11E8-B48F-1D18A9856A87 last_name: Safari - first_name: Aldo full_name: Antognini, Aldo last_name: Antognini - first_name: Paul full_name: Indelicato, Paul last_name: Indelicato - first_name: Randolf full_name: Pohl, Randolf last_name: Pohl - first_name: José full_name: Santos, José last_name: Santos citation: ama: Amaro P, Fratini F, Safari L, et al. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 2015;92(6). doi:10.1103/PhysRevA.92.062506 apa: Amaro, P., Fratini, F., Safari, L., Antognini, A., Indelicato, P., Pohl, R., & Santos, J. (2015). Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.92.062506 chicago: Amaro, Pedro, Filippo Fratini, Laleh Safari, Aldo Antognini, Paul Indelicato, Randolf Pohl, and José Santos. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.062506. ieee: P. Amaro et al., “Quantum interference shifts in laser spectroscopy with elliptical polarization,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6. American Physical Society, 2015. ista: Amaro P, Fratini F, Safari L, Antognini A, Indelicato P, Pohl R, Santos J. 2015. Quantum interference shifts in laser spectroscopy with elliptical polarization. Physical Review A - Atomic, Molecular, and Optical Physics. 92(6), 062506. mla: Amaro, Pedro, et al. “Quantum Interference Shifts in Laser Spectroscopy with Elliptical Polarization.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 92, no. 6, 062506, American Physical Society, 2015, doi:10.1103/PhysRevA.92.062506. short: P. Amaro, F. Fratini, L. Safari, A. Antognini, P. Indelicato, R. Pohl, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 92 (2015). date_created: 2018-12-11T11:52:53Z date_published: 2015-12-31T00:00:00Z date_updated: 2021-01-12T06:51:47Z day: '31' department: - _id: MiLe doi: 10.1103/PhysRevA.92.062506 ec_funded: 1 external_id: arxiv: - '1511.03585' intvolume: ' 92' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1511.03585 month: '12' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review A - Atomic, Molecular, and Optical Physics publication_status: published publisher: American Physical Society publist_id: '5584' quality_controlled: '1' scopus_import: 1 status: public title: Quantum interference shifts in laser spectroscopy with elliptical polarization type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2015' ... --- _id: '1588' abstract: - lang: eng text: 'We investigate the Taylor-Couette system where the radius ratio is close to unity. Systematically increasing the Reynolds number, we observe a number of previously known transitions, such as one from the classical Taylor vortex flow (TVF) to wavy vortex flow (WVF) and the transition to fully developed turbulence. Prior to the onset of turbulence, we observe intermittent bursting patterns of localized turbulent patches, confirming the experimentally observed pattern of very short wavelength bursts (VSWBs). A striking finding is that, for a Reynolds number larger than that for the onset of VSWBs, a new type of intermittently bursting behavior emerges: patterns of azimuthally closed rings of various orders. We call them ring-bursting patterns, which surround the cylinder completely but remain localized and separated in the axial direction through nonturbulent wavy structures. We employ a number of quantitative measures including the cross-flow energy to characterize the ring-bursting patterns and to distinguish them from the background flow. These patterns are interesting because they do not occur in the wide-gap Taylor-Couette flow systems. The narrow-gap regime is less studied but certainly deserves further attention to gain deeper insights into complex flow dynamics in fluids.' article_number: '053018' author: - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 - first_name: Younghae full_name: Do, Younghae last_name: Do - first_name: Ying full_name: Lai, Ying last_name: Lai citation: ama: Altmeyer S, Do Y, Lai Y. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. 2015;92(5). doi:10.1103/PhysRevE.92.053018 apa: Altmeyer, S., Do, Y., & Lai, Y. (2015). Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.92.053018 chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” Physical Review E. American Physical Society, 2015. https://doi.org/10.1103/PhysRevE.92.053018. ieee: S. Altmeyer, Y. Do, and Y. Lai, “Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows,” Physical Review E, vol. 92, no. 5. American Physical Society, 2015. ista: Altmeyer S, Do Y, Lai Y. 2015. Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows. Physical Review E. 92(5), 053018. mla: Altmeyer, Sebastian, et al. “Ring-Bursting Behavior En Route to Turbulence in Narrow-Gap Taylor-Couette Flows.” Physical Review E, vol. 92, no. 5, 053018, American Physical Society, 2015, doi:10.1103/PhysRevE.92.053018. short: S. Altmeyer, Y. Do, Y. Lai, Physical Review E 92 (2015). date_created: 2018-12-11T11:52:53Z date_published: 2015-11-24T00:00:00Z date_updated: 2021-01-12T06:51:47Z day: '24' department: - _id: BjHo doi: 10.1103/PhysRevE.92.053018 intvolume: ' 92' issue: '5' language: - iso: eng month: '11' oa_version: None publication: Physical Review E publication_status: published publisher: American Physical Society publist_id: '5583' quality_controlled: '1' scopus_import: 1 status: public title: Ring-bursting behavior en route to turbulence in narrow-gap Taylor-Couette flows type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2015' ... --- _id: '1586' abstract: - lang: eng text: Through metabolic engineering cyanobacteria can be employed in biotechnology. Combining the capacity for oxygenic photosynthesis and carbon fixation with an engineered metabolic pathway allows carbon-based product formation from CO2, light, and water directly. Such cyanobacterial 'cell factories' are constructed to produce biofuels, bioplastics, and commodity chemicals. Efforts of metabolic engineers and synthetic biologists allow the modification of the intermediary metabolism at various branching points, expanding the product range. The new biosynthesis routes 'tap' the metabolism ever more efficiently, particularly through the engineering of driving forces and utilization of cofactors generated during the light reactions of photosynthesis, resulting in higher product titers. High rates of carbon rechanneling ultimately allow an almost-complete allocation of fixed carbon to product above biomass. author: - first_name: Andreas full_name: Angermayr, Andreas id: 4677C796-F248-11E8-B48F-1D18A9856A87 last_name: Angermayr orcid: 0000-0001-8619-2223 - first_name: Aleix full_name: Gorchs, Aleix last_name: Gorchs - first_name: Klaas full_name: Hellingwerf, Klaas last_name: Hellingwerf citation: ama: Angermayr A, Gorchs A, Hellingwerf K. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. 2015;33(6):352-361. doi:10.1016/j.tibtech.2015.03.009 apa: Angermayr, A., Gorchs, A., & Hellingwerf, K. (2015). Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. Elsevier. https://doi.org/10.1016/j.tibtech.2015.03.009 chicago: Angermayr, Andreas, Aleix Gorchs, and Klaas Hellingwerf. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” Trends in Biotechnology. Elsevier, 2015. https://doi.org/10.1016/j.tibtech.2015.03.009. ieee: A. Angermayr, A. Gorchs, and K. Hellingwerf, “Metabolic engineering of cyanobacteria for the synthesis of commodity products,” Trends in Biotechnology, vol. 33, no. 6. Elsevier, pp. 352–361, 2015. ista: Angermayr A, Gorchs A, Hellingwerf K. 2015. Metabolic engineering of cyanobacteria for the synthesis of commodity products. Trends in Biotechnology. 33(6), 352–361. mla: Angermayr, Andreas, et al. “Metabolic Engineering of Cyanobacteria for the Synthesis of Commodity Products.” Trends in Biotechnology, vol. 33, no. 6, Elsevier, 2015, pp. 352–61, doi:10.1016/j.tibtech.2015.03.009. short: A. Angermayr, A. Gorchs, K. Hellingwerf, Trends in Biotechnology 33 (2015) 352–361. date_created: 2018-12-11T11:52:52Z date_published: 2015-06-01T00:00:00Z date_updated: 2021-01-12T06:51:46Z day: '01' department: - _id: ToBo doi: 10.1016/j.tibtech.2015.03.009 intvolume: ' 33' issue: '6' language: - iso: eng month: '06' oa_version: None page: 352 - 361 publication: Trends in Biotechnology publication_status: published publisher: Elsevier publist_id: '5585' quality_controlled: '1' scopus_import: 1 status: public title: Metabolic engineering of cyanobacteria for the synthesis of commodity products type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2015' ... --- _id: '1585' abstract: - lang: eng text: In this paper, we consider the fluctuation of mutual information statistics of a multiple input multiple output channel communication systems without assuming that the entries of the channel matrix have zero pseudovariance. To this end, we also establish a central limit theorem of the linear spectral statistics for sample covariance matrices under general moment conditions by removing the restrictions imposed on the second moment and fourth moment on the matrix entries in Bai and Silverstein (2004). acknowledgement: "G. Pan was supported by MOE Tier 2 under Grant 2014-T2-2-060 and in part by Tier 1 under Grant RG25/14 through the Nanyang Technological University, Singapore. W. Zhou was supported by the National University of Singapore, Singapore, under Grant R-155-000-131-112.\r\n" author: - first_name: Zhigang full_name: Bao, Zhigang id: 442E6A6C-F248-11E8-B48F-1D18A9856A87 last_name: Bao orcid: 0000-0003-3036-1475 - first_name: Guangming full_name: Pan, Guangming last_name: Pan - first_name: Wang full_name: Zhou, Wang last_name: Zhou citation: ama: Bao Z, Pan G, Zhou W. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. 2015;61(6):3413-3426. doi:10.1109/TIT.2015.2421894 apa: Bao, Z., Pan, G., & Zhou, W. (2015). Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2015.2421894 chicago: Bao, Zhigang, Guangming Pan, and Wang Zhou. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” IEEE Transactions on Information Theory. IEEE, 2015. https://doi.org/10.1109/TIT.2015.2421894. ieee: Z. Bao, G. Pan, and W. Zhou, “Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices,” IEEE Transactions on Information Theory, vol. 61, no. 6. IEEE, pp. 3413–3426, 2015. ista: Bao Z, Pan G, Zhou W. 2015. Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices. IEEE Transactions on Information Theory. 61(6), 3413–3426. mla: Bao, Zhigang, et al. “Asymptotic Mutual Information Statistics of MIMO Channels and CLT of Sample Covariance Matrices.” IEEE Transactions on Information Theory, vol. 61, no. 6, IEEE, 2015, pp. 3413–26, doi:10.1109/TIT.2015.2421894. short: Z. Bao, G. Pan, W. Zhou, IEEE Transactions on Information Theory 61 (2015) 3413–3426. date_created: 2018-12-11T11:52:52Z date_published: 2015-06-01T00:00:00Z date_updated: 2021-01-12T06:51:46Z day: '01' department: - _id: LaEr doi: 10.1109/TIT.2015.2421894 intvolume: ' 61' issue: '6' language: - iso: eng month: '06' oa_version: None page: 3413 - 3426 publication: IEEE Transactions on Information Theory publication_status: published publisher: IEEE publist_id: '5586' quality_controlled: '1' scopus_import: 1 status: public title: Asymptotic mutual information statistics of MIMO channels and CLT of sample covariance matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 61 year: '2015' ... --- _id: '1593' abstract: - lang: eng text: 'Plants are sessile organisms that are permanently restricted to their site of germination. To compensate for their lack of mobility, plants evolved unique mechanisms enabling them to rapidly react to ever changing environmental conditions and flexibly adapt their postembryonic developmental program. A prominent demonstration of this developmental plasticity is their ability to bend organs in order to reach the position most optimal for growth and utilization of light, nutrients, and other resources. Shortly after germination, dicotyledonous seedlings form a bended structure, the so-called apical hook, to protect the delicate shoot meristem and cotyledons from damage when penetrating through the soil. Upon perception of a light stimulus, the apical hook rapidly opens and the photomorphogenic developmental program is activated. After germination, plant organs are able to align their growth with the light source and adopt the most favorable orientation through bending, in a process named phototropism. On the other hand, when roots and shoots are diverted from their upright orientation, they immediately detect a change in the gravity vector and bend to maintain a vertical growth direction. Noteworthy, despite the diversity of external stimuli perceived by different plant organs, all plant tropic movements share a common mechanistic basis: differential cell growth. In our review, we will discuss the molecular principles underlying various tropic responses with the focus on mechanisms mediating the perception of external signals, transduction cascades and downstream responses that regulate differential cell growth and consequently, organ bending. In particular, we highlight common and specific features of regulatory pathways in control of the bending of organs and a role for the plant hormone auxin as a key regulatory component.' author: - first_name: Petra full_name: Žádníková, Petra last_name: Žádníková - first_name: Dajo full_name: Smet, Dajo last_name: Smet - first_name: Qiang full_name: Zhu, Qiang id: 40A4B9E6-F248-11E8-B48F-1D18A9856A87 last_name: Zhu - first_name: Dominique full_name: Van Der Straeten, Dominique last_name: Van Der Straeten - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: 'Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 2015;6(4). doi:10.3389/fpls.2015.00218' apa: 'Žádníková, P., Smet, D., Zhu, Q., Van Der Straeten, D., & Benková, E. (2015). Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. Frontiers Research Foundation. https://doi.org/10.3389/fpls.2015.00218' chicago: 'Žádníková, Petra, Dajo Smet, Qiang Zhu, Dominique Van Der Straeten, and Eva Benková. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fpls.2015.00218.' ieee: 'P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, and E. Benková, “Strategies of seedlings to overcome their sessile nature: Auxin in mobility control,” Frontiers in Plant Science, vol. 6, no. 4. Frontiers Research Foundation, 2015.' ista: 'Žádníková P, Smet D, Zhu Q, Van Der Straeten D, Benková E. 2015. Strategies of seedlings to overcome their sessile nature: Auxin in mobility control. Frontiers in Plant Science. 6(4).' mla: 'Žádníková, Petra, et al. “Strategies of Seedlings to Overcome Their Sessile Nature: Auxin in Mobility Control.” Frontiers in Plant Science, vol. 6, no. 4, Frontiers Research Foundation, 2015, doi:10.3389/fpls.2015.00218.' short: P. Žádníková, D. Smet, Q. Zhu, D. Van Der Straeten, E. Benková, Frontiers in Plant Science 6 (2015). date_created: 2018-12-11T11:52:55Z date_published: 2015-04-14T00:00:00Z date_updated: 2021-01-12T06:51:50Z day: '14' ddc: - '570' department: - _id: EvBe doi: 10.3389/fpls.2015.00218 ec_funded: 1 file: - access_level: open_access checksum: c454d642e18dfa86820b97a86cd6d3cc content_type: application/pdf creator: system date_created: 2018-12-12T10:15:23Z date_updated: 2020-07-14T12:45:03Z file_id: '5142' file_name: IST-2016-471-v1+1_fpls-06-00218.pdf file_size: 965690 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 6' issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis publication: Frontiers in Plant Science publication_status: published publisher: Frontiers Research Foundation publist_id: '5578' pubrep_id: '471' quality_controlled: '1' scopus_import: 1 status: public title: 'Strategies of seedlings to overcome their sessile nature: Auxin in mobility control' 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: 6 year: '2015' ... --- _id: '1595' abstract: - lang: eng text: 'A drawing of a graph G is radial if the vertices of G are placed on concentric circles C1, . . . , Ck with common center c, and edges are drawn radially: every edge intersects every circle centered at c at most once. G is radial planar if it has a radial embedding, that is, a crossing- free radial drawing. If the vertices of G are ordered or partitioned into ordered levels (as they are for leveled graphs), we require that the assignment of vertices to circles corresponds to the given ordering or leveling. We show that a graph G is radial planar if G has a radial drawing in which every two edges cross an even number of times; the radial embedding has the same leveling as the radial drawing. In other words, we establish the weak variant of the Hanani-Tutte theorem for radial planarity. This generalizes a result by Pach and Tóth.' acknowledgement: The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no [291734]. alternative_title: - LNCS author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Michael full_name: Pelsmajer, Michael last_name: Pelsmajer - first_name: Marcus full_name: Schaefer, Marcus last_name: Schaefer citation: ama: 'Fulek R, Pelsmajer M, Schaefer M. Hanani-Tutte for radial planarity. In: Vol 9411. Springer; 2015:99-110. doi:10.1007/978-3-319-27261-0_9' apa: 'Fulek, R., Pelsmajer, M., & Schaefer, M. (2015). Hanani-Tutte for radial planarity (Vol. 9411, pp. 99–110). Presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA: Springer. https://doi.org/10.1007/978-3-319-27261-0_9' chicago: Fulek, Radoslav, Michael Pelsmajer, and Marcus Schaefer. “Hanani-Tutte for Radial Planarity,” 9411:99–110. Springer, 2015. https://doi.org/10.1007/978-3-319-27261-0_9. ieee: 'R. Fulek, M. Pelsmajer, and M. Schaefer, “Hanani-Tutte for radial planarity,” presented at the GD: Graph Drawing and Network Visualization, Los Angeles, CA, USA, 2015, vol. 9411, pp. 99–110.' ista: 'Fulek R, Pelsmajer M, Schaefer M. 2015. Hanani-Tutte for radial planarity. GD: Graph Drawing and Network Visualization, LNCS, vol. 9411, 99–110.' mla: Fulek, Radoslav, et al. Hanani-Tutte for Radial Planarity. Vol. 9411, Springer, 2015, pp. 99–110, doi:10.1007/978-3-319-27261-0_9. short: R. Fulek, M. Pelsmajer, M. Schaefer, in:, Springer, 2015, pp. 99–110. conference: end_date: 2015-09-26 location: Los Angeles, CA, USA name: 'GD: Graph Drawing and Network Visualization' start_date: 2015-09-24 date_created: 2018-12-11T11:52:55Z date_published: 2015-11-27T00:00:00Z date_updated: 2023-02-21T16:23:36Z day: '27' ddc: - '510' department: - _id: UlWa doi: 10.1007/978-3-319-27261-0_9 ec_funded: 1 file: - access_level: open_access checksum: 685f91bd077a951ba067d42cce75409e content_type: application/pdf creator: system date_created: 2018-12-12T10:08:36Z date_updated: 2020-07-14T12:45:03Z file_id: '4697' file_name: IST-2016-594-v1+1_HTCylinder_GD_Revision.pdf file_size: 330135 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 9411' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 99 - 110 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5576' pubrep_id: '594' quality_controlled: '1' related_material: record: - id: '1113' relation: later_version status: public - id: '1164' relation: later_version status: public scopus_import: 1 status: public title: Hanani-Tutte for radial planarity type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 9411 year: '2015' ... --- _id: '1590' abstract: - lang: eng text: 'The straight skeleton of a polygon is the geometric graph obtained by tracing the vertices during a mitered offsetting process. It is known that the straight skeleton of a simple polygon is a tree, and one can naturally derive directions on the edges of the tree from the propagation of the shrinking process. In this paper, we ask the reverse question: Given a tree with directed edges, can it be the straight skeleton of a polygon? And if so, can we find a suitable simple polygon? We answer these questions for all directed trees where the order of edges around each node is fixed.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Oswin full_name: Aichholzer, Oswin last_name: Aichholzer - first_name: Therese full_name: Biedl, Therese last_name: Biedl - first_name: Thomas full_name: Hackl, Thomas last_name: Hackl - first_name: Martin full_name: Held, Martin last_name: Held - first_name: Stefan full_name: Huber, Stefan id: 4700A070-F248-11E8-B48F-1D18A9856A87 last_name: Huber orcid: 0000-0002-8871-5814 - first_name: Peter full_name: Palfrader, Peter last_name: Palfrader - first_name: Birgit full_name: Vogtenhuber, Birgit last_name: Vogtenhuber citation: ama: 'Aichholzer O, Biedl T, Hackl T, et al. Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:335-347. doi:10.1007/978-3-319-27261-0_28' apa: 'Aichholzer, O., Biedl, T., Hackl, T., Held, M., Huber, S., Palfrader, P., & Vogtenhuber, B. (2015). Representing directed trees as straight skeletons. In Graph Drawing and Network Visualization (Vol. 9411, pp. 335–347). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_28' chicago: Aichholzer, Oswin, Therese Biedl, Thomas Hackl, Martin Held, Stefan Huber, Peter Palfrader, and Birgit Vogtenhuber. “Representing Directed Trees as Straight Skeletons.” In Graph Drawing and Network Visualization, 9411:335–47. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_28. ieee: O. Aichholzer et al., “Representing directed trees as straight skeletons,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–347. ista: 'Aichholzer O, Biedl T, Hackl T, Held M, Huber S, Palfrader P, Vogtenhuber B. 2015.Representing directed trees as straight skeletons. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 335–347.' mla: Aichholzer, Oswin, et al. “Representing Directed Trees as Straight Skeletons.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 335–47, doi:10.1007/978-3-319-27261-0_28. short: O. Aichholzer, T. Biedl, T. Hackl, M. Held, S. Huber, P. Palfrader, B. Vogtenhuber, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 335–347. conference: end_date: 2015-09-26 location: Los Angeles, CA, United States name: 'GD: International Symposium on Graph Drawing' start_date: 2015-09-24 date_created: 2018-12-11T11:52:54Z date_published: 2015-11-27T00:00:00Z date_updated: 2022-01-28T09:10:37Z day: '27' department: - _id: HeEd doi: 10.1007/978-3-319-27261-0_28 intvolume: ' 9411' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1508.01076 month: '11' oa: 1 oa_version: Preprint page: 335 - 347 publication: Graph Drawing and Network Visualization publication_identifier: eisbn: - 978-3-319-27261-0 isbn: - 978-3-319-27260-3 publication_status: published publisher: Springer Nature publist_id: '5581' quality_controlled: '1' scopus_import: '1' status: public title: Representing directed trees as straight skeletons type: book_chapter user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9411 year: '2015' ... --- _id: '1594' abstract: - lang: eng text: Quantitative extensions of temporal logics have recently attracted significant attention. In this work, we study frequency LTL (fLTL), an extension of LTL which allows to speak about frequencies of events along an execution. Such an extension is particularly useful for probabilistic systems that often cannot fulfil strict qualitative guarantees on the behaviour. It has been recently shown that controller synthesis for Markov decision processes and fLTL is decidable when all the bounds on frequencies are 1. As a step towards a complete quantitative solution, we show that the problem is decidable for the fragment fLTL\GU, where U does not occur in the scope of G (but still F can). Our solution is based on a novel translation of such quantitative formulae into equivalent deterministic automata. acknowledgement: "This work is partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by the Czech Science Foundation under grant agreement P202/12/G061, by the EU 7th Framework Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the CDZ project 1023 (CAP), by the CAS/SAFEA International Partnership Program for Creative Research Teams, by the EPSRC grant EP/M023656/1, by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) REA Grant No 291734, by the Austrian Science Fund (FWF) S11407-N23 (RiSE/SHiNE), and by the ERC Start Grant (279307: Graph Games).\r\n" alternative_title: - LNCS author: - first_name: Vojtěch full_name: Forejt, Vojtěch last_name: Forejt - first_name: Jan full_name: Krčál, Jan last_name: Krčál - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 citation: ama: 'Forejt V, Krčál J, Kretinsky J. Controller synthesis for MDPs and frequency LTL\GU. In: Vol 9450. Springer; 2015:162-177. doi:10.1007/978-3-662-48899-7_12' apa: 'Forejt, V., Krčál, J., & Kretinsky, J. (2015). Controller synthesis for MDPs and frequency LTL\GU (Vol. 9450, pp. 162–177). Presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji: Springer. https://doi.org/10.1007/978-3-662-48899-7_12' chicago: Forejt, Vojtěch, Jan Krčál, and Jan Kretinsky. “Controller Synthesis for MDPs and Frequency LTL\GU,” 9450:162–77. Springer, 2015. https://doi.org/10.1007/978-3-662-48899-7_12. ieee: 'V. Forejt, J. Krčál, and J. Kretinsky, “Controller synthesis for MDPs and frequency LTL\GU,” presented at the LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, Suva, Fiji, 2015, vol. 9450, pp. 162–177.' ista: 'Forejt V, Krčál J, Kretinsky J. 2015. Controller synthesis for MDPs and frequency LTL\GU. LPAR: Logic for Programming, Artificial Intelligence, and Reasoning, LNCS, vol. 9450, 162–177.' mla: Forejt, Vojtěch, et al. Controller Synthesis for MDPs and Frequency LTL\GU. Vol. 9450, Springer, 2015, pp. 162–77, doi:10.1007/978-3-662-48899-7_12. short: V. Forejt, J. Krčál, J. Kretinsky, in:, Springer, 2015, pp. 162–177. conference: end_date: 2015-11-28 location: Suva, Fiji name: 'LPAR: Logic for Programming, Artificial Intelligence, and Reasoning' start_date: 2015-11-24 date_created: 2018-12-11T11:52:55Z date_published: 2015-11-22T00:00:00Z date_updated: 2021-01-12T06:51:50Z day: '22' department: - _id: ToHe - _id: KrCh doi: 10.1007/978-3-662-48899-7_12 ec_funded: 1 intvolume: ' 9450' language: - iso: eng month: '11' oa_version: None page: 162 - 177 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication_status: published publisher: Springer publist_id: '5577' quality_controlled: '1' scopus_import: 1 status: public title: Controller synthesis for MDPs and frequency LTL\GU type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9450 year: '2015' ... --- _id: '1596' abstract: - lang: eng text: Let C={C1,...,Cn} denote a collection of translates of a regular convex k-gon in the plane with the stacking order. The collection C forms a visibility clique if for everyi < j the intersection Ci and (Ci ∩ Cj)\⋃i<l<jCl =∅.elements that are stacked between them, i.e., We show that if C forms a visibility clique its size is bounded from above by O(k4) thereby improving the upper bound of 22k from the aforementioned paper. We also obtain an upper bound of 22(k/2)+2 on the size of a visibility clique for homothetes of a convex (not necessarily regular) k-gon. 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: Radoš full_name: Radoičić, Radoš last_name: Radoičić citation: ama: 'Fulek R, Radoičić R. Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. Vol 9411. Springer Nature; 2015:373-379. doi:10.1007/978-3-319-27261-0_31' apa: 'Fulek, R., & Radoičić, R. (2015). Vertical visibility among parallel polygons in three dimensions. In Graph Drawing and Network Visualization (Vol. 9411, pp. 373–379). Los Angeles, CA, United States: Springer Nature. https://doi.org/10.1007/978-3-319-27261-0_31' chicago: Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” In Graph Drawing and Network Visualization, 9411:373–79. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-27261-0_31. ieee: R. Fulek and R. Radoičić, “Vertical visibility among parallel polygons in three dimensions,” in Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–379. ista: 'Fulek R, Radoičić R. 2015.Vertical visibility among parallel polygons in three dimensions. In: Graph Drawing and Network Visualization. LNCS, vol. 9411, 373–379.' mla: Fulek, Radoslav, and Radoš Radoičić. “Vertical Visibility among Parallel Polygons in Three Dimensions.” Graph Drawing and Network Visualization, vol. 9411, Springer Nature, 2015, pp. 373–79, doi:10.1007/978-3-319-27261-0_31. short: R. Fulek, R. Radoičić, in:, Graph Drawing and Network Visualization, Springer Nature, 2015, pp. 373–379. conference: end_date: 2015-09-26 location: Los Angeles, CA, United States name: 'GD: Graph Drawing and Network Visualization' start_date: 2015-09-24 date_created: 2018-12-11T11:52:56Z date_published: 2015-11-27T00:00:00Z date_updated: 2022-01-28T09:20:50Z day: '27' ddc: - '510' department: - _id: UlWa doi: 10.1007/978-3-319-27261-0_31 ec_funded: 1 file: - access_level: open_access checksum: eec04f86c5921d04f025d5791db9b965 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:06Z date_updated: 2020-07-14T12:45:04Z file_id: '5258' file_name: IST-2016-595-v1+1_VerticalVisibilityGDRevision.pdf file_size: 312992 relation: main_file file_date_updated: 2020-07-14T12:45:04Z has_accepted_license: '1' intvolume: ' 9411' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 373 - 379 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Graph Drawing and Network Visualization publication_identifier: isbn: - 978-3-319-27260-3 publication_status: published publisher: Springer Nature publist_id: '5575' pubrep_id: '595' quality_controlled: '1' scopus_import: '1' status: public title: Vertical visibility among parallel polygons in three dimensions type: book_chapter user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9411 year: '2015' ... --- _id: '1601' abstract: - lang: eng text: We propose a flexible exchange format for ω-automata, as typically used in formal verification, and implement support for it in a range of established tools. Our aim is to simplify the interaction of tools, helping the research community to build upon other people’s work. A key feature of the format is the use of very generic acceptance conditions, specified by Boolean combinations of acceptance primitives, rather than being limited to common cases such as Büchi, Streett, or Rabin. Such flexibility in the choice of acceptance conditions can be exploited in applications, for example in probabilistic model checking, and furthermore encourages the development of acceptance-agnostic tools for automata manipulations. The format allows acceptance conditions that are either state-based or transition-based, and also supports alternating automata. alternative_title: - LNCS article_processing_charge: No author: - first_name: Tomáš full_name: Babiak, Tomáš last_name: Babiak - first_name: František full_name: Blahoudek, František last_name: Blahoudek - first_name: Alexandre full_name: Duret Lutz, Alexandre last_name: Duret Lutz - first_name: Joachim full_name: Klein, Joachim last_name: Klein - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Daniel full_name: Mueller, Daniel last_name: Mueller - first_name: David full_name: Parker, David last_name: Parker - first_name: Jan full_name: Strejček, Jan last_name: Strejček citation: ama: 'Babiak T, Blahoudek F, Duret Lutz A, et al. The Hanoi omega-automata format. In: Vol 9206. Springer; 2015:479-486. doi:10.1007/978-3-319-21690-4_31' apa: 'Babiak, T., Blahoudek, F., Duret Lutz, A., Klein, J., Kretinsky, J., Mueller, D., … Strejček, J. (2015). The Hanoi omega-automata format (Vol. 9206, pp. 479–486). Presented at the CAV: Computer Aided Verification, San Francisco, CA, United States: Springer. https://doi.org/10.1007/978-3-319-21690-4_31' chicago: Babiak, Tomáš, František Blahoudek, Alexandre Duret Lutz, Joachim Klein, Jan Kretinsky, Daniel Mueller, David Parker, and Jan Strejček. “The Hanoi Omega-Automata Format,” 9206:479–86. Springer, 2015. https://doi.org/10.1007/978-3-319-21690-4_31. ieee: 'T. Babiak et al., “The Hanoi omega-automata format,” presented at the CAV: Computer Aided Verification, San Francisco, CA, United States, 2015, vol. 9206, pp. 479–486.' ista: 'Babiak T, Blahoudek F, Duret Lutz A, Klein J, Kretinsky J, Mueller D, Parker D, Strejček J. 2015. The Hanoi omega-automata format. CAV: Computer Aided Verification, LNCS, vol. 9206, 479–486.' mla: Babiak, Tomáš, et al. The Hanoi Omega-Automata Format. Vol. 9206, Springer, 2015, pp. 479–86, doi:10.1007/978-3-319-21690-4_31. short: T. Babiak, F. Blahoudek, A. Duret Lutz, J. Klein, J. Kretinsky, D. Mueller, D. Parker, J. Strejček, in:, Springer, 2015, pp. 479–486. conference: end_date: 2015-07-24 location: San Francisco, CA, United States name: 'CAV: Computer Aided Verification' start_date: 2015-07-18 date_created: 2018-12-11T11:52:57Z date_published: 2015-07-16T00:00:00Z date_updated: 2021-01-12T06:51:54Z day: '16' ddc: - '000' department: - _id: ToHe - _id: KrCh doi: 10.1007/978-3-319-21690-4_31 ec_funded: 1 file: - access_level: open_access checksum: 5885236fa88a439baba9ac6f3e801e93 content_type: application/pdf creator: dernst date_created: 2020-05-15T08:38:12Z date_updated: 2020-07-14T12:45:04Z file_id: '7850' file_name: 2015_CAV_Babiak.pdf file_size: 1651779 relation: main_file file_date_updated: 2020-07-14T12:45:04Z has_accepted_license: '1' intvolume: ' 9206' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 479 - 486 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '5566' quality_controlled: '1' scopus_import: 1 status: public title: The Hanoi omega-automata format type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9206 year: '2015' ... --- _id: '1605' abstract: - lang: eng text: Multiaffine hybrid automata (MHA) represent a powerful formalism to model complex dynamical systems. This formalism is particularly suited for the representation of biological systems which often exhibit highly non-linear behavior. In this paper, we consider the problem of parameter identification for MHA. We present an abstraction of MHA based on linear hybrid automata, which can be analyzed by the SpaceEx model checker. This abstraction enables a precise handling of time-dependent properties. We demonstrate the potential of our approach on a model of a genetic regulatory network and a myocyte model. acknowledgement: This work was partly supported by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23, S11405-N23 and S11412-N23 (RiSE/SHiNE) and Z211-N23 (Wittgenstein Award), and by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS, http://www.avacs.org/). alternative_title: - LNCS article_processing_charge: No author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 - first_name: Ezio full_name: Bartocci, Ezio last_name: Bartocci - first_name: Grégory full_name: Batt, Grégory last_name: Batt - first_name: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 - first_name: Radu full_name: Grosu, Radu last_name: Grosu citation: ama: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. Abstraction-based parameter synthesis for multiaffine systems. In: Vol 9434. Springer; 2015:19-35. doi:10.1007/978-3-319-26287-1_2' apa: 'Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., & Grosu, R. (2015). Abstraction-based parameter synthesis for multiaffine systems (Vol. 9434, pp. 19–35). Presented at the HVC: Haifa Verification Conference, Haifa, Israel: Springer. https://doi.org/10.1007/978-3-319-26287-1_2' chicago: Bogomolov, Sergiy, Christian Schilling, Ezio Bartocci, Grégory Batt, Hui Kong, and Radu Grosu. “Abstraction-Based Parameter Synthesis for Multiaffine Systems,” 9434:19–35. Springer, 2015. https://doi.org/10.1007/978-3-319-26287-1_2. ieee: 'S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, and R. Grosu, “Abstraction-based parameter synthesis for multiaffine systems,” presented at the HVC: Haifa Verification Conference, Haifa, Israel, 2015, vol. 9434, pp. 19–35.' ista: 'Bogomolov S, Schilling C, Bartocci E, Batt G, Kong H, Grosu R. 2015. Abstraction-based parameter synthesis for multiaffine systems. HVC: Haifa Verification Conference, LNCS, vol. 9434, 19–35.' mla: Bogomolov, Sergiy, et al. Abstraction-Based Parameter Synthesis for Multiaffine Systems. Vol. 9434, Springer, 2015, pp. 19–35, doi:10.1007/978-3-319-26287-1_2. short: S. Bogomolov, C. Schilling, E. Bartocci, G. Batt, H. Kong, R. Grosu, in:, Springer, 2015, pp. 19–35. conference: end_date: 2015-11-19 location: Haifa, Israel name: 'HVC: Haifa Verification Conference' start_date: 2015-11-17 date_created: 2018-12-11T11:52:59Z date_published: 2015-11-28T00:00:00Z date_updated: 2021-01-12T06:51:56Z day: '28' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-26287-1_2 ec_funded: 1 file: - access_level: open_access checksum: 3aab260f3f34641d622030ba22645b3e content_type: application/pdf creator: dernst date_created: 2020-05-15T08:43:19Z date_updated: 2020-07-14T12:45:05Z file_id: '7851' file_name: 2015_LNCS_Bogomolov.pdf file_size: 1053207 relation: main_file file_date_updated: 2020-07-14T12:45:05Z has_accepted_license: '1' intvolume: ' 9434' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 19 - 35 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '5561' quality_controlled: '1' scopus_import: 1 status: public title: Abstraction-based parameter synthesis for multiaffine systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9434 year: '2015' ... --- _id: '1606' abstract: - lang: eng text: 'In this paper, we present the first steps toward a runtime verification framework for monitoring hybrid and cyber-physical systems (CPS) development tools based on randomized differential testing. The development tools include hybrid systems reachability analysis tools, model-based development environments like Simulink/Stateflow (SLSF), etc. First, hybrid automaton models are randomly generated. Next, these hybrid automaton models are translated to a number of different tools (currently, SpaceEx, dReach, Flow*, HyCreate, and the MathWorks’ Simulink/Stateflow) using the HyST source transformation and translation tool. Then, the hybrid automaton models are executed in the different tools and their outputs are parsed. The final step is the differential comparison: the outputs of the different tools are compared. If the results do not agree (in the sense that an analysis or verification result from one tool does not match that of another tool, ignoring timeouts, etc.), a candidate bug is flagged and the model is saved for future analysis by the user. The process then repeats and the monitoring continues until the user terminates the process. We present preliminary results that have been useful in identifying a few bugs in the analysis methods of different development tools, and in an earlier version of HyST.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Luan full_name: Nguyen, Luan last_name: Nguyen - first_name: Christian full_name: Schilling, Christian last_name: Schilling - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Taylor full_name: Johnson, Taylor last_name: Johnson citation: ama: 'Nguyen L, Schilling C, Bogomolov S, Johnson T. Runtime verification for hybrid analysis tools. In: 6th International Conference. Vol 9333. Springer Nature; 2015:281-286. doi:10.1007/978-3-319-23820-3_19' apa: 'Nguyen, L., Schilling, C., Bogomolov, S., & Johnson, T. (2015). Runtime verification for hybrid analysis tools. In 6th International Conference (Vol. 9333, pp. 281–286). Vienna, Austria: Springer Nature. https://doi.org/10.1007/978-3-319-23820-3_19' chicago: Nguyen, Luan, Christian Schilling, Sergiy Bogomolov, and Taylor Johnson. “Runtime Verification for Hybrid Analysis Tools.” In 6th International Conference, 9333:281–86. Springer Nature, 2015. https://doi.org/10.1007/978-3-319-23820-3_19. ieee: L. Nguyen, C. Schilling, S. Bogomolov, and T. Johnson, “Runtime verification for hybrid analysis tools,” in 6th International Conference, Vienna, Austria, 2015, vol. 9333, pp. 281–286. ista: 'Nguyen L, Schilling C, Bogomolov S, Johnson T. 2015. Runtime verification for hybrid analysis tools. 6th International Conference. RV: Runtime Verification, LNCS, vol. 9333, 281–286.' mla: Nguyen, Luan, et al. “Runtime Verification for Hybrid Analysis Tools.” 6th International Conference, vol. 9333, Springer Nature, 2015, pp. 281–86, doi:10.1007/978-3-319-23820-3_19. short: L. Nguyen, C. Schilling, S. Bogomolov, T. Johnson, in:, 6th International Conference, Springer Nature, 2015, pp. 281–286. conference: end_date: 2015-09-25 location: Vienna, Austria name: 'RV: Runtime Verification' start_date: 2015-09-22 date_created: 2018-12-11T11:52:59Z date_published: 2015-11-15T00:00:00Z date_updated: 2022-02-01T14:52:59Z day: '15' department: - _id: ToHe doi: 10.1007/978-3-319-23820-3_19 ec_funded: 1 intvolume: ' 9333' language: - iso: eng month: '11' oa_version: None page: 281 - 286 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: 6th International Conference publication_identifier: isbn: - 978-3-319-23819-7 publication_status: published publisher: Springer Nature publist_id: '5562' quality_controlled: '1' scopus_import: '1' status: public title: Runtime verification for hybrid analysis tools type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9333 year: '2015' ... --- _id: '1609' abstract: - lang: eng text: The synthesis problem asks for the automatic construction of a system from its specification. In the traditional setting, the system is “constructed from scratch” rather than composed from reusable components. However, this is rare in practice, and almost every non-trivial software system relies heavily on the use of libraries of reusable components. Recently, Lustig and Vardi introduced dataflow and controlflow synthesis from libraries of reusable components. They proved that dataflow synthesis is undecidable, while controlflow synthesis is decidable. The problem of controlflow synthesis from libraries of probabilistic components was considered by Nain, Lustig and Vardi, and was shown to be decidable for qualitative analysis (that asks that the specification be satisfied with probability 1). Our main contribution for controlflow synthesis from probabilistic components is to establish better complexity bounds for the qualitative analysis problem, and to show that the more general quantitative problem is undecidable. For the qualitative analysis, we show that the problem (i) is EXPTIME-complete when the specification is given as a deterministic parity word automaton, improving the previously known 2EXPTIME upper bound; and (ii) belongs to UP ∩ coUP and is parity-games hard, when the specification is given directly as a parity condition on the components, improving the previously known EXPTIME upper bound. acknowledgement: 'This research was supported by Austrian Science Fund (FWF) Grant No P23499- N23, FWF NFN Grant No S11407-N23 (SHiNE), ERC Start grant (279307: Graph Games), EU FP7 Project Cassting, NSF grants CNS 1049862 and CCF-1139011, by NSF Expeditions in Computing project “ExCAPE: Expeditions in Computer Augmented Program Engineering”, by BSF grant 9800096, and by gift from Intel.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - first_name: Moshe full_name: Vardi, Moshe last_name: Vardi citation: ama: 'Chatterjee K, Doyen L, Vardi M. The complexity of synthesis from probabilistic components. In: 42nd International Colloquium. Vol 9135. Springer Nature; 2015:108-120. doi:10.1007/978-3-662-47666-6_9' apa: 'Chatterjee, K., Doyen, L., & Vardi, M. (2015). The complexity of synthesis from probabilistic components. In 42nd International Colloquium (Vol. 9135, pp. 108–120). Kyoto, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-47666-6_9' chicago: Chatterjee, Krishnendu, Laurent Doyen, and Moshe Vardi. “The Complexity of Synthesis from Probabilistic Components.” In 42nd International Colloquium, 9135:108–20. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-47666-6_9. ieee: K. Chatterjee, L. Doyen, and M. Vardi, “The complexity of synthesis from probabilistic components,” in 42nd International Colloquium, Kyoto, Japan, 2015, vol. 9135, pp. 108–120. ista: 'Chatterjee K, Doyen L, Vardi M. 2015. The complexity of synthesis from probabilistic components. 42nd International Colloquium. ICALP: Automata, Languages and Programming, LNCS, vol. 9135, 108–120.' mla: Chatterjee, Krishnendu, et al. “The Complexity of Synthesis from Probabilistic Components.” 42nd International Colloquium, vol. 9135, Springer Nature, 2015, pp. 108–20, doi:10.1007/978-3-662-47666-6_9. short: K. Chatterjee, L. Doyen, M. Vardi, in:, 42nd International Colloquium, Springer Nature, 2015, pp. 108–120. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'ICALP: Automata, Languages and Programming' start_date: 2015-07-06 date_created: 2018-12-11T11:53:00Z date_published: 2015-06-20T00:00:00Z date_updated: 2022-02-01T15:04:44Z day: '20' department: - _id: KrCh doi: 10.1007/978-3-662-47666-6_9 ec_funded: 1 intvolume: ' 9135' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1502.04844 month: '06' oa: 1 oa_version: Preprint page: 108 - 120 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: 42nd International Colloquium publication_identifier: isbn: - 978-3-662-47665-9 publication_status: published publisher: Springer Nature publist_id: '5557' quality_controlled: '1' scopus_import: '1' status: public title: The complexity of synthesis from probabilistic components type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9135 year: '2015' ... --- _id: '1615' abstract: - lang: eng text: Loss-of-function mutations in the synaptic adhesion protein Neuroligin-4 are among the most common genetic abnormalities associated with autism spectrum disorders, but little is known about the function of Neuroligin-4 and the consequences of its loss. We assessed synaptic and network characteristics in Neuroligin-4 knockout mice, focusing on the hippocampus as a model brain region with a critical role in cognition and memory, and found that Neuroligin-4 deletion causes subtle defects of the protein composition and function of GABAergic synapses in the hippocampal CA3 region. Interestingly, these subtle synaptic changes are accompanied by pronounced perturbations of γ-oscillatory network activity, which has been implicated in cognitive function and is altered in multiple psychiatric and neurodevelopmental disorders. Our data provide important insights into the mechanisms by which Neuroligin-4-dependent GABAergic synapses may contribute to autism phenotypes and indicate new strategies for therapeutic approaches. acknowledgement: This work was supported by the Max Planck Society (N.B. and H.E.), the European Commission (EU-AIMS FP7-115300, N.B. and H.E.; Marie Curie IRG, D.K.-B.), the German Research Foundation (CNMPB, N.B., H.E., and F.V.), the Alexander von Humboldt-Foundation (D.K.-B.), and the Austrian Fond zur Förderung der Wissenschaftlichen Forschung (P 24909-B24, P.J.). M.H. was a student of the doctoral program Molecular Physiology of the Brain. Dr. J.-M. Fritschy generously provided the GABAARγ2 antibody. We thank F. Benseler, I. Thanhäuser, D. Schwerdtfeger, A. Ronnenberg, and D. Winkler for valuable advice and excellent technical support. We are grateful to the staff at the animal facility of the Max Planck Institute of Experimental Medicine for mouse husbandry. author: - first_name: Matthieu full_name: Hammer, Matthieu last_name: Hammer - first_name: Dilja full_name: Krueger Burg, Dilja last_name: Krueger Burg - first_name: Liam full_name: Tuffy, Liam last_name: Tuffy - first_name: Benjamin full_name: Cooper, Benjamin last_name: Cooper - first_name: Holger full_name: Taschenberger, Holger last_name: Taschenberger - first_name: Sarit full_name: Goswami, Sarit id: 3A578F32-F248-11E8-B48F-1D18A9856A87 last_name: Goswami - first_name: Hannelore full_name: Ehrenreich, Hannelore last_name: Ehrenreich - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Frederique full_name: Varoqueaux, Frederique last_name: Varoqueaux - first_name: Jeong full_name: Rhee, Jeong last_name: Rhee - first_name: Nils full_name: Brose, Nils last_name: Brose citation: ama: Hammer M, Krueger Burg D, Tuffy L, et al. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 2015;13(3):516-523. doi:10.1016/j.celrep.2015.09.011 apa: Hammer, M., Krueger Burg, D., Tuffy, L., Cooper, B., Taschenberger, H., Goswami, S., … Brose, N. (2015). Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. Cell Press. https://doi.org/10.1016/j.celrep.2015.09.011 chicago: Hammer, Matthieu, Dilja Krueger Burg, Liam Tuffy, Benjamin Cooper, Holger Taschenberger, Sarit Goswami, Hannelore Ehrenreich, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports. Cell Press, 2015. https://doi.org/10.1016/j.celrep.2015.09.011. ieee: M. Hammer et al., “Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism,” Cell Reports, vol. 13, no. 3. Cell Press, pp. 516–523, 2015. ista: Hammer M, Krueger Burg D, Tuffy L, Cooper B, Taschenberger H, Goswami S, Ehrenreich H, Jonas PM, Varoqueaux F, Rhee J, Brose N. 2015. Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism. Cell Reports. 13(3), 516–523. mla: Hammer, Matthieu, et al. “Perturbed Hippocampal Synaptic Inhibition and γ-Oscillations in a Neuroligin-4 Knockout Mouse Model of Autism.” Cell Reports, vol. 13, no. 3, Cell Press, 2015, pp. 516–23, doi:10.1016/j.celrep.2015.09.011. short: M. Hammer, D. Krueger Burg, L. Tuffy, B. Cooper, H. Taschenberger, S. Goswami, H. Ehrenreich, P.M. Jonas, F. Varoqueaux, J. Rhee, N. Brose, Cell Reports 13 (2015) 516–523. date_created: 2018-12-11T11:53:02Z date_published: 2015-10-20T00:00:00Z date_updated: 2021-01-12T06:52:01Z day: '20' ddc: - '570' department: - _id: PeJo doi: 10.1016/j.celrep.2015.09.011 file: - access_level: open_access checksum: 44d30fbb543774b076b4938bd36af9d7 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:23Z date_updated: 2020-07-14T12:45:07Z file_id: '5005' file_name: IST-2016-470-v1+1_1-s2.0-S2211124715010220-main.pdf file_size: 2314406 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 13' issue: '3' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 516 - 523 publication: Cell Reports publication_status: published publisher: Cell Press publist_id: '5551' pubrep_id: '470' quality_controlled: '1' scopus_import: 1 status: public title: Perturbed hippocampal synaptic inhibition and γ-oscillations in a neuroligin-4 knockout mouse model of autism 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: '1614' abstract: - lang: eng text: 'GABAergic perisoma-inhibiting fast-spiking interneurons (PIIs) effectively control the activity of large neuron populations by their wide axonal arborizations. It is generally assumed that the output of one PII to its target cells is strong and rapid. Here, we show that, unexpectedly, both strength and time course of PII-mediated perisomatic inhibition change with distance between synaptically connected partners in the rodent hippocampus. Synaptic signals become weaker due to lower contact numbers and decay more slowly with distance, very likely resulting from changes in GABAA receptor subunit composition. When distance-dependent synaptic inhibition is introduced to a rhythmically active neuronal network model, randomly driven principal cell assemblies are strongly synchronized by the PIIs, leading to higher precision in principal cell spike times than in a network with uniform synaptic inhibition. ' author: - first_name: Michael full_name: Strüber, Michael last_name: Strüber - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Marlene full_name: Bartos, Marlene last_name: Bartos citation: ama: Strüber M, Jonas PM, Bartos M. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 2015;112(4):1220-1225. doi:10.1073/pnas.1412996112 apa: Strüber, M., Jonas, P. M., & Bartos, M. (2015). Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1412996112 chicago: Strüber, Michael, Peter M Jonas, and Marlene Bartos. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1412996112. ieee: M. Strüber, P. M. Jonas, and M. Bartos, “Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells,” PNAS, vol. 112, no. 4. National Academy of Sciences, pp. 1220–1225, 2015. ista: Strüber M, Jonas PM, Bartos M. 2015. Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells. PNAS. 112(4), 1220–1225. mla: Strüber, Michael, et al. “Strength and Duration of Perisomatic GABAergic Inhibition Depend on Distance between Synaptically Connected Cells.” PNAS, vol. 112, no. 4, National Academy of Sciences, 2015, pp. 1220–25, doi:10.1073/pnas.1412996112. short: M. Strüber, P.M. Jonas, M. Bartos, PNAS 112 (2015) 1220–1225. date_created: 2018-12-11T11:53:02Z date_published: 2015-01-27T00:00:00Z date_updated: 2021-01-12T06:52:01Z day: '27' ddc: - '570' department: - _id: PeJo doi: 10.1073/pnas.1412996112 ec_funded: 1 external_id: pmid: - '25583495' file: - access_level: open_access checksum: 6703309a1f58493cf5a704211fb6ebed content_type: application/pdf creator: dernst date_created: 2019-01-17T07:52:40Z date_updated: 2020-07-14T12:45:07Z file_id: '5838' file_name: 2015_PNAS_Strueber.pdf file_size: 1280860 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 112' issue: '4' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 1220 - 1225 pmid: 1 project: - _id: 25C26B1E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P24909-B24 name: Mechanisms of transmitter release at GABAergic synapses - _id: 25C0F108-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '268548' name: Nanophysiology of fast-spiking, parvalbumin-expressing GABAergic interneurons publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5552' quality_controlled: '1' scopus_import: 1 status: public title: Strength and duration of perisomatic GABAergic inhibition depend on distance between synaptically connected cells type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1611' abstract: - lang: eng text: Biosensors for signaling molecules allow the study of physiological processes by bringing together the fields of protein engineering, fluorescence imaging, and cell biology. Construction of genetically encoded biosensors generally relies on the availability of a binding "core" that is both specific and stable, which can then be combined with fluorescent molecules to create a sensor. However, binding proteins with the desired properties are often not available in nature and substantial improvement to sensors can be required, particularly with regard to their durability. Ancestral protein reconstruction is a powerful protein-engineering tool able to generate highly stable and functional proteins. In this work, we sought to establish the utility of ancestral protein reconstruction to biosensor development, beginning with the construction of an l-arginine biosensor. l-arginine, as the immediate precursor to nitric oxide, is an important molecule in many physiological contexts including brain function. Using a combination of ancestral reconstruction and circular permutation, we constructed a Förster resonance energy transfer (FRET) biosensor for l-arginine (cpFLIPR). cpFLIPR displays high sensitivity and specificity, with a Kd of ∼14 μM and a maximal dynamic range of 35%. Importantly, cpFLIPR was highly robust, enabling accurate l-arginine measurement at physiological temperatures. We established that cpFLIPR is compatible with two-photon excitation fluorescence microscopy and report l-arginine concentrations in brain tissue. author: - first_name: Jason full_name: Whitfield, Jason last_name: Whitfield - first_name: William full_name: Zhang, William last_name: Zhang - first_name: Michel full_name: Herde, Michel last_name: Herde - first_name: Ben full_name: Clifton, Ben last_name: Clifton - first_name: Johanna full_name: Radziejewski, Johanna last_name: Radziejewski - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Christian full_name: Henneberger, Christian last_name: Henneberger - first_name: Colin full_name: Jackson, Colin last_name: Jackson citation: ama: Whitfield J, Zhang W, Herde M, et al. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 2015;24(9):1412-1422. doi:10.1002/pro.2721 apa: Whitfield, J., Zhang, W., Herde, M., Clifton, B., Radziejewski, J., Janovjak, H. L., … Jackson, C. (2015). Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. Wiley. https://doi.org/10.1002/pro.2721 chicago: Whitfield, Jason, William Zhang, Michel Herde, Ben Clifton, Johanna Radziejewski, Harald L Janovjak, Christian Henneberger, and Colin Jackson. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science. Wiley, 2015. https://doi.org/10.1002/pro.2721. ieee: J. Whitfield et al., “Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction,” Protein Science, vol. 24, no. 9. Wiley, pp. 1412–1422, 2015. ista: Whitfield J, Zhang W, Herde M, Clifton B, Radziejewski J, Janovjak HL, Henneberger C, Jackson C. 2015. Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction. Protein Science. 24(9), 1412–1422. mla: Whitfield, Jason, et al. “Construction of a Robust and Sensitive Arginine Biosensor through Ancestral Protein Reconstruction.” Protein Science, vol. 24, no. 9, Wiley, 2015, pp. 1412–22, doi:10.1002/pro.2721. short: J. Whitfield, W. Zhang, M. Herde, B. Clifton, J. Radziejewski, H.L. Janovjak, C. Henneberger, C. Jackson, Protein Science 24 (2015) 1412–1422. date_created: 2018-12-11T11:53:01Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:52:00Z day: '01' department: - _id: HaJa doi: 10.1002/pro.2721 external_id: pmid: - '26061224' intvolume: ' 24' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4570536/ month: '09' oa: 1 oa_version: Submitted Version page: 1412 - 1422 pmid: 1 project: - _id: 255BFFFA-B435-11E9-9278-68D0E5697425 grant_number: RGY0084/2012 name: In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator) publication: Protein Science publication_status: published publisher: Wiley publist_id: '5555' quality_controlled: '1' scopus_import: 1 status: public title: Construction of a robust and sensitive arginine biosensor through ancestral protein reconstruction type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2015' ... --- _id: '1624' abstract: - lang: eng text: Population structure can facilitate evolution of cooperation. In a structured population, cooperators can form clusters which resist exploitation by defectors. Recently, it was observed that a shift update rule is an extremely strong amplifier of cooperation in a one dimensional spatial model. For the shift update rule, an individual is chosen for reproduction proportional to fecundity; the offspring is placed next to the parent; a random individual dies. Subsequently, the population is rearranged (shifted) until all individual cells are again evenly spaced out. For large population size and a one dimensional population structure, the shift update rule favors cooperation for any benefit-to-cost ratio greater than one. But every attempt to generalize shift updating to higher dimensions while maintaining its strong effect has failed. The reason is that in two dimensions the clusters are fragmented by the movements caused by rearranging the cells. Here we introduce the natural phenomenon of a repulsive force between cells of different types. After a birth and death event, the cells are being rearranged minimizing the overall energy expenditure. If the repulsive force is sufficiently high, shift becomes a strong promoter of cooperation in two dimensions. acknowledgement: 'The research was supported by the Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 (RiSE/SHiNE), ERC Start grant (279307: Graph Games), and Microsoft Faculty Fellows award. Support from the John Templeton foundation is gratefully acknowledged.' article_number: '17147' author: - first_name: Andreas full_name: Pavlogiannis, Andreas id: 49704004-F248-11E8-B48F-1D18A9856A87 last_name: Pavlogiannis orcid: 0000-0002-8943-0722 - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ben full_name: Adlam, Ben last_name: Adlam - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. Cellular cooperation with shift updating and repulsion. Scientific Reports. 2015;5. doi:10.1038/srep17147 apa: Pavlogiannis, A., Chatterjee, K., Adlam, B., & Nowak, M. (2015). Cellular cooperation with shift updating and repulsion. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep17147 chicago: Pavlogiannis, Andreas, Krishnendu Chatterjee, Ben Adlam, and Martin Nowak. “Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep17147. ieee: A. Pavlogiannis, K. Chatterjee, B. Adlam, and M. Nowak, “Cellular cooperation with shift updating and repulsion,” Scientific Reports, vol. 5. Nature Publishing Group, 2015. ista: Pavlogiannis A, Chatterjee K, Adlam B, Nowak M. 2015. Cellular cooperation with shift updating and repulsion. Scientific Reports. 5, 17147. mla: Pavlogiannis, Andreas, et al. “Cellular Cooperation with Shift Updating and Repulsion.” Scientific Reports, vol. 5, 17147, Nature Publishing Group, 2015, doi:10.1038/srep17147. short: A. Pavlogiannis, K. Chatterjee, B. Adlam, M. Nowak, Scientific Reports 5 (2015). date_created: 2018-12-11T11:53:06Z date_published: 2015-11-25T00:00:00Z date_updated: 2021-01-12T06:52:05Z day: '25' ddc: - '000' department: - _id: KrCh doi: 10.1038/srep17147 ec_funded: 1 file: - access_level: open_access checksum: 38e06d8310d2087cae5f6d4d4bfe082b content_type: application/pdf creator: system date_created: 2018-12-12T10:12:29Z date_updated: 2020-07-14T12:45:07Z file_id: '4947' file_name: IST-2016-466-v1+1_srep17147.pdf file_size: 1021931 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _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: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '5536' pubrep_id: '466' quality_controlled: '1' scopus_import: 1 status: public title: Cellular cooperation with shift updating and repulsion 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: 5 year: '2015' ... --- _id: '1623' abstract: - lang: eng text: "Background\r\nPhotosynthetic cyanobacteria are attractive for a range of biotechnological applications including biofuel production. However, due to slow growth, screening of mutant libraries using microtiter plates is not feasible.\r\nResults\r\nWe present a method for high-throughput, single-cell analysis and sorting of genetically engineered l-lactate-producing strains of Synechocystis sp. PCC6803. A microfluidic device is used to encapsulate single cells in picoliter droplets, assay the droplets for l-lactate production, and sort strains with high productivity. We demonstrate the separation of low- and high-producing reference strains, as well as enrichment of a more productive l-lactate-synthesizing population after UV-induced mutagenesis. The droplet platform also revealed population heterogeneity in photosynthetic growth and lactate production, as well as the presence of metabolically stalled cells.\r\nConclusions\r\nThe workflow will facilitate metabolic engineering and directed evolution studies and will be useful in studies of cyanobacteria biochemistry and physiology.\r\n" article_number: '193' author: - first_name: Petter full_name: Hammar, Petter last_name: Hammar - first_name: Andreas full_name: Angermayr, Andreas id: 4677C796-F248-11E8-B48F-1D18A9856A87 last_name: Angermayr orcid: 0000-0001-8619-2223 - first_name: Staffan full_name: Sjostrom, Staffan last_name: Sjostrom - first_name: Josefin full_name: Van Der Meer, Josefin last_name: Van Der Meer - first_name: Klaas full_name: Hellingwerf, Klaas last_name: Hellingwerf - first_name: Elton full_name: Hudson, Elton last_name: Hudson - first_name: Hakaan full_name: Joensson, Hakaan last_name: Joensson citation: ama: Hammar P, Angermayr A, Sjostrom S, et al. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 2015;8(1). doi:10.1186/s13068-015-0380-2 apa: Hammar, P., Angermayr, A., Sjostrom, S., Van Der Meer, J., Hellingwerf, K., Hudson, E., & Joensson, H. (2015). Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. BioMed Central. https://doi.org/10.1186/s13068-015-0380-2 chicago: Hammar, Petter, Andreas Angermayr, Staffan Sjostrom, Josefin Van Der Meer, Klaas Hellingwerf, Elton Hudson, and Hakaan Joensson. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology for Biofuels. BioMed Central, 2015. https://doi.org/10.1186/s13068-015-0380-2. ieee: P. Hammar et al., “Single-cell screening of photosynthetic growth and lactate production by cyanobacteria,” Biotechnology for Biofuels, vol. 8, no. 1. BioMed Central, 2015. ista: Hammar P, Angermayr A, Sjostrom S, Van Der Meer J, Hellingwerf K, Hudson E, Joensson H. 2015. Single-cell screening of photosynthetic growth and lactate production by cyanobacteria. Biotechnology for Biofuels. 8(1), 193. mla: Hammar, Petter, et al. “Single-Cell Screening of Photosynthetic Growth and Lactate Production by Cyanobacteria.” Biotechnology for Biofuels, vol. 8, no. 1, 193, BioMed Central, 2015, doi:10.1186/s13068-015-0380-2. short: P. Hammar, A. Angermayr, S. Sjostrom, J. Van Der Meer, K. Hellingwerf, E. Hudson, H. Joensson, Biotechnology for Biofuels 8 (2015). date_created: 2018-12-11T11:53:05Z date_published: 2015-11-25T00:00:00Z date_updated: 2021-01-12T06:52:04Z day: '25' ddc: - '570' department: - _id: ToBo doi: 10.1186/s13068-015-0380-2 file: - access_level: open_access checksum: 172b0b6f4eb2e5c22b7cec1d57dc0107 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:11Z date_updated: 2020-07-14T12:45:07Z file_id: '4796' file_name: IST-2016-467-v1+1_s13068-015-0380-2.pdf file_size: 2914089 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 8' issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Biotechnology for Biofuels publication_status: published publisher: BioMed Central publist_id: '5537' pubrep_id: '467' quality_controlled: '1' scopus_import: 1 status: public title: Single-cell screening of photosynthetic growth and lactate production by cyanobacteria 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: 8 year: '2015' ... --- _id: '1625' abstract: - lang: eng text: In recent years we have seen numerous improvements on 3D scanning and tracking of human faces, greatly advancing the creation of digital doubles for film and video games. However, despite the high-resolution quality of the reconstruction approaches available, current methods are unable to capture one of the most important regions of the face - the eye region. In this work we present the first method for detailed spatio-temporal reconstruction of eyelids. Tracking and reconstructing eyelids is extremely challenging, as this region exhibits very complex and unique skin deformation where skin is folded under while opening the eye. Furthermore, eyelids are often only partially visible and obstructed due to selfocclusion and eyelashes. Our approach is to combine a geometric deformation model with image data, leveraging multi-view stereo, optical flow, contour tracking and wrinkle detection from local skin appearance. Our deformation model serves as a prior that enables reconstruction of eyelids even under strong self-occlusions caused by rolling and folding skin as the eye opens and closes. The output is a person-specific, time-varying eyelid reconstruction with anatomically plausible deformations. Our high-resolution detailed eyelids couple naturally with current facial performance capture approaches. As a result, our method can largely increase the fidelity of facial capture and the creation of digital doubles. article_number: '44' author: - first_name: Amit full_name: Bermano, Amit last_name: Bermano - first_name: Thabo full_name: Beeler, Thabo last_name: Beeler - first_name: Yeara full_name: Kozlov, Yeara last_name: Kozlov - first_name: Derek full_name: Bradley, Derek last_name: Bradley - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Markus full_name: Gross, Markus last_name: Gross citation: ama: 'Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. Detailed spatio-temporal reconstruction of eyelids. In: Vol 34. ACM; 2015. doi:10.1145/2766924' apa: 'Bermano, A., Beeler, T., Kozlov, Y., Bradley, D., Bickel, B., & Gross, M. (2015). Detailed spatio-temporal reconstruction of eyelids (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766924' chicago: Bermano, Amit, Thabo Beeler, Yeara Kozlov, Derek Bradley, Bernd Bickel, and Markus Gross. “Detailed Spatio-Temporal Reconstruction of Eyelids,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766924. ieee: 'A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, and M. Gross, “Detailed spatio-temporal reconstruction of eyelids,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.' ista: 'Bermano A, Beeler T, Kozlov Y, Bradley D, Bickel B, Gross M. 2015. Detailed spatio-temporal reconstruction of eyelids. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 44.' mla: Bermano, Amit, et al. Detailed Spatio-Temporal Reconstruction of Eyelids. Vol. 34, no. 4, 44, ACM, 2015, doi:10.1145/2766924. short: A. Bermano, T. Beeler, Y. Kozlov, D. Bradley, B. Bickel, M. Gross, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, United States name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:06Z date_published: 2015-07-27T00:00:00Z date_updated: 2021-01-12T06:52:05Z day: '27' department: - _id: BeBi doi: 10.1145/2766924 intvolume: ' 34' issue: '4' language: - iso: eng month: '07' oa_version: None publication_status: published publisher: ACM publist_id: '5535' quality_controlled: '1' scopus_import: 1 status: public title: Detailed spatio-temporal reconstruction of eyelids type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1626' abstract: - lang: eng text: This paper introduces "OmniAD," a novel data-driven pipeline to model and acquire the aerodynamics of three-dimensional rigid objects. Traditionally, aerodynamics are examined through elaborate wind tunnel experiments or expensive fluid dynamics computations, and are only measured for a small number of discrete wind directions. OmniAD allows the evaluation of aerodynamic forces, such as drag and lift, for any incoming wind direction using a novel representation based on spherical harmonics. Our datadriven technique acquires the aerodynamic properties of an object simply by capturing its falling motion using a single camera. Once model parameters are estimated, OmniAD enables realistic realtime simulation of rigid bodies, such as the tumbling and gliding of leaves, without simulating the surrounding air. In addition, we propose an intuitive user interface based on OmniAD to interactively design three-dimensional kites that actually fly. Various nontraditional kites were designed to demonstrate the physical validity of our model. alternative_title: - ACM Transactions on Graphics article_number: '113' author: - first_name: Tobias full_name: Martin, Tobias last_name: Martin - first_name: Nobuyuki full_name: Umetani, Nobuyuki last_name: Umetani - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: 'Martin T, Umetani N, Bickel B. OmniAD: Data-driven omni-directional aerodynamics. In: Vol 34. ACM; 2015. doi:10.1145/2766919' apa: 'Martin, T., Umetani, N., & Bickel, B. (2015). OmniAD: Data-driven omni-directional aerodynamics (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766919' chicago: 'Martin, Tobias, Nobuyuki Umetani, and Bernd Bickel. “OmniAD: Data-Driven Omni-Directional Aerodynamics,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766919.' ieee: 'T. Martin, N. Umetani, and B. Bickel, “OmniAD: Data-driven omni-directional aerodynamics,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.' ista: 'Martin T, Umetani N, Bickel B. 2015. OmniAD: Data-driven omni-directional aerodynamics. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 34, 113.' mla: 'Martin, Tobias, et al. OmniAD: Data-Driven Omni-Directional Aerodynamics. Vol. 34, no. 4, 113, ACM, 2015, doi:10.1145/2766919.' short: T. Martin, N. Umetani, B. Bickel, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, United States name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:06Z date_published: 2015-07-27T00:00:00Z date_updated: 2021-01-12T06:52:05Z day: '27' department: - _id: BeBi doi: 10.1145/2766919 intvolume: ' 34' issue: '4' language: - iso: eng month: '07' oa_version: None publication_status: published publisher: ACM publist_id: '5532' quality_controlled: '1' scopus_import: 1 status: public title: 'OmniAD: Data-driven omni-directional aerodynamics' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1628' abstract: - lang: eng text: We propose a method for fabricating deformable objects with spatially varying elasticity using 3D printing. Using a single, relatively stiff printer material, our method designs an assembly of smallscale microstructures that have the effect of a softer material at the object scale, with properties depending on the microstructure used in each part of the object. We build on work in the area of metamaterials, using numerical optimization to design tiled microstructures with desired properties, but with the key difference that our method designs families of related structures that can be interpolated to smoothly vary the material properties over a wide range. To create an object with spatially varying elastic properties, we tile the object's interior with microstructures drawn from these families, generating a different microstructure for each cell using an efficient algorithm to select compatible structures for neighboring cells. We show results computed for both 2D and 3D objects, validating several 2D and 3D printed structures using standard material tests as well as demonstrating various example applications. article_number: '136' article_processing_charge: No author: - first_name: Christian full_name: Schumacher, Christian last_name: Schumacher - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Jan full_name: Rys, Jan last_name: Rys - first_name: Steve full_name: Marschner, Steve last_name: Marschner - first_name: Chiara full_name: Daraio, Chiara last_name: Daraio - first_name: Markus full_name: Gross, Markus last_name: Gross citation: ama: 'Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. Microstructures to control elasticity in 3D printing. In: Vol 34. ACM; 2015. doi:10.1145/2766926' apa: 'Schumacher, C., Bickel, B., Rys, J., Marschner, S., Daraio, C., & Gross, M. (2015). Microstructures to control elasticity in 3D printing (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766926' chicago: Schumacher, Christian, Bernd Bickel, Jan Rys, Steve Marschner, Chiara Daraio, and Markus Gross. “Microstructures to Control Elasticity in 3D Printing,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766926. ieee: 'C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, and M. Gross, “Microstructures to control elasticity in 3D printing,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.' ista: 'Schumacher C, Bickel B, Rys J, Marschner S, Daraio C, Gross M. 2015. Microstructures to control elasticity in 3D printing. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 136.' mla: Schumacher, Christian, et al. Microstructures to Control Elasticity in 3D Printing. Vol. 34, no. 4, 136, ACM, 2015, doi:10.1145/2766926. short: C. Schumacher, B. Bickel, J. Rys, S. Marschner, C. Daraio, M. Gross, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, USA name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:07Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:52:06Z day: '01' department: - _id: BeBi doi: 10.1145/2766926 intvolume: ' 34' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/2766926 month: '08' oa: 1 oa_version: Published Version publication_status: published publisher: ACM publist_id: '5529' quality_controlled: '1' scopus_import: 1 status: public title: Microstructures to control elasticity in 3D printing type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1627' abstract: - lang: eng text: We present a computational tool for fabrication-oriented design of flexible rod meshes. Given a deformable surface and a set of deformed poses as input, our method automatically computes a printable rod mesh that, once manufactured, closely matches the input poses under the same boundary conditions. The core of our method is formed by an optimization scheme that adjusts the cross-sectional profiles of the rods and their rest centerline in order to best approximate the target deformations. This approach allows us to locally control the bending and stretching resistance of the surface with a single material, yielding high design flexibility and low fabrication cost. acknowledgement: This work was supported in part by grants from the Spanish Ministry of Economy (TIN2012-35840), and the European Research Council (ERC Starting Grant no. 280135 Animetrics). article_number: '138' author: - first_name: Jesús full_name: Pérez, Jesús last_name: Pérez - first_name: Bernhard full_name: Thomaszewski, Bernhard last_name: Thomaszewski - first_name: Stelian full_name: Coros, Stelian last_name: Coros - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: José full_name: Canabal, José last_name: Canabal - first_name: Robert full_name: Sumner, Robert last_name: Sumner - first_name: Miguel full_name: Otaduy, Miguel last_name: Otaduy citation: ama: 'Pérez J, Thomaszewski B, Coros S, et al. Design and fabrication of flexible rod meshes. In: Vol 34. ACM; 2015. doi:10.1145/2766998' apa: 'Pérez, J., Thomaszewski, B., Coros, S., Bickel, B., Canabal, J., Sumner, R., & Otaduy, M. (2015). Design and fabrication of flexible rod meshes (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766998' chicago: Pérez, Jesús, Bernhard Thomaszewski, Stelian Coros, Bernd Bickel, José Canabal, Robert Sumner, and Miguel Otaduy. “Design and Fabrication of Flexible Rod Meshes,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766998. ieee: 'J. Pérez et al., “Design and fabrication of flexible rod meshes,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.' ista: 'Pérez J, Thomaszewski B, Coros S, Bickel B, Canabal J, Sumner R, Otaduy M. 2015. Design and fabrication of flexible rod meshes. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 138.' mla: Pérez, Jesús, et al. Design and Fabrication of Flexible Rod Meshes. Vol. 34, no. 4, 138, ACM, 2015, doi:10.1145/2766998. short: J. Pérez, B. Thomaszewski, S. Coros, B. Bickel, J. Canabal, R. Sumner, M. Otaduy, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, United States name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:07Z date_published: 2015-07-27T00:00:00Z date_updated: 2021-01-12T06:52:06Z day: '27' department: - _id: BeBi doi: 10.1145/2766998 intvolume: ' 34' issue: '4' language: - iso: eng month: '07' oa_version: None publication_status: published publisher: ACM publist_id: '5530' quality_controlled: '1' scopus_import: 1 status: public title: Design and fabrication of flexible rod meshes type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1634' abstract: - lang: eng text: Simulating the delightful dynamics of soap films, bubbles, and foams has traditionally required the use of a fully three-dimensional many-phase Navier-Stokes solver, even though their visual appearance is completely dominated by the thin liquid surface. We depart from earlier work on soap bubbles and foams by noting that their dynamics are naturally described by a Lagrangian vortex sheet model in which circulation is the primary variable. This leads us to derive a novel circulation-preserving surface-only discretization of foam dynamics driven by surface tension on a non-manifold triangle mesh. We represent the surface using a mesh-based multimaterial surface tracker which supports complex bubble topology changes, and evolve the surface according to the ambient air flow induced by a scalar circulation field stored on the mesh. Surface tension forces give rise to a simple update rule for circulation, even at non-manifold Plateau borders, based on a discrete measure of signed scalar mean curvature. We further incorporate vertex constraints to enable the interaction of soap films with wires. The result is a method that is at once simple, robust, and efficient, yet able to capture an array of soap films behaviors including foam rearrangement, catenoid collapse, blowing bubbles, and double bubbles being pulled apart. article_number: '149' author: - first_name: Fang full_name: Da, Fang last_name: Da - first_name: Christopher full_name: Batty, Christopher last_name: Batty - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 - first_name: Eitan full_name: Grinspun, Eitan last_name: Grinspun citation: ama: 'Da F, Batty C, Wojtan C, Grinspun E. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. In: Vol 34. ACM; 2015. doi:10.1145/2767003' apa: 'Da, F., Batty, C., Wojtan, C., & Grinspun, E. (2015). Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2767003' chicago: 'Da, Fang, Christopher Batty, Chris Wojtan, and Eitan Grinspun. “Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2767003.' ieee: 'F. Da, C. Batty, C. Wojtan, and E. Grinspun, “Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.' ista: 'Da F, Batty C, Wojtan C, Grinspun E. 2015. Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 149.' mla: 'Da, Fang, et al. Double Bubbles sans Toil and Trouble: Discrete Circulation-Preserving Vortex Sheets for Soap Films and Foams. Vol. 34, no. 4, 149, ACM, 2015, doi:10.1145/2767003.' short: F. Da, C. Batty, C. Wojtan, E. Grinspun, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, United States name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:09Z date_published: 2015-07-27T00:00:00Z date_updated: 2023-02-23T10:07:42Z day: '27' ddc: - '000' department: - _id: ChWo doi: 10.1145/2767003 ec_funded: 1 file: - access_level: open_access checksum: 57b07d78d2d612a8052744b37d4a71fa content_type: application/pdf creator: system date_created: 2018-12-12T10:11:14Z date_updated: 2020-07-14T12:45:07Z file_id: '4867' file_name: IST-2016-608-v1+1_doublebubbles.pdf file_size: 8973215 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 34' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 2533E772-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '638176' name: Efficient Simulation of Natural Phenomena at Extremely Large Scales publication_status: published publisher: ACM publist_id: '5521' pubrep_id: '608' quality_controlled: '1' scopus_import: 1 status: public title: 'Double bubbles sans toil and trouble: discrete circulation-preserving vortex sheets for soap films and foams' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1636' abstract: - lang: eng text: "Constraint Satisfaction Problem (CSP) is a fundamental algorithmic problem that appears in many areas of Computer Science. It can be equivalently stated as computing a homomorphism R→ΓΓ between two relational structures, e.g. between two directed graphs. Analyzing its complexity has been a prominent research direction, especially for the fixed template CSPs where the right side ΓΓ is fixed and the left side R is unconstrained.\r\n\r\nFar fewer results are known for the hybrid setting that restricts both sides simultaneously. It assumes that R belongs to a certain class of relational structures (called a structural restriction in this paper). We study which structural restrictions are effective, i.e. there exists a fixed template ΓΓ (from a certain class of languages) for which the problem is tractable when R is restricted, and NP-hard otherwise. We provide a characterization for structural restrictions that are closed under inverse homomorphisms. The criterion is based on the chromatic number of a relational structure defined in this paper; it generalizes the standard chromatic number of a graph.\r\n\r\nAs our main tool, we use the algebraic machinery developed for fixed template CSPs. To apply it to our case, we introduce a new construction called a “lifted language”. We also give a characterization for structural restrictions corresponding to minor-closed families of graphs, extend results to certain Valued CSPs (namely conservative valued languages), and state implications for (valued) CSPs with ordered variables and for the maximum weight independent set problem on some restricted families of graphs." alternative_title: - LNCS article_processing_charge: No author: - first_name: Vladimir full_name: Kolmogorov, Vladimir id: 3D50B0BA-F248-11E8-B48F-1D18A9856A87 last_name: Kolmogorov - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek - first_name: Rustem full_name: Takhanov, Rustem last_name: Takhanov citation: ama: 'Kolmogorov V, Rolinek M, Takhanov R. Effectiveness of structural restrictions for hybrid CSPs. In: 26th International Symposium. Vol 9472. Springer Nature; 2015:566-577. doi:10.1007/978-3-662-48971-0_48' apa: 'Kolmogorov, V., Rolinek, M., & Takhanov, R. (2015). Effectiveness of structural restrictions for hybrid CSPs. In 26th International Symposium (Vol. 9472, pp. 566–577). Nagoya, Japan: Springer Nature. https://doi.org/10.1007/978-3-662-48971-0_48' chicago: Kolmogorov, Vladimir, Michal Rolinek, and Rustem Takhanov. “Effectiveness of Structural Restrictions for Hybrid CSPs.” In 26th International Symposium, 9472:566–77. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-48971-0_48. ieee: V. Kolmogorov, M. Rolinek, and R. Takhanov, “Effectiveness of structural restrictions for hybrid CSPs,” in 26th International Symposium, Nagoya, Japan, 2015, vol. 9472, pp. 566–577. ista: 'Kolmogorov V, Rolinek M, Takhanov R. 2015. Effectiveness of structural restrictions for hybrid CSPs. 26th International Symposium. ISAAC: International Symposium on Algorithms and Computation, LNCS, vol. 9472, 566–577.' mla: Kolmogorov, Vladimir, et al. “Effectiveness of Structural Restrictions for Hybrid CSPs.” 26th International Symposium, vol. 9472, Springer Nature, 2015, pp. 566–77, doi:10.1007/978-3-662-48971-0_48. short: V. Kolmogorov, M. Rolinek, R. Takhanov, in:, 26th International Symposium, Springer Nature, 2015, pp. 566–577. conference: end_date: 2015-12-11 location: Nagoya, Japan name: 'ISAAC: International Symposium on Algorithms and Computation' start_date: 2015-12-09 date_created: 2018-12-11T11:53:10Z date_published: 2015-12-01T00:00:00Z date_updated: 2022-02-01T15:12:35Z day: '01' department: - _id: VlKo doi: 10.1007/978-3-662-48971-0_48 ec_funded: 1 external_id: arxiv: - '1504.07067' intvolume: ' 9472' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1504.07067 month: '12' oa: 1 oa_version: Preprint page: 566 - 577 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' publication: 26th International Symposium publication_identifier: isbn: - 978-3-662-48970-3 publication_status: published publisher: Springer Nature publist_id: '5519' quality_controlled: '1' scopus_import: '1' status: public title: Effectiveness of structural restrictions for hybrid CSPs type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9472 year: '2015' ... --- _id: '1632' abstract: - lang: eng text: "This paper presents a liquid simulation technique that enforces the incompressibility condition using a stream function solve instead of a pressure projection. Previous methods have used stream function techniques for the simulation of detailed single-phase flows, but a formulation for liquid simulation has proved elusive in part due to the free surface boundary conditions. In this paper, we introduce a stream function approach to liquid simulations with novel boundary conditions for free surfaces, solid obstacles, and solid-fluid coupling.\r\n\r\nAlthough our approach increases the dimension of the linear system necessary to enforce incompressibility, it provides interesting and surprising benefits. First, the resulting flow is guaranteed to be divergence-free regardless of the accuracy of the solve. Second, our free-surface boundary conditions guarantee divergence-free motion even in the un-simulated air phase, which enables two-phase flow simulation by only computing a single phase. We implemented this method using a variant of FLIP simulation which only samples particles within a narrow band of the liquid surface, and we illustrate the effectiveness of our method for detailed two-phase flow simulations with complex boundaries, detailed bubble interactions, and two-way solid-fluid coupling." acknowledgement: The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad. This work was also supported by the ERC projects ERC-2014-StG-637014 realFlow and ERC-2014- StG-638176 BigSplash. alternative_title: - ACM Transactions on Graphics article_number: '53' author: - first_name: Ryoichi full_name: Ando, Ryoichi last_name: Ando - first_name: Nils full_name: Thuerey, Nils last_name: Thuerey - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: 'Ando R, Thuerey N, Wojtan C. A stream function solver for liquid simulations. In: Vol 34. ACM; 2015. doi:10.1145/2766935' apa: 'Ando, R., Thuerey, N., & Wojtan, C. (2015). A stream function solver for liquid simulations (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA: ACM. https://doi.org/10.1145/2766935' chicago: Ando, Ryoichi, Nils Thuerey, and Chris Wojtan. “A Stream Function Solver for Liquid Simulations,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766935. ieee: 'R. Ando, N. Thuerey, and C. Wojtan, “A stream function solver for liquid simulations,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, USA, 2015, vol. 34, no. 4.' ista: 'Ando R, Thuerey N, Wojtan C. 2015. A stream function solver for liquid simulations. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, ACM Transactions on Graphics, vol. 34, 53.' mla: Ando, Ryoichi, et al. A Stream Function Solver for Liquid Simulations. Vol. 34, no. 4, 53, ACM, 2015, doi:10.1145/2766935. short: R. Ando, N. Thuerey, C. Wojtan, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, USA name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:09Z date_published: 2015-07-27T00:00:00Z date_updated: 2023-02-23T10:07:37Z day: '27' ddc: - '000' department: - _id: ChWo doi: 10.1145/2766935 file: - access_level: open_access checksum: 7a9afdfaba9209157ce19376e15bc90b content_type: application/pdf creator: system date_created: 2018-12-12T10:11:52Z date_updated: 2020-07-14T12:45:07Z file_id: '4909' file_name: IST-2016-610-v1+1_vecpotential.pdf file_size: 21831121 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 34' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version publication_status: published publisher: ACM publist_id: '5523' pubrep_id: '610' quality_controlled: '1' scopus_import: 1 status: public title: A stream function solver for liquid simulations type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1630' abstract: - lang: eng text: We present a method to learn and propagate shape placements in 2D polygonal scenes from a few examples provided by a user. The placement of a shape is modeled as an oriented bounding box. Simple geometric relationships between this bounding box and nearby scene polygons define a feature set for the placement. The feature sets of all example placements are then used to learn a probabilistic model over all possible placements and scenes. With this model, we can generate a new set of placements with similar geometric relationships in any given scene. We introduce extensions that enable propagation and generation of shapes in 3D scenes, as well as the application of a learned modeling session to large scenes without additional user interaction. These concepts allow us to generate complex scenes with thousands of objects with relatively little user interaction. acknowledgement: This publication is based upon work supported by the KAUST Office of Competitive Research Funds (OCRF) under Award No. 62140401, the KAUST Visual Computing Center and the Austrian Science Fund (FWF) projects DEEP PICTURES (no. P24352-N23) and Data-Driven Procedural Modeling of Interiors (no. P24600-N23). article_number: '108' 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. Learning shape placements by example. In: Vol 34. ACM; 2015. doi:10.1145/2766933' apa: 'Guerrero, P., Jeschke, S., Wimmer, M., & Wonka, P. (2015). Learning shape placements by example (Vol. 34). Presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States: ACM. https://doi.org/10.1145/2766933' chicago: Guerrero, Paul, Stefan Jeschke, Michael Wimmer, and Peter Wonka. “Learning Shape Placements by Example,” Vol. 34. ACM, 2015. https://doi.org/10.1145/2766933. ieee: 'P. Guerrero, S. Jeschke, M. Wimmer, and P. Wonka, “Learning shape placements by example,” presented at the SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques, Los Angeles, CA, United States, 2015, vol. 34, no. 4.' ista: 'Guerrero P, Jeschke S, Wimmer M, Wonka P. 2015. Learning shape placements by example. SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques vol. 34, 108.' mla: Guerrero, Paul, et al. Learning Shape Placements by Example. Vol. 34, no. 4, 108, ACM, 2015, doi:10.1145/2766933. short: P. Guerrero, S. Jeschke, M. Wimmer, P. Wonka, in:, ACM, 2015. conference: end_date: 2015-08-13 location: Los Angeles, CA, United States name: 'SIGGRAPH: Special Interest Group on Computer Graphics and Interactive Techniques' start_date: 2015-08-09 date_created: 2018-12-11T11:53:08Z date_published: 2015-07-27T00:00:00Z date_updated: 2021-01-12T06:52:07Z day: '27' ddc: - '000' department: - _id: ChWo doi: 10.1145/2766933 file: - access_level: open_access checksum: 8b05a51e372c9b0b5af9a00098a9538b content_type: application/pdf creator: system date_created: 2018-12-12T10:07:49Z date_updated: 2020-07-14T12:45:07Z file_id: '4647' file_name: IST-2016-576-v1+1_guerrero-2015-lsp-paper.pdf file_size: 11902290 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 34' issue: '4' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 25357BD2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 24352-N23 name: 'Deep Pictures: Creating Visual and Haptic Vector Images' publication_status: published publisher: ACM publist_id: '5525' pubrep_id: '576' quality_controlled: '1' scopus_import: 1 status: public title: Learning shape placements by example type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1640' abstract: - lang: eng text: Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: This work was supported by the European Research Council Starting Independent Research grant (ERC-2007-Stg-207362-HCPO to E.B., M.S., C.C.), by the Ghent University Multidisciplinary Research Partnership ‘Biotechnology for a Sustainable Economy’ no.01MRB510W, by the Research Foundation—Flanders (grant 3G033711 to J.-A.O.), by the Austrian Science Fund (FWF01_I1774S) to K.Ö.,E.B., and by the Interuniversity Attraction Poles Programme (IUAP P7/29 ‘MARS’) initiated by the Belgian Science Policy Office. I.D.C. and S.V. are post-doctoral fellows of the Research Foundation—Flanders (FWO). This research was supported by the Scientific Service Units (SSU) of IST-Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF). article_number: '8717' author: - first_name: Mária full_name: Šimášková, Mária last_name: Šimášková - first_name: José full_name: O'Brien, José last_name: O'Brien - first_name: Mamoona full_name: Khan-Djamei, Mamoona id: 391B5BBC-F248-11E8-B48F-1D18A9856A87 last_name: Khan-Djamei - first_name: Giel full_name: Van Noorden, Giel last_name: Van Noorden - first_name: Krisztina full_name: Ötvös, Krisztina id: 29B901B0-F248-11E8-B48F-1D18A9856A87 last_name: Ötvös orcid: 0000-0002-5503-4983 - first_name: Anne full_name: Vieten, Anne last_name: Vieten - first_name: Inge full_name: De Clercq, Inge last_name: De Clercq - first_name: Johanna full_name: Van Haperen, Johanna last_name: Van Haperen - first_name: Candela full_name: Cuesta, Candela id: 33A3C818-F248-11E8-B48F-1D18A9856A87 last_name: Cuesta orcid: 0000-0003-1923-2410 - first_name: Klára full_name: Hoyerová, Klára last_name: Hoyerová - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Peter full_name: Marhavy, Peter id: 3F45B078-F248-11E8-B48F-1D18A9856A87 last_name: Marhavy orcid: 0000-0001-5227-5741 - first_name: Krzysztof T full_name: Wabnik, Krzysztof T id: 4DE369A4-F248-11E8-B48F-1D18A9856A87 last_name: Wabnik orcid: 0000-0001-7263-0560 - first_name: Frank full_name: Van Breusegem, Frank last_name: Van Breusegem - first_name: Moritz full_name: Nowack, Moritz last_name: Nowack - first_name: Angus full_name: Murphy, Angus last_name: Murphy - first_name: Jiřĺ full_name: Friml, Jiřĺ id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Dolf full_name: Weijers, Dolf last_name: Weijers - first_name: Tom full_name: Beeckman, Tom last_name: Beeckman - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Šimášková M, O’Brien J, Khan-Djamei M, et al. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. 2015;6. doi:10.1038/ncomms9717 apa: Šimášková, M., O’Brien, J., Khan-Djamei, M., Van Noorden, G., Ötvös, K., Vieten, A., … Benková, E. (2015). Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms9717 chicago: Šimášková, Mária, José O’Brien, Mamoona Khan-Djamei, Giel Van Noorden, Krisztina Ötvös, Anne Vieten, Inge De Clercq, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin Transporters.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms9717. ieee: M. Šimášková et al., “Cytokinin response factors regulate PIN-FORMED auxin transporters,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Šimášková M, O’Brien J, Khan-Djamei M, Van Noorden G, Ötvös K, Vieten A, De Clercq I, Van Haperen J, Cuesta C, Hoyerová K, Vanneste S, Marhavý P, Wabnik KT, Van Breusegem F, Nowack M, Murphy A, Friml J, Weijers D, Beeckman T, Benková E. 2015. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nature Communications. 6, 8717. mla: Šimášková, Mária, et al. “Cytokinin Response Factors Regulate PIN-FORMED Auxin Transporters.” Nature Communications, vol. 6, 8717, Nature Publishing Group, 2015, doi:10.1038/ncomms9717. short: M. Šimášková, J. O’Brien, M. Khan-Djamei, G. Van Noorden, K. Ötvös, A. Vieten, I. De Clercq, J. Van Haperen, C. Cuesta, K. Hoyerová, S. Vanneste, P. Marhavý, K.T. Wabnik, F. Van Breusegem, M. Nowack, A. Murphy, J. Friml, D. Weijers, T. Beeckman, E. Benková, Nature Communications 6 (2015). date_created: 2018-12-11T11:53:12Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:52:11Z day: '01' ddc: - '580' department: - _id: EvBe - _id: JiFr doi: 10.1038/ncomms9717 ec_funded: 1 file: - access_level: open_access checksum: c2c84bca37401435fedf76bad0ba0579 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:36Z date_updated: 2020-07-14T12:45:08Z file_id: '5358' file_name: IST-2018-1020-v1+1_Simaskova_et_al_NatCom_2015.pdf file_size: 1471217 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 6' language: - iso: eng month: '01' oa: 1 oa_version: Submitted Version project: - _id: 253FCA6A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '207362' name: Hormonal cross-talk in plant organogenesis - _id: 2542D156-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I 1774-B16 name: Hormone cross-talk drives nutrient dependent plant development publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5513' pubrep_id: '1020' quality_controlled: '1' scopus_import: 1 status: public title: Cytokinin response factors regulate PIN-FORMED auxin transporters type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 6 year: '2015' ... --- _id: '1642' 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 result to clustered graphs with two disjoint clusters, and show that a straightforward extension to flat clustered graphs with three or more disjoint clusters is not possible. For general clustered graphs we show a variant of the Hanani-Tutte theorem in the case when each cluster induces a connected subgraph. Di Battista and Frati proved that clustered planarity of embedded clustered graphs whose every face is incident to at most five vertices can be tested in polynomial time. We give a new and short proof of this result, using the matroid intersection algorithm. acknowledgement: e research leading to these results has received funding fromthe People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no [291734], and ESF Eurogiga project GraDR as GAˇCRGIG/11/E023. article_number: 'P4.24 ' article_processing_charge: No article_type: original 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: Malinovič, Igor last_name: Malinovič - first_name: Dömötör full_name: Pálvölgyi, Dömötör last_name: Pálvölgyi citation: ama: Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. Clustered planarity testing revisited. Electronic Journal of Combinatorics. 2015;22(4). doi:10.37236/5002 apa: Fulek, R., Kynčl, J., Malinovič, I., & Pálvölgyi, D. (2015). Clustered planarity testing revisited. Electronic Journal of Combinatorics. Electronic Journal of Combinatorics. https://doi.org/10.37236/5002 chicago: Fulek, Radoslav, Jan Kynčl, Igor Malinovič, and Dömötör Pálvölgyi. “Clustered Planarity Testing Revisited.” Electronic Journal of Combinatorics. Electronic Journal of Combinatorics, 2015. https://doi.org/10.37236/5002. ieee: R. Fulek, J. Kynčl, I. Malinovič, and D. Pálvölgyi, “Clustered planarity testing revisited,” Electronic Journal of Combinatorics, vol. 22, no. 4. Electronic Journal of Combinatorics, 2015. ista: Fulek R, Kynčl J, Malinovič I, Pálvölgyi D. 2015. Clustered planarity testing revisited. Electronic Journal of Combinatorics. 22(4), P4.24. mla: Fulek, Radoslav, et al. “Clustered Planarity Testing Revisited.” Electronic Journal of Combinatorics, vol. 22, no. 4, P4.24, Electronic Journal of Combinatorics, 2015, doi:10.37236/5002. short: R. Fulek, J. Kynčl, I. Malinovič, D. Pálvölgyi, Electronic Journal of Combinatorics 22 (2015). date_created: 2018-12-11T11:53:12Z date_published: 2015-11-13T00:00:00Z date_updated: 2023-02-21T16:03:02Z day: '13' ddc: - '514' - '516' department: - _id: UlWa doi: 10.37236/5002 ec_funded: 1 external_id: arxiv: - '1305.4519' file: - access_level: open_access checksum: 40b5920b49ee736694f59f39588ee206 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:03Z date_updated: 2020-07-14T12:45:08Z file_id: '5120' file_name: IST-2016-714-v1+1_5002-15499-3-PB.pdf file_size: 443655 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 22' issue: '4' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Electronic Journal of Combinatorics publication_identifier: eissn: - 1077-8926 publication_status: published publisher: Electronic Journal of Combinatorics publist_id: '5511' pubrep_id: '714' quality_controlled: '1' related_material: record: - id: '10793' relation: earlier_version status: public scopus_import: '1' status: public title: Clustered planarity testing revisited type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 22 year: '2015' ... --- _id: '1639' abstract: - lang: eng text: In this paper the optimal transport and the metamorphosis perspectives are combined. For a pair of given input images geodesic paths in the space of images are defined as minimizers of a resulting path energy. To this end, the underlying Riemannian metric measures the rate of transport cost and the rate of viscous dissipation. Furthermore, the model is capable to deal with strongly varying image contrast and explicitly allows for sources and sinks in the transport equations which are incorporated in the metric related to the metamorphosis approach by Trouvé and Younes. In the non-viscous case with source term existence of geodesic paths is proven in the space of measures. The proposed model is explored on the range from merely optimal transport to strongly dissipative dynamics. For this model a robust and effective variational time discretization of geodesic paths is proposed. This requires to minimize a discrete path energy consisting of a sum of consecutive image matching functionals. These functionals are defined on corresponding pairs of intensity functions and on associated pairwise matching deformations. Existence of time discrete geodesics is demonstrated. Furthermore, a finite element implementation is proposed and applied to instructive test cases and to real images. In the non-viscous case this is compared to the algorithm proposed by Benamou and Brenier including a discretization of the source term. Finally, the model is generalized to define discrete weighted barycentres with applications to textures and objects. acknowledgement: The authors acknowledge support of the Collaborative Research Centre 1060 funded by the German Science foundation. This work is further supported by the King Abdullah University for Science and Technology (KAUST) Award No. KUK-I1-007-43 and the EPSRC grant Nr. EP/M00483X/1. author: - first_name: Jan full_name: Maas, Jan id: 4C5696CE-F248-11E8-B48F-1D18A9856A87 last_name: Maas orcid: 0000-0002-0845-1338 - first_name: Martin full_name: Rumpf, Martin last_name: Rumpf - first_name: Carola full_name: Schönlieb, Carola last_name: Schönlieb - first_name: Stefan full_name: Simon, Stefan last_name: Simon citation: ama: 'Maas J, Rumpf M, Schönlieb C, Simon S. A generalized model for optimal transport of images including dissipation and density modulation. ESAIM: Mathematical Modelling and Numerical Analysis. 2015;49(6):1745-1769. doi:10.1051/m2an/2015043' apa: 'Maas, J., Rumpf, M., Schönlieb, C., & Simon, S. (2015). A generalized model for optimal transport of images including dissipation and density modulation. ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences. https://doi.org/10.1051/m2an/2015043' chicago: 'Maas, Jan, Martin Rumpf, Carola Schönlieb, and Stefan Simon. “A Generalized Model for Optimal Transport of Images Including Dissipation and Density Modulation.” ESAIM: Mathematical Modelling and Numerical Analysis. EDP Sciences, 2015. https://doi.org/10.1051/m2an/2015043.' ieee: 'J. Maas, M. Rumpf, C. Schönlieb, and S. Simon, “A generalized model for optimal transport of images including dissipation and density modulation,” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 49, no. 6. EDP Sciences, pp. 1745–1769, 2015.' ista: 'Maas J, Rumpf M, Schönlieb C, Simon S. 2015. A generalized model for optimal transport of images including dissipation and density modulation. ESAIM: Mathematical Modelling and Numerical Analysis. 49(6), 1745–1769.' mla: 'Maas, Jan, et al. “A Generalized Model for Optimal Transport of Images Including Dissipation and Density Modulation.” ESAIM: Mathematical Modelling and Numerical Analysis, vol. 49, no. 6, EDP Sciences, 2015, pp. 1745–69, doi:10.1051/m2an/2015043.' short: 'J. Maas, M. Rumpf, C. Schönlieb, S. Simon, ESAIM: Mathematical Modelling and Numerical Analysis 49 (2015) 1745–1769.' date_created: 2018-12-11T11:53:11Z date_published: 2015-11-01T00:00:00Z date_updated: 2021-01-12T06:52:10Z day: '01' department: - _id: JaMa doi: 10.1051/m2an/2015043 external_id: arxiv: - '1504.01988' intvolume: ' 49' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1504.01988 month: '11' oa: 1 oa_version: Preprint page: 1745 - 1769 publication: 'ESAIM: Mathematical Modelling and Numerical Analysis' publication_status: published publisher: EDP Sciences publist_id: '5514' quality_controlled: '1' scopus_import: 1 status: public title: A generalized model for optimal transport of images including dissipation and density modulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 49 year: '2015' ... --- _id: '1638' abstract: - lang: eng text: The mitochondrial respiratory chain, also known as the electron transport chain (ETC), is crucial to life, and energy production in the form of ATP is the main mitochondrial function. Three proton-translocating enzymes of the ETC, namely complexes I, III and IV, generate proton motive force, which in turn drives ATP synthase (complex V). The atomic structures and basic mechanisms of most respiratory complexes have previously been established, with the exception of complex I, the largest complex in the ETC. Recently, the crystal structure of the entire complex I was solved using a bacterial enzyme. The structure provided novel insights into the core architecture of the complex, the electron transfer and proton translocation pathways, as well as the mechanism that couples these two processes. author: - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: 'Sazanov LA. A giant molecular proton pump: structure and mechanism of respiratory complex I. Nature Reviews Molecular Cell Biology. 2015;16(6):375-388. doi:10.1038/nrm3997' apa: 'Sazanov, L. A. (2015). A giant molecular proton pump: structure and mechanism of respiratory complex I. Nature Reviews Molecular Cell Biology. Nature Publishing Group. https://doi.org/10.1038/nrm3997' chicago: 'Sazanov, Leonid A. “A Giant Molecular Proton Pump: Structure and Mechanism of Respiratory Complex I.” Nature Reviews Molecular Cell Biology. Nature Publishing Group, 2015. https://doi.org/10.1038/nrm3997.' ieee: 'L. A. Sazanov, “A giant molecular proton pump: structure and mechanism of respiratory complex I,” Nature Reviews Molecular Cell Biology, vol. 16, no. 6. Nature Publishing Group, pp. 375–388, 2015.' ista: 'Sazanov LA. 2015. A giant molecular proton pump: structure and mechanism of respiratory complex I. Nature Reviews Molecular Cell Biology. 16(6), 375–388.' mla: 'Sazanov, Leonid A. “A Giant Molecular Proton Pump: Structure and Mechanism of Respiratory Complex I.” Nature Reviews Molecular Cell Biology, vol. 16, no. 6, Nature Publishing Group, 2015, pp. 375–88, doi:10.1038/nrm3997.' short: L.A. Sazanov, Nature Reviews Molecular Cell Biology 16 (2015) 375–388. date_created: 2018-12-11T11:53:11Z date_published: 2015-05-22T00:00:00Z date_updated: 2021-01-12T06:52:10Z day: '22' department: - _id: LeSa doi: 10.1038/nrm3997 intvolume: ' 16' issue: '6' language: - iso: eng month: '05' oa_version: None page: 375 - 388 publication: Nature Reviews Molecular Cell Biology publication_status: published publisher: Nature Publishing Group publist_id: '5517' quality_controlled: '1' scopus_import: 1 status: public title: 'A giant molecular proton pump: structure and mechanism of respiratory complex I' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2015' ... --- _id: '1646' abstract: - lang: eng text: 'A pseudorandom function (PRF) is a keyed function F : K × X → Y where, for a random key k ∈ K, the function F(k, ·) is indistinguishable from a uniformly random function, given black-box access. A key-homomorphic PRF has the additional feature that for any keys k, k'' and any input x, we have F(k+k'', x) = F(k, x)⊕F(k'', x) for some group operations +,⊕ on K and Y, respectively. A constrained PRF for a family of setsS ⊆ P(X) has the property that, given any key k and set S ∈ S, one can efficiently compute a “constrained” key kS that enables evaluation of F(k, x) on all inputs x ∈ S, while the values F(k, x) for x /∈ S remain pseudorandom even given kS. In this paper we construct PRFs that are simultaneously constrained and key homomorphic, where the homomorphic property holds even for constrained keys. We first show that the multilinear map-based bit-fixing and circuit-constrained PRFs of Boneh and Waters (Asiacrypt 2013) can be modified to also be keyhomomorphic. We then show that the LWE-based key-homomorphic PRFs of Banerjee and Peikert (Crypto 2014) are essentially already prefix-constrained PRFs, using a (non-obvious) definition of constrained keys and associated group operation. Moreover, the constrained keys themselves are pseudorandom, and the constraining and evaluation functions can all be computed in low depth. As an application of key-homomorphic constrained PRFs,we construct a proxy re-encryption schemewith fine-grained access control. This scheme allows storing encrypted data on an untrusted server, where each file can be encrypted relative to some attributes, so that only parties whose constrained keys match the attributes can decrypt. Moreover, the server can re-key (arbitrary subsets of) the ciphertexts without learning anything about the plaintexts, thus permitting efficient and finegrained revocation.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Abishek full_name: Banerjee, Abishek last_name: Banerjee - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Chris full_name: Peikert, Chris last_name: Peikert - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Sophie full_name: Stevens, Sophie last_name: Stevens citation: ama: 'Banerjee A, Fuchsbauer G, Peikert C, Pietrzak KZ, Stevens S. Key-homomorphic constrained pseudorandom functions. In: 12th Theory of Cryptography Conference. Vol 9015. Springer Nature; 2015:31-60. doi:10.1007/978-3-662-46497-7_2' apa: 'Banerjee, A., Fuchsbauer, G., Peikert, C., Pietrzak, K. Z., & Stevens, S. (2015). Key-homomorphic constrained pseudorandom functions. In 12th Theory of Cryptography Conference (Vol. 9015, pp. 31–60). Warsaw, Poland: Springer Nature. https://doi.org/10.1007/978-3-662-46497-7_2' chicago: Banerjee, Abishek, Georg Fuchsbauer, Chris Peikert, Krzysztof Z Pietrzak, and Sophie Stevens. “Key-Homomorphic Constrained Pseudorandom Functions.” In 12th Theory of Cryptography Conference, 9015:31–60. Springer Nature, 2015. https://doi.org/10.1007/978-3-662-46497-7_2. ieee: A. Banerjee, G. Fuchsbauer, C. Peikert, K. Z. Pietrzak, and S. Stevens, “Key-homomorphic constrained pseudorandom functions,” in 12th Theory of Cryptography Conference, Warsaw, Poland, 2015, vol. 9015, pp. 31–60. ista: 'Banerjee A, Fuchsbauer G, Peikert C, Pietrzak KZ, Stevens S. 2015. Key-homomorphic constrained pseudorandom functions. 12th Theory of Cryptography Conference. TCC: Theory of Cryptography Conference, LNCS, vol. 9015, 31–60.' mla: Banerjee, Abishek, et al. “Key-Homomorphic Constrained Pseudorandom Functions.” 12th Theory of Cryptography Conference, vol. 9015, Springer Nature, 2015, pp. 31–60, doi:10.1007/978-3-662-46497-7_2. short: A. Banerjee, G. Fuchsbauer, C. Peikert, K.Z. Pietrzak, S. Stevens, in:, 12th Theory of Cryptography Conference, Springer Nature, 2015, pp. 31–60. conference: end_date: 2015-03-25 location: Warsaw, Poland name: 'TCC: Theory of Cryptography Conference' start_date: 2015-03-23 date_created: 2018-12-11T11:53:14Z date_published: 2015-03-01T00:00:00Z date_updated: 2022-02-03T08:41:46Z day: '01' ddc: - '000' - '004' department: - _id: KrPi doi: 10.1007/978-3-662-46497-7_2 ec_funded: 1 file: - access_level: open_access checksum: 3c5093bda5783c89beaacabf1aa0e60e content_type: application/pdf creator: system date_created: 2018-12-12T10:15:17Z date_updated: 2020-07-14T12:45:08Z file_id: '5136' file_name: IST-2016-679-v1+1_180.pdf file_size: 450665 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 9015' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2015/180 month: '03' oa: 1 oa_version: Submitted Version page: 31 - 60 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: 12th Theory of Cryptography Conference publication_identifier: isbn: - 978-3-662-46496-0 publication_status: published publisher: Springer Nature publist_id: '5505' pubrep_id: '679' quality_controlled: '1' scopus_import: '1' status: public title: Key-homomorphic constrained pseudorandom functions type: conference user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 volume: 9015 year: '2015' ... --- _id: '1648' abstract: - lang: eng text: Generalized Selective Decryption (GSD), introduced by Panjwani [TCC’07], is a game for a symmetric encryption scheme Enc that captures the difficulty of proving adaptive security of certain protocols, most notably the Logical Key Hierarchy (LKH) multicast encryption protocol. In the GSD game there are n keys k1,..., kn, which the adversary may adaptively corrupt (learn); moreover, it can ask for encryptions Encki (kj) of keys under other keys. The adversary’s task is to distinguish keys (which it cannot trivially compute) from random. Proving the hardness of GSD assuming only IND-CPA security of Enc is surprisingly hard. Using “complexity leveraging” loses a factor exponential in n, which makes the proof practically meaningless. We can think of the GSD game as building a graph on n vertices, where we add an edge i → j when the adversary asks for an encryption of kj under ki. If restricted to graphs of depth ℓ, Panjwani gave a reduction that loses only a factor exponential in ℓ (not n). To date, this is the only non-trivial result known for GSD. In this paper we give almost-polynomial reductions for large classes of graphs. Most importantly, we prove the security of the GSD game restricted to trees losing only a quasi-polynomial factor n3 log n+5. Trees are an important special case capturing real-world protocols like the LKH protocol. Our new bound improves upon Panjwani’s on some LKH variants proposed in the literature where the underlying tree is not balanced. Our proof builds on ideas from the “nested hybrids” technique recently introduced by Fuchsbauer et al. [Asiacrypt’14] for proving the adaptive security of constrained PRFs. alternative_title: - LNCS author: - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Zahra full_name: Jafargholi, Zahra last_name: Jafargholi - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Fuchsbauer G, Jafargholi Z, Pietrzak KZ. A quasipolynomial reduction for generalized selective decryption on trees. In: Vol 9215. Springer; 2015:601-620. doi:10.1007/978-3-662-47989-6_29' apa: 'Fuchsbauer, G., Jafargholi, Z., & Pietrzak, K. Z. (2015). A quasipolynomial reduction for generalized selective decryption on trees (Vol. 9215, pp. 601–620). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA: Springer. https://doi.org/10.1007/978-3-662-47989-6_29' chicago: Fuchsbauer, Georg, Zahra Jafargholi, and Krzysztof Z Pietrzak. “A Quasipolynomial Reduction for Generalized Selective Decryption on Trees,” 9215:601–20. Springer, 2015. https://doi.org/10.1007/978-3-662-47989-6_29. ieee: 'G. Fuchsbauer, Z. Jafargholi, and K. Z. Pietrzak, “A quasipolynomial reduction for generalized selective decryption on trees,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, USA, 2015, vol. 9215, pp. 601–620.' ista: 'Fuchsbauer G, Jafargholi Z, Pietrzak KZ. 2015. A quasipolynomial reduction for generalized selective decryption on trees. CRYPTO: International Cryptology Conference, LNCS, vol. 9215, 601–620.' mla: Fuchsbauer, Georg, et al. A Quasipolynomial Reduction for Generalized Selective Decryption on Trees. Vol. 9215, Springer, 2015, pp. 601–20, doi:10.1007/978-3-662-47989-6_29. short: G. Fuchsbauer, Z. Jafargholi, K.Z. Pietrzak, in:, Springer, 2015, pp. 601–620. conference: end_date: 2015-08-20 location: Santa Barbara, CA, USA name: 'CRYPTO: International Cryptology Conference' start_date: 2015-08-16 date_created: 2018-12-11T11:53:14Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:52:14Z day: '01' ddc: - '004' department: - _id: KrPi doi: 10.1007/978-3-662-47989-6_29 ec_funded: 1 file: - access_level: open_access checksum: 99b76b3263d5082554d0a9cbdeca3a22 content_type: application/pdf creator: system date_created: 2018-12-12T10:13:31Z date_updated: 2020-07-14T12:45:08Z file_id: '5015' file_name: IST-2016-674-v1+1_389.pdf file_size: 505618 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 9215' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 601 - 620 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5502' pubrep_id: '674' quality_controlled: '1' scopus_import: 1 status: public title: A quasipolynomial reduction for generalized selective decryption on trees tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9215 year: '2015' ... --- _id: '1649' abstract: - lang: eng text: 'We extend a commitment scheme based on the learning with errors over rings (RLWE) problem, and present efficient companion zeroknowledge proofs of knowledge. Our scheme maps elements from the ring (or equivalently, n elements from ' alternative_title: - LNCS author: - first_name: Fabrice full_name: Benhamouda, Fabrice last_name: Benhamouda - first_name: Stephan full_name: Krenn, Stephan last_name: Krenn - first_name: Vadim full_name: Lyubashevsky, Vadim last_name: Lyubashevsky - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: Benhamouda F, Krenn S, Lyubashevsky V, Pietrzak KZ. Efficient zero-knowledge proofs for commitments from learning with errors over rings. 2015;9326:305-325. doi:10.1007/978-3-319-24174-6_16 apa: 'Benhamouda, F., Krenn, S., Lyubashevsky, V., & Pietrzak, K. Z. (2015). Efficient zero-knowledge proofs for commitments from learning with errors over rings. Presented at the ESORICS: European Symposium on Research in Computer Security, Vienna, Austria: Springer. https://doi.org/10.1007/978-3-319-24174-6_16' chicago: Benhamouda, Fabrice, Stephan Krenn, Vadim Lyubashevsky, and Krzysztof Z Pietrzak. “Efficient Zero-Knowledge Proofs for Commitments from Learning with Errors over Rings.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-24174-6_16. ieee: F. Benhamouda, S. Krenn, V. Lyubashevsky, and K. Z. Pietrzak, “Efficient zero-knowledge proofs for commitments from learning with errors over rings,” vol. 9326. Springer, pp. 305–325, 2015. ista: Benhamouda F, Krenn S, Lyubashevsky V, Pietrzak KZ. 2015. Efficient zero-knowledge proofs for commitments from learning with errors over rings. 9326, 305–325. mla: Benhamouda, Fabrice, et al. Efficient Zero-Knowledge Proofs for Commitments from Learning with Errors over Rings. Vol. 9326, Springer, 2015, pp. 305–25, doi:10.1007/978-3-319-24174-6_16. short: F. Benhamouda, S. Krenn, V. Lyubashevsky, K.Z. Pietrzak, 9326 (2015) 305–325. conference: end_date: 2015-09-25 location: Vienna, Austria name: 'ESORICS: European Symposium on Research in Computer Security' start_date: 2015-09-21 date_created: 2018-12-11T11:53:15Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:52:14Z day: '01' ddc: - '000' - '004' department: - _id: KrPi doi: 10.1007/978-3-319-24174-6_16 ec_funded: 1 file: - access_level: open_access checksum: 6eac4a485b2aa644b2d3f753ed0b280b content_type: application/pdf creator: system date_created: 2018-12-12T10:11:28Z date_updated: 2020-07-14T12:45:08Z file_id: '4883' file_name: IST-2016-678-v1+1_889.pdf file_size: 494239 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 9326' language: - iso: eng license: https://creativecommons.org/licenses/by-nc/4.0/ month: '01' oa: 1 oa_version: Published Version page: 305 - 325 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5501' pubrep_id: '678' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Efficient zero-knowledge proofs for commitments from learning with errors over rings 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: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9326 year: '2015' ... --- _id: '1644' abstract: - lang: eng text: Increasing the computational complexity of evaluating a hash function, both for the honest users as well as for an adversary, is a useful technique employed for example in password-based cryptographic schemes to impede brute-force attacks, and also in so-called proofs of work (used in protocols like Bitcoin) to show that a certain amount of computation was performed by a legitimate user. A natural approach to adjust the complexity of a hash function is to iterate it c times, for some parameter c, in the hope that any query to the scheme requires c evaluations of the underlying hash function. However, results by Dodis et al. (Crypto 2012) imply that plain iteration falls short of achieving this goal, and designing schemes which provably have such a desirable property remained an open problem. This paper formalizes explicitly what it means for a given scheme to amplify the query complexity of a hash function. In the random oracle model, the goal of a secure query-complexity amplifier (QCA) scheme is captured as transforming, in the sense of indifferentiability, a random oracle allowing R queries (for the adversary) into one provably allowing only r < R queries. Turned around, this means that making r queries to the scheme requires at least R queries to the actual random oracle. Second, a new scheme, called collision-free iteration, is proposed and proven to achieve c-fold QCA for both the honest parties and the adversary, for any fixed parameter c. alternative_title: - LNCS author: - first_name: Grégory full_name: Demay, Grégory last_name: Demay - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Ueli full_name: Maurer, Ueli last_name: Maurer - first_name: Björn full_name: Tackmann, Björn last_name: Tackmann citation: ama: 'Demay G, Gazi P, Maurer U, Tackmann B. Query-complexity amplification for random oracles. In: Vol 9063. Springer; 2015:159-180. doi:10.1007/978-3-319-17470-9_10' apa: 'Demay, G., Gazi, P., Maurer, U., & Tackmann, B. (2015). Query-complexity amplification for random oracles (Vol. 9063, pp. 159–180). Presented at the ICITS: International Conference on Information Theoretic Security, Lugano, Switzerland: Springer. https://doi.org/10.1007/978-3-319-17470-9_10' chicago: Demay, Grégory, Peter Gazi, Ueli Maurer, and Björn Tackmann. “Query-Complexity Amplification for Random Oracles,” 9063:159–80. Springer, 2015. https://doi.org/10.1007/978-3-319-17470-9_10. ieee: 'G. Demay, P. Gazi, U. Maurer, and B. Tackmann, “Query-complexity amplification for random oracles,” presented at the ICITS: International Conference on Information Theoretic Security, Lugano, Switzerland, 2015, vol. 9063, pp. 159–180.' ista: 'Demay G, Gazi P, Maurer U, Tackmann B. 2015. Query-complexity amplification for random oracles. ICITS: International Conference on Information Theoretic Security, LNCS, vol. 9063, 159–180.' mla: Demay, Grégory, et al. Query-Complexity Amplification for Random Oracles. Vol. 9063, Springer, 2015, pp. 159–80, doi:10.1007/978-3-319-17470-9_10. short: G. Demay, P. Gazi, U. Maurer, B. Tackmann, in:, Springer, 2015, pp. 159–180. conference: end_date: 2015-05-05 location: Lugano, Switzerland name: 'ICITS: International Conference on Information Theoretic Security' start_date: 2015-05-02 date_created: 2018-12-11T11:53:13Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:52:13Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-319-17470-9_10 ec_funded: 1 intvolume: ' 9063' language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2015/315 month: '01' oa: 1 oa_version: Submitted Version page: 159 - 180 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5507' quality_controlled: '1' scopus_import: 1 status: public title: Query-complexity amplification for random oracles type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9063 year: '2015' ... --- _id: '1647' abstract: - lang: eng text: Round-optimal blind signatures are notoriously hard to construct in the standard model, especially in the malicious-signer model, where blindness must hold under adversarially chosen keys. This is substantiated by several impossibility results. The only construction that can be termed theoretically efficient, by Garg and Gupta (Eurocrypt’14), requires complexity leveraging, inducing an exponential security loss. We present a construction of practically efficient round-optimal blind signatures in the standard model. It is conceptually simple and builds on the recent structure-preserving signatures on equivalence classes (SPSEQ) from Asiacrypt’14. While the traditional notion of blindness follows from standard assumptions, we prove blindness under adversarially chosen keys under an interactive variant of DDH. However, we neither require non-uniform assumptions nor complexity leveraging. We then show how to extend our construction to partially blind signatures and to blind signatures on message vectors, which yield a construction of one-show anonymous credentials à la “anonymous credentials light” (CCS’13) in the standard model. Furthermore, we give the first SPS-EQ construction under noninteractive assumptions and show how SPS-EQ schemes imply conventional structure-preserving signatures, which allows us to apply optimality results for the latter to SPS-EQ. alternative_title: - LNCS article_processing_charge: No author: - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Christian full_name: Hanser, Christian last_name: Hanser - first_name: Daniel full_name: Slamanig, Daniel last_name: Slamanig citation: ama: 'Fuchsbauer G, Hanser C, Slamanig D. Practical round-optimal blind signatures in the standard model. In: Vol 9216. Springer; 2015:233-253. doi:10.1007/978-3-662-48000-7_12' apa: 'Fuchsbauer, G., Hanser, C., & Slamanig, D. (2015). Practical round-optimal blind signatures in the standard model (Vol. 9216, pp. 233–253). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_12' chicago: Fuchsbauer, Georg, Christian Hanser, and Daniel Slamanig. “Practical Round-Optimal Blind Signatures in the Standard Model,” 9216:233–53. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_12. ieee: 'G. Fuchsbauer, C. Hanser, and D. Slamanig, “Practical round-optimal blind signatures in the standard model,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 233–253.' ista: 'Fuchsbauer G, Hanser C, Slamanig D. 2015. Practical round-optimal blind signatures in the standard model. CRYPTO: International Cryptology Conference, LNCS, vol. 9216, 233–253.' mla: Fuchsbauer, Georg, et al. Practical Round-Optimal Blind Signatures in the Standard Model. Vol. 9216, Springer, 2015, pp. 233–53, doi:10.1007/978-3-662-48000-7_12. short: G. Fuchsbauer, C. Hanser, D. Slamanig, in:, Springer, 2015, pp. 233–253. conference: end_date: 2015-08-20 location: Santa Barbara, CA, United States name: 'CRYPTO: International Cryptology Conference' start_date: 2015-08-16 date_created: 2018-12-11T11:53:14Z date_published: 2015-08-01T00:00:00Z date_updated: 2023-02-21T16:44:51Z day: '01' department: - _id: KrPi doi: 10.1007/978-3-662-48000-7_12 ec_funded: 1 intvolume: ' 9216' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2015/626.pdf month: '08' oa: 1 oa_version: Submitted Version page: 233 - 253 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5503' quality_controlled: '1' related_material: record: - id: '1225' relation: later_version status: public scopus_import: 1 status: public title: Practical round-optimal blind signatures in the standard model type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9216 year: '2015' ... --- _id: '1645' abstract: - lang: eng text: Secret-key constructions are often proved secure in a model where one or more underlying components are replaced by an idealized oracle accessible to the attacker. This model gives rise to information-theoretic security analyses, and several advances have been made in this area over the last few years. This paper provides a systematic overview of what is achievable in this model, and how existing works fit into this view. article_number: '7133163' author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Stefano full_name: Tessaro, Stefano last_name: Tessaro citation: ama: 'Gazi P, Tessaro S. Secret-key cryptography from ideal primitives: A systematic verview. In: 2015 IEEE Information Theory Workshop. IEEE; 2015. doi:10.1109/ITW.2015.7133163' apa: 'Gazi, P., & Tessaro, S. (2015). Secret-key cryptography from ideal primitives: A systematic verview. In 2015 IEEE Information Theory Workshop. Jerusalem, Israel: IEEE. https://doi.org/10.1109/ITW.2015.7133163' chicago: 'Gazi, Peter, and Stefano Tessaro. “Secret-Key Cryptography from Ideal Primitives: A Systematic Verview.” In 2015 IEEE Information Theory Workshop. IEEE, 2015. https://doi.org/10.1109/ITW.2015.7133163.' ieee: 'P. Gazi and S. Tessaro, “Secret-key cryptography from ideal primitives: A systematic verview,” in 2015 IEEE Information Theory Workshop, Jerusalem, Israel, 2015.' ista: 'Gazi P, Tessaro S. 2015. Secret-key cryptography from ideal primitives: A systematic verview. 2015 IEEE Information Theory Workshop. ITW 2015: IEEE Information Theory Workshop, 7133163.' mla: 'Gazi, Peter, and Stefano Tessaro. “Secret-Key Cryptography from Ideal Primitives: A Systematic Verview.” 2015 IEEE Information Theory Workshop, 7133163, IEEE, 2015, doi:10.1109/ITW.2015.7133163.' short: P. Gazi, S. Tessaro, in:, 2015 IEEE Information Theory Workshop, IEEE, 2015. conference: end_date: 2015-05-01 location: Jerusalem, Israel name: 'ITW 2015: IEEE Information Theory Workshop' start_date: 2015-04-26 date_created: 2018-12-11T11:53:13Z date_published: 2015-06-24T00:00:00Z date_updated: 2021-01-12T06:52:13Z day: '24' department: - _id: KrPi doi: 10.1109/ITW.2015.7133163 ec_funded: 1 language: - iso: eng month: '06' oa_version: None project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: 2015 IEEE Information Theory Workshop publication_status: published publisher: IEEE publist_id: '5506' quality_controlled: '1' scopus_import: 1 status: public title: 'Secret-key cryptography from ideal primitives: A systematic verview' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1654' abstract: - lang: eng text: "HMAC and its variant NMAC are the most popular approaches to deriving a MAC (and more generally, a PRF) from a cryptographic hash function. Despite nearly two decades of research, their exact security still remains far from understood in many different contexts. Indeed, recent works have re-surfaced interest for {\\em generic} attacks, i.e., attacks that treat the compression function of the underlying hash function as a black box.\r\n\r\nGeneric security can be proved in a model where the underlying compression function is modeled as a random function -- yet, to date, the question of proving tight, non-trivial bounds on the generic security of HMAC/NMAC even as a PRF remains a challenging open question.\r\n\r\nIn this paper, we ask the question of whether a small modification to HMAC and NMAC can allow us to exactly characterize the security of the resulting constructions, while only incurring little penalty with respect to efficiency. To this end, we present simple variants of NMAC and HMAC, for which we prove tight bounds on the generic PRF security, expressed in terms of numbers of construction and compression function queries necessary to break the construction. All of our constructions are obtained via a (near) {\\em black-box} modification of NMAC and HMAC, which can be interpreted as an initial step of key-dependent message pre-processing.\r\n\r\nWhile our focus is on PRF security, a further attractive feature of our new constructions is that they clearly defeat all recent generic attacks against properties such as state recovery and universal forgery. These exploit properties of the so-called ``functional graph'' which are not directly accessible in our new constructions. " alternative_title: - LNCS author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Stefano full_name: Tessaro, Stefano last_name: Tessaro citation: ama: Gazi P, Pietrzak KZ, Tessaro S. Generic security of NMAC and HMAC with input whitening. 2015;9453:85-109. doi:10.1007/978-3-662-48800-3_4 apa: 'Gazi, P., Pietrzak, K. Z., & Tessaro, S. (2015). Generic security of NMAC and HMAC with input whitening. Presented at the ASIACRYPT: Theory and Application of Cryptology and Information Security, Auckland, New Zealand: Springer. https://doi.org/10.1007/978-3-662-48800-3_4' chicago: Gazi, Peter, Krzysztof Z Pietrzak, and Stefano Tessaro. “Generic Security of NMAC and HMAC with Input Whitening.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48800-3_4. ieee: P. Gazi, K. Z. Pietrzak, and S. Tessaro, “Generic security of NMAC and HMAC with input whitening,” vol. 9453. Springer, pp. 85–109, 2015. ista: Gazi P, Pietrzak KZ, Tessaro S. 2015. Generic security of NMAC and HMAC with input whitening. 9453, 85–109. mla: Gazi, Peter, et al. Generic Security of NMAC and HMAC with Input Whitening. Vol. 9453, Springer, 2015, pp. 85–109, doi:10.1007/978-3-662-48800-3_4. short: P. Gazi, K.Z. Pietrzak, S. Tessaro, 9453 (2015) 85–109. conference: end_date: 2015-12-03 location: Auckland, New Zealand name: 'ASIACRYPT: Theory and Application of Cryptology and Information Security' start_date: 2015-11-29 date_created: 2018-12-11T11:53:17Z date_published: 2015-12-30T00:00:00Z date_updated: 2021-01-12T06:52:16Z day: '30' ddc: - '004' - '005' department: - _id: KrPi doi: 10.1007/978-3-662-48800-3_4 ec_funded: 1 file: - access_level: open_access checksum: d1e53203db2d8573a560995ccdffac62 content_type: application/pdf creator: system date_created: 2018-12-12T10:09:09Z date_updated: 2020-07-14T12:45:08Z file_id: '4732' file_name: IST-2016-676-v1+1_881.pdf file_size: 512071 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 9453' language: - iso: eng month: '12' oa: 1 oa_version: Submitted Version page: 85 - 109 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5496' pubrep_id: '676' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Generic security of NMAC and HMAC with input whitening type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9453 year: '2015' ... --- _id: '1650' abstract: - lang: eng text: "We consider the task of deriving a key with high HILL entropy (i.e., being computationally indistinguishable from a key with high min-entropy) from an unpredictable source.\r\n\r\nPrevious to this work, the only known way to transform unpredictability into a key that was ϵ indistinguishable from having min-entropy was via pseudorandomness, for example by Goldreich-Levin (GL) hardcore bits. This approach has the inherent limitation that from a source with k bits of unpredictability entropy one can derive a key of length (and thus HILL entropy) at most k−2log(1/ϵ) bits. In many settings, e.g. when dealing with biometric data, such a 2log(1/ϵ) bit entropy loss in not an option. Our main technical contribution is a theorem that states that in the high entropy regime, unpredictability implies HILL entropy. Concretely, any variable K with |K|−d bits of unpredictability entropy has the same amount of so called metric entropy (against real-valued, deterministic distinguishers), which is known to imply the same amount of HILL entropy. The loss in circuit size in this argument is exponential in the entropy gap d, and thus this result only applies for small d (i.e., where the size of distinguishers considered is exponential in d).\r\n\r\nTo overcome the above restriction, we investigate if it’s possible to first “condense” unpredictability entropy and make the entropy gap small. We show that any source with k bits of unpredictability can be condensed into a source of length k with k−3 bits of unpredictability entropy. Our condenser simply “abuses" the GL construction and derives a k bit key from a source with k bits of unpredicatibily. The original GL theorem implies nothing when extracting that many bits, but we show that in this regime, GL still behaves like a “condenser" for unpredictability. This result comes with two caveats (1) the loss in circuit size is exponential in k and (2) we require that the source we start with has no HILL entropy (equivalently, one can efficiently check if a guess is correct). We leave it as an intriguing open problem to overcome these restrictions or to prove they’re inherent." alternative_title: - LNCS author: - first_name: Maciej full_name: Skórski, Maciej last_name: Skórski - first_name: Alexander full_name: Golovnev, Alexander last_name: Golovnev - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Skórski M, Golovnev A, Pietrzak KZ. Condensed unpredictability . In: Vol 9134. Springer; 2015:1046-1057. doi:10.1007/978-3-662-47672-7_85' apa: 'Skórski, M., Golovnev, A., & Pietrzak, K. Z. (2015). Condensed unpredictability (Vol. 9134, pp. 1046–1057). Presented at the ICALP: Automata, Languages and Programming, Kyoto, Japan: Springer. https://doi.org/10.1007/978-3-662-47672-7_85' chicago: Skórski, Maciej, Alexander Golovnev, and Krzysztof Z Pietrzak. “Condensed Unpredictability ,” 9134:1046–57. Springer, 2015. https://doi.org/10.1007/978-3-662-47672-7_85. ieee: 'M. Skórski, A. Golovnev, and K. Z. Pietrzak, “Condensed unpredictability ,” presented at the ICALP: Automata, Languages and Programming, Kyoto, Japan, 2015, vol. 9134, pp. 1046–1057.' ista: 'Skórski M, Golovnev A, Pietrzak KZ. 2015. Condensed unpredictability . ICALP: Automata, Languages and Programming, LNCS, vol. 9134, 1046–1057.' mla: Skórski, Maciej, et al. Condensed Unpredictability . Vol. 9134, Springer, 2015, pp. 1046–57, doi:10.1007/978-3-662-47672-7_85. short: M. Skórski, A. Golovnev, K.Z. Pietrzak, in:, Springer, 2015, pp. 1046–1057. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'ICALP: Automata, Languages and Programming' start_date: 2015-07-06 date_created: 2018-12-11T11:53:15Z date_published: 2015-06-20T00:00:00Z date_updated: 2021-01-12T06:52:15Z day: '20' ddc: - '000' - '005' department: - _id: KrPi doi: 10.1007/978-3-662-47672-7_85 ec_funded: 1 file: - access_level: open_access checksum: e808c7eecb631336fc9f9bf2e8d4ecae content_type: application/pdf creator: system date_created: 2018-12-12T10:08:32Z date_updated: 2020-07-14T12:45:08Z file_id: '4693' file_name: IST-2016-675-v1+1_384.pdf file_size: 525503 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 9134' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1046 - 1057 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5500' pubrep_id: '675' quality_controlled: '1' scopus_import: 1 status: public title: 'Condensed unpredictability ' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9134 year: '2015' ... --- _id: '1651' abstract: - lang: eng text: Cryptographic e-cash allows off-line electronic transactions between a bank, users and merchants in a secure and anonymous fashion. A plethora of e-cash constructions has been proposed in the literature; however, these traditional e-cash schemes only allow coins to be transferred once between users and merchants. Ideally, we would like users to be able to transfer coins between each other multiple times before deposit, as happens with physical cash. “Transferable” e-cash schemes are the solution to this problem. Unfortunately, the currently proposed schemes are either completely impractical or do not achieve the desirable anonymity properties without compromises, such as assuming the existence of a trusted “judge” who can trace all coins and users in the system. This paper presents the first efficient and fully anonymous transferable e-cash scheme without any trusted third parties. We start by revising the security and anonymity properties of transferable e-cash to capture issues that were previously overlooked. For our construction we use the recently proposed malleable signatures by Chase et al. to allow the secure and anonymous transfer of coins, combined with a new efficient double-spending detection mechanism. Finally, we discuss an instantiation of our construction. acknowledgement: Work done as an intern in Microsoft Research Redmond and as a student at Brown University, where supported by NSF grant 0964379. Supported by the European Research Council, ERC Starting Grant (259668-PSPC). alternative_title: - LNCS article_processing_charge: No author: - first_name: Foteini full_name: Baldimtsi, Foteini last_name: Baldimtsi - first_name: Melissa full_name: Chase, Melissa last_name: Chase - first_name: Georg full_name: Fuchsbauer, Georg id: 46B4C3EE-F248-11E8-B48F-1D18A9856A87 last_name: Fuchsbauer - first_name: Markulf full_name: Kohlweiss, Markulf last_name: Kohlweiss citation: ama: 'Baldimtsi F, Chase M, Fuchsbauer G, Kohlweiss M. Anonymous transferable e-cash. In: Public-Key Cryptography - PKC 2015. Vol 9020. Springer; 2015:101-124. doi:10.1007/978-3-662-46447-2_5' apa: 'Baldimtsi, F., Chase, M., Fuchsbauer, G., & Kohlweiss, M. (2015). Anonymous transferable e-cash. In Public-Key Cryptography - PKC 2015 (Vol. 9020, pp. 101–124). Gaithersburg, MD, United States: Springer. https://doi.org/10.1007/978-3-662-46447-2_5' chicago: Baldimtsi, Foteini, Melissa Chase, Georg Fuchsbauer, and Markulf Kohlweiss. “Anonymous Transferable E-Cash.” In Public-Key Cryptography - PKC 2015, 9020:101–24. Springer, 2015. https://doi.org/10.1007/978-3-662-46447-2_5. ieee: F. Baldimtsi, M. Chase, G. Fuchsbauer, and M. Kohlweiss, “Anonymous transferable e-cash,” in Public-Key Cryptography - PKC 2015, Gaithersburg, MD, United States, 2015, vol. 9020, pp. 101–124. ista: 'Baldimtsi F, Chase M, Fuchsbauer G, Kohlweiss M. 2015. Anonymous transferable e-cash. Public-Key Cryptography - PKC 2015. PKC: Public Key Crypography, LNCS, vol. 9020, 101–124.' mla: Baldimtsi, Foteini, et al. “Anonymous Transferable E-Cash.” Public-Key Cryptography - PKC 2015, vol. 9020, Springer, 2015, pp. 101–24, doi:10.1007/978-3-662-46447-2_5. short: F. Baldimtsi, M. Chase, G. Fuchsbauer, M. Kohlweiss, in:, Public-Key Cryptography - PKC 2015, Springer, 2015, pp. 101–124. conference: end_date: 2015-04-01 location: Gaithersburg, MD, United States name: 'PKC: Public Key Crypography' start_date: 2015-03-30 date_created: 2018-12-11T11:53:15Z date_published: 2015-03-17T00:00:00Z date_updated: 2022-05-23T10:08:37Z day: '17' department: - _id: KrPi doi: 10.1007/978-3-662-46447-2_5 ec_funded: 1 intvolume: ' 9020' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1007/978-3-662-46447-2_5 month: '03' oa: 1 oa_version: Published Version page: 101 - 124 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Public-Key Cryptography - PKC 2015 publication_identifier: isbn: - 978-3-662-46446-5 publication_status: published publisher: Springer publist_id: '5499' quality_controlled: '1' scopus_import: '1' status: public title: Anonymous transferable e-cash type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9020 year: '2015' ... --- _id: '1652' abstract: - lang: eng text: We develop new theoretical tools for proving lower-bounds on the (amortized) complexity of certain functions in models of parallel computation. We apply the tools to construct a class of functions with high amortized memory complexity in the parallel Random Oracle Model (pROM); a variant of the standard ROM allowing for batches of simultaneous queries. In particular we obtain a new, more robust, type of Memory-Hard Functions (MHF); a security primitive which has recently been gaining acceptance in practice as an effective means of countering brute-force attacks on security relevant functions. Along the way we also demonstrate an important shortcoming of previous definitions of MHFs and give a new definition addressing the problem. The tools we develop represent an adaptation of the powerful pebbling paradigm (initially introduced by Hewitt and Paterson [HP70] and Cook [Coo73]) to a simple and intuitive parallel setting. We define a simple pebbling game Gp over graphs which aims to abstract parallel computation in an intuitive way. As a conceptual contribution we define a measure of pebbling complexity for graphs called cumulative complexity (CC) and show how it overcomes a crucial shortcoming (in the parallel setting) exhibited by more traditional complexity measures used in the past. As a main technical contribution we give an explicit construction of a constant in-degree family of graphs whose CC in Gp approaches maximality to within a polylogarithmic factor for any graph of equal size (analogous to the graphs of Tarjan et. al. [PTC76, LT82] for sequential pebbling games). Finally, for a given graph G and related function fG, we derive a lower-bound on the amortized memory complexity of fG in the pROM in terms of the CC of G in the game Gp. author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Vladimir full_name: Serbinenko, Vladimir last_name: Serbinenko citation: ama: 'Alwen JF, Serbinenko V. High parallel complexity graphs and memory-hard functions. In: Proceedings of the 47th Annual ACM Symposium on Theory of Computing. ACM; 2015:595-603. doi:10.1145/2746539.2746622' apa: 'Alwen, J. F., & Serbinenko, V. (2015). High parallel complexity graphs and memory-hard functions. In Proceedings of the 47th annual ACM symposium on Theory of computing (pp. 595–603). Portland, OR, United States: ACM. https://doi.org/10.1145/2746539.2746622' chicago: Alwen, Joel F, and Vladimir Serbinenko. “High Parallel Complexity Graphs and Memory-Hard Functions.” In Proceedings of the 47th Annual ACM Symposium on Theory of Computing, 595–603. ACM, 2015. https://doi.org/10.1145/2746539.2746622. ieee: J. F. Alwen and V. Serbinenko, “High parallel complexity graphs and memory-hard functions,” in Proceedings of the 47th annual ACM symposium on Theory of computing, Portland, OR, United States, 2015, pp. 595–603. ista: 'Alwen JF, Serbinenko V. 2015. High parallel complexity graphs and memory-hard functions. Proceedings of the 47th annual ACM symposium on Theory of computing. STOC: Symposium on the Theory of Computing, 595–603.' mla: Alwen, Joel F., and Vladimir Serbinenko. “High Parallel Complexity Graphs and Memory-Hard Functions.” Proceedings of the 47th Annual ACM Symposium on Theory of Computing, ACM, 2015, pp. 595–603, doi:10.1145/2746539.2746622. short: J.F. Alwen, V. Serbinenko, in:, Proceedings of the 47th Annual ACM Symposium on Theory of Computing, ACM, 2015, pp. 595–603. conference: end_date: 2015-06-17 location: Portland, OR, United States name: 'STOC: Symposium on the Theory of Computing' start_date: 2015-06-14 date_created: 2018-12-11T11:53:16Z date_published: 2015-06-01T00:00:00Z date_updated: 2021-01-12T06:52:16Z day: '01' department: - _id: KrPi doi: 10.1145/2746539.2746622 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2014/238 month: '06' oa: 1 oa_version: Submitted Version page: 595 - 603 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Proceedings of the 47th annual ACM symposium on Theory of computing publication_status: published publisher: ACM publist_id: '5498' quality_controlled: '1' scopus_import: 1 status: public title: High parallel complexity graphs and memory-hard functions type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1658' abstract: - lang: eng text: Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. alternative_title: - LNCS author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - 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: Andreas full_name: Podelski, Andreas last_name: Podelski - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Christian full_name: Schilling, Christian last_name: Schilling citation: ama: Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. Adaptive moment closure for parameter inference of biochemical reaction networks. 2015;9308:77-89. doi:10.1007/978-3-319-23401-4_8 apa: 'Bogomolov, S., Henzinger, T. A., Podelski, A., Ruess, J., & Schilling, C. (2015). Adaptive moment closure for parameter inference of biochemical reaction networks. Presented at the CMSB: Computational Methods in Systems Biology, Nantes, France: Springer. https://doi.org/10.1007/978-3-319-23401-4_8' chicago: Bogomolov, Sergiy, Thomas A Henzinger, Andreas Podelski, Jakob Ruess, and Christian Schilling. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-23401-4_8. ieee: S. Bogomolov, T. A. Henzinger, A. Podelski, J. Ruess, and C. Schilling, “Adaptive moment closure for parameter inference of biochemical reaction networks,” vol. 9308. Springer, pp. 77–89, 2015. ista: Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. 2015. Adaptive moment closure for parameter inference of biochemical reaction networks. 9308, 77–89. mla: Bogomolov, Sergiy, et al. Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks. Vol. 9308, Springer, 2015, pp. 77–89, doi:10.1007/978-3-319-23401-4_8. short: S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, C. Schilling, 9308 (2015) 77–89. conference: end_date: 2015-09-18 location: Nantes, France name: 'CMSB: Computational Methods in Systems Biology' start_date: 2015-09-16 date_created: 2018-12-11T11:53:18Z date_published: 2015-09-01T00:00:00Z date_updated: 2023-02-21T16:17:24Z day: '01' department: - _id: ToHe - _id: GaTk doi: 10.1007/978-3-319-23401-4_8 ec_funded: 1 intvolume: ' 9308' language: - iso: eng month: '09' oa_version: None page: 77 - 89 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5492' quality_controlled: '1' related_material: record: - id: '1148' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Adaptive moment closure for parameter inference of biochemical reaction networks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9308 year: '2015' ... --- _id: '1660' abstract: - lang: eng text: We study the pattern frequency vector for runs in probabilistic Vector Addition Systems with States (pVASS). Intuitively, each configuration of a given pVASS is assigned one of finitely many patterns, and every run can thus be seen as an infinite sequence of these patterns. The pattern frequency vector assigns to each run the limit of pattern frequencies computed for longer and longer prefixes of the run. If the limit does not exist, then the vector is undefined. We show that for one-counter pVASS, the pattern frequency vector is defined and takes one of finitely many values for almost all runs. Further, these values and their associated probabilities can be approximated up to an arbitrarily small relative error in polynomial time. For stable two-counter pVASS, we show the same result, but we do not provide any upper complexity bound. As a byproduct of our study, we discover counterexamples falsifying some classical results about stochastic Petri nets published in the 80s. alternative_title: - LICS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Stefan full_name: Kiefer, Stefan last_name: Kiefer - first_name: Antonín full_name: Kučera, Antonín last_name: Kučera - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny citation: ama: 'Brázdil T, Kiefer S, Kučera A, Novotný P. Long-run average behaviour of probabilistic vector addition systems. In: IEEE; 2015:44-55. doi:10.1109/LICS.2015.15' apa: 'Brázdil, T., Kiefer, S., Kučera, A., & Novotný, P. (2015). Long-run average behaviour of probabilistic vector addition systems (pp. 44–55). Presented at the LICS: Logic in Computer Science, Kyoto, Japan: IEEE. https://doi.org/10.1109/LICS.2015.15' chicago: Brázdil, Tomáš, Stefan Kiefer, Antonín Kučera, and Petr Novotný. “Long-Run Average Behaviour of Probabilistic Vector Addition Systems,” 44–55. IEEE, 2015. https://doi.org/10.1109/LICS.2015.15. ieee: 'T. Brázdil, S. Kiefer, A. Kučera, and P. Novotný, “Long-run average behaviour of probabilistic vector addition systems,” presented at the LICS: Logic in Computer Science, Kyoto, Japan, 2015, pp. 44–55.' ista: 'Brázdil T, Kiefer S, Kučera A, Novotný P. 2015. Long-run average behaviour of probabilistic vector addition systems. LICS: Logic in Computer Science, LICS, , 44–55.' mla: Brázdil, Tomáš, et al. Long-Run Average Behaviour of Probabilistic Vector Addition Systems. IEEE, 2015, pp. 44–55, doi:10.1109/LICS.2015.15. short: T. Brázdil, S. Kiefer, A. Kučera, P. Novotný, in:, IEEE, 2015, pp. 44–55. conference: end_date: 2015-07-10 location: Kyoto, Japan name: 'LICS: Logic in Computer Science' start_date: 2015-07-06 date_created: 2018-12-11T11:53:19Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:52:20Z day: '01' department: - _id: KrCh doi: 10.1109/LICS.2015.15 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1505.02655 month: '07' oa: 1 oa_version: Preprint page: 44 - 55 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: IEEE publist_id: '5490' quality_controlled: '1' scopus_import: 1 status: public title: Long-run average behaviour of probabilistic vector addition systems type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1665' abstract: - lang: eng text: Which genetic alterations drive tumorigenesis and how they evolve over the course of disease and therapy are central questions in cancer biology. Here we identify 44 recurrently mutated genes and 11 recurrent somatic copy number variations through whole-exome sequencing of 538 chronic lymphocytic leukaemia (CLL) and matched germline DNA samples, 278 of which were collected in a prospective clinical trial. These include previously unrecognized putative cancer drivers (RPS15, IKZF3), and collectively identify RNA processing and export, MYC activity, and MAPK signalling as central pathways involved in CLL. Clonality analysis of this large data set further enabled reconstruction of temporal relationships between driver events. Direct comparison between matched pre-treatment and relapse samples from 59 patients demonstrated highly frequent clonal evolution. Thus, large sequencing data sets of clinically informative samples enable the discovery of novel genes associated with cancer, the network of relationships between the driver events, and their impact on disease relapse and clinical outcome. article_processing_charge: No article_type: original author: - first_name: Dan full_name: Landau, Dan last_name: Landau - first_name: Eugen full_name: Tausch, Eugen last_name: Tausch - first_name: Amaro full_name: Taylor Weiner, Amaro last_name: Taylor Weiner - first_name: Chip full_name: Stewart, Chip last_name: Stewart - first_name: Johannes full_name: Reiter, Johannes id: 4A918E98-F248-11E8-B48F-1D18A9856A87 last_name: Reiter orcid: 0000-0002-0170-7353 - first_name: Jasmin full_name: Bahlo, Jasmin last_name: Bahlo - first_name: Sandra full_name: Kluth, Sandra last_name: Kluth - first_name: Ivana full_name: Božić, Ivana last_name: Božić - first_name: Michael full_name: Lawrence, Michael last_name: Lawrence - first_name: Sebastian full_name: Böttcher, Sebastian last_name: Böttcher - first_name: Scott full_name: Carter, Scott last_name: Carter - first_name: Kristian full_name: Cibulskis, Kristian last_name: Cibulskis - first_name: Daniel full_name: Mertens, Daniel last_name: Mertens - first_name: Carrie full_name: Sougnez, Carrie last_name: Sougnez - first_name: Mara full_name: Rosenberg, Mara last_name: Rosenberg - first_name: Julian full_name: Hess, Julian last_name: Hess - first_name: Jennifer full_name: Edelmann, Jennifer last_name: Edelmann - first_name: Sabrina full_name: Kless, Sabrina last_name: Kless - first_name: Michael full_name: Kneba, Michael last_name: Kneba - first_name: Matthias full_name: Ritgen, Matthias last_name: Ritgen - first_name: Anna full_name: Fink, Anna last_name: Fink - first_name: Kirsten full_name: Fischer, Kirsten last_name: Fischer - first_name: Stacey full_name: Gabriel, Stacey last_name: Gabriel - first_name: Eric full_name: Lander, Eric last_name: Lander - first_name: Martin full_name: Nowak, Martin last_name: Nowak - first_name: Hartmut full_name: Döhner, Hartmut last_name: Döhner - first_name: Michael full_name: Hallek, Michael last_name: Hallek - first_name: Donna full_name: Neuberg, Donna last_name: Neuberg - first_name: Gad full_name: Getz, Gad last_name: Getz - first_name: Stephan full_name: Stilgenbauer, Stephan last_name: Stilgenbauer - first_name: Catherine full_name: Wu, Catherine last_name: Wu citation: ama: Landau D, Tausch E, Taylor Weiner A, et al. Mutations driving CLL and their evolution in progression and relapse. Nature. 2015;526(7574):525-530. doi:10.1038/nature15395 apa: Landau, D., Tausch, E., Taylor Weiner, A., Stewart, C., Reiter, J., Bahlo, J., … Wu, C. (2015). Mutations driving CLL and their evolution in progression and relapse. Nature. Nature Publishing Group. https://doi.org/10.1038/nature15395 chicago: Landau, Dan, Eugen Tausch, Amaro Taylor Weiner, Chip Stewart, Johannes Reiter, Jasmin Bahlo, Sandra Kluth, et al. “Mutations Driving CLL and Their Evolution in Progression and Relapse.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature15395. ieee: D. Landau et al., “Mutations driving CLL and their evolution in progression and relapse,” Nature, vol. 526, no. 7574. Nature Publishing Group, pp. 525–530, 2015. ista: Landau D, Tausch E, Taylor Weiner A, Stewart C, Reiter J, Bahlo J, Kluth S, Božić I, Lawrence M, Böttcher S, Carter S, Cibulskis K, Mertens D, Sougnez C, Rosenberg M, Hess J, Edelmann J, Kless S, Kneba M, Ritgen M, Fink A, Fischer K, Gabriel S, Lander E, Nowak M, Döhner H, Hallek M, Neuberg D, Getz G, Stilgenbauer S, Wu C. 2015. Mutations driving CLL and their evolution in progression and relapse. Nature. 526(7574), 525–530. mla: Landau, Dan, et al. “Mutations Driving CLL and Their Evolution in Progression and Relapse.” Nature, vol. 526, no. 7574, Nature Publishing Group, 2015, pp. 525–30, doi:10.1038/nature15395. short: D. Landau, E. Tausch, A. Taylor Weiner, C. Stewart, J. Reiter, J. Bahlo, S. Kluth, I. Božić, M. Lawrence, S. Böttcher, S. Carter, K. Cibulskis, D. Mertens, C. Sougnez, M. Rosenberg, J. Hess, J. Edelmann, S. Kless, M. Kneba, M. Ritgen, A. Fink, K. Fischer, S. Gabriel, E. Lander, M. Nowak, H. Döhner, M. Hallek, D. Neuberg, G. Getz, S. Stilgenbauer, C. Wu, Nature 526 (2015) 525–530. date_created: 2018-12-11T11:53:21Z date_published: 2015-10-22T00:00:00Z date_updated: 2021-01-12T06:52:23Z day: '22' department: - _id: KrCh doi: 10.1038/nature15395 ec_funded: 1 external_id: pmid: - '26466571' intvolume: ' 526' issue: '7574' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4815041/ month: '10' oa: 1 oa_version: Submitted Version page: 525 - 530 pmid: 1 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5484' quality_controlled: '1' scopus_import: 1 status: public title: Mutations driving CLL and their evolution in progression and relapse type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 526 year: '2015' ... --- _id: '1663' abstract: - lang: eng text: CREB-binding protein (CBP) and p300 are transcriptional coactivators involved in numerous biological processes that affect cell growth, transformation, differentiation, and development. In this study, we provide evidence of the involvement of homeodomain-interacting protein kinase 2 (HIPK2) in the regulation of CBP activity. We show that HIPK2 interacts with and phosphorylates several regions of CBP. We demonstrate that serines 2361, 2363, 2371, 2376, and 2381 are responsible for the HIPK2-induced mobility shift of CBP C-terminal activation domain. Moreover, we show that HIPK2 strongly potentiates the transcriptional activity of CBP. However, our data suggest that HIPK2 activates CBP mainly by counteracting the repressive action of cell cycle regulatory domain 1 (CRD1), located between amino acids 977 and 1076, independently of CBP phosphorylation. Our findings thus highlight a complex regulation of CBP activity by HIPK2, which might be relevant for the control of specific sets of target genes involved in cellular proliferation, differentiation and apoptosis. author: - first_name: Krisztián full_name: Kovács, Krisztián id: 2AB5821E-F248-11E8-B48F-1D18A9856A87 last_name: Kovács - first_name: Myriam full_name: Steinmann, Myriam last_name: Steinmann - first_name: Olivier full_name: Halfon, Olivier last_name: Halfon - first_name: Pierre full_name: Magistretti, Pierre last_name: Magistretti - first_name: Jean full_name: Cardinaux, Jean last_name: Cardinaux citation: ama: Kovács K, Steinmann M, Halfon O, Magistretti P, Cardinaux J. Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. 2015;27(11):2252-2260. doi:10.1016/j.cellsig.2015.08.001 apa: Kovács, K., Steinmann, M., Halfon, O., Magistretti, P., & Cardinaux, J. (2015). Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. Elsevier. https://doi.org/10.1016/j.cellsig.2015.08.001 chicago: Kovács, Krisztián, Myriam Steinmann, Olivier Halfon, Pierre Magistretti, and Jean Cardinaux. “Complex Regulation of CREB-Binding Protein by Homeodomain-Interacting Protein Kinase 2.” Cellular Signalling. Elsevier, 2015. https://doi.org/10.1016/j.cellsig.2015.08.001. ieee: K. Kovács, M. Steinmann, O. Halfon, P. Magistretti, and J. Cardinaux, “Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2,” Cellular Signalling, vol. 27, no. 11. Elsevier, pp. 2252–2260, 2015. ista: Kovács K, Steinmann M, Halfon O, Magistretti P, Cardinaux J. 2015. Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2. Cellular Signalling. 27(11), 2252–2260. mla: Kovács, Krisztián, et al. “Complex Regulation of CREB-Binding Protein by Homeodomain-Interacting Protein Kinase 2.” Cellular Signalling, vol. 27, no. 11, Elsevier, 2015, pp. 2252–60, doi:10.1016/j.cellsig.2015.08.001. short: K. Kovács, M. Steinmann, O. Halfon, P. Magistretti, J. Cardinaux, Cellular Signalling 27 (2015) 2252–2260. date_created: 2018-12-11T11:53:20Z date_published: 2015-11-01T00:00:00Z date_updated: 2021-01-12T06:52:22Z day: '01' ddc: - '570' department: - _id: JoCs doi: 10.1016/j.cellsig.2015.08.001 ec_funded: 1 file: - access_level: local checksum: 4ee690b6444b7a43523237f0941457d1 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:03Z date_updated: 2020-07-14T12:45:10Z file_id: '5321' file_name: IST-2016-578-v1+1_CLS-D-15-00072R1_.pdf file_size: 1735337 relation: main_file file_date_updated: 2020-07-14T12:45:10Z has_accepted_license: '1' intvolume: ' 27' issue: '11' language: - iso: eng month: '11' oa_version: Published Version page: 2252 - 2260 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Cellular Signalling publication_status: published publisher: Elsevier publist_id: '5487' pubrep_id: '578' quality_controlled: '1' scopus_import: 1 status: public title: Complex regulation of CREB-binding protein by homeodomain-interacting protein kinase 2 tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2015' ... --- _id: '1667' abstract: - lang: eng text: We consider parametric version of fixed-delay continuoustime Markov chains (or equivalently deterministic and stochastic Petri nets, DSPN) where fixed-delay transitions are specified by parameters, rather than concrete values. Our goal is to synthesize values of these parameters that, for a given cost function, minimise expected total cost incurred before reaching a given set of target states. We show that under mild assumptions, optimal values of parameters can be effectively approximated using translation to a Markov decision process (MDP) whose actions correspond to discretized values of these parameters. To this end we identify and overcome several interesting phenomena arising in systems with fixed delays. acknowledgement: The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n∘ [291734]. This work is partly supported by the German Research Council (DFG) as part of the Transregional Collaborative Research Center AVACS (SFB/TR 14), by the EU 7th Framework Programme under grant agreement no. 295261 (MEALS) and 318490 (SENSATION), by the Czech Science Foundation, grant No. 15-17564S, and by the CAS/SAFEA International Partnership Program for Creative Research Teams. alternative_title: - LNCS author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: L'Uboš full_name: Korenčiak, L'Uboš last_name: Korenčiak - first_name: Jan full_name: Krčál, Jan last_name: Krčál - first_name: Petr full_name: Novotny, Petr id: 3CC3B868-F248-11E8-B48F-1D18A9856A87 last_name: Novotny - first_name: Vojtěch full_name: Řehák, Vojtěch last_name: Řehák citation: ama: Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. Optimizing performance of continuous-time stochastic systems using timeout synthesis. 2015;9259:141-159. doi:10.1007/978-3-319-22264-6_10 apa: 'Brázdil, T., Korenčiak, L., Krčál, J., Novotný, P., & Řehák, V. (2015). Optimizing performance of continuous-time stochastic systems using timeout synthesis. Presented at the QEST: Quantitative Evaluation of Systems, Madrid, Spain: Springer. https://doi.org/10.1007/978-3-319-22264-6_10' chicago: Brázdil, Tomáš, L’Uboš Korenčiak, Jan Krčál, Petr Novotný, and Vojtěch Řehák. “Optimizing Performance of Continuous-Time Stochastic Systems Using Timeout Synthesis.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-22264-6_10. ieee: T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, and V. Řehák, “Optimizing performance of continuous-time stochastic systems using timeout synthesis,” vol. 9259. Springer, pp. 141–159, 2015. ista: Brázdil T, Korenčiak L, Krčál J, Novotný P, Řehák V. 2015. Optimizing performance of continuous-time stochastic systems using timeout synthesis. 9259, 141–159. mla: Brázdil, Tomáš, et al. Optimizing Performance of Continuous-Time Stochastic Systems Using Timeout Synthesis. Vol. 9259, Springer, 2015, pp. 141–59, doi:10.1007/978-3-319-22264-6_10. short: T. Brázdil, L. Korenčiak, J. Krčál, P. Novotný, V. Řehák, 9259 (2015) 141–159. conference: end_date: 2015-09-03 location: Madrid, Spain name: 'QEST: Quantitative Evaluation of Systems' start_date: 2015-09-01 date_created: 2018-12-11T11:53:22Z date_published: 2015-08-22T00:00:00Z date_updated: 2021-01-12T06:52:24Z day: '22' department: - _id: KrCh doi: 10.1007/978-3-319-22264-6_10 ec_funded: 1 intvolume: ' 9259' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.4777 month: '08' oa: 1 oa_version: Preprint page: 141 - 159 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5482' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Optimizing performance of continuous-time stochastic systems using timeout synthesis type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9259 year: '2015' ... --- _id: '1664' abstract: - lang: eng text: Over a century of research into the origin of turbulence in wall-bounded shear flows has resulted in a puzzling picture in which turbulence appears in a variety of different states competing with laminar background flow. At moderate flow speeds, turbulence is confined to localized patches; it is only at higher speeds that the entire flow becomes turbulent. The origin of the different states encountered during this transition, the front dynamics of the turbulent regions and the transformation to full turbulence have yet to be explained. By combining experiments, theory and computer simulations, here we uncover a bifurcation scenario that explains the transformation to fully turbulent pipe flow and describe the front dynamics of the different states encountered in the process. Key to resolving this problem is the interpretation of the flow as a bistable system with nonlinear propagation (advection) of turbulent fronts. These findings bridge the gap between our understanding of the onset of turbulence and fully turbulent flows. acknowledgement: We acknowledge the Deutsche Forschungsgemeinschaft (Project No. FOR 1182), and the European Research Council under the European Union’s Seventh Framework Programme (FP/2007-2013)/ERC Grant Agreement 306589 for financial support. B.S. acknowledges financial support from the Chinese State Scholarship Fund under grant number 2010629145. B.S. acknowledges support from the International Max Planck Research School for the Physics of Biological and Complex Systems and the Göttingen Graduate School for Neurosciences and Molecular Biosciences. We acknowledge computing resources from GWDG (Gesellschaft für wissenschaftliche Datenverarbeitung Göttingen) and the Jülich Supercomputing Centre (grant HGU16) where the simulations were performed. author: - first_name: Dwight full_name: Barkley, Dwight last_name: Barkley - first_name: Baofang full_name: Song, Baofang last_name: Song - first_name: Mukund full_name: Vasudevan, Mukund id: 3C5A959A-F248-11E8-B48F-1D18A9856A87 last_name: Vasudevan - first_name: Grégoire M full_name: Lemoult, Grégoire M id: 4787FE80-F248-11E8-B48F-1D18A9856A87 last_name: Lemoult - first_name: Marc full_name: Avila, Marc last_name: Avila - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. The rise of fully turbulent flow. Nature. 2015;526(7574):550-553. doi:10.1038/nature15701 apa: Barkley, D., Song, B., Vasudevan, M., Lemoult, G. M., Avila, M., & Hof, B. (2015). The rise of fully turbulent flow. Nature. Nature Publishing Group. https://doi.org/10.1038/nature15701 chicago: Barkley, Dwight, Baofang Song, Mukund Vasudevan, Grégoire M Lemoult, Marc Avila, and Björn Hof. “The Rise of Fully Turbulent Flow.” Nature. Nature Publishing Group, 2015. https://doi.org/10.1038/nature15701. ieee: D. Barkley, B. Song, M. Vasudevan, G. M. Lemoult, M. Avila, and B. Hof, “The rise of fully turbulent flow,” Nature, vol. 526, no. 7574. Nature Publishing Group, pp. 550–553, 2015. ista: Barkley D, Song B, Vasudevan M, Lemoult GM, Avila M, Hof B. 2015. The rise of fully turbulent flow. Nature. 526(7574), 550–553. mla: Barkley, Dwight, et al. “The Rise of Fully Turbulent Flow.” Nature, vol. 526, no. 7574, Nature Publishing Group, 2015, pp. 550–53, doi:10.1038/nature15701. short: D. Barkley, B. Song, M. Vasudevan, G.M. Lemoult, M. Avila, B. Hof, Nature 526 (2015) 550–553. date_created: 2018-12-11T11:53:20Z date_published: 2015-10-21T00:00:00Z date_updated: 2021-01-12T06:52:22Z day: '21' department: - _id: BjHo doi: 10.1038/nature15701 ec_funded: 1 intvolume: ' 526' issue: '7574' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1510.09143 month: '10' oa: 1 oa_version: Preprint page: 550 - 553 project: - _id: 25152F3A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '306589' name: Decoding the complexity of turbulence at its origin publication: Nature publication_status: published publisher: Nature Publishing Group publist_id: '5485' quality_controlled: '1' scopus_import: 1 status: public title: The rise of fully turbulent flow type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 526 year: '2015' ... --- _id: '1672' abstract: - lang: eng text: Composable notions of incoercibility aim to forbid a coercer from using anything beyond the coerced parties’ inputs and outputs to catch them when they try to deceive him. Existing definitions are restricted to weak coercion types, and/or are not universally composable. Furthermore, they often make too strong assumptions on the knowledge of coerced parties—e.g., they assume they known the identities and/or the strategies of other coerced parties, or those of corrupted parties— which makes them unsuitable for applications of incoercibility such as e-voting, where colluding adversarial parties may attempt to coerce honest voters, e.g., by offering them money for a promised vote, and use their own view to check that the voter keeps his end of the bargain. In this work we put forward the first universally composable notion of incoercible multi-party computation, which satisfies the above intuition and does not assume collusions among coerced parties or knowledge of the corrupted set. We define natural notions of UC incoercibility corresponding to standard coercion-types, i.e., receipt-freeness and resistance to full-active coercion. Importantly, our suggested notion has the unique property that it builds on top of the well studied UC framework by Canetti instead of modifying it. This guarantees backwards compatibility, and allows us to inherit results from the rich UC literature. We then present MPC protocols which realize our notions of UC incoercibility given access to an arguably minimal setup—namely honestly generate tamper-proof hardware performing a very simple cryptographic operation—e.g., a smart card. This is, to our knowledge, the first proposed construction of an MPC protocol (for more than two parties) that is incoercibly secure and universally composable, and therefore the first construction of a universally composable receipt-free e-voting protocol. acknowledgement: Joël Alwen was supported by the ERC starting grant (259668-PSPC). Rafail Ostrovsky was supported in part by NSF grants 09165174, 1065276, 1118126 and 1136174, US-Israel BSF grant 2008411, OKAWA Foundation Research Award, IBM Faculty Research Award, Xerox Faculty Research Award, B. John Garrick Foundation Award, Teradata Research Award, Lockheed-Martin Corporation Research Award, and the Defense Advanced Research Projects Agency through the U.S. Office of Naval Research under Contract N00014 -11 -1-0392. The views expressed are those of the author and do not reflect the official policy or position of the Department of Defense or the U.S. Government. Vassilis Zikas was supported in part by the Swiss National Science Foundation (SNF) via the Ambizione grant PZ00P-2142549. alternative_title: - LNCS article_processing_charge: No author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Rafail full_name: Ostrovsky, Rafail last_name: Ostrovsky - first_name: Hongsheng full_name: Zhou, Hongsheng last_name: Zhou - first_name: Vassilis full_name: Zikas, Vassilis last_name: Zikas citation: ama: 'Alwen JF, Ostrovsky R, Zhou H, Zikas V. Incoercible multi-party computation and universally composable receipt-free voting. In: Advances in Cryptology - CRYPTO 2015. Vol 9216. Lecture Notes in Computer Science. Springer; 2015:763-780. doi:10.1007/978-3-662-48000-7_37' apa: 'Alwen, J. F., Ostrovsky, R., Zhou, H., & Zikas, V. (2015). Incoercible multi-party computation and universally composable receipt-free voting. In Advances in Cryptology - CRYPTO 2015 (Vol. 9216, pp. 763–780). Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-48000-7_37' chicago: Alwen, Joel F, Rafail Ostrovsky, Hongsheng Zhou, and Vassilis Zikas. “Incoercible Multi-Party Computation and Universally Composable Receipt-Free Voting.” In Advances in Cryptology - CRYPTO 2015, 9216:763–80. Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48000-7_37. ieee: J. F. Alwen, R. Ostrovsky, H. Zhou, and V. Zikas, “Incoercible multi-party computation and universally composable receipt-free voting,” in Advances in Cryptology - CRYPTO 2015, Santa Barbara, CA, United States, 2015, vol. 9216, pp. 763–780. ista: 'Alwen JF, Ostrovsky R, Zhou H, Zikas V. 2015. Incoercible multi-party computation and universally composable receipt-free voting. Advances in Cryptology - CRYPTO 2015. CRYPTO: International Cryptology ConferenceLecture Notes in Computer Science, LNCS, vol. 9216, 763–780.' mla: Alwen, Joel F., et al. “Incoercible Multi-Party Computation and Universally Composable Receipt-Free Voting.” Advances in Cryptology - CRYPTO 2015, vol. 9216, Springer, 2015, pp. 763–80, doi:10.1007/978-3-662-48000-7_37. short: J.F. Alwen, R. Ostrovsky, H. Zhou, V. Zikas, in:, Advances in Cryptology - CRYPTO 2015, Springer, 2015, pp. 763–780. conference: end_date: 2015-08-20 location: Santa Barbara, CA, United States name: 'CRYPTO: International Cryptology Conference' start_date: 2015-08-16 date_created: 2018-12-11T11:53:23Z date_published: 2015-08-01T00:00:00Z date_updated: 2022-06-07T09:51:55Z day: '01' ddc: - '000' department: - _id: KrPi doi: 10.1007/978-3-662-48000-7_37 ec_funded: 1 file: - access_level: open_access checksum: 5b6649e80d1f781a8910f7cce6427f78 content_type: application/pdf creator: dernst date_created: 2020-05-15T08:55:29Z date_updated: 2020-07-14T12:45:11Z file_id: '7853' file_name: 2015_CRYPTO_Alwen.pdf file_size: 397363 relation: main_file file_date_updated: 2020-07-14T12:45:11Z has_accepted_license: '1' intvolume: ' 9216' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 763 - 780 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Advances in Cryptology - CRYPTO 2015 publication_identifier: eisbn: - 978-3-662-48000-7 isbn: - 978-3-662-47999-5 publication_status: published publisher: Springer publist_id: '5476' quality_controlled: '1' scopus_import: '1' series_title: Lecture Notes in Computer Science status: public title: Incoercible multi-party computation and universally composable receipt-free voting type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9216 year: '2015' ... --- _id: '1669' abstract: - lang: eng text: Computational notions of entropy (a.k.a. pseudoentropy) have found many applications, including leakage-resilient cryptography, deterministic encryption or memory delegation. The most important tools to argue about pseudoentropy are chain rules, which quantify by how much (in terms of quantity and quality) the pseudoentropy of a given random variable X decreases when conditioned on some other variable Z (think for example of X as a secret key and Z as information leaked by a side-channel). In this paper we give a very simple and modular proof of the chain rule for HILL pseudoentropy, improving best known parameters. Our version allows for increasing the acceptable length of leakage in applications up to a constant factor compared to the best previous bounds. As a contribution of independent interest, we provide a comprehensive study of all known versions of the chain rule, comparing their worst-case strength and limitations. alternative_title: - LNCS author: - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Maciej full_name: Skórski, Maciej last_name: Skórski citation: ama: Pietrzak KZ, Skórski M. The chain rule for HILL pseudoentropy, revisited. 2015;9230:81-98. doi:10.1007/978-3-319-22174-8_5 apa: 'Pietrzak, K. Z., & Skórski, M. (2015). The chain rule for HILL pseudoentropy, revisited. Presented at the LATINCRYPT: Cryptology and Information Security in Latin America, Guadalajara, Mexico: Springer. https://doi.org/10.1007/978-3-319-22174-8_5' chicago: Pietrzak, Krzysztof Z, and Maciej Skórski. “The Chain Rule for HILL Pseudoentropy, Revisited.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-22174-8_5. ieee: K. Z. Pietrzak and M. Skórski, “The chain rule for HILL pseudoentropy, revisited,” vol. 9230. Springer, pp. 81–98, 2015. ista: Pietrzak KZ, Skórski M. 2015. The chain rule for HILL pseudoentropy, revisited. 9230, 81–98. mla: Pietrzak, Krzysztof Z., and Maciej Skórski. The Chain Rule for HILL Pseudoentropy, Revisited. Vol. 9230, Springer, 2015, pp. 81–98, doi:10.1007/978-3-319-22174-8_5. short: K.Z. Pietrzak, M. Skórski, 9230 (2015) 81–98. conference: end_date: 2015-08-26 location: Guadalajara, Mexico name: 'LATINCRYPT: Cryptology and Information Security in Latin America' start_date: 2015-08-23 date_created: 2018-12-11T11:53:22Z date_published: 2015-08-15T00:00:00Z date_updated: 2021-01-12T06:52:24Z day: '15' ddc: - '005' department: - _id: KrPi doi: 10.1007/978-3-319-22174-8_5 ec_funded: 1 file: - access_level: open_access checksum: 8cd4215b83efba720e8cf27c23ff4781 content_type: application/pdf creator: system date_created: 2018-12-12T10:18:29Z date_updated: 2020-07-14T12:45:11Z file_id: '5351' file_name: IST-2016-669-v1+1_599.pdf file_size: 443340 relation: main_file file_date_updated: 2020-07-14T12:45:11Z has_accepted_license: '1' intvolume: ' 9230' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 81 - 98 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5480' pubrep_id: '669' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: The chain rule for HILL pseudoentropy, revisited type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9230 year: '2015' ... --- _id: '1671' abstract: - lang: eng text: This paper studies the concrete security of PRFs and MACs obtained by keying hash functions based on the sponge paradigm. One such hash function is KECCAK, selected as NIST’s new SHA-3 standard. In contrast to other approaches like HMAC, the exact security of keyed sponges is not well understood. Indeed, recent security analyses delivered concrete security bounds which are far from existing attacks. This paper aims to close this gap. We prove (nearly) exact bounds on the concrete PRF security of keyed sponges using a random permutation. These bounds are tight for the most relevant ranges of parameters, i.e., for messages of length (roughly) l ≤ min{2n/4, 2r} blocks, where n is the state size and r is the desired output length; and for l ≤ q queries (to the construction or the underlying permutation). Moreover, we also improve standard-model bounds. As an intermediate step of independent interest, we prove tight bounds on the PRF security of the truncated CBC-MAC construction, which operates as plain CBC-MAC, but only returns a prefix of the output. alternative_title: - LNCS author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Stefano full_name: Tessaro, Stefano last_name: Tessaro citation: ama: 'Gazi P, Pietrzak KZ, Tessaro S. The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC. In: Vol 9215. Springer; 2015:368-387. doi:10.1007/978-3-662-47989-6_18' apa: 'Gazi, P., Pietrzak, K. Z., & Tessaro, S. (2015). The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC (Vol. 9215, pp. 368–387). Presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States: Springer. https://doi.org/10.1007/978-3-662-47989-6_18' chicago: 'Gazi, Peter, Krzysztof Z Pietrzak, and Stefano Tessaro. “The Exact PRF Security of Truncation: Tight Bounds for Keyed Sponges and Truncated CBC,” 9215:368–87. Springer, 2015. https://doi.org/10.1007/978-3-662-47989-6_18.' ieee: 'P. Gazi, K. Z. Pietrzak, and S. Tessaro, “The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC,” presented at the CRYPTO: International Cryptology Conference, Santa Barbara, CA, United States, 2015, vol. 9215, pp. 368–387.' ista: 'Gazi P, Pietrzak KZ, Tessaro S. 2015. The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC. CRYPTO: International Cryptology Conference, LNCS, vol. 9215, 368–387.' mla: 'Gazi, Peter, et al. The Exact PRF Security of Truncation: Tight Bounds for Keyed Sponges and Truncated CBC. Vol. 9215, Springer, 2015, pp. 368–87, doi:10.1007/978-3-662-47989-6_18.' short: P. Gazi, K.Z. Pietrzak, S. Tessaro, in:, Springer, 2015, pp. 368–387. conference: end_date: 2015-08-20 location: Santa Barbara, CA, United States name: 'CRYPTO: International Cryptology Conference' start_date: 2015-08-16 date_created: 2018-12-11T11:53:23Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:52:25Z day: '01' ddc: - '004' - '005' department: - _id: KrPi doi: 10.1007/978-3-662-47989-6_18 ec_funded: 1 file: - access_level: open_access checksum: 17d854227b3b753fd34f5d29e5b5a32e content_type: application/pdf creator: system date_created: 2018-12-12T10:10:38Z date_updated: 2020-07-14T12:45:11Z file_id: '4827' file_name: IST-2016-673-v1+1_053.pdf file_size: 592296 relation: main_file file_date_updated: 2020-07-14T12:45:11Z has_accepted_license: '1' intvolume: ' 9215' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 368 - 387 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5478' pubrep_id: '673' quality_controlled: '1' scopus_import: 1 status: public title: 'The exact PRF security of truncation: Tight bounds for keyed sponges and truncated CBC' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9215 year: '2015' ... --- _id: '1673' abstract: - lang: eng text: 'When a new mutant arises in a population, there is a probability it outcompetes the residents and fixes. The structure of the population can affect this fixation probability. Suppressing population structures reduce the difference between two competing variants, while amplifying population structures enhance the difference. Suppressors are ubiquitous and easy to construct, but amplifiers for the large population limit are more elusive and only a few examples have been discovered. Whether or not a population structure is an amplifier of selection depends on the probability distribution for the placement of the invading mutant. First, we prove that there exist only bounded amplifiers for adversarial placement-that is, for arbitrary initial conditions. Next, we show that the Star population structure, which is known to amplify for mutants placed uniformly at random, does not amplify for mutants that arise through reproduction and are therefore placed proportional to the temperatures of the vertices. Finally, we construct population structures that amplify for all mutational events that arise through reproduction, uniformly at random, or through some combination of the two. ' acknowledgement: 'K.C. gratefully acknowledges support from ERC Start grant no. (279307: Graph Games), Austrian Science Fund (FWF) grant no. P23499-N23, and FWF NFN grant no. S11407-N23 (RiSE). ' article_number: '20150114' author: - first_name: Ben full_name: Adlam, Ben last_name: Adlam - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: 'Adlam B, Chatterjee K, Nowak M. Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 2015;471(2181). doi:10.1098/rspa.2015.0114' apa: 'Adlam, B., Chatterjee, K., & Nowak, M. (2015). Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London. https://doi.org/10.1098/rspa.2015.0114' chicago: 'Adlam, Ben, Krishnendu Chatterjee, and Martin Nowak. “Amplifiers of Selection.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. Royal Society of London, 2015. https://doi.org/10.1098/rspa.2015.0114.' ieee: 'B. Adlam, K. Chatterjee, and M. Nowak, “Amplifiers of selection,” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 471, no. 2181. Royal Society of London, 2015.' ista: 'Adlam B, Chatterjee K, Nowak M. 2015. Amplifiers of selection. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences. 471(2181), 20150114.' mla: 'Adlam, Ben, et al. “Amplifiers of Selection.” Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, vol. 471, no. 2181, 20150114, Royal Society of London, 2015, doi:10.1098/rspa.2015.0114.' short: 'B. Adlam, K. Chatterjee, M. Nowak, Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences 471 (2015).' date_created: 2018-12-11T11:53:24Z date_published: 2015-09-08T00:00:00Z date_updated: 2021-01-12T06:52:26Z day: '08' ddc: - '000' department: - _id: KrCh doi: 10.1098/rspa.2015.0114 ec_funded: 1 file: - access_level: open_access checksum: e613d94d283c776322403a28aad11bdd content_type: application/pdf creator: kschuh date_created: 2019-04-18T12:39:56Z date_updated: 2020-07-14T12:45:11Z file_id: '6342' file_name: 2015_rspa_Adlam.pdf file_size: 391466 relation: main_file file_date_updated: 2020-07-14T12:45:11Z has_accepted_license: '1' intvolume: ' 471' issue: '2181' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication: 'Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences' publication_status: published publisher: Royal Society of London publist_id: '5477' quality_controlled: '1' scopus_import: 1 status: public title: Amplifiers of selection type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 471 year: '2015' ... --- _id: '1668' abstract: - lang: eng text: "We revisit the security (as a pseudorandom permutation) of cascading-based constructions for block-cipher key-length extension. Previous works typically considered the extreme case where the adversary is given the entire codebook of the construction, the only complexity measure being the number qe of queries to the underlying ideal block cipher, representing adversary’s secret-key-independent computation. Here, we initiate a systematic study of the more natural case of an adversary restricted to adaptively learning a number qc of plaintext/ciphertext pairs that is less than the entire codebook. For any such qc, we aim to determine the highest number of block-cipher queries qe the adversary can issue without being able to successfully distinguish the construction (under a secret key) from a random permutation.\r\nMore concretely, we show the following results for key-length extension schemes using a block cipher with n-bit blocks and κ-bit keys:\r\nPlain cascades of length ℓ=2r+1 are secure whenever qcqre≪2r(κ+n), qc≪2κ and qe≪22κ. The bound for r=1 also applies to two-key triple encryption (as used within Triple DES).\r\nThe r-round XOR-cascade is secure as long as qcqre≪2r(κ+n), matching an attack by Gaži (CRYPTO 2013).\r\nWe fully characterize the security of Gaži and Tessaro’s two-call " alternative_title: - LNCS author: - first_name: Peter full_name: Gazi, Peter id: 3E0BFE38-F248-11E8-B48F-1D18A9856A87 last_name: Gazi - first_name: Jooyoung full_name: Lee, Jooyoung last_name: Lee - first_name: Yannick full_name: Seurin, Yannick last_name: Seurin - first_name: John full_name: Steinberger, John last_name: Steinberger - first_name: Stefano full_name: Tessaro, Stefano last_name: Tessaro citation: ama: 'Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. Relaxing full-codebook security: A refined analysis of key-length extension schemes. 2015;9054:319-341. doi:10.1007/978-3-662-48116-5_16' apa: 'Gazi, P., Lee, J., Seurin, Y., Steinberger, J., & Tessaro, S. (2015). Relaxing full-codebook security: A refined analysis of key-length extension schemes. Presented at the FSE: Fast Software Encryption, Istanbul, Turkey: Springer. https://doi.org/10.1007/978-3-662-48116-5_16' chicago: 'Gazi, Peter, Jooyoung Lee, Yannick Seurin, John Steinberger, and Stefano Tessaro. “Relaxing Full-Codebook Security: A Refined Analysis of Key-Length Extension Schemes.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-662-48116-5_16.' ieee: 'P. Gazi, J. Lee, Y. Seurin, J. Steinberger, and S. Tessaro, “Relaxing full-codebook security: A refined analysis of key-length extension schemes,” vol. 9054. Springer, pp. 319–341, 2015.' ista: 'Gazi P, Lee J, Seurin Y, Steinberger J, Tessaro S. 2015. Relaxing full-codebook security: A refined analysis of key-length extension schemes. 9054, 319–341.' mla: 'Gazi, Peter, et al. Relaxing Full-Codebook Security: A Refined Analysis of Key-Length Extension Schemes. Vol. 9054, Springer, 2015, pp. 319–41, doi:10.1007/978-3-662-48116-5_16.' short: P. Gazi, J. Lee, Y. Seurin, J. Steinberger, S. Tessaro, 9054 (2015) 319–341. conference: end_date: 2015-03-11 location: Istanbul, Turkey name: 'FSE: Fast Software Encryption' start_date: 2015-03-08 date_created: 2018-12-11T11:53:22Z date_published: 2015-08-12T00:00:00Z date_updated: 2020-08-11T10:09:26Z day: '12' department: - _id: KrPi doi: 10.1007/978-3-662-48116-5_16 ec_funded: 1 intvolume: ' 9054' language: - iso: eng main_file_link: - open_access: '1' url: http://eprint.iacr.org/2015/397 month: '08' oa: 1 oa_version: Submitted Version page: 319 - 341 project: - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication_status: published publisher: Springer publist_id: '5481' quality_controlled: '1' scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: 'Relaxing full-codebook security: A refined analysis of key-length extension schemes' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9054 year: '2015' ... --- _id: '1670' abstract: - lang: eng text: Planning in hybrid domains poses a special challenge due to the involved mixed discrete-continuous dynamics. A recent solving approach for such domains is based on applying model checking techniques on a translation of PDDL+ planning problems to hybrid automata. However, the proposed translation is limited because must behavior is only overapproximated, and hence, processes and events are not reflected exactly. In this paper, we present the theoretical foundation of an exact PDDL+ translation. We propose a schema to convert a hybrid automaton with must transitions into an equivalent hybrid automaton featuring only may transitions. acknowledgement: This work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS, http://www.avacs.org/), by the European Research Council (ERC) under grant 267989 (QUAREM), by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award), and by the Swiss National Science Foundation (SNSF) as part of the project “Automated Reformulation and Pruning in Factored State Spaces (ARAP)”. author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Daniele full_name: Magazzeni, Daniele last_name: Magazzeni - first_name: Stefano full_name: Minopoli, Stefano last_name: Minopoli - first_name: Martin full_name: Wehrle, Martin last_name: Wehrle citation: ama: 'Bogomolov S, Magazzeni D, Minopoli S, Wehrle M. PDDL+ planning with hybrid automata: Foundations of translating must behavior. In: AAAI Press; 2015:42-46.' apa: 'Bogomolov, S., Magazzeni, D., Minopoli, S., & Wehrle, M. (2015). PDDL+ planning with hybrid automata: Foundations of translating must behavior (pp. 42–46). Presented at the ICAPS: International Conference on Automated Planning and Scheduling, Jerusalem, Israel: AAAI Press.' chicago: 'Bogomolov, Sergiy, Daniele Magazzeni, Stefano Minopoli, and Martin Wehrle. “PDDL+ Planning with Hybrid Automata: Foundations of Translating Must Behavior,” 42–46. AAAI Press, 2015.' ieee: 'S. Bogomolov, D. Magazzeni, S. Minopoli, and M. Wehrle, “PDDL+ planning with hybrid automata: Foundations of translating must behavior,” presented at the ICAPS: International Conference on Automated Planning and Scheduling, Jerusalem, Israel, 2015, pp. 42–46.' ista: 'Bogomolov S, Magazzeni D, Minopoli S, Wehrle M. 2015. PDDL+ planning with hybrid automata: Foundations of translating must behavior. ICAPS: International Conference on Automated Planning and Scheduling, 42–46.' mla: 'Bogomolov, Sergiy, et al. PDDL+ Planning with Hybrid Automata: Foundations of Translating Must Behavior. AAAI Press, 2015, pp. 42–46.' short: S. Bogomolov, D. Magazzeni, S. Minopoli, M. Wehrle, in:, AAAI Press, 2015, pp. 42–46. conference: end_date: 2015-06-11 location: Jerusalem, Israel name: 'ICAPS: International Conference on Automated Planning and Scheduling' start_date: 2015-06-07 date_created: 2018-12-11T11:53:23Z date_published: 2015-06-01T00:00:00Z date_updated: 2021-01-12T06:52:25Z day: '01' department: - _id: ToHe ec_funded: 1 language: - iso: eng main_file_link: - url: https://www.aaai.org/ocs/index.php/ICAPS/ICAPS15/paper/view/10606/10394 month: '06' oa_version: None page: 42 - 46 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: AAAI Press publist_id: '5479' quality_controlled: '1' scopus_import: 1 status: public title: 'PDDL+ planning with hybrid automata: Foundations of translating must behavior' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1674' abstract: - lang: eng text: We consider N × N random matrices of the form H = W + V where W is a real symmetric Wigner matrix and V a random or deterministic, real, diagonal matrix whose entries are independent of W. We assume subexponential decay for the matrix entries of W and we choose V so that the eigenvalues of W and V are typically of the same order. For a large class of diagonal matrices V, we show that the rescaled distribution of the extremal eigenvalues is given by the Tracy-Widom distribution F1 in the limit of large N. Our proofs also apply to the complex Hermitian setting, i.e. when W is a complex Hermitian Wigner matrix. article_number: '1550018' author: - first_name: Jioon full_name: Lee, Jioon last_name: Lee - first_name: Kevin full_name: Schnelli, Kevin id: 434AD0AE-F248-11E8-B48F-1D18A9856A87 last_name: Schnelli orcid: 0000-0003-0954-3231 citation: ama: Lee J, Schnelli K. Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. 2015;27(8). doi:10.1142/S0129055X1550018X apa: Lee, J., & Schnelli, K. (2015). Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. World Scientific Publishing. https://doi.org/10.1142/S0129055X1550018X chicago: Lee, Jioon, and Kevin Schnelli. “Edge Universality for Deformed Wigner Matrices.” Reviews in Mathematical Physics. World Scientific Publishing, 2015. https://doi.org/10.1142/S0129055X1550018X. ieee: J. Lee and K. Schnelli, “Edge universality for deformed Wigner matrices,” Reviews in Mathematical Physics, vol. 27, no. 8. World Scientific Publishing, 2015. ista: Lee J, Schnelli K. 2015. Edge universality for deformed Wigner matrices. Reviews in Mathematical Physics. 27(8), 1550018. mla: Lee, Jioon, and Kevin Schnelli. “Edge Universality for Deformed Wigner Matrices.” Reviews in Mathematical Physics, vol. 27, no. 8, 1550018, World Scientific Publishing, 2015, doi:10.1142/S0129055X1550018X. short: J. Lee, K. Schnelli, Reviews in Mathematical Physics 27 (2015). date_created: 2018-12-11T11:53:24Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:52:26Z day: '01' department: - _id: LaEr doi: 10.1142/S0129055X1550018X intvolume: ' 27' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1407.8015 month: '09' oa: 1 oa_version: Preprint publication: Reviews in Mathematical Physics publication_status: published publisher: World Scientific Publishing publist_id: '5475' quality_controlled: '1' scopus_import: 1 status: public title: Edge universality for deformed Wigner matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2015' ... --- _id: '1679' article_number: '091102' author: - first_name: Grégoire M full_name: Lemoult, Grégoire M id: 4787FE80-F248-11E8-B48F-1D18A9856A87 last_name: Lemoult - first_name: Philipp full_name: Maier, Philipp id: 384F7C04-F248-11E8-B48F-1D18A9856A87 last_name: Maier - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Lemoult GM, Maier P, Hof B. Taylor’s Forest. Physics of Fluids. 2015;27(9). doi:10.1063/1.4930850 apa: Lemoult, G. M., Maier, P., & Hof, B. (2015). Taylor’s Forest. Physics of Fluids. American Institute of Physics. https://doi.org/10.1063/1.4930850 chicago: Lemoult, Grégoire M, Philipp Maier, and Björn Hof. “Taylor’s Forest.” Physics of Fluids. American Institute of Physics, 2015. https://doi.org/10.1063/1.4930850. ieee: G. M. Lemoult, P. Maier, and B. Hof, “Taylor’s Forest,” Physics of Fluids, vol. 27, no. 9. American Institute of Physics, 2015. ista: Lemoult GM, Maier P, Hof B. 2015. Taylor’s Forest. Physics of Fluids. 27(9), 091102. mla: Lemoult, Grégoire M., et al. “Taylor’s Forest.” Physics of Fluids, vol. 27, no. 9, 091102, American Institute of Physics, 2015, doi:10.1063/1.4930850. short: G.M. Lemoult, P. Maier, B. Hof, Physics of Fluids 27 (2015). date_created: 2018-12-11T11:53:26Z date_published: 2015-09-24T00:00:00Z date_updated: 2021-01-12T06:52:28Z day: '24' ddc: - '532' department: - _id: BjHo doi: 10.1063/1.4930850 file: - access_level: open_access checksum: 604bba3c2496aadb3efcff77de01ce6c content_type: application/pdf creator: system date_created: 2018-12-12T10:13:35Z date_updated: 2020-07-14T12:45:12Z file_id: '5019' file_name: IST-2017-748-v1+1_1.4930850.pdf file_size: 872366 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 27' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version publication: Physics of Fluids publication_status: published publisher: American Institute of Physics publist_id: '5469' pubrep_id: '748' quality_controlled: '1' scopus_import: 1 status: public title: Taylor's Forest 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: 27 year: '2015' ... --- _id: '1676' author: - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Erez full_name: Raz, Erez last_name: Raz citation: ama: 'Sixt MK, Raz E. Editorial overview: Cell adhesion and migration. Current Opinion in Cell Biology. 2015;36(10):4-6. doi:10.1016/j.ceb.2015.09.004' apa: 'Sixt, M. K., & Raz, E. (2015). Editorial overview: Cell adhesion and migration. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.09.004' chicago: 'Sixt, Michael K, and Erez Raz. “Editorial Overview: Cell Adhesion and Migration.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.09.004.' ieee: 'M. K. Sixt and E. Raz, “Editorial overview: Cell adhesion and migration,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 4–6, 2015.' ista: 'Sixt MK, Raz E. 2015. Editorial overview: Cell adhesion and migration. Current Opinion in Cell Biology. 36(10), 4–6.' mla: 'Sixt, Michael K., and Erez Raz. “Editorial Overview: Cell Adhesion and Migration.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 4–6, doi:10.1016/j.ceb.2015.09.004.' short: M.K. Sixt, E. Raz, Current Opinion in Cell Biology 36 (2015) 4–6. date_created: 2018-12-11T11:53:25Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:52:27Z day: '01' department: - _id: MiSi doi: 10.1016/j.ceb.2015.09.004 intvolume: ' 36' issue: '10' language: - iso: eng month: '10' oa_version: None page: 4 - 6 publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '5473' scopus_import: 1 status: public title: 'Editorial overview: Cell adhesion and migration' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2015' ... --- _id: '1687' abstract: - lang: eng text: Guided cell movement is essential for development and integrity of animals and crucially involved in cellular immune responses. Leukocytes are professional migratory cells that can navigate through most types of tissues and sense a wide range of directional cues. The responses of these cells to attractants have been mainly explored in tissue culture settings. How leukocytes make directional decisions in situ, within the challenging environment of a tissue maze, is less understood. Here we review recent advances in how leukocytes sense chemical cues in complex tissue settings and make links with paradigms of directed migration in development and Dictyostelium discoideum amoebae. author: - first_name: Milka full_name: Sarris, Milka last_name: Sarris - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: 'Sarris M, Sixt MK. Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. 2015;36(10):93-102. doi:10.1016/j.ceb.2015.08.001' apa: 'Sarris, M., & Sixt, M. K. (2015). Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.08.001' chicago: 'Sarris, Milka, and Michael K Sixt. “Navigating in Tissue Mazes: Chemoattractant Interpretation in Complex Environments.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.08.001.' ieee: 'M. Sarris and M. K. Sixt, “Navigating in tissue mazes: Chemoattractant interpretation in complex environments,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 93–102, 2015.' ista: 'Sarris M, Sixt MK. 2015. Navigating in tissue mazes: Chemoattractant interpretation in complex environments. Current Opinion in Cell Biology. 36(10), 93–102.' mla: 'Sarris, Milka, and Michael K. Sixt. “Navigating in Tissue Mazes: Chemoattractant Interpretation in Complex Environments.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 93–102, doi:10.1016/j.ceb.2015.08.001.' short: M. Sarris, M.K. Sixt, Current Opinion in Cell Biology 36 (2015) 93–102. date_created: 2018-12-11T11:53:28Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:52:31Z day: '01' ddc: - '570' department: - _id: MiSi doi: 10.1016/j.ceb.2015.08.001 ec_funded: 1 file: - access_level: open_access checksum: c29973924b790aab02fdd91857759cfb content_type: application/pdf creator: system date_created: 2018-12-12T10:11:21Z date_updated: 2020-07-14T12:45:12Z file_id: '4875' file_name: IST-2016-445-v1+1_1-s2.0-S0955067415001064-main.pdf file_size: 797964 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 36' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 93 - 102 project: - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '5458' pubrep_id: '445' quality_controlled: '1' scopus_import: 1 status: public title: 'Navigating in tissue mazes: Chemoattractant interpretation in complex environments' 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: 36 year: '2015' ... --- _id: '1685' abstract: - lang: eng text: "Given a graph G cellularly embedded on a surface Σ of genus g, a cut graph is a subgraph of G such that cutting Σ along G yields a topological disk. We provide a fixed parameter tractable approximation scheme for the problem of computing the shortest cut graph, that is, for any ε > 0, we show how to compute a (1 + ε) approximation of the shortest cut graph in time f(ε, g)n3.\r\nOur techniques first rely on the computation of a spanner for the problem using the technique of brick decompositions, to reduce the problem to the case of bounded tree-width. Then, to solve the bounded tree-width case, we introduce a variant of the surface-cut decomposition of Rué, Sau and Thilikos, which may be of independent interest." alternative_title: - LNCS author: - first_name: Vincent full_name: Cohen Addad, Vincent last_name: Cohen Addad - first_name: Arnaud N full_name: De Mesmay, Arnaud N id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87 last_name: De Mesmay citation: ama: 'Cohen Addad V, de Mesmay AN. A fixed parameter tractable approximation scheme for the optimal cut graph of a surface. In: Vol 9294. Springer; 2015:386-398. doi:10.1007/978-3-662-48350-3_33' apa: 'Cohen Addad, V., & de Mesmay, A. N. (2015). A fixed parameter tractable approximation scheme for the optimal cut graph of a surface (Vol. 9294, pp. 386–398). Presented at the ESA: European Symposium on Algorithms, Patras, Greece: Springer. https://doi.org/10.1007/978-3-662-48350-3_33' chicago: Cohen Addad, Vincent, and Arnaud N de Mesmay. “A Fixed Parameter Tractable Approximation Scheme for the Optimal Cut Graph of a Surface,” 9294:386–98. Springer, 2015. https://doi.org/10.1007/978-3-662-48350-3_33. ieee: 'V. Cohen Addad and A. N. de Mesmay, “A fixed parameter tractable approximation scheme for the optimal cut graph of a surface,” presented at the ESA: European Symposium on Algorithms, Patras, Greece, 2015, vol. 9294, pp. 386–398.' ista: 'Cohen Addad V, de Mesmay AN. 2015. A fixed parameter tractable approximation scheme for the optimal cut graph of a surface. ESA: European Symposium on Algorithms, LNCS, vol. 9294, 386–398.' mla: Cohen Addad, Vincent, and Arnaud N. de Mesmay. A Fixed Parameter Tractable Approximation Scheme for the Optimal Cut Graph of a Surface. Vol. 9294, Springer, 2015, pp. 386–98, doi:10.1007/978-3-662-48350-3_33. short: V. Cohen Addad, A.N. de Mesmay, in:, Springer, 2015, pp. 386–398. conference: end_date: 2015-09-16 location: Patras, Greece name: 'ESA: European Symposium on Algorithms' start_date: 2015-09-14 date_created: 2018-12-11T11:53:27Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:52:31Z day: '01' department: - _id: UlWa doi: 10.1007/978-3-662-48350-3_33 ec_funded: 1 intvolume: ' 9294' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1507.01688 month: '09' oa: 1 oa_version: Preprint page: 386 - 398 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5462' quality_controlled: '1' scopus_import: 1 status: public title: A fixed parameter tractable approximation scheme for the optimal cut graph of a surface type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9294 year: '2015' ... --- _id: '1688' abstract: - lang: eng text: 'We estimate the selection constant in the following geometric selection theorem by Pach: For every positive integer d, there is a constant (Formula presented.) such that whenever (Formula presented.) are n-element subsets of (Formula presented.), we can find a point (Formula presented.) and subsets (Formula presented.) for every i∈[d+1], each of size at least cdn, such that p belongs to all rainbowd-simplices determined by (Formula presented.) simplices with one vertex in each Yi. We show a super-exponentially decreasing upper bound (Formula presented.). The ideas used in the proof of the upper bound also help us to prove Pach’s theorem with (Formula presented.), which is a lower bound doubly exponentially decreasing in d (up to some polynomial in the exponent). For comparison, Pach’s original approach yields a triply exponentially decreasing lower bound. On the other hand, Fox, Pach, and Suk recently obtained a hypergraph density result implying a proof of Pach’s theorem with (Formula presented.). In our construction for the upper bound, we use the fact that the minimum solid angle of every d-simplex is super-exponentially small. This fact was previously unknown and might be of independent interest. For the lower bound, we improve the ‘separation’ part of the argument by showing that in one of the key steps only d+1 separations are necessary, compared to 2d separations in the original proof. We also provide a measure version of Pach’s theorem.' acknowledgement: R. K. was supported by the Russian Foundation for Basic Research Grant 15-31-20403 (mol_a_ved) and grant 15-01-99563. J. K., Z. P., and M. T. were partially supported by ERC Advanced Research Grant No. 267165 (DISCONV) and by the project CE-ITI (GAČR P202/12/G061) of the Czech Science Foundation. J. K. was also partially supported by Swiss National Science Foundation Grants 200021-137574 and 200020-14453. P. P., Z. P., and M. T. were partially supported by the Charles University Grant GAUK 421511. P. P. was also partially supported by the Charles University Grant SVV-2014-260107. Z. P. was also partially supported by the Charles University Grant SVV-2014-260103. author: - first_name: Roman full_name: Karasev, Roman last_name: Karasev - first_name: Jan full_name: Kynčl, Jan last_name: Kynčl - first_name: Pavel full_name: Paták, Pavel last_name: Paták - first_name: Zuzana full_name: Patakova, Zuzana last_name: Patakova orcid: 0000-0002-3975-1683 - first_name: Martin full_name: Tancer, Martin id: 38AC689C-F248-11E8-B48F-1D18A9856A87 last_name: Tancer orcid: 0000-0002-1191-6714 citation: ama: Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. 2015;54(3):610-636. doi:10.1007/s00454-015-9720-z apa: Karasev, R., Kynčl, J., Paták, P., Patakova, Z., & Tancer, M. (2015). Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9720-z chicago: Karasev, Roman, Jan Kynčl, Pavel Paták, Zuzana Patakova, and Martin Tancer. “Bounds for Pach’s Selection Theorem and for the Minimum Solid Angle in a Simplex.” Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9720-z. ieee: R. Karasev, J. Kynčl, P. Paták, Z. Patakova, and M. Tancer, “Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex,” Discrete & Computational Geometry, vol. 54, no. 3. Springer, pp. 610–636, 2015. ista: Karasev R, Kynčl J, Paták P, Patakova Z, Tancer M. 2015. Bounds for Pach’s selection theorem and for the minimum solid angle in a simplex. Discrete & Computational Geometry. 54(3), 610–636. mla: Karasev, Roman, et al. “Bounds for Pach’s Selection Theorem and for the Minimum Solid Angle in a Simplex.” Discrete & Computational Geometry, vol. 54, no. 3, Springer, 2015, pp. 610–36, doi:10.1007/s00454-015-9720-z. short: R. Karasev, J. Kynčl, P. Paták, Z. Patakova, M. Tancer, Discrete & Computational Geometry 54 (2015) 610–636. date_created: 2018-12-11T11:53:28Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:52:32Z day: '01' department: - _id: UlWa doi: 10.1007/s00454-015-9720-z intvolume: ' 54' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1403.8147 month: '10' oa: 1 oa_version: Preprint page: 610 - 636 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '5457' quality_controlled: '1' scopus_import: 1 status: public title: Bounds for Pach's selection theorem and for the minimum solid angle in a simplex type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2015' ... --- _id: '1680' abstract: - lang: eng text: We consider the satisfiability problem for modal logic over first-order definable classes of frames.We confirm the conjecture from Hemaspaandra and Schnoor [2008] that modal logic is decidable over classes definable by universal Horn formulae. We provide a full classification of Horn formulae with respect to the complexity of the corresponding satisfiability problem. It turns out, that except for the trivial case of inconsistent formulae, local satisfiability is eitherNP-complete or PSPACE-complete, and global satisfiability is NP-complete, PSPACE-complete, or ExpTime-complete. We also show that the finite satisfiability problem for modal logic over Horn definable classes of frames is decidable. On the negative side, we show undecidability of two related problems. First, we exhibit a simple universal three-variable formula defining the class of frames over which modal logic is undecidable. Second, we consider the satisfiability problem of bimodal logic over Horn definable classes of frames, and also present a formula leading to undecidability. article_number: '2' author: - first_name: Jakub full_name: Michaliszyn, Jakub last_name: Michaliszyn - first_name: Jan full_name: Otop, Jan id: 2FC5DA74-F248-11E8-B48F-1D18A9856A87 last_name: Otop - first_name: Emanuel full_name: Kieroňski, Emanuel last_name: Kieroňski citation: ama: Michaliszyn J, Otop J, Kieroňski E. On the decidability of elementary modal logics. ACM Transactions on Computational Logic. 2015;17(1). doi:10.1145/2817825 apa: Michaliszyn, J., Otop, J., & Kieroňski, E. (2015). On the decidability of elementary modal logics. ACM Transactions on Computational Logic. ACM. https://doi.org/10.1145/2817825 chicago: Michaliszyn, Jakub, Jan Otop, and Emanuel Kieroňski. “On the Decidability of Elementary Modal Logics.” ACM Transactions on Computational Logic. ACM, 2015. https://doi.org/10.1145/2817825. ieee: J. Michaliszyn, J. Otop, and E. Kieroňski, “On the decidability of elementary modal logics,” ACM Transactions on Computational Logic, vol. 17, no. 1. ACM, 2015. ista: Michaliszyn J, Otop J, Kieroňski E. 2015. On the decidability of elementary modal logics. ACM Transactions on Computational Logic. 17(1), 2. mla: Michaliszyn, Jakub, et al. “On the Decidability of Elementary Modal Logics.” ACM Transactions on Computational Logic, vol. 17, no. 1, 2, ACM, 2015, doi:10.1145/2817825. short: J. Michaliszyn, J. Otop, E. Kieroňski, ACM Transactions on Computational Logic 17 (2015). date_created: 2018-12-11T11:53:26Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:52:29Z day: '01' department: - _id: ToHe doi: 10.1145/2817825 ec_funded: 1 intvolume: ' 17' issue: '1' language: - iso: eng month: '09' oa_version: None 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 - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: ACM Transactions on Computational Logic publication_status: published publisher: ACM publist_id: '5468' quality_controlled: '1' status: public title: On the decidability of elementary modal logics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2015' ... --- _id: '1682' abstract: - lang: eng text: 'We study the problem of robust satisfiability of systems of nonlinear equations, namely, whether for a given continuous function f:K→ ℝn on a finite simplicial complex K and α > 0, it holds that each function g: K → ℝn such that ||g - f || ∞ < α, has a root in K. Via a reduction to the extension problem of maps into a sphere, we particularly show that this problem is decidable in polynomial time for every fixed n, assuming dimK ≤ 2n - 3. This is a substantial extension of previous computational applications of topological degree and related concepts in numerical and interval analysis. Via a reverse reduction, we prove that the problem is undecidable when dim K > 2n - 2, where the threshold comes from the stable range in homotopy theory. For the lucidity of our exposition, we focus on the setting when f is simplexwise linear. Such functions can approximate general continuous functions, and thus we get approximation schemes and undecidability of the robust satisfiability in other possible settings.' article_number: '26' author: - first_name: Peter full_name: Franek, Peter last_name: Franek - first_name: Marek full_name: Krcál, Marek id: 33E21118-F248-11E8-B48F-1D18A9856A87 last_name: Krcál citation: ama: Franek P, Krcál M. Robust satisfiability of systems of equations. Journal of the ACM. 2015;62(4). doi:10.1145/2751524 apa: Franek, P., & Krcál, M. (2015). Robust satisfiability of systems of equations. Journal of the ACM. ACM. https://doi.org/10.1145/2751524 chicago: Franek, Peter, and Marek Krcál. “Robust Satisfiability of Systems of Equations.” Journal of the ACM. ACM, 2015. https://doi.org/10.1145/2751524. ieee: P. Franek and M. Krcál, “Robust satisfiability of systems of equations,” Journal of the ACM, vol. 62, no. 4. ACM, 2015. ista: Franek P, Krcál M. 2015. Robust satisfiability of systems of equations. Journal of the ACM. 62(4), 26. mla: Franek, Peter, and Marek Krcál. “Robust Satisfiability of Systems of Equations.” Journal of the ACM, vol. 62, no. 4, 26, ACM, 2015, doi:10.1145/2751524. short: P. Franek, M. Krcál, Journal of the ACM 62 (2015). date_created: 2018-12-11T11:53:27Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:52:30Z day: '01' department: - _id: UlWa - _id: HeEd doi: 10.1145/2751524 intvolume: ' 62' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.0858 month: '08' oa: 1 oa_version: Preprint publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '5466' quality_controlled: '1' scopus_import: 1 status: public title: Robust satisfiability of systems of equations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2015' ... --- _id: '1683' abstract: - lang: eng text: The 1 MDa, 45-subunit proton-pumping NADH-ubiquinone oxidoreductase (complex I) is the largest complex of the mitochondrial electron transport chain. The molecular mechanism of complex I is central to the metabolism of cells, but has yet to be fully characterized. The last two years have seen steady progress towards this goal with the first atomic-resolution structure of the entire bacterial complex I, a 5 Å cryo-electron microscopy map of bovine mitochondrial complex I and a ∼3.8 Å resolution X-ray crystallographic study of mitochondrial complex I from yeast Yarrowia lipotytica. In this review we will discuss what we have learned from these studies and what remains to be elucidated. author: - first_name: Jame A full_name: Letts, Jame A id: 322DA418-F248-11E8-B48F-1D18A9856A87 last_name: Letts orcid: 0000-0002-9864-3586 - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: 'Letts JA, Sazanov LA. Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. 2015;33(8):135-145. doi:10.1016/j.sbi.2015.08.008' apa: 'Letts, J. A., & Sazanov, L. A. (2015). Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2015.08.008' chicago: 'Letts, James A, and Leonid A Sazanov. “Gaining Mass: The Structure of Respiratory Complex I-from Bacterial towards Mitochondrial Versions.” Current Opinion in Structural Biology. Elsevier, 2015. https://doi.org/10.1016/j.sbi.2015.08.008.' ieee: 'J. A. Letts and L. A. Sazanov, “Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions,” Current Opinion in Structural Biology, vol. 33, no. 8. Elsevier, pp. 135–145, 2015.' ista: 'Letts JA, Sazanov LA. 2015. Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions. Current Opinion in Structural Biology. 33(8), 135–145.' mla: 'Letts, James A., and Leonid A. Sazanov. “Gaining Mass: The Structure of Respiratory Complex I-from Bacterial towards Mitochondrial Versions.” Current Opinion in Structural Biology, vol. 33, no. 8, Elsevier, 2015, pp. 135–45, doi:10.1016/j.sbi.2015.08.008.' short: J.A. Letts, L.A. Sazanov, Current Opinion in Structural Biology 33 (2015) 135–145. date_created: 2018-12-11T11:53:27Z date_published: 2015-08-01T00:00:00Z date_updated: 2021-01-12T06:52:30Z day: '01' department: - _id: LeSa doi: 10.1016/j.sbi.2015.08.008 intvolume: ' 33' issue: '8' language: - iso: eng month: '08' oa_version: None page: 135 - 145 publication: Current Opinion in Structural Biology publication_status: published publisher: Elsevier publist_id: '5465' quality_controlled: '1' scopus_import: 1 status: public title: 'Gaining mass: The structure of respiratory complex I-from bacterial towards mitochondrial versions' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2015' ... --- _id: '1686' author: - first_name: Eva full_name: Kiermaier, Eva id: 3EB04B78-F248-11E8-B48F-1D18A9856A87 last_name: Kiermaier orcid: 0000-0001-6165-5738 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: 'Kiermaier E, Sixt MK. Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. 2015;349(6252):1055-1056. doi:10.1126/science.aad0867' apa: 'Kiermaier, E., & Sixt, M. K. (2015). Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aad0867' chicago: 'Kiermaier, Eva, and Michael K Sixt. “Fragmented Communication between Immune Cells: Neutrophils Blaze a Trail with Migratory Cues for T Cells to Follow to Sites of Infection.” Science. American Association for the Advancement of Science, 2015. https://doi.org/10.1126/science.aad0867.' ieee: 'E. Kiermaier and M. K. Sixt, “Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection,” Science, vol. 349, no. 6252. American Association for the Advancement of Science, pp. 1055–1056, 2015.' ista: 'Kiermaier E, Sixt MK. 2015. Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection. Science. 349(6252), 1055–1056.' mla: 'Kiermaier, Eva, and Michael K. Sixt. “Fragmented Communication between Immune Cells: Neutrophils Blaze a Trail with Migratory Cues for T Cells to Follow to Sites of Infection.” Science, vol. 349, no. 6252, American Association for the Advancement of Science, 2015, pp. 1055–56, doi:10.1126/science.aad0867.' short: E. Kiermaier, M.K. Sixt, Science 349 (2015) 1055–1056. date_created: 2018-12-11T11:53:28Z date_published: 2015-09-04T00:00:00Z date_updated: 2021-01-12T06:52:31Z day: '04' department: - _id: MiSi doi: 10.1126/science.aad0867 intvolume: ' 349' issue: '6252' language: - iso: eng month: '09' oa_version: None page: 1055 - 1056 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5459' quality_controlled: '1' scopus_import: 1 status: public title: 'Fragmented communication between immune cells: Neutrophils blaze a trail with migratory cues for T cells to follow to sites of infection' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 349 year: '2015' ... --- _id: '1692' abstract: - lang: eng text: Computing an approximation of the reachable states of a hybrid system is a challenge, mainly because overapproximating the solutions of ODEs with a finite number of sets does not scale well. Using template polyhedra can greatly reduce the computational complexity, since it replaces complex operations on sets with a small number of optimization problems. However, the use of templates may make the over-approximation too conservative. Spurious transitions, which are falsely considered reachable, are particularly detrimental to performance and accuracy, and may exacerbate the state explosion problem. In this paper, we examine how spurious transitions can be avoided with minimal computational effort. To this end, detecting spurious transitions is reduced to the well-known problem of showing that two convex sets are disjoint by finding a hyperplane that separates them. We generalize this to owpipes by considering hyperplanes that evolve with time in correspondence to the dynamics of the system. The approach is implemented in the model checker SpaceEx and demonstrated on examples. author: - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Marius full_name: Greitschus, Marius last_name: Greitschus - first_name: Thomas full_name: Strump, Thomas last_name: Strump - first_name: Andreas full_name: Podelski, Andreas last_name: Podelski citation: ama: 'Frehse G, Bogomolov S, Greitschus M, Strump T, Podelski A. Eliminating spurious transitions in reachability with support functions. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:149-158. doi:10.1145/2728606.2728622' apa: 'Frehse, G., Bogomolov, S., Greitschus, M., Strump, T., & Podelski, A. (2015). Eliminating spurious transitions in reachability with support functions. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 149–158). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728622' chicago: 'Frehse, Goran, Sergiy Bogomolov, Marius Greitschus, Thomas Strump, and Andreas Podelski. “Eliminating Spurious Transitions in Reachability with Support Functions.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 149–58. ACM, 2015. https://doi.org/10.1145/2728606.2728622.' ieee: 'G. Frehse, S. Bogomolov, M. Greitschus, T. Strump, and A. Podelski, “Eliminating spurious transitions in reachability with support functions,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 149–158.' ista: 'Frehse G, Bogomolov S, Greitschus M, Strump T, Podelski A. 2015. Eliminating spurious transitions in reachability with support functions. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 149–158.' mla: 'Frehse, Goran, et al. “Eliminating Spurious Transitions in Reachability with Support Functions.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 149–58, doi:10.1145/2728606.2728622.' short: 'G. Frehse, S. Bogomolov, M. Greitschus, T. Strump, A. Podelski, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 149–158.' conference: end_date: 2015-04-16 location: Seattle, WA, United States name: 'HSCC: Hybrid Systems - Computation and Control' start_date: 2015-04-14 date_created: 2018-12-11T11:53:30Z date_published: 2015-04-14T00:00:00Z date_updated: 2021-01-12T06:52:33Z day: '14' department: - _id: ToHe doi: 10.1145/2728606.2728622 ec_funded: 1 language: - iso: eng month: '04' oa_version: None page: 149 - 158 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 - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: 'Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control' publication_identifier: isbn: - 978-1-4503-3433-4 publication_status: published publisher: ACM publist_id: '5452' quality_controlled: '1' scopus_import: 1 status: public title: Eliminating spurious transitions in reachability with support functions type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1693' abstract: - lang: eng text: Quantum interference between energetically close states is theoretically investigated, with the state structure being observed via laser spectroscopy. In this work, we focus on hyperfine states of selected hydrogenic muonic isotopes, and on how quantum interference affects the measured Lamb shift. The process of photon excitation and subsequent photon decay is implemented within the framework of nonrelativistic second-order perturbation theory. Due to its experimental interest, calculations are performed for muonic hydrogen, deuterium, and helium-3. We restrict our analysis to the case of photon scattering by incident linear polarized photons and the polarization of the scattered photons not being observed. We conclude that while quantum interference effects can be safely neglected in muonic hydrogen and helium-3, in the case of muonic deuterium there are resonances with close proximity, where quantum interference effects can induce shifts up to a few percent of the linewidth, assuming a pointlike detector. However, by taking into account the geometry of the setup used by the CREMA collaboration, this effect is reduced to less than 0.2% of the linewidth in all possible cases, which makes it irrelevant at the present level of accuracy. © 2015 American Physical Society. article_number: '022514' author: - first_name: Pedro full_name: Amaro, Pedro last_name: Amaro - first_name: Beatrice full_name: Franke, Beatrice last_name: Franke - first_name: Julian full_name: Krauth, Julian last_name: Krauth - first_name: Marc full_name: Diepold, Marc last_name: Diepold - first_name: Filippo full_name: Fratini, Filippo last_name: Fratini - first_name: Laleh full_name: Safari, Laleh id: 3C325E5E-F248-11E8-B48F-1D18A9856A87 last_name: Safari - first_name: Jorge full_name: Machado, Jorge last_name: Machado - first_name: Aldo full_name: Antognini, Aldo last_name: Antognini - first_name: Franz full_name: Kottmann, Franz last_name: Kottmann - first_name: Paul full_name: Indelicato, Paul last_name: Indelicato - first_name: Randolf full_name: Pohl, Randolf last_name: Pohl - first_name: José full_name: Santos, José last_name: Santos citation: ama: Amaro P, Franke B, Krauth J, et al. Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. 2015;92(2). doi:10.1103/PhysRevA.92.022514 apa: Amaro, P., Franke, B., Krauth, J., Diepold, M., Fratini, F., Safari, L., … Santos, J. (2015). Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.92.022514 chicago: Amaro, Pedro, Beatrice Franke, Julian Krauth, Marc Diepold, Filippo Fratini, Laleh Safari, Jorge Machado, et al. “Quantum Interference Effects in Laser Spectroscopy of Muonic Hydrogen, Deuterium, and Helium-3.” Physical Review A. American Physical Society, 2015. https://doi.org/10.1103/PhysRevA.92.022514. ieee: P. Amaro et al., “Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3,” Physical Review A, vol. 92, no. 2. American Physical Society, 2015. ista: Amaro P, Franke B, Krauth J, Diepold M, Fratini F, Safari L, Machado J, Antognini A, Kottmann F, Indelicato P, Pohl R, Santos J. 2015. Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3. Physical Review A. 92(2), 022514. mla: Amaro, Pedro, et al. “Quantum Interference Effects in Laser Spectroscopy of Muonic Hydrogen, Deuterium, and Helium-3.” Physical Review A, vol. 92, no. 2, 022514, American Physical Society, 2015, doi:10.1103/PhysRevA.92.022514. short: P. Amaro, B. Franke, J. Krauth, M. Diepold, F. Fratini, L. Safari, J. Machado, A. Antognini, F. Kottmann, P. Indelicato, R. Pohl, J. Santos, Physical Review A 92 (2015). date_created: 2018-12-11T11:53:30Z date_published: 2015-08-28T00:00:00Z date_updated: 2021-01-12T06:52:34Z day: '28' department: - _id: MiLe doi: 10.1103/PhysRevA.92.022514 ec_funded: 1 intvolume: ' 92' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1506.02734 month: '08' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review A publication_status: published publisher: American Physical Society publist_id: '5451' quality_controlled: '1' scopus_import: 1 status: public title: Quantum interference effects in laser spectroscopy of muonic hydrogen, deuterium, and helium-3 type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2015' ... --- _id: '1690' abstract: - lang: eng text: A number of powerful and scalable hybrid systems model checkers have recently emerged. Although all of them honor roughly the same hybrid systems semantics, they have drastically different model description languages. This situation (a) makes it difficult to quickly evaluate a specific hybrid automaton model using the different tools, (b) obstructs comparisons of reachability approaches, and (c) impedes the widespread application of research results that perform model modification and could benefit many of the tools. In this paper, we present Hyst, a Hybrid Source Transformer. Hyst is a source-to-source translation tool, currently taking input in the SpaceEx model format, and translating to the formats of HyCreate, Flow∗, or dReach. Internally, the tool supports generic model-to-model transformation passes that serve to both ease the translation and potentially improve reachability results for the supported tools. Although these model transformation passes could be implemented within each tool, the Hyst approach provides a single place for model modification, generating modified input sources for the unmodified target tools. Our evaluation demonstrates Hyst is capable of automatically translating benchmarks in several classes (including affine and nonlinear hybrid automata) to the input formats of several tools. Additionally, we illustrate a general model transformation pass based on pseudo-invariants implemented in Hyst that illustrates the reachability improvement. acknowledgement: The material presented in this paper is based upon work sup-ported by the Air Force Research Laboratory’s Information Directorate (AFRL/RI) through the Visiting Faculty Research Program (VFRP) under contract number FA8750-13-2-0115 and the Air Force Office of Scientific Research (AFOSR). Any opinions,findings, and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of the AFRL/RI or AFOSR. This work was also partly supported in part by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR14 AVACS, http://www.avacs.org/), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). author: - first_name: Stanley full_name: Bak, Stanley last_name: Bak - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Taylor full_name: Johnson, Taylor last_name: Johnson citation: ama: 'Bak S, Bogomolov S, Johnson T. HYST: A source transformation and translation tool for hybrid automaton models. In: Springer; 2015:128-133. doi:10.1145/2728606.2728630' apa: 'Bak, S., Bogomolov, S., & Johnson, T. (2015). HYST: A source transformation and translation tool for hybrid automaton models (pp. 128–133). Presented at the HSCC: Hybrid Systems - Computation and Control, Seattle, WA, United States: Springer. https://doi.org/10.1145/2728606.2728630' chicago: 'Bak, Stanley, Sergiy Bogomolov, and Taylor Johnson. “HYST: A Source Transformation and Translation Tool for Hybrid Automaton Models,” 128–33. Springer, 2015. https://doi.org/10.1145/2728606.2728630.' ieee: 'S. Bak, S. Bogomolov, and T. Johnson, “HYST: A source transformation and translation tool for hybrid automaton models,” presented at the HSCC: Hybrid Systems - Computation and Control, Seattle, WA, United States, 2015, pp. 128–133.' ista: 'Bak S, Bogomolov S, Johnson T. 2015. HYST: A source transformation and translation tool for hybrid automaton models. HSCC: Hybrid Systems - Computation and Control, 128–133.' mla: 'Bak, Stanley, et al. HYST: A Source Transformation and Translation Tool for Hybrid Automaton Models. Springer, 2015, pp. 128–33, doi:10.1145/2728606.2728630.' short: S. Bak, S. Bogomolov, T. Johnson, in:, Springer, 2015, pp. 128–133. conference: end_date: 2015-04-16 location: Seattle, WA, United States name: 'HSCC: Hybrid Systems - Computation and Control' start_date: 2015-04-14 date_created: 2018-12-11T11:53:29Z date_published: 2015-04-14T00:00:00Z date_updated: 2021-01-12T06:52:33Z day: '14' department: - _id: ToHe doi: 10.1145/2728606.2728630 ec_funded: 1 language: - iso: eng month: '04' oa_version: None page: 128 - 133 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Springer publist_id: '5454' quality_controlled: '1' status: public title: 'HYST: A source transformation and translation tool for hybrid automaton models' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1691' abstract: - lang: eng text: We consider a case study of the problem of deploying an autonomous air vehicle in a partially observable, dynamic, indoor environment from a specification given as a linear temporal logic (LTL) formula over regions of interest. We model the motion and sensing capabilities of the vehicle as a partially observable Markov decision process (POMDP). We adapt recent results for solving POMDPs with parity objectives to generate a control policy. We also extend the existing framework with a policy minimization technique to obtain a better implementable policy, while preserving its correctness. The proposed techniques are illustrated in an experimental setup involving an autonomous quadrotor performing surveillance in a dynamic environment. author: - first_name: Mária full_name: Svoreňová, Mária last_name: Svoreňová - first_name: Martin full_name: Chmelik, Martin id: 3624234E-F248-11E8-B48F-1D18A9856A87 last_name: Chmelik - first_name: Kevin full_name: Leahy, Kevin last_name: Leahy - first_name: Hasan full_name: Eniser, Hasan last_name: Eniser - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Ivana full_name: Cěrná, Ivana last_name: Cěrná - first_name: Cǎlin full_name: Belta, Cǎlin last_name: Belta citation: ama: 'Svoreňová M, Chmelik M, Leahy K, et al. Temporal logic motion planning using POMDPs with parity objectives: Case study paper. In: Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. ACM; 2015:233-238. doi:10.1145/2728606.2728617' apa: 'Svoreňová, M., Chmelik, M., Leahy, K., Eniser, H., Chatterjee, K., Cěrná, I., & Belta, C. (2015). Temporal logic motion planning using POMDPs with parity objectives: Case study paper. In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control (pp. 233–238). Seattle, WA, United States: ACM. https://doi.org/10.1145/2728606.2728617' chicago: 'Svoreňová, Mária, Martin Chmelik, Kevin Leahy, Hasan Eniser, Krishnendu Chatterjee, Ivana Cěrná, and Cǎlin Belta. “Temporal Logic Motion Planning Using POMDPs with Parity Objectives: Case Study Paper.” In Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, 233–38. ACM, 2015. https://doi.org/10.1145/2728606.2728617.' ieee: 'M. Svoreňová et al., “Temporal logic motion planning using POMDPs with parity objectives: Case study paper,” in Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, Seattle, WA, United States, 2015, pp. 233–238.' ista: 'Svoreňová M, Chmelik M, Leahy K, Eniser H, Chatterjee K, Cěrná I, Belta C. 2015. Temporal logic motion planning using POMDPs with parity objectives: Case study paper. Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems - Computation and Control, 233–238.' mla: 'Svoreňová, Mária, et al. “Temporal Logic Motion Planning Using POMDPs with Parity Objectives: Case Study Paper.” Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 233–38, doi:10.1145/2728606.2728617.' short: 'M. Svoreňová, M. Chmelik, K. Leahy, H. Eniser, K. Chatterjee, I. Cěrná, C. Belta, in:, Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control, ACM, 2015, pp. 233–238.' conference: end_date: 2015-04-16 location: Seattle, WA, United States name: 'HSCC: Hybrid Systems - Computation and Control' start_date: 2015-04-14 date_created: 2018-12-11T11:53:29Z date_published: 2015-04-14T00:00:00Z date_updated: 2021-01-12T06:52:33Z day: '14' department: - _id: KrCh doi: 10.1145/2728606.2728617 ec_funded: 1 language: - iso: eng month: '04' oa_version: None page: 233 - 238 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' publication: 'Proceedings of the 18th International Conference on Hybrid Systems: Computation and Control' publication_status: published publisher: ACM publist_id: '5453' scopus_import: 1 status: public title: 'Temporal logic motion planning using POMDPs with parity objectives: Case study paper' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2015' ... --- _id: '1694' abstract: - lang: eng text: "\r\nWe introduce quantitative timed refinement and timed simulation (directed) metrics, incorporating zenoness checks, for timed systems. These metrics assign positive real numbers which quantify the timing mismatches between two timed systems, amongst non-zeno runs. We quantify timing mismatches in three ways: (1) the maximal timing mismatch that can arise, (2) the “steady-state” maximal timing mismatches, where initial transient timing mismatches are ignored; and (3) the (long-run) average timing mismatches amongst two systems. These three kinds of mismatches constitute three important types of timing differences. Our event times are the global times, measured from the start of the system execution, not just the time durations of individual steps. We present algorithms over timed automata for computing the three quantitative simulation distances to within any desired degree of accuracy. In order to compute the values of the quantitative simulation distances, we use a game theoretic formulation. We introduce two new kinds of objectives for two player games on finite-state game graphs: (1) eventual debit-sum level objectives, and (2) average debit-sum level objectives. We present algorithms for computing the optimal values for these objectives in graph games, and then use these algorithms to compute the values of the timed simulation distances over timed automata.\r\n" author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Vinayak full_name: Prabhu, Vinayak last_name: Prabhu citation: ama: Chatterjee K, Prabhu V. Quantitative temporal simulation and refinement distances for timed systems. IEEE Transactions on Automatic Control. 2015;60(9):2291-2306. doi:10.1109/TAC.2015.2404612 apa: Chatterjee, K., & Prabhu, V. (2015). Quantitative temporal simulation and refinement distances for timed systems. IEEE Transactions on Automatic Control. IEEE. https://doi.org/10.1109/TAC.2015.2404612 chicago: Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Temporal Simulation and Refinement Distances for Timed Systems.” IEEE Transactions on Automatic Control. IEEE, 2015. https://doi.org/10.1109/TAC.2015.2404612. ieee: K. Chatterjee and V. Prabhu, “Quantitative temporal simulation and refinement distances for timed systems,” IEEE Transactions on Automatic Control, vol. 60, no. 9. IEEE, pp. 2291–2306, 2015. ista: Chatterjee K, Prabhu V. 2015. Quantitative temporal simulation and refinement distances for timed systems. IEEE Transactions on Automatic Control. 60(9), 2291–2306. mla: Chatterjee, Krishnendu, and Vinayak Prabhu. “Quantitative Temporal Simulation and Refinement Distances for Timed Systems.” IEEE Transactions on Automatic Control, vol. 60, no. 9, IEEE, 2015, pp. 2291–306, doi:10.1109/TAC.2015.2404612. short: K. Chatterjee, V. Prabhu, IEEE Transactions on Automatic Control 60 (2015) 2291–2306. date_created: 2018-12-11T11:53:30Z date_published: 2015-02-24T00:00:00Z date_updated: 2021-01-12T06:52:34Z day: '24' department: - _id: KrCh doi: 10.1109/TAC.2015.2404612 ec_funded: 1 intvolume: ' 60' issue: '9' language: - iso: eng month: '02' oa_version: None page: 2291 - 2306 project: - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _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: IEEE Transactions on Automatic Control publication_status: published publisher: IEEE publist_id: '5450' quality_controlled: '1' scopus_import: 1 status: public title: Quantitative temporal simulation and refinement distances for timed systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 60 year: '2015' ... --- _id: '1695' abstract: - lang: eng text: We give a comprehensive introduction into a diagrammatic method that allows for the evaluation of Gutzwiller wave functions in finite spatial dimensions. We discuss in detail some numerical schemes that turned out to be useful in the real-space evaluation of the diagrams. The method is applied to the problem of d-wave superconductivity in a two-dimensional single-band Hubbard model. Here, we discuss in particular the role of long-range contributions in our diagrammatic expansion. We further reconsider our previous analysis on the kinetic energy gain in the superconducting state. author: - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 - first_name: Tobias full_name: Schickling, Tobias last_name: Schickling - first_name: Jörg full_name: Bünemann, Jörg last_name: Bünemann citation: ama: 'Kaczmarczyk J, Schickling T, Bünemann J. Evaluation techniques for Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B): Basic Solid State Physics. 2015;252(9):2059-2071. doi:10.1002/pssb.201552082' apa: 'Kaczmarczyk, J., Schickling, T., & Bünemann, J. (2015). Evaluation techniques for Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B): Basic Solid State Physics. Wiley. https://doi.org/10.1002/pssb.201552082' chicago: 'Kaczmarczyk, Jan, Tobias Schickling, and Jörg Bünemann. “Evaluation Techniques for Gutzwiller Wave Functions in Finite Dimensions.” Physica Status Solidi (B): Basic Solid State Physics. Wiley, 2015. https://doi.org/10.1002/pssb.201552082.' ieee: 'J. Kaczmarczyk, T. Schickling, and J. Bünemann, “Evaluation techniques for Gutzwiller wave functions in finite dimensions,” Physica Status Solidi (B): Basic Solid State Physics, vol. 252, no. 9. Wiley, pp. 2059–2071, 2015.' ista: 'Kaczmarczyk J, Schickling T, Bünemann J. 2015. Evaluation techniques for Gutzwiller wave functions in finite dimensions. Physica Status Solidi (B): Basic Solid State Physics. 252(9), 2059–2071.' mla: 'Kaczmarczyk, Jan, et al. “Evaluation Techniques for Gutzwiller Wave Functions in Finite Dimensions.” Physica Status Solidi (B): Basic Solid State Physics, vol. 252, no. 9, Wiley, 2015, pp. 2059–71, doi:10.1002/pssb.201552082.' short: 'J. Kaczmarczyk, T. Schickling, J. Bünemann, Physica Status Solidi (B): Basic Solid State Physics 252 (2015) 2059–2071.' date_created: 2018-12-11T11:53:31Z date_published: 2015-09-01T00:00:00Z date_updated: 2021-01-12T06:52:34Z day: '01' department: - _id: MiLe doi: 10.1002/pssb.201552082 ec_funded: 1 intvolume: ' 252' issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1503.03738 month: '09' oa: 1 oa_version: Preprint page: 2059 - 2071 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: 'Physica Status Solidi (B): Basic Solid State Physics' publication_status: published publisher: Wiley publist_id: '5449' quality_controlled: '1' scopus_import: 1 status: public title: Evaluation techniques for Gutzwiller wave functions in finite dimensions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 252 year: '2015' ... --- _id: '1697' abstract: - lang: eng text: Motion tracking is a challenge the visual system has to solve by reading out the retinal population. It is still unclear how the information from different neurons can be combined together to estimate the position of an object. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar’s position can be reconstructed from retinal activity with a precision in the hyperacuity regime using a linear decoder acting on 100+ cells. We then took advantage of this unprecedented precision to explore the spatial structure of the retina’s population code. The classical view would have suggested that the firing rates of the cells form a moving hill of activity tracking the bar’s position. Instead, we found that most ganglion cells in the salamander fired sparsely and idiosyncratically, so that their neural image did not track the bar. Furthermore, ganglion cell activity spanned an area much larger than predicted by their receptive fields, with cells coding for motion far in their surround. As a result, population redundancy was high, and we could find multiple, disjoint subsets of neurons that encoded the trajectory with high precision. This organization allows for diverse collections of ganglion cells to represent high-accuracy motion information in a form easily read out by downstream neural circuits. acknowledgement: 'This work was supported by grants EY 014196 and EY 017934 to MJB, ANR OPTIMA, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche [LIFESENSES: ANR-10-LABX-65], and by a EC grant from the Human Brain Project (CLAP) to OM, the Austrian Research Foundation FWF P25651 to VBS and GT. VBS is partially supported by contracts MEC, Spain (Grant No. AYA2010- 22111-C03-02, Grant No. AYA2013-48623-C2-2 and FEDER Funds).' article_number: e1004304 author: - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Vicente full_name: Botella Soler, Vicente id: 421234E8-F248-11E8-B48F-1D18A9856A87 last_name: Botella Soler orcid: 0000-0002-8790-1914 - first_name: Kristina full_name: Simmons, Kristina last_name: Simmons - first_name: Thierry full_name: Mora, Thierry last_name: Mora - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Michael full_name: Berry, Michael last_name: Berry citation: ama: Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 2015;11(7). doi:10.1371/journal.pcbi.1004304 apa: Marre, O., Botella Soler, V., Simmons, K., Mora, T., Tkačik, G., & Berry, M. (2015). High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004304 chicago: Marre, Olivier, Vicente Botella Soler, Kristina Simmons, Thierry Mora, Gašper Tkačik, and Michael Berry. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004304. ieee: O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7. Public Library of Science, 2015. ista: Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. 2015. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 11(7), e1004304. mla: Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304. short: O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS Computational Biology 11 (2015). date_created: 2018-12-11T11:53:31Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:52:35Z day: '01' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pcbi.1004304 file: - access_level: open_access checksum: 472b979f3f1cffb37b3e503f085115ca content_type: application/pdf creator: system date_created: 2018-12-12T10:16:25Z date_updated: 2020-07-14T12:45:12Z file_id: '5212' file_name: IST-2016-455-v1+1_journal.pcbi.1004304.pdf file_size: 4673930 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 11' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5447' pubrep_id: '455' quality_controlled: '1' scopus_import: 1 status: public title: High accuracy decoding of dynamical motion from a large retinal population 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: 11 year: '2015' ... --- _id: '1699' abstract: - lang: eng text: By hybridization and backcrossing, alleles can surmount species boundaries and be incorporated into the genome of a related species. This introgression of genes is of particular evolutionary relevance if it involves the transfer of adaptations between populations. However, any beneficial allele will typically be associated with other alien alleles that are often deleterious and hamper the introgression process. In order to describe the introgression of an adaptive allele, we set up a stochastic model with an explicit genetic makeup of linked and unlinked deleterious alleles. Based on the theory of reducible multitype branching processes, we derive a recursive expression for the establishment probability of the beneficial allele after a single hybridization event. We furthermore study the probability that slightly deleterious alleles hitchhike to fixation. The key to the analysis is a split of the process into a stochastic phase in which the advantageous alleles establishes and a deterministic phase in which it sweeps to fixation. We thereafter apply the theory to a set of biologically relevant scenarios such as introgression in the presence of many unlinked or few closely linked deleterious alleles. A comparison to computer simulations shows that the approximations work well over a large parameter range. acknowledgement: This work was made possible with financial support by the Vienna Science and Technology Fund (WWTF), by the Deutsche Forschungsgemeinschaft (DFG), Research Unit 1078 Natural selection in structured populations, by the Austrian Science Fund (FWF) via funding for the Vienna Graduate School for Population Genetics, and by a “For Women in Science” fellowship (L’Oréal Österreich in cooperation with the Austrian Commission for UNESCO and the Austrian Academy of Sciences with financial support from the Federal Ministry for Science and Research Austria). author: - first_name: Hildegard full_name: Uecker, Hildegard id: 2DB8F68A-F248-11E8-B48F-1D18A9856A87 last_name: Uecker orcid: 0000-0001-9435-2813 - first_name: Derek full_name: Setter, Derek last_name: Setter - first_name: Joachim full_name: Hermisson, Joachim last_name: Hermisson citation: ama: Uecker H, Setter D, Hermisson J. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 2015;70(7):1523-1580. doi:10.1007/s00285-014-0802-y apa: Uecker, H., Setter, D., & Hermisson, J. (2015). Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. Springer. https://doi.org/10.1007/s00285-014-0802-y chicago: Uecker, Hildegard, Derek Setter, and Joachim Hermisson. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology. Springer, 2015. https://doi.org/10.1007/s00285-014-0802-y. ieee: H. Uecker, D. Setter, and J. Hermisson, “Adaptive gene introgression after secondary contact,” Journal of Mathematical Biology, vol. 70, no. 7. Springer, pp. 1523–1580, 2015. ista: Uecker H, Setter D, Hermisson J. 2015. Adaptive gene introgression after secondary contact. Journal of Mathematical Biology. 70(7), 1523–1580. mla: Uecker, Hildegard, et al. “Adaptive Gene Introgression after Secondary Contact.” Journal of Mathematical Biology, vol. 70, no. 7, Springer, 2015, pp. 1523–80, doi:10.1007/s00285-014-0802-y. short: H. Uecker, D. Setter, J. Hermisson, Journal of Mathematical Biology 70 (2015) 1523–1580. date_created: 2018-12-11T11:53:32Z date_published: 2015-06-01T00:00:00Z date_updated: 2023-02-23T10:10:36Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1007/s00285-014-0802-y file: - access_level: open_access checksum: 00e3a67bda05d4cc165b3a48b41ef9ad content_type: application/pdf creator: system date_created: 2018-12-12T10:14:27Z date_updated: 2020-07-14T12:45:12Z file_id: '5079' file_name: IST-2016-458-v1+1_s00285-014-0802-y.pdf file_size: 1321527 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 70' issue: '7' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1523 - 1580 project: - _id: 25B67606-B435-11E9-9278-68D0E5697425 name: L'OREAL Fellowship publication: Journal of Mathematical Biology publication_status: published publisher: Springer publist_id: '5442' pubrep_id: '458' quality_controlled: '1' scopus_import: 1 status: public title: Adaptive gene introgression after secondary contact 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: 70 year: '2015' ... --- _id: '1696' abstract: - lang: eng text: The recently proposed diagrammatic expansion (DE) technique for the full Gutzwiller wave function (GWF) is applied to the Anderson lattice model. This approach allows for a systematic evaluation of the expectation values with full Gutzwiller wave function in finite-dimensional systems. It introduces results extending in an essential manner those obtained by means of the standard Gutzwiller approximation (GA), which is variationally exact only in infinite dimensions. Within the DE-GWF approach we discuss the principal paramagnetic properties and their relevance to heavy-fermion systems. We demonstrate the formation of an effective, narrow f band originating from atomic f-electron states and subsequently interpret this behavior as a direct itineracy of f electrons; it represents a combined effect of both the hybridization and the correlations induced by the Coulomb repulsive interaction. Such a feature is absent on the level of GA, which is equivalent to the zeroth order of our expansion. Formation of the hybridization- and electron-concentration-dependent narrow f band rationalizes the common assumption of such dispersion of f levels in the phenomenological modeling of the band structure of CeCoIn5. Moreover, it is shown that the emerging f-electron direct itineracy leads in a natural manner to three physically distinct regimes within a single model that are frequently discussed for 4f- or 5f-electron compounds as separate model situations. We identify these regimes as (i) the mixed-valence regime, (ii) Kondo/almost-Kondo insulating regime, and (iii) the Kondo-lattice limit when the f-electron occupancy is very close to the f-state half filling, ⟨nˆf⟩→1. The nonstandard features of the emerging correlated quantum liquid state are stressed. acknowledgement: The work was partly supported by the National Science Centre (NCN) under MAESTRO, Grant No. DEC-2012/04/A/ST3/00342. M.W. acknowledges the hospitality of the Institute of Science and Technology Austria during the final stage of development of the present work, as well as partial financial support from the Society-Environment-Technology project of the Jagiellonian University for that stay. J.K. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA Grant Agreement No. [291734 ]. article_number: '125135' author: - first_name: Marcin full_name: Wysokiński, Marcin last_name: Wysokiński - first_name: Jan full_name: Kaczmarczyk, Jan id: 46C405DE-F248-11E8-B48F-1D18A9856A87 last_name: Kaczmarczyk orcid: 0000-0002-1629-3675 - first_name: Jozef full_name: Spałek, Jozef last_name: Spałek citation: ama: 'Wysokiński M, Kaczmarczyk J, Spałek J. Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. 2015;92(12). doi:10.1103/PhysRevB.92.125135' apa: 'Wysokiński, M., Kaczmarczyk, J., & Spałek, J. (2015). Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.92.125135' chicago: 'Wysokiński, Marcin, Jan Kaczmarczyk, and Jozef Spałek. “Gutzwiller Wave Function Solution for Anderson Lattice Model: Emerging Universal Regimes of Heavy Quasiparticle States.” Physical Review B. American Physical Society, 2015. https://doi.org/10.1103/PhysRevB.92.125135.' ieee: 'M. Wysokiński, J. Kaczmarczyk, and J. Spałek, “Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states,” Physical Review B, vol. 92, no. 12. American Physical Society, 2015.' ista: 'Wysokiński M, Kaczmarczyk J, Spałek J. 2015. Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states. Physical Review B. 92(12), 125135.' mla: 'Wysokiński, Marcin, et al. “Gutzwiller Wave Function Solution for Anderson Lattice Model: Emerging Universal Regimes of Heavy Quasiparticle States.” Physical Review B, vol. 92, no. 12, 125135, American Physical Society, 2015, doi:10.1103/PhysRevB.92.125135.' short: M. Wysokiński, J. Kaczmarczyk, J. Spałek, Physical Review B 92 (2015). date_created: 2018-12-11T11:53:31Z date_published: 2015-09-18T00:00:00Z date_updated: 2021-01-12T06:52:35Z day: '18' department: - _id: MiLe doi: 10.1103/PhysRevB.92.125135 ec_funded: 1 intvolume: ' 92' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1505.07003 month: '09' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '5448' quality_controlled: '1' scopus_import: 1 status: public title: 'Gutzwiller wave function solution for Anderson lattice model: Emerging universal regimes of heavy quasiparticle states' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2015' ... --- _id: '1701' abstract: - lang: eng text: 'The activity of a neural network is defined by patterns of spiking and silence from the individual neurons. Because spikes are (relatively) sparse, patterns of activity with increasing numbers of spikes are less probable, but, with more spikes, the number of possible patterns increases. This tradeoff between probability and numerosity is mathematically equivalent to the relationship between entropy and energy in statistical physics. We construct this relationship for populations of up to N = 160 neurons in a small patch of the vertebrate retina, using a combination of direct and model-based analyses of experiments on the response of this network to naturalistic movies. We see signs of a thermodynamic limit, where the entropy per neuron approaches a smooth function of the energy per neuron as N increases. The form of this function corresponds to the distribution of activity being poised near an unusual kind of critical point. We suggest further tests of criticality, and give a brief discussion of its functional significance. ' acknowledgement: "Research was supported in part by National Science Foundation Grants PHY-1305525, PHY-1451171, and CCF-0939370, by National Institutes of Health Grant R01 EY14196, and by Austrian Science Foundation Grant FWF P25651. Additional support was provided by the\r\nFannie and John Hertz Foundation, by the Swartz Foundation, by the W. M. Keck Foundation, and by the Simons Foundation." author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Thierry full_name: Mora, Thierry last_name: Mora - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Dario full_name: Amodei, Dario last_name: Amodei - first_name: Stephanie full_name: Palmer, Stephanie last_name: Palmer - first_name: Michael full_name: Berry Ii, Michael last_name: Berry Ii - first_name: William full_name: Bialek, William last_name: Bialek citation: ama: Tkačik G, Mora T, Marre O, et al. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 2015;112(37):11508-11513. doi:10.1073/pnas.1514188112 apa: Tkačik, G., Mora, T., Marre, O., Amodei, D., Palmer, S., Berry Ii, M., & Bialek, W. (2015). Thermodynamics and signatures of criticality in a network of neurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1514188112 chicago: Tkačik, Gašper, Thierry Mora, Olivier Marre, Dario Amodei, Stephanie Palmer, Michael Berry Ii, and William Bialek. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1514188112. ieee: G. Tkačik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37. National Academy of Sciences, pp. 11508–11513, 2015. ista: Tkačik G, Mora T, Marre O, Amodei D, Palmer S, Berry Ii M, Bialek W. 2015. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 112(37), 11508–11513. mla: Tkačik, Gašper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112. short: G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513. date_created: 2018-12-11T11:53:33Z date_published: 2015-09-15T00:00:00Z date_updated: 2021-01-12T06:52:37Z day: '15' department: - _id: GaTk doi: 10.1073/pnas.1514188112 external_id: pmid: - '26330611' intvolume: ' 112' issue: '37' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577210/ month: '09' oa: 1 oa_version: Submitted Version page: 11508 - 11513 pmid: 1 project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5440' quality_controlled: '1' scopus_import: 1 status: public title: Thermodynamics and signatures of criticality in a network of neurons type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1698' abstract: - lang: eng text: 'In mean-payoff games, the objective of the protagonist is to ensure that the limit average of an infinite sequence of numeric weights is nonnegative. In energy games, the objective is to ensure that the running sum of weights is always nonnegative. Multi-mean-payoff and multi-energy games replace individual weights by tuples, and the limit average (resp., running sum) of each coordinate must be (resp., remain) nonnegative. We prove finite-memory determinacy of multi-energy games and show inter-reducibility of multi-mean-payoff and multi-energy games for finite-memory strategies. We improve the computational complexity for solving both classes with finite-memory strategies: we prove coNP-completeness improving the previous known EXPSPACE bound. For memoryless strategies, we show that deciding the existence of a winning strategy for the protagonist is NP-complete. We present the first solution of multi-mean-payoff games with infinite-memory strategies: we show that mean-payoff-sup objectives can be decided in NP∩coNP, whereas mean-payoff-inf objectives are coNP-complete.' acknowledgement: 'The research was partly supported by Austrian Science Fund (FWF) Grant No P23499-N23, FWF NFN Grant No S11407-N23 and S11402-N23 (RiSE), ERC Start grant (279307: Graph Games), Microsoft faculty fellows award, the ERC Advanced Grant QUAREM (267989: Quantitative Reactive Modeling), European project Cassting (FP7-601148), ERC Start grant (279499: inVEST).' author: - first_name: Yaron full_name: Velner, Yaron last_name: Velner - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Laurent full_name: Doyen, Laurent last_name: Doyen - 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: Alexander full_name: Rabinovich, Alexander last_name: Rabinovich - first_name: Jean full_name: Raskin, Jean last_name: Raskin citation: ama: Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. The complexity of multi-mean-payoff and multi-energy games. Information and Computation. 2015;241(4):177-196. doi:10.1016/j.ic.2015.03.001 apa: Velner, Y., Chatterjee, K., Doyen, L., Henzinger, T. A., Rabinovich, A., & Raskin, J. (2015). The complexity of multi-mean-payoff and multi-energy games. Information and Computation. Elsevier. https://doi.org/10.1016/j.ic.2015.03.001 chicago: Velner, Yaron, Krishnendu Chatterjee, Laurent Doyen, Thomas A Henzinger, Alexander Rabinovich, and Jean Raskin. “The Complexity of Multi-Mean-Payoff and Multi-Energy Games.” Information and Computation. Elsevier, 2015. https://doi.org/10.1016/j.ic.2015.03.001. ieee: Y. Velner, K. Chatterjee, L. Doyen, T. A. Henzinger, A. Rabinovich, and J. Raskin, “The complexity of multi-mean-payoff and multi-energy games,” Information and Computation, vol. 241, no. 4. Elsevier, pp. 177–196, 2015. ista: Velner Y, Chatterjee K, Doyen L, Henzinger TA, Rabinovich A, Raskin J. 2015. The complexity of multi-mean-payoff and multi-energy games. Information and Computation. 241(4), 177–196. mla: Velner, Yaron, et al. “The Complexity of Multi-Mean-Payoff and Multi-Energy Games.” Information and Computation, vol. 241, no. 4, Elsevier, 2015, pp. 177–96, doi:10.1016/j.ic.2015.03.001. short: Y. Velner, K. Chatterjee, L. Doyen, T.A. Henzinger, A. Rabinovich, J. Raskin, Information and Computation 241 (2015) 177–196. date_created: 2018-12-11T11:53:32Z date_published: 2015-04-01T00:00:00Z date_updated: 2021-01-12T06:52:36Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1016/j.ic.2015.03.001 ec_funded: 1 intvolume: ' 241' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1209.3234 month: '04' oa: 1 oa_version: Preprint page: 177 - 196 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: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _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 - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling publication: Information and Computation publication_status: published publisher: Elsevier publist_id: '5443' quality_controlled: '1' scopus_import: 1 status: public title: The complexity of multi-mean-payoff and multi-energy games type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 241 year: '2015' ... --- _id: '1700' abstract: - lang: eng text: We use the dual boson approach to reveal the phase diagram of the Fermi-Hubbard model with long-range dipole-dipole interactions. By using a large-scale finite-temperature calculation on a 64×64 square lattice we demonstrate the existence of a novel phase, possessing an "ultralong-range" order. The fingerprint of this phase - the density correlation function - features a nontrivial behavior on a scale of tens of lattice sites. We study the properties and the stability of the ultralong-range-ordered phase, and show that it is accessible in modern experiments with ultracold polar molecules and magnetic atoms. acknowledgement: The work is supported by European Research Council (ERC) Advanced Grant No. 338957 FEMTO/NANO. article_number: '081106' author: - first_name: Erik full_name: Van Loon, Erik last_name: Van Loon - first_name: Mikhail full_name: Katsnelson, Mikhail last_name: Katsnelson - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Van Loon E, Katsnelson M, Lemeshko M. Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. 2015;92(8). doi:10.1103/PhysRevB.92.081106 apa: Van Loon, E., Katsnelson, M., & Lemeshko, M. (2015). Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.92.081106 chicago: Van Loon, Erik, Mikhail Katsnelson, and Mikhail Lemeshko. “Ultralong-Range Order in the Fermi-Hubbard Model with Long-Range Interactions.” Physical Review B. American Physical Society, 2015. https://doi.org/10.1103/PhysRevB.92.081106. ieee: E. Van Loon, M. Katsnelson, and M. Lemeshko, “Ultralong-range order in the Fermi-Hubbard model with long-range interactions,” Physical Review B, vol. 92, no. 8. American Physical Society, 2015. ista: Van Loon E, Katsnelson M, Lemeshko M. 2015. Ultralong-range order in the Fermi-Hubbard model with long-range interactions. Physical Review B. 92(8), 081106. mla: Van Loon, Erik, et al. “Ultralong-Range Order in the Fermi-Hubbard Model with Long-Range Interactions.” Physical Review B, vol. 92, no. 8, 081106, American Physical Society, 2015, doi:10.1103/PhysRevB.92.081106. short: E. Van Loon, M. Katsnelson, M. Lemeshko, Physical Review B 92 (2015). date_created: 2018-12-11T11:53:32Z date_published: 2015-08-10T00:00:00Z date_updated: 2021-01-12T06:52:37Z day: '10' department: - _id: MiLe doi: 10.1103/PhysRevB.92.081106 intvolume: ' 92' issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1506.06007 month: '08' oa: 1 oa_version: Preprint publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '5441' scopus_import: 1 status: public title: Ultralong-range order in the Fermi-Hubbard model with long-range interactions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 92 year: '2015' ... --- _id: '1704' abstract: - lang: eng text: Given a convex function (Formula presented.) and two hermitian matrices A and B, Lewin and Sabin study in (Lett Math Phys 104:691–705, 2014) the relative entropy defined by (Formula presented.). Among other things, they prove that the so-defined quantity is monotone if and only if (Formula presented.) is operator monotone. The monotonicity is then used to properly define (Formula presented.) for bounded self-adjoint operators acting on an infinite-dimensional Hilbert space by a limiting procedure. More precisely, for an increasing sequence of finite-dimensional projections (Formula presented.) with (Formula presented.) strongly, the limit (Formula presented.) is shown to exist and to be independent of the sequence of projections (Formula presented.). The question whether this sequence converges to its "obvious" limit, namely (Formula presented.), has been left open. We answer this question in principle affirmatively and show that (Formula presented.). If the operators A and B are regular enough, that is (A − B), (Formula presented.) and (Formula presented.) are trace-class, the identity (Formula presented.) holds. author: - first_name: Andreas full_name: Deuchert, Andreas last_name: Deuchert orcid: 0000-0003-3146-6746 - 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: Deuchert A, Hainzl C, Seiringer R. Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. 2015;105(10):1449-1466. doi:10.1007/s11005-015-0787-5 apa: Deuchert, A., Hainzl, C., & Seiringer, R. (2015). Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. Springer. https://doi.org/10.1007/s11005-015-0787-5 chicago: Deuchert, Andreas, Christian Hainzl, and Robert Seiringer. “Note on a Family of Monotone Quantum Relative Entropies.” Letters in Mathematical Physics. Springer, 2015. https://doi.org/10.1007/s11005-015-0787-5. ieee: A. Deuchert, C. Hainzl, and R. Seiringer, “Note on a family of monotone quantum relative entropies,” Letters in Mathematical Physics, vol. 105, no. 10. Springer, pp. 1449–1466, 2015. ista: Deuchert A, Hainzl C, Seiringer R. 2015. Note on a family of monotone quantum relative entropies. Letters in Mathematical Physics. 105(10), 1449–1466. mla: Deuchert, Andreas, et al. “Note on a Family of Monotone Quantum Relative Entropies.” Letters in Mathematical Physics, vol. 105, no. 10, Springer, 2015, pp. 1449–66, doi:10.1007/s11005-015-0787-5. short: A. Deuchert, C. Hainzl, R. Seiringer, Letters in Mathematical Physics 105 (2015) 1449–1466. date_created: 2018-12-11T11:53:34Z date_published: 2015-08-05T00:00:00Z date_updated: 2021-01-12T06:52:38Z day: '05' ddc: - '510' department: - _id: RoSe doi: 10.1007/s11005-015-0787-5 file: - access_level: open_access checksum: fd7307282a314cc1fbbaef77b187516b content_type: application/pdf creator: dernst date_created: 2019-01-15T14:42:07Z date_updated: 2020-07-14T12:45:13Z file_id: '5836' file_name: 2015_LettersMathPhys_Deuchert.pdf file_size: 484967 relation: main_file file_date_updated: 2020-07-14T12:45:13Z has_accepted_license: '1' intvolume: ' 105' issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1502.07205 month: '08' oa: 1 oa_version: Preprint page: 1449 - 1466 publication: Letters in Mathematical Physics publication_status: published publisher: Springer publist_id: '5432' quality_controlled: '1' scopus_import: 1 status: public title: Note on a family of monotone quantum relative entropies 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: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 105 year: '2015' ... --- _id: '1703' abstract: - lang: eng text: Vegetation clearing and land-use change have depleted many natural plant communities to the point where restoration is required. A major impediment to the success of rebuilding complex vegetation communities is having regular access to sufficient quantities of high-quality seed. Seed-production areas (SPAs) can help generate this seed, but these must be underpinned by a broad genetic base to maximise the evolutionary potential of restored populations. However, genetic bottlenecks can occur at the collection, establishment and production stages in SPAs, requiring genetic evaluation. This is especially relevant for species that may take many years before a return on SPA investment is realised. Two recently established yellow box (Eucalyptus melliodora A.Cunn. ex Schauer, Myrtaceae) SPAs were evaluated to determine whether genetic bottlenecks had occurred between seed collection and SPA establishment. No evidence was found to suggest that a significant loss of genetic diversity had occurred at this stage, although there was a significant difference in diversity between the two SPAs. Complex population genetic structure was also observed in the seed used to source the SPAs, with up to eight groups identified. Plant survival in the SPAs was influenced by seed collection location but not by SPA location and was not associated with genetic diversity. There were also no associations between genetic diversity and plant growth. These data highlighted the importance of chance events when establishing SPAs and indicated that the two yellow box SPAs are likely to provide genetically diverse seed sources for future restoration projects, especially by pooling seed from both SPAs. author: - first_name: Linda full_name: Broadhurst, Linda last_name: Broadhurst - first_name: Graham full_name: Fifield, Graham last_name: Fifield - first_name: Bindi full_name: Vanzella, Bindi last_name: Vanzella - first_name: Melinda full_name: Pickup, Melinda id: 2C78037E-F248-11E8-B48F-1D18A9856A87 last_name: Pickup orcid: 0000-0001-6118-0541 citation: ama: Broadhurst L, Fifield G, Vanzella B, Pickup M. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 2015;63(5):455-466. doi:10.1071/BT15023 apa: Broadhurst, L., Fifield, G., Vanzella, B., & Pickup, M. (2015). An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. CSIRO. https://doi.org/10.1071/BT15023 chicago: Broadhurst, Linda, Graham Fifield, Bindi Vanzella, and Melinda Pickup. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany. CSIRO, 2015. https://doi.org/10.1071/BT15023. ieee: L. Broadhurst, G. Fifield, B. Vanzella, and M. Pickup, “An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas,” Australian Journal of Botany, vol. 63, no. 5. CSIRO, pp. 455–466, 2015. ista: Broadhurst L, Fifield G, Vanzella B, Pickup M. 2015. An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas. Australian Journal of Botany. 63(5), 455–466. mla: Broadhurst, Linda, et al. “An Evaluation of the Genetic Structure of Seed Sources and the Maintenance of Genetic Diversity during Establishment of Two Yellow Box (Eucalyptus Melliodora) Seed-Production Areas.” Australian Journal of Botany, vol. 63, no. 5, CSIRO, 2015, pp. 455–66, doi:10.1071/BT15023. short: L. Broadhurst, G. Fifield, B. Vanzella, M. Pickup, Australian Journal of Botany 63 (2015) 455–466. date_created: 2018-12-11T11:53:34Z date_published: 2015-05-26T00:00:00Z date_updated: 2021-01-12T06:52:38Z day: '26' department: - _id: NiBa doi: 10.1071/BT15023 intvolume: ' 63' issue: '5' language: - iso: eng month: '05' oa_version: None page: 455 - 466 publication: Australian Journal of Botany publication_status: published publisher: CSIRO publist_id: '5434' quality_controlled: '1' scopus_import: 1 status: public title: An evaluation of the genetic structure of seed sources and the maintenance of genetic diversity during establishment of two yellow box (Eucalyptus melliodora) seed-production areas type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 63 year: '2015' ... --- _id: '1706' abstract: - lang: eng text: We consider a problem of learning kernels for use in SVM classification in the multi-task and lifelong scenarios and provide generalization bounds on the error of a large margin classifier. Our results show that, under mild conditions on the family of kernels used for learning, solving several related tasks simultaneously is beneficial over single task learning. In particular, as the number of observed tasks grows, assuming that in the considered family of kernels there exists one that yields low approximation error on all tasks, the overhead associated with learning such a kernel vanishes and the complexity converges to that of learning when this good kernel is given to the learner. alternative_title: - LNCS author: - first_name: Anastasia full_name: Pentina, Anastasia id: 42E87FC6-F248-11E8-B48F-1D18A9856A87 last_name: Pentina - first_name: Shai full_name: Ben David, Shai last_name: Ben David citation: ama: 'Pentina A, Ben David S. Multi-task and lifelong learning of kernels. In: Vol 9355. Springer; 2015:194-208. doi:10.1007/978-3-319-24486-0_13' apa: 'Pentina, A., & Ben David, S. (2015). Multi-task and lifelong learning of kernels (Vol. 9355, pp. 194–208). Presented at the ALT: Algorithmic Learning Theory, Banff, AB, Canada: Springer. https://doi.org/10.1007/978-3-319-24486-0_13' chicago: Pentina, Anastasia, and Shai Ben David. “Multi-Task and Lifelong Learning of Kernels,” 9355:194–208. Springer, 2015. https://doi.org/10.1007/978-3-319-24486-0_13. ieee: 'A. Pentina and S. Ben David, “Multi-task and lifelong learning of kernels,” presented at the ALT: Algorithmic Learning Theory, Banff, AB, Canada, 2015, vol. 9355, pp. 194–208.' ista: 'Pentina A, Ben David S. 2015. Multi-task and lifelong learning of kernels. ALT: Algorithmic Learning Theory, LNCS, vol. 9355, 194–208.' mla: Pentina, Anastasia, and Shai Ben David. Multi-Task and Lifelong Learning of Kernels. Vol. 9355, Springer, 2015, pp. 194–208, doi:10.1007/978-3-319-24486-0_13. short: A. Pentina, S. Ben David, in:, Springer, 2015, pp. 194–208. conference: end_date: 2015-10-06 location: Banff, AB, Canada name: 'ALT: Algorithmic Learning Theory' start_date: 2015-10-04 date_created: 2018-12-11T11:53:35Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:52:39Z day: '01' department: - _id: ChLa doi: 10.1007/978-3-319-24486-0_13 ec_funded: 1 intvolume: ' 9355' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1602.06531 month: '01' oa: 1 oa_version: Preprint page: 194 - 208 project: - _id: 2532554C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '308036' name: Lifelong Learning of Visual Scene Understanding publication_status: published publisher: Springer publist_id: '5430' quality_controlled: '1' scopus_import: 1 status: public title: Multi-task and lifelong learning of kernels type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9355 year: '2015' ... --- _id: '1712' abstract: - lang: eng text: The majority of immune cells in Drosophila melanogaster are plasmatocytes; they carry out similar functions to vertebrate macrophages, influencing development as well as protecting against infection and cancer. Plasmatocytes, sometimes referred to with the broader term of hemocytes, migrate widely during embryonic development and cycle in the larvae between sessile and circulating positions. Here we discuss the similarities of plasmatocyte developmental migration and its functions to that of vertebrate macrophages, considering the recent controversy regarding the functions of Drosophila PDGF/VEGF related ligands. We also examine recent findings on the significance of adhesion for plasmatocyte migration in the embryo, as well as proliferation, trans-differentiation, and tumor responses in the larva. We spotlight parallels throughout to vertebrate immune responses. author: - first_name: Aparna full_name: Ratheesh, Aparna id: 2F064CFE-F248-11E8-B48F-1D18A9856A87 last_name: Ratheesh - first_name: Vera full_name: Belyaeva, Vera id: 47F080FE-F248-11E8-B48F-1D18A9856A87 last_name: Belyaeva - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 citation: ama: Ratheesh A, Belyaeva V, Siekhaus DE. Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. 2015;36(10):71-79. doi:10.1016/j.ceb.2015.07.003 apa: Ratheesh, A., Belyaeva, V., & Siekhaus, D. E. (2015). Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2015.07.003 chicago: Ratheesh, Aparna, Vera Belyaeva, and Daria E Siekhaus. “Drosophila Immune Cell Migration and Adhesion during Embryonic Development and Larval Immune Responses.” Current Opinion in Cell Biology. Elsevier, 2015. https://doi.org/10.1016/j.ceb.2015.07.003. ieee: A. Ratheesh, V. Belyaeva, and D. E. Siekhaus, “Drosophila immune cell migration and adhesion during embryonic development and larval immune responses,” Current Opinion in Cell Biology, vol. 36, no. 10. Elsevier, pp. 71–79, 2015. ista: Ratheesh A, Belyaeva V, Siekhaus DE. 2015. Drosophila immune cell migration and adhesion during embryonic development and larval immune responses. Current Opinion in Cell Biology. 36(10), 71–79. mla: Ratheesh, Aparna, et al. “Drosophila Immune Cell Migration and Adhesion during Embryonic Development and Larval Immune Responses.” Current Opinion in Cell Biology, vol. 36, no. 10, Elsevier, 2015, pp. 71–79, doi:10.1016/j.ceb.2015.07.003. short: A. Ratheesh, V. Belyaeva, D.E. Siekhaus, Current Opinion in Cell Biology 36 (2015) 71–79. date_created: 2018-12-11T11:53:36Z date_published: 2015-10-01T00:00:00Z date_updated: 2021-01-12T06:52:41Z day: '01' ddc: - '573' department: - _id: DaSi doi: 10.1016/j.ceb.2015.07.003 ec_funded: 1 file: - access_level: open_access checksum: bbb1ee39ca52929aefe4f48752b166ee content_type: application/pdf creator: system date_created: 2018-12-12T10:14:44Z date_updated: 2020-07-14T12:45:13Z file_id: '5098' file_name: IST-2015-346-v1+1_Current_Opinion_Review_Ratheesh_et_al_2015.pdf file_size: 1023680 relation: main_file file_date_updated: 2020-07-14T12:45:13Z has_accepted_license: '1' intvolume: ' 36' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 71 - 79 project: - _id: 2536F660-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '334077' name: Investigating the role of transporters in invasive migration through junctions publication: Current Opinion in Cell Biology publication_status: published publisher: Elsevier publist_id: '5421' pubrep_id: '346' quality_controlled: '1' scopus_import: 1 status: public title: Drosophila immune cell migration and adhesion during embryonic development and larval immune responses tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 36 year: '2015' ... --- _id: '1710' abstract: - lang: eng text: 'We consider the hollow on the half-plane {(x, y) : y ≤ 0} ⊂ ℝ2 defined by a function u : (-1, 1) → ℝ, u(x) < 0, and a vertical flow of point particles incident on the hollow. It is assumed that u satisfies the so-called single impact condition (SIC): each incident particle is elastically reflected by graph(u) and goes away without hitting the graph of u anymore. We solve the problem: find the function u minimizing the force of resistance created by the flow. We show that the graph of the minimizer is formed by two arcs of parabolas symmetric to each other with respect to the y-axis. Assuming that the resistance of u ≡ 0 equals 1, we show that the minimal resistance equals π/2 - 2arctan(1/2) ≈ 0.6435. This result completes the previously obtained result [SIAM J. Math. Anal., 46 (2014), pp. 2730-2742] stating in particular that the minimal resistance of a hollow in higher dimensions equals 0.5. We additionally consider a similar problem of minimal resistance, where the hollow in the half-space {(x1,...,xd,y) : y ≤ 0} ⊂ ℝd+1 is defined by a radial function U satisfying the SIC, U(x) = u(|x|), with x = (x1,...,xd), u(ξ) < 0 for 0 ≤ ξ < 1, and u(ξ) = 0 for ξ ≥ 1, and the flow is parallel to the y-axis. The minimal resistance is greater than 0.5 (and coincides with 0.6435 when d = 1) and converges to 0.5 as d → ∞.' author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Alexander full_name: Plakhov, Alexander last_name: Plakhov citation: ama: Akopyan A, Plakhov A. Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. 2015;47(4):2754-2769. doi:10.1137/140993843 apa: Akopyan, A., & Plakhov, A. (2015). Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. SIAM. https://doi.org/10.1137/140993843 chicago: Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” Society for Industrial and Applied Mathematics. SIAM, 2015. https://doi.org/10.1137/140993843. ieee: A. Akopyan and A. Plakhov, “Minimal resistance of curves under the single impact assumption,” Society for Industrial and Applied Mathematics, vol. 47, no. 4. SIAM, pp. 2754–2769, 2015. ista: Akopyan A, Plakhov A. 2015. Minimal resistance of curves under the single impact assumption. Society for Industrial and Applied Mathematics. 47(4), 2754–2769. mla: Akopyan, Arseniy, and Alexander Plakhov. “Minimal Resistance of Curves under the Single Impact Assumption.” Society for Industrial and Applied Mathematics, vol. 47, no. 4, SIAM, 2015, pp. 2754–69, doi:10.1137/140993843. short: A. Akopyan, A. Plakhov, Society for Industrial and Applied Mathematics 47 (2015) 2754–2769. date_created: 2018-12-11T11:53:36Z date_published: 2015-07-14T00:00:00Z date_updated: 2021-01-12T06:52:41Z day: '14' department: - _id: HeEd doi: 10.1137/140993843 ec_funded: 1 intvolume: ' 47' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1410.3736 month: '07' oa: 1 oa_version: Preprint page: 2754 - 2769 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Society for Industrial and Applied Mathematics publication_status: published publisher: SIAM publist_id: '5423' quality_controlled: '1' scopus_import: 1 status: public title: Minimal resistance of curves under the single impact assumption type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 47 year: '2015' ... --- _id: '1730' abstract: - lang: eng text: How much cutting is needed to simplify the topology of a surface? We provide bounds for several instances of this question, for the minimum length of topologically non-trivial closed curves, pants decompositions, and cut graphs with a given combinatorial map in triangulated combinatorial surfaces (or their dual cross-metric counterpart). Our work builds upon Riemannian systolic inequalities, which bound the minimum length of non-trivial closed curves in terms of the genus and the area of the surface. We first describe a systematic way to translate Riemannian systolic inequalities to a discrete setting, and vice-versa. This implies a conjecture by Przytycka and Przytycki (Graph structure theory. Contemporary Mathematics, vol. 147, 1993), a number of new systolic inequalities in the discrete setting, and the fact that a theorem of Hutchinson on the edge-width of triangulated surfaces and Gromov’s systolic inequality for surfaces are essentially equivalent. We also discuss how these proofs generalize to higher dimensions. Then we focus on topological decompositions of surfaces. Relying on ideas of Buser, we prove the existence of pants decompositions of length O(g^(3/2)n^(1/2)) for any triangulated combinatorial surface of genus g with n triangles, and describe an O(gn)-time algorithm to compute such a decomposition. Finally, we consider the problem of embedding a cut graph (or more generally a cellular graph) with a given combinatorial map on a given surface. Using random triangulations, we prove (essentially) that, for any choice of a combinatorial map, there are some surfaces on which any cellular embedding with that combinatorial map has length superlinear in the number of triangles of the triangulated combinatorial surface. There is also a similar result for graphs embedded on polyhedral triangulations. author: - first_name: Éric full_name: Colin De Verdière, Éric last_name: Colin De Verdière - first_name: Alfredo full_name: Hubard, Alfredo last_name: Hubard - first_name: Arnaud N full_name: De Mesmay, Arnaud N id: 3DB2F25C-F248-11E8-B48F-1D18A9856A87 last_name: De Mesmay citation: ama: Colin De Verdière É, Hubard A, de Mesmay AN. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 2015;53(3):587-620. doi:10.1007/s00454-015-9679-9 apa: Colin De Verdière, É., Hubard, A., & de Mesmay, A. N. (2015). Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. Springer. https://doi.org/10.1007/s00454-015-9679-9 chicago: Colin De Verdière, Éric, Alfredo Hubard, and Arnaud N de Mesmay. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry. Springer, 2015. https://doi.org/10.1007/s00454-015-9679-9. ieee: É. Colin De Verdière, A. Hubard, and A. N. de Mesmay, “Discrete systolic inequalities and decompositions of triangulated surfaces,” Discrete & Computational Geometry, vol. 53, no. 3. Springer, pp. 587–620, 2015. ista: Colin De Verdière É, Hubard A, de Mesmay AN. 2015. Discrete systolic inequalities and decompositions of triangulated surfaces. Discrete & Computational Geometry. 53(3), 587–620. mla: Colin De Verdière, Éric, et al. “Discrete Systolic Inequalities and Decompositions of Triangulated Surfaces.” Discrete & Computational Geometry, vol. 53, no. 3, Springer, 2015, pp. 587–620, doi:10.1007/s00454-015-9679-9. short: É. Colin De Verdière, A. Hubard, A.N. de Mesmay, Discrete & Computational Geometry 53 (2015) 587–620. date_created: 2018-12-11T11:53:42Z date_published: 2015-04-02T00:00:00Z date_updated: 2021-01-12T06:52:49Z day: '02' department: - _id: UlWa doi: 10.1007/s00454-015-9679-9 intvolume: ' 53' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1408.4036 month: '04' oa: 1 oa_version: Preprint page: 587 - 620 publication: Discrete & Computational Geometry publication_status: published publisher: Springer publist_id: '5397' quality_controlled: '1' scopus_import: 1 status: public title: Discrete systolic inequalities and decompositions of triangulated surfaces type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 53 year: '2015' ... --- _id: '1735' abstract: - lang: eng text: This work presents a method for efficiently simplifying the pressure projection step in a liquid simulation. We first devise a straightforward dimension reduction technique that dramatically reduces the cost of solving the pressure projection. Next, we introduce a novel change of basis that satisfies free-surface boundary conditions exactly, regardless of the accuracy of the pressure solve. When combined, these ideas greatly reduce the computational complexity of the pressure solve without compromising free surface boundary conditions at the highest level of detail. Our techniques are easy to parallelize, and they effectively eliminate the computational bottleneck for large liquid simulations. acknowledgement: The first author was supported by a JSPS Postdoctoral Fellowship for Research Abroad author: - first_name: Ryoichi full_name: Ando, Ryoichi last_name: Ando - first_name: Nils full_name: Thürey, Nils last_name: Thürey - first_name: Christopher J full_name: Wojtan, Christopher J id: 3C61F1D2-F248-11E8-B48F-1D18A9856A87 last_name: Wojtan orcid: 0000-0001-6646-5546 citation: ama: Ando R, Thürey N, Wojtan C. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 2015;34(2):473-480. doi:10.1111/cgf.12576 apa: Ando, R., Thürey, N., & Wojtan, C. (2015). A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. Wiley. https://doi.org/10.1111/cgf.12576 chicago: Ando, Ryoichi, Nils Thürey, and Chris Wojtan. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum. Wiley, 2015. https://doi.org/10.1111/cgf.12576. ieee: R. Ando, N. Thürey, and C. Wojtan, “A dimension-reduced pressure solver for liquid simulations,” Computer Graphics Forum, vol. 34, no. 2. Wiley, pp. 473–480, 2015. ista: Ando R, Thürey N, Wojtan C. 2015. A dimension-reduced pressure solver for liquid simulations. Computer Graphics Forum. 34(2), 473–480. mla: Ando, Ryoichi, et al. “A Dimension-Reduced Pressure Solver for Liquid Simulations.” Computer Graphics Forum, vol. 34, no. 2, Wiley, 2015, pp. 473–80, doi:10.1111/cgf.12576. short: R. Ando, N. Thürey, C. Wojtan, Computer Graphics Forum 34 (2015) 473–480. date_created: 2018-12-11T11:53:44Z date_published: 2015-05-01T00:00:00Z date_updated: 2023-02-23T10:12:11Z day: '01' ddc: - '000' department: - _id: ChWo doi: 10.1111/cgf.12576 file: - access_level: open_access checksum: 590752bf977855b337a80f78a9bc2404 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:30Z date_updated: 2020-07-14T12:45:15Z file_id: '5218' file_name: IST-2016-607-v1+1_coarsegrid.pdf file_size: 6312352 relation: main_file file_date_updated: 2020-07-14T12:45:15Z has_accepted_license: '1' intvolume: ' 34' issue: '2' language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 473 - 480 publication: Computer Graphics Forum publication_status: published publisher: Wiley publist_id: '5389' pubrep_id: '607' quality_controlled: '1' scopus_import: 1 status: public title: A dimension-reduced pressure solver for liquid simulations type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1734' abstract: - lang: eng text: Facial appearance capture is now firmly established within academic research and used extensively across various application domains, perhaps most prominently in the entertainment industry through the design of virtual characters in video games and films. While significant progress has occurred over the last two decades, no single survey currently exists that discusses the similarities, differences, and practical considerations of the available appearance capture techniques as applied to human faces. A central difficulty of facial appearance capture is the way light interacts with skin-which has a complex multi-layered structure-and the interactions that occur below the skin surface can, by definition, only be observed indirectly. In this report, we distinguish between two broad strategies for dealing with this complexity. "Image-based methods" try to exhaustively capture the exact face appearance under different lighting and viewing conditions, and then render the face through weighted image combinations. "Parametric methods" instead fit the captured reflectance data to some parametric appearance model used during rendering, allowing for a more lightweight and flexible representation but at the cost of potentially increased rendering complexity or inexact reproduction. The goal of this report is to provide an overview that can guide practitioners and researchers in assessing the tradeoffs between current approaches and identifying directions for future advances in facial appearance capture. author: - first_name: Oliver full_name: Klehm, Oliver last_name: Klehm - first_name: Fabrice full_name: Rousselle, Fabrice last_name: Rousselle - first_name: Marios full_name: Papas, Marios last_name: Papas - first_name: Derek full_name: Bradley, Derek last_name: Bradley - first_name: Christophe full_name: Hery, Christophe last_name: Hery - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Wojciech full_name: Jarosz, Wojciech last_name: Jarosz - first_name: Thabo full_name: Beeler, Thabo last_name: Beeler citation: ama: Klehm O, Rousselle F, Papas M, et al. Recent advances in facial appearance capture. Computer Graphics Forum. 2015;34(2):709-733. doi:10.1111/cgf.12594 apa: Klehm, O., Rousselle, F., Papas, M., Bradley, D., Hery, C., Bickel, B., … Beeler, T. (2015). Recent advances in facial appearance capture. Computer Graphics Forum. Wiley-Blackwell. https://doi.org/10.1111/cgf.12594 chicago: Klehm, Oliver, Fabrice Rousselle, Marios Papas, Derek Bradley, Christophe Hery, Bernd Bickel, Wojciech Jarosz, and Thabo Beeler. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum. Wiley-Blackwell, 2015. https://doi.org/10.1111/cgf.12594. ieee: O. Klehm et al., “Recent advances in facial appearance capture,” Computer Graphics Forum, vol. 34, no. 2. Wiley-Blackwell, pp. 709–733, 2015. ista: Klehm O, Rousselle F, Papas M, Bradley D, Hery C, Bickel B, Jarosz W, Beeler T. 2015. Recent advances in facial appearance capture. Computer Graphics Forum. 34(2), 709–733. mla: Klehm, Oliver, et al. “Recent Advances in Facial Appearance Capture.” Computer Graphics Forum, vol. 34, no. 2, Wiley-Blackwell, 2015, pp. 709–33, doi:10.1111/cgf.12594. short: O. Klehm, F. Rousselle, M. Papas, D. Bradley, C. Hery, B. Bickel, W. Jarosz, T. Beeler, Computer Graphics Forum 34 (2015) 709–733. date_created: 2018-12-11T11:53:43Z date_published: 2015-05-01T00:00:00Z date_updated: 2021-01-12T06:52:52Z day: '01' department: - _id: BeBi doi: 10.1111/cgf.12594 intvolume: ' 34' issue: '2' language: - iso: eng main_file_link: - url: https://graphics.ethz.ch/~mpapas/publications/fac_star.pdf month: '05' oa_version: None page: 709 - 733 publication: Computer Graphics Forum publication_status: published publisher: Wiley-Blackwell publist_id: '5391' quality_controlled: '1' scopus_import: 1 status: public title: Recent advances in facial appearance capture type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 34 year: '2015' ... --- _id: '1789' abstract: - lang: eng text: Intellectual disability (ID) has an estimated prevalence of 2-3%. Due to its extreme heterogeneity, the genetic basis of ID remains elusive in many cases. Recently, whole exome sequencing (WES) studies revealed that a large proportion of sporadic cases are caused by de novo gene variants. To identify further genes involved in ID, we performed WES in 250 patients with unexplained ID and their unaffected parents and included exomes of 51 previously sequenced child-parents trios in the analysis. Exome analysis revealed de novo intragenic variants in SET domain-containing 5 (SETD5) in two patients. One patient carried a nonsense variant, and the other an 81 bp deletion located across a splice-donor site. Chromosomal microarray diagnostics further identified four de novo non-recurrent microdeletions encompassing SETD5. CRISPR/Cas9 mutation modelling of the two intragenic variants demonstrated nonsense-mediated decay of the resulting transcripts, pointing to a loss-of-function (LoF) and haploinsufficiency as the common disease-causing mechanism of intragenic SETD5 sequence variants and SETD5-containing microdeletions. In silico domain prediction of SETD5, a predicted SET domain-containing histone methyltransferase (HMT), substantiated the presence of a SET domain and identified a novel putative PHD domain, strengthening a functional link to well-known histone-modifying ID genes. All six patients presented with ID and certain facial dysmorphisms, suggesting that SETD5 sequence variants contribute substantially to the microdeletion 3p25.3 phenotype. The present report of two SETD5 LoF variants in 301 patients demonstrates a prevalence of 0.7% and thus SETD5 variants as a relatively frequent cause of ID. author: - first_name: Alma full_name: Kuechler, Alma last_name: Kuechler - first_name: Alexander full_name: Zink, Alexander last_name: Zink - first_name: Thomas full_name: Wieland, Thomas last_name: Wieland - first_name: Hermann full_name: Lüdecke, Hermann last_name: Lüdecke - first_name: Kirsten full_name: Cremer, Kirsten last_name: Cremer - first_name: Leonardo full_name: Salviati, Leonardo last_name: Salviati - first_name: Pamela full_name: Magini, Pamela last_name: Magini - first_name: Kimia full_name: Najafi, Kimia last_name: Najafi - first_name: Christiane full_name: Zweier, Christiane last_name: Zweier - first_name: Johanna full_name: Czeschik, Johanna last_name: Czeschik - first_name: Stefan full_name: Aretz, Stefan last_name: Aretz - first_name: Sabine full_name: Endele, Sabine last_name: Endele - first_name: Federica full_name: Tamburrino, Federica last_name: Tamburrino - first_name: Claudia full_name: Pinato, Claudia last_name: Pinato - first_name: Maurizio full_name: Clementi, Maurizio last_name: Clementi - first_name: Jasmin full_name: Gundlach, Jasmin last_name: Gundlach - first_name: Carina full_name: Maylahn, Carina last_name: Maylahn - first_name: Laura full_name: Mazzanti, Laura last_name: Mazzanti - first_name: Eva full_name: Wohlleber, Eva last_name: Wohlleber - first_name: Thomas full_name: Schwarzmayr, Thomas last_name: Schwarzmayr - first_name: Roxana full_name: Kariminejad, Roxana last_name: Kariminejad - first_name: Avner full_name: Schlessinger, Avner last_name: Schlessinger - first_name: Dagmar full_name: Wieczorek, Dagmar last_name: Wieczorek - first_name: Tim full_name: Strom, Tim last_name: Strom - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Hartmut full_name: Engels, Hartmut last_name: Engels citation: ama: Kuechler A, Zink A, Wieland T, et al. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 2015;23(6):753-760. doi:10.1038/ejhg.2014.165 apa: Kuechler, A., Zink, A., Wieland, T., Lüdecke, H., Cremer, K., Salviati, L., … Engels, H. (2015). Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. Nature Publishing Group. https://doi.org/10.1038/ejhg.2014.165 chicago: Kuechler, Alma, Alexander Zink, Thomas Wieland, Hermann Lüdecke, Kirsten Cremer, Leonardo Salviati, Pamela Magini, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics. Nature Publishing Group, 2015. https://doi.org/10.1038/ejhg.2014.165. ieee: A. Kuechler et al., “Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome,” European Journal of Human Genetics, vol. 23, no. 6. Nature Publishing Group, pp. 753–760, 2015. ista: Kuechler A, Zink A, Wieland T, Lüdecke H, Cremer K, Salviati L, Magini P, Najafi K, Zweier C, Czeschik J, Aretz S, Endele S, Tamburrino F, Pinato C, Clementi M, Gundlach J, Maylahn C, Mazzanti L, Wohlleber E, Schwarzmayr T, Kariminejad R, Schlessinger A, Wieczorek D, Strom T, Novarino G, Engels H. 2015. Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome. European Journal of Human Genetics. 23(6), 753–760. mla: Kuechler, Alma, et al. “Loss-of-Function Variants of SETD5 Cause Intellectual Disability and the Core Phenotype of Microdeletion 3p25.3 Syndrome.” European Journal of Human Genetics, vol. 23, no. 6, Nature Publishing Group, 2015, pp. 753–60, doi:10.1038/ejhg.2014.165. short: A. Kuechler, A. Zink, T. Wieland, H. Lüdecke, K. Cremer, L. Salviati, P. Magini, K. Najafi, C. Zweier, J. Czeschik, S. Aretz, S. Endele, F. Tamburrino, C. Pinato, M. Clementi, J. Gundlach, C. Maylahn, L. Mazzanti, E. Wohlleber, T. Schwarzmayr, R. Kariminejad, A. Schlessinger, D. Wieczorek, T. Strom, G. Novarino, H. Engels, European Journal of Human Genetics 23 (2015) 753–760. date_created: 2018-12-11T11:54:01Z date_published: 2015-06-15T00:00:00Z date_updated: 2021-01-12T06:53:12Z day: '15' department: - _id: GaNo doi: 10.1038/ejhg.2014.165 external_id: pmid: - '25138099' intvolume: ' 23' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4795044/ month: '06' oa: 1 oa_version: Submitted Version page: 753 - 760 pmid: 1 publication: European Journal of Human Genetics publication_status: published publisher: Nature Publishing Group publist_id: '5324' quality_controlled: '1' status: public title: Loss-of-function variants of SETD5 cause intellectual disability and the core phenotype of microdeletion 3p25.3 syndrome type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 23 year: '2015' ... --- _id: '1804' abstract: - lang: eng text: It is known that in classical fluids turbulence typically occurs at high Reynolds numbers. But can turbulence occur at low Reynolds numbers? Here we investigate the transition to turbulence in the classic Taylor-Couette system in which the rotating fluids are manufactured ferrofluids with magnetized nanoparticles embedded in liquid carriers. We find that, in the presence of a magnetic field transverse to the symmetry axis of the system, turbulence can occur at Reynolds numbers that are at least one order of magnitude smaller than those in conventional fluids. This is established by extensive computational ferrohydrodynamics through a detailed investigation of transitions in the flow structure, and characterization of behaviors of physical quantities such as the energy, the wave number, and the angular momentum through the bifurcations. A finding is that, as the magnetic field is increased, onset of turbulence can be determined accurately and reliably. Our results imply that experimental investigation of turbulence may be feasible by using ferrofluids. Our study of transition to and evolution of turbulence in the Taylor-Couette ferrofluidic flow system provides insights into the challenging problem of turbulence control. article_number: '10781' author: - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 - first_name: Younghae full_name: Do, Younghae last_name: Do - first_name: Ying full_name: Lai, Ying last_name: Lai citation: ama: Altmeyer S, Do Y, Lai Y. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 2015;5. doi:10.1038/srep10781 apa: Altmeyer, S., Do, Y., & Lai, Y. (2015). Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/srep10781 chicago: Altmeyer, Sebastian, Younghae Do, and Ying Lai. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” Scientific Reports. Nature Publishing Group, 2015. https://doi.org/10.1038/srep10781. ieee: S. Altmeyer, Y. Do, and Y. Lai, “Transition to turbulence in Taylor-Couette ferrofluidic flow,” Scientific Reports, vol. 5. Nature Publishing Group, 2015. ista: Altmeyer S, Do Y, Lai Y. 2015. Transition to turbulence in Taylor-Couette ferrofluidic flow. Scientific Reports. 5, 10781. mla: Altmeyer, Sebastian, et al. “Transition to Turbulence in Taylor-Couette Ferrofluidic Flow.” Scientific Reports, vol. 5, 10781, Nature Publishing Group, 2015, doi:10.1038/srep10781. short: S. Altmeyer, Y. Do, Y. Lai, Scientific Reports 5 (2015). date_created: 2018-12-11T11:54:06Z date_published: 2015-06-12T00:00:00Z date_updated: 2021-01-12T06:53:18Z day: '12' ddc: - '530' department: - _id: BjHo doi: 10.1038/srep10781 file: - access_level: open_access checksum: 7716f582f8c9d82d8f2bf80bf896b440 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:26Z date_updated: 2020-07-14T12:45:16Z file_id: '5280' file_name: IST-2016-450-v1+1_srep10781.pdf file_size: 2449723 relation: main_file file_date_updated: 2020-07-14T12:45:16Z has_accepted_license: '1' intvolume: ' 5' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '5306' pubrep_id: '450' quality_controlled: '1' scopus_import: 1 status: public title: Transition to turbulence in Taylor-Couette ferrofluidic flow 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: 5 year: '2015' ...