--- _id: '3361' abstract: - lang: eng text: In this paper, we investigate the computational complexity of quantitative information flow (QIF) problems. Information-theoretic quantitative relaxations of noninterference (based on Shannon entropy)have been introduced to enable more fine-grained reasoning about programs in situations where limited information flow is acceptable. The QIF bounding problem asks whether the information flow in a given program is bounded by a constant $d$. Our first result is that the QIF bounding problem is PSPACE-complete. The QIF memoryless synthesis problem asks whether it is possible to resolve nondeterministic choices in a given partial program in such a way that in the resulting deterministic program, the quantitative information flow is bounded by a given constant $d$. Our second result is that the QIF memoryless synthesis problem is also EXPTIME-complete. The QIF memoryless synthesis problem generalizes to QIF general synthesis problem which does not impose the memoryless requirement (that is, by allowing the synthesized program to have more variables then the original partial program). Our third result is that the QIF general synthesis problem is EXPTIME-hard. author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Cerny P, Chatterjee K, Henzinger TA. The complexity of quantitative information flow problems. In: IEEE; 2011:205-217. doi:10.1109/CSF.2011.21' apa: 'Cerny, P., Chatterjee, K., & Henzinger, T. A. (2011). The complexity of quantitative information flow problems (pp. 205–217). Presented at the CSF: Computer Security Foundations, Cernay-la-Ville, France: IEEE. https://doi.org/10.1109/CSF.2011.21' chicago: Cerny, Pavol, Krishnendu Chatterjee, and Thomas A Henzinger. “The Complexity of Quantitative Information Flow Problems,” 205–17. IEEE, 2011. https://doi.org/10.1109/CSF.2011.21. ieee: 'P. Cerny, K. Chatterjee, and T. A. Henzinger, “The complexity of quantitative information flow problems,” presented at the CSF: Computer Security Foundations, Cernay-la-Ville, France, 2011, pp. 205–217.' ista: 'Cerny P, Chatterjee K, Henzinger TA. 2011. The complexity of quantitative information flow problems. CSF: Computer Security Foundations, 205–217.' mla: Cerny, Pavol, et al. The Complexity of Quantitative Information Flow Problems. IEEE, 2011, pp. 205–17, doi:10.1109/CSF.2011.21. short: P. Cerny, K. Chatterjee, T.A. Henzinger, in:, IEEE, 2011, pp. 205–217. conference: end_date: 2011-06-29 location: Cernay-la-Ville, France name: 'CSF: Computer Security Foundations' start_date: 2011-06-27 date_created: 2018-12-11T12:02:54Z date_published: 2011-06-27T00:00:00Z date_updated: 2021-01-12T07:42:56Z day: '27' ddc: - '000' - '005' department: - _id: ToHe - _id: KrCh doi: 10.1109/CSF.2011.21 ec_funded: 1 file: - access_level: open_access checksum: 1a25be0c62459fc7640db88af08ff63a content_type: application/pdf creator: system date_created: 2018-12-12T10:10:07Z date_updated: 2020-07-14T12:46:10Z file_id: '4792' file_name: IST-2012-81-v1+1_The_complexity_of_quantitative_information_flow_problems.pdf file_size: 299069 relation: main_file file_date_updated: 2020-07-14T12:46:10Z has_accepted_license: '1' language: - iso: eng month: '06' oa: 1 oa_version: Submitted Version page: 205 - 217 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2587B514-B435-11E9-9278-68D0E5697425 name: Microsoft Research Faculty Fellowship publication_status: published publisher: IEEE publist_id: '3254' pubrep_id: '81' quality_controlled: '1' scopus_import: 1 status: public title: The complexity of quantitative information flow problems type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3358' abstract: - lang: eng text: The static scheduling problem often arises as a fundamental problem in real-time systems and grid computing. We consider the problem of statically scheduling a large job expressed as a task graph on a large number of computing nodes, such as a data center. This paper solves the large-scale static scheduling problem using abstraction refinement, a technique commonly used in formal verification to efficiently solve computationally hard problems. A scheduler based on abstraction refinement first attempts to solve the scheduling problem with abstract representations of the job and the computing resources. As abstract representations are generally small, the scheduling can be done reasonably fast. If the obtained schedule does not meet specified quality conditions (like data center utilization or schedule makespan) then the scheduler refines the job and data center abstractions and, again solves the scheduling problem. We develop different schedulers based on abstraction refinement. We implemented these schedulers and used them to schedule task graphs from various computing domains on simulated data centers with realistic topologies. We compared the speed of scheduling and the quality of the produced schedules with our abstraction refinement schedulers against a baseline scheduler that does not use any abstraction. We conclude that abstraction refinement techniques give a significant speed-up compared to traditional static scheduling heuristics, at a reasonable cost in the quality of the produced schedules. We further used our static schedulers in an actual system that we deployed on Amazon EC2 and compared it against the Hadoop dynamic scheduler for large MapReduce jobs. Our experiments indicate that there is great potential for static scheduling techniques. article_processing_charge: No author: - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Vasu full_name: Singh, Vasu id: 4DAE2708-F248-11E8-B48F-1D18A9856A87 last_name: Singh - first_name: Thomas full_name: Wies, Thomas id: 447BFB88-F248-11E8-B48F-1D18A9856A87 last_name: Wies - first_name: Damien full_name: Zufferey, Damien id: 4397AC76-F248-11E8-B48F-1D18A9856A87 last_name: Zufferey orcid: 0000-0002-3197-8736 citation: ama: 'Henzinger TA, Singh V, Wies T, Zufferey D. Scheduling large jobs by abstraction refinement. In: ACM; 2011:329-342. doi:10.1145/1966445.1966476' apa: 'Henzinger, T. A., Singh, V., Wies, T., & Zufferey, D. (2011). Scheduling large jobs by abstraction refinement (pp. 329–342). Presented at the EuroSys, Salzburg, Austria: ACM. https://doi.org/10.1145/1966445.1966476' chicago: Henzinger, Thomas A, Vasu Singh, Thomas Wies, and Damien Zufferey. “Scheduling Large Jobs by Abstraction Refinement,” 329–42. ACM, 2011. https://doi.org/10.1145/1966445.1966476. ieee: T. A. Henzinger, V. Singh, T. Wies, and D. Zufferey, “Scheduling large jobs by abstraction refinement,” presented at the EuroSys, Salzburg, Austria, 2011, pp. 329–342. ista: Henzinger TA, Singh V, Wies T, Zufferey D. 2011. Scheduling large jobs by abstraction refinement. EuroSys, 329–342. mla: Henzinger, Thomas A., et al. Scheduling Large Jobs by Abstraction Refinement. ACM, 2011, pp. 329–42, doi:10.1145/1966445.1966476. short: T.A. Henzinger, V. Singh, T. Wies, D. Zufferey, in:, ACM, 2011, pp. 329–342. conference: end_date: 2011-04-13 location: Salzburg, Austria name: EuroSys start_date: 2011-04-10 date_created: 2018-12-11T12:02:53Z date_published: 2011-04-10T00:00:00Z date_updated: 2021-01-12T07:42:55Z day: '10' department: - _id: ToHe doi: 10.1145/1966445.1966476 language: - iso: eng main_file_link: - open_access: '1' url: http://cs.nyu.edu/wies/publ/scheduling_large_jobs_by_abstraction_refinement.pdf month: '04' oa: 1 oa_version: Published Version page: 329 - 342 publication_status: published publisher: ACM publist_id: '3257' quality_controlled: '1' scopus_import: 1 status: public title: Scheduling large jobs by abstraction refinement type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3359' abstract: - lang: eng text: "Motivated by improvements in constraint-solving technology and by the increase of routinely available computational power, partial-program synthesis is emerging as an effective approach for increasing programmer productivity. The goal of the approach is to allow the programmer to specify a part of her intent imperatively (that is, give a partial program) and a part of her intent declaratively, by specifying which conditions need to be achieved or maintained. The task of the synthesizer is to construct a program that satisfies the specification. As an example, consider a partial program where threads access shared data without using any synchronization mechanism, and a declarative specification that excludes data races and deadlocks. The task of the synthesizer is then to place locks into the program code in order for the program to meet the specification.\r\n\r\nIn this paper, we argue that quantitative objectives are needed in partial-program synthesis in order to produce higher-quality programs, while enabling simpler specifications. Returning to the example, the synthesizer could construct a naive solution that uses one global lock for shared data. This can be prevented either by constraining the solution space further (which is error-prone and partly defeats the point of synthesis), or by optimizing a quantitative objective that models performance. Other quantitative notions useful in synthesis include fault tolerance, robustness, resource (memory, power) consumption, and information flow." acknowledgement: This work was partially supported by the ERC Advanced Grant QUAREM, the FWF NFN Grant S11402-N23 (RiSE), and the EU NOE Grant ArtistDesign. author: - first_name: Pavol full_name: Cerny, Pavol id: 4DCBEFFE-F248-11E8-B48F-1D18A9856A87 last_name: Cerny - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 citation: ama: 'Cerny P, Henzinger TA. From boolean to quantitative synthesis. In: ACM; 2011:149-154. doi:10.1145/2038642.2038666' apa: 'Cerny, P., & Henzinger, T. A. (2011). From boolean to quantitative synthesis (pp. 149–154). Presented at the EMSOFT: Embedded Software , Taipei; Taiwan: ACM. https://doi.org/10.1145/2038642.2038666' chicago: Cerny, Pavol, and Thomas A Henzinger. “From Boolean to Quantitative Synthesis,” 149–54. ACM, 2011. https://doi.org/10.1145/2038642.2038666. ieee: 'P. Cerny and T. A. Henzinger, “From boolean to quantitative synthesis,” presented at the EMSOFT: Embedded Software , Taipei; Taiwan, 2011, pp. 149–154.' ista: 'Cerny P, Henzinger TA. 2011. From boolean to quantitative synthesis. EMSOFT: Embedded Software , 149–154.' mla: Cerny, Pavol, and Thomas A. Henzinger. From Boolean to Quantitative Synthesis. ACM, 2011, pp. 149–54, doi:10.1145/2038642.2038666. short: P. Cerny, T.A. Henzinger, in:, ACM, 2011, pp. 149–154. conference: end_date: 2011-10-14 location: Taipei; Taiwan name: 'EMSOFT: Embedded Software ' start_date: 2011-10-09 date_created: 2018-12-11T12:02:53Z date_published: 2011-10-09T00:00:00Z date_updated: 2021-01-12T07:42:55Z day: '09' department: - _id: ToHe doi: 10.1145/2038642.2038666 ec_funded: 1 language: - iso: eng month: '10' oa_version: None page: 149 - 154 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F1337C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '214373' name: Design for Embedded Systems publication_status: published publisher: ACM publist_id: '3256' quality_controlled: '1' status: public title: From boolean to quantitative synthesis type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2011' ... --- _id: '3357' abstract: - lang: eng text: We consider two-player graph games whose objectives are request-response condition, i.e conjunctions of conditions of the form "if a state with property Rq is visited, then later a state with property Rp is visited". The winner of such games can be decided in EXPTIME and the problem is known to be NP-hard. In this paper, we close this gap by showing that this problem is, in fact, EXPTIME-complete. We show that the problem becomes PSPACE-complete if we only consider games played on DAGs, and NP-complete or PTIME-complete if there is only one player (depending on whether he wants to enforce or spoil the request-response condition). We also present near-optimal bounds on the memory needed to design winning strategies for each player, in each case. alternative_title: - LNCS author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - 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: Florian full_name: Horn, Florian id: 37327ACE-F248-11E8-B48F-1D18A9856A87 last_name: Horn citation: ama: 'Chatterjee K, Henzinger TA, Horn F. The complexity of request-response games. In: Dediu A-H, Inenaga S, Martín-Vide C, eds. Vol 6638. Springer; 2011:227-237. doi:10.1007/978-3-642-21254-3_17' apa: 'Chatterjee, K., Henzinger, T. A., & Horn, F. (2011). The complexity of request-response games. In A.-H. Dediu, S. Inenaga, & C. Martín-Vide (Eds.) (Vol. 6638, pp. 227–237). Presented at the LATA: Language and Automata Theory and Applications, Tarragona, Spain: Springer. https://doi.org/10.1007/978-3-642-21254-3_17' chicago: Chatterjee, Krishnendu, Thomas A Henzinger, and Florian Horn. “The Complexity of Request-Response Games.” edited by Adrian-Horia Dediu, Shunsuke Inenaga, and Carlos Martín-Vide, 6638:227–37. Springer, 2011. https://doi.org/10.1007/978-3-642-21254-3_17. ieee: 'K. Chatterjee, T. A. Henzinger, and F. Horn, “The complexity of request-response games,” presented at the LATA: Language and Automata Theory and Applications, Tarragona, Spain, 2011, vol. 6638, pp. 227–237.' ista: 'Chatterjee K, Henzinger TA, Horn F. 2011. The complexity of request-response games. LATA: Language and Automata Theory and Applications, LNCS, vol. 6638, 227–237.' mla: Chatterjee, Krishnendu, et al. The Complexity of Request-Response Games. Edited by Adrian-Horia Dediu et al., vol. 6638, Springer, 2011, pp. 227–37, doi:10.1007/978-3-642-21254-3_17. short: K. Chatterjee, T.A. Henzinger, F. Horn, in:, A.-H. Dediu, S. Inenaga, C. Martín-Vide (Eds.), Springer, 2011, pp. 227–237. conference: end_date: 2011-05-31 location: Tarragona, Spain name: 'LATA: Language and Automata Theory and Applications' start_date: 2011-05-26 date_created: 2018-12-11T12:02:52Z date_published: 2011-01-01T00:00:00Z date_updated: 2021-01-12T07:42:54Z day: '01' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-642-21254-3_17 editor: - first_name: Adrian-Horia full_name: Dediu, Adrian-Horia last_name: Dediu - first_name: Shunsuke full_name: Inenaga, Shunsuke last_name: Inenaga - first_name: Carlos full_name: Martín-Vide, Carlos last_name: Martín-Vide intvolume: ' 6638' language: - iso: eng month: '01' oa_version: None page: 227 - 237 publication_status: published publisher: Springer publist_id: '3258' quality_controlled: '1' scopus_import: 1 status: public title: The complexity of request-response games type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 6638 year: '2011' ... --- _id: '336' abstract: - lang: eng text: 'The growth kinetics of colloidal Bi2S3 nanorods was investigated. After nucleation, the length distribution of the growing Bi 2S3 nanorods narrows with the reaction time until a bimodal length distribution appears. From this critical reaction time on, the smallest nanorods of the ensemble dissolve, feeding with monomer the growth of the largest ones. A comprehensive characterization of the size-distribution evolution of Bi2S3 nanorods is used here to illustrate the dependences of the anisotropic growth rates of cylindrical nanoparticles on the nanoparticle dimensions and the monomer concentration in solution. With this goal in mind, a diffusion-reaction model is presented to explain the origin of the experimentally obtained length distribution focusing mechanism. The model is able to reproduce the decrease of the growth rate in the nanorod axial direction with both its thickness and length. On the other hand, low lateral reaction rates prevent the nanorod thickness distribution to be focused. In both crystallographic growth directions, a concentration-dependent critical thickness exists, which discriminates between nanorods with positive growth rates and those dissolving in the reaction solution. ' acknowledgement: This work was supported by the Spanish MICINN Projects MAT2008-05779, MAT2008-03400-E/MAT, and ENE2008-03277-E/CON. Maria Ibáñez thanks the Ph.D. grant from the Spanish MICINN. article_processing_charge: No article_type: original author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Pablo full_name: Guardia, Pablo last_name: Guardia - first_name: Alexey full_name: Shavel, Alexey last_name: Shavel - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Joan full_name: Morante, Joan last_name: Morante - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot citation: ama: 'Ibáñez M, Guardia P, Shavel A, et al. Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods. Journal of Physical Chemistry C. 2011;115(16):7947-7955. doi:10.1021/jp2002904' apa: 'Ibáñez, M., Guardia, P., Shavel, A., Cadavid, D., Arbiol, J., Morante, J., & Cabot, A. (2011). Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods. Journal of Physical Chemistry C. American Chemical Society. https://doi.org/10.1021/jp2002904' chicago: 'Ibáñez, Maria, Pablo Guardia, Alexey Shavel, Doris Cadavid, Jordi Arbiol, Joan Morante, and Andreu Cabot. “Growth Kinetics of Asymmetric Bi2S3 Nanocrystals: Size Distribution Focusing in Nanorods.” Journal of Physical Chemistry C. American Chemical Society, 2011. https://doi.org/10.1021/jp2002904.' ieee: 'M. Ibáñez et al., “Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods,” Journal of Physical Chemistry C, vol. 115, no. 16. American Chemical Society, pp. 7947–7955, 2011.' ista: 'Ibáñez M, Guardia P, Shavel A, Cadavid D, Arbiol J, Morante J, Cabot A. 2011. Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods. Journal of Physical Chemistry C. 115(16), 7947–7955.' mla: 'Ibáñez, Maria, et al. “Growth Kinetics of Asymmetric Bi2S3 Nanocrystals: Size Distribution Focusing in Nanorods.” Journal of Physical Chemistry C, vol. 115, no. 16, American Chemical Society, 2011, pp. 7947–55, doi:10.1021/jp2002904.' short: M. Ibáñez, P. Guardia, A. Shavel, D. Cadavid, J. Arbiol, J. Morante, A. Cabot, Journal of Physical Chemistry C 115 (2011) 7947–7955. date_created: 2018-12-11T11:45:53Z date_published: 2011-04-28T00:00:00Z date_updated: 2021-01-12T07:42:56Z day: '28' doi: 10.1021/jp2002904 extern: '1' intvolume: ' 115' issue: '16' language: - iso: eng month: '04' oa_version: None page: 7947 - 7955 publication: Journal of Physical Chemistry C publication_status: published publisher: American Chemical Society publist_id: '7493' quality_controlled: '1' status: public title: 'Growth kinetics of asymmetric Bi2S3 nanocrystals: Size distribution focusing in nanorods' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2011' ... --- _id: '3379' abstract: - lang: eng text: The process of gastrulation is highly conserved across vertebrates on both the genetic and morphological levels, despite great variety in embryonic shape and speed of development. This mechanism spatially separates the germ layers and establishes the organizational foundation for future development. Mesodermal identity is specified in a superficial layer of cells, the epiblast, where cells maintain an epithelioid morphology. These cells involute to join the deeper hypoblast layer where they adopt a migratory, mesenchymal morphology. Expression of a cascade of related transcription factors orchestrates the parallel genetic transition from primitive to mature mesoderm. Although the early and late stages of this process are increasingly well understood, the transition between them has remained largely mysterious. We present here the first high resolution in vivo observations of the blebby transitional morphology of involuting mesodermal cells in a vertebrate embryo. We further demonstrate that the zebrafish spadetail mutation creates a reversible block in the maturation program, stalling cells in the transition state. This mutation creates an ideal system for dissecting the specific properties of cells undergoing the morphological transition of maturing mesoderm, as we demonstrate with a direct measurement of cell–cell adhesion. article_type: original author: - first_name: Richard full_name: Row, Richard last_name: Row - first_name: Jean-Léon full_name: Maître, Jean-Léon id: 48F1E0D8-F248-11E8-B48F-1D18A9856A87 last_name: Maître orcid: 0000-0002-3688-1474 - first_name: Benjamin full_name: Martin, Benjamin last_name: Martin - first_name: Petra full_name: Stockinger, Petra id: 261CB030-E90D-11E9-B182-F697D44B663C last_name: Stockinger - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 - first_name: David full_name: Kimelman, David last_name: Kimelman citation: ama: Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. 2011;354(1):102-110. doi:10.1016/j.ydbio.2011.03.025 apa: Row, R., Maître, J.-L., Martin, B., Stockinger, P., Heisenberg, C.-P. J., & Kimelman, D. (2011). Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. Elsevier. https://doi.org/10.1016/j.ydbio.2011.03.025 chicago: Row, Richard, Jean-Léon Maître, Benjamin Martin, Petra Stockinger, Carl-Philipp J Heisenberg, and David Kimelman. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology. Elsevier, 2011. https://doi.org/10.1016/j.ydbio.2011.03.025. ieee: R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P. J. Heisenberg, and D. Kimelman, “Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail,” Developmental Biology, vol. 354, no. 1. Elsevier, pp. 102–110, 2011. ista: Row R, Maître J-L, Martin B, Stockinger P, Heisenberg C-PJ, Kimelman D. 2011. Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail. Developmental Biology. 354(1), 102–110. mla: Row, Richard, et al. “Completion of the Epithelial to Mesenchymal Transition in Zebrafish Mesoderm Requires Spadetail.” Developmental Biology, vol. 354, no. 1, Elsevier, 2011, pp. 102–10, doi:10.1016/j.ydbio.2011.03.025. short: R. Row, J.-L. Maître, B. Martin, P. Stockinger, C.-P.J. Heisenberg, D. Kimelman, Developmental Biology 354 (2011) 102–110. date_created: 2018-12-11T12:03:00Z date_published: 2011-06-01T00:00:00Z date_updated: 2021-01-12T07:43:04Z day: '01' department: - _id: CaHe doi: 10.1016/j.ydbio.2011.03.025 external_id: pmid: - '1463614' intvolume: ' 354' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3090540/ month: '06' oa: 1 oa_version: Submitted Version page: 102 - 110 pmid: 1 publication: Developmental Biology publication_status: published publisher: Elsevier publist_id: '3228' quality_controlled: '1' scopus_import: 1 status: public title: Completion of the epithelial to mesenchymal transition in zebrafish mesoderm requires Spadetail type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 354 year: '2011' ... --- _id: '3376' abstract: - lang: eng text: Regulatory conflicts occur when two signals that individually trigger opposite cellular responses are present simultaneously. Here, we investigate regulatory conflicts in the bacterial response to antibiotic combinations. We use an Escherichia coli promoter-GFP library to study the transcriptional response of many promoters to either additive or antagonistic drug pairs at fine two-dimensional (2D) resolution of drug concentration. Surprisingly, we find that this data set can be characterized as a linear sum of only two principal components. Component one, accounting for over 70% of the response, represents the response to growth inhibition by the drugs. Component two describes how regulatory conflicts are resolved. For the additive drug pair, conflicts are resolved by linearly interpolating the single drug responses, while for the antagonistic drug pair, the growth-limiting drug dominates the response. Importantly, for a given drug pair, the same conflict resolution strategy applies to almost all genes. These results provide a recipe for predicting gene expression responses to antibiotic combinations. acknowledgement: This work was supported by a Feodor Lynen Fellowship of the Alexander von Humboldt Foundation (to T.B.). 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: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Bollenbach MT, Kishony R. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 2011;42(4):413-425. doi:10.1016/j.molcel.2011.04.016 apa: Bollenbach, M. T., & Kishony, R. (2011). Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. Cell Press. https://doi.org/10.1016/j.molcel.2011.04.016 chicago: Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” Molecular Cell. Cell Press, 2011. https://doi.org/10.1016/j.molcel.2011.04.016. ieee: M. T. Bollenbach and R. Kishony, “Resolution of gene regulatory conflicts caused by combinations of antibiotics,” Molecular Cell, vol. 42, no. 4. Cell Press, pp. 413–425, 2011. ista: Bollenbach MT, Kishony R. 2011. Resolution of gene regulatory conflicts caused by combinations of antibiotics. Molecular Cell. 42(4), 413–425. mla: Bollenbach, Mark Tobias, and Roy Kishony. “Resolution of Gene Regulatory Conflicts Caused by Combinations of Antibiotics.” Molecular Cell, vol. 42, no. 4, Cell Press, 2011, pp. 413–25, doi:10.1016/j.molcel.2011.04.016. short: M.T. Bollenbach, R. Kishony, Molecular Cell 42 (2011) 413–425. date_created: 2018-12-11T12:02:59Z date_published: 2011-05-20T00:00:00Z date_updated: 2021-01-12T07:43:03Z day: '20' department: - _id: ToBo doi: 10.1016/j.molcel.2011.04.016 intvolume: ' 42' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3143497/ month: '05' oa: 1 oa_version: Submitted Version page: 413 - 425 publication: Molecular Cell publication_status: published publisher: Cell Press publist_id: '3231' quality_controlled: '1' scopus_import: 1 status: public title: Resolution of gene regulatory conflicts caused by combinations of antibiotics type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2011' ... --- _id: '3380' abstract: - lang: eng text: Linkage between markers and genes that affect a phenotype of interest may be determined by examining differences in marker allele frequency in the extreme progeny of a cross between two inbred lines. This strategy is usually employed when pooling is used to reduce genotyping costs. When the cross progeny are asexual, the extreme progeny may be selected by multiple generations of asexual reproduction and selection. We analyse this method of measuring phenotype in asexual progeny and examine the changes in marker allele frequency due to selection over many generations. Stochasticity in marker frequency in the selected population arises due to the finite initial population size. We derive the distribution of marker frequency as a result of selection at a single major locus, and show that in order to avoid spurious changes in marker allele frequency in the selected population, the initial population size should be in the low to mid hundreds. article_processing_charge: No article_type: original author: - first_name: Sayanthan full_name: Logeswaran, Sayanthan last_name: Logeswaran - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Logeswaran S, Barton NH. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 2011;93(3):221-232. doi:10.1017/S0016672311000115 apa: Logeswaran, S., & Barton, N. H. (2011). Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. Cambridge University Press. https://doi.org/10.1017/S0016672311000115 chicago: Logeswaran, Sayanthan, and Nicholas H Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research. Cambridge University Press, 2011. https://doi.org/10.1017/S0016672311000115. ieee: S. Logeswaran and N. H. Barton, “Mapping Mendelian traits in asexual progeny using changes in marker allele frequency,” Genetical Research, vol. 93, no. 3. Cambridge University Press, pp. 221–232, 2011. ista: Logeswaran S, Barton NH. 2011. Mapping Mendelian traits in asexual progeny using changes in marker allele frequency. Genetical Research. 93(3), 221–232. mla: Logeswaran, Sayanthan, and Nicholas H. Barton. “Mapping Mendelian Traits in Asexual Progeny Using Changes in Marker Allele Frequency.” Genetical Research, vol. 93, no. 3, Cambridge University Press, 2011, pp. 221–32, doi:10.1017/S0016672311000115. short: S. Logeswaran, N.H. Barton, Genetical Research 93 (2011) 221–232. date_created: 2018-12-11T12:03:00Z date_published: 2011-05-18T00:00:00Z date_updated: 2021-01-12T07:43:05Z day: '18' department: - _id: NiBa doi: 10.1017/S0016672311000115 intvolume: ' 93' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://www.pure.ed.ac.uk/ws/files/8144621/GR_2011_Barton.pdf month: '05' oa: 1 oa_version: Published Version page: 221 - 232 publication: Genetical Research publication_status: published publisher: Cambridge University Press publist_id: '3227' quality_controlled: '1' scopus_import: 1 status: public title: Mapping Mendelian traits in asexual progeny using changes in marker allele frequency type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 93 year: '2011' ... --- _id: '3377' abstract: - lang: eng text: By definition, transverse intersections are stable under in- finitesimal perturbations. Using persistent homology, we ex- tend this notion to sizeable perturbations. Specifically, we assign to each homology class of the intersection its robust- ness, the magnitude of a perturbation necessary to kill it, and prove that robustness is stable. Among the applications of this result is a stable notion of robustness for fixed points of continuous mappings and a statement of stability for con- tours of smooth mappings. acknowledgement: This research is partially supported by the Defense Advanced Research Projects Agency (DARPA) under grants HR0011-05-1-0007 and HR0011-05-1-0057. author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Dmitriy full_name: Morozov, Dmitriy last_name: Morozov - first_name: Amit full_name: Patel, Amit id: 34A254A0-F248-11E8-B48F-1D18A9856A87 last_name: Patel citation: ama: Edelsbrunner H, Morozov D, Patel A. Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. 2011;11(3):345-361. doi:10.1007/s10208-011-9090-8 apa: Edelsbrunner, H., Morozov, D., & Patel, A. (2011). Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-011-9090-8 chicago: Edelsbrunner, Herbert, Dmitriy Morozov, and Amit Patel. “Quantifying Transversality by Measuring the Robustness of Intersections.” Foundations of Computational Mathematics. Springer, 2011. https://doi.org/10.1007/s10208-011-9090-8. ieee: H. Edelsbrunner, D. Morozov, and A. Patel, “Quantifying transversality by measuring the robustness of intersections,” Foundations of Computational Mathematics, vol. 11, no. 3. Springer, pp. 345–361, 2011. ista: Edelsbrunner H, Morozov D, Patel A. 2011. Quantifying transversality by measuring the robustness of intersections. Foundations of Computational Mathematics. 11(3), 345–361. mla: Edelsbrunner, Herbert, et al. “Quantifying Transversality by Measuring the Robustness of Intersections.” Foundations of Computational Mathematics, vol. 11, no. 3, Springer, 2011, pp. 345–61, doi:10.1007/s10208-011-9090-8. short: H. Edelsbrunner, D. Morozov, A. Patel, Foundations of Computational Mathematics 11 (2011) 345–361. date_created: 2018-12-11T12:02:59Z date_published: 2011-06-01T00:00:00Z date_updated: 2021-01-12T07:43:04Z day: '01' department: - _id: HeEd doi: 10.1007/s10208-011-9090-8 intvolume: ' 11' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/0911.2142 month: '06' oa: 1 oa_version: Submitted Version page: 345 - 361 publication: Foundations of Computational Mathematics publication_status: published publisher: Springer publist_id: '3230' quality_controlled: '1' scopus_import: 1 status: public title: Quantifying transversality by measuring the robustness of intersections type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2011' ... --- _id: '3378' abstract: - lang: eng text: The theory of intersection homology was developed to study the singularities of a topologically stratified space. This paper in- corporates this theory into the already developed framework of persistent homology. We demonstrate that persistent intersec- tion homology gives useful information about the relationship between an embedded stratified space and its singularities. We give, and prove the correctness of, an algorithm for the computa- tion of the persistent intersection homology groups of a filtered simplicial complex equipped with a stratification by subcom- plexes. We also derive, from Poincare ́ Duality, some structural results about persistent intersection homology. acknowledgement: This research was partially supported by the Defense Advanced Research Projects Agency (DARPA) under grant HR0011-05-1-0007. author: - first_name: Paul full_name: Bendich, Paul id: 43F6EC54-F248-11E8-B48F-1D18A9856A87 last_name: Bendich - first_name: John full_name: Harer, John last_name: Harer citation: ama: Bendich P, Harer J. Persistent intersection homology. Foundations of Computational Mathematics. 2011;11(3):305-336. doi:10.1007/s10208-010-9081-1 apa: Bendich, P., & Harer, J. (2011). Persistent intersection homology. Foundations of Computational Mathematics. Springer. https://doi.org/10.1007/s10208-010-9081-1 chicago: Bendich, Paul, and John Harer. “Persistent Intersection Homology.” Foundations of Computational Mathematics. Springer, 2011. https://doi.org/10.1007/s10208-010-9081-1. ieee: P. Bendich and J. Harer, “Persistent intersection homology,” Foundations of Computational Mathematics, vol. 11, no. 3. Springer, pp. 305–336, 2011. ista: Bendich P, Harer J. 2011. Persistent intersection homology. Foundations of Computational Mathematics. 11(3), 305–336. mla: Bendich, Paul, and John Harer. “Persistent Intersection Homology.” Foundations of Computational Mathematics, vol. 11, no. 3, Springer, 2011, pp. 305–36, doi:10.1007/s10208-010-9081-1. short: P. Bendich, J. Harer, Foundations of Computational Mathematics 11 (2011) 305–336. date_created: 2018-12-11T12:02:59Z date_published: 2011-06-01T00:00:00Z date_updated: 2021-01-12T07:43:04Z day: '01' department: - _id: HeEd doi: 10.1007/s10208-010-9081-1 intvolume: ' 11' issue: '3' language: - iso: eng month: '06' oa_version: None page: 305 - 336 publication: Foundations of Computational Mathematics publication_status: published publisher: Springer publist_id: '3229' quality_controlled: '1' scopus_import: 1 status: public title: Persistent intersection homology type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2011' ...