--- _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 license: https://creativecommons.org/licenses/by/4.0/ 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 license: https://creativecommons.org/licenses/by-nc/4.0/ 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 license: https://creativecommons.org/licenses/by-nc-nd/4.0/ 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: '1728' abstract: - lang: eng text: 'In the vertebrate neural tube, the morphogen Sonic Hedgehog (Shh) establishes a characteristic pattern of gene expression. Here we quantify the Shh gradient in the developing mouse neural tube and show that while the amplitude of the gradient increases over time, the activity of the pathway transcriptional effectors, Gli proteins, initially increases but later decreases. Computational analysis of the pathway suggests three mechanisms that could contribute to this adaptation: transcriptional upregulation of the inhibitory receptor Ptch1, transcriptional downregulation of Gli and the differential stability of active and inactive Gli isoforms. Consistent with this, Gli2 protein expression is downregulated during neural tube patterning and adaptation continues when the pathway is stimulated downstream of Ptch1. Moreover, the Shh-induced upregulation of Gli2 transcription prevents Gli activity levels from adapting in a different cell type, NIH3T3 fibroblasts, despite the upregulation of Ptch1. Multiple mechanisms therefore contribute to the intracellular dynamics of Shh signalling, resulting in different signalling dynamics in different cell types.' acknowledgement: C.P.B. gratefully acknowledges funding from the Wellcome Trust through a Research Career Development Fellowship (097319/Z/11/Z). This work was supported by the Medical Research Council (U117560541) and Wellcome Trust (WT098326MA, WT098325MA). author: - first_name: Michael full_name: Cohen, Michael H last_name: Cohen - first_name: Anna full_name: Anna Kicheva id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Ana full_name: Ribeiro, Ana C last_name: Ribeiro - first_name: Robert full_name: Blassberg, Robert A last_name: Blassberg - first_name: Karen full_name: Page, Karen M last_name: Page - first_name: Chris full_name: Barnes, Chris P last_name: Barnes - first_name: James full_name: Briscoe, James last_name: Briscoe citation: ama: Cohen M, Kicheva A, Ribeiro A, et al. Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. 2015;6. doi:10.1038/ncomms7709 apa: Cohen, M., Kicheva, A., Ribeiro, A., Blassberg, R., Page, K., Barnes, C., & Briscoe, J. (2015). Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms7709 chicago: Cohen, Michael, Anna Kicheva, Ana Ribeiro, Robert Blassberg, Karen Page, Chris Barnes, and James Briscoe. “Ptch1 and Gli Regulate Shh Signalling Dynamics via Multiple Mechanisms.” Nature Communications. Nature Publishing Group, 2015. https://doi.org/10.1038/ncomms7709. ieee: M. Cohen et al., “Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms,” Nature Communications, vol. 6. Nature Publishing Group, 2015. ista: Cohen M, Kicheva A, Ribeiro A, Blassberg R, Page K, Barnes C, Briscoe J. 2015. Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms. Nature Communications. 6. mla: Cohen, Michael, et al. “Ptch1 and Gli Regulate Shh Signalling Dynamics via Multiple Mechanisms.” Nature Communications, vol. 6, Nature Publishing Group, 2015, doi:10.1038/ncomms7709. short: M. Cohen, A. Kicheva, A. Ribeiro, R. Blassberg, K. Page, C. Barnes, J. Briscoe, Nature Communications 6 (2015). date_created: 2018-12-11T11:53:42Z date_published: 2015-04-02T00:00:00Z date_updated: 2021-01-12T06:52:48Z day: '02' doi: 10.1038/ncomms7709 extern: 1 intvolume: ' 6' month: '04' publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5399' quality_controlled: 0 status: public title: Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms 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 volume: 6 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' ...