--- _id: '14198' abstract: - lang: eng text: "High-dimensional time series are common in many domains. Since human\r\ncognition is not optimized to work well in high-dimensional spaces, these areas\r\ncould benefit from interpretable low-dimensional representations. However, most\r\nrepresentation learning algorithms for time series data are difficult to\r\ninterpret. This is due to non-intuitive mappings from data features to salient\r\nproperties of the representation and non-smoothness over time. To address this\r\nproblem, we propose a new representation learning framework building on ideas\r\nfrom interpretable discrete dimensionality reduction and deep generative\r\nmodeling. This framework allows us to learn discrete representations of time\r\nseries, which give rise to smooth and interpretable embeddings with superior\r\nclustering performance. We introduce a new way to overcome the\r\nnon-differentiability in discrete representation learning and present a\r\ngradient-based version of the traditional self-organizing map algorithm that is\r\nmore performant than the original. Furthermore, to allow for a probabilistic\r\ninterpretation of our method, we integrate a Markov model in the representation\r\nspace. This model uncovers the temporal transition structure, improves\r\nclustering performance even further and provides additional explanatory\r\ninsights as well as a natural representation of uncertainty. We evaluate our\r\nmodel in terms of clustering performance and interpretability on static\r\n(Fashion-)MNIST data, a time series of linearly interpolated (Fashion-)MNIST\r\nimages, a chaotic Lorenz attractor system with two macro states, as well as on\r\na challenging real world medical time series application on the eICU data set.\r\nOur learned representations compare favorably with competitor methods and\r\nfacilitate downstream tasks on the real world data." article_processing_charge: No author: - first_name: Vincent full_name: Fortuin, Vincent last_name: Fortuin - first_name: Matthias full_name: Hüser, Matthias last_name: Hüser - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Heiko full_name: Strathmann, Heiko last_name: Strathmann - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch citation: ama: 'Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. SOM-VAE: Interpretable discrete representation learning on time series. In: International Conference on Learning Representations. ; 2018.' apa: 'Fortuin, V., Hüser, M., Locatello, F., Strathmann, H., & Rätsch, G. (2018). SOM-VAE: Interpretable discrete representation learning on time series. In International Conference on Learning Representations. New Orleans, LA, United States.' chicago: 'Fortuin, Vincent, Matthias Hüser, Francesco Locatello, Heiko Strathmann, and Gunnar Rätsch. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” In International Conference on Learning Representations, 2018.' ieee: 'V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, and G. Rätsch, “SOM-VAE: Interpretable discrete representation learning on time series,” in International Conference on Learning Representations, New Orleans, LA, United States, 2018.' ista: 'Fortuin V, Hüser M, Locatello F, Strathmann H, Rätsch G. 2018. SOM-VAE: Interpretable discrete representation learning on time series. International Conference on Learning Representations. ICLR: International Conference on Learning Representations.' mla: 'Fortuin, Vincent, et al. “SOM-VAE: Interpretable Discrete Representation Learning on Time Series.” International Conference on Learning Representations, 2018.' short: V. Fortuin, M. Hüser, F. Locatello, H. Strathmann, G. Rätsch, in:, International Conference on Learning Representations, 2018. conference: end_date: 2019-05-09 location: New Orleans, LA, United States name: 'ICLR: International Conference on Learning Representations' start_date: 2019-05-06 date_created: 2023-08-22T14:12:48Z date_published: 2018-06-06T00:00:00Z date_updated: 2023-09-13T06:35:12Z day: '06' department: - _id: FrLo extern: '1' external_id: arxiv: - '1806.02199' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.02199 month: '06' oa: 1 oa_version: Preprint publication: International Conference on Learning Representations publication_status: published quality_controlled: '1' status: public title: 'SOM-VAE: Interpretable discrete representation learning on time series' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '14203' abstract: - lang: eng text: We propose a conditional gradient framework for a composite convex minimization template with broad applications. Our approach combines smoothing and homotopy techniques under the CGM framework, and provably achieves the optimal O(1/k−−√) convergence rate. We demonstrate that the same rate holds if the linear subproblems are solved approximately with additive or multiplicative error. In contrast with the relevant work, we are able to characterize the convergence when the non-smooth term is an indicator function. Specific applications of our framework include the non-smooth minimization, semidefinite programming, and minimization with linear inclusion constraints over a compact domain. Numerical evidence demonstrates the benefits of our framework. alternative_title: - PMLR article_processing_charge: No author: - first_name: Alp full_name: Yurtsever, Alp last_name: Yurtsever - first_name: Olivier full_name: Fercoq, Olivier last_name: Fercoq - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Volkan full_name: Cevher, Volkan last_name: Cevher citation: ama: 'Yurtsever A, Fercoq O, Locatello F, Cevher V. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:5727-5736.' apa: 'Yurtsever, A., Fercoq, O., Locatello, F., & Cevher, V. (2018). A conditional gradient framework for composite convex minimization with applications to semidefinite programming. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 5727–5736). Stockholm, Sweden: ML Research Press.' chicago: Yurtsever, Alp, Olivier Fercoq, Francesco Locatello, and Volkan Cevher. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” In Proceedings of the 35th International Conference on Machine Learning, 80:5727–36. ML Research Press, 2018. ieee: A. Yurtsever, O. Fercoq, F. Locatello, and V. Cevher, “A conditional gradient framework for composite convex minimization with applications to semidefinite programming,” in Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden, 2018, vol. 80, pp. 5727–5736. ista: 'Yurtsever A, Fercoq O, Locatello F, Cevher V. 2018. A conditional gradient framework for composite convex minimization with applications to semidefinite programming. Proceedings of the 35th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 80, 5727–5736.' mla: Yurtsever, Alp, et al. “A Conditional Gradient Framework for Composite Convex Minimization with Applications to Semidefinite Programming.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 5727–36. short: A. Yurtsever, O. Fercoq, F. Locatello, V. Cevher, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 5727–5736. conference: end_date: 2018-07-15 location: Stockholm, Sweden name: 'ICML: International Conference on Machine Learning' start_date: 2018-07-10 date_created: 2023-08-22T14:16:01Z date_published: 2018-07-15T00:00:00Z date_updated: 2023-09-13T08:13:39Z day: '15' department: - _id: FrLo extern: '1' external_id: arxiv: - '1804.08544' intvolume: ' 80' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.08544 month: '07' oa: 1 oa_version: Preprint page: 5727-5736 publication: Proceedings of the 35th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' status: public title: A conditional gradient framework for composite convex minimization with applications to semidefinite programming type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 80 year: '2018' ... --- _id: '282' abstract: - lang: eng text: Adaptive introgression is common in nature and can be driven by selection acting on multiple, linked genes. We explore the effects of polygenic selection on introgression under the infinitesimal model with linkage. This model assumes that the introgressing block has an effectively infinite number of genes, each with an infinitesimal effect on the trait under selection. The block is assumed to introgress under directional selection within a native population that is genetically homogeneous. We use individual-based simulations and a branching process approximation to compute various statistics of the introgressing block, and explore how these depend on parameters such as the map length and initial trait value associated with the introgressing block, the genetic variability along the block, and the strength of selection. Our results show that the introgression dynamics of a block under infinitesimal selection is qualitatively different from the dynamics of neutral introgression. We also find that in the long run, surviving descendant blocks are likely to have intermediate lengths, and clarify how the length is shaped by the interplay between linkage and infinitesimal selection. Our results suggest that it may be difficult to distinguish introgression of single loci from that of genomic blocks with multiple, tightly linked and weakly selected loci. article_processing_charge: No author: - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva - 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: Sachdeva H, Barton NH. Introgression of a block of genome under infinitesimal selection. Genetics. 2018;209(4):1279-1303. doi:10.1534/genetics.118.301018 apa: Sachdeva, H., & Barton, N. H. (2018). Introgression of a block of genome under infinitesimal selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301018 chicago: Sachdeva, Himani, and Nicholas H Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301018. ieee: H. Sachdeva and N. H. Barton, “Introgression of a block of genome under infinitesimal selection,” Genetics, vol. 209, no. 4. Genetics Society of America, pp. 1279–1303, 2018. ista: Sachdeva H, Barton NH. 2018. Introgression of a block of genome under infinitesimal selection. Genetics. 209(4), 1279–1303. mla: Sachdeva, Himani, and Nicholas H. Barton. “Introgression of a Block of Genome under Infinitesimal Selection.” Genetics, vol. 209, no. 4, Genetics Society of America, 2018, pp. 1279–303, doi:10.1534/genetics.118.301018. short: H. Sachdeva, N.H. Barton, Genetics 209 (2018) 1279–1303. date_created: 2018-12-11T11:45:36Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-09-13T08:22:32Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.118.301018 external_id: isi: - '000440014100020' intvolume: ' 209' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/early/2017/11/30/227082 month: '08' oa: 1 oa_version: Submitted Version page: 1279 - 1303 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '7617' quality_controlled: '1' scopus_import: '1' status: public title: Introgression of a block of genome under infinitesimal selection type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 209 year: '2018' ... --- _id: '108' abstract: - lang: eng text: Universal hashing found a lot of applications in computer science. In cryptography the most important fact about universal families is the so called Leftover Hash Lemma, proved by Impagliazzo, Levin and Luby. In the language of modern cryptography it states that almost universal families are good extractors. In this work we provide a somewhat surprising characterization in the opposite direction. Namely, every extractor with sufficiently good parameters yields a universal family on a noticeable fraction of its inputs. Our proof technique is based on tools from extremal graph theory applied to the \'collision graph\' induced by the extractor, and may be of independent interest. We discuss possible applications to the theory of randomness extractors and non-malleable codes. alternative_title: - ISIT Proceedings article_processing_charge: No author: - first_name: Marciej full_name: Obremski, Marciej last_name: Obremski - first_name: Maciej full_name: Skorski, Maciej id: EC09FA6A-02D0-11E9-8223-86B7C91467DD last_name: Skorski citation: ama: 'Obremski M, Skórski M. Inverted leftover hash lemma. In: Vol 2018. IEEE; 2018. doi:10.1109/ISIT.2018.8437654' apa: 'Obremski, M., & Skórski, M. (2018). Inverted leftover hash lemma (Vol. 2018). Presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA: IEEE. https://doi.org/10.1109/ISIT.2018.8437654' chicago: Obremski, Marciej, and Maciej Skórski. “Inverted Leftover Hash Lemma,” Vol. 2018. IEEE, 2018. https://doi.org/10.1109/ISIT.2018.8437654. ieee: 'M. Obremski and M. Skórski, “Inverted leftover hash lemma,” presented at the ISIT: International Symposium on Information Theory, Vail, CO, USA, 2018, vol. 2018.' ista: 'Obremski M, Skórski M. 2018. Inverted leftover hash lemma. ISIT: International Symposium on Information Theory, ISIT Proceedings, vol. 2018.' mla: Obremski, Marciej, and Maciej Skórski. Inverted Leftover Hash Lemma. Vol. 2018, IEEE, 2018, doi:10.1109/ISIT.2018.8437654. short: M. Obremski, M. Skórski, in:, IEEE, 2018. conference: end_date: 2018-06-22 location: Vail, CO, USA name: 'ISIT: International Symposium on Information Theory' start_date: '2018-06-17 ' date_created: 2018-12-11T11:44:40Z date_published: 2018-08-16T00:00:00Z date_updated: 2023-09-13T08:23:18Z day: '16' department: - _id: KrPi doi: 10.1109/ISIT.2018.8437654 external_id: isi: - '000448139300368' intvolume: ' 2018' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2017/507 month: '08' oa: 1 oa_version: Submitted Version publication_status: published publisher: IEEE publist_id: '7946' quality_controlled: '1' scopus_import: '1' status: public title: Inverted leftover hash lemma type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2018 year: '2018' ... --- _id: '14204' abstract: - lang: eng text: Two popular examples of first-order optimization methods over linear spaces are coordinate descent and matching pursuit algorithms, with their randomized variants. While the former targets the optimization by moving along coordinates, the latter considers a generalized notion of directions. Exploiting the connection between the two algorithms, we present a unified analysis of both, providing affine invariant sublinear O(1/t) rates on smooth objectives and linear convergence on strongly convex objectives. As a byproduct of our affine invariant analysis of matching pursuit, our rates for steepest coordinate descent are the tightest known. Furthermore, we show the first accelerated convergence rate O(1/t2) for matching pursuit and steepest coordinate descent on convex objectives. alternative_title: - PMLR article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Anant full_name: Raj, Anant last_name: Raj - first_name: Sai Praneeth full_name: Karimireddy, Sai Praneeth last_name: Karimireddy - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Sebastian U. full_name: Stich, Sebastian U. last_name: Stich - first_name: Martin full_name: Jaggi, Martin last_name: Jaggi citation: ama: 'Locatello F, Raj A, Karimireddy SP, et al. On matching pursuit and coordinate descent. In: Proceedings of the 35th International Conference on Machine Learning. Vol 80. ML Research Press; 2018:3198-3207.' apa: Locatello, F., Raj, A., Karimireddy, S. P., Rätsch, G., Schölkopf, B., Stich, S. U., & Jaggi, M. (2018). On matching pursuit and coordinate descent. In Proceedings of the 35th International Conference on Machine Learning (Vol. 80, pp. 3198–3207). ML Research Press. chicago: Locatello, Francesco, Anant Raj, Sai Praneeth Karimireddy, Gunnar Rätsch, Bernhard Schölkopf, Sebastian U. Stich, and Martin Jaggi. “On Matching Pursuit and Coordinate Descent.” In Proceedings of the 35th International Conference on Machine Learning, 80:3198–3207. ML Research Press, 2018. ieee: F. Locatello et al., “On matching pursuit and coordinate descent,” in Proceedings of the 35th International Conference on Machine Learning, 2018, vol. 80, pp. 3198–3207. ista: Locatello F, Raj A, Karimireddy SP, Rätsch G, Schölkopf B, Stich SU, Jaggi M. 2018. On matching pursuit and coordinate descent. Proceedings of the 35th International Conference on Machine Learning. , PMLR, vol. 80, 3198–3207. mla: Locatello, Francesco, et al. “On Matching Pursuit and Coordinate Descent.” Proceedings of the 35th International Conference on Machine Learning, vol. 80, ML Research Press, 2018, pp. 3198–207. short: F. Locatello, A. Raj, S.P. Karimireddy, G. Rätsch, B. Schölkopf, S.U. Stich, M. Jaggi, in:, Proceedings of the 35th International Conference on Machine Learning, ML Research Press, 2018, pp. 3198–3207. date_created: 2023-08-22T14:16:25Z date_published: 2018-07-01T00:00:00Z date_updated: 2023-09-13T08:19:05Z day: '01' department: - _id: FrLo extern: '1' external_id: arxiv: - '1803.09539' intvolume: ' 80' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.09539 month: '07' oa: 1 oa_version: Preprint page: 3198-3207 publication: Proceedings of the 35th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' scopus_import: '1' status: public title: On matching pursuit and coordinate descent type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 80 year: '2018' ... --- _id: '160' abstract: - lang: eng text: We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs. alternative_title: - LNCS article_processing_charge: No author: - first_name: Bernhard full_name: Kragl, Bernhard id: 320FC952-F248-11E8-B48F-1D18A9856A87 last_name: Kragl orcid: 0000-0001-7745-9117 - first_name: Shaz full_name: Qadeer, Shaz last_name: Qadeer citation: ama: 'Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:10.1007/978-3-319-96145-3_5' apa: 'Kragl, B., & Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-96145-3_5' chicago: Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_5. ieee: 'B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.' ista: 'Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.' mla: Kragl, Bernhard, and Shaz Qadeer. Layered Concurrent Programs. Vol. 10981, Springer, 2018, pp. 79–102, doi:10.1007/978-3-319-96145-3_5. short: B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102. conference: end_date: 2018-07-17 location: Oxford, UK name: 'CAV: Computer Aided Verification' start_date: 2018-07-14 date_created: 2018-12-11T11:44:57Z date_published: 2018-07-18T00:00:00Z date_updated: 2023-09-13T08:45:09Z day: '18' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-96145-3_5 external_id: isi: - '000491481600005' file: - access_level: open_access checksum: c64fff560fe5a7532ec10626ad1c215e content_type: application/pdf creator: dernst date_created: 2018-12-17T12:52:12Z date_updated: 2020-07-14T12:45:04Z file_id: '5705' file_name: 2018_LNCS_Kragl.pdf file_size: 1603844 relation: main_file file_date_updated: 2020-07-14T12:45:04Z has_accepted_license: '1' intvolume: ' 10981' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 79 - 102 project: - _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: '7761' quality_controlled: '1' related_material: record: - id: '8332' relation: dissertation_contains status: public scopus_import: '1' status: public title: Layered Concurrent Programs tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10981 year: '2018' ... --- _id: '280' abstract: - lang: eng text: Flowers have a species-specific functional life span that determines the time window in which pollination, fertilization and seed set can occur. The stigma tissue plays a key role in flower receptivity by intercepting pollen and initiating pollen tube growth toward the ovary. In this article, we show that a developmentally controlled cell death programme terminates the functional life span of stigma cells in Arabidopsis. We identified the leaf senescence regulator ORESARA1 (also known as ANAC092) and the previously uncharacterized KIRA1 (also known as ANAC074) as partially redundant transcription factors that modulate stigma longevity by controlling the expression of programmed cell death-associated genes. KIRA1 expression is sufficient to induce cell death and terminate floral receptivity, whereas lack of both KIRA1 and ORESARA1 substantially increases stigma life span. Surprisingly, the extension of stigma longevity is accompanied by only a moderate extension of flower receptivity, suggesting that additional processes participate in the control of the flower's receptive life span. acknowledgement: We gratefully acknowledge funding from the Chinese Scholarship Council (CSC; project number 201206910025 to Z.G.), the Fonds Wetenschappelijk Onderzoek (FWO; project number G005112N to A.D.; fellowship number 12I7417N to Z.L.), the Belgian Federal Science Policy Office (BELSPO; to Y.S.), the Agency for Innovation by Science and Technology of Belgium (IWT; fellowship number 121110 to M.V.D.), the Hercules foundation (grant AUGE-09-029 to K.D.), and the ERC StG PROCELLDEATH (project number 639234 to M.K.N.). article_processing_charge: No author: - first_name: Zhen full_name: Gao, Zhen last_name: Gao - first_name: Anna full_name: Daneva, Anna last_name: Daneva - first_name: Yuliya full_name: Salanenka, Yuliya id: 46DAAE7E-F248-11E8-B48F-1D18A9856A87 last_name: Salanenka - first_name: Matthias full_name: Van Durme, Matthias last_name: Van Durme - first_name: Marlies full_name: Huysmans, Marlies last_name: Huysmans - first_name: Zongcheng full_name: Lin, Zongcheng last_name: Lin - first_name: Freya full_name: De Winter, Freya last_name: De Winter - first_name: Steffen full_name: Vanneste, Steffen last_name: Vanneste - first_name: Mansour full_name: Karimi, Mansour last_name: Karimi - first_name: Jan full_name: Van De Velde, Jan last_name: Van De Velde - first_name: Klaas full_name: Vandepoele, Klaas last_name: Vandepoele - first_name: Davy full_name: Van De Walle, Davy last_name: Van De Walle - first_name: Koen full_name: Dewettinck, Koen last_name: Dewettinck - first_name: Bart full_name: Lambrecht, Bart last_name: Lambrecht - first_name: Moritz full_name: Nowack, Moritz last_name: Nowack citation: ama: Gao Z, Daneva A, Salanenka Y, et al. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 2018;4(6):365-375. doi:10.1038/s41477-018-0160-7 apa: Gao, Z., Daneva, A., Salanenka, Y., Van Durme, M., Huysmans, M., Lin, Z., … Nowack, M. (2018). KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0160-7 chicago: Gao, Zhen, Anna Daneva, Yuliya Salanenka, Matthias Van Durme, Marlies Huysmans, Zongcheng Lin, Freya De Winter, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0160-7. ieee: Z. Gao et al., “KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis,” Nature Plants, vol. 4, no. 6. Nature Publishing Group, pp. 365–375, 2018. ista: Gao Z, Daneva A, Salanenka Y, Van Durme M, Huysmans M, Lin Z, De Winter F, Vanneste S, Karimi M, Van De Velde J, Vandepoele K, Van De Walle D, Dewettinck K, Lambrecht B, Nowack M. 2018. KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis. Nature Plants. 4(6), 365–375. mla: Gao, Zhen, et al. “KIRA1 and ORESARA1 Terminate Flower Receptivity by Promoting Cell Death in the Stigma of Arabidopsis.” Nature Plants, vol. 4, no. 6, Nature Publishing Group, 2018, pp. 365–75, doi:10.1038/s41477-018-0160-7. short: Z. Gao, A. Daneva, Y. Salanenka, M. Van Durme, M. Huysmans, Z. Lin, F. De Winter, S. Vanneste, M. Karimi, J. Van De Velde, K. Vandepoele, D. Van De Walle, K. Dewettinck, B. Lambrecht, M. Nowack, Nature Plants 4 (2018) 365–375. date_created: 2018-12-11T11:45:35Z date_published: 2018-05-28T00:00:00Z date_updated: 2023-09-13T08:24:17Z day: '28' department: - _id: JiFr doi: 10.1038/s41477-018-0160-7 external_id: isi: - '000435571000017' intvolume: ' 4' isi: 1 issue: '6' language: - iso: eng month: '05' oa_version: None page: 365 - 375 publication: Nature Plants publication_status: published publisher: Nature Publishing Group publist_id: '7619' quality_controlled: '1' scopus_import: '1' status: public title: KIRA1 and ORESARA1 terminate flower receptivity by promoting cell death in the stigma of Arabidopsis type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 4 year: '2018' ... --- _id: '503' abstract: - lang: eng text: Buffers are essential for diluting bacterial cultures for flow cytometry analysis in order to study bacterial physiology and gene expression parameters based on fluorescence signals. Using a variety of constitutively expressed fluorescent proteins in Escherichia coli K-12 strain MG1655, we found strong artifactual changes in fluorescence levels after dilution into the commonly used flow cytometry buffer phosphate-buffered saline (PBS) and two other buffer solutions, Tris-HCl and M9 salts. These changes appeared very rapidly after dilution, and were linked to increased membrane permeability and loss in cell viability. We observed buffer-related effects in several different E. coli strains, K-12, C and W, but not E. coli B, which can be partially explained by differences in lipopolysaccharide (LPS) and outer membrane composition. Supplementing the buffers with divalent cations responsible for outer membrane stability, Mg2+ and Ca2+, preserved fluorescence signals, membrane integrity and viability of E. coli. Thus, stabilizing the bacterial outer membrane is essential for precise and unbiased measurements of fluorescence parameters using flow cytometry. acknowledged_ssus: - _id: Bio acknowledgement: "We thank R Chait and M Lagator for sharing Bacillus subtilis CR_Y1 and pZS*_2R-cIPtet-Venus-Prm, respectively. We are grateful to T Pilizota and all members of the Guet lab for critically reading the manuscript. We also thank the Bioimaging facility at IST Austria for assistance using the FACSAria III system.\r\n\r\n" article_processing_charge: No author: - first_name: Kathrin full_name: Tomasek, Kathrin id: 3AEC8556-F248-11E8-B48F-1D18A9856A87 last_name: Tomasek orcid: 0000-0003-3768-877X - first_name: Tobias full_name: Bergmiller, Tobias id: 2C471CFA-F248-11E8-B48F-1D18A9856A87 last_name: Bergmiller orcid: 0000-0001-5396-4346 - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Tomasek K, Bergmiller T, Guet CC. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 2018;268:40-52. doi:10.1016/j.jbiotec.2018.01.008 apa: Tomasek, K., Bergmiller, T., & Guet, C. C. (2018). Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. Elsevier. https://doi.org/10.1016/j.jbiotec.2018.01.008 chicago: Tomasek, Kathrin, Tobias Bergmiller, and Calin C Guet. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology. Elsevier, 2018. https://doi.org/10.1016/j.jbiotec.2018.01.008. ieee: K. Tomasek, T. Bergmiller, and C. C. Guet, “Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains,” Journal of Biotechnology, vol. 268. Elsevier, pp. 40–52, 2018. ista: Tomasek K, Bergmiller T, Guet CC. 2018. Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains. Journal of Biotechnology. 268, 40–52. mla: Tomasek, Kathrin, et al. “Lack of Cations in Flow Cytometry Buffers Affect Fluorescence Signals by Reducing Membrane Stability and Viability of Escherichia Coli Strains.” Journal of Biotechnology, vol. 268, Elsevier, 2018, pp. 40–52, doi:10.1016/j.jbiotec.2018.01.008. short: K. Tomasek, T. Bergmiller, C.C. Guet, Journal of Biotechnology 268 (2018) 40–52. date_created: 2018-12-11T11:46:50Z date_published: 2018-02-20T00:00:00Z date_updated: 2023-09-13T08:24:51Z day: '20' department: - _id: CaGu doi: 10.1016/j.jbiotec.2018.01.008 external_id: isi: - '000425715100006' intvolume: ' 268' isi: 1 language: - iso: eng month: '02' oa_version: None page: 40 - 52 publication: Journal of Biotechnology publication_status: published publisher: Elsevier publist_id: '7317' quality_controlled: '1' scopus_import: '1' status: public title: Lack of cations in flow cytometry buffers affect fluorescence signals by reducing membrane stability and viability of Escherichia coli strains type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 268 year: '2018' ... --- _id: '82' abstract: - lang: eng text: In experimental cultures, when bacteria are mixed with lytic (virulent) bacteriophage, bacterial cells resistant to the phage commonly emerge and become the dominant population of bacteria. Following the ascent of resistant mutants, the densities of bacteria in these simple communities become limited by resources rather than the phage. Despite the evolution of resistant hosts, upon which the phage cannot replicate, the lytic phage population is most commonly maintained in an apparently stable state with the resistant bacteria. Several mechanisms have been put forward to account for this result. Here we report the results of population dynamic/evolution experiments with a virulent mutant of phage Lambda, λVIR, and Escherichia coli in serial transfer cultures. We show that, following the ascent of λVIR-resistant bacteria, λVIRis maintained in the majority of cases in maltose-limited minimal media and in all cases in nutrient-rich broth. Using mathematical models and experiments, we show that the dominant mechanism responsible for maintenance of λVIRin these resource-limited populations dominated by resistant E. coli is a high rate of either phenotypic or genetic transition from resistance to susceptibility—a hitherto undemonstrated mechanism we term "leaky resistance." We discuss the implications of leaky resistance to our understanding of the conditions for the maintenance of phage in populations of bacteria—their “existence conditions.”. article_number: '2005971' article_processing_charge: Yes author: - first_name: Waqas full_name: Chaudhry, Waqas last_name: Chaudhry - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Nilang full_name: Shah, Nilang last_name: Shah - first_name: Howard full_name: Weiss, Howard last_name: Weiss - first_name: Ingrid full_name: Mccall, Ingrid last_name: Mccall - first_name: Justin full_name: Meyer, Justin last_name: Meyer - first_name: Animesh full_name: Gupta, Animesh last_name: Gupta - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Bruce full_name: Levin, Bruce last_name: Levin citation: ama: Chaudhry W, Pleska M, Shah N, et al. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 2018;16(8). doi:10.1371/journal.pbio.2005971 apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971 chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology. Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971. ieee: W. Chaudhry et al., “Leaky resistance and the conditions for the existence of lytic bacteriophage,” PLoS Biology, vol. 16, no. 8. Public Library of Science, 2018. ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Leaky resistance and the conditions for the existence of lytic bacteriophage. PLoS Biology. 16(8), 2005971. mla: Chaudhry, Waqas, et al. “Leaky Resistance and the Conditions for the Existence of Lytic Bacteriophage.” PLoS Biology, vol. 16, no. 8, 2005971, Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971. short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, PLoS Biology 16 (2018). date_created: 2018-12-11T11:44:32Z date_published: 2018-08-16T00:00:00Z date_updated: 2023-09-13T08:45:41Z day: '16' ddc: - '570' department: - _id: CaGu doi: 10.1371/journal.pbio.2005971 external_id: isi: - '000443383300024' file: - access_level: open_access checksum: 527076f78265cd4ea192cd1569851587 content_type: application/pdf creator: dernst date_created: 2018-12-17T12:55:31Z date_updated: 2020-07-14T12:48:10Z file_id: '5706' file_name: 2018_Plos_Chaudhry.pdf file_size: 4007095 relation: main_file file_date_updated: 2020-07-14T12:48:10Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '8' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: PLoS Biology publication_status: published publisher: Public Library of Science publist_id: '7972' quality_controlled: '1' related_material: record: - id: '9810' relation: research_data status: public scopus_import: '1' status: public title: Leaky resistance and the conditions for the existence of lytic bacteriophage 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 16 year: '2018' ... --- _id: '4' abstract: - lang: eng text: We present a data-driven technique to instantly predict how fluid flows around various three-dimensional objects. Such simulation is useful for computational fabrication and engineering, but is usually computationally expensive since it requires solving the Navier-Stokes equation for many time steps. To accelerate the process, we propose a machine learning framework which predicts aerodynamic forces and velocity and pressure fields given a threedimensional shape input. Handling detailed free-form three-dimensional shapes in a data-driven framework is challenging because machine learning approaches usually require a consistent parametrization of input and output. We present a novel PolyCube maps-based parametrization that can be computed for three-dimensional shapes at interactive rates. This allows us to efficiently learn the nonlinear response of the flow using a Gaussian process regression. We demonstrate the effectiveness of our approach for the interactive design and optimization of a car body. article_number: '89' article_processing_charge: No author: - first_name: Nobuyuki full_name: Umetani, Nobuyuki last_name: Umetani - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: Umetani N, Bickel B. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201325 apa: Umetani, N., & Bickel, B. (2018). Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201325 chicago: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201325. ieee: N. Umetani and B. Bickel, “Learning three-dimensional flow for interactive aerodynamic design,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018. ista: Umetani N, Bickel B. 2018. Learning three-dimensional flow for interactive aerodynamic design. ACM Trans. Graph. 37(4), 89. mla: Umetani, Nobuyuki, and Bernd Bickel. “Learning Three-Dimensional Flow for Interactive Aerodynamic Design.” ACM Trans. Graph., vol. 37, no. 4, 89, ACM, 2018, doi:10.1145/3197517.3201325. short: N. Umetani, B. Bickel, ACM Trans. Graph. 37 (2018). date_created: 2018-12-11T11:44:06Z date_published: 2018-08-04T00:00:00Z date_updated: 2023-09-13T08:46:15Z day: '04' ddc: - '003' - '004' department: - _id: BeBi doi: 10.1145/3197517.3201325 ec_funded: 1 external_id: isi: - '000448185000050' file: - access_level: open_access checksum: 7a2243668f215821bc6aecad0320079a content_type: application/pdf creator: system date_created: 2018-12-12T10:16:28Z date_updated: 2020-07-14T12:46:22Z file_id: '5216' file_name: IST-2018-1049-v1+1_2018_sigg_Learning3DAerodynamics.pdf file_size: 22803163 relation: main_file file_date_updated: 2020-07-14T12:46:22Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: ACM Trans. Graph. publication_status: published publisher: ACM publist_id: '8053' pubrep_id: '1049' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-interactive-machine-learning-tool-makes-car-designs-more-aerodynamic/ scopus_import: '1' status: public title: Learning three-dimensional flow for interactive aerodynamic design type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2018' ... --- _id: '183' abstract: - lang: eng text: 'Fault-localization is considered to be a very tedious and time-consuming activity in the design of complex Cyber-Physical Systems (CPS). This laborious task essentially requires expert knowledge of the system in order to discover the cause of the fault. In this context, we propose a new procedure that AIDS designers in debugging Simulink/Stateflow hybrid system models, guided by Signal Temporal Logic (STL) specifications. The proposed method relies on three main ingredients: (1) a monitoring and a trace diagnostics procedure that checks whether a tested behavior satisfies or violates an STL specification, localizes time segments and interfaces variables contributing to the property violations; (2) a slicing procedure that maps these observable behavior segments to the internal states and transitions of the Simulink model; and (3) a spectrum-based fault-localization method that combines the previous analysis from multiple tests to identify the internal states and/or transitions that are the most likely to explain the fault. We demonstrate the applicability of our approach on two Simulink models from the automotive and the avionics domain.' acknowledgement: This work was partially supported by the Austrian Science Fund (FWF) under grants S11402-N23 and S11405-N23 (RiSE/SHiNE), the CPS/IoT project (HRSM), the EU ICT COST Action IC1402 on Run-time Verification beyond Monitoring (ARVI), the AMASS project (ECSEL 692474), and the ENABLE-S3 project (ECSEL 692455). The CPS/IoT project receives support from the Austrian government through the Federal Ministry of Science, Research and Economy (BMWFW) in the funding program Hochschulraum-Strukturmittel (HRSM) 2016. The ECSEL Joint Undertaking receives support from the European Union’s Horizon 2020 research and innovation programme and Austria, Denmark, Germany, Finland, Czech Republic, Italy, Spain, Portugal, Poland, Ireland, Belgium, France, Netherlands, United Kingdom, Slovakia, Norway. alternative_title: - HSCC Proceedings article_processing_charge: No author: - first_name: Ezio full_name: Bartocci, Ezio last_name: Bartocci - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Niveditha full_name: Manjunath, Niveditha last_name: Manjunath - first_name: Dejan full_name: Nickovic, Dejan last_name: Nickovic citation: ama: 'Bartocci E, Ferrere T, Manjunath N, Nickovic D. Localizing faults in simulink/stateflow models with STL. In: Association for Computing Machinery, Inc; 2018:197-206. doi:10.1145/3178126.3178131' apa: 'Bartocci, E., Ferrere, T., Manjunath, N., & Nickovic, D. (2018). Localizing faults in simulink/stateflow models with STL (pp. 197–206). Presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal: Association for Computing Machinery, Inc. https://doi.org/10.1145/3178126.3178131' chicago: Bartocci, Ezio, Thomas Ferrere, Niveditha Manjunath, and Dejan Nickovic. “Localizing Faults in Simulink/Stateflow Models with STL,” 197–206. Association for Computing Machinery, Inc, 2018. https://doi.org/10.1145/3178126.3178131. ieee: 'E. Bartocci, T. Ferrere, N. Manjunath, and D. Nickovic, “Localizing faults in simulink/stateflow models with STL,” presented at the HSCC: Hybrid Systems: Computation and Control, Porto, Portugal, 2018, pp. 197–206.' ista: 'Bartocci E, Ferrere T, Manjunath N, Nickovic D. 2018. Localizing faults in simulink/stateflow models with STL. HSCC: Hybrid Systems: Computation and Control, HSCC Proceedings, , 197–206.' mla: Bartocci, Ezio, et al. Localizing Faults in Simulink/Stateflow Models with STL. Association for Computing Machinery, Inc, 2018, pp. 197–206, doi:10.1145/3178126.3178131. short: E. Bartocci, T. Ferrere, N. Manjunath, D. Nickovic, in:, Association for Computing Machinery, Inc, 2018, pp. 197–206. conference: end_date: 2018-04-13 location: Porto, Portugal name: 'HSCC: Hybrid Systems: Computation and Control' start_date: 2018-04-11 date_created: 2018-12-11T11:45:04Z date_published: 2018-04-11T00:00:00Z date_updated: 2023-09-13T08:48:46Z day: '11' department: - _id: ToHe doi: 10.1145/3178126.3178131 external_id: isi: - '000474781600022' isi: 1 language: - iso: eng month: '04' oa_version: None page: 197 - 206 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering publication_status: published publisher: Association for Computing Machinery, Inc publist_id: '7738' quality_controlled: '1' scopus_import: '1' status: public title: Localizing faults in simulink/stateflow models with STL type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '566' abstract: - lang: eng text: "We consider large random matrices X with centered, independent entries which have comparable but not necessarily identical variances. Girko's circular law asserts that the spectrum is supported in a disk and in case of identical variances, the limiting density is uniform. In this special case, the local circular law by Bourgade et. al. [11,12] shows that the empirical density converges even locally on scales slightly above the typical eigenvalue spacing. In the general case, the limiting density is typically inhomogeneous and it is obtained via solving a system of deterministic equations. Our main result is the local inhomogeneous circular law in the bulk spectrum on the optimal scale for a general variance profile of the entries of X. \r\n\r\n" article_processing_charge: No article_type: original author: - first_name: Johannes full_name: Alt, Johannes id: 36D3D8B6-F248-11E8-B48F-1D18A9856A87 last_name: Alt - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 citation: ama: Alt J, Erdös L, Krüger TH. Local inhomogeneous circular law. Annals Applied Probability . 2018;28(1):148-203. doi:10.1214/17-AAP1302 apa: Alt, J., Erdös, L., & Krüger, T. H. (2018). Local inhomogeneous circular law. Annals Applied Probability . Institute of Mathematical Statistics. https://doi.org/10.1214/17-AAP1302 chicago: Alt, Johannes, László Erdös, and Torben H Krüger. “Local Inhomogeneous Circular Law.” Annals Applied Probability . Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/17-AAP1302. ieee: J. Alt, L. Erdös, and T. H. Krüger, “Local inhomogeneous circular law,” Annals Applied Probability , vol. 28, no. 1. Institute of Mathematical Statistics, pp. 148–203, 2018. ista: Alt J, Erdös L, Krüger TH. 2018. Local inhomogeneous circular law. Annals Applied Probability . 28(1), 148–203. mla: Alt, Johannes, et al. “Local Inhomogeneous Circular Law.” Annals Applied Probability , vol. 28, no. 1, Institute of Mathematical Statistics, 2018, pp. 148–203, doi:10.1214/17-AAP1302. short: J. Alt, L. Erdös, T.H. Krüger, Annals Applied Probability 28 (2018) 148–203. date_created: 2018-12-11T11:47:13Z date_published: 2018-03-03T00:00:00Z date_updated: 2023-09-13T08:47:52Z day: '03' department: - _id: LaEr doi: 10.1214/17-AAP1302 ec_funded: 1 external_id: arxiv: - '1612.07776 ' isi: - '000431721800005' intvolume: ' 28' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'https://arxiv.org/abs/1612.07776 ' month: '03' oa: 1 oa_version: Preprint page: 148-203 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems publication: 'Annals Applied Probability ' publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' related_material: record: - id: '149' relation: dissertation_contains status: public scopus_import: '1' status: public title: Local inhomogeneous circular law type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 28 year: '2018' ... --- _id: '106' abstract: - lang: eng text: The goal of this article is to introduce the reader to the theory of intrinsic geometry of convex surfaces. We illustrate the power of the tools by proving a theorem on convex surfaces containing an arbitrarily long closed simple geodesic. Let us remind ourselves that a curve in a surface is called geodesic if every sufficiently short arc of the curve is length minimizing; if, in addition, it has no self-intersections, we call it simple geodesic. A tetrahedron with equal opposite edges is called isosceles. The axiomatic method of Alexandrov geometry allows us to work with the metrics of convex surfaces directly, without approximating it first by a smooth or polyhedral metric. Such approximations destroy the closed geodesics on the surface; therefore it is difficult (if at all possible) to apply approximations in the proof of our theorem. On the other hand, a proof in the smooth or polyhedral case usually admits a translation into Alexandrov’s language; such translation makes the result more general. In fact, our proof resembles a translation of the proof given by Protasov. Note that the main theorem implies in particular that a smooth convex surface does not have arbitrarily long simple closed geodesics. However we do not know a proof of this corollary that is essentially simpler than the one presented below. article_processing_charge: No author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X - first_name: Anton full_name: Petrunin, Anton last_name: Petrunin citation: ama: Akopyan A, Petrunin A. Long geodesics on convex surfaces. Mathematical Intelligencer. 2018;40(3):26-31. doi:10.1007/s00283-018-9795-5 apa: Akopyan, A., & Petrunin, A. (2018). Long geodesics on convex surfaces. Mathematical Intelligencer. Springer. https://doi.org/10.1007/s00283-018-9795-5 chicago: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer. Springer, 2018. https://doi.org/10.1007/s00283-018-9795-5. ieee: A. Akopyan and A. Petrunin, “Long geodesics on convex surfaces,” Mathematical Intelligencer, vol. 40, no. 3. Springer, pp. 26–31, 2018. ista: Akopyan A, Petrunin A. 2018. Long geodesics on convex surfaces. Mathematical Intelligencer. 40(3), 26–31. mla: Akopyan, Arseniy, and Anton Petrunin. “Long Geodesics on Convex Surfaces.” Mathematical Intelligencer, vol. 40, no. 3, Springer, 2018, pp. 26–31, doi:10.1007/s00283-018-9795-5. short: A. Akopyan, A. Petrunin, Mathematical Intelligencer 40 (2018) 26–31. date_created: 2018-12-11T11:44:40Z date_published: 2018-09-01T00:00:00Z date_updated: 2023-09-13T08:49:16Z day: '01' department: - _id: HeEd doi: 10.1007/s00283-018-9795-5 external_id: arxiv: - '1702.05172' isi: - '000444141200005' intvolume: ' 40' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.05172 month: '09' oa: 1 oa_version: Preprint page: 26 - 31 publication: Mathematical Intelligencer publication_status: published publisher: Springer publist_id: '7948' quality_controlled: '1' scopus_import: '1' status: public title: Long geodesics on convex surfaces type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 40 year: '2018' ... --- _id: '9810' article_processing_charge: No author: - first_name: Waqas full_name: Chaudhry, Waqas last_name: Chaudhry - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Nilang full_name: Shah, Nilang last_name: Shah - first_name: Howard full_name: Weiss, Howard last_name: Weiss - first_name: Ingrid full_name: Mccall, Ingrid last_name: Mccall - first_name: Justin full_name: Meyer, Justin last_name: Meyer - first_name: Animesh full_name: Gupta, Animesh last_name: Gupta - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Bruce full_name: Levin, Bruce last_name: Levin citation: ama: Chaudhry W, Pleska M, Shah N, et al. Numerical data used in figures. 2018. doi:10.1371/journal.pbio.2005971.s008 apa: Chaudhry, W., Pleska, M., Shah, N., Weiss, H., Mccall, I., Meyer, J., … Levin, B. (2018). Numerical data used in figures. Public Library of Science. https://doi.org/10.1371/journal.pbio.2005971.s008 chicago: Chaudhry, Waqas, Maros Pleska, Nilang Shah, Howard Weiss, Ingrid Mccall, Justin Meyer, Animesh Gupta, Calin C Guet, and Bruce Levin. “Numerical Data Used in Figures.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pbio.2005971.s008. ieee: W. Chaudhry et al., “Numerical data used in figures.” Public Library of Science, 2018. ista: Chaudhry W, Pleska M, Shah N, Weiss H, Mccall I, Meyer J, Gupta A, Guet CC, Levin B. 2018. Numerical data used in figures, Public Library of Science, 10.1371/journal.pbio.2005971.s008. mla: Chaudhry, Waqas, et al. Numerical Data Used in Figures. Public Library of Science, 2018, doi:10.1371/journal.pbio.2005971.s008. short: W. Chaudhry, M. Pleska, N. Shah, H. Weiss, I. Mccall, J. Meyer, A. Gupta, C.C. Guet, B. Levin, (2018). date_created: 2021-08-06T12:43:44Z date_published: 2018-08-16T00:00:00Z date_updated: 2023-09-13T08:45:41Z day: '16' department: - _id: CaGu doi: 10.1371/journal.pbio.2005971.s008 month: '08' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '82' relation: used_in_publication status: public status: public title: Numerical data used in figures type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '275' abstract: - lang: eng text: Lymphatic endothelial cells (LECs) release extracellular chemokines to guide the migration of dendritic cells. In this study, we report that LECs also release basolateral exosome-rich endothelial vesicles (EEVs) that are secreted in greater numbers in the presence of inflammatory cytokines and accumulate in the perivascular stroma of small lymphatic vessels in human chronic inflammatory diseases. Proteomic analyses of EEV fractions identified > 1,700 cargo proteins and revealed a dominant motility-promoting protein signature. In vitro and ex vivo EEV fractions augmented cellular protrusion formation in a CX3CL1/fractalkine-dependent fashion and enhanced the directional migratory response of human dendritic cells along guidance cues. We conclude that perilymphatic LEC exosomes enhance exploratory behavior and thus promote directional migration of CX3CR1-expressing cells in complex tissue environments. acknowledgement: M. Brown was supported by the Cell Communication in Health and Disease Graduate Study Program of the Austrian Science Fund and Medizinische Universität Wien, M. Sixt by the European Research Council (ERC GA 281556) and an Austrian Science Fund START award, K.L. Bennett by the Austrian Academy of Sciences, D.G. Jackson and L.A. Johnson by Unit Funding (MC_UU_12010/2) and project grants from the Medical Research Council (G1100134 and MR/L008610/1), and M. Detmar by the Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung and Advanced European Research Council grant LYVICAM. K. Vaahtomeri was supported by an Academy of Finland postdoctoral research grant (287853). This project has received funding from the European Union’s Horizon 2020 research and innovation program under grant agreement No. 668036 (RELENT). article_processing_charge: No author: - first_name: Markus full_name: Brown, Markus id: 3DAB9AFC-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Louise full_name: Johnson, Louise last_name: Johnson - first_name: Dario full_name: Leone, Dario last_name: Leone - first_name: Peter full_name: Májek, Peter last_name: Májek - first_name: Kari full_name: Vaahtomeri, Kari id: 368EE576-F248-11E8-B48F-1D18A9856A87 last_name: Vaahtomeri orcid: 0000-0001-7829-3518 - first_name: Daniel full_name: Senfter, Daniel last_name: Senfter - first_name: Nora full_name: Bukosza, Nora last_name: Bukosza - first_name: Helga full_name: Schachner, Helga last_name: Schachner - first_name: Gabriele full_name: Asfour, Gabriele last_name: Asfour - first_name: Brigitte full_name: Langer, Brigitte last_name: Langer - first_name: Robert full_name: Hauschild, Robert id: 4E01D6B4-F248-11E8-B48F-1D18A9856A87 last_name: Hauschild orcid: 0000-0001-9843-3522 - first_name: Katja full_name: Parapatics, Katja last_name: Parapatics - first_name: Young full_name: Hong, Young last_name: Hong - first_name: Keiryn full_name: Bennett, Keiryn last_name: Bennett - first_name: Renate full_name: Kain, Renate last_name: Kain - first_name: Michael full_name: Detmar, Michael last_name: Detmar - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: David full_name: Jackson, David last_name: Jackson - first_name: Dontscho full_name: Kerjaschki, Dontscho last_name: Kerjaschki citation: ama: Brown M, Johnson L, Leone D, et al. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 2018;217(6):2205-2221. doi:10.1083/jcb.201612051 apa: Brown, M., Johnson, L., Leone, D., Májek, P., Vaahtomeri, K., Senfter, D., … Kerjaschki, D. (2018). Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201612051 chicago: Brown, Markus, Louise Johnson, Dario Leone, Peter Májek, Kari Vaahtomeri, Daniel Senfter, Nora Bukosza, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201612051. ieee: M. Brown et al., “Lymphatic exosomes promote dendritic cell migration along guidance cues,” Journal of Cell Biology, vol. 217, no. 6. Rockefeller University Press, pp. 2205–2221, 2018. ista: Brown M, Johnson L, Leone D, Májek P, Vaahtomeri K, Senfter D, Bukosza N, Schachner H, Asfour G, Langer B, Hauschild R, Parapatics K, Hong Y, Bennett K, Kain R, Detmar M, Sixt MK, Jackson D, Kerjaschki D. 2018. Lymphatic exosomes promote dendritic cell migration along guidance cues. Journal of Cell Biology. 217(6), 2205–2221. mla: Brown, Markus, et al. “Lymphatic Exosomes Promote Dendritic Cell Migration along Guidance Cues.” Journal of Cell Biology, vol. 217, no. 6, Rockefeller University Press, 2018, pp. 2205–21, doi:10.1083/jcb.201612051. short: M. Brown, L. Johnson, D. Leone, P. Májek, K. Vaahtomeri, D. Senfter, N. Bukosza, H. Schachner, G. Asfour, B. Langer, R. Hauschild, K. Parapatics, Y. Hong, K. Bennett, R. Kain, M. Detmar, M.K. Sixt, D. Jackson, D. Kerjaschki, Journal of Cell Biology 217 (2018) 2205–2221. date_created: 2018-12-11T11:45:33Z date_published: 2018-04-12T00:00:00Z date_updated: 2023-09-13T08:51:29Z day: '12' ddc: - '570' department: - _id: MiSi - _id: Bio doi: 10.1083/jcb.201612051 ec_funded: 1 external_id: isi: - '000438077800026' pmid: - '29650776' file: - access_level: open_access checksum: 9c7eba51a35c62da8c13f98120b64df4 content_type: application/pdf creator: dernst date_created: 2018-12-17T12:50:07Z date_updated: 2020-07-14T12:45:45Z file_id: '5704' file_name: 2018_JournalCellBiology_Brown.pdf file_size: 2252043 relation: main_file file_date_updated: 2020-07-14T12:45:45Z has_accepted_license: '1' intvolume: ' 217' isi: 1 issue: '6' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 2205 - 2221 pmid: 1 project: - _id: 25A8E5EA-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Y 564-B12 name: Cytoskeletal force generation and transduction of leukocytes (FWF) - _id: 25A603A2-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '281556' name: Cytoskeletal force generation and force transduction of migrating leukocytes (EU) publication: Journal of Cell Biology publication_status: published publisher: Rockefeller University Press publist_id: '7627' quality_controlled: '1' scopus_import: '1' status: public title: Lymphatic exosomes promote dendritic cell migration along guidance cues 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 217 year: '2018' ... --- _id: '158' abstract: - lang: eng text: 'The angiosperm seed is composed of three genetically distinct tissues: the diploid embryo that originates from the fertilized egg cell, the triploid endosperm that is produced from the fertilized central cell, and the maternal sporophytic integuments that develop into the seed coat1. At the onset of embryo development in Arabidopsis thaliana, the zygote divides asymmetrically, producing a small apical embryonic cell and a larger basal cell that connects the embryo to the maternal tissue2. The coordinated and synchronous development of the embryo and the surrounding integuments, and the alignment of their growth axes, suggest communication between maternal tissues and the embryo. In contrast to animals, however, where a network of maternal factors that direct embryo patterning have been identified3,4, only a few maternal mutations have been described to affect embryo development in plants5–7. Early embryo patterning in Arabidopsis requires accumulation of the phytohormone auxin in the apical cell by directed transport from the suspensor8–10. However, the origin of this auxin has remained obscure. Here we investigate the source of auxin for early embryogenesis and provide evidence that the mother plant coordinates seed development by supplying auxin to the early embryo from the integuments of the ovule. We show that auxin response increases in ovules after fertilization, due to upregulated auxin biosynthesis in the integuments, and this maternally produced auxin is required for correct embryo development.' acknowledgement: This work was further supported by the Czech Science Foundation GACR (GA13-40637S) to J.F.; article_processing_charge: No author: - first_name: Hélène full_name: Robert, Hélène last_name: Robert - first_name: Chulmin full_name: Park, Chulmin last_name: Park - first_name: Carla full_name: Gutièrrez, Carla last_name: Gutièrrez - first_name: Barbara full_name: Wójcikowska, Barbara last_name: Wójcikowska - first_name: Aleš full_name: Pěnčík, Aleš last_name: Pěnčík - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Junyi full_name: Chen, Junyi last_name: Chen - first_name: Wim full_name: Grunewald, Wim last_name: Grunewald - first_name: Thomas full_name: Dresselhaus, Thomas last_name: Dresselhaus - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Thomas full_name: Laux, Thomas last_name: Laux citation: ama: Robert H, Park C, Gutièrrez C, et al. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 2018;4(8):548-553. doi:10.1038/s41477-018-0204-z apa: Robert, H., Park, C., Gutièrrez, C., Wójcikowska, B., Pěnčík, A., Novák, O., … Laux, T. (2018). Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0204-z chicago: Robert, Hélène, Chulmin Park, Carla Gutièrrez, Barbara Wójcikowska, Aleš Pěnčík, Ondřej Novák, Junyi Chen, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0204-z. ieee: H. Robert et al., “Maternal auxin supply contributes to early embryo patterning in Arabidopsis,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 548–553, 2018. ista: Robert H, Park C, Gutièrrez C, Wójcikowska B, Pěnčík A, Novák O, Chen J, Grunewald W, Dresselhaus T, Friml J, Laux T. 2018. Maternal auxin supply contributes to early embryo patterning in Arabidopsis. Nature Plants. 4(8), 548–553. mla: Robert, Hélène, et al. “Maternal Auxin Supply Contributes to Early Embryo Patterning in Arabidopsis.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 548–53, doi:10.1038/s41477-018-0204-z. short: H. Robert, C. Park, C. Gutièrrez, B. Wójcikowska, A. Pěnčík, O. Novák, J. Chen, W. Grunewald, T. Dresselhaus, J. Friml, T. Laux, Nature Plants 4 (2018) 548–553. date_created: 2018-12-11T11:44:56Z date_published: 2018-07-16T00:00:00Z date_updated: 2023-09-13T08:53:28Z day: '16' department: - _id: JiFr doi: 10.1038/s41477-018-0204-z ec_funded: 1 external_id: isi: - '000443861300011' pmid: - '30013211' intvolume: ' 4' isi: 1 issue: '8' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30013211 month: '07' oa: 1 oa_version: Submitted Version page: 548 - 553 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants publication: Nature Plants publication_status: published publisher: Nature Publishing Group publist_id: '7763' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/plant-mothers-talk-to-their-embryos-via-the-hormone-auxin/ scopus_import: '1' status: public title: Maternal auxin supply contributes to early embryo patterning in Arabidopsis type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 4 year: '2018' ... --- _id: '152' abstract: - lang: eng text: Complex I has an essential role in ATP production by coupling electron transfer from NADH to quinone with translocation of protons across the inner mitochondrial membrane. Isolated complex I deficiency is a frequent cause of mitochondrial inherited diseases. Complex I has also been implicated in cancer, ageing, and neurodegenerative conditions. Until recently, the understanding of complex I deficiency on the molecular level was limited due to the lack of high-resolution structures of the enzyme. However, due to developments in single particle cryo-electron microscopy (cryo-EM), recent studies have reported nearly atomic resolution maps and models of mitochondrial complex I. These structures significantly add to our understanding of complex I mechanism and assembly. The disease-causing mutations are discussed here in their structural context. article_processing_charge: No article_type: original author: - first_name: Karol full_name: Fiedorczuk, Karol id: 5BFF67CE-02D1-11E9-B11A-A5A4D7DFFFD0 last_name: Fiedorczuk - first_name: Leonid A full_name: Sazanov, Leonid A id: 338D39FE-F248-11E8-B48F-1D18A9856A87 last_name: Sazanov orcid: 0000-0002-0977-7989 citation: ama: Fiedorczuk K, Sazanov LA. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 2018;28(10):835-867. doi:10.1016/j.tcb.2018.06.006 apa: Fiedorczuk, K., & Sazanov, L. A. (2018). Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. Elsevier. https://doi.org/10.1016/j.tcb.2018.06.006 chicago: Fiedorczuk, Karol, and Leonid A Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology. Elsevier, 2018. https://doi.org/10.1016/j.tcb.2018.06.006. ieee: K. Fiedorczuk and L. A. Sazanov, “Mammalian mitochondrial complex I structure and disease causing mutations,” Trends in Cell Biology, vol. 28, no. 10. Elsevier, pp. 835–867, 2018. ista: Fiedorczuk K, Sazanov LA. 2018. Mammalian mitochondrial complex I structure and disease causing mutations. Trends in Cell Biology. 28(10), 835–867. mla: Fiedorczuk, Karol, and Leonid A. Sazanov. “Mammalian Mitochondrial Complex I Structure and Disease Causing Mutations.” Trends in Cell Biology, vol. 28, no. 10, Elsevier, 2018, pp. 835–67, doi:10.1016/j.tcb.2018.06.006. short: K. Fiedorczuk, L.A. Sazanov, Trends in Cell Biology 28 (2018) 835–867. date_created: 2018-12-11T11:44:54Z date_published: 2018-07-26T00:00:00Z date_updated: 2023-09-13T08:51:56Z day: '26' ddc: - '572' department: - _id: LeSa doi: 10.1016/j.tcb.2018.06.006 external_id: isi: - '000445118200007' file: - access_level: open_access checksum: ef6d2b4e1fd63948539639242610bfa6 content_type: application/pdf creator: lsazanov date_created: 2019-11-07T12:55:20Z date_updated: 2020-07-14T12:45:00Z file_id: '6994' file_name: SasanovFinalMS+EdComments_LS_allacc_withFigs.pdf file_size: 2185385 relation: main_file file_date_updated: 2020-07-14T12:45:00Z has_accepted_license: '1' intvolume: ' 28' isi: 1 issue: '10' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 835 - 867 publication: Trends in Cell Biology publication_status: published publisher: Elsevier publist_id: '7769' quality_controlled: '1' scopus_import: '1' status: public title: Mammalian mitochondrial complex I structure and disease causing mutations 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 28 year: '2018' ... --- _id: '310' abstract: - lang: eng text: A model of computation that is widely used in the formal analysis of reactive systems is symbolic algorithms. In this model the access to the input graph is restricted to consist of symbolic operations, which are expensive in comparison to the standard RAM operations. We give lower bounds on the number of symbolic operations for basic graph problems such as the computation of the strongly connected components and of the approximate diameter as well as for fundamental problems in model checking such as safety, liveness, and coliveness. Our lower bounds are linear in the number of vertices of the graph, even for constant-diameter graphs. For none of these problems lower bounds on the number of symbolic operations were known before. The lower bounds show an interesting separation of these problems from the reachability problem, which can be solved with O(D) symbolic operations, where D is the diameter of the graph. Additionally we present an approximation algorithm for the graph diameter which requires Õ(n/D) symbolic steps to achieve a (1 +ϵ)-approximation for any constant > 0. This compares to O(n/D) symbolic steps for the (naive) exact algorithm and O(D) symbolic steps for a 2-approximation. Finally we also give a refined analysis of the strongly connected components algorithms of [15], showing that it uses an optimal number of symbolic steps that is proportional to the sum of the diameters of the strongly connected components. article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Wolfgang full_name: Dvorák, Wolfgang last_name: Dvorák - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer citation: ama: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. In: ACM; 2018:2341-2356. doi:10.1137/1.9781611975031.151' apa: 'Chatterjee, K., Dvorák, W., Henzinger, M. H., & Loitzenbauer, V. (2018). Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter (pp. 2341–2356). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States: ACM. https://doi.org/10.1137/1.9781611975031.151' chicago: 'Chatterjee, Krishnendu, Wolfgang Dvorák, Monika H Henzinger, and Veronika Loitzenbauer. “Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter,” 2341–56. ACM, 2018. https://doi.org/10.1137/1.9781611975031.151.' ieee: 'K. Chatterjee, W. Dvorák, M. H. Henzinger, and V. Loitzenbauer, “Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, Louisiana, United States, 2018, pp. 2341–2356.' ista: 'Chatterjee K, Dvorák W, Henzinger MH, Loitzenbauer V. 2018. Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter. SODA: Symposium on Discrete Algorithms, 2341–2356.' mla: 'Chatterjee, Krishnendu, et al. Lower Bounds for Symbolic Computation on Graphs: Strongly Connected Components, Liveness, Safety, and Diameter. ACM, 2018, pp. 2341–56, doi:10.1137/1.9781611975031.151.' short: K. Chatterjee, W. Dvorák, M.H. Henzinger, V. Loitzenbauer, in:, ACM, 2018, pp. 2341–2356. conference: end_date: 2018-01-10 location: New Orleans, Louisiana, United States name: 'SODA: Symposium on Discrete Algorithms' start_date: 2018-01-07 date_created: 2018-12-11T11:45:45Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-09-13T08:50:16Z day: '01' department: - _id: KrCh doi: 10.1137/1.9781611975031.151 ec_funded: 1 external_id: arxiv: - '1711.09148' isi: - '000483921200152' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1711.09148 month: '01' oa: 1 oa_version: Preprint page: 2341 - 2356 project: - _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: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication_status: published publisher: ACM publist_id: '7555' quality_controlled: '1' scopus_import: '1' status: public title: 'Lower bounds for symbolic computation on graphs: Strongly connected components, liveness, safety, and diameter' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '436' abstract: - lang: eng text: There has been significant interest recently in using complex quantum systems to create effective nonreciprocal dynamics. Proposals have been put forward for the realization of artificial magnetic fields for photons and phonons; experimental progress is fast making these proposals a reality. Much work has concentrated on the use of such systems for controlling the flow of signals, e.g., to create isolators or directional amplifiers for optical signals. In this Letter, we build on this work but move in a different direction. We develop the theory of and discuss a potential realization for the controllable flow of thermal noise in quantum systems. We demonstrate theoretically that the unidirectional flow of thermal noise is possible within quantum cascaded systems. Viewing an optomechanical platform as a cascaded system we show here that one can ultimately control the direction of the flow of thermal noise. By appropriately engineering the mechanical resonator, which acts as an artificial reservoir, the flow of thermal noise can be constrained to a desired direction, yielding a thermal rectifier. The proposed quantum thermal noise rectifier could potentially be used to develop devices such as a thermal modulator, a thermal router, and a thermal amplifier for nanoelectronic devices and superconducting circuits. article_number: '060601 ' article_processing_charge: No author: - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Matteo full_name: Aquilina, Matteo last_name: Aquilina - first_name: André full_name: Xuereb, André last_name: Xuereb citation: ama: Barzanjeh S, Aquilina M, Xuereb A. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 2018;120(6). doi:10.1103/PhysRevLett.120.060601 apa: Barzanjeh, S., Aquilina, M., & Xuereb, A. (2018). Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.120.060601 chicago: Barzanjeh, Shabir, Matteo Aquilina, and André Xuereb. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.120.060601. ieee: S. Barzanjeh, M. Aquilina, and A. Xuereb, “Manipulating the flow of thermal noise in quantum devices,” Physical Review Letters, vol. 120, no. 6. American Physical Society, 2018. ista: Barzanjeh S, Aquilina M, Xuereb A. 2018. Manipulating the flow of thermal noise in quantum devices. Physical Review Letters. 120(6), 060601. mla: Barzanjeh, Shabir, et al. “Manipulating the Flow of Thermal Noise in Quantum Devices.” Physical Review Letters, vol. 120, no. 6, 060601, American Physical Society, 2018, doi:10.1103/PhysRevLett.120.060601. short: S. Barzanjeh, M. Aquilina, A. Xuereb, Physical Review Letters 120 (2018). date_created: 2018-12-11T11:46:28Z date_published: 2018-02-07T00:00:00Z date_updated: 2023-09-13T08:52:27Z day: '07' department: - _id: JoFi doi: 10.1103/PhysRevLett.120.060601 ec_funded: 1 external_id: arxiv: - '1706.09051' isi: - '000424382100004' intvolume: ' 120' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.09051 month: '02' oa: 1 oa_version: Preprint project: - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 258047B6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '707438' name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM' publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '7387' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/interference-as-a-new-method-for-cooling-quantum-devices/ scopus_import: '1' status: public title: Manipulating the flow of thermal noise in quantum devices type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 120 year: '2018' ... --- _id: '5858' abstract: - lang: eng text: Spatial patterns are ubiquitous on the subcellular, cellular and tissue level, and can be studied using imaging techniques such as light and fluorescence microscopy. Imaging data provide quantitative information about biological systems; however, mechanisms causing spatial patterning often remain elusive. In recent years, spatio-temporal mathematical modelling has helped to overcome this problem. Yet, outliers and structured noise limit modelling of whole imaging data, and models often consider spatial summary statistics. Here, we introduce an integrated data-driven modelling approach that can cope with measurement artefacts and whole imaging data. Our approach combines mechanistic models of the biological processes with robust statistical models of the measurement process. The parameters of the integrated model are calibrated using a maximum-likelihood approach. We used this integrated modelling approach to study in vivo gradients of the chemokine (C-C motif) ligand 21 (CCL21). CCL21 gradients guide dendritic cells and are important in the adaptive immune response. Using artificial data, we verified that the integrated modelling approach provides reliable parameter estimates in the presence of measurement noise and that bias and variance of these estimates are reduced compared to conventional approaches. The application to experimental data allowed the parametrization and subsequent refinement of the model using additional mechanisms. Among other results, model-based hypothesis testing predicted lymphatic vessel-dependent concentration of heparan sulfate, the binding partner of CCL21. The selected model provided an accurate description of the experimental data and was partially validated using published data. Our findings demonstrate that integrated statistical modelling of whole imaging data is computationally feasible and can provide novel biological insights. article_number: '20180600' article_processing_charge: No author: - first_name: Sabrina full_name: Hross, Sabrina last_name: Hross - first_name: Fabian J. full_name: Theis, Fabian J. last_name: Theis - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Jan full_name: Hasenauer, Jan last_name: Hasenauer citation: ama: Hross S, Theis FJ, Sixt MK, Hasenauer J. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0600 apa: Hross, S., Theis, F. J., Sixt, M. K., & Hasenauer, J. (2018). Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0600 chicago: Hross, Sabrina, Fabian J. Theis, Michael K Sixt, and Jan Hasenauer. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0600. ieee: S. Hross, F. J. Theis, M. K. Sixt, and J. Hasenauer, “Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018. ista: Hross S, Theis FJ, Sixt MK, Hasenauer J. 2018. Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data. Journal of the Royal Society Interface. 15(149), 20180600. mla: Hross, Sabrina, et al. “Mechanistic Description of Spatial Processes Using Integrative Modelling of Noise-Corrupted Imaging Data.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180600, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0600. short: S. Hross, F.J. Theis, M.K. Sixt, J. Hasenauer, Journal of the Royal Society Interface 15 (2018). date_created: 2019-01-20T22:59:18Z date_published: 2018-12-05T00:00:00Z date_updated: 2023-09-13T08:55:05Z day: '05' ddc: - '570' department: - _id: MiSi doi: 10.1098/rsif.2018.0600 external_id: isi: - '000456783800011' file: - access_level: open_access checksum: 56eb4308a15b7190bff938fab1f780e8 content_type: application/pdf creator: dernst date_created: 2019-02-05T14:46:44Z date_updated: 2020-07-14T12:47:13Z file_id: '5925' file_name: 2018_Interface_Hross.pdf file_size: 1464288 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 15' isi: 1 issue: '149' language: - iso: eng month: '12' oa: 1 oa_version: Published Version publication: Journal of the Royal Society Interface publication_identifier: issn: - '17425689' publication_status: published publisher: Royal Society Publishing quality_controlled: '1' scopus_import: '1' status: public title: Mechanistic description of spatial processes using integrative modelling of noise-corrupted imaging data 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 15 year: '2018' ... --- _id: '16' abstract: - lang: eng text: We report quantitative evidence of mixing-layer elastic instability in a viscoelastic fluid flow between two widely spaced obstacles hindering a channel flow at Re 1 and Wi 1. Two mixing layers with nonuniform shear velocity profiles are formed in the region between the obstacles. The mixing-layer instability arises in the vicinity of an inflection point on the shear velocity profile with a steep variation in the elastic stress. The instability results in an intermittent appearance of small vortices in the mixing layers and an amplification of spatiotemporal averaged vorticity in the elastic turbulence regime. The latter is characterized through scaling of friction factor with Wi and both pressure and velocity spectra. Furthermore, the observations reported provide improved understanding of the stability of the mixing layer in a viscoelastic fluid at large elasticity, i.e., Wi 1 and Re 1 and oppose the current view of suppression of vorticity solely by polymer additives. acknowledgement: This work was partially supported by the Israel Science Foundation (ISF; Grant No. 882/15) and the Binational USA-Israel Foundation (BSF; Grant No. 2016145). article_number: '103303' article_processing_charge: No article_type: original author: - first_name: Atul full_name: Varshney, Atul id: 2A2006B2-F248-11E8-B48F-1D18A9856A87 last_name: Varshney orcid: 0000-0002-3072-5999 - first_name: Victor full_name: Steinberg, Victor last_name: Steinberg citation: ama: Varshney A, Steinberg V. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 2018;3(10). doi:10.1103/PhysRevFluids.3.103303 apa: Varshney, A., & Steinberg, V. (2018). Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. American Physical Society. https://doi.org/10.1103/PhysRevFluids.3.103303 chicago: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids. American Physical Society, 2018. https://doi.org/10.1103/PhysRevFluids.3.103303. ieee: A. Varshney and V. Steinberg, “Mixing layer instability and vorticity amplification in a creeping viscoelastic flow,” Physical Review Fluids, vol. 3, no. 10. American Physical Society, 2018. ista: Varshney A, Steinberg V. 2018. Mixing layer instability and vorticity amplification in a creeping viscoelastic flow. Physical Review Fluids. 3(10), 103303. mla: Varshney, Atul, and Victor Steinberg. “Mixing Layer Instability and Vorticity Amplification in a Creeping Viscoelastic Flow.” Physical Review Fluids, vol. 3, no. 10, 103303, American Physical Society, 2018, doi:10.1103/PhysRevFluids.3.103303. short: A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018). date_created: 2018-12-11T11:44:10Z date_published: 2018-10-16T00:00:00Z date_updated: 2023-09-13T08:57:05Z day: '16' ddc: - '532' department: - _id: BjHo doi: 10.1103/PhysRevFluids.3.103303 ec_funded: 1 external_id: isi: - '000447469200001' file: - access_level: open_access checksum: 7fc0a2322214d1c04debef36d5bf2e8a content_type: application/pdf creator: system date_created: 2018-12-12T10:13:56Z date_updated: 2020-07-14T12:45:04Z file_id: '5043' file_name: IST-2018-1062-v1+1_PhysRevFluids.3.103303.pdf file_size: 1838431 relation: main_file file_date_updated: 2020-07-14T12:45:04Z has_accepted_license: '1' intvolume: ' 3' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Physical Review Fluids publication_status: published publisher: American Physical Society publist_id: '8039' pubrep_id: '1062' quality_controlled: '1' scopus_import: '1' status: public title: Mixing layer instability and vorticity amplification in a creeping viscoelastic flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 3 year: '2018' ... --- _id: '43' abstract: - lang: eng text: 'The initial amount of pathogens required to start an infection within a susceptible host is called the infective dose and is known to vary to a large extent between different pathogen species. We investigate the hypothesis that the differences in infective doses are explained by the mode of action in the underlying mechanism of pathogenesis: Pathogens with locally acting mechanisms tend to have smaller infective doses than pathogens with distantly acting mechanisms. While empirical evidence tends to support the hypothesis, a formal theoretical explanation has been lacking. We give simple analytical models to gain insight into this phenomenon and also investigate a stochastic, spatially explicit, mechanistic within-host model for toxin-dependent bacterial infections. The model shows that pathogens secreting locally acting toxins have smaller infective doses than pathogens secreting diffusive toxins, as hypothesized. While local pathogenetic mechanisms require smaller infective doses, pathogens with distantly acting toxins tend to spread faster and may cause more damage to the host. The proposed model can serve as a basis for the spatially explicit analysis of various virulence factors also in the context of other problems in infection dynamics.' acknowledgement: J.R. and J.V.A. were also supported by the Academy of Finland Grants 1273253 and 267541. article_processing_charge: No author: - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 - first_name: Eva full_name: Kisdi, Eva last_name: Kisdi - first_name: Jani full_name: Anttila, Jani last_name: Anttila citation: ama: Rybicki J, Kisdi E, Anttila J. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 2018;115(42):10690-10695. doi:10.1073/pnas.1721061115 apa: Rybicki, J., Kisdi, E., & Anttila, J. (2018). Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1721061115 chicago: Rybicki, Joel, Eva Kisdi, and Jani Anttila. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1721061115. ieee: J. Rybicki, E. Kisdi, and J. Anttila, “Model of bacterial toxin-dependent pathogenesis explains infective dose,” PNAS, vol. 115, no. 42. National Academy of Sciences, pp. 10690–10695, 2018. ista: Rybicki J, Kisdi E, Anttila J. 2018. Model of bacterial toxin-dependent pathogenesis explains infective dose. PNAS. 115(42), 10690–10695. mla: Rybicki, Joel, et al. “Model of Bacterial Toxin-Dependent Pathogenesis Explains Infective Dose.” PNAS, vol. 115, no. 42, National Academy of Sciences, 2018, pp. 10690–95, doi:10.1073/pnas.1721061115. short: J. Rybicki, E. Kisdi, J. Anttila, PNAS 115 (2018) 10690–10695. date_created: 2018-12-11T11:44:19Z date_published: 2018-10-02T00:00:00Z date_updated: 2023-09-13T08:57:38Z day: '02' ddc: - '570' - '577' department: - _id: DaAl doi: 10.1073/pnas.1721061115 ec_funded: 1 external_id: isi: - '000447491300057' file: - access_level: open_access checksum: df7ac544a587c06b75692653b9fabd18 content_type: application/pdf creator: dernst date_created: 2019-04-09T08:02:50Z date_updated: 2020-07-14T12:46:26Z file_id: '6258' file_name: 2018_PNAS_Rybicki.pdf file_size: 4070777 relation: main_file file_date_updated: 2020-07-14T12:46:26Z has_accepted_license: '1' intvolume: ' 115' isi: 1 issue: '42' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 10690 - 10695 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '8011' pubrep_id: '1063' quality_controlled: '1' scopus_import: '1' status: public title: Model of bacterial toxin-dependent pathogenesis explains infective dose type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '13' abstract: - lang: eng text: We propose a new method for fabricating digital objects through reusable silicone molds. Molds are generated by casting liquid silicone into custom 3D printed containers called metamolds. Metamolds automatically define the cuts that are needed to extract the cast object from the silicone mold. The shape of metamolds is designed through a novel segmentation technique, which takes into account both geometric and topological constraints involved in the process of mold casting. Our technique is simple, does not require changing the shape or topology of the input objects, and only requires off-the- shelf materials and technologies. We successfully tested our method on a set of challenging examples with complex shapes and rich geometric detail. © 2018 Association for Computing Machinery. article_number: '136' article_processing_charge: No author: - first_name: Thomas full_name: Alderighi, Thomas last_name: Alderighi - first_name: Luigi full_name: Malomo, Luigi last_name: Malomo - first_name: Daniela full_name: Giorgi, Daniela last_name: Giorgi - first_name: Nico full_name: Pietroni, Nico last_name: Pietroni - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Paolo full_name: Cignoni, Paolo last_name: Cignoni citation: ama: 'Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. Metamolds: Computational design of silicone molds. ACM Trans Graph. 2018;37(4). doi:10.1145/3197517.3201381' apa: 'Alderighi, T., Malomo, L., Giorgi, D., Pietroni, N., Bickel, B., & Cignoni, P. (2018). Metamolds: Computational design of silicone molds. ACM Trans. Graph. ACM. https://doi.org/10.1145/3197517.3201381' chicago: 'Alderighi, Thomas, Luigi Malomo, Daniela Giorgi, Nico Pietroni, Bernd Bickel, and Paolo Cignoni. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph. ACM, 2018. https://doi.org/10.1145/3197517.3201381.' ieee: 'T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, and P. Cignoni, “Metamolds: Computational design of silicone molds,” ACM Trans. Graph., vol. 37, no. 4. ACM, 2018.' ista: 'Alderighi T, Malomo L, Giorgi D, Pietroni N, Bickel B, Cignoni P. 2018. Metamolds: Computational design of silicone molds. ACM Trans. Graph. 37(4), 136.' mla: 'Alderighi, Thomas, et al. “Metamolds: Computational Design of Silicone Molds.” ACM Trans. Graph., vol. 37, no. 4, 136, ACM, 2018, doi:10.1145/3197517.3201381.' short: T. Alderighi, L. Malomo, D. Giorgi, N. Pietroni, B. Bickel, P. Cignoni, ACM Trans. Graph. 37 (2018). date_created: 2018-12-11T11:44:09Z date_published: 2018-08-04T00:00:00Z date_updated: 2023-09-13T08:56:07Z day: '04' ddc: - '004' department: - _id: BeBi doi: 10.1145/3197517.3201381 ec_funded: 1 external_id: isi: - '000448185000097' file: - access_level: open_access checksum: 61d46273dca4de626accef1d17a0aaad content_type: application/pdf creator: system date_created: 2018-12-12T10:18:52Z date_updated: 2020-07-14T12:44:43Z file_id: '5374' file_name: IST-2018-1038-v1+1_metamolds_authorversion.pdf file_size: 91939066 relation: main_file file_date_updated: 2020-07-14T12:44:43Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '4' language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: ACM Trans. Graph. publication_status: published publisher: ACM publist_id: '8043' pubrep_id: '1038' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/metamolds-molding-a-mold/ scopus_import: '1' status: public title: 'Metamolds: Computational design of silicone molds' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2018' ... --- _id: '137' abstract: - lang: eng text: Fluorescent sensors are an essential part of the experimental toolbox of the life sciences, where they are used ubiquitously to visualize intra- and extracellular signaling. In the brain, optical neurotransmitter sensors can shed light on temporal and spatial aspects of signal transmission by directly observing, for instance, neurotransmitter release and spread. Here we report the development and application of the first optical sensor for the amino acid glycine, which is both an inhibitory neurotransmitter and a co-agonist of the N-methyl-d-aspartate receptors (NMDARs) involved in synaptic plasticity. Computational design of a glycine-specific binding protein allowed us to produce the optical glycine FRET sensor (GlyFS), which can be used with single and two-photon excitation fluorescence microscopy. We took advantage of this newly developed sensor to test predictions about the uneven spatial distribution of glycine in extracellular space and to demonstrate that extracellular glycine levels are controlled by plasticity-inducing stimuli. article_processing_charge: No article_type: original author: - first_name: William full_name: Zhang, William last_name: Zhang - first_name: Michel full_name: Herde, Michel last_name: Herde - first_name: Joshua full_name: Mitchell, Joshua last_name: Mitchell - first_name: Jason full_name: Whitfield, Jason last_name: Whitfield - first_name: Andreas full_name: Wulff, Andreas last_name: Wulff - first_name: Vanessa full_name: Vongsouthi, Vanessa last_name: Vongsouthi - first_name: Inmaculada full_name: Sanchez Romero, Inmaculada id: 3D9C5D30-F248-11E8-B48F-1D18A9856A87 last_name: Sanchez Romero - first_name: Polina full_name: Gulakova, Polina last_name: Gulakova - first_name: Daniel full_name: Minge, Daniel last_name: Minge - first_name: Björn full_name: Breithausen, Björn last_name: Breithausen - first_name: Susanne full_name: Schoch, Susanne last_name: Schoch - first_name: Harald L full_name: Janovjak, Harald L id: 33BA6C30-F248-11E8-B48F-1D18A9856A87 last_name: Janovjak orcid: 0000-0002-8023-9315 - first_name: Colin full_name: Jackson, Colin last_name: Jackson - first_name: Christian full_name: Henneberger, Christian last_name: Henneberger citation: ama: Zhang W, Herde M, Mitchell J, et al. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 2018;14(9):861-869. doi:10.1038/s41589-018-0108-2 apa: Zhang, W., Herde, M., Mitchell, J., Whitfield, J., Wulff, A., Vongsouthi, V., … Henneberger, C. (2018). Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0108-2 chicago: Zhang, William, Michel Herde, Joshua Mitchell, Jason Whitfield, Andreas Wulff, Vanessa Vongsouthi, Inmaculada Sanchez-Romero, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0108-2. ieee: W. Zhang et al., “Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS,” Nature Chemical Biology, vol. 14, no. 9. Nature Publishing Group, pp. 861–869, 2018. ista: Zhang W, Herde M, Mitchell J, Whitfield J, Wulff A, Vongsouthi V, Sanchez-Romero I, Gulakova P, Minge D, Breithausen B, Schoch S, Janovjak HL, Jackson C, Henneberger C. 2018. Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS. Nature Chemical Biology. 14(9), 861–869. mla: Zhang, William, et al. “Monitoring Hippocampal Glycine with the Computationally Designed Optical Sensor GlyFS.” Nature Chemical Biology, vol. 14, no. 9, Nature Publishing Group, 2018, pp. 861–69, doi:10.1038/s41589-018-0108-2. short: W. Zhang, M. Herde, J. Mitchell, J. Whitfield, A. Wulff, V. Vongsouthi, I. Sanchez-Romero, P. Gulakova, D. Minge, B. Breithausen, S. Schoch, H.L. Janovjak, C. Jackson, C. Henneberger, Nature Chemical Biology 14 (2018) 861–869. date_created: 2018-12-11T11:44:49Z date_published: 2018-07-30T00:00:00Z date_updated: 2023-09-13T08:58:05Z day: '30' department: - _id: HaJa doi: 10.1038/s41589-018-0108-2 external_id: isi: - '000442174500013' pmid: - '30061718 ' intvolume: ' 14' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30061718 month: '07' oa: 1 oa_version: Submitted Version page: 861 - 869 pmid: 1 project: - _id: 255BFFFA-B435-11E9-9278-68D0E5697425 grant_number: RGY0084/2012 name: In situ real-time imaging of neurotransmitter signaling using designer optical sensors (HFSP Young Investigator) publication: Nature Chemical Biology publication_status: published publisher: Nature Publishing Group publist_id: '7786' quality_controlled: '1' scopus_import: '1' status: public title: Monitoring hippocampal glycine with the computationally designed optical sensor GlyFS type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2018' ... --- _id: '153' abstract: - lang: eng text: Cells migrating in multicellular organisms steadily traverse complex three-dimensional (3D) environments. To decipher the underlying cell biology, current experimental setups either use simplified 2D, tissue-mimetic 3D (e.g., collagen matrices) or in vivo environments. While only in vivo experiments are truly physiological, they do not allow for precise manipulation of environmental parameters. 2D in vitro experiments do allow mechanical and chemical manipulations, but increasing evidence demonstrates substantial differences of migratory mechanisms in 2D and 3D. Here, we describe simple, robust, and versatile “pillar forests” to investigate cell migration in complex but fully controllable 3D environments. Pillar forests are polydimethylsiloxane-based setups, in which two closely adjacent surfaces are interconnected by arrays of micrometer-sized pillars. Changing the pillar shape, size, height and the inter-pillar distance precisely manipulates microenvironmental parameters (e.g., pore sizes, micro-geometry, micro-topology), while being easily combined with chemotactic cues, surface coatings, diverse cell types and advanced imaging techniques. Thus, pillar forests combine the advantages of 2D cell migration assays with the precise definition of 3D environmental parameters. article_processing_charge: No author: - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Anne full_name: Reversat, Anne id: 35B76592-F248-11E8-B48F-1D18A9856A87 last_name: Reversat orcid: 0000-0003-0666-8928 - first_name: Alexander F full_name: Leithner, Alexander F id: 3B1B77E4-F248-11E8-B48F-1D18A9856A87 last_name: Leithner orcid: 0000-0002-1073-744X - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 citation: ama: 'Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. Vol 147. Academic Press; 2018:79-91. doi:10.1016/bs.mcb.2018.07.004' apa: Renkawitz, J., Reversat, A., Leithner, A. F., Merrin, J., & Sixt, M. K. (2018). Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In Methods in Cell Biology (Vol. 147, pp. 79–91). Academic Press. https://doi.org/10.1016/bs.mcb.2018.07.004 chicago: Renkawitz, Jörg, Anne Reversat, Alexander F Leithner, Jack Merrin, and Michael K Sixt. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” In Methods in Cell Biology, 147:79–91. Academic Press, 2018. https://doi.org/10.1016/bs.mcb.2018.07.004. ieee: J. Renkawitz, A. Reversat, A. F. Leithner, J. Merrin, and M. K. Sixt, “Micro-engineered ‘pillar forests’ to study cell migration in complex but controlled 3D environments,” in Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91. ista: 'Renkawitz J, Reversat A, Leithner AF, Merrin J, Sixt MK. 2018.Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments. In: Methods in Cell Biology. vol. 147, 79–91.' mla: Renkawitz, Jörg, et al. “Micro-Engineered ‘Pillar Forests’ to Study Cell Migration in Complex but Controlled 3D Environments.” Methods in Cell Biology, vol. 147, Academic Press, 2018, pp. 79–91, doi:10.1016/bs.mcb.2018.07.004. short: J. Renkawitz, A. Reversat, A.F. Leithner, J. Merrin, M.K. Sixt, in:, Methods in Cell Biology, Academic Press, 2018, pp. 79–91. date_created: 2018-12-11T11:44:54Z date_published: 2018-07-27T00:00:00Z date_updated: 2023-09-13T08:56:35Z day: '27' department: - _id: MiSi - _id: NanoFab doi: 10.1016/bs.mcb.2018.07.004 external_id: isi: - '000452412300006' pmid: - '30165964' intvolume: ' 147' isi: 1 language: - iso: eng month: '07' oa_version: None page: 79 - 91 pmid: 1 publication: Methods in Cell Biology publication_identifier: issn: - 0091679X publication_status: published publisher: Academic Press publist_id: '7768' quality_controlled: '1' scopus_import: '1' status: public title: Micro-engineered “pillar forests” to study cell migration in complex but controlled 3D environments type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 147 year: '2018' ... --- _id: '54' abstract: - lang: eng text: During epithelial tissue development, repair, and homeostasis, adherens junctions (AJs) ensure intercellular adhesion and tissue integrity while allowing for cell and tissue dynamics. Mechanical forces play critical roles in AJs’ composition and dynamics. Recent findings highlight that beyond a well-established role in reinforcing cell-cell adhesion, AJ mechanosensitivity promotes junctional remodeling and polarization, thereby regulating critical processes such as cell intercalation, division, and collective migration. Here, we provide an integrated view of mechanosensing mechanisms that regulate cell-cell contact composition, geometry, and integrity under tension and highlight pivotal roles for mechanosensitive AJ remodeling in preserving epithelial integrity and sustaining tissue dynamics. acknowledgement: Research in the Bellaïche laboratory is supported by the European Research Council (ERC Advanced, TiMoprh, 340784), the Fondation ARC pour la Recherche sur le Cancer (SL220130607097), the Agence Nationale de la Recherche (ANR lLabex DEEP; 11-LBX-0044, ANR-10-IDEX-0001-02), the Centre National de la Recherche Scientifique, the Institut National de la Santé et de la Recherche Médicale, and Institut Curie and PSL Research University funding or grants. article_processing_charge: No article_type: review author: - first_name: Diana C full_name: Nunes Pinheiro, Diana C id: 2E839F16-F248-11E8-B48F-1D18A9856A87 last_name: Nunes Pinheiro orcid: 0000-0003-4333-7503 - first_name: Yohanns full_name: Bellaïche, Yohanns last_name: Bellaïche citation: ama: Nunes Pinheiro DC, Bellaïche Y. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 2018;47(1):3-19. doi:10.1016/j.devcel.2018.09.014 apa: Nunes Pinheiro, D. C., & Bellaïche, Y. (2018). Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. Cell Press. https://doi.org/10.1016/j.devcel.2018.09.014 chicago: Nunes Pinheiro, Diana C, and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell. Cell Press, 2018. https://doi.org/10.1016/j.devcel.2018.09.014. ieee: D. C. Nunes Pinheiro and Y. Bellaïche, “Mechanical force-driven adherents junction remodeling and epithelial dynamics,” Developmental Cell, vol. 47, no. 1. Cell Press, pp. 3–19, 2018. ista: Nunes Pinheiro DC, Bellaïche Y. 2018. Mechanical force-driven adherents junction remodeling and epithelial dynamics. Developmental Cell. 47(1), 3–19. mla: Nunes Pinheiro, Diana C., and Yohanns Bellaïche. “Mechanical Force-Driven Adherents Junction Remodeling and Epithelial Dynamics.” Developmental Cell, vol. 47, no. 1, Cell Press, 2018, pp. 3–19, doi:10.1016/j.devcel.2018.09.014. short: D.C. Nunes Pinheiro, Y. Bellaïche, Developmental Cell 47 (2018) 3–19. date_created: 2018-12-11T11:44:23Z date_published: 2018-10-08T00:00:00Z date_updated: 2023-09-13T08:54:38Z day: '08' department: - _id: CaHe doi: 10.1016/j.devcel.2018.09.014 external_id: isi: - '000446579900002' intvolume: ' 47' isi: 1 issue: '1' language: - iso: eng main_file_link: - url: https://doi.org/10.1016/j.devcel.2018.09.014 month: '10' oa_version: Published Version page: 3 - 19 publication: Developmental Cell publication_status: published publisher: Cell Press publist_id: '8000' quality_controlled: '1' scopus_import: '1' status: public title: Mechanical force-driven adherents junction remodeling and epithelial dynamics type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 47 year: '2018' ... --- _id: '276' abstract: - lang: eng text: Directed migration of cells relies on their ability to sense directional guidance cues and to interact with pericellular structures in order to transduce contractile cytoskeletal- into mechanical forces. These biomechanical processes depend highly on microenvironmental factors such as exposure to 2D surfaces or 3D matrices. In vivo, the majority of cells are exposed to 3D environments. Data on 3D cell migration are mostly derived from intravital microscopy or collagen-based in vitro assays. Both approaches offer only limited controlla-bility of experimental conditions. Here, we developed an automated microfluidic system that allows positioning of cells in 3D microenvironments containing highly controlled diffusion-based chemokine gradients. Tracking migration in such gradients was feasible in real time at the single cell level. Moreover, the setup allowed on-chip immunocytochemistry and thus linking of functional with phenotypical properties in individual cells. Spatially defined retrieval of cells from the device allows down-stream off-chip analysis. Using dendritic cells as a model, our setup specifically allowed us for the first time to quantitate key migration characteristics of cells exposed to identical gradients of the chemokine CCL19 yet placed on 2D vs in 3D environments. Migration properties between 2D and 3D migration were distinct. Morphological features of cells migrating in an in vitro 3D environment were similar to those of cells migrating in animal tissues, but different from cells migrating on a surface. Our system thus offers a highly controllable in vitro-mimic of a 3D environment that cells traffic in vivo. acknowledgement: This work was supported by the Swiss National Science Foundation (MD-PhD fellowships, 323530_164221 to C.F.; and 323630_151483 to A.J.; grant PZ00P3_144863 to M.R, grant 31003A_156431 to T.S.; PZ00P3_148000 to C.T.B.; PZ00P3_154733 to M.M.), a Novartis “FreeNovation” grant to M.M. and T.S. and an EMBO long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409) to J.R.. M.R. was supported by the Gebert Rüf Foundation (GRS 058/14). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. article_number: e0198330 article_processing_charge: No article_type: original author: - first_name: Corina full_name: Frick, Corina last_name: Frick - first_name: Philip full_name: Dettinger, Philip last_name: Dettinger - first_name: Jörg full_name: Renkawitz, Jörg id: 3F0587C8-F248-11E8-B48F-1D18A9856A87 last_name: Renkawitz orcid: 0000-0003-2856-3369 - first_name: Annaïse full_name: Jauch, Annaïse last_name: Jauch - first_name: Christoph full_name: Berger, Christoph last_name: Berger - first_name: Mike full_name: Recher, Mike last_name: Recher - first_name: Timm full_name: Schroeder, Timm last_name: Schroeder - first_name: Matthias full_name: Mehling, Matthias last_name: Mehling citation: ama: Frick C, Dettinger P, Renkawitz J, et al. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 2018;13(6). doi:10.1371/journal.pone.0198330 apa: Frick, C., Dettinger, P., Renkawitz, J., Jauch, A., Berger, C., Recher, M., … Mehling, M. (2018). Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0198330 chicago: Frick, Corina, Philip Dettinger, Jörg Renkawitz, Annaïse Jauch, Christoph Berger, Mike Recher, Timm Schroeder, and Matthias Mehling. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0198330. ieee: C. Frick et al., “Nano-scale microfluidics to study 3D chemotaxis at the single cell level,” PLoS One, vol. 13, no. 6. Public Library of Science, 2018. ista: Frick C, Dettinger P, Renkawitz J, Jauch A, Berger C, Recher M, Schroeder T, Mehling M. 2018. Nano-scale microfluidics to study 3D chemotaxis at the single cell level. PLoS One. 13(6), e0198330. mla: Frick, Corina, et al. “Nano-Scale Microfluidics to Study 3D Chemotaxis at the Single Cell Level.” PLoS One, vol. 13, no. 6, e0198330, Public Library of Science, 2018, doi:10.1371/journal.pone.0198330. short: C. Frick, P. Dettinger, J. Renkawitz, A. Jauch, C. Berger, M. Recher, T. Schroeder, M. Mehling, PLoS One 13 (2018). date_created: 2018-12-11T11:45:34Z date_published: 2018-06-07T00:00:00Z date_updated: 2023-09-13T09:00:15Z day: '07' ddc: - '570' department: - _id: MiSi doi: 10.1371/journal.pone.0198330 external_id: isi: - '000434384900031' file: - access_level: open_access checksum: 95fc5dc3938b3ad3b7697d10c83cc143 content_type: application/pdf creator: dernst date_created: 2018-12-17T14:10:32Z date_updated: 2020-07-14T12:45:45Z file_id: '5709' file_name: 2018_Plos_Frick.pdf file_size: 7682167 relation: main_file file_date_updated: 2020-07-14T12:45:45Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '7626' quality_controlled: '1' scopus_import: '1' status: public title: Nano-scale microfluidics to study 3D chemotaxis at the single cell level 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 13 year: '2018' ... --- _id: '283' abstract: - lang: eng text: Light represents the principal signal driving circadian clock entrainment. However, how light influences the evolution of the clock remains poorly understood. The cavefish Phreatichthys andruzzii represents a fascinating model to explore how evolution under extreme aphotic conditions shapes the circadian clock, since in this species the clock is unresponsive to light. We have previously demonstrated that loss-of-function mutations targeting non-visual opsins contribute in part to this blind clock phenotype. Here, we have compared orthologs of two core clock genes that play a key role in photic entrainment, cry1a and per2, in both zebrafish and P. andruzzii. We encountered aberrantly spliced variants for the P. andruzzii per2 transcript. The most abundant transcript encodes a truncated protein lacking the C-terminal Cry binding domain and incorporating an intronic, transposon-derived coding sequence. We demonstrate that the transposon insertion leads to a predominantly cytoplasmic localization of the cavefish Per2 protein in contrast to the zebrafish ortholog which is distributed in both the nucleus and cytoplasm. Thus, it seems that during evolution in complete darkness, the photic entrainment pathway of the circadian clock has been subject to mutation at multiple levels, extending from opsin photoreceptors to nuclear effectors. article_number: '8754' article_processing_charge: No author: - first_name: Rosa Maria full_name: Ceinos, Rosa Maria last_name: Ceinos - first_name: Elena full_name: Frigato, Elena last_name: Frigato - first_name: Cristina full_name: Pagano, Cristina last_name: Pagano - first_name: Nadine full_name: Frohlich, Nadine last_name: Frohlich - first_name: Pietro full_name: Negrini, Pietro last_name: Negrini - first_name: Nicola full_name: Cavallari, Nicola id: 457160E6-F248-11E8-B48F-1D18A9856A87 last_name: Cavallari - first_name: Daniela full_name: Vallone, Daniela last_name: Vallone - first_name: Silvia full_name: Fuselli, Silvia last_name: Fuselli - first_name: Cristiano full_name: Bertolucci, Cristiano last_name: Bertolucci - first_name: Nicholas S full_name: Foulkes, Nicholas S last_name: Foulkes citation: ama: Ceinos RM, Frigato E, Pagano C, et al. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-27080-2 apa: Ceinos, R. M., Frigato, E., Pagano, C., Frohlich, N., Negrini, P., Cavallari, N., … Foulkes, N. S. (2018). Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-27080-2 chicago: Ceinos, Rosa Maria, Elena Frigato, Cristina Pagano, Nadine Frohlich, Pietro Negrini, Nicola Cavallari, Daniela Vallone, Silvia Fuselli, Cristiano Bertolucci, and Nicholas S Foulkes. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-27080-2. ieee: R. M. Ceinos et al., “Mutations in blind cavefish target the light regulated circadian clock gene period 2,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018. ista: Ceinos RM, Frigato E, Pagano C, Frohlich N, Negrini P, Cavallari N, Vallone D, Fuselli S, Bertolucci C, Foulkes NS. 2018. Mutations in blind cavefish target the light regulated circadian clock gene period 2. Scientific Reports. 8(1), 8754. mla: Ceinos, Rosa Maria, et al. “Mutations in Blind Cavefish Target the Light Regulated Circadian Clock Gene Period 2.” Scientific Reports, vol. 8, no. 1, 8754, Nature Publishing Group, 2018, doi:10.1038/s41598-018-27080-2. short: R.M. Ceinos, E. Frigato, C. Pagano, N. Frohlich, P. Negrini, N. Cavallari, D. Vallone, S. Fuselli, C. Bertolucci, N.S. Foulkes, Scientific Reports 8 (2018). date_created: 2018-12-11T11:45:36Z date_published: 2018-06-08T00:00:00Z date_updated: 2023-09-13T08:59:27Z day: '08' ddc: - '570' department: - _id: EvBe doi: 10.1038/s41598-018-27080-2 external_id: isi: - '000434640800008' file: - access_level: open_access checksum: 9c3942d772f84f3df032ffde0ed9a8ea content_type: application/pdf creator: dernst date_created: 2018-12-17T13:04:46Z date_updated: 2020-07-14T12:45:49Z file_id: '5707' file_name: 2018_ScientificReports_Ceinos.pdf file_size: 1855324 relation: main_file file_date_updated: 2020-07-14T12:45:49Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '7616' quality_controlled: '1' scopus_import: '1' status: public title: Mutations in blind cavefish target the light regulated circadian clock gene period 2 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2018' ... --- _id: '81' abstract: - lang: eng text: We solve the offline monitoring problem for timed propositional temporal logic (TPTL), interpreted over dense-time Boolean signals. The variant of TPTL we consider extends linear temporal logic (LTL) with clock variables and reset quantifiers, providing a mechanism to specify real-time constraints. We first describe a general monitoring algorithm based on an exhaustive computation of the set of satisfying clock assignments as a finite union of zones. We then propose a specialized monitoring algorithm for the one-variable case using a partition of the time domain based on the notion of region equivalence, whose complexity is linear in the length of the signal, thereby generalizing a known result regarding the monitoring of metric temporal logic (MTL). The region and zone representations of time constraints are known from timed automata verification and can also be used in the discrete-time case. Our prototype implementation appears to outperform previous discrete-time implementations of TPTL monitoring, alternative_title: - LNCS article_processing_charge: No author: - first_name: Adrian full_name: Elgyütt, Adrian id: 4A2E9DBA-F248-11E8-B48F-1D18A9856A87 last_name: Elgyütt - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - 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: 'Elgyütt A, Ferrere T, Henzinger TA. Monitoring temporal logic with clock variables. In: Vol 11022. Springer; 2018:53-70. doi:10.1007/978-3-030-00151-3_4' apa: 'Elgyütt, A., Ferrere, T., & Henzinger, T. A. (2018). Monitoring temporal logic with clock variables (Vol. 11022, pp. 53–70). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_4' chicago: Elgyütt, Adrian, Thomas Ferrere, and Thomas A Henzinger. “Monitoring Temporal Logic with Clock Variables,” 11022:53–70. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_4. ieee: 'A. Elgyütt, T. Ferrere, and T. A. Henzinger, “Monitoring temporal logic with clock variables,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Beijing, China, 2018, vol. 11022, pp. 53–70.' ista: 'Elgyütt A, Ferrere T, Henzinger TA. 2018. Monitoring temporal logic with clock variables. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 53–70.' mla: Elgyütt, Adrian, et al. Monitoring Temporal Logic with Clock Variables. Vol. 11022, Springer, 2018, pp. 53–70, doi:10.1007/978-3-030-00151-3_4. short: A. Elgyütt, T. Ferrere, T.A. Henzinger, in:, Springer, 2018, pp. 53–70. conference: end_date: 2018-09-06 location: Beijing, China name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' start_date: 2018-09-04 date_created: 2018-12-11T11:44:31Z date_published: 2018-08-26T00:00:00Z date_updated: 2023-09-13T08:58:34Z day: '26' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-00151-3_4 external_id: isi: - '000884993200004' file: - access_level: open_access checksum: e5d81c9b50a6bd9d8a2c16953aad7e23 content_type: application/pdf creator: dernst date_created: 2020-10-09T06:24:21Z date_updated: 2020-10-09T06:24:21Z file_id: '8638' file_name: 2018_LNCS_Elgyuett.pdf file_size: 537219 relation: main_file success: 1 file_date_updated: 2020-10-09T06:24:21Z has_accepted_license: '1' intvolume: ' 11022' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 53 - 70 project: - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_status: published publisher: Springer publist_id: '7973' quality_controlled: '1' scopus_import: '1' status: public title: Monitoring temporal logic with clock variables type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11022 year: '2018' ... --- _id: '76' abstract: - lang: eng text: 'Consider a fully-connected synchronous distributed system consisting of n nodes, where up to f nodes may be faulty and every node starts in an arbitrary initial state. In the synchronous C-counting problem, all nodes need to eventually agree on a counter that is increased by one modulo C in each round for given C>1. In the self-stabilising firing squad problem, the task is to eventually guarantee that all non-faulty nodes have simultaneous responses to external inputs: if a subset of the correct nodes receive an external “go” signal as input, then all correct nodes should agree on a round (in the not-too-distant future) in which to jointly output a “fire” signal. Moreover, no node should generate a “fire” signal without some correct node having previously received a “go” signal as input. We present a framework reducing both tasks to binary consensus at very small cost. For example, we obtain a deterministic algorithm for self-stabilising Byzantine firing squads with optimal resilience f<n/3, asymptotically optimal stabilisation and response time O(f), and message size O(log f). As our framework does not restrict the type of consensus routines used, we also obtain efficient randomised solutions.' article_processing_charge: Yes (via OA deal) author: - first_name: Christoph full_name: Lenzen, Christoph last_name: Lenzen - first_name: Joel full_name: Rybicki, Joel id: 334EFD2E-F248-11E8-B48F-1D18A9856A87 last_name: Rybicki orcid: 0000-0002-6432-6646 citation: ama: Lenzen C, Rybicki J. Near-optimal self-stabilising counting and firing squads. Distributed Computing. 2018. doi:10.1007/s00446-018-0342-6 apa: Lenzen, C., & Rybicki, J. (2018). Near-optimal self-stabilising counting and firing squads. Distributed Computing. Springer. https://doi.org/10.1007/s00446-018-0342-6 chicago: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing. Springer, 2018. https://doi.org/10.1007/s00446-018-0342-6. ieee: C. Lenzen and J. Rybicki, “Near-optimal self-stabilising counting and firing squads,” Distributed Computing. Springer, 2018. ista: Lenzen C, Rybicki J. 2018. Near-optimal self-stabilising counting and firing squads. Distributed Computing. mla: Lenzen, Christoph, and Joel Rybicki. “Near-Optimal Self-Stabilising Counting and Firing Squads.” Distributed Computing, Springer, 2018, doi:10.1007/s00446-018-0342-6. short: C. Lenzen, J. Rybicki, Distributed Computing (2018). date_created: 2018-12-11T11:44:30Z date_published: 2018-09-12T00:00:00Z date_updated: 2023-09-13T09:01:06Z day: '12' ddc: - '000' department: - _id: DaAl doi: 10.1007/s00446-018-0342-6 external_id: isi: - '000475627800005' file: - access_level: open_access checksum: 872db70bba9b401500abe3c6ae2f1a61 content_type: application/pdf creator: dernst date_created: 2018-12-17T14:21:22Z date_updated: 2020-07-14T12:48:01Z file_id: '5711' file_name: 2018_DistributedComputing_Lenzen.pdf file_size: 799337 relation: main_file file_date_updated: 2020-07-14T12:48:01Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Distributed Computing publication_status: published publisher: Springer publist_id: '7978' quality_controlled: '1' scopus_import: '1' status: public title: Near-optimal self-stabilising counting and firing squads 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '530' abstract: - lang: eng text: Inclusion–exclusion is an effective method for computing the volume of a union of measurable sets. We extend it to multiple coverings, proving short inclusion–exclusion formulas for the subset of Rn covered by at least k balls in a finite set. We implement two of the formulas in dimension n=3 and report on results obtained with our software. article_processing_charge: No author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham citation: ama: 'Edelsbrunner H, Iglesias Ham M. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 2018;68:119-133. doi:10.1016/j.comgeo.2017.06.014' apa: 'Edelsbrunner, H., & Iglesias Ham, M. (2018). Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. Elsevier. https://doi.org/10.1016/j.comgeo.2017.06.014' chicago: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications. Elsevier, 2018. https://doi.org/10.1016/j.comgeo.2017.06.014.' ieee: 'H. Edelsbrunner and M. Iglesias Ham, “Multiple covers with balls I: Inclusion–exclusion,” Computational Geometry: Theory and Applications, vol. 68. Elsevier, pp. 119–133, 2018.' ista: 'Edelsbrunner H, Iglesias Ham M. 2018. Multiple covers with balls I: Inclusion–exclusion. Computational Geometry: Theory and Applications. 68, 119–133.' mla: 'Edelsbrunner, Herbert, and Mabel Iglesias Ham. “Multiple Covers with Balls I: Inclusion–Exclusion.” Computational Geometry: Theory and Applications, vol. 68, Elsevier, 2018, pp. 119–33, doi:10.1016/j.comgeo.2017.06.014.' short: 'H. Edelsbrunner, M. Iglesias Ham, Computational Geometry: Theory and Applications 68 (2018) 119–133.' date_created: 2018-12-11T11:46:59Z date_published: 2018-03-01T00:00:00Z date_updated: 2023-09-13T08:59:00Z day: '01' ddc: - '000' department: - _id: HeEd doi: 10.1016/j.comgeo.2017.06.014 ec_funded: 1 external_id: isi: - '000415778300010' file: - access_level: open_access checksum: 1c8d58cd489a66cd3e2064c1141c8c5e content_type: application/pdf creator: dernst date_created: 2019-02-12T06:47:52Z date_updated: 2020-07-14T12:46:38Z file_id: '5953' file_name: 2018_Edelsbrunner.pdf file_size: 708357 relation: main_file file_date_updated: 2020-07-14T12:46:38Z has_accepted_license: '1' intvolume: ' 68' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Preprint page: 119 - 133 project: - _id: 255D761E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '318493' name: Topological Complex Systems publication: 'Computational Geometry: Theory and Applications' publication_status: published publisher: Elsevier publist_id: '7289' quality_controlled: '1' scopus_import: '1' status: public title: 'Multiple covers with balls I: Inclusion–exclusion' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 68 year: '2018' ... --- _id: '307' abstract: - lang: eng text: 'Spontaneous emission spectra of two initially excited closely spaced identical atoms are very sensitive to the strength and the direction of the applied magnetic field. We consider the relevant schemes that ensure the determination of the mutual spatial orientation of the atoms and the distance between them by entirely optical means. A corresponding theoretical description is given accounting for the dipole-dipole interaction between the two atoms in the presence of a magnetic field and for polarizations of the quantum field interacting with magnetic sublevels of the two-atom system. ' acknowledgement: The work was partially supported by Russian Foundation for Basic Research (Grant No. 15-02-05657a) and by the Basic research program of Higher School of Economics (HSE). article_number: ' 043812 ' article_processing_charge: No article_type: original author: - first_name: Elena full_name: Redchenko, Elena id: 2C21D6E8-F248-11E8-B48F-1D18A9856A87 last_name: Redchenko - first_name: Alexander full_name: Makarov, Alexander last_name: Makarov - first_name: Vladimir full_name: Yudson, Vladimir last_name: Yudson citation: ama: Redchenko E, Makarov A, Yudson V. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043812 apa: Redchenko, E., Makarov, A., & Yudson, V. (2018). Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043812 chicago: Redchenko, Elena, Alexander Makarov, and Vladimir Yudson. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043812. ieee: E. Redchenko, A. Makarov, and V. Yudson, “Nanoscopy of pairs of atoms by fluorescence in a magnetic field,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018. ista: Redchenko E, Makarov A, Yudson V. 2018. Nanoscopy of pairs of atoms by fluorescence in a magnetic field. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4), 043812. mla: Redchenko, Elena, et al. “Nanoscopy of Pairs of Atoms by Fluorescence in a Magnetic Field.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, 043812, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043812. short: E. Redchenko, A. Makarov, V. Yudson, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018). date_created: 2018-12-11T11:45:44Z date_published: 2018-04-09T00:00:00Z date_updated: 2023-09-13T09:00:41Z day: '09' department: - _id: JoFi doi: 10.1103/PhysRevA.97.043812 external_id: arxiv: - '1712.10127' isi: - '000429454000015' intvolume: ' 97' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.10127 month: '04' oa: 1 oa_version: Submitted Version publication: ' Physical Review A - Atomic, Molecular, and Optical Physics' publication_status: published publisher: American Physical Society publist_id: '7572' quality_controlled: '1' scopus_import: '1' status: public title: Nanoscopy of pairs of atoms by fluorescence in a magnetic field type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 97 year: '2018' ... --- _id: '279' abstract: - lang: eng text: 'Background: Natural selection shapes cancer genomes. Previous studies used signatures of positive selection to identify genes driving malignant transformation. However, the contribution of negative selection against somatic mutations that affect essential tumor functions or specific domains remains a controversial topic. Results: Here, we analyze 7546 individual exomes from 26 tumor types from TCGA data to explore the portion of the cancer exome under negative selection. Although we find most of the genes neutrally evolving in a pan-cancer framework, we identify essential cancer genes and immune-exposed protein regions under significant negative selection. Moreover, our simulations suggest that the amount of negative selection is underestimated. We therefore choose an empirical approach to identify genes, functions, and protein regions under negative selection. We find that expression and mutation status of negatively selected genes is indicative of patient survival. Processes that are most strongly conserved are those that play fundamental cellular roles such as protein synthesis, glucose metabolism, and molecular transport. Intriguingly, we observe strong signals of selection in the immunopeptidome and proteins controlling peptide exposition, highlighting the importance of immune surveillance evasion. Additionally, tumor type-specific immune activity correlates with the strength of negative selection on human epitopes. Conclusions: In summary, our results show that negative selection is a hallmark of cell essentiality and immune response in cancer. The functional domains identified could be exploited therapeutically, ultimately allowing for the development of novel cancer treatments.' article_number: '67' article_processing_charge: No author: - first_name: Luis full_name: Zapata, Luis last_name: Zapata - first_name: Oriol full_name: Pich, Oriol last_name: Pich - first_name: Luis full_name: Serrano, Luis last_name: Serrano - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephan full_name: Ossowski, Stephan last_name: Ossowski - first_name: Martin full_name: Schaefer, Martin last_name: Schaefer citation: ama: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 2018;19. doi:10.1186/s13059-018-1434-0 apa: Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. BioMed Central. https://doi.org/10.1186/s13059-018-1434-0 chicago: Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology. BioMed Central, 2018. https://doi.org/10.1186/s13059-018-1434-0. ieee: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome,” Genome Biology, vol. 19. BioMed Central, 2018. ista: Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Genome Biology. 19, 67. mla: Zapata, Luis, et al. “Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Genome Biology, vol. 19, 67, BioMed Central, 2018, doi:10.1186/s13059-018-1434-0. short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, Genome Biology 19 (2018). date_created: 2018-12-11T11:45:35Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-13T09:01:32Z day: '31' ddc: - '570' department: - _id: FyKo doi: 10.1186/s13059-018-1434-0 ec_funded: 1 external_id: isi: - '000433986200001' file: - access_level: open_access checksum: f3e4922486bd9bf1483271bdbed394a7 content_type: application/pdf creator: dernst date_created: 2018-12-17T14:05:01Z date_updated: 2020-07-14T12:45:47Z file_id: '5708' file_name: 2018_GenomeBiology_Zapata.pdf file_size: 1414722 relation: main_file file_date_updated: 2020-07-14T12:45:47Z has_accepted_license: '1' intvolume: ' 19' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Published Version project: - _id: 26120F5C-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335980' name: Systematic investigation of epistasis in molecular evolution publication: Genome Biology publication_status: published publisher: BioMed Central publist_id: '7620' quality_controlled: '1' related_material: record: - id: '9811' relation: research_data status: public - id: '9812' relation: research_data status: public scopus_import: '1' status: public title: Negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '145' abstract: - lang: eng text: Aged proteins can become hazardous to cellular function, by accumulating molecular damage. This implies that cells should preferentially rely on newly produced ones. We tested this hypothesis in cultured hippocampal neurons, focusing on synaptic transmission. We found that newly synthesized vesicle proteins were incorporated in the actively recycling pool of vesicles responsible for all neurotransmitter release during physiological activity. We observed this for the calcium sensor Synaptotagmin 1, for the neurotransmitter transporter VGAT, and for the fusion protein VAMP2 (Synaptobrevin 2). Metabolic labeling of proteins and visualization by secondary ion mass spectrometry enabled us to query the entire protein makeup of the actively recycling vesicles, which we found to be younger than that of non-recycling vesicles. The young vesicle proteins remained in use for up to ~ 24 h, during which they participated in recycling a few hundred times. They were afterward reluctant to release and were degraded after an additional ~ 24–48 h. We suggest that the recycling pool of synaptic vesicles relies on newly synthesized proteins, while the inactive reserve pool contains older proteins. acknowledgement: We thank Reinhard Jahn for providing a plasmid for YFP-SNAP25. We thank Erwin Neher for help with the development of the mathematical model of the synaptic vesicle life cycle. We thank Martin Meschkat, Andreas Höbartner, Annedore Punge, and Peer Hoopmann for help with the experiments. We thank Burkhard Rammner for providing the illustrations of synaptic vesicle and protein dynamics. We thank Manuel Maidorn, Martin Helm, and Katharina N. Richter for critically reading the manuscript. S.T. was supported by an Excellence Stipend of the Göttingen Graduate School for Neurosciences, Biophysics, and Molecular Biosciences (GGNB). E.F.F. is a recipient of long-term fellowships from the European Molecular Biology Organization (ALTF_797-2012) and from the Human Frontier Science Program (HFSP_LT000830/2013). The work was supported by grants to S.O.R. from the European Research Council (ERC-2013-CoG NeuroMolAnatomy) and from the Deutsche Forschungsgemeinschaft (Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, SFB1190/P09, SFB889/A05, and SFB1286/A03, and DFG RI 1967 7/1). The nanoSIMS instrument was funded by the German Federal Ministry of Education and Research (03F0626A). article_number: e98044 article_processing_charge: No article_type: original author: - first_name: Sven M full_name: Truckenbrodt, Sven M id: 45812BD4-F248-11E8-B48F-1D18A9856A87 last_name: Truckenbrodt - first_name: Abhiyan full_name: Viplav, Abhiyan last_name: Viplav - first_name: Sebsatian full_name: Jähne, Sebsatian last_name: Jähne - first_name: Angela full_name: Vogts, Angela last_name: Vogts - first_name: Annette full_name: Denker, Annette last_name: Denker - first_name: Hanna full_name: Wildhagen, Hanna last_name: Wildhagen - first_name: Eugenio full_name: Fornasiero, Eugenio last_name: Fornasiero - first_name: Silvio full_name: Rizzoli, Silvio last_name: Rizzoli citation: ama: Truckenbrodt SM, Viplav A, Jähne S, et al. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 2018;37(15). doi:10.15252/embj.201798044 apa: Truckenbrodt, S. M., Viplav, A., Jähne, S., Vogts, A., Denker, A., Wildhagen, H., … Rizzoli, S. (2018). Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. Wiley. https://doi.org/10.15252/embj.201798044 chicago: Truckenbrodt, Sven M, Abhiyan Viplav, Sebsatian Jähne, Angela Vogts, Annette Denker, Hanna Wildhagen, Eugenio Fornasiero, and Silvio Rizzoli. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal. Wiley, 2018. https://doi.org/10.15252/embj.201798044. ieee: S. M. Truckenbrodt et al., “Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission,” The EMBO Journal, vol. 37, no. 15. Wiley, 2018. ista: Truckenbrodt SM, Viplav A, Jähne S, Vogts A, Denker A, Wildhagen H, Fornasiero E, Rizzoli S. 2018. Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission. The EMBO Journal. 37(15), e98044. mla: Truckenbrodt, Sven M., et al. “Newly Produced Synaptic Vesicle Proteins Are Preferentially Used in Synaptic Transmission.” The EMBO Journal, vol. 37, no. 15, e98044, Wiley, 2018, doi:10.15252/embj.201798044. short: S.M. Truckenbrodt, A. Viplav, S. Jähne, A. Vogts, A. Denker, H. Wildhagen, E. Fornasiero, S. Rizzoli, The EMBO Journal 37 (2018). date_created: 2018-12-11T11:44:52Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-09-13T09:02:48Z day: '01' ddc: - '570' department: - _id: JoDa doi: 10.15252/embj.201798044 external_id: isi: - '000440416900005' pmid: - '29950309' file: - access_level: open_access checksum: a540feb6c9af6aefc78de531461a8835 content_type: application/pdf creator: dernst date_created: 2018-12-17T14:17:29Z date_updated: 2020-07-14T12:44:56Z file_id: '5710' file_name: 2018_EMBO_Truckenbrodt.pdf file_size: 2846470 relation: main_file file_date_updated: 2020-07-14T12:44:56Z has_accepted_license: '1' intvolume: ' 37' isi: 1 issue: '15' language: - iso: eng month: '08' oa: 1 oa_version: Published Version pmid: 1 publication: The EMBO Journal publication_identifier: issn: - 0261-4189 publication_status: published publisher: Wiley publist_id: '7778' quality_controlled: '1' scopus_import: '1' status: public title: Newly produced synaptic vesicle proteins are preferentially used in synaptic transmission 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2018' ... --- _id: '462' abstract: - lang: eng text: 'AtNHX5 and AtNHX6 are endosomal Na+,K+/H+ antiporters that are critical for growth and development in Arabidopsis, but the mechanism behind their action remains unknown. Here, we report that AtNHX5 and AtNHX6, functioning as H+ leak, control auxin homeostasis and auxin-mediated development. We found that nhx5 nhx6 exhibited growth variations of auxin-related defects. We further showed that nhx5 nhx6 was affected in auxin homeostasis. Genetic analysis showed that AtNHX5 and AtNHX6 were required for the function of the ER-localized auxin transporter PIN5. Although AtNHX5 and AtNHX6 were co-localized with PIN5 at ER, they did not interact directly. Instead, the conserved acidic residues in AtNHX5 and AtNHX6, which are essential for exchange activity, were required for PIN5 function. AtNHX5 and AtNHX6 regulated the pH in ER. Overall, AtNHX5 and AtNHX6 may regulate auxin transport across the ER via the pH gradient created by their transport activity. H+-leak pathway provides a fine-tuning mechanism that controls cellular auxin fluxes. ' acknowledgement: 'This work was supported by the National Natural Science Foundation of China (31571464, 31371438 and 31070222 to Q.S.Q.), the National Basic Research Program of China (973 project, 2013CB429904 to Q.S.Q.), the Research Fund for the Doctoral Program of Higher Education of China (20130211110001 to Q.S.Q.), the Ministry of Education, Youth and Sports of the Czech Republic (the National Program for Sustainability I, LO1204), and The Czech Science Foundation GAČR (GA13–40637S) to JF. We thank Dr. Tom J. Guilfoyle for DR5::GUS line and Dr. Jia Li for pBIB‐RFP vector and DR5::GFP line. We thank Liping Guan and Yang Zhao for their help with the confocal microscope assay. ' article_processing_charge: No article_type: original author: - first_name: Ligang full_name: Fan, Ligang last_name: Fan - first_name: Lei full_name: Zhao, Lei last_name: Zhao - first_name: Wei full_name: Hu, Wei last_name: Hu - first_name: Weina full_name: Li, Weina last_name: Li - first_name: Ondřej full_name: Novák, Ondřej last_name: Novák - first_name: Miroslav full_name: Strnad, Miroslav last_name: Strnad - first_name: Sibu full_name: Simon, Sibu id: 4542EF9A-F248-11E8-B48F-1D18A9856A87 last_name: Simon orcid: 0000-0002-1998-6741 - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jinbo full_name: Shen, Jinbo last_name: Shen - first_name: Liwen full_name: Jiang, Liwen last_name: Jiang - first_name: Quan full_name: Qiu, Quan last_name: Qiu citation: ama: Fan L, Zhao L, Hu W, et al. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 2018;41:850-864. doi:10.1111/pce.13153 apa: Fan, L., Zhao, L., Hu, W., Li, W., Novák, O., Strnad, M., … Qiu, Q. (2018). NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. Wiley-Blackwell. https://doi.org/10.1111/pce.13153 chicago: Fan, Ligang, Lei Zhao, Wei Hu, Weina Li, Ondřej Novák, Miroslav Strnad, Sibu Simon, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment. Wiley-Blackwell, 2018. https://doi.org/10.1111/pce.13153. ieee: L. Fan et al., “NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development,” Plant, Cell and Environment, vol. 41. Wiley-Blackwell, pp. 850–864, 2018. ista: Fan L, Zhao L, Hu W, Li W, Novák O, Strnad M, Simon S, Friml J, Shen J, Jiang L, Qiu Q. 2018. NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development. Plant, Cell and Environment. 41, 850–864. mla: Fan, Ligang, et al. “NHX Antiporters Regulate the PH of Endoplasmic Reticulum and Auxin-Mediated Development.” Plant, Cell and Environment, vol. 41, Wiley-Blackwell, 2018, pp. 850–64, doi:10.1111/pce.13153. short: L. Fan, L. Zhao, W. Hu, W. Li, O. Novák, M. Strnad, S. Simon, J. Friml, J. Shen, L. Jiang, Q. Qiu, Plant, Cell and Environment 41 (2018) 850–864. date_created: 2018-12-11T11:46:36Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-09-13T09:03:18Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/pce.13153 external_id: isi: - '000426870500012' pmid: - '29360148' file: - access_level: open_access checksum: 6a20f843565f962cb20281cdf5e40914 content_type: application/pdf creator: dernst date_created: 2019-11-18T16:22:22Z date_updated: 2020-07-14T12:46:32Z file_id: '7042' file_name: 2018_PlantCellEnv_Fan.pdf file_size: 1937976 relation: main_file file_date_updated: 2020-07-14T12:46:32Z has_accepted_license: '1' intvolume: ' 41' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 850 - 864 pmid: 1 publication: Plant, Cell and Environment publication_status: published publisher: Wiley-Blackwell publist_id: '7359' quality_controlled: '1' scopus_import: '1' status: public title: NHX antiporters regulate the pH of endoplasmic reticulum and auxin-mediated development 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 41 year: '2018' ... --- _id: '519' abstract: - lang: eng text: 'This study treats with the influence of a symmetry-breaking transversal magnetic field on the nonlinear dynamics of ferrofluidic Taylor-Couette flow – flow confined between two concentric independently rotating cylinders. We detected alternating ‘flip’ solutions which are flow states featuring typical characteristics of slow-fast-dynamics in dynamical systems. The flip corresponds to a temporal change in the axial wavenumber and we find them to appear either as pure 2-fold axisymmetric (due to the symmetry-breaking nature of the applied transversal magnetic field) or involving non-axisymmetric, helical modes in its interim solution. The latter ones show features of typical ribbon solutions. In any case the flip solutions have a preferential first axial wavenumber which corresponds to the more stable state (slow dynamics) and second axial wavenumber, corresponding to the short appearing more unstable state (fast dynamics). However, in both cases the flip time grows exponential with increasing the magnetic field strength before the flip solutions, living on 2-tori invariant manifolds, cease to exist, with lifetime going to infinity. Further we show that ferrofluidic flow turbulence differ from the classical, ordinary (usually at high Reynolds number) turbulence. The applied magnetic field hinders the free motion of ferrofluid partials and therefore smoothen typical turbulent quantities and features so that speaking of mildly chaotic dynamics seems to be a more appropriate expression for the observed motion. ' acknowledgement: S.Altmeyer is a Serra Húnter Fellow article_processing_charge: No article_type: original author: - first_name: Sebastian full_name: Altmeyer, Sebastian id: 2EE67FDC-F248-11E8-B48F-1D18A9856A87 last_name: Altmeyer orcid: 0000-0001-5964-0203 citation: ama: Altmeyer S. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 2018;452:427-441. doi:10.1016/j.jmmm.2017.12.073 apa: Altmeyer, S. (2018). Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. Elsevier. https://doi.org/10.1016/j.jmmm.2017.12.073 chicago: Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials. Elsevier, 2018. https://doi.org/10.1016/j.jmmm.2017.12.073. ieee: S. Altmeyer, “Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow,” Journal of Magnetism and Magnetic Materials, vol. 452. Elsevier, pp. 427–441, 2018. ista: Altmeyer S. 2018. Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow. Journal of Magnetism and Magnetic Materials. 452, 427–441. mla: Altmeyer, Sebastian. “Non-Linear Dynamics and Alternating ‘Flip’ Solutions in Ferrofluidic Taylor-Couette Flow.” Journal of Magnetism and Magnetic Materials, vol. 452, Elsevier, 2018, pp. 427–41, doi:10.1016/j.jmmm.2017.12.073. short: S. Altmeyer, Journal of Magnetism and Magnetic Materials 452 (2018) 427–441. date_created: 2018-12-11T11:46:56Z date_published: 2018-04-15T00:00:00Z date_updated: 2023-09-13T09:03:44Z day: '15' ddc: - '530' department: - _id: BjHo doi: 10.1016/j.jmmm.2017.12.073 external_id: isi: - '000425547700061' file: - access_level: open_access checksum: 431f5cd4a628d7ca21161f82b14ccb4f content_type: application/pdf creator: dernst date_created: 2020-05-14T14:41:17Z date_updated: 2020-07-14T12:46:37Z file_id: '7838' file_name: 2018_Magnetism_Altmeyer.pdf file_size: 17309535 relation: main_file file_date_updated: 2020-07-14T12:46:37Z has_accepted_license: '1' intvolume: ' 452' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 427 - 441 publication: Journal of Magnetism and Magnetic Materials publication_status: published publisher: Elsevier publist_id: '7297' quality_controlled: '1' scopus_import: '1' status: public title: Non-linear dynamics and alternating ‘flip’ solutions in ferrofluidic Taylor-Couette flow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 452 year: '2018' ... --- _id: '5679' abstract: - lang: eng text: We study the almost-sure termination problem for probabilistic programs. First, we show that supermartingales with lower bounds on conditional absolute difference provide a sound approach for the almost-sure termination problem. Moreover, using this approach we can obtain explicit optimal bounds on tail probabilities of non-termination within a given number of steps. Second, we present a new approach based on Central Limit Theorem for the almost-sure termination problem, and show that this approach can establish almost-sure termination of programs which none of the existing approaches can handle. Finally, we discuss algorithmic approaches for the two above methods that lead to automated analysis techniques for almost-sure termination of probabilistic programs. alternative_title: - LNCS article_processing_charge: No author: - first_name: Mingzhang full_name: Huang, Mingzhang last_name: Huang - first_name: Hongfei full_name: Fu, Hongfei last_name: Fu - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X citation: ama: 'Huang M, Fu H, Chatterjee K. New approaches for almost-sure termination of probabilistic programs. In: Ryu S, ed. Vol 11275. Springer; 2018:181-201. doi:10.1007/978-3-030-02768-1_11' apa: 'Huang, M., Fu, H., & Chatterjee, K. (2018). New approaches for almost-sure termination of probabilistic programs. In S. Ryu (Ed.) (Vol. 11275, pp. 181–201). Presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand: Springer. https://doi.org/10.1007/978-3-030-02768-1_11' chicago: Huang, Mingzhang, Hongfei Fu, and Krishnendu Chatterjee. “New Approaches for Almost-Sure Termination of Probabilistic Programs.” edited by Sukyoung Ryu, 11275:181–201. Springer, 2018. https://doi.org/10.1007/978-3-030-02768-1_11. ieee: M. Huang, H. Fu, and K. Chatterjee, “New approaches for almost-sure termination of probabilistic programs,” presented at the 16th Asian Symposium on Programming Languages and Systems, APLAS, Wellington, New Zealand, 2018, vol. 11275, pp. 181–201. ista: Huang M, Fu H, Chatterjee K. 2018. New approaches for almost-sure termination of probabilistic programs. 16th Asian Symposium on Programming Languages and Systems, APLAS, LNCS, vol. 11275, 181–201. mla: Huang, Mingzhang, et al. New Approaches for Almost-Sure Termination of Probabilistic Programs. Edited by Sukyoung Ryu, vol. 11275, Springer, 2018, pp. 181–201, doi:10.1007/978-3-030-02768-1_11. short: M. Huang, H. Fu, K. Chatterjee, in:, S. Ryu (Ed.), Springer, 2018, pp. 181–201. conference: end_date: 2018-12-06 location: Wellington, New Zealand name: 16th Asian Symposium on Programming Languages and Systems, APLAS start_date: 2018-12-02 date_created: 2018-12-16T22:59:20Z date_published: 2018-12-01T00:00:00Z date_updated: 2023-09-13T09:02:22Z day: '01' department: - _id: KrCh doi: 10.1007/978-3-030-02768-1_11 editor: - first_name: Sukyoung full_name: Ryu, Sukyoung last_name: Ryu external_id: arxiv: - '1806.06683' isi: - '000916310900011' intvolume: ' 11275' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1806.06683 month: '12' oa: 1 oa_version: Preprint page: 181-201 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification publication_identifier: isbn: - '9783030027674' issn: - '03029743' publisher: Springer quality_controlled: '1' scopus_import: '1' status: public title: New approaches for almost-sure termination of probabilistic programs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11275 year: '2018' ... --- _id: '546' abstract: - lang: eng text: The precise control of neural stem cell (NSC) proliferation and differentiation is crucial for the development and function of the human brain. Here, we review the emerging links between the alteration of embryonic and adult neurogenesis and the etiology of neuropsychiatric disorders (NPDs) such as autism spectrum disorders (ASDs) and schizophrenia (SCZ), as well as the advances in stem cell-based modeling and the novel therapeutic targets derived from these studies. article_processing_charge: No author: - first_name: Roberto full_name: Sacco, Roberto id: 42C9F57E-F248-11E8-B48F-1D18A9856A87 last_name: Sacco - first_name: Emanuele full_name: Cacci, Emanuele last_name: Cacci - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Sacco R, Cacci E, Novarino G. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 2018;48(2):131-138. doi:10.1016/j.conb.2017.12.005 apa: Sacco, R., Cacci, E., & Novarino, G. (2018). Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. Elsevier. https://doi.org/10.1016/j.conb.2017.12.005 chicago: Sacco, Roberto, Emanuele Cacci, and Gaia Novarino. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology. Elsevier, 2018. https://doi.org/10.1016/j.conb.2017.12.005. ieee: R. Sacco, E. Cacci, and G. Novarino, “Neural stem cells in neuropsychiatric disorders,” Current Opinion in Neurobiology, vol. 48, no. 2. Elsevier, pp. 131–138, 2018. ista: Sacco R, Cacci E, Novarino G. 2018. Neural stem cells in neuropsychiatric disorders. Current Opinion in Neurobiology. 48(2), 131–138. mla: Sacco, Roberto, et al. “Neural Stem Cells in Neuropsychiatric Disorders.” Current Opinion in Neurobiology, vol. 48, no. 2, Elsevier, 2018, pp. 131–38, doi:10.1016/j.conb.2017.12.005. short: R. Sacco, E. Cacci, G. Novarino, Current Opinion in Neurobiology 48 (2018) 131–138. date_created: 2018-12-11T11:47:06Z date_published: 2018-02-01T00:00:00Z date_updated: 2023-09-13T09:01:56Z day: '01' department: - _id: GaNo doi: 10.1016/j.conb.2017.12.005 external_id: isi: - '000427101600018' intvolume: ' 48' isi: 1 issue: '2' language: - iso: eng month: '02' oa_version: None page: 131 - 138 publication: Current Opinion in Neurobiology publication_status: published publisher: Elsevier publist_id: '7268' quality_controlled: '1' scopus_import: '1' status: public title: Neural stem cells in neuropsychiatric disorders type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 48 year: '2018' ... --- _id: '9812' abstract: - lang: eng text: This document contains the full list of genes with their respective significance and dN/dS values. (TXT 4499Â kb) article_processing_charge: No author: - first_name: Luis full_name: Zapata, Luis last_name: Zapata - first_name: Oriol full_name: Pich, Oriol last_name: Pich - first_name: Luis full_name: Serrano, Luis last_name: Serrano - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephan full_name: Ossowski, Stephan last_name: Ossowski - first_name: Martin full_name: Schaefer, Martin last_name: Schaefer citation: ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401414.v1' apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401414.v1' chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401414.v1.' ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.' ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401414.v1.' mla: 'Zapata, Luis, et al. Additional File 2: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401414.v1.' short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018). date_created: 2021-08-06T12:58:25Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-13T09:01:31Z day: '31' department: - _id: FyKo doi: 10.6084/m9.figshare.6401414.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.6401414.v1 month: '05' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '279' relation: used_in_publication status: public status: public title: 'Additional file 2: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '9811' abstract: - lang: eng text: This document contains additional supporting evidence presented as supplemental tables. (XLSX 50Â kb) article_processing_charge: No author: - first_name: Luis full_name: Zapata, Luis last_name: Zapata - first_name: Oriol full_name: Pich, Oriol last_name: Pich - first_name: Luis full_name: Serrano, Luis last_name: Serrano - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 - first_name: Stephan full_name: Ossowski, Stephan last_name: Ossowski - first_name: Martin full_name: Schaefer, Martin last_name: Schaefer citation: ama: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. 2018. doi:10.6084/m9.figshare.6401390.v1' apa: 'Zapata, L., Pich, O., Serrano, L., Kondrashov, F., Ossowski, S., & Schaefer, M. (2018). Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome. Springer Nature. https://doi.org/10.6084/m9.figshare.6401390.v1' chicago: 'Zapata, Luis, Oriol Pich, Luis Serrano, Fyodor Kondrashov, Stephan Ossowski, and Martin Schaefer. “Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.6401390.v1.' ieee: 'L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, and M. Schaefer, “Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome.” Springer Nature, 2018.' ista: 'Zapata L, Pich O, Serrano L, Kondrashov F, Ossowski S, Schaefer M. 2018. Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome, Springer Nature, 10.6084/m9.figshare.6401390.v1.' mla: 'Zapata, Luis, et al. Additional File 1: Of Negative Selection in Tumor Genome Evolution Acts on Essential Cellular Functions and the Immunopeptidome. Springer Nature, 2018, doi:10.6084/m9.figshare.6401390.v1.' short: L. Zapata, O. Pich, L. Serrano, F. Kondrashov, S. Ossowski, M. Schaefer, (2018). date_created: 2021-08-06T12:53:49Z date_published: 2018-05-31T00:00:00Z date_updated: 2023-09-13T09:01:31Z day: '31' department: - _id: FyKo doi: 10.6084/m9.figshare.6401390.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.6401390.v1 month: '05' oa: 1 oa_version: Preprint publisher: Springer Nature related_material: record: - id: '279' relation: used_in_publication status: public status: public title: 'Additional file 1: Of negative selection in tumor genome evolution acts on essential cellular functions and the immunopeptidome' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '20' abstract: - lang: eng text: 'Background: Norepinephrine (NE) signaling has a key role in white adipose tissue (WAT) functions, including lipolysis, free fatty acid liberation and, under certain conditions, conversion of white into brite (brown-in-white) adipocytes. However, acute effects of NE stimulation have not been described at the transcriptional network level. Results: We used RNA-seq to uncover a broad transcriptional response. The inference of protein-protein and protein-DNA interaction networks allowed us to identify a set of immediate-early genes (IEGs) with high betweenness, validating our approach and suggesting a hierarchical control of transcriptional regulation. In addition, we identified a transcriptional regulatory network with IEGs as master regulators, including HSF1 and NFIL3 as novel NE-induced IEG candidates. Moreover, a functional enrichment analysis and gene clustering into functional modules suggest a crosstalk between metabolic, signaling, and immune responses. Conclusions: Altogether, our network biology approach explores for the first time the immediate-early systems level response of human adipocytes to acute sympathetic activation, thereby providing a first network basis of early cell fate programs and crosstalks between metabolic and transcriptional networks required for proper WAT function.' acknowledgement: This work was funded by the German Centre for Diabetes Research (DZD) and the Austrian Science Fund (FWF, P25729-B19). article_processing_charge: No article_type: original author: - first_name: Juan full_name: Higareda Almaraz, Juan last_name: Higareda Almaraz - first_name: Michael full_name: Karbiener, Michael last_name: Karbiener - first_name: Maude full_name: Giroud, Maude last_name: Giroud - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Teresa full_name: Gerhalter, Teresa last_name: Gerhalter - first_name: Stephan full_name: Herzig, Stephan last_name: Herzig - first_name: Marcel full_name: Scheideler, Marcel last_name: Scheideler citation: ama: Higareda Almaraz J, Karbiener M, Giroud M, et al. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 2018;19(1). doi:10.1186/s12864-018-5173-0 apa: Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. BioMed Central. https://doi.org/10.1186/s12864-018-5173-0 chicago: Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics. BioMed Central, 2018. https://doi.org/10.1186/s12864-018-5173-0. ieee: J. Higareda Almaraz et al., “Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes,” BMC Genomics, vol. 19, no. 1. BioMed Central, 2018. ista: Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. BMC Genomics. 19(1). mla: Higareda Almaraz, Juan, et al. “Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” BMC Genomics, vol. 19, no. 1, BioMed Central, 2018, doi:10.1186/s12864-018-5173-0. short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, BMC Genomics 19 (2018). date_created: 2018-12-11T11:44:12Z date_published: 2018-11-03T00:00:00Z date_updated: 2023-09-13T09:10:47Z day: '03' ddc: - '570' department: - _id: SiHi doi: 10.1186/s12864-018-5173-0 external_id: isi: - '000450976700002' file: - access_level: open_access checksum: a56516e734dab589dc7f3e1915973b4d content_type: application/pdf creator: dernst date_created: 2018-12-17T14:52:57Z date_updated: 2020-07-14T12:45:23Z file_id: '5712' file_name: 2018_BMCGenomics_Higareda.pdf file_size: 4629784 relation: main_file file_date_updated: 2020-07-14T12:45:23Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: BMC Genomics publication_identifier: issn: - 1471-2164 publication_status: published publisher: BioMed Central publist_id: '8035' quality_controlled: '1' related_material: record: - id: '9807' relation: research_data status: public - id: '9808' relation: research_data status: public scopus_import: '1' status: public title: Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '107' abstract: - lang: eng text: 'We introduce the notion of “non-malleable codes” which relaxes the notion of error correction and error detection. Informally, a code is non-malleable if the message contained in a modified codeword is either the original message, or a completely unrelated value. In contrast to error correction and error detection, non-malleability can be achieved for very rich classes of modifications. We construct an efficient code that is non-malleable with respect to modifications that affect each bit of the codeword arbitrarily (i.e., leave it untouched, flip it, or set it to either 0 or 1), but independently of the value of the other bits of the codeword. Using the probabilistic method, we also show a very strong and general statement: there exists a non-malleable code for every “small enough” family F of functions via which codewords can be modified. Although this probabilistic method argument does not directly yield efficient constructions, it gives us efficient non-malleable codes in the random-oracle model for very general classes of tampering functions—e.g., functions where every bit in the tampered codeword can depend arbitrarily on any 99% of the bits in the original codeword. As an application of non-malleable codes, we show that they provide an elegant algorithmic solution to the task of protecting functionalities implemented in hardware (e.g., signature cards) against “tampering attacks.” In such attacks, the secret state of a physical system is tampered, in the hopes that future interaction with the modified system will reveal some secret information. This problem was previously studied in the work of Gennaro et al. in 2004 under the name “algorithmic tamper proof security” (ATP). We show that non-malleable codes can be used to achieve important improvements over the prior work. In particular, we show that any functionality can be made secure against a large class of tampering attacks, simply by encoding the secret state with a non-malleable code while it is stored in memory.' article_number: '20' article_processing_charge: No article_type: original author: - first_name: Stefan full_name: Dziembowski, Stefan last_name: Dziembowski - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Daniel full_name: Wichs, Daniel last_name: Wichs citation: ama: Dziembowski S, Pietrzak KZ, Wichs D. Non-malleable codes. Journal of the ACM. 2018;65(4). doi:10.1145/3178432 apa: Dziembowski, S., Pietrzak, K. Z., & Wichs, D. (2018). Non-malleable codes. Journal of the ACM. ACM. https://doi.org/10.1145/3178432 chicago: Dziembowski, Stefan, Krzysztof Z Pietrzak, and Daniel Wichs. “Non-Malleable Codes.” Journal of the ACM. ACM, 2018. https://doi.org/10.1145/3178432. ieee: S. Dziembowski, K. Z. Pietrzak, and D. Wichs, “Non-malleable codes,” Journal of the ACM, vol. 65, no. 4. ACM, 2018. ista: Dziembowski S, Pietrzak KZ, Wichs D. 2018. Non-malleable codes. Journal of the ACM. 65(4), 20. mla: Dziembowski, Stefan, et al. “Non-Malleable Codes.” Journal of the ACM, vol. 65, no. 4, 20, ACM, 2018, doi:10.1145/3178432. short: S. Dziembowski, K.Z. Pietrzak, D. Wichs, Journal of the ACM 65 (2018). date_created: 2018-12-11T11:44:40Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-09-13T09:05:17Z day: '01' department: - _id: KrPi doi: 10.1145/3178432 ec_funded: 1 external_id: isi: - '000442938200004' intvolume: ' 65' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2009/608 month: '08' oa: 1 oa_version: Preprint project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks - _id: 258C570E-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '259668' name: Provable Security for Physical Cryptography publication: Journal of the ACM publication_status: published publisher: ACM publist_id: '7947' quality_controlled: '1' scopus_import: '1' status: public title: Non-malleable codes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 65 year: '2018' ... --- _id: '5676' abstract: - lang: eng text: 'In epithelial tissues, cells tightly connect to each other through cell–cell junctions, but they also present the remarkable capacity of reorganizing themselves without compromising tissue integrity. Upon injury, simple epithelia efficiently resolve small lesions through the action of actin cytoskeleton contractile structures at the wound edge and cellular rearrangements. However, the underlying mechanisms and how they cooperate are still poorly understood. In this study, we combine live imaging and theoretical modeling to reveal a novel and indispensable role for occluding junctions (OJs) in this process. We demonstrate that OJ loss of function leads to defects in wound-closure dynamics: instead of contracting, wounds dramatically increase their area. OJ mutants exhibit phenotypes in cell shape, cellular rearrangements, and mechanical properties as well as in actin cytoskeleton dynamics at the wound edge. We propose that OJs are essential for wound closure by impacting on epithelial mechanics at the tissue level, which in turn is crucial for correct regulation of the cellular events occurring at the wound edge.' article_processing_charge: No author: - first_name: Lara full_name: Carvalho, Lara last_name: Carvalho - first_name: Pedro full_name: Patricio, Pedro last_name: Patricio - first_name: Susana full_name: Ponte, Susana last_name: Ponte - 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: Luis full_name: Almeida, Luis last_name: Almeida - first_name: André S. full_name: Nunes, André S. last_name: Nunes - first_name: Nuno A.M. full_name: Araújo, Nuno A.M. last_name: Araújo - first_name: Antonio full_name: Jacinto, Antonio last_name: Jacinto citation: ama: Carvalho L, Patricio P, Ponte S, et al. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 2018;217(12):4267-4283. doi:10.1083/jcb.201804048 apa: Carvalho, L., Patricio, P., Ponte, S., Heisenberg, C.-P. J., Almeida, L., Nunes, A. S., … Jacinto, A. (2018). Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.201804048 chicago: Carvalho, Lara, Pedro Patricio, Susana Ponte, Carl-Philipp J Heisenberg, Luis Almeida, André S. Nunes, Nuno A.M. Araújo, and Antonio Jacinto. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology. Rockefeller University Press, 2018. https://doi.org/10.1083/jcb.201804048. ieee: L. Carvalho et al., “Occluding junctions as novel regulators of tissue mechanics during wound repair,” Journal of Cell Biology, vol. 217, no. 12. Rockefeller University Press, pp. 4267–4283, 2018. ista: Carvalho L, Patricio P, Ponte S, Heisenberg C-PJ, Almeida L, Nunes AS, Araújo NAM, Jacinto A. 2018. Occluding junctions as novel regulators of tissue mechanics during wound repair. Journal of Cell Biology. 217(12), 4267–4283. mla: Carvalho, Lara, et al. “Occluding Junctions as Novel Regulators of Tissue Mechanics during Wound Repair.” Journal of Cell Biology, vol. 217, no. 12, Rockefeller University Press, 2018, pp. 4267–83, doi:10.1083/jcb.201804048. short: L. Carvalho, P. Patricio, S. Ponte, C.-P.J. Heisenberg, L. Almeida, A.S. Nunes, N.A.M. Araújo, A. Jacinto, Journal of Cell Biology 217 (2018) 4267–4283. date_created: 2018-12-16T22:59:19Z date_published: 2018-12-01T00:00:00Z date_updated: 2023-09-13T09:11:17Z day: '01' department: - _id: CaHe doi: 10.1083/jcb.201804048 ec_funded: 1 external_id: isi: - '000451960800018' pmid: - '30228162 ' intvolume: ' 217' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30228162 month: '12' oa: 1 oa_version: Submitted Version page: 4267-4283 pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Cell Biology publication_identifier: issn: - '00219525' publication_status: published publisher: Rockefeller University Press quality_controlled: '1' scopus_import: '1' status: public title: Occluding junctions as novel regulators of tissue mechanics during wound repair type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 217 year: '2018' ... --- _id: '14224' abstract: - lang: eng text: Clustering is a cornerstone of unsupervised learning which can be thought as disentangling multiple generative mechanisms underlying the data. In this paper we introduce an algorithmic framework to train mixtures of implicit generative models which we particularize for variational autoencoders. Relying on an additional set of discriminators, we propose a competitive procedure in which the models only need to approximate the portion of the data distribution from which they can produce realistic samples. As a byproduct, each model is simpler to train, and a clustering interpretation arises naturally from the partitioning of the training points among the models. We empirically show that our approach splits the training distribution in a reasonable way and increases the quality of the generated samples. article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Damien full_name: Vincent, Damien last_name: Vincent - first_name: Ilya full_name: Tolstikhin, Ilya last_name: Tolstikhin - first_name: Gunnar full_name: Ratsch, Gunnar last_name: Ratsch - first_name: Sylvain full_name: Gelly, Sylvain last_name: Gelly - first_name: Bernhard full_name: Scholkopf, Bernhard last_name: Scholkopf citation: ama: 'Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. Clustering meets implicit generative models. In: 6th International Conference on Learning Representations. ; 2018.' apa: Locatello, F., Vincent, D., Tolstikhin, I., Ratsch, G., Gelly, S., & Scholkopf, B. (2018). Clustering meets implicit generative models. In 6th International Conference on Learning Representations. Vancouver, Canada. chicago: Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Ratsch, Sylvain Gelly, and Bernhard Scholkopf. “Clustering Meets Implicit Generative Models.” In 6th International Conference on Learning Representations, 2018. ieee: F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, and B. Scholkopf, “Clustering meets implicit generative models,” in 6th International Conference on Learning Representations, Vancouver, Canada, 2018. ista: Locatello F, Vincent D, Tolstikhin I, Ratsch G, Gelly S, Scholkopf B. 2018. Clustering meets implicit generative models. 6th International Conference on Learning Representations. International Conference on Machine Learning. mla: Locatello, Francesco, et al. “Clustering Meets Implicit Generative Models.” 6th International Conference on Learning Representations, 2018. short: F. Locatello, D. Vincent, I. Tolstikhin, G. Ratsch, S. Gelly, B. Scholkopf, in:, 6th International Conference on Learning Representations, 2018. conference: end_date: 2018-05-03 location: Vancouver, Canada name: International Conference on Machine Learning start_date: 2018-04-30 date_created: 2023-08-22T14:25:34Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-09-13T09:08:24Z day: '01' department: - _id: FrLo extern: '1' external_id: arxiv: - '1804.11130' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1804.11130 month: '05' oa: 1 oa_version: Preprint publication: 6th International Conference on Learning Representations publication_status: published quality_controlled: '1' scopus_import: '1' status: public title: Clustering meets implicit generative models type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '9807' abstract: - lang: eng text: Table S1. Genes with highest betweenness. Table S2. Local and Master regulators up-regulated. Table S3. Local and Master regulators down-regulated (XLSX 23 kb). article_processing_charge: No author: - first_name: Juan full_name: Higareda Almaraz, Juan last_name: Higareda Almaraz - first_name: Michael full_name: Karbiener, Michael last_name: Karbiener - first_name: Maude full_name: Giroud, Maude last_name: Giroud - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Teresa full_name: Gerhalter, Teresa last_name: Gerhalter - first_name: Stephan full_name: Herzig, Stephan last_name: Herzig - first_name: Marcel full_name: Scheideler, Marcel last_name: Scheideler citation: ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295339.v1' apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295339.v1' chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295339.v1.' ieee: 'J. Higareda Almaraz et al., “Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.' ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295339.v1.' mla: 'Higareda Almaraz, Juan, et al. Additional File 1: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295339.v1.' short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018). date_created: 2021-08-06T12:26:53Z date_published: 2018-11-03T00:00:00Z date_updated: 2023-09-13T09:10:47Z day: '03' department: - _id: SiHi doi: 10.6084/m9.figshare.7295339.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.7295339.v1 month: '11' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '20' relation: used_in_publication status: public status: public title: 'Additional file 1: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '9808' abstract: - lang: eng text: Table S4. Counts per Gene per Million Reads Mapped. (XLSX 2751 kb). article_processing_charge: No author: - first_name: Juan full_name: Higareda Almaraz, Juan last_name: Higareda Almaraz - first_name: Michael full_name: Karbiener, Michael last_name: Karbiener - first_name: Maude full_name: Giroud, Maude last_name: Giroud - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Teresa full_name: Gerhalter, Teresa last_name: Gerhalter - first_name: Stephan full_name: Herzig, Stephan last_name: Herzig - first_name: Marcel full_name: Scheideler, Marcel last_name: Scheideler citation: ama: 'Higareda Almaraz J, Karbiener M, Giroud M, et al. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. 2018. doi:10.6084/m9.figshare.7295369.v1' apa: 'Higareda Almaraz, J., Karbiener, M., Giroud, M., Pauler, F., Gerhalter, T., Herzig, S., & Scheideler, M. (2018). Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes. Springer Nature. https://doi.org/10.6084/m9.figshare.7295369.v1' chicago: 'Higareda Almaraz, Juan, Michael Karbiener, Maude Giroud, Florian Pauler, Teresa Gerhalter, Stephan Herzig, and Marcel Scheideler. “Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes.” Springer Nature, 2018. https://doi.org/10.6084/m9.figshare.7295369.v1.' ieee: 'J. Higareda Almaraz et al., “Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes.” Springer Nature, 2018.' ista: 'Higareda Almaraz J, Karbiener M, Giroud M, Pauler F, Gerhalter T, Herzig S, Scheideler M. 2018. Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes, Springer Nature, 10.6084/m9.figshare.7295369.v1.' mla: 'Higareda Almaraz, Juan, et al. Additional File 3: Of Norepinephrine Triggers an Immediate-Early Regulatory Network Response in Primary Human White Adipocytes. Springer Nature, 2018, doi:10.6084/m9.figshare.7295369.v1.' short: J. Higareda Almaraz, M. Karbiener, M. Giroud, F. Pauler, T. Gerhalter, S. Herzig, M. Scheideler, (2018). date_created: 2021-08-06T12:31:57Z date_published: 2018-11-03T00:00:00Z date_updated: 2023-09-13T09:10:47Z day: '03' department: - _id: SiHi doi: 10.6084/m9.figshare.7295369.v1 main_file_link: - open_access: '1' url: https://doi.org/10.6084/m9.figshare.7295369.v1 month: '11' oa: 1 oa_version: Published Version publisher: Springer Nature related_material: record: - id: '20' relation: used_in_publication status: public status: public title: 'Additional file 3: Of Norepinephrine triggers an immediate-early regulatory network response in primary human white adipocytes' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '193' abstract: - lang: eng text: 'We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki''16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block''16] for analyzing the hardware costs of an iMHF.' acknowledgement: Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria. article_processing_charge: No author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Peter full_name: Gazi, Peter last_name: Gazi - first_name: Chethan full_name: Kamath Hosdurg, Chethan id: 4BD3F30E-F248-11E8-B48F-1D18A9856A87 last_name: Kamath Hosdurg - first_name: Karen full_name: Klein, Karen id: 3E83A2F8-F248-11E8-B48F-1D18A9856A87 last_name: Klein - first_name: Georg F full_name: Osang, Georg F id: 464B40D6-F248-11E8-B48F-1D18A9856A87 last_name: Osang orcid: 0000-0002-8882-5116 - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 - first_name: Lenoid full_name: Reyzin, Lenoid last_name: Reyzin - first_name: Michal full_name: Rolinek, Michal id: 3CB3BC06-F248-11E8-B48F-1D18A9856A87 last_name: Rolinek - first_name: Michal full_name: Rybar, Michal id: 2B3E3DE8-F248-11E8-B48F-1D18A9856A87 last_name: Rybar citation: ama: 'Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ACM; 2018:51-65. doi:10.1145/3196494.3196534' apa: 'Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In Proceedings of the 2018 on Asia Conference on Computer and Communication Security (pp. 51–65). Incheon, Republic of Korea: ACM. https://doi.org/10.1145/3196494.3196534' chicago: Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In Proceedings of the 2018 on Asia Conference on Computer and Communication Security, 51–65. ACM, 2018. https://doi.org/10.1145/3196494.3196534. ieee: J. F. Alwen et al., “On the memory hardness of data independent password hashing functions,” in Proceedings of the 2018 on Asia Conference on Computer and Communication Security, Incheon, Republic of Korea, 2018, pp. 51–65. ista: 'Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.' mla: Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65, doi:10.1145/3196494.3196534. short: J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65. conference: end_date: 2018-06-08 location: Incheon, Republic of Korea name: 'ASIACCS: Asia Conference on Computer and Communications Security ' start_date: 2018-06-04 date_created: 2018-12-11T11:45:07Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-13T09:13:12Z day: '01' department: - _id: KrPi - _id: HeEd - _id: VlKo doi: 10.1145/3196494.3196534 ec_funded: 1 external_id: isi: - '000516620100005' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2016/783 month: '06' oa: 1 oa_version: Submitted Version page: 51 - 65 project: - _id: 25FBA906-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '616160' name: 'Discrete Optimization in Computer Vision: Theory and Practice' - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication: Proceedings of the 2018 on Asia Conference on Computer and Communication Security publication_status: published publisher: ACM publist_id: '7723' quality_controlled: '1' scopus_import: '1' status: public title: On the memory hardness of data independent password hashing functions type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '300' abstract: - lang: eng text: We introduce a formal quantitative notion of “bit security” for a general type of cryptographic games (capturing both decision and search problems), aimed at capturing the intuition that a cryptographic primitive with k-bit security is as hard to break as an ideal cryptographic function requiring a brute force attack on a k-bit key space. Our new definition matches the notion of bit security commonly used by cryptographers and cryptanalysts when studying search (e.g., key recovery) problems, where the use of the traditional definition is well established. However, it produces a quantitatively different metric in the case of decision (indistinguishability) problems, where the use of (a straightforward generalization of) the traditional definition is more problematic and leads to a number of paradoxical situations or mismatches between theoretical/provable security and practical/common sense intuition. Key to our new definition is to consider adversaries that may explicitly declare failure of the attack. We support and justify the new definition by proving a number of technical results, including tight reductions between several standard cryptographic problems, a new hybrid theorem that preserves bit security, and an application to the security analysis of indistinguishability primitives making use of (approximate) floating point numbers. This is the first result showing that (standard precision) 53-bit floating point numbers can be used to achieve 100-bit security in the context of cryptographic primitives with general indistinguishability-based security definitions. Previous results of this type applied only to search problems, or special types of decision problems. acknowledgement: Research supported in part by the Defense Advanced Research Projects Agency (DARPA) and the U.S. Army Research Office under the SafeWare program. Opinions, findings and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views, position or policy of the Government. The second author was also supported by the European Research Council, ERC consolidator grant (682815 - TOCNeT). alternative_title: - LNCS article_processing_charge: No author: - first_name: Daniele full_name: Micciancio, Daniele last_name: Micciancio - first_name: Michael full_name: Walter, Michael id: 488F98B0-F248-11E8-B48F-1D18A9856A87 last_name: Walter orcid: 0000-0003-3186-2482 citation: ama: 'Micciancio D, Walter M. On the bit security of cryptographic primitives. In: Vol 10820. Springer; 2018:3-28. doi:10.1007/978-3-319-78381-9_1' apa: 'Micciancio, D., & Walter, M. (2018). On the bit security of cryptographic primitives (Vol. 10820, pp. 3–28). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78381-9_1' chicago: Micciancio, Daniele, and Michael Walter. “On the Bit Security of Cryptographic Primitives,” 10820:3–28. Springer, 2018. https://doi.org/10.1007/978-3-319-78381-9_1. ieee: 'D. Micciancio and M. Walter, “On the bit security of cryptographic primitives,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10820, pp. 3–28.' ista: 'Micciancio D, Walter M. 2018. On the bit security of cryptographic primitives. Eurocrypt: Advances in Cryptology, LNCS, vol. 10820, 3–28.' mla: Micciancio, Daniele, and Michael Walter. On the Bit Security of Cryptographic Primitives. Vol. 10820, Springer, 2018, pp. 3–28, doi:10.1007/978-3-319-78381-9_1. short: D. Micciancio, M. Walter, in:, Springer, 2018, pp. 3–28. conference: end_date: 2018-05-03 location: Tel Aviv, Israel name: 'Eurocrypt: Advances in Cryptology' start_date: 2018-04-29 date_created: 2018-12-11T11:45:42Z date_published: 2018-03-31T00:00:00Z date_updated: 2023-09-13T09:12:04Z day: '31' department: - _id: KrPi doi: 10.1007/978-3-319-78381-9_1 ec_funded: 1 external_id: isi: - '000517097500001' intvolume: ' 10820' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2018/077 month: '03' oa: 1 oa_version: Submitted Version page: 3 - 28 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_status: published publisher: Springer publist_id: '7581' quality_controlled: '1' scopus_import: '1' status: public title: On the bit security of cryptographic primitives type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10820 year: '2018' ... --- _id: '312' abstract: - lang: eng text: Motivated by biological questions, we study configurations of equal spheres that neither pack nor cover. Placing their centers on a lattice, we define the soft density of the configuration by penalizing multiple overlaps. Considering the 1-parameter family of diagonally distorted 3-dimensional integer lattices, we show that the soft density is maximized at the FCC lattice. acknowledgement: This work was partially supported by the DFG Collaborative Research Center TRR 109, “Discretization in Geometry and Dynamics,” through grant I02979-N35 of the Austrian Science Fund (FWF). article_processing_charge: No article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Mabel full_name: Iglesias Ham, Mabel id: 41B58C0C-F248-11E8-B48F-1D18A9856A87 last_name: Iglesias Ham citation: ama: Edelsbrunner H, Iglesias Ham M. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 2018;32(1):750-782. doi:10.1137/16M1097201 apa: Edelsbrunner, H., & Iglesias Ham, M. (2018). On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/16M1097201 chicago: Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/16M1097201. ieee: H. Edelsbrunner and M. Iglesias Ham, “On the optimality of the FCC lattice for soft sphere packing,” SIAM J Discrete Math, vol. 32, no. 1. Society for Industrial and Applied Mathematics , pp. 750–782, 2018. ista: Edelsbrunner H, Iglesias Ham M. 2018. On the optimality of the FCC lattice for soft sphere packing. SIAM J Discrete Math. 32(1), 750–782. mla: Edelsbrunner, Herbert, and Mabel Iglesias Ham. “On the Optimality of the FCC Lattice for Soft Sphere Packing.” SIAM J Discrete Math, vol. 32, no. 1, Society for Industrial and Applied Mathematics , 2018, pp. 750–82, doi:10.1137/16M1097201. short: H. Edelsbrunner, M. Iglesias Ham, SIAM J Discrete Math 32 (2018) 750–782. date_created: 2018-12-11T11:45:46Z date_published: 2018-03-29T00:00:00Z date_updated: 2023-09-13T09:34:38Z day: '29' department: - _id: HeEd doi: 10.1137/16M1097201 external_id: isi: - '000428958900038' intvolume: ' 32' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://pdfs.semanticscholar.org/d2d5/6da00fbc674e6a8b1bb9d857167e54200dc6.pdf month: '03' oa: 1 oa_version: Submitted Version page: 750 - 782 project: - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: SIAM J Discrete Math publication_identifier: issn: - '08954801' publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '7553' quality_controlled: '1' scopus_import: '1' status: public title: On the optimality of the FCC lattice for soft sphere packing type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2018' ... --- _id: '409' abstract: - lang: eng text: We give a simple proof of T. Stehling's result [4], whereby in any normal tiling of the plane with convex polygons with number of sides not less than six, all tiles except a finite number are hexagons. article_processing_charge: No article_type: original author: - first_name: Arseniy full_name: Akopyan, Arseniy id: 430D2C90-F248-11E8-B48F-1D18A9856A87 last_name: Akopyan orcid: 0000-0002-2548-617X citation: ama: Akopyan A. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 2018;356(4):412-414. doi:10.1016/j.crma.2018.03.005 apa: Akopyan, A. (2018). On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. Elsevier. https://doi.org/10.1016/j.crma.2018.03.005 chicago: Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique. Elsevier, 2018. https://doi.org/10.1016/j.crma.2018.03.005. ieee: A. Akopyan, “On the number of non-hexagons in a planar tiling,” Comptes Rendus Mathematique, vol. 356, no. 4. Elsevier, pp. 412–414, 2018. ista: Akopyan A. 2018. On the number of non-hexagons in a planar tiling. Comptes Rendus Mathematique. 356(4), 412–414. mla: Akopyan, Arseniy. “On the Number of Non-Hexagons in a Planar Tiling.” Comptes Rendus Mathematique, vol. 356, no. 4, Elsevier, 2018, pp. 412–14, doi:10.1016/j.crma.2018.03.005. short: A. Akopyan, Comptes Rendus Mathematique 356 (2018) 412–414. date_created: 2018-12-11T11:46:19Z date_published: 2018-04-01T00:00:00Z date_updated: 2023-09-13T09:34:12Z day: '01' department: - _id: HeEd doi: 10.1016/j.crma.2018.03.005 external_id: arxiv: - '1805.01652' isi: - '000430402700009' intvolume: ' 356' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1805.01652 month: '04' oa: 1 oa_version: Preprint page: 412-414 publication: Comptes Rendus Mathematique publication_identifier: issn: - 1631073X publication_status: published publisher: Elsevier publist_id: '7420' quality_controlled: '1' scopus_import: '1' status: public title: On the number of non-hexagons in a planar tiling type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 356 year: '2018' ... --- _id: '419' abstract: - lang: eng text: 'Reciprocity is a major factor in human social life and accounts for a large part of cooperation in our communities. Direct reciprocity arises when repeated interactions occur between the same individuals. The framework of iterated games formalizes this phenomenon. Despite being introduced more than five decades ago, the concept keeps offering beautiful surprises. Recent theoretical research driven by new mathematical tools has proposed a remarkable dichotomy among the crucial strategies: successful individuals either act as partners or as rivals. Rivals strive for unilateral advantages by applying selfish or extortionate strategies. Partners aim to share the payoff for mutual cooperation, but are ready to fight back when being exploited. Which of these behaviours evolves depends on the environment. Whereas small population sizes and a limited number of rounds favour rivalry, partner strategies are selected when populations are large and relationships stable. Only partners allow for evolution of cooperation, while the rivals’ attempt to put themselves first leads to defection. Hilbe et al. synthesize recent theoretical work on zero-determinant and ‘rival’ versus ‘partner’ strategies in social dilemmas. They describe the environments under which these contrasting selfish or cooperative strategies emerge in evolution.' article_processing_charge: No article_type: review author: - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Hilbe C, Chatterjee K, Nowak M. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2018;2:469–477. doi:10.1038/s41562-018-0320-9 apa: Hilbe, C., Chatterjee, K., & Nowak, M. (2018). Partners and rivals in direct reciprocity. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0320-9 chicago: Hilbe, Christian, Krishnendu Chatterjee, and Martin Nowak. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0320-9. ieee: C. Hilbe, K. Chatterjee, and M. Nowak, “Partners and rivals in direct reciprocity,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 469–477, 2018. ista: Hilbe C, Chatterjee K, Nowak M. 2018. Partners and rivals in direct reciprocity. Nature Human Behaviour. 2, 469–477. mla: Hilbe, Christian, et al. “Partners and Rivals in Direct Reciprocity.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 469–477, doi:10.1038/s41562-018-0320-9. short: C. Hilbe, K. Chatterjee, M. Nowak, Nature Human Behaviour 2 (2018) 469–477. date_created: 2018-12-11T11:46:22Z date_published: 2018-03-19T00:00:00Z date_updated: 2023-09-13T09:38:54Z day: '19' ddc: - '000' department: - _id: KrCh doi: 10.1038/s41562-018-0320-9 ec_funded: 1 external_id: isi: - '000446612000016' file: - access_level: open_access checksum: 571b8cc0ba14e8d5d8b18e439a9835eb content_type: application/pdf creator: dernst date_created: 2019-11-19T08:19:51Z date_updated: 2020-07-14T12:46:25Z file_id: '7052' file_name: 2018_NatureHumanBeh_Hilbe.pdf file_size: 598033 relation: main_file file_date_updated: 2020-07-14T12:46:25Z has_accepted_license: '1' intvolume: ' 2' isi: 1 language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version page: 469–477 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 2584A770-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 23499-N23 name: Modern Graph Algorithmic Techniques in Formal Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Nature Human Behaviour publication_status: published publisher: Nature Publishing Group publist_id: '7404' quality_controlled: '1' related_material: link: - relation: erratum url: http://doi.org/10.1038/s41562-018-0342-3 scopus_import: '1' status: public title: Partners and rivals in direct reciprocity type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2 year: '2018' ... --- _id: '78' abstract: - lang: eng text: We provide a procedure for detecting the sub-segments of an incrementally observed Boolean signal ω that match a given temporal pattern ϕ. As a pattern specification language, we use timed regular expressions, a formalism well-suited for expressing properties of concurrent asynchronous behaviors embedded in metric time. We construct a timed automaton accepting the timed language denoted by ϕ and modify it slightly for the purpose of matching. We then apply zone-based reachability computation to this automaton while it reads ω, and retrieve all the matching segments from the results. Since the procedure is automaton based, it can be applied to patterns specified by other formalisms such as timed temporal logics reducible to timed automata or directly encoded as timed automata. The procedure has been implemented and its performance on synthetic examples is demonstrated. alternative_title: - LNCS article_processing_charge: No author: - first_name: Alexey full_name: Bakhirkin, Alexey last_name: Bakhirkin - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Dejan full_name: Nickovic, Dejan last_name: Nickovic - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Eugene full_name: Asarin, Eugene last_name: Asarin citation: ama: 'Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. Online timed pattern matching using automata. In: Vol 11022. Springer; 2018:215-232. doi:10.1007/978-3-030-00151-3_13' apa: 'Bakhirkin, A., Ferrere, T., Nickovic, D., Maler, O., & Asarin, E. (2018). Online timed pattern matching using automata (Vol. 11022, pp. 215–232). Presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China: Springer. https://doi.org/10.1007/978-3-030-00151-3_13' chicago: Bakhirkin, Alexey, Thomas Ferrere, Dejan Nickovic, Oded Maler, and Eugene Asarin. “Online Timed Pattern Matching Using Automata,” 11022:215–32. Springer, 2018. https://doi.org/10.1007/978-3-030-00151-3_13. ieee: 'A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, and E. Asarin, “Online timed pattern matching using automata,” presented at the FORMATS: Formal Modeling and Analysis of Timed Systems, Bejing, China, 2018, vol. 11022, pp. 215–232.' ista: 'Bakhirkin A, Ferrere T, Nickovic D, Maler O, Asarin E. 2018. Online timed pattern matching using automata. FORMATS: Formal Modeling and Analysis of Timed Systems, LNCS, vol. 11022, 215–232.' mla: Bakhirkin, Alexey, et al. Online Timed Pattern Matching Using Automata. Vol. 11022, Springer, 2018, pp. 215–32, doi:10.1007/978-3-030-00151-3_13. short: A. Bakhirkin, T. Ferrere, D. Nickovic, O. Maler, E. Asarin, in:, Springer, 2018, pp. 215–232. conference: end_date: 2018-09-06 location: Bejing, China name: 'FORMATS: Formal Modeling and Analysis of Timed Systems' start_date: 2018-09-04 date_created: 2018-12-11T11:44:31Z date_published: 2018-08-26T00:00:00Z date_updated: 2023-09-13T09:35:46Z day: '26' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-030-00151-3_13 external_id: isi: - '000884993200013' file: - access_level: open_access checksum: 436b7574934324cfa7d1d3986fddc65b content_type: application/pdf creator: dernst date_created: 2020-05-14T11:34:34Z date_updated: 2020-07-14T12:48:03Z file_id: '7831' file_name: 2018_LNCS_Bakhirkin.pdf file_size: 374851 relation: main_file file_date_updated: 2020-07-14T12:48:03Z has_accepted_license: '1' intvolume: ' 11022' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Submitted Version page: 215 - 232 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_identifier: isbn: - 978-3-030-00150-6 publication_status: published publisher: Springer publist_id: '7976' quality_controlled: '1' scopus_import: '1' status: public title: Online timed pattern matching using automata type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11022 year: '2018' ... --- _id: '317' abstract: - lang: eng text: We replace the established aluminium gates for the formation of quantum dots in silicon with gates made from palladium. We study the morphology of both aluminium and palladium gates with transmission electron microscopy. The native aluminium oxide is found to be formed all around the aluminium gates, which could lead to the formation of unintentional dots. Therefore, we report on a novel fabrication route that replaces aluminium and its native oxide by palladium with atomic-layer-deposition-grown aluminium oxide. Using this approach, we show the formation of low-disorder gate-defined quantum dots, which are reproducibly fabricated. Furthermore, palladium enables us to further shrink the gate design, allowing us to perform electron transport measurements in the few-electron regime in devices comprising only two gate layers, a major technological advancement. It remains to be seen, whether the introduction of palladium gates can improve the excellent results on electron and nuclear spin qubits defined with an aluminium gate stack. article_number: '5690' article_processing_charge: No author: - first_name: Matthias full_name: Brauns, Matthias id: 33F94E3C-F248-11E8-B48F-1D18A9856A87 last_name: Brauns - first_name: Sergey full_name: Amitonov, Sergey last_name: Amitonov - first_name: Paul full_name: Spruijtenburg, Paul last_name: Spruijtenburg - first_name: Floris full_name: Zwanenburg, Floris last_name: Zwanenburg citation: ama: Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 2018;8(1). doi:10.1038/s41598-018-24004-y apa: Brauns, M., Amitonov, S., Spruijtenburg, P., & Zwanenburg, F. (2018). Palladium gates for reproducible quantum dots in silicon. Scientific Reports. Nature Publishing Group. https://doi.org/10.1038/s41598-018-24004-y chicago: Brauns, Matthias, Sergey Amitonov, Paul Spruijtenburg, and Floris Zwanenburg. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports. Nature Publishing Group, 2018. https://doi.org/10.1038/s41598-018-24004-y. ieee: M. Brauns, S. Amitonov, P. Spruijtenburg, and F. Zwanenburg, “Palladium gates for reproducible quantum dots in silicon,” Scientific Reports, vol. 8, no. 1. Nature Publishing Group, 2018. ista: Brauns M, Amitonov S, Spruijtenburg P, Zwanenburg F. 2018. Palladium gates for reproducible quantum dots in silicon. Scientific Reports. 8(1), 5690. mla: Brauns, Matthias, et al. “Palladium Gates for Reproducible Quantum Dots in Silicon.” Scientific Reports, vol. 8, no. 1, 5690, Nature Publishing Group, 2018, doi:10.1038/s41598-018-24004-y. short: M. Brauns, S. Amitonov, P. Spruijtenburg, F. Zwanenburg, Scientific Reports 8 (2018). date_created: 2018-12-11T11:45:47Z date_published: 2018-04-09T00:00:00Z date_updated: 2023-09-13T09:38:00Z day: '09' ddc: - '539' department: - _id: GeKa doi: 10.1038/s41598-018-24004-y external_id: isi: - '000429404300013' file: - access_level: open_access checksum: 20af238ca4ba6491b77270be8d826bf5 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:04Z date_updated: 2020-07-14T12:46:02Z file_id: '5256' file_name: IST-2018-1016-v1+1_2018_Brauns_Palladium_gates.pdf file_size: 1850530 relation: main_file file_date_updated: 2020-07-14T12:46:02Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: Scientific Reports publication_status: published publisher: Nature Publishing Group publist_id: '7548' pubrep_id: '1016' quality_controlled: '1' scopus_import: '1' status: public title: Palladium gates for reproducible quantum dots in silicon 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2018' ... --- _id: '194' abstract: - lang: eng text: Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion. article_processing_charge: No article_type: original author: - first_name: Zita full_name: Liutkeviciute, Zita last_name: Liutkeviciute - first_name: Esther full_name: Gil Mansilla, Esther last_name: Gil Mansilla - first_name: Thomas full_name: Eder, Thomas last_name: Eder - first_name: Barbara E full_name: Casillas Perez, Barbara E id: 351ED2AA-F248-11E8-B48F-1D18A9856A87 last_name: Casillas Perez - first_name: Maria full_name: Giulia Di Giglio, Maria last_name: Giulia Di Giglio - first_name: Edin full_name: Muratspahić, Edin last_name: Muratspahić - first_name: Florian full_name: Grebien, Florian last_name: Grebien - first_name: Thomas full_name: Rattei, Thomas last_name: Rattei - first_name: Markus full_name: Muttenthaler, Markus last_name: Muttenthaler - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Christian full_name: Gruber, Christian last_name: Gruber citation: ama: Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 2018;32(12):6808-6821. doi:10.1096/fj.201800443 apa: Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. FASEB. https://doi.org/10.1096/fj.201800443 chicago: Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal. FASEB, 2018. https://doi.org/10.1096/fj.201800443. ieee: Z. Liutkeviciute et al., “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” The FASEB Journal, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018. ista: Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821. mla: Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” The FASEB Journal, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:10.1096/fj.201800443. short: Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821. date_created: 2018-12-11T11:45:08Z date_published: 2018-11-29T00:00:00Z date_updated: 2023-09-13T09:37:32Z day: '29' department: - _id: SyCr doi: 10.1096/fj.201800443 external_id: isi: - '000449359700035' pmid: - '29939785' intvolume: ' 32' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.1096/fj.201800443' month: '11' oa: 1 oa_version: Published Version page: 6808-6821 pmid: 1 project: - _id: 25E3D34E-B435-11E9-9278-68D0E5697425 name: Individual function and social role of oxytocin-like neuropeptides in ants publication: The FASEB Journal publication_identifier: issn: - '08926638' publication_status: published publisher: FASEB publist_id: '7721' quality_controlled: '1' scopus_import: '1' status: public title: Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2018' ... --- _id: '159' abstract: - lang: eng text: L-type Ca2+ channels (LTCCs) play a crucial role in excitation-contraction coupling and release of hormones from secretory cells. They are targets of antihypertensive and antiarrhythmic drugs such as diltiazem. Here, we present a photoswitchable diltiazem, FHU-779, which can be used to reversibly block endogenous LTCCs by light. FHU-779 is as potent as diltiazem and can be used to place pancreatic β-cell function and cardiac activity under optical control. article_processing_charge: No article_type: original author: - first_name: Timm full_name: Fehrentz, Timm last_name: Fehrentz - first_name: Florian full_name: Huber, Florian last_name: Huber - first_name: Nina full_name: Hartrampf, Nina last_name: Hartrampf - first_name: Tobias full_name: Bruegmann, Tobias last_name: Bruegmann - first_name: James full_name: Frank, James last_name: Frank - first_name: Nicholas full_name: Fine, Nicholas last_name: Fine - first_name: Daniela full_name: Malan, Daniela last_name: Malan - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Denis full_name: Tikhonov, Denis last_name: Tikhonov - first_name: Maritn full_name: Sumser, Maritn last_name: Sumser - first_name: Philipp full_name: Sasse, Philipp last_name: Sasse - first_name: David full_name: Hodson, David last_name: Hodson - first_name: Boris full_name: Zhorov, Boris last_name: Zhorov - first_name: Nikolaj full_name: Klocker, Nikolaj last_name: Klocker - first_name: Dirk full_name: Trauner, Dirk last_name: Trauner citation: ama: Fehrentz T, Huber F, Hartrampf N, et al. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 2018;14(8):764-767. doi:10.1038/s41589-018-0090-8 apa: Fehrentz, T., Huber, F., Hartrampf, N., Bruegmann, T., Frank, J., Fine, N., … Trauner, D. (2018). Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/s41589-018-0090-8 chicago: Fehrentz, Timm, Florian Huber, Nina Hartrampf, Tobias Bruegmann, James Frank, Nicholas Fine, Daniela Malan, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology. Nature Publishing Group, 2018. https://doi.org/10.1038/s41589-018-0090-8. ieee: T. Fehrentz et al., “Optical control of L-type Ca2+ channels using a diltiazem photoswitch,” Nature Chemical Biology, vol. 14, no. 8. Nature Publishing Group, pp. 764–767, 2018. ista: Fehrentz T, Huber F, Hartrampf N, Bruegmann T, Frank J, Fine N, Malan D, Danzl JG, Tikhonov D, Sumser M, Sasse P, Hodson D, Zhorov B, Klocker N, Trauner D. 2018. Optical control of L-type Ca2+ channels using a diltiazem photoswitch. Nature Chemical Biology. 14(8), 764–767. mla: Fehrentz, Timm, et al. “Optical Control of L-Type Ca2+ Channels Using a Diltiazem Photoswitch.” Nature Chemical Biology, vol. 14, no. 8, Nature Publishing Group, 2018, pp. 764–67, doi:10.1038/s41589-018-0090-8. short: T. Fehrentz, F. Huber, N. Hartrampf, T. Bruegmann, J. Frank, N. Fine, D. Malan, J.G. Danzl, D. Tikhonov, M. Sumser, P. Sasse, D. Hodson, B. Zhorov, N. Klocker, D. Trauner, Nature Chemical Biology 14 (2018) 764–767. date_created: 2018-12-11T11:44:56Z date_published: 2018-07-16T00:00:00Z date_updated: 2023-09-13T09:36:35Z day: '16' ddc: - '570' department: - _id: JoDa doi: 10.1038/s41589-018-0090-8 external_id: isi: - '000438970200010' file: - access_level: open_access checksum: d42935094ec845f54a0688bf12986d62 content_type: application/pdf creator: dernst date_created: 2020-05-14T12:14:09Z date_updated: 2020-07-14T12:45:03Z file_id: '7832' file_name: 2018_NatureChemicalBiology_Fehrentz.pdf file_size: 6321000 relation: main_file file_date_updated: 2020-07-14T12:45:03Z has_accepted_license: '1' intvolume: ' 14' isi: 1 issue: '8' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 764 - 767 publication: Nature Chemical Biology publication_status: published publisher: Nature Publishing Group publist_id: '7762' quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1038/s41589-021-00744-3 scopus_import: '1' status: public title: Optical control of L-type Ca2+ channels using a diltiazem photoswitch type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2018' ... --- _id: '79' abstract: - lang: eng text: 'Markov Decision Processes (MDPs) are a popular class of models suitable for solving control decision problems in probabilistic reactive systems. We consider parametric MDPs (pMDPs) that include parameters in some of the transition probabilities to account for stochastic uncertainties of the environment such as noise or input disturbances. We study pMDPs with reachability objectives where the parameter values are unknown and impossible to measure directly during execution, but there is a probability distribution known over the parameter values. We study for the first time computing parameter-independent strategies that are expectation optimal, i.e., optimize the expected reachability probability under the probability distribution over the parameters. We present an encoding of our problem to partially observable MDPs (POMDPs), i.e., a reduction of our problem to computing optimal strategies in POMDPs. We evaluate our method experimentally on several benchmarks: a motivating (repeated) learner model; a series of benchmarks of varying configurations of a robot moving on a grid; and a consensus protocol.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Sebastian full_name: Arming, Sebastian last_name: Arming - first_name: Ezio full_name: Bartocci, Ezio last_name: Bartocci - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Joost P full_name: Katoen, Joost P id: 4524F760-F248-11E8-B48F-1D18A9856A87 last_name: Katoen - first_name: Ana full_name: Sokolova, Ana last_name: Sokolova citation: ama: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. Parameter-independent strategies for pMDPs via POMDPs. In: Vol 11024. Springer; 2018:53-70. doi:10.1007/978-3-319-99154-2_4' apa: 'Arming, S., Bartocci, E., Chatterjee, K., Katoen, J. P., & Sokolova, A. (2018). Parameter-independent strategies for pMDPs via POMDPs (Vol. 11024, pp. 53–70). Presented at the QEST: Quantitative Evaluation of Systems, Beijing, China: Springer. https://doi.org/10.1007/978-3-319-99154-2_4' chicago: Arming, Sebastian, Ezio Bartocci, Krishnendu Chatterjee, Joost P Katoen, and Ana Sokolova. “Parameter-Independent Strategies for PMDPs via POMDPs,” 11024:53–70. Springer, 2018. https://doi.org/10.1007/978-3-319-99154-2_4. ieee: 'S. Arming, E. Bartocci, K. Chatterjee, J. P. Katoen, and A. Sokolova, “Parameter-independent strategies for pMDPs via POMDPs,” presented at the QEST: Quantitative Evaluation of Systems, Beijing, China, 2018, vol. 11024, pp. 53–70.' ista: 'Arming S, Bartocci E, Chatterjee K, Katoen JP, Sokolova A. 2018. Parameter-independent strategies for pMDPs via POMDPs. QEST: Quantitative Evaluation of Systems, LNCS, vol. 11024, 53–70.' mla: Arming, Sebastian, et al. Parameter-Independent Strategies for PMDPs via POMDPs. Vol. 11024, Springer, 2018, pp. 53–70, doi:10.1007/978-3-319-99154-2_4. short: S. Arming, E. Bartocci, K. Chatterjee, J.P. Katoen, A. Sokolova, in:, Springer, 2018, pp. 53–70. conference: end_date: 2018-09-07 location: Beijing, China name: 'QEST: Quantitative Evaluation of Systems' start_date: 2018-09-04 date_created: 2018-12-11T11:44:31Z date_published: 2018-08-15T00:00:00Z date_updated: 2023-09-13T09:38:28Z day: '15' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-319-99154-2_4 external_id: arxiv: - '1806.05126' isi: - '000548912200004' intvolume: ' 11024' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.05126 month: '08' oa: 1 oa_version: Preprint page: 53-70 publication_status: published publisher: Springer publist_id: '7975' quality_controlled: '1' scopus_import: '1' status: public title: Parameter-independent strategies for pMDPs via POMDPs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11024 year: '2018' ... --- _id: '14327' abstract: - lang: eng text: "A common assumption in causal modeling posits that the data is generated by a\r\nset of independent mechanisms, and algorithms should aim to recover this\r\nstructure. Standard unsupervised learning, however, is often concerned with\r\ntraining a single model to capture the overall distribution or aspects thereof.\r\nInspired by clustering approaches, we consider mixtures of implicit generative\r\nmodels that ``disentangle'' the independent generative mechanisms underlying\r\nthe data. Relying on an additional set of discriminators, we propose a\r\ncompetitive training procedure in which the models only need to capture the\r\nportion of the data distribution from which they can produce realistic samples.\r\nAs a by-product, each model is simpler and faster to train. We empirically show\r\nthat our approach splits the training distribution in a sensible way and\r\nincreases the quality of the generated samples." article_number: '1804.11130' article_processing_charge: No author: - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Damien full_name: Vincent, Damien last_name: Vincent - first_name: Ilya full_name: Tolstikhin, Ilya last_name: Tolstikhin - first_name: Gunnar full_name: Rätsch, Gunnar last_name: Rätsch - first_name: Sylvain full_name: Gelly, Sylvain last_name: Gelly - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf citation: ama: Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv. doi:10.48550/arXiv.1804.11130 apa: Locatello, F., Vincent, D., Tolstikhin, I., Rätsch, G., Gelly, S., & Schölkopf, B. (n.d.). Competitive training of mixtures of independent deep generative models. arXiv. https://doi.org/10.48550/arXiv.1804.11130 chicago: Locatello, Francesco, Damien Vincent, Ilya Tolstikhin, Gunnar Rätsch, Sylvain Gelly, and Bernhard Schölkopf. “Competitive Training of Mixtures of Independent Deep Generative Models.” ArXiv, n.d. https://doi.org/10.48550/arXiv.1804.11130. ieee: F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, and B. Schölkopf, “Competitive training of mixtures of independent deep generative models,” arXiv. . ista: Locatello F, Vincent D, Tolstikhin I, Rätsch G, Gelly S, Schölkopf B. Competitive training of mixtures of independent deep generative models. arXiv, 1804.11130. mla: Locatello, Francesco, et al. “Competitive Training of Mixtures of Independent Deep Generative Models.” ArXiv, 1804.11130, doi:10.48550/arXiv.1804.11130. short: F. Locatello, D. Vincent, I. Tolstikhin, G. Rätsch, S. Gelly, B. Schölkopf, ArXiv (n.d.). date_created: 2023-09-13T12:20:49Z date_published: 2018-04-30T00:00:00Z date_updated: 2023-09-13T12:23:03Z day: '30' department: - _id: FrLo doi: 10.48550/arXiv.1804.11130 extern: '1' external_id: arxiv: - '1804.11130' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1804.11130 month: '04' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Competitive training of mixtures of independent deep generative models type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2018' ... --- _id: '400' abstract: - lang: eng text: We consider the two-dimensional BCS functional with a radial pair interaction. We show that the translational symmetry is not broken in a certain temperature interval below the critical temperature. In the case of vanishing angular momentum, our results carry over to the three-dimensional case. article_processing_charge: Yes (via OA deal) author: - first_name: Andreas full_name: Deuchert, Andreas id: 4DA65CD0-F248-11E8-B48F-1D18A9856A87 last_name: Deuchert orcid: 0000-0003-3146-6746 - first_name: Alissa full_name: Geisinge, Alissa last_name: Geisinge - first_name: Christian full_name: Hainzl, Christian last_name: Hainzl - first_name: Michael full_name: Loss, Michael last_name: Loss citation: ama: Deuchert A, Geisinge A, Hainzl C, Loss M. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 2018;19(5):1507-1527. doi:10.1007/s00023-018-0665-7 apa: Deuchert, A., Geisinge, A., Hainzl, C., & Loss, M. (2018). Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. Springer. https://doi.org/10.1007/s00023-018-0665-7 chicago: Deuchert, Andreas, Alissa Geisinge, Christian Hainzl, and Michael Loss. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare. Springer, 2018. https://doi.org/10.1007/s00023-018-0665-7. ieee: A. Deuchert, A. Geisinge, C. Hainzl, and M. Loss, “Persistence of translational symmetry in the BCS model with radial pair interaction,” Annales Henri Poincare, vol. 19, no. 5. Springer, pp. 1507–1527, 2018. ista: Deuchert A, Geisinge A, Hainzl C, Loss M. 2018. Persistence of translational symmetry in the BCS model with radial pair interaction. Annales Henri Poincare. 19(5), 1507–1527. mla: Deuchert, Andreas, et al. “Persistence of Translational Symmetry in the BCS Model with Radial Pair Interaction.” Annales Henri Poincare, vol. 19, no. 5, Springer, 2018, pp. 1507–27, doi:10.1007/s00023-018-0665-7. short: A. Deuchert, A. Geisinge, C. Hainzl, M. Loss, Annales Henri Poincare 19 (2018) 1507–1527. date_created: 2018-12-11T11:46:15Z date_published: 2018-05-01T00:00:00Z date_updated: 2023-09-15T12:04:15Z day: '01' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00023-018-0665-7 ec_funded: 1 external_id: isi: - '000429799900008' file: - access_level: open_access checksum: 04d2c9bd7cbf3ca1d7acaaf4e7dca3e5 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:47Z date_updated: 2020-07-14T12:46:22Z file_id: '4966' file_name: IST-2018-1011-v1+1_2018_Deuchert_Persistence.pdf file_size: 582680 relation: main_file file_date_updated: 2020-07-14T12:46:22Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '5' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: 1507 - 1527 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Annales Henri Poincare publication_status: published publisher: Springer publist_id: '7429' pubrep_id: '1011' quality_controlled: '1' scopus_import: '1' status: public title: Persistence of translational symmetry in the BCS model with radial pair interaction 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '406' abstract: - lang: eng text: 'Recent developments in automated tracking allow uninterrupted, high-resolution recording of animal trajectories, sometimes coupled with the identification of stereotyped changes of body pose or other behaviors of interest. Analysis and interpretation of such data represents a challenge: the timing of animal behaviors may be stochastic and modulated by kinematic variables, by the interaction with the environment or with the conspecifics within the animal group, and dependent on internal cognitive or behavioral state of the individual. Existing models for collective motion typically fail to incorporate the discrete, stochastic, and internal-state-dependent aspects of behavior, while models focusing on individual animal behavior typically ignore the spatial aspects of the problem. Here we propose a probabilistic modeling framework to address this gap. Each animal can switch stochastically between different behavioral states, with each state resulting in a possibly different law of motion through space. Switching rates for behavioral transitions can depend in a very general way, which we seek to identify from data, on the effects of the environment as well as the interaction between the animals. We represent the switching dynamics as a Generalized Linear Model and show that: (i) forward simulation of multiple interacting animals is possible using a variant of the Gillespie’s Stochastic Simulation Algorithm; (ii) formulated properly, the maximum likelihood inference of switching rate functions is tractably solvable by gradient descent; (iii) model selection can be used to identify factors that modulate behavioral state switching and to appropriately adjust model complexity to data. To illustrate our framework, we apply it to two synthetic models of animal motion and to real zebrafish tracking data. ' acknowledgement: This work was supported by the Human Frontier Science Program RGP0065/2012 (GT, ES). article_processing_charge: Yes author: - first_name: Katarína full_name: Bod’Ová, Katarína last_name: Bod’Ová - first_name: Gabriel full_name: Mitchell, Gabriel id: 315BCD80-F248-11E8-B48F-1D18A9856A87 last_name: Mitchell - first_name: Roy full_name: Harpaz, Roy last_name: Harpaz - first_name: Elad full_name: Schneidman, Elad last_name: Schneidman - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Probabilistic models of individual and collective animal behavior. PLoS One. 2018;13(3). doi:10.1371/journal.pone.0193049 apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Probabilistic models of individual and collective animal behavior. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049 chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One. Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049. ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Probabilistic models of individual and collective animal behavior,” PLoS One, vol. 13, no. 3. Public Library of Science, 2018. ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Probabilistic models of individual and collective animal behavior. PLoS One. 13(3). mla: Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049. short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, PLoS One 13 (2018). date_created: 2018-12-11T11:46:18Z date_published: 2018-03-07T00:00:00Z date_updated: 2023-09-15T12:06:19Z day: '07' ddc: - '530' - '571' department: - _id: GaTk doi: 10.1371/journal.pone.0193049 external_id: isi: - '000426896800032' file: - access_level: open_access checksum: 684229493db75b43e98a46cd922da497 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:43Z date_updated: 2020-07-14T12:46:22Z file_id: '5165' file_name: IST-2018-995-v1+1_2018_Bodova_Probabilistic.pdf file_size: 6887358 relation: main_file file_date_updated: 2020-07-14T12:46:22Z has_accepted_license: '1' intvolume: ' 13' isi: 1 issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Submitted Version project: - _id: 255008E4-B435-11E9-9278-68D0E5697425 grant_number: RGP0065/2012 name: Information processing and computation in fish groups publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '7423' pubrep_id: '995' quality_controlled: '1' related_material: record: - id: '9831' relation: research_data status: public scopus_import: '1' status: public title: Probabilistic models of individual and collective animal behavior 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 13 year: '2018' ... --- _id: '457' abstract: - lang: eng text: Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages. We show that although restriction-modification systems as mechanisms of innate immunity prevent both lytic and lysogenic infections indiscriminately in individual bacteria, they increase the number of prophage-acquiring individuals at the population level. We find that this counterintuitive result is a consequence of phage-host population dynamics, in which restriction-modification systems delay infection onset until bacteria reach densities at which the probability of lysogeny increases. These results underscore the importance of population-level dynamics as a key factor modulating costs and benefits of immunity to temperate bacteriophages article_processing_charge: No author: - first_name: Maros full_name: Pleska, Maros id: 4569785E-F248-11E8-B48F-1D18A9856A87 last_name: Pleska orcid: 0000-0001-7460-7479 - first_name: Moritz full_name: Lang, Moritz id: 29E0800A-F248-11E8-B48F-1D18A9856A87 last_name: Lang - first_name: Dominik full_name: Refardt, Dominik last_name: Refardt - first_name: Bruce full_name: Levin, Bruce last_name: Levin - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 citation: ama: Pleska M, Lang M, Refardt D, Levin B, Guet CC. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2018;2(2):359-366. doi:10.1038/s41559-017-0424-z apa: Pleska, M., Lang, M., Refardt, D., Levin, B., & Guet, C. C. (2018). Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. Springer Nature. https://doi.org/10.1038/s41559-017-0424-z chicago: Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution. Springer Nature, 2018. https://doi.org/10.1038/s41559-017-0424-z. ieee: M. Pleska, M. Lang, D. Refardt, B. Levin, and C. C. Guet, “Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity,” Nature Ecology and Evolution, vol. 2, no. 2. Springer Nature, pp. 359–366, 2018. ista: Pleska M, Lang M, Refardt D, Levin B, Guet CC. 2018. Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity. Nature Ecology and Evolution. 2(2), 359–366. mla: Pleska, Maros, et al. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.” Nature Ecology and Evolution, vol. 2, no. 2, Springer Nature, 2018, pp. 359–66, doi:10.1038/s41559-017-0424-z. short: M. Pleska, M. Lang, D. Refardt, B. Levin, C.C. Guet, Nature Ecology and Evolution 2 (2018) 359–366. date_created: 2018-12-11T11:46:35Z date_published: 2018-02-01T00:00:00Z date_updated: 2023-09-15T12:04:57Z day: '01' department: - _id: CaGu - _id: GaTk doi: 10.1038/s41559-017-0424-z ec_funded: 1 external_id: isi: - '000426516400027' intvolume: ' 2' isi: 1 issue: '2' language: - iso: eng month: '02' oa_version: None page: 359 - 366 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 251BCBEC-B435-11E9-9278-68D0E5697425 grant_number: RGY0079/2011 name: Multi-Level Conflicts in Evolutionary Dynamics of Restriction-Modification Systems (HFSP Young investigators' grant) - _id: 251D65D8-B435-11E9-9278-68D0E5697425 grant_number: '24210' name: Effects of Stochasticity on the Function of Restriction-Modi cation Systems at the Single-Cell Level (DOC Fellowship) publication: Nature Ecology and Evolution publication_status: published publisher: Springer Nature publist_id: '7364' quality_controlled: '1' related_material: record: - id: '202' relation: dissertation_contains status: public scopus_import: '1' status: public title: Phage-host population dynamics promotes prophage acquisition in bacteria with innate immunity type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2 year: '2018' ... --- _id: '55' abstract: - lang: eng text: Many animals use antimicrobials to prevent or cure disease [1,2]. For example, some animals will ingest plants with medicinal properties, both prophylactically to prevent infection and therapeutically to self-medicate when sick. Antimicrobial substances are also used as topical disinfectants, to prevent infection, protect offspring and to sanitise their surroundings [1,2]. Social insects (ants, bees, wasps and termites) build nests in environments with a high abundance and diversity of pathogenic microorganisms — such as soil and rotting wood — and colonies are often densely crowded, creating conditions that favour disease outbreaks. Consequently, social insects have evolved collective disease defences to protect their colonies from epidemics. These traits can be seen as functionally analogous to the immune system of individual organisms [3,4]. This ‘social immunity’ utilises antimicrobials to prevent and eradicate infections, and to keep the brood and nest clean. However, these antimicrobial compounds can be harmful to the insects themselves, and it is unknown how colonies prevent collateral damage when using them. Here, we demonstrate that antimicrobial acids, produced by workers to disinfect the colony, are harmful to the delicate pupal brood stage, but that the pupae are protected from the acids by the presence of a silk cocoon. Garden ants spray their nests with an antimicrobial poison to sanitize contaminated nestmates and brood. Here, Pull et al show that they also prophylactically sanitise their colonies, and that the silk cocoon serves as a barrier to protect developing pupae, thus preventing collateral damage during nest sanitation. article_processing_charge: No article_type: original author: - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Sina full_name: Metzler, Sina id: 48204546-F248-11E8-B48F-1D18A9856A87 last_name: Metzler orcid: 0000-0002-9547-2494 - first_name: Elisabeth full_name: Naderlinger, Elisabeth id: 31757262-F248-11E8-B48F-1D18A9856A87 last_name: Naderlinger - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Pull C, Metzler S, Naderlinger E, Cremer S. Protection against the lethal side effects of social immunity in ants. Current Biology. 2018;28(19):R1139-R1140. doi:10.1016/j.cub.2018.08.063 apa: Pull, C., Metzler, S., Naderlinger, E., & Cremer, S. (2018). Protection against the lethal side effects of social immunity in ants. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2018.08.063 chicago: Pull, Christopher, Sina Metzler, Elisabeth Naderlinger, and Sylvia Cremer. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology. Cell Press, 2018. https://doi.org/10.1016/j.cub.2018.08.063. ieee: C. Pull, S. Metzler, E. Naderlinger, and S. Cremer, “Protection against the lethal side effects of social immunity in ants,” Current Biology, vol. 28, no. 19. Cell Press, pp. R1139–R1140, 2018. ista: Pull C, Metzler S, Naderlinger E, Cremer S. 2018. Protection against the lethal side effects of social immunity in ants. Current Biology. 28(19), R1139–R1140. mla: Pull, Christopher, et al. “Protection against the Lethal Side Effects of Social Immunity in Ants.” Current Biology, vol. 28, no. 19, Cell Press, 2018, pp. R1139–40, doi:10.1016/j.cub.2018.08.063. short: C. Pull, S. Metzler, E. Naderlinger, S. Cremer, Current Biology 28 (2018) R1139–R1140. date_created: 2018-12-11T11:44:23Z date_published: 2018-10-08T00:00:00Z date_updated: 2023-09-15T12:06:46Z day: '08' department: - _id: SyCr doi: 10.1016/j.cub.2018.08.063 external_id: isi: - '000446693400008' intvolume: ' 28' isi: 1 issue: '19' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cub.2018.08.063 month: '10' oa: 1 oa_version: Published Version page: R1139 - R1140 publication: Current Biology publication_status: published publisher: Cell Press publist_id: '7999' quality_controlled: '1' scopus_import: '1' status: public title: Protection against the lethal side effects of social immunity in ants type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 28 year: '2018' ... --- _id: '181' abstract: - lang: eng text: We consider large random matrices X with centered, independent entries but possibly di erent variances. We compute the normalized trace of f(X)g(X∗) for f, g functions analytic on the spectrum of X. We use these results to compute the long time asymptotics for systems of coupled di erential equations with random coe cients. We show that when the coupling is critical, the norm squared of the solution decays like t−1/2. acknowledgement: The work of the second author was also partially supported by the Hausdorff Center of Mathematics. article_processing_charge: No author: - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Torben H full_name: Krüger, Torben H id: 3020C786-F248-11E8-B48F-1D18A9856A87 last_name: Krüger orcid: 0000-0002-4821-3297 - first_name: David T full_name: Renfrew, David T id: 4845BF6A-F248-11E8-B48F-1D18A9856A87 last_name: Renfrew orcid: 0000-0003-3493-121X citation: ama: Erdös L, Krüger TH, Renfrew DT. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 2018;50(3):3271-3290. doi:10.1137/17M1143125 apa: Erdös, L., Krüger, T. H., & Renfrew, D. T. (2018). Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics . https://doi.org/10.1137/17M1143125 chicago: Erdös, László, Torben H Krüger, and David T Renfrew. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis. Society for Industrial and Applied Mathematics , 2018. https://doi.org/10.1137/17M1143125. ieee: L. Erdös, T. H. Krüger, and D. T. Renfrew, “Power law decay for systems of randomly coupled differential equations,” SIAM Journal on Mathematical Analysis, vol. 50, no. 3. Society for Industrial and Applied Mathematics , pp. 3271–3290, 2018. ista: Erdös L, Krüger TH, Renfrew DT. 2018. Power law decay for systems of randomly coupled differential equations. SIAM Journal on Mathematical Analysis. 50(3), 3271–3290. mla: Erdös, László, et al. “Power Law Decay for Systems of Randomly Coupled Differential Equations.” SIAM Journal on Mathematical Analysis, vol. 50, no. 3, Society for Industrial and Applied Mathematics , 2018, pp. 3271–90, doi:10.1137/17M1143125. short: L. Erdös, T.H. Krüger, D.T. Renfrew, SIAM Journal on Mathematical Analysis 50 (2018) 3271–3290. date_created: 2018-12-11T11:45:03Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-09-15T12:05:52Z day: '01' department: - _id: LaEr doi: 10.1137/17M1143125 ec_funded: 1 external_id: arxiv: - '1708.01546' isi: - '000437018500032' intvolume: ' 50' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1708.01546 month: '01' oa: 1 oa_version: Published Version page: 3271 - 3290 project: - _id: 258DCDE6-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '338804' name: Random matrices, universality and disordered quantum systems - _id: 258F40A4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02080 name: Structured Non-Hermitian Random Matrices publication: SIAM Journal on Mathematical Analysis publication_status: published publisher: 'Society for Industrial and Applied Mathematics ' publist_id: '7740' quality_controlled: '1' scopus_import: '1' status: public title: Power law decay for systems of randomly coupled differential equations type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 50 year: '2018' ... --- _id: '322' abstract: - lang: eng text: We construct quantizations of multiplicative hypertoric varieties using an algebra of q-difference operators on affine space, where q is a root of unity in C. The quantization defines a matrix bundle (i.e. Azumaya algebra) over the multiplicative hypertoric variety and admits an explicit finite étale splitting. The global sections of this Azumaya algebra is a hypertoric quantum group, and we prove a localization theorem. We introduce a general framework of Frobenius quantum moment maps and their Hamiltonian reductions; our results shed light on an instance of this framework. acknowledgement: "National Science Foundation: Graduate Research Fellowship and grant No.0932078000; ERC Advanced Grant “Arithmetic and Physics of Higgs moduli spaces” No. 320593 \r\nThe author is grateful to David Jordan for suggesting this project and providing guidance throughout, particularly for the formulation of Frobenius quantum moment maps and key ideas in the proofs of Theorems 3.12 and 4.8. Special thanks to David Ben-Zvi (the author's PhD advisor) for numerous discussions and constant encouragement, and for suggesting the term ‘hypertoric quantum group.’ Many results appearing in the current paper were proven independently by Nicholas Cooney; the author is grateful to Nicholas for sharing his insight on various topics, including Proposition 3.8. The author also thanks Nicholas Proudfoot for relating the definition of multiplicative hypertoric varieties, as well as the content of Remark 2.14. The author also benefited immensely from the close reading and detailed comments of an anonymous referee, and from conversations with Justin Hilburn, Kobi Kremnitzer, Michael McBreen, Tom Nevins, Travis Schedler, and Ben Webster. \r\n\r\n\r\n\r\n" article_processing_charge: No author: - first_name: Iordan V full_name: Ganev, Iordan V id: 447491B8-F248-11E8-B48F-1D18A9856A87 last_name: Ganev citation: ama: Ganev IV. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 2018;506:92-128. doi:10.1016/j.jalgebra.2018.03.015 apa: Ganev, I. V. (2018). Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. World Scientific Publishing. https://doi.org/10.1016/j.jalgebra.2018.03.015 chicago: Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra. World Scientific Publishing, 2018. https://doi.org/10.1016/j.jalgebra.2018.03.015. ieee: I. V. Ganev, “Quantizations of multiplicative hypertoric varieties at a root of unity,” Journal of Algebra, vol. 506. World Scientific Publishing, pp. 92–128, 2018. ista: Ganev IV. 2018. Quantizations of multiplicative hypertoric varieties at a root of unity. Journal of Algebra. 506, 92–128. mla: Ganev, Iordan V. “Quantizations of Multiplicative Hypertoric Varieties at a Root of Unity.” Journal of Algebra, vol. 506, World Scientific Publishing, 2018, pp. 92–128, doi:10.1016/j.jalgebra.2018.03.015. short: I.V. Ganev, Journal of Algebra 506 (2018) 92–128. date_created: 2018-12-11T11:45:49Z date_published: 2018-07-15T00:00:00Z date_updated: 2023-09-15T12:08:38Z day: '15' department: - _id: TaHa doi: 10.1016/j.jalgebra.2018.03.015 ec_funded: 1 external_id: arxiv: - '1412.7211' isi: - '000433270600005' intvolume: ' 506' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1412.7211 month: '07' oa: 1 oa_version: Preprint page: 92 - 128 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces publication: Journal of Algebra publication_status: published publisher: World Scientific Publishing publist_id: '7543' quality_controlled: '1' scopus_import: '1' status: public title: Quantizations of multiplicative hypertoric varieties at a root of unity type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 506 year: '2018' ... --- _id: '9831' abstract: - lang: eng text: 'Implementation of the inference method in Matlab, including three applications of the method: The first one for the model of ant motion, the second one for bacterial chemotaxis, and the third one for the motion of fish.' article_processing_charge: No author: - first_name: Katarína full_name: Bod’Ová, Katarína last_name: Bod’Ová - first_name: Gabriel full_name: Mitchell, Gabriel id: 315BCD80-F248-11E8-B48F-1D18A9856A87 last_name: Mitchell - first_name: Roy full_name: Harpaz, Roy last_name: Harpaz - first_name: Elad full_name: Schneidman, Elad last_name: Schneidman - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. Implementation of the inference method in Matlab. 2018. doi:10.1371/journal.pone.0193049.s001 apa: Bod’Ová, K., Mitchell, G., Harpaz, R., Schneidman, E., & Tkačik, G. (2018). Implementation of the inference method in Matlab. Public Library of Science. https://doi.org/10.1371/journal.pone.0193049.s001 chicago: Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gašper Tkačik. “Implementation of the Inference Method in Matlab.” Public Library of Science, 2018. https://doi.org/10.1371/journal.pone.0193049.s001. ieee: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, and G. Tkačik, “Implementation of the inference method in Matlab.” Public Library of Science, 2018. ista: Bod’Ová K, Mitchell G, Harpaz R, Schneidman E, Tkačik G. 2018. Implementation of the inference method in Matlab, Public Library of Science, 10.1371/journal.pone.0193049.s001. mla: Bod’Ová, Katarína, et al. Implementation of the Inference Method in Matlab. Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.s001. short: K. Bod’Ová, G. Mitchell, R. Harpaz, E. Schneidman, G. Tkačik, (2018). date_created: 2021-08-09T07:01:24Z date_published: 2018-03-07T00:00:00Z date_updated: 2023-09-15T12:06:18Z day: '07' department: - _id: GaTk doi: 10.1371/journal.pone.0193049.s001 month: '03' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '406' relation: used_in_publication status: public status: public title: Implementation of the inference method in Matlab type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '142' abstract: - lang: eng text: We address the problem of analyzing the reachable set of a polynomial nonlinear continuous system by over-approximating the flowpipe of its dynamics. The common approach to tackle this problem is to perform a numerical integration over a given time horizon based on Taylor expansion and interval arithmetic. However, this method results to be very conservative when there is a large difference in speed between trajectories as time progresses. In this paper, we propose to use combinations of barrier functions, which we call piecewise barrier tube (PBT), to over-approximate flowpipe. The basic idea of PBT is that for each segment of a flowpipe, a coarse box which is big enough to contain the segment is constructed using sampled simulation and then in the box we compute by linear programming a set of barrier functions (called barrier tube or BT for short) which work together to form a tube surrounding the flowpipe. The benefit of using PBT is that (1) BT is independent of time and hence can avoid being stretched and deformed by time; and (2) a small number of BTs can form a tight over-approximation for the flowpipe, which means that the computation required to decide whether the BTs intersect the unsafe set can be reduced significantly. We implemented a prototype called PBTS in C++. Experiments on some benchmark systems show that our approach is effective. acknowledgement: 'Austrian Science Fund FWF: S11402-N23, S11405-N23, Z211-N32' alternative_title: - LNCS article_processing_charge: No author: - first_name: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 - first_name: Ezio full_name: Bartocci, Ezio last_name: Bartocci - 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: 'Kong H, Bartocci E, Henzinger TA. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. In: Vol 10981. Springer; 2018:449-467. doi:10.1007/978-3-319-96145-3_24' apa: 'Kong, H., Bartocci, E., & Henzinger, T. A. (2018). Reachable set over-approximation for nonlinear systems using piecewise barrier tubes (Vol. 10981, pp. 449–467). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_24' chicago: Kong, Hui, Ezio Bartocci, and Thomas A Henzinger. “Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes,” 10981:449–67. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_24. ieee: 'H. Kong, E. Bartocci, and T. A. Henzinger, “Reachable set over-approximation for nonlinear systems using piecewise barrier tubes,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 449–467.' ista: 'Kong H, Bartocci E, Henzinger TA. 2018. Reachable set over-approximation for nonlinear systems using piecewise barrier tubes. CAV: Computer Aided Verification, LNCS, vol. 10981, 449–467.' mla: Kong, Hui, et al. Reachable Set Over-Approximation for Nonlinear Systems Using Piecewise Barrier Tubes. Vol. 10981, Springer, 2018, pp. 449–67, doi:10.1007/978-3-319-96145-3_24. short: H. Kong, E. Bartocci, T.A. Henzinger, in:, Springer, 2018, pp. 449–467. conference: end_date: 2018-07-17 location: Oxford, United Kingdom name: 'CAV: Computer Aided Verification' start_date: 2018-07-14 date_created: 2018-12-11T11:44:51Z date_published: 2018-07-18T00:00:00Z date_updated: 2023-09-15T12:12:08Z day: '18' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-96145-3_24 external_id: isi: - '000491481600024' file: - access_level: open_access checksum: fd95e8026deacef3dc752a733bb9355f content_type: application/pdf creator: dernst date_created: 2018-12-17T15:57:06Z date_updated: 2020-07-14T12:44:53Z file_id: '5718' file_name: 2018_LNCS_Kong.pdf file_size: 5591566 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 10981' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 449 - 467 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication_status: published publisher: Springer publist_id: '7781' quality_controlled: '1' scopus_import: '1' status: public title: Reachable set over-approximation for nonlinear systems using piecewise barrier tubes tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10981 year: '2018' ... --- _id: '427' abstract: - lang: eng text: We investigate the quantum interference induced shifts between energetically close states in highly charged ions, with the energy structure being observed by laser spectroscopy. In this work, we focus on hyperfine states of lithiumlike heavy-Z isotopes and quantify how much quantum interference changes the observed transition frequencies. The process of photon excitation and subsequent photon decay for the transition 2s→2p→2s is implemented with fully relativistic and full-multipole frameworks, which are relevant for such relativistic atomic systems. We consider the isotopes Pb79+207 and Bi80+209 due to experimental interest, as well as other examples of isotopes with lower Z, namely Pr56+141 and Ho64+165. We conclude that quantum interference can induce shifts up to 11% of the linewidth in the measurable resonances of the considered isotopes, if interference between resonances is neglected. The inclusion of relativity decreases the cross section by 35%, mainly due to the complete retardation form of the electric dipole multipole. However, the contribution of the next higher multipoles (e.g., magnetic quadrupole) to the cross section is negligible. This makes the contribution of relativity and higher-order multipoles to the quantum interference induced shifts a minor effect, even for heavy-Z elements. acknowledgement: "This work was funded by the Portuguese Fundação para a Ciência e a Tecnologia (FCT/MCTES/PIDDAC) under Grant No. UID/FIS/04559/2013 (LIBPhys). P.A. acknowledges the support of the FCT, under Contract No. SFRH/BPD/92329/2013. L.S. acknowledges financial 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). Laboratoire Kastler Brossel (LKB) is “Unité Mixte de Recherche de Sorbonne Université, de ENS-PSL Research University, du Collège de France et du CNRS No. 8552.” APPENDIX:\r\n" article_number: '022510' article_processing_charge: No article_type: original author: - first_name: Pedro full_name: Amaro, Pedro last_name: Amaro - first_name: Ulisses full_name: Loureiro, Ulisses last_name: Loureiro - first_name: Laleh full_name: Safari, Laleh id: 3C325E5E-F248-11E8-B48F-1D18A9856A87 last_name: Safari - first_name: Filippo full_name: Fratini, Filippo last_name: Fratini - first_name: Paul full_name: Indelicato, Paul last_name: Indelicato - first_name: Thomas full_name: Stöhlker, Thomas last_name: Stöhlker - first_name: José full_name: Santos, José last_name: Santos citation: ama: Amaro P, Loureiro U, Safari L, et al. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(2). doi:10.1103/PhysRevA.97.022510 apa: Amaro, P., Loureiro, U., Safari, L., Fratini, F., Indelicato, P., Stöhlker, T., & Santos, J. (2018). Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.022510 chicago: Amaro, Pedro, Ulisses Loureiro, Laleh Safari, Filippo Fratini, Paul Indelicato, Thomas Stöhlker, and José Santos. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.022510. ieee: P. Amaro et al., “Quantum interference in laser spectroscopy of highly charged lithiumlike ions,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2. American Physical Society, 2018. ista: Amaro P, Loureiro U, Safari L, Fratini F, Indelicato P, Stöhlker T, Santos J. 2018. Quantum interference in laser spectroscopy of highly charged lithiumlike ions. Physical Review A - Atomic, Molecular, and Optical Physics. 97(2), 022510. mla: Amaro, Pedro, et al. “Quantum Interference in Laser Spectroscopy of Highly Charged Lithiumlike Ions.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 2, 022510, American Physical Society, 2018, doi:10.1103/PhysRevA.97.022510. short: P. Amaro, U. Loureiro, L. Safari, F. Fratini, P. Indelicato, T. Stöhlker, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018). date_created: 2018-12-11T11:46:25Z date_published: 2018-02-21T00:00:00Z date_updated: 2023-09-15T12:09:35Z day: '21' department: - _id: MiLe doi: 10.1103/PhysRevA.97.022510 ec_funded: 1 external_id: arxiv: - '1802.07920' isi: - '000425601000004' intvolume: ' 97' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1802.07920 month: '02' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ' Physical Review A - Atomic, Molecular, and Optical Physics' publication_status: published publisher: American Physical Society publist_id: '7396' quality_controlled: '1' scopus_import: '1' status: public title: Quantum interference in laser spectroscopy of highly charged lithiumlike ions type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 97 year: '2018' ... --- _id: '309' abstract: - lang: eng text: 'We present an efficient algorithm for a problem in the interface between clustering and graph embeddings. An embedding '' : G ! M of a graph G into a 2manifold M maps the vertices in V (G) to distinct points and the edges in E(G) to interior-disjoint Jordan arcs between the corresponding vertices. In applications in clustering, cartography, and visualization, nearby vertices and edges are often bundled to a common node or arc, due to data compression or low resolution. This raises the computational problem of deciding whether a given map '' : G ! M comes from an embedding. A map '' : G ! M is a weak embedding if it can be perturbed into an embedding ψ: G ! M with k'' "k < " for every " > 0. A polynomial-time algorithm for recognizing weak embeddings was recently found by Fulek and Kyncl [14], which reduces to solving a system of linear equations over Z2. It runs in O(n2!) O(n4:75) time, where 2:373 is the matrix multiplication exponent and n is the number of vertices and edges of G. We improve the running time to O(n log n). Our algorithm is also conceptually simpler than [14]: We perform a sequence of local operations that gradually "untangles" the image ''(G) into an embedding (G), or reports that '' is not a weak embedding. It generalizes a recent technique developed for the case that G is a cycle and the embedding is a simple polygon [1], and combines local constraints on the orientation of subgraphs directly, thereby eliminating the need for solving large systems of linear equations.' acknowledgement: '∗Research supported in part by the NSF awards CCF-1422311 and CCF-1423615, and the Science Without Borders program. The second author gratefully acknowledges support from Austrian Science Fund (FWF): M2281-N35.' article_processing_charge: No author: - first_name: Hugo full_name: Akitaya, Hugo last_name: Akitaya - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Csaba full_name: Tóth, Csaba last_name: Tóth citation: ama: 'Akitaya H, Fulek R, Tóth C. Recognizing weak embeddings of graphs. In: ACM; 2018:274-292. doi:10.1137/1.9781611975031.20' apa: 'Akitaya, H., Fulek, R., & Tóth, C. (2018). Recognizing weak embeddings of graphs (pp. 274–292). Presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA: ACM. https://doi.org/10.1137/1.9781611975031.20' chicago: Akitaya, Hugo, Radoslav Fulek, and Csaba Tóth. “Recognizing Weak Embeddings of Graphs,” 274–92. ACM, 2018. https://doi.org/10.1137/1.9781611975031.20. ieee: 'H. Akitaya, R. Fulek, and C. Tóth, “Recognizing weak embeddings of graphs,” presented at the SODA: Symposium on Discrete Algorithms, New Orleans, LA, USA, 2018, pp. 274–292.' ista: 'Akitaya H, Fulek R, Tóth C. 2018. Recognizing weak embeddings of graphs. SODA: Symposium on Discrete Algorithms, 274–292.' mla: Akitaya, Hugo, et al. Recognizing Weak Embeddings of Graphs. ACM, 2018, pp. 274–92, doi:10.1137/1.9781611975031.20. short: H. Akitaya, R. Fulek, C. Tóth, in:, ACM, 2018, pp. 274–292. conference: end_date: 2018-01-10 location: New Orleans, LA, USA name: 'SODA: Symposium on Discrete Algorithms' start_date: 2018-01-07 date_created: 2018-12-11T11:45:45Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-09-15T12:19:32Z day: '01' department: - _id: UlWa doi: 10.1137/1.9781611975031.20 external_id: arxiv: - '1709.09209' isi: - '000483921200021' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.09209 month: '01' oa: 1 oa_version: Preprint page: 274 - 292 project: - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication_status: published publisher: ACM publist_id: '7556' quality_controlled: '1' related_material: record: - id: '6982' relation: later_version status: public scopus_import: '1' status: public title: Recognizing weak embeddings of graphs type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '5794' abstract: - lang: eng text: We present an approach to interacting quantum many-body systems based on the notion of quantum groups, also known as q-deformed Lie algebras. In particular, we show that, if the symmetry of a free quantum particle corresponds to a Lie group G, in the presence of a many-body environment this particle can be described by a deformed group, Gq. Crucially, the single deformation parameter, q, contains all the information about the many-particle interactions in the system. We exemplify our approach by considering a quantum rotor interacting with a bath of bosons, and demonstrate that extracting the value of q from closed-form solutions in the perturbative regime allows one to predict the behavior of the system for arbitrary values of the impurity-bath coupling strength, in good agreement with nonperturbative calculations. Furthermore, the value of the deformation parameter allows one to predict at which coupling strengths rotor-bath interactions result in a formation of a stable quasiparticle. The approach based on quantum groups does not only allow for a drastic simplification of impurity problems, but also provides valuable insights into hidden symmetries of interacting many-particle systems. article_number: '255302' article_processing_charge: No article_type: original author: - first_name: Enderalp full_name: Yakaboylu, Enderalp id: 38CB71F6-F248-11E8-B48F-1D18A9856A87 last_name: Yakaboylu orcid: 0000-0001-5973-0874 - first_name: Mikhail full_name: Shkolnikov, Mikhail id: 35084A62-F248-11E8-B48F-1D18A9856A87 last_name: Shkolnikov orcid: 0000-0002-4310-178X - first_name: Mikhail full_name: Lemeshko, Mikhail id: 37CB05FA-F248-11E8-B48F-1D18A9856A87 last_name: Lemeshko orcid: 0000-0002-6990-7802 citation: ama: Yakaboylu E, Shkolnikov M, Lemeshko M. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 2018;121(25). doi:10.1103/PhysRevLett.121.255302 apa: Yakaboylu, E., Shkolnikov, M., & Lemeshko, M. (2018). Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.121.255302 chicago: Yakaboylu, Enderalp, Mikhail Shkolnikov, and Mikhail Lemeshko. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters. American Physical Society, 2018. https://doi.org/10.1103/PhysRevLett.121.255302. ieee: E. Yakaboylu, M. Shkolnikov, and M. Lemeshko, “Quantum groups as hidden symmetries of quantum impurities,” Physical Review Letters, vol. 121, no. 25. American Physical Society, 2018. ista: Yakaboylu E, Shkolnikov M, Lemeshko M. 2018. Quantum groups as hidden symmetries of quantum impurities. Physical Review Letters. 121(25), 255302. mla: Yakaboylu, Enderalp, et al. “Quantum Groups as Hidden Symmetries of Quantum Impurities.” Physical Review Letters, vol. 121, no. 25, 255302, American Physical Society, 2018, doi:10.1103/PhysRevLett.121.255302. short: E. Yakaboylu, M. Shkolnikov, M. Lemeshko, Physical Review Letters 121 (2018). date_created: 2019-01-06T22:59:12Z date_published: 2018-12-17T00:00:00Z date_updated: 2023-09-15T12:09:06Z day: '17' department: - _id: MiLe doi: 10.1103/PhysRevLett.121.255302 ec_funded: 1 external_id: arxiv: - '1809.00222' isi: - '000454178600009' intvolume: ' 121' isi: 1 issue: '25' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1809.00222 month: '12' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 26031614-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P29902 name: Quantum rotations in the presence of a many-body environment publication: Physical Review Letters publication_identifier: issn: - '00319007' publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Quantum groups as hidden symmetries of quantum impurities type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 121 year: '2018' ... --- _id: '87' abstract: - lang: eng text: Using the geodesic distance on the n-dimensional sphere, we study the expected radius function of the Delaunay mosaic of a random set of points. Specifically, we consider the partition of the mosaic into intervals of the radius function and determine the expected number of intervals whose radii are less than or equal to a given threshold. We find that the expectations are essentially the same as for the Poisson–Delaunay mosaic in n-dimensional Euclidean space. Assuming the points are not contained in a hemisphere, the Delaunay mosaic is isomorphic to the boundary complex of the convex hull in Rn+1, so we also get the expected number of faces of a random inscribed polytope. As proved in Antonelli et al. [Adv. in Appl. Probab. 9–12 (1977–1980)], an orthant section of the n-sphere is isometric to the standard n-simplex equipped with the Fisher information metric. It follows that the latter space has similar stochastic properties as the n-dimensional Euclidean space. Our results are therefore relevant in information geometry and in population genetics. article_processing_charge: No article_type: original author: - first_name: Herbert full_name: Edelsbrunner, Herbert id: 3FB178DA-F248-11E8-B48F-1D18A9856A87 last_name: Edelsbrunner orcid: 0000-0002-9823-6833 - first_name: Anton full_name: Nikitenko, Anton id: 3E4FF1BA-F248-11E8-B48F-1D18A9856A87 last_name: Nikitenko orcid: 0000-0002-0659-3201 citation: ama: Edelsbrunner H, Nikitenko A. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 2018;28(5):3215-3238. doi:10.1214/18-AAP1389 apa: Edelsbrunner, H., & Nikitenko, A. (2018). Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/18-AAP1389 chicago: Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability. Institute of Mathematical Statistics, 2018. https://doi.org/10.1214/18-AAP1389. ieee: H. Edelsbrunner and A. Nikitenko, “Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics,” Annals of Applied Probability, vol. 28, no. 5. Institute of Mathematical Statistics, pp. 3215–3238, 2018. ista: Edelsbrunner H, Nikitenko A. 2018. Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics. Annals of Applied Probability. 28(5), 3215–3238. mla: Edelsbrunner, Herbert, and Anton Nikitenko. “Random Inscribed Polytopes Have Similar Radius Functions as Poisson-Delaunay Mosaics.” Annals of Applied Probability, vol. 28, no. 5, Institute of Mathematical Statistics, 2018, pp. 3215–38, doi:10.1214/18-AAP1389. short: H. Edelsbrunner, A. Nikitenko, Annals of Applied Probability 28 (2018) 3215–3238. date_created: 2018-12-11T11:44:33Z date_published: 2018-10-01T00:00:00Z date_updated: 2023-09-15T12:10:35Z day: '01' department: - _id: HeEd doi: 10.1214/18-AAP1389 external_id: arxiv: - '1705.02870' isi: - '000442893500018' intvolume: ' 28' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.02870 month: '10' oa: 1 oa_version: Preprint page: 3215 - 3238 project: - _id: 2561EBF4-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I02979-N35 name: Persistence and stability of geometric complexes publication: Annals of Applied Probability publication_status: published publisher: Institute of Mathematical Statistics publist_id: '7967' quality_controlled: '1' related_material: record: - id: '6287' relation: dissertation_contains status: public scopus_import: '1' status: public title: Random inscribed polytopes have similar radius functions as Poisson-Delaunay mosaics type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 28 year: '2018' ... --- _id: '192' abstract: - lang: eng text: The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway. article_processing_charge: No article_type: original author: - first_name: Matyas full_name: Fendrych, Matyas id: 43905548-F248-11E8-B48F-1D18A9856A87 last_name: Fendrych orcid: 0000-0002-9767-8699 - first_name: Maria full_name: Akhmanova, Maria id: 3425EC26-F248-11E8-B48F-1D18A9856A87 last_name: Akhmanova orcid: 0000-0003-1522-3162 - first_name: Jack full_name: Merrin, Jack id: 4515C308-F248-11E8-B48F-1D18A9856A87 last_name: Merrin orcid: 0000-0001-5145-4609 - first_name: Matous full_name: Glanc, Matous last_name: Glanc - first_name: Shinya full_name: Hagihara, Shinya last_name: Hagihara - first_name: Koji full_name: Takahashi, Koji last_name: Takahashi - first_name: Naoyuki full_name: Uchida, Naoyuki last_name: Uchida - first_name: Keiko U full_name: Torii, Keiko U last_name: Torii - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 2018;4(7):453-459. doi:10.1038/s41477-018-0190-1 apa: Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-018-0190-1 chicago: Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants. Springer Nature, 2018. https://doi.org/10.1038/s41477-018-0190-1. ieee: M. Fendrych et al., “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” Nature Plants, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018. ista: Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459. mla: Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” Nature Plants, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:10.1038/s41477-018-0190-1. short: M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459. date_created: 2018-12-11T11:45:07Z date_published: 2018-06-25T00:00:00Z date_updated: 2023-09-15T12:11:03Z day: '25' department: - _id: JiFr - _id: DaSi - _id: NanoFab doi: 10.1038/s41477-018-0190-1 external_id: isi: - '000443221200017' pmid: - '29942048' intvolume: ' 4' isi: 1 issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/29942048 month: '06' oa: 1 oa_version: Submitted Version page: 453 - 459 pmid: 1 publication: Nature Plants publication_status: published publisher: Springer Nature publist_id: '7728' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/ scopus_import: '1' status: public title: Rapid and reversible root growth inhibition by TIR1 auxin signalling type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 4 year: '2018' ... --- _id: '14' abstract: - lang: eng text: The intercellular transport of auxin is driven by PIN-formed (PIN) auxin efflux carriers. PINs are localized at the plasma membrane (PM) and on constitutively recycling endomembrane vesicles. Therefore, PINs can mediate auxin transport either by direct translocation across the PM or by pumping auxin into secretory vesicles (SVs), leading to its secretory release upon fusion with the PM. Which of these two mechanisms dominates is a matter of debate. Here, we addressed the issue with a mathematical modeling approach. We demonstrate that the efficiency of secretory transport depends on SV size, half-life of PINs on the PM, pH, exocytosis frequency and PIN density. 3D structured illumination microscopy (SIM) was used to determine PIN density on the PM. Combining this data with published values of the other parameters, we show that the transport activity of PINs in SVs would have to be at least 1000× greater than on the PM in order to produce a comparable macroscopic auxin transport. If both transport mechanisms operated simultaneously and PINs were equally active on SVs and PM, the contribution of secretion to the total auxin flux would be negligible. In conclusion, while secretory vesicle-mediated transport of auxin is an intriguing and theoretically possible model, it is unlikely to be a major mechanism of auxin transport inplanta. acknowledgement: 'European Research Council (ERC): 742985 to Jiri Friml; M.A. was supported by the Austrian Science Fund (FWF) (M2379-B28); AJ was supported by the Austria Science Fund (FWF): I03630 to Jiri Friml.' article_processing_charge: No article_type: original author: - first_name: Sander full_name: Hille, Sander last_name: Hille - first_name: Maria full_name: Akhmanova, Maria id: 3425EC26-F248-11E8-B48F-1D18A9856A87 last_name: Akhmanova orcid: 0000-0003-1522-3162 - first_name: Matous full_name: Glanc, Matous id: 1AE1EA24-02D0-11E9-9BAA-DAF4881429F2 last_name: Glanc orcid: 0000-0003-0619-7783 - first_name: Alexander J full_name: Johnson, Alexander J id: 46A62C3A-F248-11E8-B48F-1D18A9856A87 last_name: Johnson orcid: 0000-0002-2739-8843 - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 2018;19(11). doi:10.3390/ijms19113566' apa: 'Hille, S., Akhmanova, M., Glanc, M., Johnson, A. J., & Friml, J. (2018). Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms19113566' chicago: 'Hille, Sander, Maria Akhmanova, Matous Glanc, Alexander J Johnson, and Jiří Friml. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences. MDPI, 2018. https://doi.org/10.3390/ijms19113566.' ieee: 'S. Hille, M. Akhmanova, M. Glanc, A. J. Johnson, and J. Friml, “Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation,” International Journal of Molecular Sciences, vol. 19, no. 11. MDPI, 2018.' ista: 'Hille S, Akhmanova M, Glanc M, Johnson AJ, Friml J. 2018. Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation. International Journal of Molecular Sciences. 19(11).' mla: 'Hille, Sander, et al. “Relative Contribution of PIN-Containing Secretory Vesicles and Plasma Membrane PINs to the Directed Auxin Transport: Theoretical Estimation.” International Journal of Molecular Sciences, vol. 19, no. 11, MDPI, 2018, doi:10.3390/ijms19113566.' short: S. Hille, M. Akhmanova, M. Glanc, A.J. Johnson, J. Friml, International Journal of Molecular Sciences 19 (2018). date_created: 2018-12-11T11:44:09Z date_published: 2018-11-12T00:00:00Z date_updated: 2023-09-18T08:09:32Z day: '12' ddc: - '580' department: - _id: DaSi - _id: JiFr doi: 10.3390/ijms19113566 ec_funded: 1 external_id: isi: - '000451528500282' file: - access_level: open_access checksum: e4b59c2599b0ca26ebf5b8434bcde94a content_type: application/pdf creator: dernst date_created: 2018-12-17T16:04:11Z date_updated: 2020-07-14T12:44:50Z file_id: '5719' file_name: 2018_IJMS_Hille.pdf file_size: 2200593 relation: main_file file_date_updated: 2020-07-14T12:44:50Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants - _id: 26538374-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03630 name: Molecular mechanisms of endocytic cargo recognition in plants publication: International Journal of Molecular Sciences publication_identifier: eissn: - 1422-0067 publication_status: published publisher: MDPI publist_id: '8042' quality_controlled: '1' scopus_import: '1' status: public title: 'Relative contribution of PIN-containing secretory vesicles and plasma membrane PINs to the directed auxin transport: Theoretical estimation' 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '39' abstract: - lang: eng text: We study how a block of genome with a large number of weakly selected loci introgresses under directional selection into a genetically homogeneous population. We derive exact expressions for the expected rate of growth of any fragment of the introduced block during the initial phase of introgression, and show that the growth rate of a single-locus variant is largely insensitive to its own additive effect, but depends instead on the combined effect of all loci within a characteristic linkage scale. The expected growth rate of a fragment is highly correlated with its long-term introgression probability in populations of moderate size, and can hence identify variants that are likely to introgress across replicate populations. We clarify how the introgression probability of an individual variant is determined by the interplay between hitchhiking with relatively large fragments during the early phase of introgression and selection on fine-scale variation within these, which at longer times results in differential introgression probabilities for beneficial and deleterious loci within successful fragments. By simulating individuals, we also investigate how introgression probabilities at individual loci depend on the variance of fitness effects, the net fitness of the introduced block, and the size of the recipient population, and how this shapes the net advance under selection. Our work suggests that even highly replicable substitutions may be associated with a range of selective effects, which makes it challenging to fine map the causal loci that underlie polygenic adaptation. article_processing_charge: No article_type: original author: - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva - 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: Sachdeva H, Barton NH. Replicability of introgression under linked, polygenic selection. Genetics. 2018;210(4):1411-1427. doi:10.1534/genetics.118.301429 apa: Sachdeva, H., & Barton, N. H. (2018). Replicability of introgression under linked, polygenic selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.301429 chicago: Sachdeva, Himani, and Nicholas H Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.301429. ieee: H. Sachdeva and N. H. Barton, “Replicability of introgression under linked, polygenic selection,” Genetics, vol. 210, no. 4. Genetics Society of America, pp. 1411–1427, 2018. ista: Sachdeva H, Barton NH. 2018. Replicability of introgression under linked, polygenic selection. Genetics. 210(4), 1411–1427. mla: Sachdeva, Himani, and Nicholas H. Barton. “Replicability of Introgression under Linked, Polygenic Selection.” Genetics, vol. 210, no. 4, Genetics Society of America, 2018, pp. 1411–27, doi:10.1534/genetics.118.301429. short: H. Sachdeva, N.H. Barton, Genetics 210 (2018) 1411–1427. date_created: 2018-12-11T11:44:18Z date_published: 2018-12-04T00:00:00Z date_updated: 2023-09-18T08:10:29Z day: '04' department: - _id: NiBa doi: 10.1534/genetics.118.301429 external_id: isi: - '000452315900021' intvolume: ' 210' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/379578v1 month: '12' oa: 1 oa_version: Preprint page: 1411-1427 publication: Genetics publication_identifier: issn: - '00166731' publication_status: published publisher: Genetics Society of America quality_controlled: '1' scopus_import: '1' status: public title: Replicability of introgression under linked, polygenic selection type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 210 year: '2018' ... --- _id: '420' abstract: - lang: eng text: We analyze the theoretical derivation of the beyond-mean-field equation of state for two-dimensional gas of dilute, ultracold alkali-metal atoms in the Bardeen–Cooper–Schrieffer (BCS) to Bose–Einstein condensate (BEC) crossover. We show that at zero temperature our theory — considering Gaussian fluctuations on top of the mean-field equation of state — is in very good agreement with experimental data. Subsequently, we investigate the superfluid density at finite temperature and its renormalization due to the proliferation of vortex–antivortex pairs. By doing so, we determine the Berezinskii–Kosterlitz–Thouless (BKT) critical temperature — at which the renormalized superfluid density jumps to zero — as a function of the inter-atomic potential strength. We find that the Nelson–Kosterlitz criterion overestimates the BKT temperature with respect to the renormalization group equations, this effect being particularly relevant in the intermediate regime of the crossover. article_processing_charge: No author: - first_name: Giacomo full_name: Bighin, Giacomo id: 4CA96FD4-F248-11E8-B48F-1D18A9856A87 last_name: Bighin orcid: 0000-0001-8823-9777 - first_name: Luca full_name: Salasnich, Luca last_name: Salasnich citation: ama: Bighin G, Salasnich L. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 2018;32(17):1840022. doi:10.1142/S0217979218400222 apa: Bighin, G., & Salasnich, L. (2018). Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. World Scientific Publishing. https://doi.org/10.1142/S0217979218400222 chicago: Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B. World Scientific Publishing, 2018. https://doi.org/10.1142/S0217979218400222. ieee: G. Bighin and L. Salasnich, “Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover,” International Journal of Modern Physics B, vol. 32, no. 17. World Scientific Publishing, p. 1840022, 2018. ista: Bighin G, Salasnich L. 2018. Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover. International Journal of Modern Physics B. 32(17), 1840022. mla: Bighin, Giacomo, and Luca Salasnich. “Renormalization of the Superfluid Density in the Two-Dimensional BCS-BEC Crossover.” International Journal of Modern Physics B, vol. 32, no. 17, World Scientific Publishing, 2018, p. 1840022, doi:10.1142/S0217979218400222. short: G. Bighin, L. Salasnich, International Journal of Modern Physics B 32 (2018) 1840022. date_created: 2018-12-11T11:46:22Z date_published: 2018-07-10T00:00:00Z date_updated: 2023-09-18T08:09:59Z day: '10' department: - _id: MiLe doi: 10.1142/S0217979218400222 external_id: isi: - '000438217300007' intvolume: ' 32' isi: 1 issue: '17' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1710.11171 month: '07' oa: 1 oa_version: Preprint page: '1840022' publication: International Journal of Modern Physics B publication_status: published publisher: World Scientific Publishing publist_id: '7402' quality_controlled: '1' scopus_import: '1' status: public title: Renormalization of the superfluid density in the two-dimensional BCS-BEC crossover type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 32 year: '2018' ... --- _id: '38' abstract: - lang: eng text: 'Genomes of closely-related species or populations often display localized regions of enhanced relative sequence divergence, termed genomic islands. It has been proposed that these islands arise through selective sweeps and/or barriers to gene flow. Here, we genetically dissect a genomic island that controls flower color pattern differences between two subspecies of Antirrhinum majus, A.m.striatum and A.m.pseudomajus, and relate it to clinal variation across a natural hybrid zone. We show that selective sweeps likely raised relative divergence at two tightly-linked MYB-like transcription factors, leading to distinct flower patterns in the two subspecies. The two patterns provide alternate floral guides and create a strong barrier to gene flow where populations come into contact. This barrier affects the selected flower color genes and tightlylinked loci, but does not extend outside of this domain, allowing gene flow to lower relative divergence for the rest of the chromosome. Thus, both selective sweeps and barriers to gene flow play a role in shaping genomic islands: sweeps cause elevation in relative divergence, while heterogeneous gene flow flattens the surrounding "sea," making the island of divergence stand out. By showing how selective sweeps establish alternative adaptive phenotypes that lead to barriers to gene flow, our study sheds light on possible mechanisms leading to reproductive isolation and speciation.' acknowledgement: ' ERC Grant 201252 (to N.H.B.)' article_processing_charge: No author: - first_name: Hugo full_name: Tavares, Hugo last_name: Tavares - first_name: Annabel full_name: Whitley, Annabel last_name: Whitley - first_name: David full_name: Field, David id: 419049E2-F248-11E8-B48F-1D18A9856A87 last_name: Field orcid: 0000-0002-4014-8478 - first_name: Desmond full_name: Bradley, Desmond last_name: Bradley - first_name: Matthew full_name: Couchman, Matthew last_name: Couchman - first_name: Lucy full_name: Copsey, Lucy last_name: Copsey - first_name: Joane full_name: Elleouet, Joane last_name: Elleouet - first_name: Monique full_name: Burrus, Monique last_name: Burrus - first_name: Christophe full_name: Andalo, Christophe last_name: Andalo - first_name: Miaomiao full_name: Li, Miaomiao last_name: Li - first_name: Qun full_name: Li, Qun last_name: Li - first_name: Yongbiao full_name: Xue, Yongbiao last_name: Xue - first_name: Alexandra B full_name: Rebocho, Alexandra B last_name: Rebocho - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Enrico full_name: Coen, Enrico last_name: Coen citation: ama: Tavares H, Whitley A, Field D, et al. Selection and gene flow shape genomic islands that control floral guides. PNAS. 2018;115(43):11006-11011. doi:10.1073/pnas.1801832115 apa: Tavares, H., Whitley, A., Field, D., Bradley, D., Couchman, M., Copsey, L., … Coen, E. (2018). Selection and gene flow shape genomic islands that control floral guides. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1801832115 chicago: Tavares, Hugo, Annabel Whitley, David Field, Desmond Bradley, Matthew Couchman, Lucy Copsey, Joane Elleouet, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1801832115. ieee: H. Tavares et al., “Selection and gene flow shape genomic islands that control floral guides,” PNAS, vol. 115, no. 43. National Academy of Sciences, pp. 11006–11011, 2018. ista: Tavares H, Whitley A, Field D, Bradley D, Couchman M, Copsey L, Elleouet J, Burrus M, Andalo C, Li M, Li Q, Xue Y, Rebocho AB, Barton NH, Coen E. 2018. Selection and gene flow shape genomic islands that control floral guides. PNAS. 115(43), 11006–11011. mla: Tavares, Hugo, et al. “Selection and Gene Flow Shape Genomic Islands That Control Floral Guides.” PNAS, vol. 115, no. 43, National Academy of Sciences, 2018, pp. 11006–11, doi:10.1073/pnas.1801832115. short: H. Tavares, A. Whitley, D. Field, D. Bradley, M. Couchman, L. Copsey, J. Elleouet, M. Burrus, C. Andalo, M. Li, Q. Li, Y. Xue, A.B. Rebocho, N.H. Barton, E. Coen, PNAS 115 (2018) 11006–11011. date_created: 2018-12-11T11:44:18Z date_published: 2018-10-23T00:00:00Z date_updated: 2023-09-18T08:36:49Z day: '23' ddc: - '570' department: - _id: NiBa doi: 10.1073/pnas.1801832115 external_id: isi: - '000448040500065' pmid: - '30297406' file: - access_level: open_access checksum: d2305d0cc81dbbe4c1c677d64ad6f6d1 content_type: application/pdf creator: dernst date_created: 2018-12-17T08:44:03Z date_updated: 2020-07-14T12:46:16Z file_id: '5683' file_name: 11006.full.pdf file_size: 1911302 relation: main_file file_date_updated: 2020-07-14T12:46:16Z has_accepted_license: '1' intvolume: ' 115' isi: 1 issue: '43' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 11006 - 11011 pmid: 1 publication: PNAS publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '8017' quality_controlled: '1' scopus_import: '1' status: public title: Selection and gene flow shape genomic islands that control floral guides 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '155' abstract: - lang: eng text: There is currently significant interest in operating devices in the quantum regime, where their behaviour cannot be explained through classical mechanics. Quantum states, including entangled states, are fragile and easily disturbed by excessive thermal noise. Here we address the question of whether it is possible to create non-reciprocal devices that encourage the flow of thermal noise towards or away from a particular quantum device in a network. Our work makes use of the cascaded systems formalism to answer this question in the affirmative, showing how a three-port device can be used as an effective thermal transistor, and illustrates how this formalism maps onto an experimentally-realisable optomechanical system. Our results pave the way to more resilient quantum devices and to the use of thermal noise as a resource. alternative_title: - Proceedings of SPIE article_number: 106721N article_processing_charge: No author: - first_name: André full_name: Xuereb, André last_name: Xuereb - first_name: Matteo full_name: Aquilina, Matteo last_name: Aquilina - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 citation: ama: 'Xuereb A, Aquilina M, Barzanjeh S. Routing thermal noise through quantum networks. In: Andrews DL, Ostendorf A, Bain AJ, Nunzi JM, eds. Vol 10672. SPIE; 2018. doi:10.1117/12.2309928' apa: 'Xuereb, A., Aquilina, M., & Barzanjeh, S. (2018). Routing thermal noise through quantum networks. In D. L. Andrews, A. Ostendorf, A. J. Bain, & J. M. Nunzi (Eds.) (Vol. 10672). Presented at the SPIE: The international society for optical engineering, Strasbourg, France: SPIE. https://doi.org/10.1117/12.2309928' chicago: Xuereb, André, Matteo Aquilina, and Shabir Barzanjeh. “Routing Thermal Noise through Quantum Networks.” edited by D L Andrews, A Ostendorf, A J Bain, and J M Nunzi, Vol. 10672. SPIE, 2018. https://doi.org/10.1117/12.2309928. ieee: 'A. Xuereb, M. Aquilina, and S. Barzanjeh, “Routing thermal noise through quantum networks,” presented at the SPIE: The international society for optical engineering, Strasbourg, France, 2018, vol. 10672.' ista: 'Xuereb A, Aquilina M, Barzanjeh S. 2018. Routing thermal noise through quantum networks. SPIE: The international society for optical engineering, Proceedings of SPIE, vol. 10672, 106721N.' mla: Xuereb, André, et al. Routing Thermal Noise through Quantum Networks. Edited by D L Andrews et al., vol. 10672, 106721N, SPIE, 2018, doi:10.1117/12.2309928. short: A. Xuereb, M. Aquilina, S. Barzanjeh, in:, D.L. Andrews, A. Ostendorf, A.J. Bain, J.M. Nunzi (Eds.), SPIE, 2018. conference: end_date: 2018-04-26 location: Strasbourg, France name: 'SPIE: The international society for optical engineering' start_date: 2018-04-22 date_created: 2018-12-11T11:44:55Z date_published: 2018-05-04T00:00:00Z date_updated: 2023-09-18T08:12:24Z day: '04' department: - _id: JoFi doi: 10.1117/12.2309928 editor: - first_name: D L full_name: Andrews, D L last_name: Andrews - first_name: A full_name: Ostendorf, A last_name: Ostendorf - first_name: A J full_name: Bain, A J last_name: Bain - first_name: J M full_name: Nunzi, J M last_name: Nunzi external_id: arxiv: - '1806.01000' isi: - '000453298500019' intvolume: ' 10672' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.01000 month: '05' oa: 1 oa_version: Preprint publication_status: published publisher: SPIE publist_id: '7766' quality_controlled: '1' scopus_import: '1' status: public title: Routing thermal noise through quantum networks type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10672 year: '2018' ... --- _id: '5767' abstract: - lang: eng text: 'Cuprate superconductors have long been thought of as having strong electronic correlations but negligible spin-orbit coupling. Using spin- and angle-resolved photoemission spectroscopy, we discovered that one of the most studied cuprate superconductors, Bi2212, has a nontrivial spin texture with a spin-momentum locking that circles the Brillouin zone center and a spin-layer locking that allows states of opposite spin to be localized in different parts of the unit cell. Our findings pose challenges for the vast majority of models of cuprates, such as the Hubbard model and its variants, where spin-orbit interaction has been mostly neglected, and open the intriguing question of how the high-temperature superconducting state emerges in the presence of this nontrivial spin texture. ' acknowledgement: ' M.S. was supported by the Gordon and Betty Moore Foundation s EPiQS Initiative through grant GBMF4307' article_processing_charge: No article_type: original author: - first_name: Kenneth full_name: Gotlieb, Kenneth last_name: Gotlieb - first_name: Chiu-Yun full_name: Lin, Chiu-Yun last_name: Lin - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Wentao full_name: Zhang, Wentao last_name: Zhang - first_name: Christopher L. full_name: Smallwood, Christopher L. last_name: Smallwood - first_name: Christopher full_name: Jozwiak, Christopher last_name: Jozwiak - first_name: Hiroshi full_name: Eisaki, Hiroshi last_name: Eisaki - first_name: Zahid full_name: Hussain, Zahid last_name: Hussain - first_name: Ashvin full_name: Vishwanath, Ashvin last_name: Vishwanath - first_name: Alessandra full_name: Lanzara, Alessandra last_name: Lanzara citation: ama: Gotlieb K, Lin C-Y, Serbyn M, et al. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 2018;362(6420):1271-1275. doi:10.1126/science.aao0980 apa: Gotlieb, K., Lin, C.-Y., Serbyn, M., Zhang, W., Smallwood, C. L., Jozwiak, C., … Lanzara, A. (2018). Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aao0980 chicago: Gotlieb, Kenneth, Chiu-Yun Lin, Maksym Serbyn, Wentao Zhang, Christopher L. Smallwood, Christopher Jozwiak, Hiroshi Eisaki, Zahid Hussain, Ashvin Vishwanath, and Alessandra Lanzara. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science. American Association for the Advancement of Science, 2018. https://doi.org/10.1126/science.aao0980. ieee: K. Gotlieb et al., “Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor,” Science, vol. 362, no. 6420. American Association for the Advancement of Science, pp. 1271–1275, 2018. ista: Gotlieb K, Lin C-Y, Serbyn M, Zhang W, Smallwood CL, Jozwiak C, Eisaki H, Hussain Z, Vishwanath A, Lanzara A. 2018. Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor. Science. 362(6420), 1271–1275. mla: Gotlieb, Kenneth, et al. “Revealing Hidden Spin-Momentum Locking in a High-Temperature Cuprate Superconductor.” Science, vol. 362, no. 6420, American Association for the Advancement of Science, 2018, pp. 1271–75, doi:10.1126/science.aao0980. short: K. Gotlieb, C.-Y. Lin, M. Serbyn, W. Zhang, C.L. Smallwood, C. Jozwiak, H. Eisaki, Z. Hussain, A. Vishwanath, A. Lanzara, Science 362 (2018) 1271–1275. date_created: 2018-12-19T14:53:50Z date_published: 2018-12-14T00:00:00Z date_updated: 2023-09-18T08:11:56Z day: '14' department: - _id: MaSe doi: 10.1126/science.aao0980 external_id: isi: - '000452994400048' intvolume: ' 362' isi: 1 issue: '6420' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1126/science.aao0980 month: '12' oa: 1 oa_version: Published Version page: 1271-1275 publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: American Association for the Advancement of Science quality_controlled: '1' scopus_import: '1' status: public title: Revealing hidden spin-momentum locking in a high-temperature cuprate superconductor type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 362 year: '2018' ... --- _id: '434' abstract: - lang: eng text: In this paper, we present a formal model-driven design approach to establish a safety-assured implementation of multifunction vehicle bus controller (MVBC), which controls the data transmission among the devices of the vehicle. First, the generic models and safety requirements described in International Electrotechnical Commission Standard 61375 are formalized as time automata and timed computation tree logic formulas, respectively. With model checking tool Uppaal, we verify whether or not the constructed timed automata satisfy the formulas and several logic inconsistencies in the original standard are detected and corrected. Then, we apply the code generation tool Times to generate C code from the verified model, which is later synthesized into a real MVBC chip, with some handwriting glue code. Furthermore, the runtime verification tool RMOR is applied on the integrated code, to verify some safety requirements that cannot be formalized on the timed automata. For evaluation, we compare the proposed approach with existing MVBC design methods, such as BeagleBone, Galsblock, and Simulink. Experiments show that more ambiguousness or bugs in the standard are detected during Uppaal verification, and the generated code of Times outperforms the C code generated by others in terms of the synthesized binary code size. The errors in the standard have been confirmed and the resulting MVBC has been deployed in the real train communication network. article_processing_charge: No author: - first_name: Yu full_name: Jiang, Yu last_name: Jiang - first_name: Han full_name: Liu, Han last_name: Liu - first_name: Huobing full_name: Song, Huobing last_name: Song - first_name: Hui full_name: Kong, Hui id: 3BDE25AA-F248-11E8-B48F-1D18A9856A87 last_name: Kong orcid: 0000-0002-3066-6941 - first_name: Rui full_name: Wang, Rui last_name: Wang - first_name: Yong full_name: Guan, Yong last_name: Guan - first_name: Lui full_name: Sha, Lui last_name: Sha citation: ama: Jiang Y, Liu H, Song H, et al. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 2018;19(10):3320-3333. doi:10.1109/TITS.2017.2778077 apa: Jiang, Y., Liu, H., Song, H., Kong, H., Wang, R., Guan, Y., & Sha, L. (2018). Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. IEEE. https://doi.org/10.1109/TITS.2017.2778077 chicago: Jiang, Yu, Han Liu, Huobing Song, Hui Kong, Rui Wang, Yong Guan, and Lui Sha. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems. IEEE, 2018. https://doi.org/10.1109/TITS.2017.2778077. ieee: Y. Jiang et al., “Safety-assured model-driven design of the multifunction vehicle bus controller,” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10. IEEE, pp. 3320–3333, 2018. ista: Jiang Y, Liu H, Song H, Kong H, Wang R, Guan Y, Sha L. 2018. Safety-assured model-driven design of the multifunction vehicle bus controller. IEEE Transactions on Intelligent Transportation Systems. 19(10), 3320–3333. mla: Jiang, Yu, et al. “Safety-Assured Model-Driven Design of the Multifunction Vehicle Bus Controller.” IEEE Transactions on Intelligent Transportation Systems, vol. 19, no. 10, IEEE, 2018, pp. 3320–33, doi:10.1109/TITS.2017.2778077. short: Y. Jiang, H. Liu, H. Song, H. Kong, R. Wang, Y. Guan, L. Sha, IEEE Transactions on Intelligent Transportation Systems 19 (2018) 3320–3333. date_created: 2018-12-11T11:46:27Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-09-18T08:12:49Z day: '01' department: - _id: ToHe doi: 10.1109/TITS.2017.2778077 external_id: isi: - '000446651100020' intvolume: ' 19' isi: 1 issue: '10' language: - iso: eng month: '01' oa_version: None page: 3320 - 3333 publication: IEEE Transactions on Intelligent Transportation Systems publication_status: published publisher: IEEE publist_id: '7389' quality_controlled: '1' related_material: record: - id: '1205' relation: earlier_version status: public scopus_import: '1' status: public title: Safety-assured model-driven design of the multifunction vehicle bus controller type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 19 year: '2018' ... --- _id: '162' abstract: - lang: eng text: 'Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.' article_number: e34465 article_processing_charge: No author: - first_name: Marketa full_name: Kaucka, Marketa last_name: Kaucka - first_name: Julian full_name: Petersen, Julian last_name: Petersen - first_name: Marketa full_name: Tesarova, Marketa last_name: Tesarova - first_name: Bara full_name: Szarowska, Bara last_name: Szarowska - first_name: Maria full_name: Kastriti, Maria last_name: Kastriti - first_name: Meng full_name: Xie, Meng last_name: Xie - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Karl full_name: Annusver, Karl last_name: Annusver - first_name: Maria full_name: Kasper, Maria last_name: Kasper - first_name: Orsolya full_name: Symmons, Orsolya last_name: Symmons - first_name: Leslie full_name: Pan, Leslie last_name: Pan - first_name: Francois full_name: Spitz, Francois last_name: Spitz - first_name: Jozef full_name: Kaiser, Jozef last_name: Kaiser - first_name: Maria full_name: Hovorakova, Maria last_name: Hovorakova - first_name: Tomas full_name: Zikmund, Tomas last_name: Zikmund - first_name: Kazunori full_name: Sunadome, Kazunori last_name: Sunadome - first_name: Michael P full_name: Matise, Michael P last_name: Matise - first_name: Hui full_name: Wang, Hui last_name: Wang - first_name: Ulrika full_name: Marklund, Ulrika last_name: Marklund - first_name: Hind full_name: Abdo, Hind last_name: Abdo - first_name: Patrik full_name: Ernfors, Patrik last_name: Ernfors - first_name: Pascal full_name: Maire, Pascal last_name: Maire - first_name: Maud full_name: Wurmser, Maud last_name: Wurmser - first_name: Andrei S full_name: Chagin, Andrei S last_name: Chagin - first_name: Kaj full_name: Fried, Kaj last_name: Fried - first_name: Igor full_name: Adameyko, Igor last_name: Adameyko citation: ama: Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 2018;7. doi:10.7554/eLife.34465 apa: Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.34465 chicago: Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.34465. ieee: M. Kaucka et al., “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” eLife, vol. 7. eLife Sciences Publications, 2018. ista: Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465. mla: Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” ELife, vol. 7, e34465, eLife Sciences Publications, 2018, doi:10.7554/eLife.34465. short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018). date_created: 2018-12-11T11:44:57Z date_published: 2018-06-13T00:00:00Z date_updated: 2023-09-18T09:29:07Z day: '13' ddc: - '571' department: - _id: AnKi doi: 10.7554/eLife.34465 ec_funded: 1 external_id: isi: - '000436227500001' file: - access_level: open_access checksum: da2378cdcf6b5461dcde194e4d608343 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:41:58Z date_updated: 2020-07-14T12:45:07Z file_id: '5727' file_name: 2018_eLife_Kaucka.pdf file_size: 9816484 relation: main_file file_date_updated: 2020-07-14T12:45:07Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '7759' quality_controlled: '1' related_material: record: - id: '9838' relation: research_data status: public scopus_import: '1' status: public title: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 7 year: '2018' ... --- _id: '302' abstract: - lang: eng text: At ITCS 2013, Mahmoody, Moran and Vadhan [MMV13] introduce and construct publicly verifiable proofs of sequential work, which is a protocol for proving that one spent sequential computational work related to some statement. The original motivation for such proofs included non-interactive time-stamping and universally verifiable CPU benchmarks. A more recent application, and our main motivation, are blockchain designs, where proofs of sequential work can be used – in combination with proofs of space – as a more ecological and economical substitute for proofs of work which are currently used to secure Bitcoin and other cryptocurrencies. The construction proposed by [MMV13] is based on a hash function and can be proven secure in the random oracle model, or assuming inherently sequential hash-functions, which is a new standard model assumption introduced in their work. In a proof of sequential work, a prover gets a “statement” χ, a time parameter N and access to a hash-function H, which for the security proof is modelled as a random oracle. Correctness requires that an honest prover can make a verifier accept making only N queries to H, while soundness requires that any prover who makes the verifier accept must have made (almost) N sequential queries to H. Thus a solution constitutes a proof that N time passed since χ was received. Solutions must be publicly verifiable in time at most polylogarithmic in N. The construction of [MMV13] is based on “depth-robust” graphs, and as a consequence has rather poor concrete parameters. But the major drawback is that the prover needs not just N time, but also N space to compute a proof. In this work we propose a proof of sequential work which is much simpler, more efficient and achieves much better concrete bounds. Most importantly, the space required can be as small as log (N) (but we get better soundness using slightly more memory than that). An open problem stated by [MMV13] that our construction does not solve either is achieving a “unique” proof, where even a cheating prover can only generate a single accepting proof. This property would be extremely useful for applications to blockchains. alternative_title: - LNCS article_processing_charge: No author: - first_name: Bram full_name: Cohen, Bram last_name: Cohen - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Cohen B, Pietrzak KZ. Simple proofs of sequential work. In: Vol 10821. Springer; 2018:451-467. doi:10.1007/978-3-319-78375-8_15' apa: 'Cohen, B., & Pietrzak, K. Z. (2018). Simple proofs of sequential work (Vol. 10821, pp. 451–467). Presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_15' chicago: Cohen, Bram, and Krzysztof Z Pietrzak. “Simple Proofs of Sequential Work,” 10821:451–67. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_15. ieee: 'B. Cohen and K. Z. Pietrzak, “Simple proofs of sequential work,” presented at the Eurocrypt: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 451–467.' ista: 'Cohen B, Pietrzak KZ. 2018. Simple proofs of sequential work. Eurocrypt: Advances in Cryptology, LNCS, vol. 10821, 451–467.' mla: Cohen, Bram, and Krzysztof Z. Pietrzak. Simple Proofs of Sequential Work. Vol. 10821, Springer, 2018, pp. 451–67, doi:10.1007/978-3-319-78375-8_15. short: B. Cohen, K.Z. Pietrzak, in:, Springer, 2018, pp. 451–467. conference: end_date: 2018-05-03 location: Tel Aviv, Israel name: 'Eurocrypt: Advances in Cryptology' start_date: 2018-04-29 date_created: 2018-12-11T11:45:42Z date_published: 2018-05-29T00:00:00Z date_updated: 2023-09-18T09:29:33Z day: '29' department: - _id: KrPi doi: 10.1007/978-3-319-78375-8_15 ec_funded: 1 external_id: isi: - '000517098700015' intvolume: ' 10821' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2018/183.pdf month: '05' oa: 1 oa_version: Submitted Version page: 451 - 467 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_status: published publisher: Springer publist_id: '7579' quality_controlled: '1' scopus_import: '1' status: public title: Simple proofs of sequential work type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10821 year: '2018' ... --- _id: '31' abstract: - lang: eng text: Correlations in sensory neural networks have both extrinsic and intrinsic origins. Extrinsic or stimulus correlations arise from shared inputs to the network and, thus, depend strongly on the stimulus ensemble. Intrinsic or noise correlations reflect biophysical mechanisms of interactions between neurons, which are expected to be robust to changes in the stimulus ensemble. Despite the importance of this distinction for understanding how sensory networks encode information collectively, no method exists to reliably separate intrinsic interactions from extrinsic correlations in neural activity data, limiting our ability to build predictive models of the network response. In this paper we introduce a general strategy to infer population models of interacting neurons that collectively encode stimulus information. The key to disentangling intrinsic from extrinsic correlations is to infer the couplings between neurons separately from the encoding model and to combine the two using corrections calculated in a mean-field approximation. We demonstrate the effectiveness of this approach in retinal recordings. The same coupling network is inferred from responses to radically different stimulus ensembles, showing that these couplings indeed reflect stimulus-independent interactions between neurons. The inferred model predicts accurately the collective response of retinal ganglion cell populations as a function of the stimulus. acknowledgement: This work was supported by ANR Trajectory, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche (LIFESENSES; ANR-10-LABX-65), EC Grant No. H2020-785907 from the Human Brain Project, NIH Grant No. U01NS090501, and an AVIESAN-UNADEV grant to O.M. M.C. was supported by the Agence Nationale de la Recherche Jeune Chercheur/Jeune Chercheuse grant (ANR-17-CE37-0013). article_number: '042410' article_processing_charge: No article_type: original author: - first_name: Ulisse full_name: Ferrari, Ulisse last_name: Ferrari - first_name: Stephane full_name: Deny, Stephane last_name: Deny - first_name: Matthew J full_name: Chalk, Matthew J last_name: Chalk - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Thierry full_name: Mora, Thierry last_name: Mora citation: ama: Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 2018;98(4). doi:10.1103/PhysRevE.98.042410 apa: Ferrari, U., Deny, S., Chalk, M. J., Tkačik, G., Marre, O., & Mora, T. (2018). Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. American Physical Society. https://doi.org/10.1103/PhysRevE.98.042410 chicago: Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gašper Tkačik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E. American Physical Society, 2018. https://doi.org/10.1103/PhysRevE.98.042410. ieee: U. Ferrari, S. Deny, M. J. Chalk, G. Tkačik, O. Marre, and T. Mora, “Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons,” Physical Review E, vol. 98, no. 4. American Physical Society, 2018. ista: Ferrari U, Deny S, Chalk MJ, Tkačik G, Marre O, Mora T. 2018. Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons. Physical Review E. 98(4), 042410. mla: Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410. short: U. Ferrari, S. Deny, M.J. Chalk, G. Tkačik, O. Marre, T. Mora, Physical Review E 98 (2018). date_created: 2018-12-11T11:44:15Z date_published: 2018-10-17T00:00:00Z date_updated: 2023-09-18T09:18:44Z day: '17' department: - _id: GaTk doi: 10.1103/PhysRevE.98.042410 ec_funded: 1 external_id: isi: - '000447486100004' intvolume: ' 98' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/243816v2.full month: '10' oa: 1 oa_version: Preprint project: - _id: 26436750-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '785907' name: Human Brain Project Specific Grant Agreement 2 (HBP SGA 2) publication: Physical Review E publication_identifier: issn: - '24700045' publication_status: published publisher: American Physical Society publist_id: '8024' quality_controlled: '1' scopus_import: '1' status: public title: Separating intrinsic interactions from extrinsic correlations in a network of sensory neurons type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 98 year: '2018' ... --- _id: '64' abstract: - lang: eng text: Tropical geometry, an established field in pure mathematics, is a place where string theory, mirror symmetry, computational algebra, auction theory, and so forth meet and influence one another. In this paper, we report on our discovery of a tropical model with self-organized criticality (SOC) behavior. Our model is continuous, in contrast to all known models of SOC, and is a certain scaling limit of the sandpile model, the first and archetypical model of SOC. We describe how our model is related to pattern formation and proportional growth phenomena and discuss the dichotomy between continuous and discrete models in several contexts. Our aim in this context is to present an idealized tropical toy model (cf. Turing reaction-diffusion model), requiring further investigation. article_processing_charge: No article_type: original author: - first_name: Nikita full_name: Kalinin, Nikita last_name: Kalinin - first_name: Aldo full_name: Guzmán Sáenz, Aldo last_name: Guzmán Sáenz - first_name: Y full_name: Prieto, Y last_name: Prieto - first_name: Mikhail full_name: Shkolnikov, Mikhail id: 35084A62-F248-11E8-B48F-1D18A9856A87 last_name: Shkolnikov orcid: 0000-0002-4310-178X - first_name: V full_name: Kalinina, V last_name: Kalinina - first_name: Ernesto full_name: Lupercio, Ernesto last_name: Lupercio citation: ama: 'Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 2018;115(35):E8135-E8142. doi:10.1073/pnas.1805847115' apa: 'Kalinin, N., Guzmán Sáenz, A., Prieto, Y., Shkolnikov, M., Kalinina, V., & Lupercio, E. (2018). Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences. https://doi.org/10.1073/pnas.1805847115' chicago: 'Kalinin, Nikita, Aldo Guzmán Sáenz, Y Prieto, Mikhail Shkolnikov, V Kalinina, and Ernesto Lupercio. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1805847115.' ieee: 'N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, and E. Lupercio, “Self-organized criticality and pattern emergence through the lens of tropical geometry,” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35. National Academy of Sciences, pp. E8135–E8142, 2018.' ista: 'Kalinin N, Guzmán Sáenz A, Prieto Y, Shkolnikov M, Kalinina V, Lupercio E. 2018. Self-organized criticality and pattern emergence through the lens of tropical geometry. PNAS: Proceedings of the National Academy of Sciences of the United States of America. 115(35), E8135–E8142.' mla: 'Kalinin, Nikita, et al. “Self-Organized Criticality and Pattern Emergence through the Lens of Tropical Geometry.” PNAS: Proceedings of the National Academy of Sciences of the United States of America, vol. 115, no. 35, National Academy of Sciences, 2018, pp. E8135–42, doi:10.1073/pnas.1805847115.' short: 'N. Kalinin, A. Guzmán Sáenz, Y. Prieto, M. Shkolnikov, V. Kalinina, E. Lupercio, PNAS: Proceedings of the National Academy of Sciences of the United States of America 115 (2018) E8135–E8142.' date_created: 2018-12-11T11:44:26Z date_published: 2018-08-28T00:00:00Z date_updated: 2023-09-18T08:41:16Z day: '28' department: - _id: TaHa doi: 10.1073/pnas.1805847115 ec_funded: 1 external_id: arxiv: - '1806.09153' isi: - '000442861600009' intvolume: ' 115' isi: 1 issue: '35' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1806.09153 month: '08' oa: 1 oa_version: Preprint page: E8135 - E8142 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: 'PNAS: Proceedings of the National Academy of Sciences of the United States of America' publication_identifier: issn: - '00278424' publication_status: published publisher: National Academy of Sciences publist_id: '7990' quality_controlled: '1' scopus_import: '1' status: public title: Self-organized criticality and pattern emergence through the lens of tropical geometry type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '9838' abstract: - lang: eng text: 'Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.' article_processing_charge: No author: - first_name: Marketa full_name: Kaucka, Marketa last_name: Kaucka - first_name: Julian full_name: Petersen, Julian last_name: Petersen - first_name: Marketa full_name: Tesarova, Marketa last_name: Tesarova - first_name: Bara full_name: Szarowska, Bara last_name: Szarowska - first_name: Maria Eleni full_name: Kastriti, Maria Eleni last_name: Kastriti - first_name: Meng full_name: Xie, Meng last_name: Xie - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Karl full_name: Annusver, Karl last_name: Annusver - first_name: Maria full_name: Kasper, Maria last_name: Kasper - first_name: Orsolya full_name: Symmons, Orsolya last_name: Symmons - first_name: Leslie full_name: Pan, Leslie last_name: Pan - first_name: Francois full_name: Spitz, Francois last_name: Spitz - first_name: Jozef full_name: Kaiser, Jozef last_name: Kaiser - first_name: Maria full_name: Hovorakova, Maria last_name: Hovorakova - first_name: Tomas full_name: Zikmund, Tomas last_name: Zikmund - first_name: Kazunori full_name: Sunadome, Kazunori last_name: Sunadome - first_name: Michael P full_name: Matise, Michael P last_name: Matise - first_name: Hui full_name: Wang, Hui last_name: Wang - first_name: Ulrika full_name: Marklund, Ulrika last_name: Marklund - first_name: Hind full_name: Abdo, Hind last_name: Abdo - first_name: Patrik full_name: Ernfors, Patrik last_name: Ernfors - first_name: Pascal full_name: Maire, Pascal last_name: Maire - first_name: Maud full_name: Wurmser, Maud last_name: Wurmser - first_name: Andrei S full_name: Chagin, Andrei S last_name: Chagin - first_name: Kaj full_name: Fried, Kaj last_name: Fried - first_name: Igor full_name: Adameyko, Igor last_name: Adameyko citation: ama: 'Kaucka M, Petersen J, Tesarova M, et al. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. 2018. doi:10.5061/dryad.f1s76f2' apa: 'Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M. E., Xie, M., … Adameyko, I. (2018). Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. Dryad. https://doi.org/10.5061/dryad.f1s76f2' chicago: 'Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Eleni Kastriti, Meng Xie, Anna Kicheva, et al. “Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” Dryad, 2018. https://doi.org/10.5061/dryad.f1s76f2.' ieee: 'M. Kaucka et al., “Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage.” Dryad, 2018.' ista: 'Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti ME, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage, Dryad, 10.5061/dryad.f1s76f2.' mla: 'Kaucka, Marketa, et al. Data from: Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage. Dryad, 2018, doi:10.5061/dryad.f1s76f2.' short: M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M.E. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, (2018). date_created: 2021-08-09T12:54:35Z date_published: 2018-06-14T00:00:00Z date_updated: 2023-09-18T09:29:07Z day: '14' department: - _id: AnKi doi: 10.5061/dryad.f1s76f2 main_file_link: - open_access: '1' url: https://doi.org/10.5061/dryad.f1s76f2 month: '06' oa: 1 oa_version: Published Version publisher: Dryad related_material: record: - id: '162' relation: used_in_publication status: public status: public title: 'Data from: Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage' type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2018' ... --- _id: '41' abstract: - lang: eng text: 'The small-conductance, Ca2+-activated K+ (SK) channel subtype SK2 regulates the spike rate and firing frequency, as well as Ca2+ transients in Purkinje cells (PCs). To understand the molecular basis by which SK2 channels mediate these functions, we analyzed the exact location and densities of SK2 channels along the neuronal surface of the mouse cerebellar PCs using SDS-digested freeze-fracture replica labeling (SDS-FRL) of high sensitivity combined with quantitative analyses. Immunogold particles for SK2 were observed on post- and pre-synaptic compartments showing both scattered and clustered distribution patterns. We found an axo-somato-dendritic gradient of the SK2 particle density increasing 12-fold from soma to dendritic spines. Using two different immunogold approaches, we also found that SK2 immunoparticles were frequently adjacent to, but never overlap with, the postsynaptic density of excitatory synapses in PC spines. Co-immunoprecipitation analysis demonstrated that SK2 channels form macromolecular complexes with two types of proteins that mobilize Ca2+: CaV2.1 channels and mGlu1α receptors in the cerebellum. Freeze-fracture replica double-labeling showed significant co-clustering of particles for SK2 with those for CaV2.1 channels and mGlu1α receptors. SK2 channels were also detected at presynaptic sites, mostly at the presynaptic active zone (AZ), where they are close to CaV2.1 channels, though they are not significantly co-clustered. These data demonstrate that SK2 channels located in different neuronal compartments can associate with distinct proteins mobilizing Ca2+, and suggest that the ultrastructural association of SK2 with CaV2.1 and mGlu1α provides the mechanism that ensures voltage (excitability) regulation by distinct intracellular Ca2+ transients in PCs.' article_number: '311' article_processing_charge: No article_type: original author: - first_name: Rafæl full_name: Luján, Rafæl last_name: Luján - first_name: Carolina full_name: Aguado, Carolina last_name: Aguado - first_name: Francisco full_name: Ciruela, Francisco last_name: Ciruela - first_name: Xavier full_name: Arus, Xavier last_name: Arus - first_name: Alejandro full_name: Martín Belmonte, Alejandro last_name: Martín Belmonte - first_name: Rocío full_name: Alfaro Ruiz, Rocío last_name: Alfaro Ruiz - first_name: Jesus full_name: Martinez Gomez, Jesus last_name: Martinez Gomez - first_name: Luis full_name: De La Ossa, Luis last_name: De La Ossa - first_name: Masahiko full_name: Watanabe, Masahiko last_name: Watanabe - first_name: John full_name: Adelman, John last_name: Adelman - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Yugo full_name: Fukazawa, Yugo last_name: Fukazawa citation: ama: Luján R, Aguado C, Ciruela F, et al. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 2018;12. doi:10.3389/fncel.2018.00311 apa: Luján, R., Aguado, C., Ciruela, F., Arus, X., Martín Belmonte, A., Alfaro Ruiz, R., … Fukazawa, Y. (2018). Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. Frontiers Media. https://doi.org/10.3389/fncel.2018.00311 chicago: Luján, Rafæl, Carolina Aguado, Francisco Ciruela, Xavier Arus, Alejandro Martín Belmonte, Rocío Alfaro Ruiz, Jesus Martinez Gomez, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience. Frontiers Media, 2018. https://doi.org/10.3389/fncel.2018.00311. ieee: R. Luján et al., “Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells,” Frontiers in Cellular Neuroscience, vol. 12. Frontiers Media, 2018. ista: Luján R, Aguado C, Ciruela F, Arus X, Martín Belmonte A, Alfaro Ruiz R, Martinez Gomez J, De La Ossa L, Watanabe M, Adelman J, Shigemoto R, Fukazawa Y. 2018. Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells. Frontiers in Cellular Neuroscience. 12, 311. mla: Luján, Rafæl, et al. “Sk2 Channels Associate with MGlu1α Receptors and CaV2.1 Channels in Purkinje Cells.” Frontiers in Cellular Neuroscience, vol. 12, 311, Frontiers Media, 2018, doi:10.3389/fncel.2018.00311. short: R. Luján, C. Aguado, F. Ciruela, X. Arus, A. Martín Belmonte, R. Alfaro Ruiz, J. Martinez Gomez, L. De La Ossa, M. Watanabe, J. Adelman, R. Shigemoto, Y. Fukazawa, Frontiers in Cellular Neuroscience 12 (2018). date_created: 2018-12-11T11:44:19Z date_published: 2018-09-19T00:00:00Z date_updated: 2023-09-18T09:31:18Z day: '19' ddc: - '570' department: - _id: RySh doi: 10.3389/fncel.2018.00311 ec_funded: 1 external_id: isi: - '000445090100002' file: - access_level: open_access checksum: 0bcaec8d596162af0b7fe3f31325d480 content_type: application/pdf creator: dernst date_created: 2018-12-17T08:49:03Z date_updated: 2020-07-14T12:46:23Z file_id: '5684' file_name: fncel-12-00311.pdf file_size: 6834251 relation: main_file file_date_updated: 2020-07-14T12:46:23Z has_accepted_license: '1' intvolume: ' 12' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25CBA828-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '720270' name: Human Brain Project Specific Grant Agreement 1 (HBP SGA 1) publication: Frontiers in Cellular Neuroscience publication_identifier: issn: - '16625102' publication_status: published publisher: Frontiers Media publist_id: '8013' quality_controlled: '1' scopus_import: '1' status: public title: Sk2 channels associate with mGlu1α receptors and CaV2.1 channels in Purkinje cells tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 12 year: '2018' ... --- _id: '23' abstract: - lang: eng text: The strong atomistic spin–orbit coupling of holes makes single-shot spin readout measurements difficult because it reduces the spin lifetimes. By integrating the charge sensor into a high bandwidth radio frequency reflectometry setup, we were able to demonstrate single-shot readout of a germanium quantum dot hole spin and measure the spin lifetime. Hole spin relaxation times of about 90 μs at 500 mT are reported, with a total readout visibility of about 70%. By analyzing separately the spin-to-charge conversion and charge readout fidelities, we have obtained insight into the processes limiting the visibilities of hole spins. The analyses suggest that high hole visibilities are feasible at realistic experimental conditions, underlying the potential of hole spins for the realization of viable qubit devices. acknowledged_ssus: - _id: M-Shop - _id: NanoFab article_processing_charge: No author: - first_name: Lada full_name: Vukušić, Lada id: 31E9F056-F248-11E8-B48F-1D18A9856A87 last_name: Vukušić orcid: 0000-0003-2424-8636 - first_name: Josip full_name: Kukucka, Josip id: 3F5D8856-F248-11E8-B48F-1D18A9856A87 last_name: Kukucka - first_name: Hannes full_name: Watzinger, Hannes id: 35DF8E50-F248-11E8-B48F-1D18A9856A87 last_name: Watzinger - first_name: Joshua M full_name: Milem, Joshua M id: 4CDE0A96-F248-11E8-B48F-1D18A9856A87 last_name: Milem - first_name: Friedrich full_name: Schäffler, Friedrich last_name: Schäffler - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. Single-shot readout of hole spins in Ge. Nano Letters. 2018;18(11):7141-7145. doi:10.1021/acs.nanolett.8b03217 apa: Vukušić, L., Kukucka, J., Watzinger, H., Milem, J. M., Schäffler, F., & Katsaros, G. (2018). Single-shot readout of hole spins in Ge. Nano Letters. American Chemical Society. https://doi.org/10.1021/acs.nanolett.8b03217 chicago: Vukušić, Lada, Josip Kukucka, Hannes Watzinger, Joshua M Milem, Friedrich Schäffler, and Georgios Katsaros. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters. American Chemical Society, 2018. https://doi.org/10.1021/acs.nanolett.8b03217. ieee: L. Vukušić, J. Kukucka, H. Watzinger, J. M. Milem, F. Schäffler, and G. Katsaros, “Single-shot readout of hole spins in Ge,” Nano Letters, vol. 18, no. 11. American Chemical Society, pp. 7141–7145, 2018. ista: Vukušić L, Kukucka J, Watzinger H, Milem JM, Schäffler F, Katsaros G. 2018. Single-shot readout of hole spins in Ge. Nano Letters. 18(11), 7141–7145. mla: Vukušić, Lada, et al. “Single-Shot Readout of Hole Spins in Ge.” Nano Letters, vol. 18, no. 11, American Chemical Society, 2018, pp. 7141–45, doi:10.1021/acs.nanolett.8b03217. short: L. Vukušić, J. Kukucka, H. Watzinger, J.M. Milem, F. Schäffler, G. Katsaros, Nano Letters 18 (2018) 7141–7145. date_created: 2018-12-11T11:44:13Z date_published: 2018-10-25T00:00:00Z date_updated: 2023-09-18T09:30:37Z day: '25' ddc: - '530' department: - _id: GeKa doi: 10.1021/acs.nanolett.8b03217 ec_funded: 1 external_id: isi: - '000451102100064' pmid: - '30359041' file: - access_level: open_access checksum: 3e6034a94c6b5335e939145d88bdb371 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:08Z date_updated: 2020-07-14T12:45:37Z file_id: '5194' file_name: IST-2018-1065-v1+1_ACS_nanoletters_8b03217.pdf file_size: 1361441 relation: main_file file_date_updated: 2020-07-14T12:45:37Z has_accepted_license: '1' intvolume: ' 18' isi: 1 issue: '11' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 7141 - 7145 pmid: 1 project: - _id: 25517E86-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '335497' name: Towards Spin qubits and Majorana fermions in Germanium selfassembled hut-wires publication: Nano Letters publication_identifier: issn: - '15306984' publication_status: published publisher: American Chemical Society publist_id: '8032' pubrep_id: '1065' quality_controlled: '1' related_material: record: - id: '7977' relation: popular_science - id: '69' relation: dissertation_contains status: public - id: '7996' relation: dissertation_contains status: public scopus_import: '1' status: public title: Single-shot readout of hole spins in Ge 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 18 year: '2018' ... --- _id: '85' abstract: - lang: eng text: Concurrent accesses to shared data structures must be synchronized to avoid data races. Coarse-grained synchronization, which locks the entire data structure, is easy to implement but does not scale. Fine-grained synchronization can scale well, but can be hard to reason about. Hand-over-hand locking, in which operations are pipelined as they traverse the data structure, combines fine-grained synchronization with ease of use. However, the traditional implementation suffers from inherent overheads. This paper introduces snapshot-based synchronization (SBS), a novel hand-over-hand locking mechanism. SBS decouples the synchronization state from the data, significantly improving cache utilization. Further, it relies on guarantees provided by pipelining to minimize synchronization that requires cross-thread communication. Snapshot-based synchronization thus scales much better than traditional hand-over-hand locking, while maintaining the same ease of use. acknowledgement: Trevor Brown was supported in part by the ISF (grants 2005/17 & 1749/14) and by a NSERC post-doctoral fellowship. alternative_title: - LNCS article_processing_charge: No author: - first_name: Eran full_name: Gilad, Eran last_name: Gilad - first_name: Trevor A full_name: Brown, Trevor A id: 3569F0A0-F248-11E8-B48F-1D18A9856A87 last_name: Brown - first_name: Mark full_name: Oskin, Mark last_name: Oskin - first_name: Yoav full_name: Etsion, Yoav last_name: Etsion citation: ama: 'Gilad E, Brown TA, Oskin M, Etsion Y. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. In: Vol 11014. Springer; 2018:465-479. doi:10.1007/978-3-319-96983-1_33' apa: 'Gilad, E., Brown, T. A., Oskin, M., & Etsion, Y. (2018). Snapshot based synchronization: A fast replacement for Hand-over-Hand locking (Vol. 11014, pp. 465–479). Presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy: Springer. https://doi.org/10.1007/978-3-319-96983-1_33' chicago: 'Gilad, Eran, Trevor A Brown, Mark Oskin, and Yoav Etsion. “Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking,” 11014:465–79. Springer, 2018. https://doi.org/10.1007/978-3-319-96983-1_33.' ieee: 'E. Gilad, T. A. Brown, M. Oskin, and Y. Etsion, “Snapshot based synchronization: A fast replacement for Hand-over-Hand locking,” presented at the Euro-Par: European Conference on Parallel Processing, Turin, Italy, 2018, vol. 11014, pp. 465–479.' ista: 'Gilad E, Brown TA, Oskin M, Etsion Y. 2018. Snapshot based synchronization: A fast replacement for Hand-over-Hand locking. Euro-Par: European Conference on Parallel Processing, LNCS, vol. 11014, 465–479.' mla: 'Gilad, Eran, et al. Snapshot Based Synchronization: A Fast Replacement for Hand-over-Hand Locking. Vol. 11014, Springer, 2018, pp. 465–79, doi:10.1007/978-3-319-96983-1_33.' short: E. Gilad, T.A. Brown, M. Oskin, Y. Etsion, in:, Springer, 2018, pp. 465–479. conference: end_date: 2018-08-31 location: Turin, Italy name: 'Euro-Par: European Conference on Parallel Processing' start_date: 2018-08-27 date_created: 2018-12-11T11:44:33Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-09-18T09:32:36Z day: '01' ddc: - '000' department: - _id: DaAl doi: 10.1007/978-3-319-96983-1_33 external_id: isi: - '000851042300031' file: - access_level: open_access checksum: 13a3f250be8878405e791b53c19722ad content_type: application/pdf creator: dernst date_created: 2019-02-12T07:40:40Z date_updated: 2020-07-14T12:48:14Z file_id: '5954' file_name: 2018_Brown.pdf file_size: 665372 relation: main_file file_date_updated: 2020-07-14T12:48:14Z has_accepted_license: '1' intvolume: ' 11014' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Preprint page: 465 - 479 project: - _id: 26450934-B435-11E9-9278-68D0E5697425 name: NSERC Postdoctoral fellowship publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '7969' quality_controlled: '1' scopus_import: '1' status: public title: 'Snapshot based synchronization: A fast replacement for Hand-over-Hand locking' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11014 year: '2018' ... --- _id: '327' abstract: - lang: eng text: Many-body quantum systems typically display fast dynamics and ballistic spreading of information. Here we address the open problem of how slow the dynamics can be after a generic breaking of integrability by local interactions. We develop a method based on degenerate perturbation theory that reveals slow dynamical regimes and delocalization processes in general translation invariant models, along with accurate estimates of their delocalization time scales. Our results shed light on the fundamental questions of the robustness of quantum integrable systems and the possibility of many-body localization without disorder. As an example, we construct a large class of one-dimensional lattice models where, despite the absence of asymptotic localization, the transient dynamics is exceptionally slow, i.e., the dynamics is indistinguishable from that of many-body localized systems for the system sizes and time scales accessible in experiments and numerical simulations. acknowledgement: 'We thank F. Huveneers for useful discussions. Z.P. and A.M. acknowledge support by EPSRC Grant No. EP/P009409/1 and and the Royal Society Research Grant No. RG160635. Statement of compliance with EPSRC policy framework on research data: This publication is theoretical work that does not require supporting research data. D.A. acknowledges support by the Swiss National Science Foundation. M.Z., M.M. and T.P. acknowledge Grants J1-7279 (M.Z.) and N1-0025 (M.M. and T.P.) of Slovenian Research Agency, and Advanced Grant of European Research Council, Grant No. 694544 - OMNES (T.P.).' article_number: '104307' article_processing_charge: No author: - first_name: Alexios full_name: Michailidis, Alexios id: 36EBAD38-F248-11E8-B48F-1D18A9856A87 last_name: Michailidis orcid: 0000-0002-8443-1064 - first_name: Marko full_name: Žnidarič, Marko last_name: Žnidarič - first_name: Mariya full_name: Medvedyeva, Mariya last_name: Medvedyeva - first_name: Dmitry full_name: Abanin, Dmitry last_name: Abanin - first_name: Tomaž full_name: Prosen, Tomaž last_name: Prosen - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić citation: ama: Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 2018;97(10). doi:10.1103/PhysRevB.97.104307 apa: Michailidis, A., Žnidarič, M., Medvedyeva, M., Abanin, D., Prosen, T., & Papić, Z. (2018). Slow dynamics in translation-invariant quantum lattice models. Physical Review B. American Physical Society. https://doi.org/10.1103/PhysRevB.97.104307 chicago: Michailidis, Alexios, Marko Žnidarič, Mariya Medvedyeva, Dmitry Abanin, Tomaž Prosen, and Zlatko Papić. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B. American Physical Society, 2018. https://doi.org/10.1103/PhysRevB.97.104307. ieee: A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, and Z. Papić, “Slow dynamics in translation-invariant quantum lattice models,” Physical Review B, vol. 97, no. 10. American Physical Society, 2018. ista: Michailidis A, Žnidarič M, Medvedyeva M, Abanin D, Prosen T, Papić Z. 2018. Slow dynamics in translation-invariant quantum lattice models. Physical Review B. 97(10), 104307. mla: Michailidis, Alexios, et al. “Slow Dynamics in Translation-Invariant Quantum Lattice Models.” Physical Review B, vol. 97, no. 10, 104307, American Physical Society, 2018, doi:10.1103/PhysRevB.97.104307. short: A. Michailidis, M. Žnidarič, M. Medvedyeva, D. Abanin, T. Prosen, Z. Papić, Physical Review B 97 (2018). date_created: 2018-12-11T11:45:50Z date_published: 2018-03-19T00:00:00Z date_updated: 2023-09-18T09:31:46Z day: '19' department: - _id: MaSe doi: 10.1103/PhysRevB.97.104307 external_id: isi: - '000427798800005' intvolume: ' 97' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1706.05026 month: '03' oa: 1 oa_version: Preprint publication: Physical Review B publication_status: published publisher: American Physical Society publist_id: '7538' quality_controlled: '1' scopus_import: '1' status: public title: Slow dynamics in translation-invariant quantum lattice models type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 97 year: '2018' ... --- _id: '29' abstract: - lang: eng text: Social insects have evolved enormous capacities to collectively build nests and defend their colonies against both predators and pathogens. The latter is achieved by a combination of individual immune responses and sophisticated collective behavioral and organizational disease defenses, that is, social immunity. We investigated how the presence or absence of these social defense lines affects individual-level immunity in ant queens after bacterial infection. To this end, we injected queens of the ant Linepithema humile with a mix of gram+ and gram− bacteria or a control solution, reared them either with workers or alone and analyzed their gene expression patterns at 2, 4, 8, and 12 hr post-injection, using RNA-seq. This allowed us to test for the effect of bacterial infection, social context, as well as the interaction between the two over the course of infection and raising of an immune response. We found that social isolation per se affected queen gene expression for metabolism genes, but not for immune genes. When infected, queens reared with and without workers up-regulated similar numbers of innate immune genes revealing activation of Toll and Imd signaling pathways and melanization. Interestingly, however, they mostly regulated different genes along the pathways and showed a different pattern of overall gene up-regulation or down-regulation. Hence, we can conclude that the absence of workers does not compromise the onset of an individual immune response by the queens, but that the social environment impacts the route of the individual innate immune responses. article_processing_charge: No author: - first_name: Lumi full_name: Viljakainen, Lumi last_name: Viljakainen - first_name: Jaana full_name: Jurvansuu, Jaana last_name: Jurvansuu - first_name: Ida full_name: Holmberg, Ida last_name: Holmberg - first_name: Tobias full_name: Pamminger, Tobias last_name: Pamminger - first_name: Silvio full_name: Erler, Silvio last_name: Erler - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 citation: ama: Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 2018;8(22):11031-11070. doi:10.1002/ece3.4573 apa: Viljakainen, L., Jurvansuu, J., Holmberg, I., Pamminger, T., Erler, S., & Cremer, S. (2018). Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. Wiley. https://doi.org/10.1002/ece3.4573 chicago: Viljakainen, Lumi, Jaana Jurvansuu, Ida Holmberg, Tobias Pamminger, Silvio Erler, and Sylvia Cremer. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution. Wiley, 2018. https://doi.org/10.1002/ece3.4573. ieee: L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, and S. Cremer, “Social environment affects the transcriptomic response to bacteria in ant queens,” Ecology and Evolution, vol. 8, no. 22. Wiley, pp. 11031–11070, 2018. ista: Viljakainen L, Jurvansuu J, Holmberg I, Pamminger T, Erler S, Cremer S. 2018. Social environment affects the transcriptomic response to bacteria in ant queens. Ecology and Evolution. 8(22), 11031–11070. mla: Viljakainen, Lumi, et al. “Social Environment Affects the Transcriptomic Response to Bacteria in Ant Queens.” Ecology and Evolution, vol. 8, no. 22, Wiley, 2018, pp. 11031–70, doi:10.1002/ece3.4573. short: L. Viljakainen, J. Jurvansuu, I. Holmberg, T. Pamminger, S. Erler, S. Cremer, Ecology and Evolution 8 (2018) 11031–11070. date_created: 2018-12-11T11:44:15Z date_published: 2018-11-01T00:00:00Z date_updated: 2023-09-19T09:29:12Z day: '01' ddc: - '576' - '591' department: - _id: SyCr doi: 10.1002/ece3.4573 external_id: isi: - '000451611000032' file: - access_level: open_access checksum: 0d1355c78627ca7210aadd9a17a01915 content_type: application/pdf creator: dernst date_created: 2018-12-17T08:27:04Z date_updated: 2020-07-14T12:45:52Z file_id: '5682' file_name: Viljakainen_et_al-2018-Ecology_and_Evolution.pdf file_size: 1272096 relation: main_file file_date_updated: 2020-07-14T12:45:52Z has_accepted_license: '1' intvolume: ' 8' isi: 1 issue: '22' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 11031-11070 publication: Ecology and Evolution publication_identifier: issn: - '20457758' publication_status: published publisher: Wiley publist_id: '8026' quality_controlled: '1' scopus_import: '1' status: public title: Social environment affects the transcriptomic response to bacteria in ant queens 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 8 year: '2018' ... --- _id: '806' abstract: - lang: eng text: Social insect colonies have evolved many collectively performed adaptations that reduce the impact of infectious disease and that are expected to maximize their fitness. This colony-level protection is termed social immunity, and it enhances the health and survival of the colony. In this review, we address how social immunity emerges from its mechanistic components to produce colony-level disease avoidance, resistance, and tolerance. To understand the evolutionary causes and consequences of social immunity, we highlight the need for studies that evaluate the effects of social immunity on colony fitness. We discuss the role that host life history and ecology have on predicted eco-evolutionary dynamics, which differ among the social insect lineages. Throughout the review, we highlight current gaps in our knowledge and promising avenues for future research, which we hope will bring us closer to an integrated understanding of socio-eco-evo-immunology. article_processing_charge: No author: - first_name: Sylvia full_name: Cremer, Sylvia id: 2F64EC8C-F248-11E8-B48F-1D18A9856A87 last_name: Cremer orcid: 0000-0002-2193-3868 - first_name: Christopher full_name: Pull, Christopher id: 3C7F4840-F248-11E8-B48F-1D18A9856A87 last_name: Pull orcid: 0000-0003-1122-3982 - first_name: Matthias full_name: Fürst, Matthias id: 393B1196-F248-11E8-B48F-1D18A9856A87 last_name: Fürst orcid: 0000-0002-3712-925X citation: ama: 'Cremer S, Pull C, Fürst M. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 2018;63:105-123. doi:10.1146/annurev-ento-020117-043110' apa: 'Cremer, S., Pull, C., & Fürst, M. (2018). Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. Annual Reviews. https://doi.org/10.1146/annurev-ento-020117-043110' chicago: 'Cremer, Sylvia, Christopher Pull, and Matthias Fürst. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” Annual Review of Entomology. Annual Reviews, 2018. https://doi.org/10.1146/annurev-ento-020117-043110.' ieee: 'S. Cremer, C. Pull, and M. Fürst, “Social immunity: Emergence and evolution of colony-level disease protection,” Annual Review of Entomology, vol. 63. Annual Reviews, pp. 105–123, 2018.' ista: 'Cremer S, Pull C, Fürst M. 2018. Social immunity: Emergence and evolution of colony-level disease protection. Annual Review of Entomology. 63, 105–123.' mla: 'Cremer, Sylvia, et al. “Social Immunity: Emergence and Evolution of Colony-Level Disease Protection.” Annual Review of Entomology, vol. 63, Annual Reviews, 2018, pp. 105–23, doi:10.1146/annurev-ento-020117-043110.' short: S. Cremer, C. Pull, M. Fürst, Annual Review of Entomology 63 (2018) 105–123. date_created: 2018-12-11T11:48:36Z date_published: 2018-01-07T00:00:00Z date_updated: 2023-09-19T09:29:45Z day: '07' department: - _id: SyCr doi: 10.1146/annurev-ento-020117-043110 external_id: isi: - '000424633700008' intvolume: ' 63' isi: 1 language: - iso: eng month: '01' oa_version: None page: 105 - 123 publication: Annual Review of Entomology publication_identifier: issn: - 1545-4487 publication_status: published publisher: Annual Reviews publist_id: '6844' quality_controlled: '1' related_material: record: - id: '819' relation: dissertation_contains status: public scopus_import: '1' status: public title: 'Social immunity: Emergence and evolution of colony-level disease protection' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 63 year: '2018' ... --- _id: '140' abstract: - lang: eng text: Reachability analysis is difficult for hybrid automata with affine differential equations, because the reach set needs to be approximated. Promising abstraction techniques usually employ interval methods or template polyhedra. Interval methods account for dense time and guarantee soundness, and there are interval-based tools that overapproximate affine flowpipes. But interval methods impose bounded and rigid shapes, which make refinement expensive and fixpoint detection difficult. Template polyhedra, on the other hand, can be adapted flexibly and can be unbounded, but sound template refinement for unbounded reachability analysis has been implemented only for systems with piecewise constant dynamics. We capitalize on the advantages of both techniques, combining interval arithmetic and template polyhedra, using the former to abstract time and the latter to abstract space. During a CEGAR loop, whenever a spurious error trajectory is found, we compute additional space constraints and split time intervals, and use these space-time interpolants to eliminate the counterexample. Space-time interpolation offers a lazy, flexible framework for increasing precision while guaranteeing soundness, both for error avoidance and fixpoint detection. To the best of out knowledge, this is the first abstraction refinement scheme for the reachability analysis over unbounded and dense time of affine hybrid systems, which is both sound and automatic. We demonstrate the effectiveness of our algorithm with several benchmark examples, which cannot be handled by other tools. alternative_title: - LNCS article_processing_charge: No author: - first_name: Goran full_name: Frehse, Goran last_name: Frehse - first_name: Mirco full_name: Giacobbe, Mirco id: 3444EA5E-F248-11E8-B48F-1D18A9856A87 last_name: Giacobbe orcid: 0000-0001-8180-0904 - 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: 'Frehse G, Giacobbe M, Henzinger TA. Space-time interpolants. In: Vol 10981. Springer; 2018:468-486. doi:10.1007/978-3-319-96145-3_25' apa: 'Frehse, G., Giacobbe, M., & Henzinger, T. A. (2018). Space-time interpolants (Vol. 10981, pp. 468–486). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96145-3_25' chicago: Frehse, Goran, Mirco Giacobbe, and Thomas A Henzinger. “Space-Time Interpolants,” 10981:468–86. Springer, 2018. https://doi.org/10.1007/978-3-319-96145-3_25. ieee: 'G. Frehse, M. Giacobbe, and T. A. Henzinger, “Space-time interpolants,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10981, pp. 468–486.' ista: 'Frehse G, Giacobbe M, Henzinger TA. 2018. Space-time interpolants. CAV: Computer Aided Verification, LNCS, vol. 10981, 468–486.' mla: Frehse, Goran, et al. Space-Time Interpolants. Vol. 10981, Springer, 2018, pp. 468–86, doi:10.1007/978-3-319-96145-3_25. short: G. Frehse, M. Giacobbe, T.A. Henzinger, in:, Springer, 2018, pp. 468–486. conference: end_date: 2018-07-17 location: Oxford, United Kingdom name: 'CAV: Computer Aided Verification' start_date: 2018-07-14 date_created: 2018-12-11T11:44:50Z date_published: 2018-07-18T00:00:00Z date_updated: 2023-09-19T09:30:43Z day: '18' ddc: - '005' department: - _id: ToHe doi: 10.1007/978-3-319-96145-3_25 external_id: isi: - '000491481600025' file: - access_level: open_access checksum: 6dca832f575d6b3f0ea9dff56f579142 content_type: application/pdf creator: system date_created: 2018-12-12T10:17:53Z date_updated: 2020-07-14T12:44:50Z file_id: '5310' file_name: IST-2018-1010-v1+1_space-time_interpolants.pdf file_size: 563710 relation: main_file file_date_updated: 2020-07-14T12:44:50Z has_accepted_license: '1' intvolume: ' 10981' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 468 - 486 project: - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F5A88A-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S11402-N23 name: Moderne Concurrency Paradigms publication_identifier: issn: - '03029743' publication_status: published publisher: Springer publist_id: '7783' pubrep_id: '1010' quality_controlled: '1' related_material: record: - id: '6894' relation: dissertation_contains status: public scopus_import: '1' status: public title: Space-time interpolants tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10981 year: '2018' ... --- _id: '154' abstract: - lang: eng text: We give a lower bound on the ground state energy of a system of two fermions of one species interacting with two fermions of another species via point interactions. We show that there is a critical mass ratio m2 ≈ 0.58 such that the system is stable, i.e., the energy is bounded from below, for m∈[m2,m2−1]. So far it was not known whether this 2 + 2 system exhibits a stable region at all or whether the formation of four-body bound states causes an unbounded spectrum for all mass ratios, similar to the Thomas effect. Our result gives further evidence for the stability of the more general N + M system. acknowledgement: Open access funding provided by Austrian Science Fund (FWF). article_number: '19' article_processing_charge: No article_type: original author: - first_name: Thomas full_name: Moser, Thomas id: 2B5FC9A4-F248-11E8-B48F-1D18A9856A87 last_name: Moser - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: Moser T, Seiringer R. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 2018;21(3). doi:10.1007/s11040-018-9275-3 apa: Moser, T., & Seiringer, R. (2018). Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. Springer. https://doi.org/10.1007/s11040-018-9275-3 chicago: Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry. Springer, 2018. https://doi.org/10.1007/s11040-018-9275-3. ieee: T. Moser and R. Seiringer, “Stability of the 2+2 fermionic system with point interactions,” Mathematical Physics Analysis and Geometry, vol. 21, no. 3. Springer, 2018. ista: Moser T, Seiringer R. 2018. Stability of the 2+2 fermionic system with point interactions. Mathematical Physics Analysis and Geometry. 21(3), 19. mla: Moser, Thomas, and Robert Seiringer. “Stability of the 2+2 Fermionic System with Point Interactions.” Mathematical Physics Analysis and Geometry, vol. 21, no. 3, 19, Springer, 2018, doi:10.1007/s11040-018-9275-3. short: T. Moser, R. Seiringer, Mathematical Physics Analysis and Geometry 21 (2018). date_created: 2018-12-11T11:44:55Z date_published: 2018-09-01T00:00:00Z date_updated: 2023-09-19T09:31:15Z day: '01' ddc: - '530' department: - _id: RoSe doi: 10.1007/s11040-018-9275-3 ec_funded: 1 external_id: isi: - '000439639700001' file: - access_level: open_access checksum: 411c4db5700d7297c9cd8ebc5dd29091 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:49:02Z date_updated: 2020-07-14T12:45:01Z file_id: '5729' file_name: 2018_MathPhysics_Moser.pdf file_size: 496973 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 21' isi: 1 issue: '3' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: 25C878CE-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27533_N27 name: Structure of the Excitation Spectrum for Many-Body Quantum Systems - _id: 3AC91DDA-15DF-11EA-824D-93A3E7B544D1 call_identifier: FWF name: FWF Open Access Fund publication: Mathematical Physics Analysis and Geometry publication_identifier: eissn: - '15729656' issn: - '13850172' publication_status: published publisher: Springer publist_id: '7767' quality_controlled: '1' related_material: record: - id: '52' relation: dissertation_contains status: public scopus_import: '1' status: public title: Stability of the 2+2 fermionic system with point interactions 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 21 year: '2018' ... --- _id: '5787' abstract: - lang: eng text: "Branching morphogenesis remains a subject of abiding interest. Although \ much is \r\nknown about the gene regulatory programs and signaling pathways that operate at \r\nthe cellular scale, it has remained unclear how the macroscopic features of branched \r\norgans, including their size, network topology and \ spatial patterning, are encoded. \r\nLately, it has been proposed that, these features can be explained quantitatively in \r\nseveral organs within a single unifying framework. Based on large-\r\nscale organ recon\r\n-\r\nstructions \ and cell lineage tracing, it has been argued that morphogenesis follows \ \r\nfrom the collective dynamics of sublineage- \r\nrestricted self- \r\nrenewing progenitor cells, \r\nlocalized at ductal tips, that act cooperatively to drive a serial process of ductal elon\r\n-\r\ngation and stochastic tip bifurcation. By correlating differentiation or cell cycle exit \r\nwith proximity to maturing ducts, this dynamic results in the specification of a com-\r\nplex network of \ defined density and statistical organization. These results suggest \r\nthat, for several mammalian tissues, branched epithelial structures develop as a self- \r\norganized process, reliant upon a strikingly simple, but generic, \ set of local rules, \r\nwithout recourse to a rigid and deterministic \ sequence of genetically programmed \r\nevents. Here, we review the basis of these findings and discuss their implications." article_processing_charge: No author: - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Benjamin D. full_name: Simons, Benjamin D. last_name: Simons citation: ama: Hannezo EB, Simons BD. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 2018;60(9):512-521. doi:10.1111/dgd.12570 apa: Hannezo, E. B., & Simons, B. D. (2018). Statistical theory of branching morphogenesis. Development Growth and Differentiation. Wiley. https://doi.org/10.1111/dgd.12570 chicago: Hannezo, Edouard B, and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation. Wiley, 2018. https://doi.org/10.1111/dgd.12570. ieee: E. B. Hannezo and B. D. Simons, “Statistical theory of branching morphogenesis,” Development Growth and Differentiation, vol. 60, no. 9. Wiley, pp. 512–521, 2018. ista: Hannezo EB, Simons BD. 2018. Statistical theory of branching morphogenesis. Development Growth and Differentiation. 60(9), 512–521. mla: Hannezo, Edouard B., and Benjamin D. Simons. “Statistical Theory of Branching Morphogenesis.” Development Growth and Differentiation, vol. 60, no. 9, Wiley, 2018, pp. 512–21, doi:10.1111/dgd.12570. short: E.B. Hannezo, B.D. Simons, Development Growth and Differentiation 60 (2018) 512–521. date_created: 2018-12-30T22:59:14Z date_published: 2018-12-09T00:00:00Z date_updated: 2023-09-19T09:32:49Z day: '09' ddc: - '570' department: - _id: EdHa doi: 10.1111/dgd.12570 external_id: isi: - '000453555100002' file: - access_level: open_access checksum: a6d30b0785db902c734a84fecb2eadd9 content_type: application/pdf creator: dernst date_created: 2019-02-06T10:40:46Z date_updated: 2020-07-14T12:47:11Z file_id: '5933' file_name: 2018_DevGrowh_Hannezo.pdf file_size: 1313606 relation: main_file file_date_updated: 2020-07-14T12:47:11Z has_accepted_license: '1' intvolume: ' 60' isi: 1 issue: '9' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 512-521 publication: Development Growth and Differentiation publication_identifier: issn: - '00121592' publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Statistical theory of branching morphogenesis 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 60 year: '2018' ... --- _id: '297' abstract: - lang: eng text: Graph games played by two players over finite-state graphs are central in many problems in computer science. In particular, graph games with ω -regular winning conditions, specified as parity objectives, which can express properties such as safety, liveness, fairness, are the basic framework for verification and synthesis of reactive systems. The decisions for a player at various states of the graph game are represented as strategies. While the algorithmic problem for solving graph games with parity objectives has been widely studied, the most prominent data-structure for strategy representation in graph games has been binary decision diagrams (BDDs). However, due to the bit-level representation, BDDs do not retain the inherent flavor of the decisions of strategies, and are notoriously hard to minimize to obtain succinct representation. In this work we propose decision trees for strategy representation in graph games. Decision trees retain the flavor of decisions of strategies and allow entropy-based minimization to obtain succinct trees. However, decision trees work in settings (e.g., probabilistic models) where errors are allowed, and overfitting of data is typically avoided. In contrast, for strategies in graph games no error is allowed, and the decision tree must represent the entire strategy. We develop new techniques to extend decision trees to overcome the above obstacles, while retaining the entropy-based techniques to obtain succinct trees. We have implemented our techniques to extend the existing decision tree solvers. We present experimental results for problems in reactive synthesis to show that decision trees provide a much more efficient data-structure for strategy representation as compared to BDDs. alternative_title: - LNCS article_processing_charge: No author: - first_name: Tomáš full_name: Brázdil, Tomáš last_name: Brázdil - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Jan full_name: Kretinsky, Jan id: 44CEF464-F248-11E8-B48F-1D18A9856A87 last_name: Kretinsky orcid: 0000-0002-8122-2881 - first_name: Viktor full_name: Toman, Viktor id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87 last_name: Toman orcid: 0000-0001-9036-063X citation: ama: 'Brázdil T, Chatterjee K, Kretinsky J, Toman V. Strategy representation by decision trees in reactive synthesis. In: Vol 10805. Springer; 2018:385-407. doi:10.1007/978-3-319-89960-2_21' apa: 'Brázdil, T., Chatterjee, K., Kretinsky, J., & Toman, V. (2018). Strategy representation by decision trees in reactive synthesis (Vol. 10805, pp. 385–407). Presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece: Springer. https://doi.org/10.1007/978-3-319-89960-2_21' chicago: Brázdil, Tomáš, Krishnendu Chatterjee, Jan Kretinsky, and Viktor Toman. “Strategy Representation by Decision Trees in Reactive Synthesis,” 10805:385–407. Springer, 2018. https://doi.org/10.1007/978-3-319-89960-2_21. ieee: 'T. Brázdil, K. Chatterjee, J. Kretinsky, and V. Toman, “Strategy representation by decision trees in reactive synthesis,” presented at the TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, Thessaloniki, Greece, 2018, vol. 10805, pp. 385–407.' ista: 'Brázdil T, Chatterjee K, Kretinsky J, Toman V. 2018. Strategy representation by decision trees in reactive synthesis. TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 10805, 385–407.' mla: Brázdil, Tomáš, et al. Strategy Representation by Decision Trees in Reactive Synthesis. Vol. 10805, Springer, 2018, pp. 385–407, doi:10.1007/978-3-319-89960-2_21. short: T. Brázdil, K. Chatterjee, J. Kretinsky, V. Toman, in:, Springer, 2018, pp. 385–407. conference: end_date: 2018-04-20 location: Thessaloniki, Greece name: 'TACAS 2018: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2018-04-14 date_created: 2018-12-11T11:45:41Z date_published: 2018-04-12T00:00:00Z date_updated: 2023-09-19T09:57:08Z day: '12' ddc: - '000' department: - _id: KrCh - _id: ToHe doi: 10.1007/978-3-319-89960-2_21 ec_funded: 1 external_id: isi: - '000546326300021' file: - access_level: open_access checksum: b13874ffb114932ad9cc2586b7469db4 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:29:08Z date_updated: 2020-07-14T12:45:57Z file_id: '5723' file_name: 2018_LNCS_Brazdil.pdf file_size: 1829940 relation: main_file file_date_updated: 2020-07-14T12:45:57Z has_accepted_license: '1' intvolume: ' 10805' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 385 - 407 project: - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided 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: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_status: published publisher: Springer publist_id: '7584' quality_controlled: '1' scopus_import: '1' status: public title: Strategy representation by decision trees in reactive synthesis tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10805 year: '2018' ... --- _id: '141' abstract: - lang: eng text: 'Given a model and a specification, the fundamental model-checking problem asks for algorithmic verification of whether the model satisfies the specification. We consider graphs and Markov decision processes (MDPs), which are fundamental models for reactive systems. One of the very basic specifications that arise in verification of reactive systems is the strong fairness (aka Streett) objective. Given different types of requests and corresponding grants, the objective requires that for each type, if the request event happens infinitely often, then the corresponding grant event must also happen infinitely often. All ω -regular objectives can be expressed as Streett objectives and hence they are canonical in verification. To handle the state-space explosion, symbolic algorithms are required that operate on a succinct implicit representation of the system rather than explicitly accessing the system. While explicit algorithms for graphs and MDPs with Streett objectives have been widely studied, there has been no improvement of the basic symbolic algorithms. The worst-case numbers of symbolic steps required for the basic symbolic algorithms are as follows: quadratic for graphs and cubic for MDPs. In this work we present the first sub-quadratic symbolic algorithm for graphs with Streett objectives, and our algorithm is sub-quadratic even for MDPs. Based on our algorithmic insights we present an implementation of the new symbolic approach and show that it improves the existing approach on several academic benchmark examples.' acknowledgement: 'Acknowledgements. K. C. and M. H. are partially supported by the Vienna Science and Technology Fund (WWTF) grant ICT15-003. K. C. is partially supported by the Austrian Science Fund (FWF): S11407-N23 (RiSE/SHiNE), and an ERC Start Grant (279307: Graph Games). V. T. is partially supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Sk lodowska-Curie Grant Agreement No. 665385.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Veronika full_name: Loitzenbauer, Veronika last_name: Loitzenbauer - first_name: Simin full_name: Oraee, Simin last_name: Oraee - first_name: Viktor full_name: Toman, Viktor id: 3AF3DA7C-F248-11E8-B48F-1D18A9856A87 last_name: Toman orcid: 0000-0001-9036-063X citation: ama: 'Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. In: Vol 10982. Springer; 2018:178-197. doi:10.1007/978-3-319-96142-2_13' apa: 'Chatterjee, K., Henzinger, M. H., Loitzenbauer, V., Oraee, S., & Toman, V. (2018). Symbolic algorithms for graphs and Markov decision processes with fairness objectives (Vol. 10982, pp. 178–197). Presented at the CAV: Computer Aided Verification, Oxford, United Kingdom: Springer. https://doi.org/10.1007/978-3-319-96142-2_13' chicago: Chatterjee, Krishnendu, Monika H Henzinger, Veronika Loitzenbauer, Simin Oraee, and Viktor Toman. “Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives,” 10982:178–97. Springer, 2018. https://doi.org/10.1007/978-3-319-96142-2_13. ieee: 'K. Chatterjee, M. H. Henzinger, V. Loitzenbauer, S. Oraee, and V. Toman, “Symbolic algorithms for graphs and Markov decision processes with fairness objectives,” presented at the CAV: Computer Aided Verification, Oxford, United Kingdom, 2018, vol. 10982, pp. 178–197.' ista: 'Chatterjee K, Henzinger MH, Loitzenbauer V, Oraee S, Toman V. 2018. Symbolic algorithms for graphs and Markov decision processes with fairness objectives. CAV: Computer Aided Verification, LNCS, vol. 10982, 178–197.' mla: Chatterjee, Krishnendu, et al. Symbolic Algorithms for Graphs and Markov Decision Processes with Fairness Objectives. Vol. 10982, Springer, 2018, pp. 178–97, doi:10.1007/978-3-319-96142-2_13. short: K. Chatterjee, M.H. Henzinger, V. Loitzenbauer, S. Oraee, V. Toman, in:, Springer, 2018, pp. 178–197. conference: end_date: 2018-07-17 location: Oxford, United Kingdom name: 'CAV: Computer Aided Verification' start_date: 2018-07-14 date_created: 2018-12-11T11:44:51Z date_published: 2018-07-18T00:00:00Z date_updated: 2023-09-19T09:59:55Z day: '18' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-319-96142-2_13 ec_funded: 1 external_id: isi: - '000491469700013' file: - access_level: open_access checksum: 1a6ffa4febe8bb8ac28be3adb3eafebc content_type: application/pdf creator: dernst date_created: 2018-12-18T08:52:38Z date_updated: 2020-07-14T12:44:53Z file_id: '5737' file_name: 2018_LNCS_Chatterjee.pdf file_size: 675606 relation: main_file file_date_updated: 2020-07-14T12:44:53Z has_accepted_license: '1' intvolume: ' 10982' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 178-197 project: - _id: 2581B60A-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '279307' name: 'Quantitative Graph Games: Theory and Applications' - _id: 25892FC0-B435-11E9-9278-68D0E5697425 grant_number: ICT15-003 name: Efficient Algorithms for Computer Aided Verification - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program publication_status: published publisher: Springer publist_id: '7782' quality_controlled: '1' related_material: record: - id: '10199' relation: dissertation_contains status: public scopus_import: '1' status: public title: Symbolic algorithms for graphs and Markov decision processes with fairness objectives tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10982 year: '2018' ... --- _id: '298' abstract: - lang: eng text: "Memory-hard functions (MHF) are functions whose evaluation cost is dominated by memory cost. MHFs are egalitarian, in the sense that evaluating them on dedicated hardware (like FPGAs or ASICs) is not much cheaper than on off-the-shelf hardware (like x86 CPUs). MHFs have interesting cryptographic applications, most notably to password hashing and securing blockchains.\r\n\r\nAlwen and Serbinenko [STOC’15] define the cumulative memory complexity (cmc) of a function as the sum (over all time-steps) of the amount of memory required to compute the function. They advocate that a good MHF must have high cmc. Unlike previous notions, cmc takes into account that dedicated hardware might exploit amortization and parallelism. Still, cmc has been critizised as insufficient, as it fails to capture possible time-memory trade-offs; as memory cost doesn’t scale linearly, functions with the same cmc could still have very different actual hardware cost.\r\n\r\nIn this work we address this problem, and introduce the notion of sustained-memory complexity, which requires that any algorithm evaluating the function must use a large amount of memory for many steps. We construct functions (in the parallel random oracle model) whose sustained-memory complexity is almost optimal: our function can be evaluated using n steps and O(n/log(n)) memory, in each step making one query to the (fixed-input length) random oracle, while any algorithm that can make arbitrary many parallel queries to the random oracle, still needs Ω(n/log(n)) memory for Ω(n) steps.\r\n\r\nAs has been done for various notions (including cmc) before, we reduce the task of constructing an MHFs with high sustained-memory complexity to proving pebbling lower bounds on DAGs. Our main technical contribution is the construction is a family of DAGs on n nodes with constant indegree with high “sustained-space complexity”, meaning that any parallel black-pebbling strategy requires Ω(n/log(n)) pebbles for at least Ω(n) steps.\r\n\r\nAlong the way we construct a family of maximally “depth-robust” DAGs with maximum indegree O(logn) , improving upon the construction of Mahmoody et al. [ITCS’13] which had maximum indegree O(log2n⋅" alternative_title: - LNCS article_processing_charge: No author: - first_name: Joel F full_name: Alwen, Joel F id: 2A8DFA8C-F248-11E8-B48F-1D18A9856A87 last_name: Alwen - first_name: Jeremiah full_name: Blocki, Jeremiah last_name: Blocki - first_name: Krzysztof Z full_name: Pietrzak, Krzysztof Z id: 3E04A7AA-F248-11E8-B48F-1D18A9856A87 last_name: Pietrzak orcid: 0000-0002-9139-1654 citation: ama: 'Alwen JF, Blocki J, Pietrzak KZ. Sustained space complexity. In: Vol 10821. Springer; 2018:99-130. doi:10.1007/978-3-319-78375-8_4' apa: 'Alwen, J. F., Blocki, J., & Pietrzak, K. Z. (2018). Sustained space complexity (Vol. 10821, pp. 99–130). Presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel: Springer. https://doi.org/10.1007/978-3-319-78375-8_4' chicago: Alwen, Joel F, Jeremiah Blocki, and Krzysztof Z Pietrzak. “Sustained Space Complexity,” 10821:99–130. Springer, 2018. https://doi.org/10.1007/978-3-319-78375-8_4. ieee: 'J. F. Alwen, J. Blocki, and K. Z. Pietrzak, “Sustained space complexity,” presented at the Eurocrypt 2018: Advances in Cryptology, Tel Aviv, Israel, 2018, vol. 10821, pp. 99–130.' ista: 'Alwen JF, Blocki J, Pietrzak KZ. 2018. Sustained space complexity. Eurocrypt 2018: Advances in Cryptology, LNCS, vol. 10821, 99–130.' mla: Alwen, Joel F., et al. Sustained Space Complexity. Vol. 10821, Springer, 2018, pp. 99–130, doi:10.1007/978-3-319-78375-8_4. short: J.F. Alwen, J. Blocki, K.Z. Pietrzak, in:, Springer, 2018, pp. 99–130. conference: end_date: 2018-05-03 location: Tel Aviv, Israel name: 'Eurocrypt 2018: Advances in Cryptology' start_date: 2018-04-29 date_created: 2018-12-11T11:45:41Z date_published: 2018-03-31T00:00:00Z date_updated: 2023-09-19T09:59:30Z day: '31' department: - _id: KrPi doi: 10.1007/978-3-319-78375-8_4 ec_funded: 1 external_id: arxiv: - '1705.05313' isi: - '000517098700004' intvolume: ' 10821' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1705.05313 month: '03' oa: 1 oa_version: Preprint page: 99 - 130 project: - _id: 258AA5B2-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '682815' name: Teaching Old Crypto New Tricks publication_status: published publisher: Springer publist_id: '7583' quality_controlled: '1' scopus_import: '1' status: public title: Sustained space complexity type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10821 year: '2018' ... --- _id: '36' abstract: - lang: eng text: Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower, and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental, and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term and mild increase in temperature on the wheat leaf and spikelet phosphoproteome. In total, 3822 (containing 5178 phosphosites) and 5581 phosphopeptides (containing 7023 phosphosites) were identified in leaf and spikelet samples, respectively. Following statistical analysis, the resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature. This community resource on the high temperature-mediated wheat phosphoproteome will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which probably impacts protein activity. acknowledgement: TZ is supported by a grant from the Chinese Scholarship Council. article_processing_charge: No author: - first_name: Lam full_name: Vu, Lam last_name: Vu - first_name: Tingting full_name: Zhu, Tingting last_name: Zhu - first_name: Inge full_name: Verstraeten, Inge id: 362BF7FE-F248-11E8-B48F-1D18A9856A87 last_name: Verstraeten orcid: 0000-0001-7241-2328 - first_name: Brigitte full_name: Van De Cotte, Brigitte last_name: Van De Cotte - first_name: Kris full_name: Gevaert, Kris last_name: Gevaert - first_name: Ive full_name: De Smet, Ive last_name: De Smet citation: ama: Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 2018;69(19):4609-4624. doi:10.1093/jxb/ery204 apa: Vu, L., Zhu, T., Verstraeten, I., Van De Cotte, B., Gevaert, K., & De Smet, I. (2018). Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. Oxford University Press. https://doi.org/10.1093/jxb/ery204 chicago: Vu, Lam, Tingting Zhu, Inge Verstraeten, Brigitte Van De Cotte, Kris Gevaert, and Ive De Smet. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany. Oxford University Press, 2018. https://doi.org/10.1093/jxb/ery204. ieee: L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, and I. De Smet, “Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms,” Journal of Experimental Botany, vol. 69, no. 19. Oxford University Press, pp. 4609–4624, 2018. ista: Vu L, Zhu T, Verstraeten I, Van De Cotte B, Gevaert K, De Smet I. 2018. Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms. Journal of Experimental Botany. 69(19), 4609–4624. mla: Vu, Lam, et al. “Temperature-Induced Changes in the Wheat Phosphoproteome Reveal Temperature-Regulated Interconversion of Phosphoforms.” Journal of Experimental Botany, vol. 69, no. 19, Oxford University Press, 2018, pp. 4609–24, doi:10.1093/jxb/ery204. short: L. Vu, T. Zhu, I. Verstraeten, B. Van De Cotte, K. Gevaert, I. De Smet, Journal of Experimental Botany 69 (2018) 4609–4624. date_created: 2018-12-11T11:44:17Z date_published: 2018-08-31T00:00:00Z date_updated: 2023-09-19T10:00:46Z day: '31' ddc: - '581' department: - _id: JiFr doi: 10.1093/jxb/ery204 external_id: isi: - '000443568700010' file: - access_level: open_access checksum: 34cb0a1611588b75bd6f4913fb4e30f1 content_type: application/pdf creator: dernst date_created: 2018-12-18T09:47:51Z date_updated: 2020-07-14T12:46:13Z file_id: '5741' file_name: 2018_JournalExperimBotany_Vu.pdf file_size: 3359316 relation: main_file file_date_updated: 2020-07-14T12:46:13Z has_accepted_license: '1' intvolume: ' 69' isi: 1 issue: '19' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 4609 - 4624 publication: Journal of Experimental Botany publication_status: published publisher: Oxford University Press publist_id: '8019' quality_controlled: '1' scopus_import: '1' status: public title: Temperature-induced changes in the wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 69 year: '2018' ... --- _id: '326' abstract: - lang: eng text: Three-dimensional (3D) super-resolution microscopy technique structured illumination microscopy (SIM) imaging of dendritic spines along the dendrite has not been previously performed in fixed tissues, mainly due to deterioration of the stripe pattern of the excitation laser induced by light scattering and optical aberrations. To address this issue and solve these optical problems, we applied a novel clearing reagent, LUCID, to fixed brains. In SIM imaging, the penetration depth and the spatial resolution were improved in LUCID-treated slices, and 160-nm spatial resolution was obtained in a large portion of the imaging volume on a single apical dendrite. Furthermore, in a morphological analysis of spine heads of layer V pyramidal neurons (L5PNs) in the medial prefrontal cortex (mPFC) of chronic dexamethasone (Dex)-treated mice, SIM imaging revealed an altered distribution of spine forms that could not be detected by high-NA confocal imaging. Thus, super-resolution SIM imaging represents a promising high-throughput method for revealing spine morphologies in single dendrites. acknowledged_ssus: - _id: EM-Fac article_processing_charge: No author: - first_name: Kazuaki full_name: Sawada, Kazuaki last_name: Sawada - first_name: Ryosuke full_name: Kawakami, Ryosuke last_name: Kawakami - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Tomomi full_name: Nemoto, Tomomi last_name: Nemoto citation: ama: Sawada K, Kawakami R, Shigemoto R, Nemoto T. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 2018;47(9):1033-1042. doi:10.1111/ejn.13901 apa: Sawada, K., Kawakami, R., Shigemoto, R., & Nemoto, T. (2018). Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. Wiley. https://doi.org/10.1111/ejn.13901 chicago: Sawada, Kazuaki, Ryosuke Kawakami, Ryuichi Shigemoto, and Tomomi Nemoto. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience. Wiley, 2018. https://doi.org/10.1111/ejn.13901. ieee: K. Sawada, R. Kawakami, R. Shigemoto, and T. Nemoto, “Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices,” European Journal of Neuroscience, vol. 47, no. 9. Wiley, pp. 1033–1042, 2018. ista: Sawada K, Kawakami R, Shigemoto R, Nemoto T. 2018. Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices. European Journal of Neuroscience. 47(9), 1033–1042. mla: Sawada, Kazuaki, et al. “Super Resolution Structural Analysis of Dendritic Spines Using Three-Dimensional Structured Illumination Microscopy in Cleared Mouse Brain Slices.” European Journal of Neuroscience, vol. 47, no. 9, Wiley, 2018, pp. 1033–42, doi:10.1111/ejn.13901. short: K. Sawada, R. Kawakami, R. Shigemoto, T. Nemoto, European Journal of Neuroscience 47 (2018) 1033–1042. date_created: 2018-12-11T11:45:50Z date_published: 2018-03-07T00:00:00Z date_updated: 2023-09-19T09:58:40Z day: '07' ddc: - '570' department: - _id: RySh doi: 10.1111/ejn.13901 external_id: isi: - '000431496400001' file: - access_level: open_access checksum: 98e901d8229e44aa8f3b51d248dedd09 content_type: application/pdf creator: dernst date_created: 2018-12-17T16:16:50Z date_updated: 2020-07-14T12:46:06Z file_id: '5721' file_name: 2018_EJN_Sawada.pdf file_size: 4850261 relation: main_file file_date_updated: 2020-07-14T12:46:06Z has_accepted_license: '1' intvolume: ' 47' isi: 1 issue: '9' language: - iso: eng month: '03' oa: 1 oa_version: Published Version page: 1033 - 1042 publication: European Journal of Neuroscience publication_status: published publisher: Wiley publist_id: '7539' quality_controlled: '1' scopus_import: '1' status: public title: Super resolution structural analysis of dendritic spines using three-dimensional structured illumination microscopy in cleared mouse brain slices 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: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 47 year: '2018' ... --- _id: '5770' abstract: - lang: eng text: Retroviruses assemble and bud from infected cells in an immature form and require proteolytic maturation for infectivity. The CA (capsid) domains of the Gag polyproteins assemble a protein lattice as a truncated sphere in the immature virion. Proteolytic cleavage of Gag induces dramatic structural rearrangements; a subset of cleaved CA subsequently assembles into the mature core, whose architecture varies among retroviruses. Murine leukemia virus (MLV) is the prototypical γ-retrovirus and serves as the basis of retroviral vectors, but the structure of the MLV CA layer is unknown. Here we have combined X-ray crystallography with cryoelectron tomography to determine the structures of immature and mature MLV CA layers within authentic viral particles. This reveals the structural changes associated with maturation, and, by comparison with HIV-1, uncovers conserved and variable features. In contrast to HIV-1, most MLV CA is used for assembly of the mature core, which adopts variable, multilayered morphologies and does not form a closed structure. Unlike in HIV-1, there is similarity between protein–protein interfaces in the immature MLV CA layer and those in the mature CA layer, and structural maturation of MLV could be achieved through domain rotations that largely maintain hexameric interactions. Nevertheless, the dramatic architectural change on maturation indicates that extensive disassembly and reassembly are required for mature core growth. The core morphology suggests that wrapping of the genome in CA sheets may be sufficient to protect the MLV ribonucleoprotein during cell entry. article_processing_charge: No author: - first_name: Kun full_name: Qu, Kun last_name: Qu - first_name: Bärbel full_name: Glass, Bärbel last_name: Glass - first_name: Michal full_name: Doležal, Michal last_name: Doležal - first_name: Florian full_name: Schur, Florian id: 48AD8942-F248-11E8-B48F-1D18A9856A87 last_name: Schur orcid: 0000-0003-4790-8078 - first_name: Brice full_name: Murciano, Brice last_name: Murciano - first_name: Alan full_name: Rein, Alan last_name: Rein - first_name: Michaela full_name: Rumlová, Michaela last_name: Rumlová - first_name: Tomáš full_name: Ruml, Tomáš last_name: Ruml - first_name: Hans-Georg full_name: Kräusslich, Hans-Georg last_name: Kräusslich - first_name: John A. G. full_name: Briggs, John A. G. last_name: Briggs citation: ama: Qu K, Glass B, Doležal M, et al. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 2018;115(50):E11751-E11760. doi:10.1073/pnas.1811580115 apa: Qu, K., Glass, B., Doležal, M., Schur, F. K., Murciano, B., Rein, A., … Briggs, J. A. G. (2018). Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.1811580115 chicago: Qu, Kun, Bärbel Glass, Michal Doležal, Florian KM Schur, Brice Murciano, Alan Rein, Michaela Rumlová, Tomáš Ruml, Hans-Georg Kräusslich, and John A. G. Briggs. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences. Proceedings of the National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1811580115. ieee: K. Qu et al., “Structure and architecture of immature and mature murine leukemia virus capsids,” Proceedings of the National Academy of Sciences, vol. 115, no. 50. Proceedings of the National Academy of Sciences, pp. E11751–E11760, 2018. ista: Qu K, Glass B, Doležal M, Schur FK, Murciano B, Rein A, Rumlová M, Ruml T, Kräusslich H-G, Briggs JAG. 2018. Structure and architecture of immature and mature murine leukemia virus capsids. Proceedings of the National Academy of Sciences. 115(50), E11751–E11760. mla: Qu, Kun, et al. “Structure and Architecture of Immature and Mature Murine Leukemia Virus Capsids.” Proceedings of the National Academy of Sciences, vol. 115, no. 50, Proceedings of the National Academy of Sciences, 2018, pp. E11751–60, doi:10.1073/pnas.1811580115. short: K. Qu, B. Glass, M. Doležal, F.K. Schur, B. Murciano, A. Rein, M. Rumlová, T. Ruml, H.-G. Kräusslich, J.A.G. Briggs, Proceedings of the National Academy of Sciences 115 (2018) E11751–E11760. date_created: 2018-12-20T21:09:37Z date_published: 2018-12-11T00:00:00Z date_updated: 2023-09-19T09:57:45Z day: '11' department: - _id: FlSc doi: 10.1073/pnas.1811580115 external_id: isi: - '000452866000022' pmid: - '30478053' intvolume: ' 115' isi: 1 issue: '50' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30478053 month: '12' oa: 1 oa_version: Submitted Version page: E11751-E11760 pmid: 1 publication: Proceedings of the National Academy of Sciences publication_identifier: issn: - '00278424' publication_status: published publisher: Proceedings of the National Academy of Sciences quality_controlled: '1' scopus_import: '1' status: public title: Structure and architecture of immature and mature murine leukemia virus capsids type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '608' abstract: - lang: eng text: Synthesis is the automated construction of a system from its specification. In real life, hardware and software systems are rarely constructed from scratch. Rather, a system is typically constructed from a library of components. Lustig and Vardi formalized this intuition and studied LTL synthesis from component libraries. In real life, designers seek optimal systems. In this paper we add optimality considerations to the setting. We distinguish between quality considerations (for example, size - the smaller a system is, the better it is), and pricing (for example, the payment to the company who manufactured the component). We study the problem of designing systems with minimal quality-cost and price. A key point is that while the quality cost is individual - the choices of a designer are independent of choices made by other designers that use the same library, pricing gives rise to a resource-allocation game - designers that use the same component share its price, with the share being proportional to the number of uses (a component can be used several times in a design). We study both closed and open settings, and in both we solve the problem of finding an optimal design. In a setting with multiple designers, we also study the game-theoretic problems of the induced resource-allocation game. article_processing_charge: No article_type: original author: - first_name: Guy full_name: Avni, Guy id: 463C8BC2-F248-11E8-B48F-1D18A9856A87 last_name: Avni orcid: 0000-0001-5588-8287 - first_name: Orna full_name: Kupferman, Orna last_name: Kupferman citation: ama: Avni G, Kupferman O. Synthesis from component libraries with costs. Theoretical Computer Science. 2018;712:50-72. doi:10.1016/j.tcs.2017.11.001 apa: Avni, G., & Kupferman, O. (2018). Synthesis from component libraries with costs. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2017.11.001 chicago: Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science. Elsevier, 2018. https://doi.org/10.1016/j.tcs.2017.11.001. ieee: G. Avni and O. Kupferman, “Synthesis from component libraries with costs,” Theoretical Computer Science, vol. 712. Elsevier, pp. 50–72, 2018. ista: Avni G, Kupferman O. 2018. Synthesis from component libraries with costs. Theoretical Computer Science. 712, 50–72. mla: Avni, Guy, and Orna Kupferman. “Synthesis from Component Libraries with Costs.” Theoretical Computer Science, vol. 712, Elsevier, 2018, pp. 50–72, doi:10.1016/j.tcs.2017.11.001. short: G. Avni, O. Kupferman, Theoretical Computer Science 712 (2018) 50–72. date_created: 2018-12-11T11:47:28Z date_published: 2018-02-15T00:00:00Z date_updated: 2023-09-19T10:00:21Z day: '15' department: - _id: ToHe doi: 10.1016/j.tcs.2017.11.001 ec_funded: 1 external_id: isi: - '000424959200003' intvolume: ' 712' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.636.4529 month: '02' oa: 1 oa_version: Published Version page: 50 - 72 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize publication: Theoretical Computer Science publication_status: published publisher: Elsevier publist_id: '7197' quality_controlled: '1' scopus_import: '1' status: public title: Synthesis from component libraries with costs type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 712 year: '2018' ... --- _id: '705' abstract: - lang: eng text: Although dopamine receptors D1 and D2 play key roles in hippocampal function, their synaptic localization within the hippocampus has not been fully elucidated. In order to understand precise functions of pre- or postsynaptic dopamine receptors (DRs), the development of protocols to differentiate pre- and postsynaptic DRs is essential. So far, most studies on determination and quantification of DRs did not discriminate between subsynaptic localization. Therefore, the aim of the study was to generate a robust workflow for the localization of DRs. This work provides the basis for future work on hippocampal DRs, in light that DRs may have different functions at pre- or postsynaptic sites. Synaptosomes from rat hippocampi isolated by a sucrose gradient protocol were prepared for super-resolution direct stochastic optical reconstruction microscopy (dSTORM) using Bassoon as a presynaptic zone and Homer1 as postsynaptic density marker. Direct labeling of primary validated antibodies against dopamine receptors D1 (D1R) and D2 (D2R) with Alexa Fluor 594 enabled unequivocal assignment of D1R and D2R to both, pre- and postsynaptic sites. D1R immunoreactivity clusters were observed within the presynaptic active zone as well as at perisynaptic sites at the edge of the presynaptic active zone. The results may be useful for the interpretation of previous studies and the design of future work on DRs in the hippocampus. Moreover, the reduction of the complexity of brain tissue by the use of synaptosomal preparations and dSTORM technology may represent a useful tool for synaptic localization of brain proteins. article_processing_charge: No author: - first_name: Andras full_name: Miklosi, Andras last_name: Miklosi - first_name: Giorgia full_name: Del Favero, Giorgia last_name: Del Favero - first_name: Tanja full_name: Bulat, Tanja last_name: Bulat - first_name: Harald full_name: Höger, Harald last_name: Höger - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Doris full_name: Marko, Doris last_name: Marko - first_name: Gert full_name: Lubec, Gert last_name: Lubec citation: ama: Miklosi A, Del Favero G, Bulat T, et al. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 2018;55(6):4857 – 4869. doi:10.1007/s12035-017-0688-y apa: Miklosi, A., Del Favero, G., Bulat, T., Höger, H., Shigemoto, R., Marko, D., & Lubec, G. (2018). Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. Springer. https://doi.org/10.1007/s12035-017-0688-y chicago: Miklosi, Andras, Giorgia Del Favero, Tanja Bulat, Harald Höger, Ryuichi Shigemoto, Doris Marko, and Gert Lubec. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology. Springer, 2018. https://doi.org/10.1007/s12035-017-0688-y. ieee: A. Miklosi et al., “Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes,” Molecular Neurobiology, vol. 55, no. 6. Springer, pp. 4857 – 4869, 2018. ista: Miklosi A, Del Favero G, Bulat T, Höger H, Shigemoto R, Marko D, Lubec G. 2018. Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes. Molecular Neurobiology. 55(6), 4857 – 4869. mla: Miklosi, Andras, et al. “Super Resolution Microscopical Localization of Dopamine Receptors 1 and 2 in Rat Hippocampal Synaptosomes.” Molecular Neurobiology, vol. 55, no. 6, Springer, 2018, pp. 4857 – 4869, doi:10.1007/s12035-017-0688-y. short: A. Miklosi, G. Del Favero, T. Bulat, H. Höger, R. Shigemoto, D. Marko, G. Lubec, Molecular Neurobiology 55 (2018) 4857 – 4869. date_created: 2018-12-11T11:48:02Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-19T09:58:11Z day: '01' department: - _id: RySh doi: 10.1007/s12035-017-0688-y external_id: isi: - '000431991500025' intvolume: ' 55' isi: 1 issue: '6' language: - iso: eng month: '06' oa_version: None page: 4857 – 4869 publication: Molecular Neurobiology publication_status: published publisher: Springer publist_id: '6991' quality_controlled: '1' scopus_import: '1' status: public title: Super resolution microscopical localization of dopamine receptors 1 and 2 in rat hippocampal synaptosomes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 55 year: '2018' ... --- _id: '148' abstract: - lang: eng text: 'Land plants evolved from charophytic algae, among which Charophyceae possess the most complex body plans. We present the genome of Chara braunii; comparison of the genome to those of land plants identified evolutionary novelties for plant terrestrialization and land plant heritage genes. C. braunii employs unique xylan synthases for cell wall biosynthesis, a phragmoplast (cell separation) mechanism similar to that of land plants, and many phytohormones. C. braunii plastids are controlled via land-plant-like retrograde signaling, and transcriptional regulation is more elaborate than in other algae. The morphological complexity of this organism may result from expanded gene families, with three cases of particular note: genes effecting tolerance to reactive oxygen species (ROS), LysM receptor-like kinases, and transcription factors (TFs). Transcriptomic analysis of sexual reproductive structures reveals intricate control by TFs, activity of the ROS gene network, and the ancestral use of plant-like storage and stress protection proteins in the zygote.' acknowledgement: In-Data-Review article_processing_charge: No author: - first_name: Tomoaki full_name: Nishiyama, Tomoaki last_name: Nishiyama - first_name: Hidetoshi full_name: Sakayama, Hidetoshi last_name: Sakayama - first_name: Jan full_name: De Vries, Jan last_name: De Vries - first_name: Henrik full_name: Buschmann, Henrik last_name: Buschmann - first_name: Denis full_name: Saint Marcoux, Denis last_name: Saint Marcoux - first_name: Kristian full_name: Ullrich, Kristian last_name: Ullrich - first_name: Fabian full_name: Haas, Fabian last_name: Haas - first_name: Lisa full_name: Vanderstraeten, Lisa last_name: Vanderstraeten - first_name: Dirk full_name: Becker, Dirk last_name: Becker - first_name: Daniel full_name: Lang, Daniel last_name: Lang - first_name: Stanislav full_name: Vosolsobě, Stanislav last_name: Vosolsobě - first_name: Stephane full_name: Rombauts, Stephane last_name: Rombauts - first_name: Per full_name: Wilhelmsson, Per last_name: Wilhelmsson - first_name: Philipp full_name: Janitza, Philipp last_name: Janitza - first_name: Ramona full_name: Kern, Ramona last_name: Kern - first_name: Alexander full_name: Heyl, Alexander last_name: Heyl - first_name: Florian full_name: Rümpler, Florian last_name: Rümpler - first_name: Luz full_name: Calderón Villalobos, Luz last_name: Calderón Villalobos - first_name: John full_name: Clay, John last_name: Clay - first_name: Roman full_name: Skokan, Roman last_name: Skokan - first_name: Atsushi full_name: Toyoda, Atsushi last_name: Toyoda - first_name: Yutaka full_name: Suzuki, Yutaka last_name: Suzuki - first_name: Hiroshi full_name: Kagoshima, Hiroshi last_name: Kagoshima - first_name: Elio full_name: Schijlen, Elio last_name: Schijlen - first_name: Navindra full_name: Tajeshwar, Navindra last_name: Tajeshwar - first_name: Bruno full_name: Catarino, Bruno last_name: Catarino - first_name: Alexander full_name: Hetherington, Alexander last_name: Hetherington - first_name: Assia full_name: Saltykova, Assia last_name: Saltykova - first_name: Clemence full_name: Bonnot, Clemence last_name: Bonnot - first_name: Holger full_name: Breuninger, Holger last_name: Breuninger - first_name: Aikaterini full_name: Symeonidi, Aikaterini last_name: Symeonidi - first_name: Guru full_name: Radhakrishnan, Guru last_name: Radhakrishnan - first_name: Filip full_name: Van Nieuwerburgh, Filip last_name: Van Nieuwerburgh - first_name: Dieter full_name: Deforce, Dieter last_name: Deforce - first_name: Caren full_name: Chang, Caren last_name: Chang - first_name: Kenneth full_name: Karol, Kenneth last_name: Karol - first_name: Rainer full_name: Hedrich, Rainer last_name: Hedrich - first_name: Peter full_name: Ulvskov, Peter last_name: Ulvskov - first_name: Gernot full_name: Glöckner, Gernot last_name: Glöckner - first_name: Charles full_name: Delwiche, Charles last_name: Delwiche - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Yves full_name: Van De Peer, Yves last_name: Van De Peer - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Mary full_name: Beilby, Mary last_name: Beilby - first_name: Liam full_name: Dolan, Liam last_name: Dolan - first_name: Yuji full_name: Kohara, Yuji last_name: Kohara - first_name: Sumio full_name: Sugano, Sumio last_name: Sugano - first_name: Asao full_name: Fujiyama, Asao last_name: Fujiyama - first_name: Pierre Marc full_name: Delaux, Pierre Marc last_name: Delaux - first_name: Marcel full_name: Quint, Marcel last_name: Quint - first_name: Gunter full_name: Theissen, Gunter last_name: Theissen - first_name: Martin full_name: Hagemann, Martin last_name: Hagemann - first_name: Jesper full_name: Harholt, Jesper last_name: Harholt - first_name: Christophe full_name: Dunand, Christophe last_name: Dunand - first_name: Sabine full_name: Zachgo, Sabine last_name: Zachgo - first_name: Jane full_name: Langdale, Jane last_name: Langdale - first_name: Florian full_name: Maumus, Florian last_name: Maumus - first_name: Dominique full_name: Van Der Straeten, Dominique last_name: Van Der Straeten - first_name: Sven B full_name: Gould, Sven B last_name: Gould - first_name: Stefan full_name: Rensing, Stefan last_name: Rensing citation: ama: 'Nishiyama T, Sakayama H, De Vries J, et al. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 2018;174(2):448-464.e24. doi:10.1016/j.cell.2018.06.033' apa: 'Nishiyama, T., Sakayama, H., De Vries, J., Buschmann, H., Saint Marcoux, D., Ullrich, K., … Rensing, S. (2018). The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. Cell Press. https://doi.org/10.1016/j.cell.2018.06.033' chicago: 'Nishiyama, Tomoaki, Hidetoshi Sakayama, Jan De Vries, Henrik Buschmann, Denis Saint Marcoux, Kristian Ullrich, Fabian Haas, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell. Cell Press, 2018. https://doi.org/10.1016/j.cell.2018.06.033.' ieee: 'T. Nishiyama et al., “The Chara genome: Secondary complexity and implications for plant terrestrialization,” Cell, vol. 174, no. 2. Cell Press, p. 448–464.e24, 2018.' ista: 'Nishiyama T, Sakayama H, De Vries J, Buschmann H, Saint Marcoux D, Ullrich K, Haas F, Vanderstraeten L, Becker D, Lang D, Vosolsobě S, Rombauts S, Wilhelmsson P, Janitza P, Kern R, Heyl A, Rümpler F, Calderón Villalobos L, Clay J, Skokan R, Toyoda A, Suzuki Y, Kagoshima H, Schijlen E, Tajeshwar N, Catarino B, Hetherington A, Saltykova A, Bonnot C, Breuninger H, Symeonidi A, Radhakrishnan G, Van Nieuwerburgh F, Deforce D, Chang C, Karol K, Hedrich R, Ulvskov P, Glöckner G, Delwiche C, Petrášek J, Van De Peer Y, Friml J, Beilby M, Dolan L, Kohara Y, Sugano S, Fujiyama A, Delaux PM, Quint M, Theissen G, Hagemann M, Harholt J, Dunand C, Zachgo S, Langdale J, Maumus F, Van Der Straeten D, Gould SB, Rensing S. 2018. The Chara genome: Secondary complexity and implications for plant terrestrialization. Cell. 174(2), 448–464.e24.' mla: 'Nishiyama, Tomoaki, et al. “The Chara Genome: Secondary Complexity and Implications for Plant Terrestrialization.” Cell, vol. 174, no. 2, Cell Press, 2018, p. 448–464.e24, doi:10.1016/j.cell.2018.06.033.' short: T. Nishiyama, H. Sakayama, J. De Vries, H. Buschmann, D. Saint Marcoux, K. Ullrich, F. Haas, L. Vanderstraeten, D. Becker, D. Lang, S. Vosolsobě, S. Rombauts, P. Wilhelmsson, P. Janitza, R. Kern, A. Heyl, F. Rümpler, L. Calderón Villalobos, J. Clay, R. Skokan, A. Toyoda, Y. Suzuki, H. Kagoshima, E. Schijlen, N. Tajeshwar, B. Catarino, A. Hetherington, A. Saltykova, C. Bonnot, H. Breuninger, A. Symeonidi, G. Radhakrishnan, F. Van Nieuwerburgh, D. Deforce, C. Chang, K. Karol, R. Hedrich, P. Ulvskov, G. Glöckner, C. Delwiche, J. Petrášek, Y. Van De Peer, J. Friml, M. Beilby, L. Dolan, Y. Kohara, S. Sugano, A. Fujiyama, P.M. Delaux, M. Quint, G. Theissen, M. Hagemann, J. Harholt, C. Dunand, S. Zachgo, J. Langdale, F. Maumus, D. Van Der Straeten, S.B. Gould, S. Rensing, Cell 174 (2018) 448–464.e24. date_created: 2018-12-11T11:44:53Z date_published: 2018-07-12T00:00:00Z date_updated: 2023-09-19T10:02:47Z day: '12' department: - _id: JiFr doi: 10.1016/j.cell.2018.06.033 ec_funded: 1 external_id: isi: - '000438482800019' pmid: - '30007417' intvolume: ' 174' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pubmed/30007417 month: '07' oa: 1 oa_version: Published Version page: 448 - 464.e24 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Cell publication_status: published publisher: Cell Press publist_id: '7774' quality_controlled: '1' scopus_import: '1' status: public title: 'The Chara genome: Secondary complexity and implications for plant terrestrialization' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 174 year: '2018' ...