--- _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 license: https://creativecommons.org/licenses/by-nc/4.0/ 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' ... --- _id: '403' abstract: - lang: eng text: The ability to adapt growth and development to temperature variations is crucial to generate plant varieties resilient to predicted temperature changes. However, the mechanisms underlying plant response to progressive increases in temperature have just started to be elucidated. Here, we report that the Cyclin-dependent Kinase G1 (CDKG1) is a central element in a thermo-sensitive mRNA splicing cascade that transduces changes in ambient temperature into differential expression of the fundamental spliceosome component, ATU2AF65A. CDKG1 is alternatively spliced in a temperature-dependent manner. We found that this process is partly dependent on both the Cyclin-dependent Kinase G2 (CDKG2) and the interacting co-factor CYCLIN L1 resulting in two distinct messenger RNAs. Relative abundance of both CDKG1 transcripts correlates with ambient temperature and possibly with different expression levels of the associated protein isoforms. Both CDKG1 alternative transcripts are necessary to fully complement the expression of ATU2AF65A across the temperature range. Our data support a previously unidentified temperature-dependent mechanism based on the alternative splicing of CDKG1 and regulated by CDKG2 and CYCLIN L1. We propose that changes in ambient temperature affect the relative abundance of CDKG1 transcripts and this in turn translates into differential CDKG1 protein expression coordinating the alternative splicing of ATU2AF65A. This article is protected by copyright. All rights reserved. acknowledgement: CN, DD and JHD were funded by the BBSRC (grant number BB/M009459/1). NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna. AB and AF were supported by the Austrian Science Fund (FWF) [DK W1207; SFB RNAreg F43-P10] article_processing_charge: No author: - first_name: Nicola full_name: Cavallari, Nicola id: 457160E6-F248-11E8-B48F-1D18A9856A87 last_name: Cavallari - first_name: Candida full_name: Nibau, Candida last_name: Nibau - first_name: Armin full_name: Fuchs, Armin last_name: Fuchs - first_name: Despoina full_name: Dadarou, Despoina last_name: Dadarou - first_name: Andrea full_name: Barta, Andrea last_name: Barta - first_name: John full_name: Doonan, John last_name: Doonan citation: ama: Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 2018;94(6):1010-1022. doi:10.1111/tpj.13914 apa: Cavallari, N., Nibau, C., Fuchs, A., Dadarou, D., Barta, A., & Doonan, J. (2018). The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. Wiley. https://doi.org/10.1111/tpj.13914 chicago: Cavallari, Nicola, Candida Nibau, Armin Fuchs, Despoina Dadarou, Andrea Barta, and John Doonan. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal. Wiley, 2018. https://doi.org/10.1111/tpj.13914. ieee: N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, and J. Doonan, “The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A,” The Plant Journal, vol. 94, no. 6. Wiley, pp. 1010–1022, 2018. ista: Cavallari N, Nibau C, Fuchs A, Dadarou D, Barta A, Doonan J. 2018. The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A. The Plant Journal. 94(6), 1010–1022. mla: Cavallari, Nicola, et al. “The Cyclin‐dependent Kinase G Group Defines a Thermo‐sensitive Alternative Splicing Circuit Modulating the Expression of Arabidopsis ATU 2AF 65A.” The Plant Journal, vol. 94, no. 6, Wiley, 2018, pp. 1010–22, doi:10.1111/tpj.13914. short: N. Cavallari, C. Nibau, A. Fuchs, D. Dadarou, A. Barta, J. Doonan, The Plant Journal 94 (2018) 1010–1022. date_created: 2018-12-11T11:46:17Z date_published: 2018-06-01T00:00:00Z date_updated: 2023-09-19T10:07:08Z day: '01' ddc: - '580' department: - _id: EvBe doi: 10.1111/tpj.13914 external_id: isi: - '000434365500008' file: - access_level: open_access checksum: d9d3ad3215ac0e581731443fca312266 content_type: application/pdf creator: dernst date_created: 2019-02-06T11:40:54Z date_updated: 2020-07-14T12:46:22Z file_id: '5934' file_name: 2018_PlantJourn_Cavallari.pdf file_size: 1543354 relation: main_file file_date_updated: 2020-07-14T12:46:22Z has_accepted_license: '1' intvolume: ' 94' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 1010 - 1022 publication: The Plant Journal publication_status: published publisher: Wiley publist_id: '7426' quality_controlled: '1' scopus_import: '1' status: public title: The cyclin‐dependent kinase G group defines a thermo‐sensitive alternative splicing circuit modulating the expression of Arabidopsis ATU 2AF 65A 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: 94 year: '2018' ... --- _id: '156' abstract: - lang: eng text: 'Imprecision in timing can sometimes be beneficial: Metric interval temporal logic (MITL), disabling the expression of punctuality constraints, was shown to translate to timed automata, yielding an elementary decision procedure. We show how this principle extends to other forms of dense-time specification using regular expressions. By providing a clean, automaton-based formal framework for non-punctual languages, we are able to recover and extend several results in timed systems. Metric interval regular expressions (MIRE) are introduced, providing regular expressions with non-singular duration constraints. We obtain that MIRE are expressively complete relative to a class of one-clock timed automata, which can be determinized using additional clocks. Metric interval dynamic logic (MIDL) is then defined using MIRE as temporal modalities. We show that MIDL generalizes known extensions of MITL, while translating to timed automata at comparable cost.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 citation: ama: 'Ferrere T. The compound interest in relaxing punctuality. In: Vol 10951. Springer; 2018:147-164. doi:10.1007/978-3-319-95582-7_9' apa: 'Ferrere, T. (2018). The compound interest in relaxing punctuality (Vol. 10951, pp. 147–164). Presented at the FM: International Symposium on Formal Methods, Oxford, UK: Springer. https://doi.org/10.1007/978-3-319-95582-7_9' chicago: Ferrere, Thomas. “The Compound Interest in Relaxing Punctuality,” 10951:147–64. Springer, 2018. https://doi.org/10.1007/978-3-319-95582-7_9. ieee: 'T. Ferrere, “The compound interest in relaxing punctuality,” presented at the FM: International Symposium on Formal Methods, Oxford, UK, 2018, vol. 10951, pp. 147–164.' ista: 'Ferrere T. 2018. The compound interest in relaxing punctuality. FM: International Symposium on Formal Methods, LNCS, vol. 10951, 147–164.' mla: Ferrere, Thomas. The Compound Interest in Relaxing Punctuality. Vol. 10951, Springer, 2018, pp. 147–64, doi:10.1007/978-3-319-95582-7_9. short: T. Ferrere, in:, Springer, 2018, pp. 147–164. conference: end_date: 2018-07-17 location: Oxford, UK name: 'FM: International Symposium on Formal Methods' start_date: 2018-07-15 date_created: 2018-12-11T11:44:55Z date_published: 2018-07-12T00:00:00Z date_updated: 2023-09-19T10:05:37Z day: '12' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-319-95582-7_9 external_id: isi: - '000489765800009' file: - access_level: open_access checksum: a045c213c42c445f1889326f8db82a0a content_type: application/pdf creator: dernst date_created: 2020-10-09T06:22:41Z date_updated: 2020-10-09T06:22:41Z file_id: '8637' file_name: 2018_LNCS_Ferrere.pdf file_size: 485576 relation: main_file success: 1 file_date_updated: 2020-10-09T06:22:41Z has_accepted_license: '1' intvolume: ' 10951' isi: 1 language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 147 - 164 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: '7765' quality_controlled: '1' scopus_import: '1' status: public title: The compound interest in relaxing punctuality type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 10951 year: '2018' ... --- _id: '104' abstract: - lang: eng text: The biotrophic pathogen Ustilago maydis, the causative agent of corn smut disease, infects one of the most important crops worldwide – Zea mays. To successfully colonize its host, U. maydis secretes proteins, known as effectors, that suppress plant defense responses and facilitate the establishment of biotrophy. In this work, we describe the U. maydis effector protein Cce1. Cce1 is essential for virulence and is upregulated during infection. Through microscopic analysis and in vitro assays, we show that Cce1 is secreted from hyphae during filamentous growth of the fungus. Strikingly, Δcce1 mutants are blocked at early stages of infection and induce callose deposition as a plant defense response. Cce1 is highly conserved among smut fungi and the Ustilago bromivora ortholog complemented the virulence defect of the SG200Δcce1 deletion strain. These data indicate that Cce1 is a core effector with apoplastic localization that is essential for U. maydis to infect its host. acknowledgement: 'the Austrian Science Fund (FWF): [P27429‐B22, P27818‐B22, I 3033‐B22], and the Austrian Academy of Science (OEAW).' article_processing_charge: No author: - first_name: Denise full_name: Seitner, Denise last_name: Seitner - first_name: Simon full_name: Uhse, Simon last_name: Uhse - first_name: Michelle C full_name: Gallei, Michelle C id: 35A03822-F248-11E8-B48F-1D18A9856A87 last_name: Gallei orcid: 0000-0003-1286-7368 - first_name: Armin full_name: Djamei, Armin last_name: Djamei citation: ama: Seitner D, Uhse S, Gallei MC, Djamei A. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 2018;19(10):2277-2287. doi:10.1111/mpp.12698 apa: Seitner, D., Uhse, S., Gallei, M. C., & Djamei, A. (2018). The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. Wiley. https://doi.org/10.1111/mpp.12698 chicago: Seitner, Denise, Simon Uhse, Michelle C Gallei, and Armin Djamei. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology. Wiley, 2018. https://doi.org/10.1111/mpp.12698. ieee: D. Seitner, S. Uhse, M. C. Gallei, and A. Djamei, “The core effector Cce1 is required for early infection of maize by Ustilago maydis,” Molecular Plant Pathology, vol. 19, no. 10. Wiley, pp. 2277–2287, 2018. ista: Seitner D, Uhse S, Gallei MC, Djamei A. 2018. The core effector Cce1 is required for early infection of maize by Ustilago maydis. Molecular Plant Pathology. 19(10), 2277–2287. mla: Seitner, Denise, et al. “The Core Effector Cce1 Is Required for Early Infection of Maize by Ustilago Maydis.” Molecular Plant Pathology, vol. 19, no. 10, Wiley, 2018, pp. 2277–87, doi:10.1111/mpp.12698. short: D. Seitner, S. Uhse, M.C. Gallei, A. Djamei, Molecular Plant Pathology 19 (2018) 2277–2287. date_created: 2018-12-11T11:44:39Z date_published: 2018-10-01T00:00:00Z date_updated: 2023-09-19T10:06:42Z day: '01' ddc: - '580' department: - _id: GradSch doi: 10.1111/mpp.12698 external_id: isi: - '000445624100006' file: - access_level: open_access content_type: application/pdf creator: dernst date_created: 2018-12-18T09:46:00Z date_updated: 2018-12-18T09:46:00Z file_id: '5740' file_name: 2018_MolecPlantPath_Seitner.pdf file_size: 682335 relation: main_file success: 1 file_date_updated: 2018-12-18T09:46:00Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 2277 - 2287 publication: Molecular Plant Pathology publication_status: published publisher: Wiley publist_id: '7950' quality_controlled: '1' scopus_import: '1' status: public title: The core effector Cce1 is required for early infection of maize by Ustilago maydis 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: '40' abstract: - lang: eng text: Hanemaaijer et al. (Molecular Ecology, 27, 2018) describe the genetic consequences of the introgression of an insecticide resistance allele into a mosquito population. Linked alleles initially increased, but many of these later declined. It is hard to determine whether this decline was due to counter‐selection, rather than simply to chance. article_processing_charge: Yes (via OA deal) article_type: letter_note author: - 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: Barton NH. The consequences of an introgression event. Molecular Ecology. 2018;27(24):4973-4975. doi:10.1111/mec.14950 apa: Barton, N. H. (2018). The consequences of an introgression event. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.14950 chicago: Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology. Wiley, 2018. https://doi.org/10.1111/mec.14950. ieee: N. H. Barton, “The consequences of an introgression event,” Molecular Ecology, vol. 27, no. 24. Wiley, pp. 4973–4975, 2018. ista: Barton NH. 2018. The consequences of an introgression event. Molecular Ecology. 27(24), 4973–4975. mla: Barton, Nicholas H. “The Consequences of an Introgression Event.” Molecular Ecology, vol. 27, no. 24, Wiley, 2018, pp. 4973–75, doi:10.1111/mec.14950. short: N.H. Barton, Molecular Ecology 27 (2018) 4973–4975. date_created: 2018-12-11T11:44:18Z date_published: 2018-12-31T00:00:00Z date_updated: 2023-09-19T10:06:08Z day: '31' ddc: - '576' department: - _id: NiBa doi: 10.1111/mec.14950 external_id: isi: - '000454600500001' pmid: - '30599087' file: - access_level: open_access content_type: application/pdf creator: apreinsp date_created: 2019-07-19T06:54:46Z date_updated: 2020-07-14T12:46:22Z file_id: '6652' file_name: 2018_MolecularEcology_BartonNick.pdf file_size: 295452 relation: main_file file_date_updated: 2020-07-14T12:46:22Z has_accepted_license: '1' intvolume: ' 27' isi: 1 issue: '24' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 4973-4975 pmid: 1 publication: Molecular Ecology publication_identifier: issn: - 1365294X publication_status: published publisher: Wiley publist_id: '8014' quality_controlled: '1' related_material: record: - id: '9805' relation: research_data status: public scopus_import: '1' status: public title: The consequences of an introgression event 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: 27 year: '2018' ... --- _id: '5861' abstract: - lang: eng text: In zebrafish larvae, it is the cell type that determines how the cell responds to a chemokine signal. article_number: e37888 article_processing_charge: No article_type: original author: - first_name: Jonna H full_name: Alanko, Jonna H id: 2CC12E8C-F248-11E8-B48F-1D18A9856A87 last_name: Alanko orcid: 0000-0002-7698-3061 - 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: Alanko JH, Sixt MK. The cell sets the tone. eLife. 2018;7. doi:10.7554/eLife.37888 apa: Alanko, J. H., & Sixt, M. K. (2018). The cell sets the tone. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.37888 chicago: Alanko, Jonna H, and Michael K Sixt. “The Cell Sets the Tone.” ELife. eLife Sciences Publications, 2018. https://doi.org/10.7554/eLife.37888. ieee: J. H. Alanko and M. K. Sixt, “The cell sets the tone,” eLife, vol. 7. eLife Sciences Publications, 2018. ista: Alanko JH, Sixt MK. 2018. The cell sets the tone. eLife. 7, e37888. mla: Alanko, Jonna H., and Michael K. Sixt. “The Cell Sets the Tone.” ELife, vol. 7, e37888, eLife Sciences Publications, 2018, doi:10.7554/eLife.37888. short: J.H. Alanko, M.K. Sixt, ELife 7 (2018). date_created: 2019-01-20T22:59:19Z date_published: 2018-06-06T00:00:00Z date_updated: 2023-09-19T10:01:39Z day: '06' ddc: - '570' department: - _id: MiSi doi: 10.7554/eLife.37888 external_id: isi: - '000434375000001' file: - access_level: open_access checksum: f1c7ec2a809408d763c4b529a98f9a3b content_type: application/pdf creator: dernst date_created: 2019-02-13T10:52:11Z date_updated: 2020-07-14T12:47:13Z file_id: '5973' file_name: 2018_eLife_Alanko.pdf file_size: 358141 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' intvolume: ' 7' isi: 1 language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: eLife publication_identifier: issn: - 2050084X publication_status: published publisher: eLife Sciences Publications quality_controlled: '1' scopus_import: '1' status: public title: The cell sets the tone 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: '147' abstract: - lang: eng text: The trafficking of subcellular cargos in eukaryotic cells crucially depends on vesicle budding, a process mediated by ARF-GEFs (ADP-ribosylation factor guanine nucleotide exchange factors). In plants, ARF-GEFs play essential roles in endocytosis, vacuolar trafficking, recycling, secretion, and polar trafficking. Moreover, they are important for plant development, mainly through controlling the polar subcellular localization of PIN-FORMED (PIN) transporters of the plant hormone auxin. Here, using a chemical genetics screen in Arabidopsis thaliana, we identified Endosidin 4 (ES4), an inhibitor of eukaryotic ARF-GEFs. ES4 acts similarly to and synergistically with the established ARF-GEF inhibitor Brefeldin A and has broad effects on intracellular trafficking, including endocytosis, exocytosis, and vacuolar targeting. Additionally, Arabidopsis and yeast (Sacharomyces cerevisiae) mutants defective in ARF-GEF show altered sensitivity to ES4. ES4 interferes with the activation-based membrane association of the ARF1 GTPases, but not of their mutant variants that are activated independently of ARF-GEF activity. Biochemical approaches and docking simulations confirmed that ES4 specifically targets the SEC7 domain-containing ARF-GEFs. These observations collectively identify ES4 as a chemical tool enabling the study of ARF-GEF-mediated processes, including ARF-GEF-mediated plant development. acknowledgement: We thank Gerd Jürgens, Sandra Richter, and Sheng Yang He for providing antibodies; Maciek Adamowski, Fernando Aniento, Sebastian Bednarek, Nico Callewaert, Matyás Fendrych, Elena Feraru, and Mugurel I. Feraru for helpful suggestions; Siamsa Doyle for critical reading of the manuscript and helpful comments and suggestions; and Stephanie Smith and Martine De Cock for help in editing and language corrections. We acknowledge the core facility Cellular Imaging of CEITEC supported by the Czech-BioImaging large RI project (LM2015062 funded by MEYS CR) for their support with obtaining scientific data presented in this article. Plant Sciences Core Facility of CEITEC Masaryk University is gratefully acknowledged for obtaining part of the scientific data presented in this article. We acknowledge support from the Fondation pour la Recherche Médicale and from the Institut National du Cancer (J.C.). The research leading to these results was funded by the European Research Council under the European Union's 7th Framework Program (FP7/2007-2013)/ERC grant agreement numbers 282300 and 742985 and the Czech Science Foundation GAČR (GA18-26981S; J.F.); Ministry of Education, Youth, and Sports/MEYS of the Czech Republic under the Project CEITEC 2020 (LQ1601; T.N.); the China Science Council for a predoctoral fellowship (Q.L.); a joint research project within the framework of cooperation between the Research Foundation-Flanders and the Bulgarian Academy of Sciences (VS.025.13N; K.M. and E.R.); Vetenskapsrådet and Vinnova (Verket för Innovationssystem; S.R.), Knut och Alice Wallenbergs Stiftelse via “Shapesystem” Grant 2012.0050 (S.R.), Kempe stiftelserna (P.G.), Tryggers CTS410 (P.G.). article_processing_charge: No article_type: original author: - first_name: Urszula full_name: Kania, Urszula id: 4AE5C486-F248-11E8-B48F-1D18A9856A87 last_name: Kania - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Qing full_name: Lu, Qing last_name: Lu - first_name: Glenn R full_name: Hicks, Glenn R last_name: Hicks - first_name: Wim full_name: Nerinckx, Wim last_name: Nerinckx - first_name: Kiril full_name: Mishev, Kiril last_name: Mishev - first_name: Francois full_name: Peurois, Francois last_name: Peurois - first_name: Jacqueline full_name: Cherfils, Jacqueline last_name: Cherfils - first_name: Rycke Riet Maria full_name: De, Rycke Riet Maria last_name: De - first_name: Peter full_name: Grones, Peter id: 399876EC-F248-11E8-B48F-1D18A9856A87 last_name: Grones - first_name: Stéphanie full_name: Robert, Stéphanie last_name: Robert - first_name: Eugenia full_name: Russinova, Eugenia last_name: Russinova - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Kania U, Nodzyński T, Lu Q, et al. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 2018;30(10):2553-2572. doi:10.1105/tpc.18.00127 apa: Kania, U., Nodzyński, T., Lu, Q., Hicks, G. R., Nerinckx, W., Mishev, K., … Friml, J. (2018). The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. Oxford University Press. https://doi.org/10.1105/tpc.18.00127 chicago: Kania, Urszula, Tomasz Nodzyński, Qing Lu, Glenn R Hicks, Wim Nerinckx, Kiril Mishev, Francois Peurois, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell. Oxford University Press, 2018. https://doi.org/10.1105/tpc.18.00127. ieee: U. Kania et al., “The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes,” The Plant Cell, vol. 30, no. 10. Oxford University Press, pp. 2553–2572, 2018. ista: Kania U, Nodzyński T, Lu Q, Hicks GR, Nerinckx W, Mishev K, Peurois F, Cherfils J, De RRM, Grones P, Robert S, Russinova E, Friml J. 2018. The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes. The Plant Cell. 30(10), 2553–2572. mla: Kania, Urszula, et al. “The Inhibitor Endosidin 4 Targets SEC7 Domain-Type ARF GTPase Exchange Factors and Interferes with Sub Cellular Trafficking in Eukaryotes.” The Plant Cell, vol. 30, no. 10, Oxford University Press, 2018, pp. 2553–72, doi:10.1105/tpc.18.00127. short: U. Kania, T. Nodzyński, Q. Lu, G.R. Hicks, W. Nerinckx, K. Mishev, F. Peurois, J. Cherfils, R.R.M. De, P. Grones, S. Robert, E. Russinova, J. Friml, The Plant Cell 30 (2018) 2553–2572. date_created: 2018-12-11T11:44:52Z date_published: 2018-11-12T00:00:00Z date_updated: 2023-09-19T10:09:12Z day: '12' department: - _id: JiFr doi: 10.1105/tpc.18.00127 ec_funded: 1 external_id: isi: - '000450000500023' pmid: - '30018156' intvolume: ' 30' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1105/tpc.18.00127 month: '11' oa: 1 oa_version: Published Version page: 2553 - 2572 pmid: 1 project: - _id: 25716A02-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '282300' name: Polarity and subcellular dynamics in plants - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: The Plant Cell publication_identifier: issn: - 1040-4651 publication_status: published publisher: Oxford University Press publist_id: '7776' quality_controlled: '1' scopus_import: '1' status: public title: The inhibitor Endosidin 4 targets SEC7 domain-type ARF GTPase exchange factors and interferes with sub cellular trafficking in eukaryotes type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 30 year: '2018' ... --- _id: '146' abstract: - lang: eng text: The root cap protects the stem cell niche of angiosperm roots from damage. In Arabidopsis, lateral root cap (LRC) cells covering the meristematic zone are regularly lost through programmed cell death, while the outermost layer of the root cap covering the tip is repeatedly sloughed. Efficient coordination with stem cells producing new layers is needed to maintain a constant size of the cap. We present a signalling pair, the peptide IDA-LIKE1 (IDL1) and its receptor HAESA-LIKE2 (HSL2), mediating such communication. Live imaging over several days characterized this process from initial fractures in LRC cell files to full separation of a layer. Enhanced expression of IDL1 in the separating root cap layers resulted in increased frequency of sloughing, balanced with generation of new layers in a HSL2-dependent manner. Transcriptome analyses linked IDL1-HSL2 signalling to the transcription factors BEARSKIN1/2 and genes associated with programmed cell death. Mutations in either IDL1 or HSL2 slowed down cell division, maturation and separation. Thus, IDL1-HSL2 signalling potentiates dynamic regulation of the homeostatic balance between stem cell division and sloughing activity. article_processing_charge: No article_type: original author: - first_name: Chun Lin full_name: Shi, Chun Lin last_name: Shi - first_name: Daniel full_name: Von Wangenheim, Daniel id: 49E91952-F248-11E8-B48F-1D18A9856A87 last_name: Von Wangenheim orcid: 0000-0002-6862-1247 - first_name: Ullrich full_name: Herrmann, Ullrich last_name: Herrmann - first_name: Mari full_name: Wildhagen, Mari last_name: Wildhagen - first_name: Ivan full_name: Kulik, Ivan id: F0AB3FCE-02D1-11E9-BD0E-99399A5D3DEB last_name: Kulik - first_name: Andreas full_name: Kopf, Andreas last_name: Kopf - first_name: Takashi full_name: Ishida, Takashi last_name: Ishida - first_name: Vilde full_name: Olsson, Vilde last_name: Olsson - first_name: Mari Kristine full_name: Anker, Mari Kristine last_name: Anker - first_name: Markus full_name: Albert, Markus last_name: Albert - first_name: Melinka A full_name: Butenko, Melinka A last_name: Butenko - first_name: Georg full_name: Felix, Georg last_name: Felix - first_name: Shinichiro full_name: Sawa, Shinichiro last_name: Sawa - first_name: Manfred full_name: Claassen, Manfred last_name: Claassen - first_name: Jirí full_name: Friml, Jirí id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Reidunn B full_name: Aalen, Reidunn B last_name: Aalen citation: ama: Shi CL, von Wangenheim D, Herrmann U, et al. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 2018;4(8):596-604. doi:10.1038/s41477-018-0212-z apa: Shi, C. L., von Wangenheim, D., Herrmann, U., Wildhagen, M., Kulik, I., Kopf, A., … Aalen, R. B. (2018). The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. Nature Publishing Group. https://doi.org/10.1038/s41477-018-0212-z chicago: Shi, Chun Lin, Daniel von Wangenheim, Ullrich Herrmann, Mari Wildhagen, Ivan Kulik, Andreas Kopf, Takashi Ishida, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants. Nature Publishing Group, 2018. https://doi.org/10.1038/s41477-018-0212-z. ieee: C. L. Shi et al., “The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling,” Nature Plants, vol. 4, no. 8. Nature Publishing Group, pp. 596–604, 2018. ista: Shi CL, von Wangenheim D, Herrmann U, Wildhagen M, Kulik I, Kopf A, Ishida T, Olsson V, Anker MK, Albert M, Butenko MA, Felix G, Sawa S, Claassen M, Friml J, Aalen RB. 2018. The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling. Nature Plants. 4(8), 596–604. mla: Shi, Chun Lin, et al. “The Dynamics of Root Cap Sloughing in Arabidopsis Is Regulated by Peptide Signalling.” Nature Plants, vol. 4, no. 8, Nature Publishing Group, 2018, pp. 596–604, doi:10.1038/s41477-018-0212-z. short: C.L. Shi, D. von Wangenheim, U. Herrmann, M. Wildhagen, I. Kulik, A. Kopf, T. Ishida, V. Olsson, M.K. Anker, M. Albert, M.A. Butenko, G. Felix, S. Sawa, M. Claassen, J. Friml, R.B. Aalen, Nature Plants 4 (2018) 596–604. date_created: 2018-12-11T11:44:52Z date_published: 2018-07-30T00:00:00Z date_updated: 2023-09-19T10:08:45Z day: '30' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41477-018-0212-z external_id: isi: - '000443861300016' pmid: - '30061750' file: - access_level: open_access checksum: da33101c76ee1b2dc5ab28fd2ccba9d0 content_type: application/pdf creator: dernst date_created: 2019-11-18T16:24:07Z date_updated: 2020-07-14T12:44:56Z file_id: '7043' file_name: 2018_NaturePlants_Shi.pdf file_size: 226829 relation: main_file file_date_updated: 2020-07-14T12:44:56Z has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '8' language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version page: 596 - 604 pmid: 1 publication: Nature Plants publication_status: published publisher: Nature Publishing Group publist_id: '7777' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/new-process-in-root-development-discovered/ scopus_import: '1' status: public title: The dynamics of root cap sloughing in Arabidopsis is regulated by peptide signalling type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 4 year: '2018' ... --- _id: '293' abstract: - lang: eng text: People sometimes make their admirable deeds and accomplishments hard to spot, such as by giving anonymously or avoiding bragging. Such ‘buried’ signals are hard to reconcile with standard models of signalling or indirect reciprocity, which motivate costly pro-social behaviour by reputational gains. To explain these phenomena, we design a simple game theory model, which we call the signal-burying game. This game has the feature that senders can bury their signal by deliberately reducing the probability of the signal being observed. If the signal is observed, however, it is identified as having been buried. We show under which conditions buried signals can be maintained, using static equilibrium concepts and calculations of the evolutionary dynamics. We apply our analysis to shed light on a number of otherwise puzzling social phenomena, including modesty, anonymous donations, subtlety in art and fashion, and overeagerness. acknowledgement: This work was supported by a grant from the John Templeton Foundation and by the Office of Naval Research Grant N00014-16-1-2914 (M.A.N.). C.H. acknowledges generous support from the ISTFELLOW programme and by the Schrödinger scholarship of the Austrian Science Fund (FWF) J3475. article_processing_charge: No article_type: original author: - first_name: Moshe full_name: Hoffman, Moshe last_name: Hoffman - first_name: Christian full_name: Hilbe, Christian id: 2FDF8F3C-F248-11E8-B48F-1D18A9856A87 last_name: Hilbe orcid: 0000-0001-5116-955X - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Hoffman M, Hilbe C, Nowak M. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2018;2:397-404. doi:10.1038/s41562-018-0354-z apa: Hoffman, M., Hilbe, C., & Nowak, M. (2018). The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. Nature Publishing Group. https://doi.org/10.1038/s41562-018-0354-z chicago: Hoffman, Moshe, Christian Hilbe, and Martin Nowak. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour. Nature Publishing Group, 2018. https://doi.org/10.1038/s41562-018-0354-z. ieee: M. Hoffman, C. Hilbe, and M. Nowak, “The signal-burying game can explain why we obscure positive traits and good deeds,” Nature Human Behaviour, vol. 2. Nature Publishing Group, pp. 397–404, 2018. ista: Hoffman M, Hilbe C, Nowak M. 2018. The signal-burying game can explain why we obscure positive traits and good deeds. Nature Human Behaviour. 2, 397–404. mla: Hoffman, Moshe, et al. “The Signal-Burying Game Can Explain Why We Obscure Positive Traits and Good Deeds.” Nature Human Behaviour, vol. 2, Nature Publishing Group, 2018, pp. 397–404, doi:10.1038/s41562-018-0354-z. short: M. Hoffman, C. Hilbe, M. Nowak, Nature Human Behaviour 2 (2018) 397–404. date_created: 2018-12-11T11:45:39Z date_published: 2018-05-28T00:00:00Z date_updated: 2023-09-19T10:12:03Z day: '28' ddc: - '000' department: - _id: KrCh doi: 10.1038/s41562-018-0354-z ec_funded: 1 external_id: isi: - '000435551300009' file: - access_level: open_access checksum: 32efaf06a597495c184df91b3fbb19c0 content_type: application/pdf creator: dernst date_created: 2019-11-19T08:17:23Z date_updated: 2020-07-14T12:45:54Z file_id: '7051' file_name: 2018_NatureHumanBeh_Hoffman.pdf file_size: 194734 relation: main_file file_date_updated: 2020-07-14T12:45:54Z has_accepted_license: '1' intvolume: ' 2' isi: 1 language: - iso: eng month: '05' oa: 1 oa_version: Submitted Version page: 397 - 404 project: - _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: '7588' quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/the-logic-of-modesty-why-it-pays-to-be-humble/ scopus_import: '1' status: public title: The signal-burying game can explain why we obscure positive traits and good deeds type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 2 year: '2018' ... --- _id: '455' abstract: - lang: eng text: The derivation of effective evolution equations is central to the study of non-stationary quantum many-body systems, and widely used in contexts such as superconductivity, nuclear physics, Bose–Einstein condensation and quantum chemistry. We reformulate the Dirac–Frenkel approximation principle in terms of reduced density matrices and apply it to fermionic and bosonic many-body systems. We obtain the Bogoliubov–de Gennes and Hartree–Fock–Bogoliubov equations, respectively. While we do not prove quantitative error estimates, our formulation does show that the approximation is optimal within the class of quasifree states. Furthermore, we prove well-posedness of the Bogoliubov–de Gennes equations in energy space and discuss conserved quantities acknowledgement: Open access funding provided by Institute of Science and Technology (IST Austria). The authors acknowledge support by ERC Advanced Grant 321029 and by VILLUM FONDEN via the QMATH Centre of Excellence (Grant No. 10059). The authors would like to thank Sébastien Breteaux, Enno Lenzmann, Mathieu Lewin and Jochen Schmid for comments and discussions about well-posedness of the Bogoliubov–de Gennes equations. alternative_title: - Annales Henri Poincare article_processing_charge: No author: - first_name: Niels P full_name: Benedikter, Niels P id: 3DE6C32A-F248-11E8-B48F-1D18A9856A87 last_name: Benedikter orcid: 0000-0002-1071-6091 - first_name: Jérémy full_name: Sok, Jérémy last_name: Sok - first_name: Jan full_name: Solovej, Jan last_name: Solovej citation: ama: Benedikter NP, Sok J, Solovej J. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 2018;19(4):1167-1214. doi:10.1007/s00023-018-0644-z apa: Benedikter, N. P., Sok, J., & Solovej, J. (2018). The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. Birkhäuser. https://doi.org/10.1007/s00023-018-0644-z chicago: Benedikter, Niels P, Jérémy Sok, and Jan Solovej. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare. Birkhäuser, 2018. https://doi.org/10.1007/s00023-018-0644-z. ieee: N. P. Benedikter, J. Sok, and J. Solovej, “The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations,” Annales Henri Poincare, vol. 19, no. 4. Birkhäuser, pp. 1167–1214, 2018. ista: Benedikter NP, Sok J, Solovej J. 2018. The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations. Annales Henri Poincare. 19(4), 1167–1214. mla: Benedikter, Niels P., et al. “The Dirac–Frenkel Principle for Reduced Density Matrices and the Bogoliubov–de Gennes Equations.” Annales Henri Poincare, vol. 19, no. 4, Birkhäuser, 2018, pp. 1167–214, doi:10.1007/s00023-018-0644-z. short: N.P. Benedikter, J. Sok, J. Solovej, Annales Henri Poincare 19 (2018) 1167–1214. date_created: 2018-12-11T11:46:34Z date_published: 2018-04-01T00:00:00Z date_updated: 2023-09-19T10:07:41Z day: '01' ddc: - '510' - '539' department: - _id: RoSe doi: 10.1007/s00023-018-0644-z external_id: isi: - '000427578900006' file: - access_level: open_access checksum: 883eeccba8384ad7fcaa28761d99a0fa content_type: application/pdf creator: system date_created: 2018-12-12T10:11:57Z date_updated: 2020-07-14T12:46:31Z file_id: '4914' file_name: IST-2018-993-v1+1_2018_Benedikter_Dirac.pdf file_size: 923252 relation: main_file file_date_updated: 2020-07-14T12:46:31Z has_accepted_license: '1' intvolume: ' 19' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1167 - 1214 publication: Annales Henri Poincare publication_status: published publisher: Birkhäuser publist_id: '7367' pubrep_id: '993' quality_controlled: '1' scopus_import: '1' status: public title: The Dirac–Frenkel principle for reduced density matrices and the Bogoliubov–de Gennes equations 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: '314' abstract: - lang: eng text: The interface of physics and biology pro-vides a fruitful environment for generatingnew concepts and exciting ways forwardto understanding living matter. Examplesof successful studies include the estab-lishment and readout of morphogen gra-dients during development, signal pro-cessing in protein and genetic networks,the role of fluctuations in determining thefates of cells and tissues, and collectiveeffects in proteins and in tissues. It is nothard to envision that significant further ad-vances will translate to societal benefitsby initiating the development of new de-vices and strategies for curing disease.However, research at the interface posesvarious challenges, in particular for youngscientists, and current institutions arerarely designed to facilitate such scientificprograms. In this Letter, we propose aninternational initiative that addressesthese challenges through the establish-ment of a worldwide network of platformsfor cross-disciplinary training and incuba-tors for starting new collaborations. article_processing_charge: No article_type: letter_note author: - first_name: Guntram full_name: Bauer, Guntram last_name: Bauer - first_name: Nikta full_name: Fakhri, Nikta last_name: Fakhri - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: Jané full_name: Kondev, Jané last_name: Kondev - first_name: Karsten full_name: Kruse, Karsten last_name: Kruse - first_name: Hiroyuki full_name: Noji, Hiroyuki last_name: Noji - first_name: Daniel full_name: Riveline, Daniel last_name: Riveline - first_name: Timothy full_name: Saunders, Timothy last_name: Saunders - first_name: Mukund full_name: Thatta, Mukund last_name: Thatta - first_name: Eric full_name: Wieschaus, Eric last_name: Wieschaus citation: ama: Bauer G, Fakhri N, Kicheva A, et al. The science of living matter for tomorrow. Cell Systems. 2018;6(4):400-402. doi:10.1016/j.cels.2018.04.003 apa: Bauer, G., Fakhri, N., Kicheva, A., Kondev, J., Kruse, K., Noji, H., … Wieschaus, E. (2018). The science of living matter for tomorrow. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2018.04.003 chicago: Bauer, Guntram, Nikta Fakhri, Anna Kicheva, Jané Kondev, Karsten Kruse, Hiroyuki Noji, Daniel Riveline, Timothy Saunders, Mukund Thatta, and Eric Wieschaus. “The Science of Living Matter for Tomorrow.” Cell Systems. Cell Press, 2018. https://doi.org/10.1016/j.cels.2018.04.003. ieee: G. Bauer et al., “The science of living matter for tomorrow,” Cell Systems, vol. 6, no. 4. Cell Press, pp. 400–402, 2018. ista: Bauer G, Fakhri N, Kicheva A, Kondev J, Kruse K, Noji H, Riveline D, Saunders T, Thatta M, Wieschaus E. 2018. The science of living matter for tomorrow. Cell Systems. 6(4), 400–402. mla: Bauer, Guntram, et al. “The Science of Living Matter for Tomorrow.” Cell Systems, vol. 6, no. 4, Cell Press, 2018, pp. 400–02, doi:10.1016/j.cels.2018.04.003. short: G. Bauer, N. Fakhri, A. Kicheva, J. Kondev, K. Kruse, H. Noji, D. Riveline, T. Saunders, M. Thatta, E. Wieschaus, Cell Systems 6 (2018) 400–402. date_created: 2018-12-11T11:45:46Z date_published: 2018-04-25T00:00:00Z date_updated: 2023-09-19T10:11:25Z day: '25' department: - _id: AnKi doi: 10.1016/j.cels.2018.04.003 external_id: isi: - '000432192100003' pmid: - '29698645' intvolume: ' 6' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.cels.2018.04.003 month: '04' oa: 1 oa_version: Published Version page: 400 - 402 pmid: 1 publication: Cell Systems publication_identifier: eissn: - 2405-4712 publication_status: published publisher: Cell Press publist_id: '7551' quality_controlled: '1' scopus_import: '1' status: public title: The science of living matter for tomorrow type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 6 year: '2018' ... --- _id: '565' abstract: - lang: eng text: 'We re-examine the model of Kirkpatrick and Barton for the spread of an inversion into a local population. This model assumes that local selection maintains alleles at two or more loci, despite immigration of alternative alleles at these loci from another population. We show that an inversion is favored because it prevents the breakdown of linkage disequilibrium generated by migration; the selective advantage of an inversion is proportional to the amount of recombination between the loci involved, as in other cases where inversions are selected for. We derive expressions for the rate of spread of an inversion; when the loci covered by the inversion are tightly linked, these conditions deviate substantially from those proposed previously, and imply that an inversion can then have only a small advantage. ' article_processing_charge: No article_type: original author: - first_name: Brian full_name: Charlesworth, Brian last_name: Charlesworth - 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: Charlesworth B, Barton NH. The spread of an inversion with migration and selection. Genetics. 2018;208(1):377-382. doi:10.1534/genetics.117.300426 apa: Charlesworth, B., & Barton, N. H. (2018). The spread of an inversion with migration and selection. Genetics. Genetics . https://doi.org/10.1534/genetics.117.300426 chicago: Charlesworth, Brian, and Nicholas H Barton. “The Spread of an Inversion with Migration and Selection.” Genetics. Genetics , 2018. https://doi.org/10.1534/genetics.117.300426. ieee: B. Charlesworth and N. H. Barton, “The spread of an inversion with migration and selection,” Genetics, vol. 208, no. 1. Genetics , pp. 377–382, 2018. ista: Charlesworth B, Barton NH. 2018. The spread of an inversion with migration and selection. Genetics. 208(1), 377–382. mla: Charlesworth, Brian, and Nicholas H. Barton. “The Spread of an Inversion with Migration and Selection.” Genetics, vol. 208, no. 1, Genetics , 2018, pp. 377–82, doi:10.1534/genetics.117.300426. short: B. Charlesworth, N.H. Barton, Genetics 208 (2018) 377–382. date_created: 2018-12-11T11:47:12Z date_published: 2018-01-01T00:00:00Z date_updated: 2023-09-19T10:12:31Z day: '01' department: - _id: NiBa doi: 10.1534/genetics.117.300426 external_id: isi: - '000419356300025' pmid: - '29158424' intvolume: ' 208' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5753870/ month: '01' oa: 1 oa_version: Published Version page: 377 - 382 pmid: 1 publication: Genetics publication_status: published publisher: 'Genetics ' publist_id: '7249' quality_controlled: '1' scopus_import: '1' status: public title: The spread of an inversion with migration and selection type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 208 year: '2018' ... --- _id: '446' abstract: - lang: eng text: We prove that in Thomas–Fermi–Dirac–von Weizsäcker theory, a nucleus of charge Z > 0 can bind at most Z + C electrons, where C is a universal constant. This result is obtained through a comparison with Thomas-Fermi theory which, as a by-product, gives bounds on the screened nuclear potential and the radius of the minimizer. A key ingredient of the proof is a novel technique to control the particles in the exterior region, which also applies to the liquid drop model with a nuclear background potential. acknowledgement: "We thank the referee for helpful suggestions that improved the presentation of the paper. We also acknowledge partial support by National Science Foundation Grant DMS-1363432 (R.L.F.), Austrian Science Fund (FWF) Project Nr. P 27533-N27 (P.T.N.), CONICYT (Chile) through CONICYT–PCHA/ Doctorado Nacional/2014, and Iniciativa Científica Milenio (Chile) through Millenium Nucleus RC–120002 “Física Matemática” (H.V.D.B.).\r\n" article_processing_charge: No article_type: original author: - first_name: Rupert full_name: Frank, Rupert last_name: Frank - first_name: Nam full_name: Phan Thanh, Nam id: 404092F4-F248-11E8-B48F-1D18A9856A87 last_name: Phan Thanh - first_name: Hanne full_name: Van Den Bosch, Hanne last_name: Van Den Bosch citation: ama: Frank R, Nam P, Van Den Bosch H. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 2018;71(3):577-614. doi:10.1002/cpa.21717 apa: Frank, R., Nam, P., & Van Den Bosch, H. (2018). The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. Wiley-Blackwell. https://doi.org/10.1002/cpa.21717 chicago: Frank, Rupert, Phan Nam, and Hanne Van Den Bosch. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics. Wiley-Blackwell, 2018. https://doi.org/10.1002/cpa.21717. ieee: R. Frank, P. Nam, and H. Van Den Bosch, “The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory,” Communications on Pure and Applied Mathematics, vol. 71, no. 3. Wiley-Blackwell, pp. 577–614, 2018. ista: Frank R, Nam P, Van Den Bosch H. 2018. The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory. Communications on Pure and Applied Mathematics. 71(3), 577–614. mla: Frank, Rupert, et al. “The Ionization Conjecture in Thomas–Fermi–Dirac–von Weizsäcker Theory.” Communications on Pure and Applied Mathematics, vol. 71, no. 3, Wiley-Blackwell, 2018, pp. 577–614, doi:10.1002/cpa.21717. short: R. Frank, P. Nam, H. Van Den Bosch, Communications on Pure and Applied Mathematics 71 (2018) 577–614. date_created: 2018-12-11T11:46:31Z date_published: 2018-03-01T00:00:00Z date_updated: 2023-09-19T10:09:40Z day: '01' department: - _id: RoSe doi: 10.1002/cpa.21717 external_id: arxiv: - '1606.07355' isi: - '000422675800004' intvolume: ' 71' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.07355 month: '03' oa: 1 oa_version: Preprint page: 577 - 614 publication: Communications on Pure and Applied Mathematics publication_status: published publisher: Wiley-Blackwell publist_id: '7377' quality_controlled: '1' status: public title: The ionization conjecture in Thomas–Fermi–Dirac–von Weizsäcker theory type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 71 year: '2018' ... --- _id: '430' abstract: - lang: eng text: In this issue of GENETICS, a new method for detecting natural selection on polygenic traits is developed and applied to sev- eral human examples ( Racimo et al. 2018 ). By de fi nition, many loci contribute to variation in polygenic traits, and a challenge for evolutionary ge neticists has been that these traits can evolve by small, nearly undetectable shifts in allele frequencies across each of many, typically unknown, loci. Recently, a helpful remedy has arisen. Genome-wide associ- ation studies (GWAS) have been illuminating sets of loci that can be interrogated jointly for c hanges in allele frequencies. By aggregating small signal s of change across many such loci, directional natural selection is now in principle detect- able using genetic data, even for highly polygenic traits. This is an exciting arena of progress – with these methods, tests can be made for selection associated with traits, and we can now study selection in what may be its most prevalent mode. The continuing fast pace of GWAS publications suggest there will be many more polygenic tests of selection in the near future, as every new GWAS is an opportunity for an accom- panying test of polygenic selection. However, it is important to be aware of complications th at arise in interpretation, especially given that these studies may easily be misinter- preted both in and outside the evolutionary genetics commu- nity. Here, we provide context for understanding polygenic tests and urge caution regarding how these results are inter- preted and reported upon more broadly. article_processing_charge: No author: - first_name: John full_name: Novembre, John last_name: Novembre - 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: Novembre J, Barton NH. Tread lightly interpreting polygenic tests of selection. Genetics. 2018;208(4):1351-1355. doi:10.1534/genetics.118.300786 apa: Novembre, J., & Barton, N. H. (2018). Tread lightly interpreting polygenic tests of selection. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.118.300786 chicago: Novembre, John, and Nicholas H Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics. Genetics Society of America, 2018. https://doi.org/10.1534/genetics.118.300786. ieee: J. Novembre and N. H. Barton, “Tread lightly interpreting polygenic tests of selection,” Genetics, vol. 208, no. 4. Genetics Society of America, pp. 1351–1355, 2018. ista: Novembre J, Barton NH. 2018. Tread lightly interpreting polygenic tests of selection. Genetics. 208(4), 1351–1355. mla: Novembre, John, and Nicholas H. Barton. “Tread Lightly Interpreting Polygenic Tests of Selection.” Genetics, vol. 208, no. 4, Genetics Society of America, 2018, pp. 1351–55, doi:10.1534/genetics.118.300786. short: J. Novembre, N.H. Barton, Genetics 208 (2018) 1351–1355. date_created: 2018-12-11T11:46:26Z date_published: 2018-04-01T00:00:00Z date_updated: 2023-09-19T10:17:30Z day: '01' ddc: - '576' department: - _id: NiBa doi: 10.1534/genetics.118.300786 external_id: isi: - '000429094400005' file: - access_level: open_access checksum: 3d838dc285df394376555b794b6a5ad1 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:40Z date_updated: 2020-07-14T12:46:26Z file_id: '4958' file_name: IST-2018-1012-v1+1_2018_Barton_Tread.pdf file_size: 500129 relation: main_file file_date_updated: 2020-07-14T12:46:26Z has_accepted_license: '1' intvolume: ' 208' isi: 1 issue: '4' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1351 - 1355 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '7393' pubrep_id: '1012' quality_controlled: '1' scopus_import: '1' status: public title: Tread lightly interpreting polygenic tests of selection 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: 208 year: '2018' ... --- _id: '199' abstract: - lang: eng text: Sex-biased genes are central to the study of sexual selection, sexual antagonism, and sex chromosome evolution. We describe a comprehensive de novo assembled transcriptome in the common frog Rana temporaria based on five developmental stages and three adult tissues from both sexes, obtained from a population with karyotypically homomorphic but genetically differentiated sex chromosomes. This allows the study of sex-biased gene expression throughout development, and its effect on the rate of gene evolution while accounting for pleiotropic expression, which is known to negatively correlate with the evolutionary rate. Overall, sex-biased genes had little overlap among developmental stages and adult tissues. Late developmental stages and gonad tissues had the highest numbers of stage-or tissue-specific genes. We find that pleiotropic gene expression is a better predictor than sex bias for the evolutionary rate of genes, though it often interacts with sex bias. Although genetically differentiated, the sex chromosomes were not enriched in sex-biased genes, possibly due to a very recent arrest of XY recombination. These results extend our understanding of the developmental dynamics, tissue specificity, and genomic localization of sex-biased genes. article_number: '294' article_processing_charge: No author: - first_name: Wen full_name: Ma, Wen last_name: Ma - first_name: Paris full_name: Veltsos, Paris last_name: Veltsos - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Nicolas full_name: Rodrigues, Nicolas last_name: Rodrigues - first_name: Roberto full_name: Sermier, Roberto last_name: Sermier - first_name: Daniel full_name: Jeffries, Daniel last_name: Jeffries - first_name: Nicolas full_name: Perrin, Nicolas last_name: Perrin citation: ama: Ma W, Veltsos P, Toups MA, et al. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 2018;9(6). doi:10.3390/genes9060294 apa: Ma, W., Veltsos, P., Toups, M. A., Rodrigues, N., Sermier, R., Jeffries, D., & Perrin, N. (2018). Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. MDPI AG. https://doi.org/10.3390/genes9060294 chicago: Ma, Wen, Paris Veltsos, Melissa A Toups, Nicolas Rodrigues, Roberto Sermier, Daniel Jeffries, and Nicolas Perrin. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9060294. ieee: W. Ma et al., “Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes,” Genes, vol. 9, no. 6. MDPI AG, 2018. ista: Ma W, Veltsos P, Toups MA, Rodrigues N, Sermier R, Jeffries D, Perrin N. 2018. Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes. Genes. 9(6), 294. mla: Ma, Wen, et al. “Tissue Specificity and Dynamics of Sex Biased Gene Expression in a Common Frog Population with Differentiated, yet Homomorphic, Sex Chromosomes.” Genes, vol. 9, no. 6, 294, MDPI AG, 2018, doi:10.3390/genes9060294. short: W. Ma, P. Veltsos, M.A. Toups, N. Rodrigues, R. Sermier, D. Jeffries, N. Perrin, Genes 9 (2018). date_created: 2018-12-11T11:45:09Z date_published: 2018-06-12T00:00:00Z date_updated: 2023-09-19T10:15:31Z day: '12' ddc: - '570' department: - _id: BeVi doi: 10.3390/genes9060294 external_id: isi: - '000436494200026' file: - access_level: open_access checksum: 423069beb1cd3cdd25bf3f464b38f1d7 content_type: application/pdf creator: dernst date_created: 2019-02-01T07:52:28Z date_updated: 2020-07-14T12:45:22Z file_id: '5905' file_name: 2018_Genes_Ma.pdf file_size: 3985796 relation: main_file file_date_updated: 2020-07-14T12:45:22Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '6' language: - iso: eng month: '06' oa: 1 oa_version: Published Version publication: Genes publication_status: published publisher: MDPI AG publist_id: '7714' quality_controlled: '1' scopus_import: '1' status: public title: Tissue specificity and dynamics of sex biased gene expression in a common frog population with differentiated, yet homomorphic, sex chromosomes 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: 9 year: '2018' ... --- _id: '543' abstract: - lang: eng text: A central goal in theoretical neuroscience is to predict the response properties of sensory neurons from first principles. To this end, “efficient coding” posits that sensory neurons encode maximal information about their inputs given internal constraints. There exist, however, many variants of efficient coding (e.g., redundancy reduction, different formulations of predictive coding, robust coding, sparse coding, etc.), differing in their regimes of applicability, in the relevance of signals to be encoded, and in the choice of constraints. It is unclear how these types of efficient coding relate or what is expected when different coding objectives are combined. Here we present a unified framework that encompasses previously proposed efficient coding models and extends to unique regimes. We show that optimizing neural responses to encode predictive information can lead them to either correlate or decorrelate their inputs, depending on the stimulus statistics; in contrast, at low noise, efficiently encoding the past always predicts decorrelation. Later, we investigate coding of naturalistic movies and show that qualitatively different types of visual motion tuning and levels of response sparsity are predicted, depending on whether the objective is to recover the past or predict the future. Our approach promises a way to explain the observed diversity of sensory neural responses, as due to multiple functional goals and constraints fulfilled by different cell types and/or circuits. article_processing_charge: No author: - first_name: Matthew J full_name: Chalk, Matthew J id: 2BAAC544-F248-11E8-B48F-1D18A9856A87 last_name: Chalk orcid: 0000-0001-7782-4436 - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Chalk MJ, Marre O, Tkačik G. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 2018;115(1):186-191. doi:10.1073/pnas.1711114115 apa: Chalk, M. J., Marre, O., & Tkačik, G. (2018). Toward a unified theory of efficient, predictive, and sparse coding. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1711114115 chicago: Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS. National Academy of Sciences, 2018. https://doi.org/10.1073/pnas.1711114115. ieee: M. J. Chalk, O. Marre, and G. Tkačik, “Toward a unified theory of efficient, predictive, and sparse coding,” PNAS, vol. 115, no. 1. National Academy of Sciences, pp. 186–191, 2018. ista: Chalk MJ, Marre O, Tkačik G. 2018. Toward a unified theory of efficient, predictive, and sparse coding. PNAS. 115(1), 186–191. mla: Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115. short: M.J. Chalk, O. Marre, G. Tkačik, PNAS 115 (2018) 186–191. date_created: 2018-12-11T11:47:04Z date_published: 2018-01-02T00:00:00Z date_updated: 2023-09-19T10:16:35Z day: '02' department: - _id: GaTk doi: 10.1073/pnas.1711114115 external_id: isi: - '000419128700049' intvolume: ' 115' isi: 1 issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.1101/152660 ' month: '01' oa: 1 oa_version: Submitted Version page: 186 - 191 project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '7273' quality_controlled: '1' scopus_import: '1' status: public title: Toward a unified theory of efficient, predictive, and sparse coding type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 115 year: '2018' ... --- _id: '421' abstract: - lang: eng text: Cell shape is determined by a balance of intrinsic properties of the cell as well as its mechanochemical environment. Inhomogeneous shape changes underlie many morphogenetic events and involve spatial gradients in active cellular forces induced by complex chemical signaling. Here, we introduce a mechanochemical model based on the notion that cell shape changes may be induced by external diffusible biomolecules that influence cellular contractility (or equivalently, adhesions) in a concentration-dependent manner—and whose spatial profile in turn is affected by cell shape. We map out theoretically the possible interplay between chemical concentration and cellular structure. Besides providing a direct route to spatial gradients in cell shape profiles in tissues, we show that the dependence on cell shape helps create robust mechanochemical gradients. article_processing_charge: No author: - first_name: Kinjal full_name: Dasbiswas, Kinjal last_name: Dasbiswas - first_name: Claude-Edouard B full_name: Hannezo, Claude-Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Nir full_name: Gov, Nir last_name: Gov citation: ama: Dasbiswas K, Hannezo EB, Gov N. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 2018;114(4):968-977. doi:10.1016/j.bpj.2017.12.022 apa: Dasbiswas, K., Hannezo, E. B., & Gov, N. (2018). Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. Biophysical Society. https://doi.org/10.1016/j.bpj.2017.12.022 chicago: Dasbiswas, Kinjal, Edouard B Hannezo, and Nir Gov. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal. Biophysical Society, 2018. https://doi.org/10.1016/j.bpj.2017.12.022. ieee: K. Dasbiswas, E. B. Hannezo, and N. Gov, “Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients,” Biophysical Journal, vol. 114, no. 4. Biophysical Society, pp. 968–977, 2018. ista: Dasbiswas K, Hannezo EB, Gov N. 2018. Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients. Biophysical Journal. 114(4), 968–977. mla: Dasbiswas, Kinjal, et al. “Theory of Eppithelial Cell Shape Transitions Induced by Mechanoactive Chemical Gradients.” Biophysical Journal, vol. 114, no. 4, Biophysical Society, 2018, pp. 968–77, doi:10.1016/j.bpj.2017.12.022. short: K. Dasbiswas, E.B. Hannezo, N. Gov, Biophysical Journal 114 (2018) 968–977. date_created: 2018-12-11T11:46:23Z date_published: 2018-02-27T00:00:00Z date_updated: 2023-09-19T10:13:55Z day: '27' department: - _id: EdHa doi: 10.1016/j.bpj.2017.12.022 external_id: arxiv: - '1709.01486' isi: - '000428016700021' intvolume: ' 114' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.01486 month: '02' oa: 1 oa_version: Submitted Version page: 968 - 977 publication: Biophysical Journal publication_status: published publisher: Biophysical Society publist_id: '7403' quality_controlled: '1' scopus_import: '1' status: public title: Theory of eppithelial cell shape transitions induced by mechanoactive chemical gradients type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 114 year: '2018' ... --- _id: '63' abstract: - lang: eng text: African cichlids display a remarkable assortment of jaw morphologies, pigmentation patterns, and mating behaviors. In addition to this previously documented diversity, recent studies have documented a rich diversity of sex chromosomes within these fishes. Here we review the known sex-determination network within vertebrates, and the extraordinary number of sex chromosomes systems segregating in African cichlids. We also propose a model for understanding the unusual number of sex chromosome systems within this clade. acknowledgement: NSF DEB-1830753 and ISTPlus Fellowship article_number: '480' article_processing_charge: No author: - first_name: William J full_name: Gammerdinger, William J id: 3A7E01BC-F248-11E8-B48F-1D18A9856A87 last_name: Gammerdinger orcid: 0000-0001-9638-1220 - first_name: Thomas full_name: Kocher, Thomas last_name: Kocher citation: ama: Gammerdinger WJ, Kocher T. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 2018;9(10). doi:10.3390/genes9100480 apa: Gammerdinger, W. J., & Kocher, T. (2018). Unusual diversity of sex chromosomes in African cichlid fishes. Genes. MDPI AG. https://doi.org/10.3390/genes9100480 chicago: Gammerdinger, William J, and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes. MDPI AG, 2018. https://doi.org/10.3390/genes9100480. ieee: W. J. Gammerdinger and T. Kocher, “Unusual diversity of sex chromosomes in African cichlid fishes,” Genes, vol. 9, no. 10. MDPI AG, 2018. ista: Gammerdinger WJ, Kocher T. 2018. Unusual diversity of sex chromosomes in African cichlid fishes. Genes. 9(10), 480. mla: Gammerdinger, William J., and Thomas Kocher. “Unusual Diversity of Sex Chromosomes in African Cichlid Fishes.” Genes, vol. 9, no. 10, 480, MDPI AG, 2018, doi:10.3390/genes9100480. short: W.J. Gammerdinger, T. Kocher, Genes 9 (2018). date_created: 2018-12-11T11:44:26Z date_published: 2018-10-04T00:00:00Z date_updated: 2023-09-19T10:37:03Z day: '04' ddc: - '570' department: - _id: BeVi doi: 10.3390/genes9100480 ec_funded: 1 external_id: isi: - '000448656700018' file: - access_level: open_access checksum: bec527692e2c9b56919c0429634ff337 content_type: application/pdf creator: dernst date_created: 2018-12-18T09:54:46Z date_updated: 2020-07-14T12:47:27Z file_id: '5743' file_name: 2018_Genes_Gammerdinger.pdf file_size: 1415791 relation: main_file file_date_updated: 2020-07-14T12:47:27Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Genes publication_status: published publisher: MDPI AG publist_id: '7991' quality_controlled: '1' scopus_import: '1' status: public title: Unusual diversity of sex chromosomes in African cichlid fishes 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: 9 year: '2018' ... --- _id: '296' abstract: - lang: eng text: The thermodynamic description of many-particle systems rests on the assumption of ergodicity, the ability of a system to explore all allowed configurations in the phase space. Recent studies on many-body localization have revealed the existence of systems that strongly violate ergodicity in the presence of quenched disorder. Here, we demonstrate that ergodicity can be weakly broken by a different mechanism, arising from the presence of special eigenstates in the many-body spectrum that are reminiscent of quantum scars in chaotic non-interacting systems. In the single-particle case, quantum scars correspond to wavefunctions that concentrate in the vicinity of unstable periodic classical trajectories. We show that many-body scars appear in the Fibonacci chain, a model with a constrained local Hilbert space that has recently been experimentally realized in a Rydberg-atom quantum simulator. The quantum scarred eigenstates are embedded throughout the otherwise thermalizing many-body spectrum but lead to direct experimental signatures, as we show for periodic recurrences that reproduce those observed in the experiment. Our results suggest that scarred many-body bands give rise to a new universality class of quantum dynamics, opening up opportunities for the creation of novel states with long-lived coherence in systems that are now experimentally realizable. acknowledgement: C.J.T., A.M. and Z.P. acknowledge support from EPSRC grants EP/P009409/1 and EP/M50807X/1, and Royal Society Research Grant RG160635. D.A. acknowledges support from the Swiss National Science Foundation. article_processing_charge: No article_type: original author: - first_name: Christopher full_name: Turner, Christopher last_name: Turner - first_name: Alexios full_name: Michailidis, Alexios id: 36EBAD38-F248-11E8-B48F-1D18A9856A87 last_name: Michailidis orcid: 0000-0002-8443-1064 - first_name: Dmitry full_name: Abanin, Dmitry last_name: Abanin - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Zlatko full_name: Papić, Zlatko last_name: Papić citation: ama: Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 2018;14:745-749. doi:10.1038/s41567-018-0137-5 apa: Turner, C., Michailidis, A., Abanin, D., Serbyn, M., & Papić, Z. (2018). Weak ergodicity breaking from quantum many-body scars. Nature Physics. Nature Publishing Group. https://doi.org/10.1038/s41567-018-0137-5 chicago: Turner, Christopher, Alexios Michailidis, Dmitry Abanin, Maksym Serbyn, and Zlatko Papić. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics. Nature Publishing Group, 2018. https://doi.org/10.1038/s41567-018-0137-5. ieee: C. Turner, A. Michailidis, D. Abanin, M. Serbyn, and Z. Papić, “Weak ergodicity breaking from quantum many-body scars,” Nature Physics, vol. 14. Nature Publishing Group, pp. 745–749, 2018. ista: Turner C, Michailidis A, Abanin D, Serbyn M, Papić Z. 2018. Weak ergodicity breaking from quantum many-body scars. Nature Physics. 14, 745–749. mla: Turner, Christopher, et al. “Weak Ergodicity Breaking from Quantum Many-Body Scars.” Nature Physics, vol. 14, Nature Publishing Group, 2018, pp. 745–49, doi:10.1038/s41567-018-0137-5. short: C. Turner, A. Michailidis, D. Abanin, M. Serbyn, Z. Papić, Nature Physics 14 (2018) 745–749. date_created: 2018-12-11T11:45:40Z date_published: 2018-05-14T00:00:00Z date_updated: 2023-09-19T10:37:55Z day: '14' department: - _id: MaSe doi: 10.1038/s41567-018-0137-5 external_id: isi: - '000438253600028' intvolume: ' 14' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: http://eprints.whiterose.ac.uk/130860/ month: '05' oa: 1 oa_version: Submitted Version page: 745 - 749 publication: Nature Physics publication_status: published publisher: Nature Publishing Group publist_id: '7585' quality_controlled: '1' scopus_import: '1' status: public title: Weak ergodicity breaking from quantum many-body scars type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 14 year: '2018' ... --- _id: '607' abstract: - lang: eng text: We study the Fokker-Planck equation derived in the large system limit of the Markovian process describing the dynamics of quantitative traits. The Fokker-Planck equation is posed on a bounded domain and its transport and diffusion coefficients vanish on the domain's boundary. We first argue that, despite this degeneracy, the standard no-flux boundary condition is valid. We derive the weak formulation of the problem and prove the existence and uniqueness of its solutions by constructing the corresponding contraction semigroup on a suitable function space. Then, we prove that for the parameter regime with high enough mutation rate the problem exhibits a positive spectral gap, which implies exponential convergence to equilibrium.Next, we provide a simple derivation of the so-called Dynamic Maximum Entropy (DynMaxEnt) method for approximation of observables (moments) of the Fokker-Planck solution, which can be interpreted as a nonlinear Galerkin approximation. The limited applicability of the DynMaxEnt method inspires us to introduce its modified version that is valid for the whole range of admissible parameters. Finally, we present several numerical experiments to demonstrate the performance of both the original and modified DynMaxEnt methods. We observe that in the parameter regimes where both methods are valid, the modified one exhibits slightly better approximation properties compared to the original one. acknowledgement: "JH and PM are funded by KAUST baseline funds and grant no. 1000000193 .\r\nWe thank Nicholas Barton (IST Austria) for his useful comments and suggestions. \r\n\r\n" article_processing_charge: No author: - first_name: Katarina full_name: Bodova, Katarina id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bodova orcid: 0000-0002-7214-0171 - first_name: Jan full_name: Haskovec, Jan last_name: Haskovec - first_name: Peter full_name: Markowich, Peter last_name: Markowich citation: ama: 'Bodova K, Haskovec J, Markowich P. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 2018;376-377:108-120. doi:10.1016/j.physd.2017.10.015' apa: 'Bodova, K., Haskovec, J., & Markowich, P. (2018). Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. Elsevier. https://doi.org/10.1016/j.physd.2017.10.015' chicago: 'Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena. Elsevier, 2018. https://doi.org/10.1016/j.physd.2017.10.015.' ieee: 'K. Bodova, J. Haskovec, and P. Markowich, “Well posedness and maximum entropy approximation for the dynamics of quantitative traits,” Physica D: Nonlinear Phenomena, vol. 376–377. Elsevier, pp. 108–120, 2018.' ista: 'Bodova K, Haskovec J, Markowich P. 2018. Well posedness and maximum entropy approximation for the dynamics of quantitative traits. Physica D: Nonlinear Phenomena. 376–377, 108–120.' mla: 'Bodova, Katarina, et al. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.” Physica D: Nonlinear Phenomena, vol. 376–377, Elsevier, 2018, pp. 108–20, doi:10.1016/j.physd.2017.10.015.' short: 'K. Bodova, J. Haskovec, P. Markowich, Physica D: Nonlinear Phenomena 376–377 (2018) 108–120.' date_created: 2018-12-11T11:47:28Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-09-19T10:38:34Z day: '01' department: - _id: NiBa - _id: GaTk doi: 10.1016/j.physd.2017.10.015 external_id: arxiv: - '1704.08757' isi: - '000437962900012' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1704.08757 month: '08' oa: 1 oa_version: Submitted Version page: 108-120 publication: 'Physica D: Nonlinear Phenomena' publication_status: published publisher: Elsevier publist_id: '7198' quality_controlled: '1' scopus_import: '1' status: public title: Well posedness and maximum entropy approximation for the dynamics of quantitative traits type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 376-377 year: '2018' ... --- _id: '294' abstract: - lang: eng text: We developed a method to calculate two-photon processes in quantum mechanics that replaces the infinite summation over the intermediate states by a perturbation expansion. This latter consists of a series of commutators that involve position, momentum, and Hamiltonian quantum operators. We analyzed several single- and many-particle cases for which a closed-form solution to the perturbation expansion exists, as well as more complicated cases for which a solution is found by convergence. Throughout the article, Rayleigh and Raman scattering are taken as examples of two-photon processes. The present method provides a clear distinction between the Thomson scattering, regarded as classical scattering, and quantum contributions. Such a distinction lets us derive general results concerning light scattering. Finally, possible extensions to the developed formalism are discussed. article_processing_charge: No author: - first_name: Filippo full_name: Fratini, Filippo last_name: Fratini - first_name: Laleh full_name: Safari, Laleh id: 3C325E5E-F248-11E8-B48F-1D18A9856A87 last_name: Safari - first_name: Pedro full_name: Amaro, Pedro last_name: Amaro - first_name: José full_name: Santos, José last_name: Santos citation: ama: Fratini F, Safari L, Amaro P, Santos J. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 2018;97(4). doi:10.1103/PhysRevA.97.043842 apa: Fratini, F., Safari, L., Amaro, P., & Santos, J. (2018). Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society. https://doi.org/10.1103/PhysRevA.97.043842 chicago: Fratini, Filippo, Laleh Safari, Pedro Amaro, and José Santos. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics. American Physical Society, 2018. https://doi.org/10.1103/PhysRevA.97.043842. ieee: F. Fratini, L. Safari, P. Amaro, and J. Santos, “Two-photon processes based on quantum commutators,” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4. American Physical Society, 2018. ista: Fratini F, Safari L, Amaro P, Santos J. 2018. Two-photon processes based on quantum commutators. Physical Review A - Atomic, Molecular, and Optical Physics. 97(4). mla: Fratini, Filippo, et al. “Two-Photon Processes Based on Quantum Commutators.” Physical Review A - Atomic, Molecular, and Optical Physics, vol. 97, no. 4, American Physical Society, 2018, doi:10.1103/PhysRevA.97.043842. short: F. Fratini, L. Safari, P. Amaro, J. Santos, Physical Review A - Atomic, Molecular, and Optical Physics 97 (2018). date_created: 2018-12-11T11:45:40Z date_published: 2018-04-18T00:00:00Z date_updated: 2023-09-19T10:17:56Z day: '18' department: - _id: MiLe doi: 10.1103/PhysRevA.97.043842 ec_funded: 1 external_id: arxiv: - '1801.06892' isi: - '000430296800008' intvolume: ' 97' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1801.06892 month: '04' oa: 1 oa_version: Submitted Version 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: '7587' quality_controlled: '1' scopus_import: '1' status: public title: Two-photon processes based on quantum commutators type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 97 year: '2018' ... --- _id: '606' abstract: - lang: eng text: We establish the existence of a global solution for a new family of fluid-like equations, which are obtained in certain regimes in as the mean-field evolution of the supercurrent density in a (2D section of a) type-II superconductor with pinning and with imposed electric current. We also consider general vortex-sheet initial data, and investigate the uniqueness and regularity properties of the solution. For some choice of parameters, the equation under investigation coincides with the so-called lake equation from 2D shallow water fluid dynamics, and our analysis then leads to a new existence result for rough initial data. acknowledgement: "The work of the author is supported by F.R.S.-FNRS ( Fonds de la Recherche Scientifique - FNRS ) through a Research Fellowship.\r\n\r\n" article_processing_charge: No author: - first_name: Mitia full_name: Duerinckx, Mitia last_name: Duerinckx - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: Duerinckx M, Fischer JL. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 2018;35(5):1267-1319. doi:10.1016/j.anihpc.2017.11.004 apa: Duerinckx, M., & Fischer, J. L. (2018). Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier. https://doi.org/10.1016/j.anihpc.2017.11.004 chicago: Duerinckx, Mitia, and Julian L Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis. Elsevier, 2018. https://doi.org/10.1016/j.anihpc.2017.11.004. ieee: M. Duerinckx and J. L. Fischer, “Well-posedness for mean-field evolutions arising in superconductivity,” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5. Elsevier, pp. 1267–1319, 2018. ista: Duerinckx M, Fischer JL. 2018. Well-posedness for mean-field evolutions arising in superconductivity. Annales de l’Institut Henri Poincare (C) Non Linear Analysis. 35(5), 1267–1319. mla: Duerinckx, Mitia, and Julian L. Fischer. “Well-Posedness for Mean-Field Evolutions Arising in Superconductivity.” Annales de l’Institut Henri Poincare (C) Non Linear Analysis, vol. 35, no. 5, Elsevier, 2018, pp. 1267–319, doi:10.1016/j.anihpc.2017.11.004. short: M. Duerinckx, J.L. Fischer, Annales de l’Institut Henri Poincare (C) Non Linear Analysis 35 (2018) 1267–1319. date_created: 2018-12-11T11:47:27Z date_published: 2018-08-01T00:00:00Z date_updated: 2023-09-19T10:39:09Z day: '01' department: - _id: JuFi doi: 10.1016/j.anihpc.2017.11.004 external_id: arxiv: - '1607.00268' isi: - '000437975500005' intvolume: ' 35' isi: 1 issue: '5' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1607.00268 month: '08' oa: 1 oa_version: Submitted Version page: 1267-1319 publication: Annales de l'Institut Henri Poincare (C) Non Linear Analysis publication_status: published publisher: Elsevier publist_id: '7199' quality_controlled: '1' scopus_import: '1' status: public title: Well-posedness for mean-field evolutions arising in superconductivity type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 35 year: '2018' ... --- _id: '5959' abstract: - lang: eng text: Formalizing properties of systems with continuous dynamics is a challenging task. In this paper, we propose a formal framework for specifying and monitoring rich temporal properties of real-valued signals. We introduce signal first-order logic (SFO) as a specification language that combines first-order logic with linear-real arithmetic and unary function symbols interpreted as piecewise-linear signals. We first show that while the satisfiability problem for SFO is undecidable, its membership and monitoring problems are decidable. We develop an offline monitoring procedure for SFO that has polynomial complexity in the size of the input trace and the specification, for a fixed number of quantifiers and function symbols. We show that the algorithm has computation time linear in the size of the input trace for the important fragment of bounded-response specifications interpreted over input traces with finite variability. We can use our results to extend signal temporal logic with first-order quantifiers over time and value parameters, while preserving its efficient monitoring. We finally demonstrate the practical appeal of our logic through a case study in the micro-electronics domain. 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: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Deian full_name: Nickovicl, Deian last_name: Nickovicl citation: ama: 'Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. Keynote: The first-order logic of signals. In: 2018 International Conference on Embedded Software. IEEE; 2018:1-10. doi:10.1109/emsoft.2018.8537203' apa: 'Bakhirkin, A., Ferrere, T., Henzinger, T. A., & Nickovicl, D. (2018). Keynote: The first-order logic of signals. In 2018 International Conference on Embedded Software (pp. 1–10). Turin, Italy: IEEE. https://doi.org/10.1109/emsoft.2018.8537203' chicago: 'Bakhirkin, Alexey, Thomas Ferrere, Thomas A Henzinger, and Deian Nickovicl. “Keynote: The First-Order Logic of Signals.” In 2018 International Conference on Embedded Software, 1–10. IEEE, 2018. https://doi.org/10.1109/emsoft.2018.8537203.' ieee: 'A. Bakhirkin, T. Ferrere, T. A. Henzinger, and D. Nickovicl, “Keynote: The first-order logic of signals,” in 2018 International Conference on Embedded Software, Turin, Italy, 2018, pp. 1–10.' ista: 'Bakhirkin A, Ferrere T, Henzinger TA, Nickovicl D. 2018. Keynote: The first-order logic of signals. 2018 International Conference on Embedded Software. EMSOFT: International Conference on Embedded Software, 1–10.' mla: 'Bakhirkin, Alexey, et al. “Keynote: The First-Order Logic of Signals.” 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10, doi:10.1109/emsoft.2018.8537203.' short: A. Bakhirkin, T. Ferrere, T.A. Henzinger, D. Nickovicl, in:, 2018 International Conference on Embedded Software, IEEE, 2018, pp. 1–10. conference: end_date: 2018-10-05 location: Turin, Italy name: 'EMSOFT: International Conference on Embedded Software' start_date: 2018-09-30 date_created: 2019-02-13T09:19:28Z date_published: 2018-09-30T00:00:00Z date_updated: 2023-09-19T10:41:29Z day: '30' ddc: - '000' department: - _id: ToHe doi: 10.1109/emsoft.2018.8537203 external_id: isi: - '000492828500005' file: - access_level: open_access checksum: 234a33ad9055b3458fcdda6af251b33a content_type: application/pdf creator: dernst date_created: 2020-05-14T16:01:29Z date_updated: 2020-07-14T12:47:13Z file_id: '7839' file_name: 2018_EMSOFT_Bakhirkin.pdf file_size: 338006 relation: main_file file_date_updated: 2020-07-14T12:47:13Z has_accepted_license: '1' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1-10 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: 2018 International Conference on Embedded Software publication_identifier: isbn: - '9781538655603' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: 'Keynote: The first-order logic of signals' type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '5962' abstract: - lang: eng text: Stochastic Gradient Descent (SGD) is a fundamental algorithm in machine learning, representing the optimization backbone for training several classic models, from regression to neural networks. Given the recent practical focus on distributed machine learning, significant work has been dedicated to the convergence properties of this algorithm under the inconsistent and noisy updates arising from execution in a distributed environment. However, surprisingly, the convergence properties of this classic algorithm in the standard shared-memory model are still not well-understood. In this work, we address this gap, and provide new convergence bounds for lock-free concurrent stochastic gradient descent, executing in the classic asynchronous shared memory model, against a strong adaptive adversary. Our results give improved upper and lower bounds on the "price of asynchrony'' when executing the fundamental SGD algorithm in a concurrent setting. They show that this classic optimization tool can converge faster and with a wider range of parameters than previously known under asynchronous iterations. At the same time, we exhibit a fundamental trade-off between the maximum delay in the system and the rate at which SGD can converge, which governs the set of parameters under which this algorithm can still work efficiently. article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X - first_name: Christopher full_name: De Sa, Christopher last_name: De Sa - first_name: Nikola H full_name: Konstantinov, Nikola H id: 4B9D76E4-F248-11E8-B48F-1D18A9856A87 last_name: Konstantinov citation: ama: 'Alistarh D-A, De Sa C, Konstantinov NH. The convergence of stochastic gradient descent in asynchronous shared memory. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18. ACM Press; 2018:169-178. doi:10.1145/3212734.3212763' apa: 'Alistarh, D.-A., De Sa, C., & Konstantinov, N. H. (2018). The convergence of stochastic gradient descent in asynchronous shared memory. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18 (pp. 169–178). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212763' chicago: Alistarh, Dan-Adrian, Christopher De Sa, and Nikola H Konstantinov. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18, 169–78. ACM Press, 2018. https://doi.org/10.1145/3212734.3212763. ieee: D.-A. Alistarh, C. De Sa, and N. H. Konstantinov, “The convergence of stochastic gradient descent in asynchronous shared memory,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18, Egham, United Kingdom, 2018, pp. 169–178. ista: 'Alistarh D-A, De Sa C, Konstantinov NH. 2018. The convergence of stochastic gradient descent in asynchronous shared memory. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18. PODC: Principles of Distributed Computing, 169–178.' mla: Alistarh, Dan-Adrian, et al. “The Convergence of Stochastic Gradient Descent in Asynchronous Shared Memory.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18, ACM Press, 2018, pp. 169–78, doi:10.1145/3212734.3212763. short: D.-A. Alistarh, C. De Sa, N.H. Konstantinov, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18, ACM Press, 2018, pp. 169–178. conference: end_date: 2018-07-27 location: Egham, United Kingdom name: 'PODC: Principles of Distributed Computing' start_date: 2018-07-23 date_created: 2019-02-13T09:58:58Z date_published: 2018-07-23T00:00:00Z date_updated: 2023-09-19T10:42:53Z day: '23' department: - _id: DaAl doi: 10.1145/3212734.3212763 external_id: arxiv: - '1803.08841' isi: - '000458186900022' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1803.08841 month: '07' oa: 1 oa_version: Preprint page: 169-178 publication: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18 publication_identifier: isbn: - '9781450357951' publication_status: published publisher: ACM Press quality_controlled: '1' scopus_import: '1' status: public title: The convergence of stochastic gradient descent in asynchronous shared memory type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '5860' abstract: - lang: eng text: 'A major problem for evolutionary theory is understanding the so-called open-ended nature of evolutionary change, from its definition to its origins. Open-ended evolution (OEE) refers to the unbounded increase in complexity that seems to characterize evolution on multiple scales. This property seems to be a characteristic feature of biological and technological evolution and is strongly tied to the generative potential associated with combinatorics, which allows the system to grow and expand their available state spaces. Interestingly, many complex systems presumably displaying OEE, from language to proteins, share a common statistical property: the presence of Zipf''s Law. Given an inventory of basic items (such as words or protein domains) required to build more complex structures (sentences or proteins) Zipf''s Law tells us that most of these elements are rare whereas a few of them are extremely common. Using algorithmic information theory, in this paper we provide a fundamental definition for open-endedness, which can be understood as postulates. Its statistical counterpart, based on standard Shannon information theory, has the structure of a variational problem which is shown to lead to Zipf''s Law as the expected consequence of an evolutionary process displaying OEE. We further explore the problem of information conservation through an OEE process and we conclude that statistical information (standard Shannon information) is not conserved, resulting in the paradoxical situation in which the increase of information content has the effect of erasing itself. We prove that this paradox is solved if we consider non-statistical forms of information. This last result implies that standard information theory may not be a suitable theoretical framework to explore the persistence and increase of the information content in OEE systems.' article_number: '20180395' article_processing_charge: No author: - first_name: Bernat full_name: Corominas-Murtra, Bernat id: 43BE2298-F248-11E8-B48F-1D18A9856A87 last_name: Corominas-Murtra orcid: 0000-0001-9806-5643 - first_name: Luís F. full_name: Seoane, Luís F. last_name: Seoane - first_name: Ricard full_name: Solé, Ricard last_name: Solé citation: ama: Corominas-Murtra B, Seoane LF, Solé R. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 2018;15(149). doi:10.1098/rsif.2018.0395 apa: Corominas-Murtra, B., Seoane, L. F., & Solé, R. (2018). Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. Royal Society Publishing. https://doi.org/10.1098/rsif.2018.0395 chicago: Corominas-Murtra, Bernat, Luís F. Seoane, and Ricard Solé. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface. Royal Society Publishing, 2018. https://doi.org/10.1098/rsif.2018.0395. ieee: B. Corominas-Murtra, L. F. Seoane, and R. Solé, “Zipf’s Law, unbounded complexity and open-ended evolution,” Journal of the Royal Society Interface, vol. 15, no. 149. Royal Society Publishing, 2018. ista: Corominas-Murtra B, Seoane LF, Solé R. 2018. Zipf’s Law, unbounded complexity and open-ended evolution. Journal of the Royal Society Interface. 15(149), 20180395. mla: Corominas-Murtra, Bernat, et al. “Zipf’s Law, Unbounded Complexity and Open-Ended Evolution.” Journal of the Royal Society Interface, vol. 15, no. 149, 20180395, Royal Society Publishing, 2018, doi:10.1098/rsif.2018.0395. short: B. Corominas-Murtra, L.F. Seoane, R. Solé, Journal of the Royal Society Interface 15 (2018). date_created: 2019-01-20T22:59:19Z date_published: 2018-12-12T00:00:00Z date_updated: 2023-09-19T10:40:38Z day: '12' department: - _id: EdHa doi: 10.1098/rsif.2018.0395 external_id: arxiv: - '1612.01605' isi: - '000456783800002' intvolume: ' 15' isi: 1 issue: '149' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1612.01605 month: '12' oa: 1 oa_version: Preprint 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: Zipf's Law, unbounded complexity and open-ended evolution type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 15 year: '2018' ... --- _id: '5961' abstract: - lang: eng text: "The area of machine learning has made considerable progress over the past decade, enabled by the widespread availability of large datasets, as well as by improved algorithms and models. Given the large computational demands of machine learning workloads, parallelism, implemented either through single-node concurrency or through multi-node distribution, has been a third key ingredient to advances in machine learning.\r\nThe goal of this tutorial is to provide the audience with an overview of standard distribution techniques in machine learning, with an eye towards the intriguing trade-offs between synchronization and communication costs of distributed machine learning algorithms, on the one hand, and their convergence, on the other.The tutorial will focus on parallelization strategies for the fundamental stochastic gradient descent (SGD) algorithm, which is a key tool when training machine learning models, from classical instances such as linear regression, to state-of-the-art neural network architectures.\r\nThe tutorial will describe the guarantees provided by this algorithm in the sequential case, and then move on to cover both shared-memory and message-passing parallelization strategies, together with the guarantees they provide, and corresponding trade-offs. The presentation will conclude with a broad overview of ongoing research in distributed and concurrent machine learning. The tutorial will assume no prior knowledge beyond familiarity with basic concepts in algebra and analysis.\r\n" article_processing_charge: No author: - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Alistarh D-A. A brief tutorial on distributed and concurrent machine learning. In: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18. ACM Press; 2018:487-488. doi:10.1145/3212734.3212798' apa: 'Alistarh, D.-A. (2018). A brief tutorial on distributed and concurrent machine learning. In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18 (pp. 487–488). Egham, United Kingdom: ACM Press. https://doi.org/10.1145/3212734.3212798' chicago: Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine Learning.” In Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18, 487–88. ACM Press, 2018. https://doi.org/10.1145/3212734.3212798. ieee: D.-A. Alistarh, “A brief tutorial on distributed and concurrent machine learning,” in Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18, Egham, United Kingdom, 2018, pp. 487–488. ista: 'Alistarh D-A. 2018. A brief tutorial on distributed and concurrent machine learning. Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18. PODC: Principles of Distributed Computing, 487–488.' mla: Alistarh, Dan-Adrian. “A Brief Tutorial on Distributed and Concurrent Machine Learning.” Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18, ACM Press, 2018, pp. 487–88, doi:10.1145/3212734.3212798. short: D.-A. Alistarh, in:, Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing  - PODC ’18, ACM Press, 2018, pp. 487–488. conference: end_date: 2018-07-27 location: Egham, United Kingdom name: 'PODC: Principles of Distributed Computing' start_date: 2018-07-23 date_created: 2019-02-13T09:48:55Z date_published: 2018-07-27T00:00:00Z date_updated: 2023-09-19T10:42:28Z day: '27' department: - _id: DaAl doi: 10.1145/3212734.3212798 external_id: isi: - '000458186900063' isi: 1 language: - iso: eng month: '07' oa_version: None page: 487-488 publication: Proceedings of the 2018 ACM Symposium on Principles of Distributed Computing - PODC '18 publication_identifier: isbn: - '9781450357951' publication_status: published publisher: ACM Press quality_controlled: '1' scopus_import: '1' status: public title: A brief tutorial on distributed and concurrent machine learning type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2018' ... --- _id: '5960' abstract: - lang: eng text: In this paper we present a reliable method to verify the existence of loops along the uncertain trajectory of a robot, based on proprioceptive measurements only, within a bounded-error context. The loop closure detection is one of the key points in simultaneous localization and mapping (SLAM) methods, especially in homogeneous environments with difficult scenes recognitions. The proposed approach is generic and could be coupled with conventional SLAM algorithms to reliably reduce their computing burden, thus improving the localization and mapping processes in the most challenging environments such as unexplored underwater extents. To prove that a robot performed a loop whatever the uncertainties in its evolution, we employ the notion of topological degree that originates in the field of differential topology. We show that a verification tool based on the topological degree is an optimal method for proving robot loops. This is demonstrated both on datasets from real missions involving autonomous underwater vehicles and by a mathematical discussion. article_processing_charge: No author: - first_name: Simon full_name: Rohou, Simon last_name: Rohou - first_name: Peter full_name: Franek, Peter id: 473294AE-F248-11E8-B48F-1D18A9856A87 last_name: Franek orcid: 0000-0001-8878-8397 - first_name: Clément full_name: Aubry, Clément last_name: Aubry - first_name: Luc full_name: Jaulin, Luc last_name: Jaulin citation: ama: Rohou S, Franek P, Aubry C, Jaulin L. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 2018;37(12):1500-1516. doi:10.1177/0278364918808367 apa: Rohou, S., Franek, P., Aubry, C., & Jaulin, L. (2018). Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. SAGE Publications. https://doi.org/10.1177/0278364918808367 chicago: Rohou, Simon, Peter Franek, Clément Aubry, and Luc Jaulin. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research. SAGE Publications, 2018. https://doi.org/10.1177/0278364918808367. ieee: S. Rohou, P. Franek, C. Aubry, and L. Jaulin, “Proving the existence of loops in robot trajectories,” The International Journal of Robotics Research, vol. 37, no. 12. SAGE Publications, pp. 1500–1516, 2018. ista: Rohou S, Franek P, Aubry C, Jaulin L. 2018. Proving the existence of loops in robot trajectories. The International Journal of Robotics Research. 37(12), 1500–1516. mla: Rohou, Simon, et al. “Proving the Existence of Loops in Robot Trajectories.” The International Journal of Robotics Research, vol. 37, no. 12, SAGE Publications, 2018, pp. 1500–16, doi:10.1177/0278364918808367. short: S. Rohou, P. Franek, C. Aubry, L. Jaulin, The International Journal of Robotics Research 37 (2018) 1500–1516. date_created: 2019-02-13T09:36:20Z date_published: 2018-10-24T00:00:00Z date_updated: 2023-09-19T10:41:59Z day: '24' department: - _id: UlWa doi: 10.1177/0278364918808367 external_id: arxiv: - '1712.01341' isi: - '000456881100004' intvolume: ' 37' isi: 1 issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1712.01341 month: '10' oa: 1 oa_version: Preprint page: 1500-1516 publication: The International Journal of Robotics Research publication_identifier: eissn: - 1741-3176 issn: - 0278-3649 publication_status: published publisher: SAGE Publications quality_controlled: '1' scopus_import: '1' status: public title: Proving the existence of loops in robot trajectories type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 37 year: '2018' ...