--- _id: '6454' abstract: - lang: eng text: 'Adult neural stem cells and multiciliated ependymalcells are glial cells essential for neurological func-tions. Together, they make up the adult neurogenicniche. Using both high-throughput clonal analysisand single-cell resolution of progenitor division pat-terns and fate, we show that these two componentsof the neurogenic niche are lineally related: adult neu-ral stem cells are sister cells to ependymal cells,whereas most ependymal cells arise from the termi-nal symmetric divisions of the lineage. Unexpectedly,we found that the antagonist regulators of DNA repli-cation, GemC1 and Geminin, can tune the proportionof neural stem cells and ependymal cells. Our find-ings reveal the controlled dynamic of the neurogenicniche ontogeny and identify the Geminin familymembers as key regulators of the initial pool of adultneural stem cells.' article_processing_charge: No author: - first_name: G full_name: Ortiz-Álvarez, G last_name: Ortiz-Álvarez - first_name: M full_name: Daclin, M last_name: Daclin - first_name: A full_name: Shihavuddin, A last_name: Shihavuddin - first_name: P full_name: Lansade, P last_name: Lansade - first_name: A full_name: Fortoul, A last_name: Fortoul - first_name: M full_name: Faucourt, M last_name: Faucourt - first_name: S full_name: Clavreul, S last_name: Clavreul - first_name: ME full_name: Lalioti, ME last_name: Lalioti - first_name: S full_name: Taraviras, S last_name: Taraviras - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: J full_name: Livet, J last_name: Livet - first_name: A full_name: Meunier, A last_name: Meunier - first_name: A full_name: Genovesio, A last_name: Genovesio - first_name: N full_name: Spassky, N last_name: Spassky citation: ama: Ortiz-Álvarez G, Daclin M, Shihavuddin A, et al. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 2019;102(1):159-172.e7. doi:10.1016/j.neuron.2019.01.051 apa: Ortiz-Álvarez, G., Daclin, M., Shihavuddin, A., Lansade, P., Fortoul, A., Faucourt, M., … Spassky, N. (2019). Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.01.051 chicago: Ortiz-Álvarez, G, M Daclin, A Shihavuddin, P Lansade, A Fortoul, M Faucourt, S Clavreul, et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.01.051. ieee: G. Ortiz-Álvarez et al., “Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members,” Neuron, vol. 102, no. 1. Elsevier, p. 159–172.e7, 2019. ista: Ortiz-Álvarez G, Daclin M, Shihavuddin A, Lansade P, Fortoul A, Faucourt M, Clavreul S, Lalioti M, Taraviras S, Hippenmeyer S, Livet J, Meunier A, Genovesio A, Spassky N. 2019. Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members. Neuron. 102(1), 159–172.e7. mla: Ortiz-Álvarez, G., et al. “Adult Neural Stem Cells and Multiciliated Ependymal Cells Share a Common Lineage Regulated by the Geminin Family Members.” Neuron, vol. 102, no. 1, Elsevier, 2019, p. 159–172.e7, doi:10.1016/j.neuron.2019.01.051. short: G. Ortiz-Álvarez, M. Daclin, A. Shihavuddin, P. Lansade, A. Fortoul, M. Faucourt, S. Clavreul, M. Lalioti, S. Taraviras, S. Hippenmeyer, J. Livet, A. Meunier, A. Genovesio, N. Spassky, Neuron 102 (2019) 159–172.e7. date_created: 2019-05-14T13:06:30Z date_published: 2019-04-03T00:00:00Z date_updated: 2023-09-05T13:02:21Z day: '03' ddc: - '570' department: - _id: SiHi doi: 10.1016/j.neuron.2019.01.051 ec_funded: 1 external_id: isi: - '000463337900018' pmid: - '30824354' file: - access_level: open_access checksum: 1fb6e195c583eb0c5cabf26f69ff6675 content_type: application/pdf creator: dernst date_created: 2019-05-15T09:28:41Z date_updated: 2020-07-14T12:47:30Z file_id: '6457' file_name: 2019_Neuron_Ortiz.pdf file_size: 7288572 relation: main_file file_date_updated: 2020-07-14T12:47:30Z has_accepted_license: '1' intvolume: ' 102' isi: 1 issue: '1' language: - iso: eng license: https://creativecommons.org/licenses/by-nc-nd/4.0/ month: '04' oa: 1 oa_version: Published Version page: 159-172.e7 pmid: 1 project: - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development publication: Neuron publication_identifier: eissn: - 1097-4199 issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Adult neural stem cells and multiciliated ependymal cells share a common lineage regulated by the Geminin family members tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 102 year: '2019' ... --- _id: '6979' article_processing_charge: No article_type: original author: - first_name: Aglaja full_name: Kopf, Aglaja id: 31DAC7B6-F248-11E8-B48F-1D18A9856A87 last_name: Kopf orcid: 0000-0002-2187-6656 - 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: 'Kopf A, Sixt MK. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 2019;29(20):R1091-R1093. doi:10.1016/j.cub.2019.08.068' apa: 'Kopf, A., & Sixt, M. K. (2019). Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. Cell Press. https://doi.org/10.1016/j.cub.2019.08.068' chicago: 'Kopf, Aglaja, and Michael K Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” Current Biology. Cell Press, 2019. https://doi.org/10.1016/j.cub.2019.08.068.' ieee: 'A. Kopf and M. K. Sixt, “Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal,” Current Biology, vol. 29, no. 20. Cell Press, pp. R1091–R1093, 2019.' ista: 'Kopf A, Sixt MK. 2019. Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal. Current Biology. 29(20), R1091–R1093.' mla: 'Kopf, Aglaja, and Michael K. Sixt. “Gut Homeostasis: Active Migration of Intestinal Epithelial Cells in Tissue Renewal.” Current Biology, vol. 29, no. 20, Cell Press, 2019, pp. R1091–93, doi:10.1016/j.cub.2019.08.068.' short: A. Kopf, M.K. Sixt, Current Biology 29 (2019) R1091–R1093. date_created: 2019-11-04T15:18:29Z date_published: 2019-10-21T00:00:00Z date_updated: 2023-09-05T12:43:43Z day: '21' department: - _id: MiSi doi: 10.1016/j.cub.2019.08.068 external_id: isi: - '000491286200016' pmid: - '31639357' intvolume: ' 29' isi: 1 issue: '20' language: - iso: eng month: '10' oa_version: None page: R1091-R1093 pmid: 1 publication: Current Biology publication_identifier: eissn: - 1879-0445 issn: - 0960-9822 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: 'Gut homeostasis: Active migration of intestinal epithelial cells in tissue renewal' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 29 year: '2019' ... --- _id: '6980' abstract: - lang: eng text: Tissue morphogenesis in multicellular organisms is brought about by spatiotemporal coordination of mechanical and chemical signals. Extensive work on how mechanical forces together with the well‐established morphogen signalling pathways can actively shape living tissues has revealed evolutionary conserved mechanochemical features of embryonic development. More recently, attention has been drawn to the description of tissue material properties and how they can influence certain morphogenetic processes. Interestingly, besides the role of tissue material properties in determining how much tissues deform in response to force application, there is increasing theoretical and experimental evidence, suggesting that tissue material properties can abruptly and drastically change in development. These changes resemble phase transitions, pointing at the intriguing possibility that important morphogenetic processes in development, such as symmetry breaking and self‐organization, might be mediated by tissue phase transitions. In this review, we summarize recent findings on the regulation and role of tissue material properties in the context of the developing embryo. We posit that abrupt changes of tissue rheological properties may have important implications in maintaining the balance between robustness and adaptability during embryonic development. article_number: e102497 article_processing_charge: Yes (via OA deal) article_type: review author: - first_name: Nicoletta full_name: Petridou, Nicoletta id: 2A003F6C-F248-11E8-B48F-1D18A9856A87 last_name: Petridou orcid: 0000-0002-8451-1195 - first_name: Carl-Philipp J full_name: Heisenberg, Carl-Philipp J id: 39427864-F248-11E8-B48F-1D18A9856A87 last_name: Heisenberg orcid: 0000-0002-0912-4566 citation: ama: Petridou N, Heisenberg C-PJ. Tissue rheology in embryonic organization. The EMBO Journal. 2019;38(20). doi:10.15252/embj.2019102497 apa: Petridou, N., & Heisenberg, C.-P. J. (2019). Tissue rheology in embryonic organization. The EMBO Journal. EMBO. https://doi.org/10.15252/embj.2019102497 chicago: Petridou, Nicoletta, and Carl-Philipp J Heisenberg. “Tissue Rheology in Embryonic Organization.” The EMBO Journal. EMBO, 2019. https://doi.org/10.15252/embj.2019102497. ieee: N. Petridou and C.-P. J. Heisenberg, “Tissue rheology in embryonic organization,” The EMBO Journal, vol. 38, no. 20. EMBO, 2019. ista: Petridou N, Heisenberg C-PJ. 2019. Tissue rheology in embryonic organization. The EMBO Journal. 38(20), e102497. mla: Petridou, Nicoletta, and Carl-Philipp J. Heisenberg. “Tissue Rheology in Embryonic Organization.” The EMBO Journal, vol. 38, no. 20, e102497, EMBO, 2019, doi:10.15252/embj.2019102497. short: N. Petridou, C.-P.J. Heisenberg, The EMBO Journal 38 (2019). date_created: 2019-11-04T15:24:29Z date_published: 2019-10-15T00:00:00Z date_updated: 2023-09-05T13:04:13Z day: '15' ddc: - '570' department: - _id: CaHe doi: 10.15252/embj.2019102497 ec_funded: 1 external_id: isi: - '000485561900001' pmid: - '31512749' file: - access_level: open_access checksum: 76f7f4e79ab6d850c30017a69726fd85 content_type: application/pdf creator: dernst date_created: 2019-11-04T15:30:08Z date_updated: 2020-07-14T12:47:46Z file_id: '6981' file_name: 2019_Embo_Petridou.pdf file_size: 847356 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 38' isi: 1 issue: '20' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 260F1432-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742573' name: Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation - _id: 2693FD8C-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: V00736 name: Tissue material properties in embryonic development publication: The EMBO Journal publication_identifier: eissn: - 1460-2075 issn: - 0261-4189 publication_status: published publisher: EMBO quality_controlled: '1' scopus_import: '1' status: public title: Tissue rheology in embryonic organization 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: 38 year: '2019' ... --- _id: '6554' abstract: - lang: eng text: Due to the importance of zero-shot learning, i.e. classifying images where there is a lack of labeled training data, the number of proposed approaches has recently increased steadily. We argue that it is time to take a step back and to analyze the status quo of the area. The purpose of this paper is three-fold. First, given the fact that there is no agreed upon zero-shot learning benchmark, we first define a new benchmark by unifying both the evaluation protocols and data splits of publicly available datasets used for this task. This is an important contribution as published results are often not comparable and sometimes even flawed due to, e.g. pre-training on zero-shot test classes. Moreover, we propose a new zero-shot learning dataset, the Animals with Attributes 2 (AWA2) dataset which we make publicly available both in terms of image features and the images themselves. Second, we compare and analyze a significant number of the state-of-the-art methods in depth, both in the classic zero-shot setting but also in the more realistic generalized zero-shot setting. Finally, we discuss in detail the limitations of the current status of the area which can be taken as a basis for advancing it. article_processing_charge: No article_type: original author: - first_name: Yongqin full_name: Xian, Yongqin last_name: Xian - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0002-4561-241X - first_name: Bernt full_name: Schiele, Bernt last_name: Schiele - first_name: Zeynep full_name: Akata, Zeynep last_name: Akata citation: ama: Xian Y, Lampert C, Schiele B, Akata Z. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2019;41(9):2251-2265. doi:10.1109/tpami.2018.2857768 apa: Xian, Y., Lampert, C., Schiele, B., & Akata, Z. (2019). Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. Institute of Electrical and Electronics Engineers (IEEE). https://doi.org/10.1109/tpami.2018.2857768 chicago: Xian, Yongqin, Christoph Lampert, Bernt Schiele, and Zeynep Akata. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” IEEE Transactions on Pattern Analysis and Machine Intelligence. Institute of Electrical and Electronics Engineers (IEEE), 2019. https://doi.org/10.1109/tpami.2018.2857768. ieee: Y. Xian, C. Lampert, B. Schiele, and Z. Akata, “Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 41, no. 9. Institute of Electrical and Electronics Engineers (IEEE), pp. 2251–2265, 2019. ista: Xian Y, Lampert C, Schiele B, Akata Z. 2019. Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly. IEEE Transactions on Pattern Analysis and Machine Intelligence. 41(9), 2251–2265. mla: Xian, Yongqin, et al. “Zero-Shot Learning - A Comprehensive Evaluation of the Good, the Bad and the Ugly.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 41, no. 9, Institute of Electrical and Electronics Engineers (IEEE), 2019, pp. 2251–65, doi:10.1109/tpami.2018.2857768. short: Y. Xian, C. Lampert, B. Schiele, Z. Akata, IEEE Transactions on Pattern Analysis and Machine Intelligence 41 (2019) 2251–2265. date_created: 2019-06-11T14:05:59Z date_published: 2019-09-01T00:00:00Z date_updated: 2023-09-05T13:18:09Z day: '01' department: - _id: ChLa doi: 10.1109/tpami.2018.2857768 external_id: arxiv: - '1707.00600' isi: - '000480343900015' intvolume: ' 41' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1707.00600 month: '09' oa: 1 oa_version: Preprint page: 2251 - 2265 publication: IEEE Transactions on Pattern Analysis and Machine Intelligence publication_identifier: eissn: - 1939-3539 issn: - 0162-8828 publication_status: published publisher: Institute of Electrical and Electronics Engineers (IEEE) quality_controlled: '1' scopus_import: '1' status: public title: Zero-shot learning - A comprehensive evaluation of the good, the bad and the ugly type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 41 year: '2019' ... --- _id: '6259' abstract: - lang: eng text: The plant hormone auxin has crucial roles in almost all aspects of plant growth and development. Concentrations of auxin vary across different tissues, mediating distinct developmental outcomes and contributing to the functional diversity of auxin. However, the mechanisms that underlie these activities are poorly understood. Here we identify an auxin signalling mechanism, which acts in parallel to the canonical auxin pathway based on the transport inhibitor response1 (TIR1) and other auxin receptor F-box (AFB) family proteins (TIR1/AFB receptors)1,2, that translates levels of cellular auxin to mediate differential growth during apical-hook development. This signalling mechanism operates at the concave side of the apical hook, and involves auxin-mediated C-terminal cleavage of transmembrane kinase 1 (TMK1). The cytosolic and nucleus-translocated C terminus of TMK1 specifically interacts with and phosphorylates two non-canonical transcriptional repressors of the auxin or indole-3-acetic acid (Aux/IAA) family (IAA32 and IAA34), thereby regulating ARF transcription factors. In contrast to the degradation of Aux/IAA transcriptional repressors in the canonical pathway, the newly identified mechanism stabilizes the non-canonical IAA32 and IAA34 transcriptional repressors to regulate gene expression and ultimately inhibit growth. The auxin–TMK1 signalling pathway originates at the cell surface, is triggered by high levels of auxin and shares a partially overlapping set of transcription factors with the TIR1/AFB signalling pathway. This allows distinct interpretations of different concentrations of cellular auxin, and thus enables this versatile signalling molecule to mediate complex developmental outcomes. article_processing_charge: No article_type: original author: - first_name: Min full_name: Cao, Min last_name: Cao - first_name: Rong full_name: Chen, Rong last_name: Chen - first_name: Pan full_name: Li, Pan last_name: Li - first_name: Yongqiang full_name: Yu, Yongqiang last_name: Yu - first_name: Rui full_name: Zheng, Rui last_name: Zheng - first_name: Danfeng full_name: Ge, Danfeng last_name: Ge - first_name: Wei full_name: Zheng, Wei last_name: Zheng - first_name: Xuhui full_name: Wang, Xuhui last_name: Wang - first_name: Yangtao full_name: Gu, Yangtao last_name: Gu - first_name: Zuzana full_name: Gelová, Zuzana id: 0AE74790-0E0B-11E9-ABC7-1ACFE5697425 last_name: Gelová orcid: 0000-0003-4783-1752 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Heng full_name: Zhang, Heng last_name: Zhang - first_name: Renyi full_name: Liu, Renyi last_name: Liu - first_name: Jun full_name: He, Jun last_name: He - first_name: Tongda full_name: Xu, Tongda last_name: Xu citation: ama: Cao M, Chen R, Li P, et al. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 2019;568:240-243. doi:10.1038/s41586-019-1069-7 apa: Cao, M., Chen, R., Li, P., Yu, Y., Zheng, R., Ge, D., … Xu, T. (2019). TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. Springer Nature. https://doi.org/10.1038/s41586-019-1069-7 chicago: Cao, Min, Rong Chen, Pan Li, Yongqiang Yu, Rui Zheng, Danfeng Ge, Wei Zheng, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” Nature. Springer Nature, 2019. https://doi.org/10.1038/s41586-019-1069-7. ieee: M. Cao et al., “TMK1-mediated auxin signalling regulates differential growth of the apical hook,” Nature, vol. 568. Springer Nature, pp. 240–243, 2019. ista: Cao M, Chen R, Li P, Yu Y, Zheng R, Ge D, Zheng W, Wang X, Gu Y, Gelová Z, Friml J, Zhang H, Liu R, He J, Xu T. 2019. TMK1-mediated auxin signalling regulates differential growth of the apical hook. Nature. 568, 240–243. mla: Cao, Min, et al. “TMK1-Mediated Auxin Signalling Regulates Differential Growth of the Apical Hook.” Nature, vol. 568, Springer Nature, 2019, pp. 240–43, doi:10.1038/s41586-019-1069-7. short: M. Cao, R. Chen, P. Li, Y. Yu, R. Zheng, D. Ge, W. Zheng, X. Wang, Y. Gu, Z. Gelová, J. Friml, H. Zhang, R. Liu, J. He, T. Xu, Nature 568 (2019) 240–243. date_created: 2019-04-09T08:37:05Z date_published: 2019-04-11T00:00:00Z date_updated: 2023-09-05T14:58:41Z day: '11' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41586-019-1069-7 ec_funded: 1 external_id: isi: - '000464412700050' pmid: - '30944466' file: - access_level: open_access checksum: 6b84ab602a34382cf0340a37a1378c75 content_type: application/pdf creator: dernst date_created: 2020-11-13T07:37:41Z date_updated: 2020-11-13T07:37:41Z file_id: '8751' file_name: 2019_Nature _Cao_accepted.pdf file_size: 4321328 relation: main_file success: 1 file_date_updated: 2020-11-13T07:37:41Z has_accepted_license: '1' intvolume: ' 568' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Submitted Version page: 240-243 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: Nature publication_identifier: eissn: - 1476-4687 issn: - 0028-0836 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/newly-discovered-mechanism-of-plant-hormone-auxin-acts-the-opposite-way/ scopus_import: '1' status: public title: TMK1-mediated auxin signalling regulates differential growth of the apical hook type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 568 year: '2019' ... --- _id: '6987' abstract: - lang: eng text: Cells are arranged into species-specific patterns during early embryogenesis. Such cell division patterns are important since they often reflect the distribution of localized cortical factors from eggs/fertilized eggs to specific cells as well as the emergence of organismal form. However, it has proven difficult to reveal the mechanisms that underlie the emergence of cell positioning patterns that underlie embryonic shape, likely because a systems-level approach is required that integrates cell biological, genetic, developmental, and mechanical parameters. The choice of organism to address such questions is also important. Because ascidians display the most extreme form of invariant cleavage pattern among the metazoans, we have been analyzing the cell biological mechanisms that underpin three aspects of cell division (unequal cell division (UCD), oriented cell division (OCD), and asynchronous cell cycles) which affect the overall shape of the blastula-stage ascidian embryo composed of 64 cells. In ascidians, UCD creates two small cells at the 16-cell stage that in turn undergo two further successive rounds of UCD. Starting at the 16-cell stage, the cell cycle becomes asynchronous, whereby the vegetal half divides before the animal half, thus creating 24-, 32-, 44-, and then 64-cell stages. Perturbing either UCD or the alternate cell division rhythm perturbs cell position. We propose that dynamic cell shape changes propagate throughout the embryo via cell-cell contacts to create the ascidian-specific invariant cleavage pattern. alternative_title: - RESULTS article_processing_charge: No author: - first_name: Alex full_name: McDougall, Alex last_name: McDougall - first_name: Janet full_name: Chenevert, Janet last_name: Chenevert - first_name: Benoit G full_name: Godard, Benoit G id: 33280250-F248-11E8-B48F-1D18A9856A87 last_name: Godard - first_name: Remi full_name: Dumollard, Remi last_name: Dumollard citation: ama: 'McDougall A, Chenevert J, Godard BG, Dumollard R. Emergence of embryo shape during cleavage divisions. In: Tworzydlo W, Bilinski SM, eds. Evo-Devo: Non-Model Species in Cell and Developmental Biology. Vol 68. Springer Nature; 2019:127-154. doi:10.1007/978-3-030-23459-1_6' apa: 'McDougall, A., Chenevert, J., Godard, B. G., & Dumollard, R. (2019). Emergence of embryo shape during cleavage divisions. In W. Tworzydlo & S. M. Bilinski (Eds.), Evo-Devo: Non-model species in cell and developmental biology (Vol. 68, pp. 127–154). Springer Nature. https://doi.org/10.1007/978-3-030-23459-1_6' chicago: 'McDougall, Alex, Janet Chenevert, Benoit G Godard, and Remi Dumollard. “Emergence of Embryo Shape during Cleavage Divisions.” In Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, 68:127–54. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-23459-1_6.' ieee: 'A. McDougall, J. Chenevert, B. G. Godard, and R. Dumollard, “Emergence of embryo shape during cleavage divisions,” in Evo-Devo: Non-model species in cell and developmental biology, vol. 68, W. Tworzydlo and S. M. Bilinski, Eds. Springer Nature, 2019, pp. 127–154.' ista: 'McDougall A, Chenevert J, Godard BG, Dumollard R. 2019.Emergence of embryo shape during cleavage divisions. In: Evo-Devo: Non-model species in cell and developmental biology. RESULTS, vol. 68, 127–154.' mla: 'McDougall, Alex, et al. “Emergence of Embryo Shape during Cleavage Divisions.” Evo-Devo: Non-Model Species in Cell and Developmental Biology, edited by Waclaw Tworzydlo and Szczepan M. Bilinski, vol. 68, Springer Nature, 2019, pp. 127–54, doi:10.1007/978-3-030-23459-1_6.' short: 'A. McDougall, J. Chenevert, B.G. Godard, R. Dumollard, in:, W. Tworzydlo, S.M. Bilinski (Eds.), Evo-Devo: Non-Model Species in Cell and Developmental Biology, Springer Nature, 2019, pp. 127–154.' date_created: 2019-11-04T16:20:19Z date_published: 2019-10-10T00:00:00Z date_updated: 2023-09-05T15:01:12Z day: '10' ddc: - '570' department: - _id: CaHe doi: 10.1007/978-3-030-23459-1_6 editor: - first_name: Waclaw full_name: Tworzydlo, Waclaw last_name: Tworzydlo - first_name: Szczepan M. full_name: Bilinski, Szczepan M. last_name: Bilinski external_id: pmid: - '31598855' file: - access_level: open_access checksum: 7f43e1e3706d15061475c5c57efc2786 content_type: application/pdf creator: dernst date_created: 2020-05-14T10:09:30Z date_updated: 2020-07-14T12:47:46Z file_id: '7829' file_name: 2019_RESULTS_McDougall.pdf file_size: 19317348 relation: main_file file_date_updated: 2020-07-14T12:47:46Z has_accepted_license: '1' intvolume: ' 68' language: - iso: eng month: '10' oa: 1 oa_version: Submitted Version page: 127-154 pmid: 1 publication: 'Evo-Devo: Non-model species in cell and developmental biology' publication_identifier: eissn: - 1861-0412 isbn: - '9783030234584' - '9783030234591' issn: - 0080-1844 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Emergence of embryo shape during cleavage divisions type: book_chapter user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 68 year: '2019' ... --- _id: '6762' abstract: - lang: eng text: "We present and study novel optimal control problems motivated by the search for photovoltaic materials with high power-conversion efficiency. The material must perform the first step: convert light (photons) into electronic excitations. We formulate various desirable properties of the excitations as mathematical control goals at the Kohn-Sham-DFT level\r\nof theory, with the control being given by the nuclear charge distribution. We prove that nuclear distributions exist which give rise to optimal HOMO-LUMO excitations, and present illustrative numerical simulations for 1D finite nanocrystals. We observe pronounced goal-dependent features such as large electron-hole separation, and a hierarchy of length scales: internal HOMO and LUMO wavelengths < atomic spacings < (irregular) fluctuations of the doping profiles < system size." article_processing_charge: No author: - first_name: Gero full_name: Friesecke, Gero last_name: Friesecke - first_name: Michael full_name: Kniely, Michael id: 2CA2C08C-F248-11E8-B48F-1D18A9856A87 last_name: Kniely orcid: 0000-0001-5645-4333 citation: ama: Friesecke G, Kniely M. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 2019;17(3):926-947. doi:10.1137/18M1207272 apa: Friesecke, G., & Kniely, M. (2019). New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. SIAM. https://doi.org/10.1137/18M1207272 chicago: Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation. SIAM, 2019. https://doi.org/10.1137/18M1207272. ieee: G. Friesecke and M. Kniely, “New optimal control problems in density functional theory motivated by photovoltaics,” Multiscale Modeling and Simulation, vol. 17, no. 3. SIAM, pp. 926–947, 2019. ista: Friesecke G, Kniely M. 2019. New optimal control problems in density functional theory motivated by photovoltaics. Multiscale Modeling and Simulation. 17(3), 926–947. mla: Friesecke, Gero, and Michael Kniely. “New Optimal Control Problems in Density Functional Theory Motivated by Photovoltaics.” Multiscale Modeling and Simulation, vol. 17, no. 3, SIAM, 2019, pp. 926–47, doi:10.1137/18M1207272. short: G. Friesecke, M. Kniely, Multiscale Modeling and Simulation 17 (2019) 926–947. date_created: 2019-08-04T21:59:21Z date_published: 2019-07-16T00:00:00Z date_updated: 2023-09-05T15:05:45Z day: '16' department: - _id: JuFi doi: 10.1137/18M1207272 external_id: arxiv: - '1808.04200' isi: - '000487931800002' intvolume: ' 17' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1808.04200 month: '07' oa: 1 oa_version: Preprint page: 926-947 publication: Multiscale Modeling and Simulation publication_identifier: eissn: - '15403467' issn: - '15403459' publication_status: published publisher: SIAM quality_controlled: '1' scopus_import: '1' status: public title: New optimal control problems in density functional theory motivated by photovoltaics type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 17 year: '2019' ... --- _id: '10874' abstract: - lang: eng text: In this article we prove an analogue of a theorem of Lachaud, Ritzenthaler, and Zykin, which allows us to connect invariants of binary octics to Siegel modular forms of genus 3. We use this connection to show that certain modular functions, when restricted to the hyperelliptic locus, assume values whose denominators are products of powers of primes of bad reduction for the associated hyperelliptic curves. We illustrate our theorem with explicit computations. This work is motivated by the study of the values of these modular functions at CM points of the Siegel upper half-space, which, if their denominators are known, can be used to effectively compute models of (hyperelliptic, in our case) curves with CM. acknowledgement: "The authors would like to thank the Lorentz Center in Leiden for hosting the Women in Numbers Europe 2 workshop and providing a productive and enjoyable environment for our initial work on this project. We are grateful to the organizers of WIN-E2, Irene Bouw, Rachel Newton and Ekin Ozman, for making this conference and this collaboration possible. We\r\nthank Irene Bouw and Christophe Ritzenhaler for helpful discussions. Ionica acknowledges support from the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. Most of Kılıçer’s work was carried out during her stay in Universiteit Leiden and Carl von Ossietzky Universität Oldenburg. Massierer was supported by the Australian Research Council (DP150101689). Vincent is supported by the National Science Foundation under Grant No. DMS-1802323 and by the Thomas Jefferson Fund of the Embassy of France in the United States and the FACE Foundation. " article_number: '9' article_processing_charge: No article_type: original author: - first_name: Sorina full_name: Ionica, Sorina last_name: Ionica - first_name: Pınar full_name: Kılıçer, Pınar last_name: Kılıçer - first_name: Kristin full_name: Lauter, Kristin last_name: Lauter - first_name: Elisa full_name: Lorenzo García, Elisa last_name: Lorenzo García - first_name: Maria-Adelina full_name: Manzateanu, Maria-Adelina id: be8d652e-a908-11ec-82a4-e2867729459c last_name: Manzateanu - first_name: Maike full_name: Massierer, Maike last_name: Massierer - first_name: Christelle full_name: Vincent, Christelle last_name: Vincent citation: ama: Ionica S, Kılıçer P, Lauter K, et al. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 2019;5. doi:10.1007/s40993-018-0146-6 apa: Ionica, S., Kılıçer, P., Lauter, K., Lorenzo García, E., Manzateanu, M.-A., Massierer, M., & Vincent, C. (2019). Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. Springer Nature. https://doi.org/10.1007/s40993-018-0146-6 chicago: Ionica, Sorina, Pınar Kılıçer, Kristin Lauter, Elisa Lorenzo García, Maria-Adelina Manzateanu, Maike Massierer, and Christelle Vincent. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory. Springer Nature, 2019. https://doi.org/10.1007/s40993-018-0146-6. ieee: S. Ionica et al., “Modular invariants for genus 3 hyperelliptic curves,” Research in Number Theory, vol. 5. Springer Nature, 2019. ista: Ionica S, Kılıçer P, Lauter K, Lorenzo García E, Manzateanu M-A, Massierer M, Vincent C. 2019. Modular invariants for genus 3 hyperelliptic curves. Research in Number Theory. 5, 9. mla: Ionica, Sorina, et al. “Modular Invariants for Genus 3 Hyperelliptic Curves.” Research in Number Theory, vol. 5, 9, Springer Nature, 2019, doi:10.1007/s40993-018-0146-6. short: S. Ionica, P. Kılıçer, K. Lauter, E. Lorenzo García, M.-A. Manzateanu, M. Massierer, C. Vincent, Research in Number Theory 5 (2019). date_created: 2022-03-18T12:09:48Z date_published: 2019-01-02T00:00:00Z date_updated: 2023-09-05T15:39:31Z day: '02' department: - _id: TiBr doi: 10.1007/s40993-018-0146-6 external_id: arxiv: - '1807.08986' intvolume: ' 5' keyword: - Algebra and Number Theory language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1807.08986 month: '01' oa: 1 oa_version: Preprint publication: Research in Number Theory publication_identifier: eissn: - 2363-9555 issn: - 2522-0160 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Modular invariants for genus 3 hyperelliptic curves type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 5 year: '2019' ... --- _id: '7100' abstract: - lang: eng text: We present microscopic derivations of the defocusing two-dimensional cubic nonlinear Schrödinger equation and the Gross–Pitaevskii equation starting froman interacting N-particle system of bosons. We consider the interaction potential to be given either by Wβ(x)=N−1+2βW(Nβx), for any β>0, or to be given by VN(x)=e2NV(eNx), for some spherical symmetric, nonnegative and compactly supported W,V∈L∞(R2,R). In both cases we prove the convergence of the reduced density corresponding to the exact time evolution to the projector onto the solution of the corresponding nonlinear Schrödinger equation in trace norm. For the latter potential VN we show that it is crucial to take the microscopic structure of the condensate into account in order to obtain the correct dynamics. acknowledgement: OA fund by IST Austria article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Maximilian full_name: Jeblick, Maximilian last_name: Jeblick - first_name: Nikolai K full_name: Leopold, Nikolai K id: 4BC40BEC-F248-11E8-B48F-1D18A9856A87 last_name: Leopold orcid: 0000-0002-0495-6822 - first_name: Peter full_name: Pickl, Peter last_name: Pickl citation: ama: Jeblick M, Leopold NK, Pickl P. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 2019;372(1):1-69. doi:10.1007/s00220-019-03599-x apa: Jeblick, M., Leopold, N. K., & Pickl, P. (2019). Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-019-03599-x chicago: Jeblick, Maximilian, Nikolai K Leopold, and Peter Pickl. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics. Springer Nature, 2019. https://doi.org/10.1007/s00220-019-03599-x. ieee: M. Jeblick, N. K. Leopold, and P. Pickl, “Derivation of the time dependent Gross–Pitaevskii equation in two dimensions,” Communications in Mathematical Physics, vol. 372, no. 1. Springer Nature, pp. 1–69, 2019. ista: Jeblick M, Leopold NK, Pickl P. 2019. Derivation of the time dependent Gross–Pitaevskii equation in two dimensions. Communications in Mathematical Physics. 372(1), 1–69. mla: Jeblick, Maximilian, et al. “Derivation of the Time Dependent Gross–Pitaevskii Equation in Two Dimensions.” Communications in Mathematical Physics, vol. 372, no. 1, Springer Nature, 2019, pp. 1–69, doi:10.1007/s00220-019-03599-x. short: M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics 372 (2019) 1–69. date_created: 2019-11-25T08:08:02Z date_published: 2019-11-08T00:00:00Z date_updated: 2023-09-06T10:47:43Z day: '08' ddc: - '510' department: - _id: RoSe doi: 10.1007/s00220-019-03599-x ec_funded: 1 external_id: isi: - '000495193700002' file: - access_level: open_access checksum: cd283b475dd739e04655315abd46f528 content_type: application/pdf creator: dernst date_created: 2019-11-25T08:11:11Z date_updated: 2020-07-14T12:47:49Z file_id: '7101' file_name: 2019_CommMathPhys_Jeblick.pdf file_size: 884469 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' intvolume: ' 372' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1-69 project: - _id: 25C6DC12-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '694227' name: Analysis of quantum many-body systems - _id: B67AFEDC-15C9-11EA-A837-991A96BB2854 name: IST Austria Open Access Fund publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Derivation of the time dependent Gross–Pitaevskii equation in two dimensions 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: 372 year: '2019' ... --- _id: '7106' abstract: - lang: eng text: PIN-FORMED (PIN) transporters mediate directional, intercellular movement of the phytohormone auxin in land plants. To elucidate the evolutionary origins of this developmentally crucial mechanism, we analysed the single PIN homologue of a simple green alga Klebsormidium flaccidum. KfPIN functions as a plasma membrane-localized auxin exporter in land plants and heterologous models. While its role in algae remains unclear, PIN-driven auxin export is probably an ancient and conserved trait within streptophytes. article_processing_charge: No article_type: original author: - first_name: Roman full_name: Skokan, Roman last_name: Skokan - first_name: Eva full_name: Medvecká, Eva last_name: Medvecká - first_name: Tom full_name: Viaene, Tom last_name: Viaene - first_name: Stanislav full_name: Vosolsobě, Stanislav last_name: Vosolsobě - first_name: Marta full_name: Zwiewka, Marta last_name: Zwiewka - first_name: Karel full_name: Müller, Karel last_name: Müller - first_name: Petr full_name: Skůpa, Petr last_name: Skůpa - first_name: Michal full_name: Karady, Michal last_name: Karady - first_name: Yuzhou full_name: Zhang, Yuzhou last_name: Zhang - first_name: Dorina P. full_name: Janacek, Dorina P. last_name: Janacek - first_name: Ulrich Z. full_name: Hammes, Ulrich Z. last_name: Hammes - first_name: Karin full_name: Ljung, Karin last_name: Ljung - first_name: Tomasz full_name: Nodzyński, Tomasz last_name: Nodzyński - first_name: Jan full_name: Petrášek, Jan last_name: Petrášek - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Skokan R, Medvecká E, Viaene T, et al. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 2019;5(11):1114-1119. doi:10.1038/s41477-019-0542-5 apa: Skokan, R., Medvecká, E., Viaene, T., Vosolsobě, S., Zwiewka, M., Müller, K., … Friml, J. (2019). PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. Springer Nature. https://doi.org/10.1038/s41477-019-0542-5 chicago: Skokan, Roman, Eva Medvecká, Tom Viaene, Stanislav Vosolsobě, Marta Zwiewka, Karel Müller, Petr Skůpa, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants. Springer Nature, 2019. https://doi.org/10.1038/s41477-019-0542-5. ieee: R. Skokan et al., “PIN-driven auxin transport emerged early in streptophyte evolution,” Nature Plants, vol. 5, no. 11. Springer Nature, pp. 1114–1119, 2019. ista: Skokan R, Medvecká E, Viaene T, Vosolsobě S, Zwiewka M, Müller K, Skůpa P, Karady M, Zhang Y, Janacek DP, Hammes UZ, Ljung K, Nodzyński T, Petrášek J, Friml J. 2019. PIN-driven auxin transport emerged early in streptophyte evolution. Nature Plants. 5(11), 1114–1119. mla: Skokan, Roman, et al. “PIN-Driven Auxin Transport Emerged Early in Streptophyte Evolution.” Nature Plants, vol. 5, no. 11, Springer Nature, 2019, pp. 1114–19, doi:10.1038/s41477-019-0542-5. short: R. Skokan, E. Medvecká, T. Viaene, S. Vosolsobě, M. Zwiewka, K. Müller, P. Skůpa, M. Karady, Y. Zhang, D.P. Janacek, U.Z. Hammes, K. Ljung, T. Nodzyński, J. Petrášek, J. Friml, Nature Plants 5 (2019) 1114–1119. date_created: 2019-11-25T09:08:04Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-09-06T11:09:49Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1038/s41477-019-0542-5 ec_funded: 1 external_id: isi: - '000496526100010' pmid: - '31712756' file: - access_level: open_access checksum: 94e0426856aad9a9bd0135d5436efbf1 content_type: application/pdf creator: dernst date_created: 2020-10-14T08:54:49Z date_updated: 2020-10-14T08:54:49Z file_id: '8660' file_name: 2019_NaturePlants_Skokan_accepted.pdf file_size: 1980851 relation: main_file success: 1 file_date_updated: 2020-10-14T08:54:49Z has_accepted_license: '1' intvolume: ' 5' isi: 1 issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Submitted Version page: 1114-1119 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: Nature Plants publication_identifier: issn: - 2055-0278 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: PIN-driven auxin transport emerged early in streptophyte evolution type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 5 year: '2019' ... --- _id: '7105' abstract: - lang: eng text: Cell migration is hypothesized to involve a cycle of behaviours beginning with leading edge extension. However, recent evidence suggests that the leading edge may be dispensable for migration, raising the question of what actually controls cell directionality. Here, we exploit the embryonic migration of Drosophila macrophages to bridge the different temporal scales of the behaviours controlling motility. This approach reveals that edge fluctuations during random motility are not persistent and are weakly correlated with motion. In contrast, flow of the actin network behind the leading edge is highly persistent. Quantification of actin flow structure during migration reveals a stable organization and asymmetry in the cell-wide flowfield that strongly correlates with cell directionality. This organization is regulated by a gradient of actin network compression and destruction, which is controlled by myosin contraction and cofilin-mediated disassembly. It is this stable actin-flow polarity, which integrates rapid fluctuations of the leading edge, that controls inherent cellular persistence. article_processing_charge: No article_type: original author: - first_name: Lawrence full_name: Yolland, Lawrence last_name: Yolland - first_name: Mubarik full_name: Burki, Mubarik last_name: Burki - first_name: Stefania full_name: Marcotti, Stefania last_name: Marcotti - first_name: Andrei full_name: Luchici, Andrei last_name: Luchici - first_name: Fiona N. full_name: Kenny, Fiona N. last_name: Kenny - first_name: John Robert full_name: Davis, John Robert last_name: Davis - first_name: Eduardo full_name: Serna-Morales, Eduardo last_name: Serna-Morales - first_name: Jan full_name: Müller, Jan id: AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D last_name: Müller - first_name: Michael K full_name: Sixt, Michael K id: 41E9FBEA-F248-11E8-B48F-1D18A9856A87 last_name: Sixt orcid: 0000-0002-6620-9179 - first_name: Andrew full_name: Davidson, Andrew last_name: Davidson - first_name: Will full_name: Wood, Will last_name: Wood - first_name: Linus J. full_name: Schumacher, Linus J. last_name: Schumacher - first_name: Robert G. full_name: Endres, Robert G. last_name: Endres - first_name: Mark full_name: Miodownik, Mark last_name: Miodownik - first_name: Brian M. full_name: Stramer, Brian M. last_name: Stramer citation: ama: Yolland L, Burki M, Marcotti S, et al. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 2019;21(11):1370-1381. doi:10.1038/s41556-019-0411-5 apa: Yolland, L., Burki, M., Marcotti, S., Luchici, A., Kenny, F. N., Davis, J. R., … Stramer, B. M. (2019). Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. Springer Nature. https://doi.org/10.1038/s41556-019-0411-5 chicago: Yolland, Lawrence, Mubarik Burki, Stefania Marcotti, Andrei Luchici, Fiona N. Kenny, John Robert Davis, Eduardo Serna-Morales, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41556-019-0411-5. ieee: L. Yolland et al., “Persistent and polarized global actin flow is essential for directionality during cell migration,” Nature Cell Biology, vol. 21, no. 11. Springer Nature, pp. 1370–1381, 2019. ista: Yolland L, Burki M, Marcotti S, Luchici A, Kenny FN, Davis JR, Serna-Morales E, Müller J, Sixt MK, Davidson A, Wood W, Schumacher LJ, Endres RG, Miodownik M, Stramer BM. 2019. Persistent and polarized global actin flow is essential for directionality during cell migration. Nature Cell Biology. 21(11), 1370–1381. mla: Yolland, Lawrence, et al. “Persistent and Polarized Global Actin Flow Is Essential for Directionality during Cell Migration.” Nature Cell Biology, vol. 21, no. 11, Springer Nature, 2019, pp. 1370–81, doi:10.1038/s41556-019-0411-5. short: L. Yolland, M. Burki, S. Marcotti, A. Luchici, F.N. Kenny, J.R. Davis, E. Serna-Morales, J. Müller, M.K. Sixt, A. Davidson, W. Wood, L.J. Schumacher, R.G. Endres, M. Miodownik, B.M. Stramer, Nature Cell Biology 21 (2019) 1370–1381. date_created: 2019-11-25T08:55:00Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-09-06T11:08:52Z day: '01' department: - _id: MiSi doi: 10.1038/s41556-019-0411-5 external_id: isi: - '000495888300009' pmid: - '31685997' intvolume: ' 21' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7025891 month: '11' oa: 1 oa_version: Submitted Version page: 1370-1381 pmid: 1 publication: Nature Cell Biology publication_identifier: eissn: - 1476-4679 issn: - 1465-7392 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Persistent and polarized global actin flow is essential for directionality during cell migration type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 21 year: '2019' ... --- _id: '7109' abstract: - lang: eng text: We show how to construct temporal testers for the logic MITL, a prominent linear-time logic for real-time systems. A temporal tester is a transducer that inputs a signal holding the Boolean value of atomic propositions and outputs the truth value of a formula along time. Here we consider testers over continuous-time Boolean signals that use clock variables to enforce duration constraints, as in timed automata. We first rewrite the MITL formula into a “simple” formula using a limited set of temporal modalities. We then build testers for these specific modalities and show how to compose testers for simple formulae into complex ones. Temporal testers can be turned into acceptors, yielding a compositional translation from MITL to timed automata. This construction is much simpler than previously known and remains asymptotically optimal. It supports both past and future operators and can easily be extended. article_number: '19' article_processing_charge: No article_type: original author: - first_name: Thomas full_name: Ferrere, Thomas id: 40960E6E-F248-11E8-B48F-1D18A9856A87 last_name: Ferrere orcid: 0000-0001-5199-3143 - first_name: Oded full_name: Maler, Oded last_name: Maler - first_name: Dejan full_name: Ničković, Dejan last_name: Ničković - first_name: Amir full_name: Pnueli, Amir last_name: Pnueli citation: ama: Ferrere T, Maler O, Ničković D, Pnueli A. From real-time logic to timed automata. Journal of the ACM. 2019;66(3). doi:10.1145/3286976 apa: Ferrere, T., Maler, O., Ničković, D., & Pnueli, A. (2019). From real-time logic to timed automata. Journal of the ACM. ACM. https://doi.org/10.1145/3286976 chicago: Ferrere, Thomas, Oded Maler, Dejan Ničković, and Amir Pnueli. “From Real-Time Logic to Timed Automata.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3286976. ieee: T. Ferrere, O. Maler, D. Ničković, and A. Pnueli, “From real-time logic to timed automata,” Journal of the ACM, vol. 66, no. 3. ACM, 2019. ista: Ferrere T, Maler O, Ničković D, Pnueli A. 2019. From real-time logic to timed automata. Journal of the ACM. 66(3), 19. mla: Ferrere, Thomas, et al. “From Real-Time Logic to Timed Automata.” Journal of the ACM, vol. 66, no. 3, 19, ACM, 2019, doi:10.1145/3286976. short: T. Ferrere, O. Maler, D. Ničković, A. Pnueli, Journal of the ACM 66 (2019). date_created: 2019-11-26T10:22:32Z date_published: 2019-05-01T00:00:00Z date_updated: 2023-09-06T11:11:56Z day: '01' department: - _id: ToHe doi: 10.1145/3286976 external_id: isi: - '000495406300005' intvolume: ' 66' isi: 1 issue: '3' language: - iso: eng month: '05' oa_version: None 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: Journal of the ACM publication_identifier: issn: - 0004-5411 publication_status: published publisher: ACM quality_controlled: '1' scopus_import: '1' status: public title: From real-time logic to timed automata type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 66 year: '2019' ... --- _id: '7108' abstract: - lang: eng text: We prove that for every d ≥ 2, deciding if a pure, d-dimensional, simplicial complex is shellable is NP-hard, hence NP-complete. This resolves a question raised, e.g., by Danaraj and Klee in 1978. Our reduction also yields that for every d ≥ 2 and k ≥ 0, deciding if a pure, d-dimensional, simplicial complex is k-decomposable is NP-hard. For d ≥ 3, both problems remain NP-hard when restricted to contractible pure d-dimensional complexes. Another simple corollary of our result is that it is NP-hard to decide whether a given poset is CL-shellable. article_number: '21' article_processing_charge: No article_type: original author: - first_name: Xavier full_name: Goaoc, Xavier last_name: Goaoc - first_name: Pavel full_name: Patak, Pavel id: B593B804-1035-11EA-B4F1-947645A5BB83 last_name: Patak - first_name: Zuzana full_name: Patakova, Zuzana id: 48B57058-F248-11E8-B48F-1D18A9856A87 last_name: Patakova orcid: 0000-0002-3975-1683 - first_name: Martin full_name: Tancer, Martin last_name: Tancer - first_name: Uli full_name: Wagner, Uli id: 36690CA2-F248-11E8-B48F-1D18A9856A87 last_name: Wagner orcid: 0000-0002-1494-0568 citation: ama: Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. Shellability is NP-complete. Journal of the ACM. 2019;66(3). doi:10.1145/3314024 apa: Goaoc, X., Patak, P., Patakova, Z., Tancer, M., & Wagner, U. (2019). Shellability is NP-complete. Journal of the ACM. ACM. https://doi.org/10.1145/3314024 chicago: Goaoc, Xavier, Pavel Patak, Zuzana Patakova, Martin Tancer, and Uli Wagner. “Shellability Is NP-Complete.” Journal of the ACM. ACM, 2019. https://doi.org/10.1145/3314024. ieee: X. Goaoc, P. Patak, Z. Patakova, M. Tancer, and U. Wagner, “Shellability is NP-complete,” Journal of the ACM, vol. 66, no. 3. ACM, 2019. ista: Goaoc X, Patak P, Patakova Z, Tancer M, Wagner U. 2019. Shellability is NP-complete. Journal of the ACM. 66(3), 21. mla: Goaoc, Xavier, et al. “Shellability Is NP-Complete.” Journal of the ACM, vol. 66, no. 3, 21, ACM, 2019, doi:10.1145/3314024. short: X. Goaoc, P. Patak, Z. Patakova, M. Tancer, U. Wagner, Journal of the ACM 66 (2019). date_created: 2019-11-26T10:13:59Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-06T11:10:58Z day: '01' department: - _id: UlWa doi: 10.1145/3314024 external_id: arxiv: - '1711.08436' isi: - '000495406300007' intvolume: ' 66' isi: 1 issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/pdf/1711.08436.pdf month: '06' oa: 1 oa_version: Preprint publication: Journal of the ACM publication_identifier: issn: - 0004-5411 publication_status: published publisher: ACM quality_controlled: '1' related_material: record: - id: '184' relation: earlier_version status: public scopus_import: '1' status: public title: Shellability is NP-complete type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 66 year: '2019' ... --- _id: '7147' abstract: - lang: eng text: "The expression of a gene is characterised by its transcription factors and the function processing them. If the transcription factors are not affected by gene products, the regulating function is often represented as a combinational logic circuit, where the outputs (product) are determined by current input values (transcription factors) only, and are hence independent on their relative arrival times. However, the simultaneous arrival of transcription factors (TFs) in genetic circuits is a strong assumption, given that the processes of transcription and translation of a gene into a protein introduce intrinsic time delays and that there is no global synchronisation among the arrival times of different molecular species at molecular targets.\r\n\r\nIn this paper, we construct an experimentally implementable genetic circuit with two inputs and a single output, such that, in presence of small delays in input arrival, the circuit exhibits qualitatively distinct observable phenotypes. In particular, these phenotypes are long lived transients: they all converge to a single value, but so slowly, that they seem stable for an extended time period, longer than typical experiment duration. We used rule-based language to prototype our circuit, and we implemented a search for finding the parameter combinations raising the phenotypes of interest.\r\n\r\nThe behaviour of our prototype circuit has wide implications. First, it suggests that GRNs can exploit event timing to create phenotypes. Second, it opens the possibility that GRNs are using event timing to react to stimuli and memorise events, without explicit feedback in regulation. From the modelling perspective, our prototype circuit demonstrates the critical importance of analysing the transient dynamics at the promoter binding sites of the DNA, before applying rapid equilibrium assumptions." alternative_title: - LNCS article_processing_charge: No author: - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Claudia full_name: Igler, Claudia id: 46613666-F248-11E8-B48F-1D18A9856A87 last_name: Igler - first_name: Tatjana full_name: Petrov, Tatjana id: 3D5811FC-F248-11E8-B48F-1D18A9856A87 last_name: Petrov orcid: 0000-0002-9041-0905 - first_name: Ali full_name: Sezgin, Ali id: 4C7638DA-F248-11E8-B48F-1D18A9856A87 last_name: Sezgin citation: ama: 'Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. Transient memory in gene regulation. In: 17th International Conference on Computational Methods in Systems Biology. Vol 11773. Springer Nature; 2019:155-187. doi:10.1007/978-3-030-31304-3_9' apa: 'Guet, C. C., Henzinger, T. A., Igler, C., Petrov, T., & Sezgin, A. (2019). Transient memory in gene regulation. In 17th International Conference on Computational Methods in Systems Biology (Vol. 11773, pp. 155–187). Trieste, Italy: Springer Nature. https://doi.org/10.1007/978-3-030-31304-3_9' chicago: Guet, Calin C, Thomas A Henzinger, Claudia Igler, Tatjana Petrov, and Ali Sezgin. “Transient Memory in Gene Regulation.” In 17th International Conference on Computational Methods in Systems Biology, 11773:155–87. Springer Nature, 2019. https://doi.org/10.1007/978-3-030-31304-3_9. ieee: C. C. Guet, T. A. Henzinger, C. Igler, T. Petrov, and A. Sezgin, “Transient memory in gene regulation,” in 17th International Conference on Computational Methods in Systems Biology, Trieste, Italy, 2019, vol. 11773, pp. 155–187. ista: 'Guet CC, Henzinger TA, Igler C, Petrov T, Sezgin A. 2019. Transient memory in gene regulation. 17th International Conference on Computational Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNCS, vol. 11773, 155–187.' mla: Guet, Calin C., et al. “Transient Memory in Gene Regulation.” 17th International Conference on Computational Methods in Systems Biology, vol. 11773, Springer Nature, 2019, pp. 155–87, doi:10.1007/978-3-030-31304-3_9. short: C.C. Guet, T.A. Henzinger, C. Igler, T. Petrov, A. Sezgin, in:, 17th International Conference on Computational Methods in Systems Biology, Springer Nature, 2019, pp. 155–187. conference: end_date: 2019-09-20 location: Trieste, Italy name: 'CMSB: Computational Methods in Systems Biology' start_date: 2019-09-18 date_created: 2019-12-04T16:07:50Z date_published: 2019-09-17T00:00:00Z date_updated: 2023-09-06T11:18:08Z day: '17' department: - _id: CaGu - _id: ToHe doi: 10.1007/978-3-030-31304-3_9 external_id: isi: - '000557875100009' intvolume: ' 11773' isi: 1 language: - iso: eng month: '09' oa_version: None page: 155-187 project: - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 251EE76E-B435-11E9-9278-68D0E5697425 grant_number: '24573' name: Design principles underlying genetic switch architecture publication: 17th International Conference on Computational Methods in Systems Biology publication_identifier: eissn: - 1611-3349 isbn: - '9783030313036' - '9783030313043' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Transient memory in gene regulation type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 11773 year: '2019' ... --- _id: '7136' abstract: - lang: eng text: "It is well established that the notion of min-entropy fails to satisfy the \\emph{chain rule} of the form H(X,Y)=H(X|Y)+H(Y), known for Shannon Entropy. Such a property would help to analyze how min-entropy is split among smaller blocks. Problems of this kind arise for example when constructing extractors and dispersers.\r\nWe show that any sequence of variables exhibits a very strong strong block-source structure (conditional distributions of blocks are nearly flat) when we \\emph{spoil few correlated bits}. This implies, conditioned on the spoiled bits, that \\emph{splitting-recombination properties} hold. In particular, we have many nice properties that min-entropy doesn't obey in general, for example strong chain rules, \"information can't hurt\" inequalities, equivalences of average and worst-case conditional entropy definitions and others. Quantitatively, for any sequence X1,…,Xt of random variables over an alphabet X we prove that, when conditioned on m=t⋅O(loglog|X|+loglog(1/ϵ)+logt) bits of auxiliary information, all conditional distributions of the form Xi|X2019 IEEE International Symposium on Information Theory. IEEE; 2019. doi:10.1109/isit.2019.8849240' apa: 'Skórski, M. (2019). Strong chain rules for min-entropy under few bits spoiled. In 2019 IEEE International Symposium on Information Theory. Paris, France: IEEE. https://doi.org/10.1109/isit.2019.8849240' chicago: Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” In 2019 IEEE International Symposium on Information Theory. IEEE, 2019. https://doi.org/10.1109/isit.2019.8849240. ieee: M. Skórski, “Strong chain rules for min-entropy under few bits spoiled,” in 2019 IEEE International Symposium on Information Theory, Paris, France, 2019. ista: 'Skórski M. 2019. Strong chain rules for min-entropy under few bits spoiled. 2019 IEEE International Symposium on Information Theory. ISIT: International Symposium on Information Theory, 8849240.' mla: Skórski, Maciej. “Strong Chain Rules for Min-Entropy under Few Bits Spoiled.” 2019 IEEE International Symposium on Information Theory, 8849240, IEEE, 2019, doi:10.1109/isit.2019.8849240. short: M. Skórski, in:, 2019 IEEE International Symposium on Information Theory, IEEE, 2019. conference: end_date: 2019-07-12 location: Paris, France name: 'ISIT: International Symposium on Information Theory' start_date: 2019-07-07 date_created: 2019-11-28T10:19:21Z date_published: 2019-07-01T00:00:00Z date_updated: 2023-09-06T11:15:41Z day: '01' department: - _id: KrPi doi: 10.1109/isit.2019.8849240 external_id: arxiv: - '1702.08476' isi: - '000489100301043' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1702.08476 month: '07' oa: 1 oa_version: Preprint publication: 2019 IEEE International Symposium on Information Theory publication_identifier: isbn: - '9781538692912' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Strong chain rules for min-entropy under few bits spoiled type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '7122' abstract: - lang: eng text: Data-rich applications in machine-learning and control have motivated an intense research on large-scale optimization. Novel algorithms have been proposed and shown to have optimal convergence rates in terms of iteration counts. However, their practical performance is severely degraded by the cost of exchanging high-dimensional gradient vectors between computing nodes. Several gradient compression heuristics have recently been proposed to reduce communications, but few theoretical results exist that quantify how they impact algorithm convergence. This paper establishes and strengthens the convergence guarantees for gradient descent under a family of gradient compression techniques. For convex optimization problems, we derive admissible step sizes and quantify both the number of iterations and the number of bits that need to be exchanged to reach a target accuracy. Finally, we validate the performance of different gradient compression techniques in simulations. The numerical results highlight the properties of different gradient compression algorithms and confirm that fast convergence with limited information exchange is possible. article_number: '8619625' article_processing_charge: No author: - first_name: Sarit full_name: Khirirat, Sarit last_name: Khirirat - first_name: Mikael full_name: Johansson, Mikael last_name: Johansson - 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: 'Khirirat S, Johansson M, Alistarh D-A. Gradient compression for communication-limited convex optimization. In: 2018 IEEE Conference on Decision and Control. IEEE; 2019. doi:10.1109/cdc.2018.8619625' apa: 'Khirirat, S., Johansson, M., & Alistarh, D.-A. (2019). Gradient compression for communication-limited convex optimization. In 2018 IEEE Conference on Decision and Control. Miami Beach, FL, United States: IEEE. https://doi.org/10.1109/cdc.2018.8619625' chicago: Khirirat, Sarit, Mikael Johansson, and Dan-Adrian Alistarh. “Gradient Compression for Communication-Limited Convex Optimization.” In 2018 IEEE Conference on Decision and Control. IEEE, 2019. https://doi.org/10.1109/cdc.2018.8619625. ieee: S. Khirirat, M. Johansson, and D.-A. Alistarh, “Gradient compression for communication-limited convex optimization,” in 2018 IEEE Conference on Decision and Control, Miami Beach, FL, United States, 2019. ista: 'Khirirat S, Johansson M, Alistarh D-A. 2019. Gradient compression for communication-limited convex optimization. 2018 IEEE Conference on Decision and Control. CDC: Conference on Decision and Control, 8619625.' mla: Khirirat, Sarit, et al. “Gradient Compression for Communication-Limited Convex Optimization.” 2018 IEEE Conference on Decision and Control, 8619625, IEEE, 2019, doi:10.1109/cdc.2018.8619625. short: S. Khirirat, M. Johansson, D.-A. Alistarh, in:, 2018 IEEE Conference on Decision and Control, IEEE, 2019. conference: end_date: 2018-12-19 location: Miami Beach, FL, United States name: 'CDC: Conference on Decision and Control' start_date: 2018-12-17 date_created: 2019-11-26T15:07:49Z date_published: 2019-01-21T00:00:00Z date_updated: 2023-09-06T11:14:55Z day: '21' department: - _id: DaAl doi: 10.1109/cdc.2018.8619625 external_id: isi: - '000458114800023' isi: 1 language: - iso: eng month: '01' oa_version: None publication: 2018 IEEE Conference on Decision and Control publication_identifier: isbn: - '9781538613955' issn: - 0743-1546 publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Gradient compression for communication-limited convex optimization type: conference user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2019' ... --- _id: '7146' abstract: - lang: eng text: Prevailing models of sex-chromosome evolution were largely inspired by the stable and highly differentiated XY pairs of model organisms, such as those of mammals and flies. Recent work has uncovered an incredible diversity of sex-determining systems, bringing some of the assumptions of these traditional models into question. One particular question that has arisen is what drives some sex chromosomes to be maintained over millions of years and differentiate fully, while others are replaced by new sex-determining chromosomes before differentiation has occurred. Here, I review recent data on the variability of sex-determining genes and sex chromosomes in different non-model vertebrates and invertebrates, and discuss some theoretical models that have been put forward to account for this diversity. article_processing_charge: No article_type: original author: - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Vicoso B. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. 2019;3(12):1632-1641. doi:10.1038/s41559-019-1050-8 apa: Vicoso, B. (2019). Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. Springer Nature. https://doi.org/10.1038/s41559-019-1050-8 chicago: Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” Nature Ecology & Evolution. Springer Nature, 2019. https://doi.org/10.1038/s41559-019-1050-8. ieee: B. Vicoso, “Molecular and evolutionary dynamics of animal sex-chromosome turnover,” Nature Ecology & Evolution, vol. 3, no. 12. Springer Nature, pp. 1632–1641, 2019. ista: Vicoso B. 2019. Molecular and evolutionary dynamics of animal sex-chromosome turnover. Nature Ecology & Evolution. 3(12), 1632–1641. mla: Vicoso, Beatriz. “Molecular and Evolutionary Dynamics of Animal Sex-Chromosome Turnover.” Nature Ecology & Evolution, vol. 3, no. 12, Springer Nature, 2019, pp. 1632–41, doi:10.1038/s41559-019-1050-8. short: B. Vicoso, Nature Ecology & Evolution 3 (2019) 1632–1641. date_created: 2019-12-04T16:05:25Z date_published: 2019-11-25T00:00:00Z date_updated: 2023-09-06T11:18:59Z day: '25' department: - _id: BeVi doi: 10.1038/s41559-019-1050-8 ec_funded: 1 external_id: isi: - '000500728800009' intvolume: ' 3' isi: 1 issue: '12' language: - iso: eng month: '11' oa_version: None page: 1632-1641 project: - _id: 250BDE62-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715257' name: Prevalence and Influence of Sexual Antagonism on Genome Evolution publication: Nature Ecology & Evolution publication_identifier: issn: - 2397-334X publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Molecular and evolutionary dynamics of animal sex-chromosome turnover type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 3 year: '2019' ... --- _id: '7143' abstract: - lang: eng text: Roots grow downwards parallel to the gravity vector, to anchor a plant in soil and acquire water and nutrients, using a gravitropic mechanism dependent on the asymmetric distribution of the phytohormone auxin. Recently, Chang et al. demonstrate that asymmetric distribution of another phytohormone, cytokinin, directs root growth towards higher water content. article_processing_charge: No article_type: original author: - first_name: Scott A full_name: Sinclair, Scott A id: 2D99FE6A-F248-11E8-B48F-1D18A9856A87 last_name: Sinclair orcid: 0000-0002-4566-0593 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: 'Sinclair SA, Friml J. Defying gravity: a plant’s quest for moisture. Cell Research. 2019;29:965-966. doi:10.1038/s41422-019-0254-4' apa: 'Sinclair, S. A., & Friml, J. (2019). Defying gravity: a plant’s quest for moisture. Cell Research. Springer Nature. https://doi.org/10.1038/s41422-019-0254-4' chicago: 'Sinclair, Scott A, and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research. Springer Nature, 2019. https://doi.org/10.1038/s41422-019-0254-4.' ieee: 'S. A. Sinclair and J. Friml, “Defying gravity: a plant’s quest for moisture,” Cell Research, vol. 29. Springer Nature, pp. 965–966, 2019.' ista: 'Sinclair SA, Friml J. 2019. Defying gravity: a plant’s quest for moisture. Cell Research. 29, 965–966.' mla: 'Sinclair, Scott A., and Jiří Friml. “Defying Gravity: A Plant’s Quest for Moisture.” Cell Research, vol. 29, Springer Nature, 2019, pp. 965–66, doi:10.1038/s41422-019-0254-4.' short: S.A. Sinclair, J. Friml, Cell Research 29 (2019) 965–966. date_created: 2019-12-02T12:30:48Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-09-06T11:20:58Z day: '01' department: - _id: JiFr doi: 10.1038/s41422-019-0254-4 external_id: isi: - '000500749600001' pmid: - '31745287' intvolume: ' 29' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41422-019-0254-4 month: '12' oa: 1 oa_version: Published Version page: 965-966 pmid: 1 publication: Cell Research publication_identifier: eissn: - 1748-7838 issn: - 1001-0602 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: 'Defying gravity: a plant''s quest for moisture' type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 29 year: '2019' ... --- _id: '7156' abstract: - lang: eng text: We propose an efficient microwave-photonic modulator as a resource for stationary entangled microwave-optical fields and develop the theory for deterministic entanglement generation and quantum state transfer in multi-resonant electro-optic systems. The device is based on a single crystal whispering gallery mode resonator integrated into a 3D-microwave cavity. The specific design relies on a new combination of thin-film technology and conventional machining that is optimized for the lowest dissipation rates in the microwave, optical, and mechanical domains. We extract important device properties from finite-element simulations and predict continuous variable entanglement generation rates on the order of a Mebit/s for optical pump powers of only a few tens of microwatts. We compare the quantum state transfer fidelities of coherent, squeezed, and non-Gaussian cat states for both teleportation and direct conversion protocols under realistic conditions. Combining the unique capabilities of circuit quantum electrodynamics with the resilience of fiber optic communication could facilitate long-distance solid-state qubit networks, new methods for quantum signal synthesis, quantum key distribution, and quantum enhanced detection, as well as more power-efficient classical sensing and modulation. article_number: '108' article_processing_charge: No article_type: original author: - first_name: Alfredo R full_name: Rueda Sanchez, Alfredo R id: 3B82B0F8-F248-11E8-B48F-1D18A9856A87 last_name: Rueda Sanchez orcid: 0000-0001-6249-5860 - first_name: William J full_name: Hease, William J id: 29705398-F248-11E8-B48F-1D18A9856A87 last_name: Hease orcid: 0000-0001-9868-2166 - first_name: Shabir full_name: Barzanjeh, Shabir id: 2D25E1F6-F248-11E8-B48F-1D18A9856A87 last_name: Barzanjeh orcid: 0000-0003-0415-1423 - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X citation: ama: Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 2019;5. doi:10.1038/s41534-019-0220-5 apa: Rueda Sanchez, A. R., Hease, W. J., Barzanjeh, S., & Fink, J. M. (2019). Electro-optic entanglement source for microwave to telecom quantum state transfer. Npj Quantum Information. Springer Nature. https://doi.org/10.1038/s41534-019-0220-5 chicago: Rueda Sanchez, Alfredo R, William J Hease, Shabir Barzanjeh, and Johannes M Fink. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information. Springer Nature, 2019. https://doi.org/10.1038/s41534-019-0220-5. ieee: A. R. Rueda Sanchez, W. J. Hease, S. Barzanjeh, and J. M. Fink, “Electro-optic entanglement source for microwave to telecom quantum state transfer,” npj Quantum Information, vol. 5. Springer Nature, 2019. ista: Rueda Sanchez AR, Hease WJ, Barzanjeh S, Fink JM. 2019. Electro-optic entanglement source for microwave to telecom quantum state transfer. npj Quantum Information. 5, 108. mla: Rueda Sanchez, Alfredo R., et al. “Electro-Optic Entanglement Source for Microwave to Telecom Quantum State Transfer.” Npj Quantum Information, vol. 5, 108, Springer Nature, 2019, doi:10.1038/s41534-019-0220-5. short: A.R. Rueda Sanchez, W.J. Hease, S. Barzanjeh, J.M. Fink, Npj Quantum Information 5 (2019). date_created: 2019-12-09T08:18:56Z date_published: 2019-12-01T00:00:00Z date_updated: 2023-09-06T11:22:39Z day: '01' ddc: - '530' department: - _id: JoFi doi: 10.1038/s41534-019-0220-5 ec_funded: 1 external_id: arxiv: - '1909.01470' isi: - '000502996200003' file: - access_level: open_access checksum: 13e0ea1d4f9b5f5710780d9473364f58 content_type: application/pdf creator: dernst date_created: 2019-12-09T08:25:06Z date_updated: 2020-07-14T12:47:50Z file_id: '7157' file_name: 2019_NPJ_Rueda.pdf file_size: 1580132 relation: main_file file_date_updated: 2020-07-14T12:47:50Z has_accepted_license: '1' intvolume: ' 5' isi: 1 language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 26336814-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '758053' name: A Fiber Optic Transceiver for Superconducting Qubits - _id: 258047B6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '707438' name: 'Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics SUPEREOM' - _id: 257EB838-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '732894' name: Hybrid Optomechanical Technologies - _id: 26927A52-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: F07105 name: Integrating superconducting quantum circuits publication: npj Quantum Information publication_identifier: issn: - 2056-6387 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Electro-optic entanglement source for microwave to telecom quantum state transfer 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: 5 year: '2019' ... --- _id: '7165' abstract: - lang: eng text: Cell division, movement and differentiation contribute to pattern formation in developing tissues. This is the case in the vertebrate neural tube, in which neurons differentiate in a characteristic pattern from a highly dynamic proliferating pseudostratified epithelium. To investigate how progenitor proliferation and differentiation affect cell arrangement and growth of the neural tube, we used experimental measurements to develop a mechanical model of the apical surface of the neuroepithelium that incorporates the effect of interkinetic nuclear movement and spatially varying rates of neuronal differentiation. Simulations predict that tissue growth and the shape of lineage-related clones of cells differ with the rate of differentiation. Growth is isotropic in regions of high differentiation, but dorsoventrally biased in regions of low differentiation. This is consistent with experimental observations. The absence of directional signalling in the simulations indicates that global mechanical constraints are sufficient to explain the observed differences in anisotropy. This provides insight into how the tissue growth rate affects cell dynamics and growth anisotropy and opens up possibilities to study the coupling between mechanics, pattern formation and growth in the neural tube. article_number: dev176297 article_processing_charge: No article_type: original author: - first_name: Pilar full_name: Guerrero, Pilar last_name: Guerrero - first_name: Ruben full_name: Perez-Carrasco, Ruben last_name: Perez-Carrasco - first_name: Marcin P full_name: Zagórski, Marcin P id: 343DA0DC-F248-11E8-B48F-1D18A9856A87 last_name: Zagórski orcid: 0000-0001-7896-7762 - first_name: David full_name: Page, David last_name: Page - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 - first_name: James full_name: Briscoe, James last_name: Briscoe - first_name: Karen M. full_name: Page, Karen M. last_name: Page citation: ama: Guerrero P, Perez-Carrasco R, Zagórski MP, et al. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 2019;146(23). doi:10.1242/dev.176297 apa: Guerrero, P., Perez-Carrasco, R., Zagórski, M. P., Page, D., Kicheva, A., Briscoe, J., & Page, K. M. (2019). Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. The Company of Biologists. https://doi.org/10.1242/dev.176297 chicago: Guerrero, Pilar, Ruben Perez-Carrasco, Marcin P Zagórski, David Page, Anna Kicheva, James Briscoe, and Karen M. Page. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development. The Company of Biologists, 2019. https://doi.org/10.1242/dev.176297. ieee: P. Guerrero et al., “Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium,” Development, vol. 146, no. 23. The Company of Biologists, 2019. ista: Guerrero P, Perez-Carrasco R, Zagórski MP, Page D, Kicheva A, Briscoe J, Page KM. 2019. Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium. Development. 146(23), dev176297. mla: Guerrero, Pilar, et al. “Neuronal Differentiation Influences Progenitor Arrangement in the Vertebrate Neuroepithelium.” Development, vol. 146, no. 23, dev176297, The Company of Biologists, 2019, doi:10.1242/dev.176297. short: P. Guerrero, R. Perez-Carrasco, M.P. Zagórski, D. Page, A. Kicheva, J. Briscoe, K.M. Page, Development 146 (2019). date_created: 2019-12-10T14:39:50Z date_published: 2019-12-04T00:00:00Z date_updated: 2023-09-06T11:26:36Z day: '04' ddc: - '570' department: - _id: AnKi doi: 10.1242/dev.176297 ec_funded: 1 external_id: isi: - '000507575700004' pmid: - '31784457' file: - access_level: open_access checksum: b6533c37dc8fbd803ffeca216e0a8b8a content_type: application/pdf creator: dernst date_created: 2019-12-13T07:34:06Z date_updated: 2020-07-14T12:47:50Z file_id: '7177' file_name: 2019_Development_Guerrero.pdf file_size: 7797881 relation: main_file file_date_updated: 2020-07-14T12:47:50Z has_accepted_license: '1' intvolume: ' 146' isi: 1 issue: '23' language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: B6FC0238-B512-11E9-945C-1524E6697425 call_identifier: H2020 grant_number: '680037' name: Coordination of Patterning And Growth In the Spinal Cord publication: Development publication_identifier: eissn: - 1477-9129 issn: - 0950-1991 publication_status: published publisher: The Company of Biologists quality_controlled: '1' scopus_import: '1' status: public title: Neuronal differentiation influences progenitor arrangement in the vertebrate neuroepithelium 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: 146 year: '2019' ...