--- _id: '7026' abstract: - lang: eng text: Effective design of combination therapies requires understanding the changes in cell physiology that result from drug interactions. Here, we show that the genome-wide transcriptional response to combinations of two drugs, measured at a rigorously controlled growth rate, can predict higher-order antagonism with a third drug in Saccharomyces cerevisiae. Using isogrowth profiling, over 90% of the variation in cellular response can be decomposed into three principal components (PCs) that have clear biological interpretations. We demonstrate that the third PC captures emergent transcriptional programs that are dependent on both drugs and can predict antagonism with a third drug targeting the emergent pathway. We further show that emergent gene expression patterns are most pronounced at a drug ratio where the drug interaction is strongest, providing a guideline for future measurements. Our results provide a readily applicable recipe for uncovering emergent responses in other systems and for higher-order drug combinations. A record of this paper’s transparent peer review process is included in the Supplemental Information. acknowledged_ssus: - _id: LifeSc article_processing_charge: No article_type: original author: - first_name: Martin full_name: Lukacisin, Martin id: 298FFE8C-F248-11E8-B48F-1D18A9856A87 last_name: Lukacisin orcid: 0000-0001-6549-4177 - first_name: Tobias full_name: Bollenbach, Tobias id: 3E6DB97A-F248-11E8-B48F-1D18A9856A87 last_name: Bollenbach orcid: 0000-0003-4398-476X citation: ama: Lukacisin M, Bollenbach MT. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 2019;9(5):423-433.e1-e3. doi:10.1016/j.cels.2019.10.004 apa: Lukacisin, M., & Bollenbach, M. T. (2019). Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. Cell Press. https://doi.org/10.1016/j.cels.2019.10.004 chicago: Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems. Cell Press, 2019. https://doi.org/10.1016/j.cels.2019.10.004. ieee: M. Lukacisin and M. T. Bollenbach, “Emergent gene expression responses to drug combinations predict higher-order drug interactions,” Cell Systems, vol. 9, no. 5. Cell Press, pp. 423-433.e1-e3, 2019. ista: Lukacisin M, Bollenbach MT. 2019. Emergent gene expression responses to drug combinations predict higher-order drug interactions. Cell Systems. 9(5), 423-433.e1-e3. mla: Lukacisin, Martin, and Mark Tobias Bollenbach. “Emergent Gene Expression Responses to Drug Combinations Predict Higher-Order Drug Interactions.” Cell Systems, vol. 9, no. 5, Cell Press, 2019, pp. 423-433.e1-e3, doi:10.1016/j.cels.2019.10.004. short: M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 423-433.e1-e3. date_created: 2019-11-15T10:51:42Z date_published: 2019-11-27T00:00:00Z date_updated: 2023-08-30T07:24:58Z day: '27' ddc: - '570' department: - _id: ToBo doi: 10.1016/j.cels.2019.10.004 external_id: isi: - '000499495400003' file: - access_level: open_access checksum: 7a11d6c2f9523d65b049512d61733178 content_type: application/pdf creator: dernst date_created: 2019-11-15T10:57:42Z date_updated: 2020-07-14T12:47:48Z file_id: '7027' file_name: 2019_CellSystems_Lukacisin.pdf file_size: 4238460 relation: main_file file_date_updated: 2020-07-14T12:47:48Z has_accepted_license: '1' intvolume: ' 9' isi: 1 issue: '5' language: - iso: eng license: https://creativecommons.org/licenses/by/4.0/ month: '11' oa: 1 oa_version: Published Version page: 423-433.e1-e3 project: - _id: 25E9AF9E-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P27201-B22 name: Revealing the mechanisms underlying drug interactions - _id: 25EB3A80-B435-11E9-9278-68D0E5697425 grant_number: RGP0042/2013 name: Revealing the fundamental limits of cell growth publication: Cell Systems publication_identifier: issn: - 2405-4712 publication_status: published publisher: Cell Press quality_controlled: '1' scopus_import: '1' status: public title: Emergent gene expression responses to drug combinations predict higher-order drug 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ... --- _id: '7034' abstract: - lang: eng text: We find a graph of genus 5 and its drawing on the orientable surface of genus 4 with every pair of independent edges crossing an even number of times. This shows that the strong Hanani–Tutte theorem cannot be extended to the orientable surface of genus 4. As a base step in the construction we use a counterexample to an extension of the unified Hanani–Tutte theorem on the torus. article_processing_charge: No article_type: original author: - first_name: Radoslav full_name: Fulek, Radoslav id: 39F3FFE4-F248-11E8-B48F-1D18A9856A87 last_name: Fulek orcid: 0000-0001-8485-1774 - first_name: Jan full_name: Kynčl, Jan last_name: Kynčl citation: ama: Fulek R, Kynčl J. Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. 2019;39(6):1267-1279. doi:10.1007/s00493-019-3905-7 apa: Fulek, R., & Kynčl, J. (2019). Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. Springer Nature. https://doi.org/10.1007/s00493-019-3905-7 chicago: Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica. Springer Nature, 2019. https://doi.org/10.1007/s00493-019-3905-7. ieee: R. Fulek and J. Kynčl, “Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4,” Combinatorica, vol. 39, no. 6. Springer Nature, pp. 1267–1279, 2019. ista: Fulek R, Kynčl J. 2019. Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4. Combinatorica. 39(6), 1267–1279. mla: Fulek, Radoslav, and Jan Kynčl. “Counterexample to an Extension of the Hanani-Tutte Theorem on the Surface of Genus 4.” Combinatorica, vol. 39, no. 6, Springer Nature, 2019, pp. 1267–79, doi:10.1007/s00493-019-3905-7. short: R. Fulek, J. Kynčl, Combinatorica 39 (2019) 1267–1279. date_created: 2019-11-18T14:29:50Z date_published: 2019-10-29T00:00:00Z date_updated: 2023-08-30T07:26:25Z day: '29' department: - _id: UlWa doi: 10.1007/s00493-019-3905-7 ec_funded: 1 external_id: arxiv: - '1709.00508' isi: - '000493267200003' intvolume: ' 39' isi: 1 issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1709.00508 month: '10' oa: 1 oa_version: Preprint page: 1267-1279 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 261FA626-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: M02281 name: Eliminating intersections in drawings of graphs publication: Combinatorica publication_identifier: eissn: - 1439-6912 issn: - 0209-9683 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4 type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 39 year: '2019' ... --- _id: '7032' abstract: - lang: eng text: Optical frequency combs (OFCs) are light sources whose spectra consists of equally spaced frequency lines in the optical domain [1]. They have great potential for improving high-capacity data transfer, all-optical atomic clocks, spectroscopy, and high-precision measurements [2]. article_number: '8873300' article_processing_charge: No 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: Florian full_name: Sedlmeir, Florian last_name: Sedlmeir - first_name: Gerd full_name: Leuchs, Gerd last_name: Leuchs - first_name: Madhuri full_name: Kuamri, Madhuri last_name: Kuamri - first_name: Harald G. L. full_name: Schwefel, Harald G. L. last_name: Schwefel citation: ama: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. In: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. IEEE; 2019. doi:10.1109/cleoe-eqec.2019.8873300' apa: 'Rueda Sanchez, A. R., Sedlmeir, F., Leuchs, G., Kuamri, M., & Schwefel, H. G. L. (2019). Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. Munich, Germany: IEEE. https://doi.org/10.1109/cleoe-eqec.2019.8873300' chicago: Rueda Sanchez, Alfredo R, Florian Sedlmeir, Gerd Leuchs, Madhuri Kuamri, and Harald G. L. Schwefel. “Electro-Optic Frequency Comb Generation in Lithium Niobate Whispering Gallery Mode Resonators.” In 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. IEEE, 2019. https://doi.org/10.1109/cleoe-eqec.2019.8873300. ieee: A. R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, and H. G. L. Schwefel, “Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators,” in 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, Munich, Germany, 2019. ista: 'Rueda Sanchez AR, Sedlmeir F, Leuchs G, Kuamri M, Schwefel HGL. 2019. Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators. 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference. CLEO: Conference on Lasers and Electro-Optics Europe, 8873300.' mla: Rueda Sanchez, Alfredo R., et al. “Electro-Optic Frequency Comb Generation in Lithium Niobate Whispering Gallery Mode Resonators.” 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, 8873300, IEEE, 2019, doi:10.1109/cleoe-eqec.2019.8873300. short: A.R. Rueda Sanchez, F. Sedlmeir, G. Leuchs, M. Kuamri, H.G.L. Schwefel, in:, 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference, IEEE, 2019. conference: end_date: 2019-06-27 location: Munich, Germany name: 'CLEO: Conference on Lasers and Electro-Optics Europe' start_date: 2019-06-23 date_created: 2019-11-18T13:58:22Z date_published: 2019-10-17T00:00:00Z date_updated: 2023-08-30T07:26:01Z day: '17' department: - _id: JoFi doi: 10.1109/cleoe-eqec.2019.8873300 external_id: isi: - '000630002701617' isi: 1 language: - iso: eng month: '10' oa_version: None publication: 2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference publication_identifier: isbn: - '9781728104690' publication_status: published publisher: IEEE quality_controlled: '1' scopus_import: '1' status: public title: Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators type: conference user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 year: '2019' ... --- _id: '7095' abstract: - lang: eng text: BAX, a member of the BCL2 gene family, controls the committed step of the intrinsic apoptotic program. Mitochondrial fragmentation is a commonly observed feature of apoptosis, which occurs through the process of mitochondrial fission. BAX has consistently been associated with mitochondrial fission, yet how BAX participates in the process of mitochondrial fragmentation during apoptosis remains to be tested. Time-lapse imaging of BAX recruitment and mitochondrial fragmentation demonstrates that rapid mitochondrial fragmentation during apoptosis occurs after the complete recruitment of BAX to the mitochondrial outer membrane (MOM). The requirement of a fully functioning BAX protein for the fission process was demonstrated further in BAX/BAK-deficient HCT116 cells expressing a P168A mutant of BAX. The mutant performed fusion to restore the mitochondrial network. but was not demonstrably recruited to the MOM after apoptosis induction. Under these conditions, mitochondrial fragmentation was blocked. Additionally, we show that loss of the fission protein, dynamin-like protein 1 (DRP1), does not temporally affect the initiation time or rate of BAX recruitment, but does reduce the final level of BAX recruited to the MOM during the late phase of BAX recruitment. These correlative observations suggest a model where late-stage BAX oligomers play a functional part of the mitochondrial fragmentation machinery in apoptotic cells. article_number: '16565' article_processing_charge: No article_type: original author: - first_name: Margaret E full_name: Maes, Margaret E id: 3838F452-F248-11E8-B48F-1D18A9856A87 last_name: Maes orcid: 0000-0001-9642-1085 - first_name: J. A. full_name: Grosser, J. A. last_name: Grosser - first_name: R. L. full_name: Fehrman, R. L. last_name: Fehrman - first_name: C. L. full_name: Schlamp, C. L. last_name: Schlamp - first_name: R. W. full_name: Nickells, R. W. last_name: Nickells citation: ama: Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 2019;9. doi:10.1038/s41598-019-53049-w apa: Maes, M. E., Grosser, J. A., Fehrman, R. L., Schlamp, C. L., & Nickells, R. W. (2019). Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. Springer Nature. https://doi.org/10.1038/s41598-019-53049-w chicago: Maes, Margaret E, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” Scientific Reports. Springer Nature, 2019. https://doi.org/10.1038/s41598-019-53049-w. ieee: M. E. Maes, J. A. Grosser, R. L. Fehrman, C. L. Schlamp, and R. W. Nickells, “Completion of BAX recruitment correlates with mitochondrial fission during apoptosis,” Scientific Reports, vol. 9. Springer Nature, 2019. ista: Maes ME, Grosser JA, Fehrman RL, Schlamp CL, Nickells RW. 2019. Completion of BAX recruitment correlates with mitochondrial fission during apoptosis. Scientific Reports. 9, 16565. mla: Maes, Margaret E., et al. “Completion of BAX Recruitment Correlates with Mitochondrial Fission during Apoptosis.” Scientific Reports, vol. 9, 16565, Springer Nature, 2019, doi:10.1038/s41598-019-53049-w. short: M.E. Maes, J.A. Grosser, R.L. Fehrman, C.L. Schlamp, R.W. Nickells, Scientific Reports 9 (2019). date_created: 2019-11-25T07:45:17Z date_published: 2019-11-12T00:00:00Z date_updated: 2023-08-30T07:26:54Z day: '12' ddc: - '570' department: - _id: SaSi doi: 10.1038/s41598-019-53049-w external_id: isi: - '000495857600019' pmid: - '31719602' file: - access_level: open_access checksum: 9ab397ed9c1c454b34bffb8cc863d734 content_type: application/pdf creator: dernst date_created: 2019-11-25T07:49:52Z date_updated: 2020-07-14T12:47:49Z file_id: '7096' file_name: 2019_ScientificReports_Maes.pdf file_size: 6467393 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' intvolume: ' 9' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Scientific Reports publication_identifier: eissn: - 2045-2322 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Completion of BAX recruitment correlates with mitochondrial fission during apoptosis 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 9 year: '2019' ... --- _id: '7097' abstract: - lang: eng text: Early endosomes, also called sorting endosomes, are known to mature into late endosomesvia the Rab5-mediated endolysosomal trafficking pathway. Thus, early endosome existence isthought to be maintained by the continual fusion of transport vesicles from the plasmamembrane and thetrans-Golgi network (TGN). Here we show instead that endocytosis isdispensable and post-Golgi vesicle transport is crucial for the formation of endosomes andthe subsequent endolysosomal traffic regulated by yeast Rab5 Vps21p. Fittingly, all threeproteins required for endosomal nucleotide exchange on Vps21p arefirst recruited to theTGN before transport to the endosome, namely the GEF Vps9p and the epsin-relatedadaptors Ent3/5p. The TGN recruitment of these components is distinctly controlled, withVps9p appearing to require the Arf1p GTPase, and the Rab11s, Ypt31p/32p. These resultsprovide a different view of endosome formation and identify the TGN as a critical location forregulating progress through the endolysosomal trafficking pathway. article_number: '419' article_processing_charge: No article_type: original author: - first_name: Makoto full_name: Nagano, Makoto last_name: Nagano - first_name: Junko Y. full_name: Toshima, Junko Y. last_name: Toshima - first_name: Daria E full_name: Siekhaus, Daria E id: 3D224B9E-F248-11E8-B48F-1D18A9856A87 last_name: Siekhaus orcid: 0000-0001-8323-8353 - first_name: Jiro full_name: Toshima, Jiro last_name: Toshima citation: ama: Nagano M, Toshima JY, Siekhaus DE, Toshima J. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2019;2(1). doi:10.1038/s42003-019-0670-5 apa: Nagano, M., Toshima, J. Y., Siekhaus, D. E., & Toshima, J. (2019). Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. Springer Nature. https://doi.org/10.1038/s42003-019-0670-5 chicago: Nagano, Makoto, Junko Y. Toshima, Daria E Siekhaus, and Jiro Toshima. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications Biology. Springer Nature, 2019. https://doi.org/10.1038/s42003-019-0670-5. ieee: M. Nagano, J. Y. Toshima, D. E. Siekhaus, and J. Toshima, “Rab5-mediated endosome formation is regulated at the trans-Golgi network,” Communications Biology, vol. 2, no. 1. Springer Nature, 2019. ista: Nagano M, Toshima JY, Siekhaus DE, Toshima J. 2019. Rab5-mediated endosome formation is regulated at the trans-Golgi network. Communications Biology. 2(1), 419. mla: Nagano, Makoto, et al. “Rab5-Mediated Endosome Formation Is Regulated at the Trans-Golgi Network.” Communications Biology, vol. 2, no. 1, 419, Springer Nature, 2019, doi:10.1038/s42003-019-0670-5. short: M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology 2 (2019). date_created: 2019-11-25T07:55:01Z date_published: 2019-11-15T00:00:00Z date_updated: 2023-08-30T07:27:55Z day: '15' ddc: - '570' department: - _id: DaSi doi: 10.1038/s42003-019-0670-5 external_id: isi: - '000496767800005' file: - access_level: open_access checksum: c63c69a264fc8a0e52f2b0d482f3bdae content_type: application/pdf creator: dernst date_created: 2019-11-25T07:58:05Z date_updated: 2020-07-14T12:47:49Z file_id: '7098' file_name: 2019_CommunicBiology_Nagano.pdf file_size: 2626069 relation: main_file file_date_updated: 2020-07-14T12:47:49Z has_accepted_license: '1' intvolume: ' 2' isi: 1 issue: '1' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Communications Biology publication_identifier: issn: - 2399-3642 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Rab5-mediated endosome formation is regulated at the trans-Golgi network 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: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 2 year: '2019' ... --- _id: '7099' acknowledgement: "The authors thank Gabi Schmid for excellent technical support. We also thank\r\nDr. H. Harada, Dr. W. Kaufmann, and Dr. B. Kapelari for testing the specificity\r\nof some of the antibodies used in this study on replicas. Funding was provided\r\nby the Austrian Science Fund (Fonds zur Fo¨ rderung der Wissenschaftlichen\r\nForschung) Sonderforschungsbereich grants F44-17 (to F.jF.), F44-10 and\r\nP25375-B24 (to N.S.), and P26680 (to G.S.) and by the Novartis Research\r\nFoundation and the Swiss National Science Foundation (to A.L). We also thank\r\nProf. M. Capogna for reading a previous version of the manuscript." article_processing_charge: No article_type: original author: - first_name: Yu full_name: Kasugai, Yu last_name: Kasugai - first_name: Elisabeth full_name: Vogel, Elisabeth last_name: Vogel - first_name: Heide full_name: Hörtnagl, Heide last_name: Hörtnagl - first_name: Sabine full_name: Schönherr, Sabine last_name: Schönherr - first_name: Enrica full_name: Paradiso, Enrica last_name: Paradiso - first_name: Markus full_name: Hauschild, Markus last_name: Hauschild - first_name: Georg full_name: Göbel, Georg last_name: Göbel - first_name: Ivan full_name: Milenkovic, Ivan last_name: Milenkovic - first_name: Yvan full_name: Peterschmitt, Yvan last_name: Peterschmitt - first_name: Ramon full_name: Tasan, Ramon last_name: Tasan - first_name: Günther full_name: Sperk, Günther last_name: Sperk - first_name: Ryuichi full_name: Shigemoto, Ryuichi id: 499F3ABC-F248-11E8-B48F-1D18A9856A87 last_name: Shigemoto orcid: 0000-0001-8761-9444 - first_name: Werner full_name: Sieghart, Werner last_name: Sieghart - first_name: Nicolas full_name: Singewald, Nicolas last_name: Singewald - first_name: Andreas full_name: Lüthi, Andreas last_name: Lüthi - first_name: Francesco full_name: Ferraguti, Francesco last_name: Ferraguti citation: ama: Kasugai Y, Vogel E, Hörtnagl H, et al. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 2019;104(4):781-794.e4. doi:10.1016/j.neuron.2019.08.013 apa: Kasugai, Y., Vogel, E., Hörtnagl, H., Schönherr, S., Paradiso, E., Hauschild, M., … Ferraguti, F. (2019). Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. Elsevier. https://doi.org/10.1016/j.neuron.2019.08.013 chicago: Kasugai, Yu, Elisabeth Vogel, Heide Hörtnagl, Sabine Schönherr, Enrica Paradiso, Markus Hauschild, Georg Göbel, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” Neuron. Elsevier, 2019. https://doi.org/10.1016/j.neuron.2019.08.013. ieee: Y. Kasugai et al., “Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning,” Neuron, vol. 104, no. 4. Elsevier, p. 781–794.e4, 2019. ista: Kasugai Y, Vogel E, Hörtnagl H, Schönherr S, Paradiso E, Hauschild M, Göbel G, Milenkovic I, Peterschmitt Y, Tasan R, Sperk G, Shigemoto R, Sieghart W, Singewald N, Lüthi A, Ferraguti F. 2019. Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning. Neuron. 104(4), 781–794.e4. mla: Kasugai, Yu, et al. “Structural and Functional Remodeling of Amygdala GABAergic Synapses in Associative Fear Learning.” Neuron, vol. 104, no. 4, Elsevier, 2019, p. 781–794.e4, doi:10.1016/j.neuron.2019.08.013. short: Y. Kasugai, E. Vogel, H. Hörtnagl, S. Schönherr, E. Paradiso, M. Hauschild, G. Göbel, I. Milenkovic, Y. Peterschmitt, R. Tasan, G. Sperk, R. Shigemoto, W. Sieghart, N. Singewald, A. Lüthi, F. Ferraguti, Neuron 104 (2019) 781–794.e4. date_created: 2019-11-25T08:02:39Z date_published: 2019-11-20T00:00:00Z date_updated: 2023-08-30T07:28:22Z day: '20' ddc: - '571' - '599' department: - _id: RySh doi: 10.1016/j.neuron.2019.08.013 external_id: isi: - '000497963500017' pmid: - '31543297' has_accepted_license: '1' intvolume: ' 104' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.neuron.2019.08.013 month: '11' oa: 1 oa_version: Published Version page: 781-794.e4 pmid: 1 publication: Neuron publication_identifier: issn: - 0896-6273 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 104 year: '2019' ... --- _id: '6455' abstract: - lang: eng text: During corticogenesis, distinct subtypes of neurons are sequentially born from ventricular zone progenitors. How these cells are molecularly temporally patterned is poorly understood. We used single-cell RNA sequencing at high temporal resolution to trace the lineage of the molecular identities of successive generations of apical progenitors (APs) and their daughter neurons in mouse embryos. We identified a core set of evolutionarily conserved, temporally patterned genes that drive APs from internally driven to more exteroceptive states. We found that the Polycomb repressor complex 2 (PRC2) epigenetically regulates AP temporal progression. Embryonic age–dependent AP molecular states are transmitted to their progeny as successive ground states, onto which essentially conserved early postmitotic differentiation programs are applied, and are complemented by later-occurring environment-dependent signals. Thus, epigenetically regulated temporal molecular birthmarks present in progenitors act in their postmitotic progeny to seed adult neuronal diversity. article_number: eaav2522 article_processing_charge: No article_type: original author: - first_name: L full_name: Telley, L last_name: Telley - first_name: G full_name: Agirman, G last_name: Agirman - first_name: J full_name: Prados, J last_name: Prados - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: S full_name: Fièvre, S last_name: Fièvre - first_name: P full_name: Oberst, P last_name: Oberst - first_name: G full_name: Bartolini, G last_name: Bartolini - first_name: I full_name: Vitali, I last_name: Vitali - first_name: C full_name: Cadilhac, C last_name: Cadilhac - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: L full_name: Nguyen, L last_name: Nguyen - first_name: A full_name: Dayer, A last_name: Dayer - first_name: D full_name: Jabaudon, D last_name: Jabaudon citation: ama: Telley L, Agirman G, Prados J, et al. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 2019;364(6440). doi:10.1126/science.aav2522 apa: Telley, L., Agirman, G., Prados, J., Amberg, N., Fièvre, S., Oberst, P., … Jabaudon, D. (2019). Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. AAAS. https://doi.org/10.1126/science.aav2522 chicago: Telley, L, G Agirman, J Prados, Nicole Amberg, S Fièvre, P Oberst, G Bartolini, et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” Science. AAAS, 2019. https://doi.org/10.1126/science.aav2522. ieee: L. Telley et al., “Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex,” Science, vol. 364, no. 6440. AAAS, 2019. ista: Telley L, Agirman G, Prados J, Amberg N, Fièvre S, Oberst P, Bartolini G, Vitali I, Cadilhac C, Hippenmeyer S, Nguyen L, Dayer A, Jabaudon D. 2019. Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex. Science. 364(6440), eaav2522. mla: Telley, L., et al. “Temporal Patterning of Apical Progenitors and Their Daughter Neurons in the Developing Neocortex.” Science, vol. 364, no. 6440, eaav2522, AAAS, 2019, doi:10.1126/science.aav2522. short: L. Telley, G. Agirman, J. Prados, N. Amberg, S. Fièvre, P. Oberst, G. Bartolini, I. Vitali, C. Cadilhac, S. Hippenmeyer, L. Nguyen, A. Dayer, D. Jabaudon, Science 364 (2019). date_created: 2019-05-14T13:07:47Z date_published: 2019-05-10T00:00:00Z date_updated: 2023-09-05T11:51:09Z day: '10' department: - _id: SiHi doi: 10.1126/science.aav2522 ec_funded: 1 external_id: isi: - '000467631800034' pmid: - '31073041' intvolume: ' 364' isi: 1 issue: '6440' language: - iso: eng main_file_link: - open_access: '1' url: https://orbi.uliege.be/bitstream/2268/239604/1/Telley_Agirman_Science2019.pdf month: '05' oa: 1 oa_version: Published Version 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 - _id: 268F8446-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: T0101031 name: Role of Eed in neural stem cell lineage progression publication: Science publication_identifier: eissn: - 1095-9203 issn: - 0036-8075 publication_status: published publisher: AAAS quality_controlled: '1' related_material: link: - description: News on IST Homepage relation: press_release url: https://ist.ac.at/en/news/how-to-generate-a-brain-of-correct-size-and-composition/ scopus_import: '1' status: public title: Temporal patterning of apical progenitors and their daughter neurons in the developing neocortex type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 364 year: '2019' ... --- _id: '6586' abstract: - lang: eng text: The bottom-up assembly of colloidal nanocrystals is a versatile methodology to produce composite nanomaterials with precisely tuned electronic properties. Beyond the synthetic control over crystal domain size, shape, crystal phase, and composition, solution-processed nanocrystals allow exquisite surface engineering. This provides additional means to modulate the nanomaterial characteristics and particularly its electronic transport properties. For instance, inorganic surface ligands can be used to tune the type and concentration of majority carriers or to modify the electronic band structure. Herein, we report the thermoelectric properties of SnTe nanocomposites obtained from the consolidation of surface-engineered SnTe nanocrystals into macroscopic pellets. A CdSe-based ligand is selected to (i) converge the light and heavy bands through partial Cd alloying and (ii) generate CdSe nanoinclusions as a secondary phase within the SnTe matrix, thereby reducing the thermal conductivity. These SnTe-CdSe nanocomposites possess thermoelectric figures of merit of up to 1.3 at 850 K, which is, to the best of our knowledge, the highest thermoelectric figure of merit reported for solution-processed SnTe. article_processing_charge: No article_type: original author: - first_name: Maria full_name: Ibáñez, Maria id: 43C61214-F248-11E8-B48F-1D18A9856A87 last_name: Ibáñez orcid: 0000-0001-5013-2843 - first_name: Roger full_name: Hasler, Roger last_name: Hasler - first_name: Aziz full_name: Genç, Aziz last_name: Genç - first_name: Yu full_name: Liu, Yu id: 2A70014E-F248-11E8-B48F-1D18A9856A87 last_name: Liu orcid: 0000-0001-7313-6740 - first_name: Beatrice full_name: Kuster, Beatrice last_name: Kuster - first_name: Maximilian full_name: Schuster, Maximilian last_name: Schuster - first_name: Oleksandr full_name: Dobrozhan, Oleksandr last_name: Dobrozhan - first_name: Doris full_name: Cadavid, Doris last_name: Cadavid - first_name: Jordi full_name: Arbiol, Jordi last_name: Arbiol - first_name: Andreu full_name: Cabot, Andreu last_name: Cabot - first_name: Maksym V. full_name: Kovalenko, Maksym V. last_name: Kovalenko citation: ama: Ibáñez M, Hasler R, Genç A, et al. Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. 2019;141(20):8025-8029. doi:10.1021/jacs.9b01394 apa: Ibáñez, M., Hasler, R., Genç, A., Liu, Y., Kuster, B., Schuster, M., … Kovalenko, M. V. (2019). Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.9b01394 chicago: Ibáñez, Maria, Roger Hasler, Aziz Genç, Yu Liu, Beatrice Kuster, Maximilian Schuster, Oleksandr Dobrozhan, et al. “Ligand-Mediated Band Engineering in Bottom-up Assembled SnTe Nanocomposites for Thermoelectric Energy Conversion.” Journal of the American Chemical Society. American Chemical Society, 2019. https://doi.org/10.1021/jacs.9b01394. ieee: M. Ibáñez et al., “Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion,” Journal of the American Chemical Society, vol. 141, no. 20. American Chemical Society, pp. 8025–8029, 2019. ista: Ibáñez M, Hasler R, Genç A, Liu Y, Kuster B, Schuster M, Dobrozhan O, Cadavid D, Arbiol J, Cabot A, Kovalenko MV. 2019. Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion. Journal of the American Chemical Society. 141(20), 8025–8029. mla: Ibáñez, Maria, et al. “Ligand-Mediated Band Engineering in Bottom-up Assembled SnTe Nanocomposites for Thermoelectric Energy Conversion.” Journal of the American Chemical Society, vol. 141, no. 20, American Chemical Society, 2019, pp. 8025–29, doi:10.1021/jacs.9b01394. short: M. Ibáñez, R. Hasler, A. Genç, Y. Liu, B. Kuster, M. Schuster, O. Dobrozhan, D. Cadavid, J. Arbiol, A. Cabot, M.V. Kovalenko, Journal of the American Chemical Society 141 (2019) 8025–8029. date_created: 2019-06-25T11:53:35Z date_published: 2019-04-19T00:00:00Z date_updated: 2023-09-05T12:03:45Z day: '19' ddc: - '540' department: - _id: MaIb doi: 10.1021/jacs.9b01394 ec_funded: 1 external_id: isi: - '000469292300004' pmid: - '31017419 ' file: - access_level: open_access checksum: 34d7ec837869cc6a07996b54f75696b7 content_type: application/pdf creator: cpetz date_created: 2019-06-25T11:59:00Z date_updated: 2020-07-14T12:47:34Z file_id: '6587' file_name: JACS_April2019.pdf file_size: 6234004 relation: main_file file_date_updated: 2020-07-14T12:47:34Z has_accepted_license: '1' intvolume: ' 141' isi: 1 issue: '20' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 8025-8029 pmid: 1 project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Journal of the American Chemical Society publication_identifier: eissn: - 1520-5126 issn: - 0002-7863 publication_status: published publisher: American Chemical Society quality_controlled: '1' scopus_import: '1' status: public title: Ligand-mediated band engineering in bottom-up assembled SnTe nanocomposites for thermoelectric energy conversion type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 141 year: '2019' ... --- _id: '6174' abstract: - lang: eng text: We propose a scaling theory for the many-body localization (MBL) phase transition in one dimension, building on the idea that it proceeds via a “quantum avalanche.” We argue that the critical properties can be captured at a coarse-grained level by a Kosterlitz-Thouless (KT) renormalization group (RG) flow. On phenomenological grounds, we identify the scaling variables as the density of thermal regions and the length scale that controls the decay of typical matrix elements. Within this KT picture, the MBL phase is a line of fixed points that terminates at the delocalization transition. We discuss two possible scenarios distinguished by the distribution of rare, fractal thermal inclusions within the MBL phase. In the first scenario, these regions have a stretched exponential distribution in the MBL phase. In the second scenario, the near-critical MBL phase hosts rare thermal regions that are power-law-distributed in size. This points to the existence of a second transition within the MBL phase, at which these power laws change to the stretched exponential form expected at strong disorder. We numerically simulate two different phenomenological RGs previously proposed to describe the MBL transition. Both RGs display a universal power-law length distribution of thermal regions at the transition with a critical exponent αc=2, and continuously varying exponents in the MBL phase consistent with the KT picture. article_number: '094205' article_processing_charge: No article_type: original author: - first_name: Philipp T. full_name: Dumitrescu, Philipp T. last_name: Dumitrescu - first_name: Anna full_name: Goremykina, Anna last_name: Goremykina - first_name: Siddharth A. full_name: Parameswaran, Siddharth A. last_name: Parameswaran - first_name: Maksym full_name: Serbyn, Maksym id: 47809E7E-F248-11E8-B48F-1D18A9856A87 last_name: Serbyn orcid: 0000-0002-2399-5827 - first_name: Romain full_name: Vasseur, Romain last_name: Vasseur citation: ama: Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. 2019;99(9). doi:10.1103/physrevb.99.094205 apa: Dumitrescu, P. T., Goremykina, A., Parameswaran, S. A., Serbyn, M., & Vasseur, R. (2019). Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.99.094205 chicago: Dumitrescu, Philipp T., Anna Goremykina, Siddharth A. Parameswaran, Maksym Serbyn, and Romain Vasseur. “Kosterlitz-Thouless Scaling at Many-Body Localization Phase Transitions.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.99.094205. ieee: P. T. Dumitrescu, A. Goremykina, S. A. Parameswaran, M. Serbyn, and R. Vasseur, “Kosterlitz-Thouless scaling at many-body localization phase transitions,” Physical Review B, vol. 99, no. 9. American Physical Society, 2019. ista: Dumitrescu PT, Goremykina A, Parameswaran SA, Serbyn M, Vasseur R. 2019. Kosterlitz-Thouless scaling at many-body localization phase transitions. Physical Review B. 99(9), 094205. mla: Dumitrescu, Philipp T., et al. “Kosterlitz-Thouless Scaling at Many-Body Localization Phase Transitions.” Physical Review B, vol. 99, no. 9, 094205, American Physical Society, 2019, doi:10.1103/physrevb.99.094205. short: P.T. Dumitrescu, A. Goremykina, S.A. Parameswaran, M. Serbyn, R. Vasseur, Physical Review B 99 (2019). date_created: 2019-03-25T07:32:08Z date_published: 2019-03-22T00:00:00Z date_updated: 2023-09-05T12:11:13Z day: '22' department: - _id: MaSe doi: 10.1103/physrevb.99.094205 external_id: arxiv: - '1811.03103' isi: - '000462883200001' intvolume: ' 99' isi: 1 issue: '9' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1811.03103 month: '03' oa: 1 oa_version: Preprint publication: Physical Review B publication_identifier: eissn: - 2469-9969 issn: - 2469-9950 publication_status: published publisher: American Physical Society quality_controlled: '1' scopus_import: '1' status: public title: Kosterlitz-Thouless scaling at many-body localization phase transitions type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 99 year: '2019' ... --- _id: '6366' abstract: - lang: eng text: Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl. article_processing_charge: No article_type: original author: - first_name: Julia full_name: Bellstaedt, Julia last_name: Bellstaedt - first_name: Jana full_name: Trenner, Jana last_name: Trenner - first_name: Rebecca full_name: Lippmann, Rebecca last_name: Lippmann - first_name: Yvonne full_name: Poeschl, Yvonne last_name: Poeschl - first_name: Xixi full_name: Zhang, Xixi id: 61A66458-47E9-11EA-85BA-8AEAAF14E49A last_name: Zhang orcid: 0000-0001-7048-4627 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Marcel full_name: Quint, Marcel last_name: Quint - first_name: Carolin full_name: Delker, Carolin last_name: Delker citation: ama: Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 2019;180(2):757-766. doi:10.1104/pp.18.01377 apa: Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J., … Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. ASPB. https://doi.org/10.1104/pp.18.01377 chicago: Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology. ASPB, 2019. https://doi.org/10.1104/pp.18.01377. ieee: J. Bellstaedt et al., “A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls,” Plant Physiology, vol. 180, no. 2. ASPB, pp. 757–766, 2019. ista: Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M, Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766. mla: Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” Plant Physiology, vol. 180, no. 2, ASPB, 2019, pp. 757–66, doi:10.1104/pp.18.01377. short: J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766. date_created: 2019-04-30T15:24:22Z date_published: 2019-06-01T00:00:00Z date_updated: 2023-09-05T12:25:19Z day: '01' department: - _id: JiFr doi: 10.1104/pp.18.01377 external_id: isi: - '000470086100019' pmid: - '31000634' intvolume: ' 180' isi: 1 issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: www.doi.org/10.1104/pp.18.01377 month: '06' oa: 1 oa_version: Published Version page: 757-766 pmid: 1 publication: Plant Physiology publication_identifier: eissn: - 1532-2548 issn: - 0032-0889 publication_status: published publisher: ASPB quality_controlled: '1' scopus_import: '1' status: public title: A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 180 year: '2019' ... --- _id: '6986' abstract: - lang: eng text: 'Li-Nadler proposed a conjecture about traces of Hecke categories, which implies the semistable part of the Betti geometric Langlands conjecture of Ben-Zvi-Nadler in genus 1. We prove a Weyl group analogue of this conjecture. Our theorem holds in the natural generality of reflection groups in Euclidean or hyperbolic space. As a corollary, we give an expression of the centralizer of a finite order element in a reflection group using homotopy theory. ' article_processing_charge: No article_type: original author: - first_name: Penghui full_name: Li, Penghui id: 42A24CCC-F248-11E8-B48F-1D18A9856A87 last_name: Li citation: ama: Li P. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 2019;147(11):4597-4604. doi:10.1090/proc/14586 apa: Li, P. (2019). A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. AMS. https://doi.org/10.1090/proc/14586 chicago: Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society. AMS, 2019. https://doi.org/10.1090/proc/14586. ieee: P. Li, “A colimit of traces of reflection groups,” Proceedings of the American Mathematical Society, vol. 147, no. 11. AMS, pp. 4597–4604, 2019. ista: Li P. 2019. A colimit of traces of reflection groups. Proceedings of the American Mathematical Society. 147(11), 4597–4604. mla: Li, Penghui. “A Colimit of Traces of Reflection Groups.” Proceedings of the American Mathematical Society, vol. 147, no. 11, AMS, 2019, pp. 4597–604, doi:10.1090/proc/14586. short: P. Li, Proceedings of the American Mathematical Society 147 (2019) 4597–4604. date_created: 2019-11-04T16:10:50Z date_published: 2019-11-01T00:00:00Z date_updated: 2023-09-05T12:22:21Z day: '01' department: - _id: TaHa doi: 10.1090/proc/14586 ec_funded: 1 external_id: arxiv: - '1810.07039' isi: - '000488621700004' intvolume: ' 147' isi: 1 issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1810.07039 month: '11' oa: 1 oa_version: Preprint page: 4597-4604 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces publication: Proceedings of the American Mathematical Society publication_identifier: eissn: - 1088-6826 issn: - 0002-9939 publication_status: published publisher: AMS quality_controlled: '1' scopus_import: '1' status: public title: A colimit of traces of reflection groups type: journal_article user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 volume: 147 year: '2019' ... --- _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' ...