[{"date_updated":"2023-08-30T07:20:32Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://doi.org/10.1007/s40314-019-0955-9","open_access":"1"}],"abstract":[{"text":"The main contributions of this paper are the proposition and the convergence analysis of a class of inertial projection-type algorithm for solving variational inequality problems in real Hilbert spaces where the underline operator is monotone and uniformly continuous. We carry out a unified analysis of the proposed method under very mild assumptions. In particular, weak convergence of the generated sequence is established and nonasymptotic O(1 / n) rate of convergence is established, where n denotes the iteration counter. We also present some experimental results to illustrate the profits gained by introducing the inertial extrapolation steps.","lang":"eng"}],"scopus_import":"1","status":"public","author":[{"full_name":"Shehu, Yekini","last_name":"Shehu","orcid":"0000-0001-9224-7139","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87","first_name":"Yekini"},{"first_name":"Olaniyi S.","last_name":"Iyiola","full_name":"Iyiola, Olaniyi S."},{"last_name":"Li","full_name":"Li, Xiao-Huan","first_name":"Xiao-Huan"},{"last_name":"Dong","full_name":"Dong, Qiao-Li","first_name":"Qiao-Li"}],"publisher":"Springer Nature","ddc":["510","515","518"],"type":"journal_article","oa_version":"Published Version","external_id":{"isi":["000488973100005"],"arxiv":["2101.09081"]},"publication_status":"published","issue":"4","_id":"7000","publication_identifier":{"issn":["2238-3603"],"eissn":["1807-0302"]},"isi":1,"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","name":"Discrete Optimization in Computer Vision: Theory and Practice","call_identifier":"FP7","grant_number":"616160"}],"month":"12","year":"2019","department":[{"_id":"VlKo"}],"article_type":"original","day":"01","publication":"Computational and Applied Mathematics","volume":38,"has_accepted_license":"1","intvolume":" 38","date_published":"2019-12-01T00:00:00Z","doi":"10.1007/s40314-019-0955-9","article_processing_charge":"No","ec_funded":1,"oa":1,"article_number":"161","citation":{"ama":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 2019;38(4). doi:10.1007/s40314-019-0955-9","ista":"Shehu Y, Iyiola OS, Li X-H, Dong Q-L. 2019. Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. 38(4), 161.","short":"Y. Shehu, O.S. Iyiola, X.-H. Li, Q.-L. Dong, Computational and Applied Mathematics 38 (2019).","ieee":"Y. Shehu, O. S. Iyiola, X.-H. Li, and Q.-L. Dong, “Convergence analysis of projection method for variational inequalities,” Computational and Applied Mathematics, vol. 38, no. 4. Springer Nature, 2019.","mla":"Shehu, Yekini, et al. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics, vol. 38, no. 4, 161, Springer Nature, 2019, doi:10.1007/s40314-019-0955-9.","apa":"Shehu, Y., Iyiola, O. S., Li, X.-H., & Dong, Q.-L. (2019). Convergence analysis of projection method for variational inequalities. Computational and Applied Mathematics. Springer Nature. https://doi.org/10.1007/s40314-019-0955-9","chicago":"Shehu, Yekini, Olaniyi S. Iyiola, Xiao-Huan Li, and Qiao-Li Dong. “Convergence Analysis of Projection Method for Variational Inequalities.” Computational and Applied Mathematics. Springer Nature, 2019. https://doi.org/10.1007/s40314-019-0955-9."},"date_created":"2019-11-12T12:41:44Z","quality_controlled":"1","arxiv":1,"title":"Convergence analysis of projection method for variational inequalities"},{"date_updated":"2024-03-25T23:30:21Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"id":"7186","status":"public","relation":"dissertation_contains"},{"id":"8350","relation":"dissertation_contains","status":"public"}],"link":[{"description":"News auf IST Website","url":"https://ist.ac.at/en/news/biochemistry-meets-mechanics-the-sensitive-nature-of-cell-cell-contact-formation-in-embryo-development/","relation":"press_release"}]},"scopus_import":"1","status":"public","author":[{"id":"3436488C-F248-11E8-B48F-1D18A9856A87","first_name":"Cornelia","last_name":"Schwayer","full_name":"Schwayer, Cornelia","orcid":"0000-0001-5130-2226"},{"first_name":"Shayan","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","last_name":"Shamipour","full_name":"Shamipour, Shayan"},{"full_name":"Pranjic-Ferscha, Kornelija","last_name":"Pranjic-Ferscha","id":"4362B3C2-F248-11E8-B48F-1D18A9856A87","first_name":"Kornelija"},{"first_name":"Alexandra","id":"30A536BA-F248-11E8-B48F-1D18A9856A87","full_name":"Schauer, Alexandra","last_name":"Schauer","orcid":"0000-0001-7659-9142"},{"full_name":"Balda, M","last_name":"Balda","first_name":"M"},{"last_name":"Tada","full_name":"Tada, M","first_name":"M"},{"full_name":"Matter, K","last_name":"Matter","first_name":"K"},{"id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","orcid":"0000-0002-0912-4566","full_name":"Heisenberg, Carl-Philipp J","last_name":"Heisenberg"}],"publisher":"Cell Press","ddc":["570"],"type":"journal_article","oa_version":"Submitted Version","file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-10-21T07:09:45Z","checksum":"33dac4bb77ee630e2666e936b4d57980","file_size":8805878,"success":1,"date_created":"2020-10-21T07:09:45Z","file_name":"2019_Cell_Schwayer_accepted.pdf","file_id":"8684","creator":"dernst","relation":"main_file"}],"publication_status":"published","external_id":{"pmid":["31675500"],"isi":["000493898000012"]},"_id":"7001","issue":"4","publication_identifier":{"issn":["0092-8674"],"eissn":["1097-4172"]},"isi":1,"project":[{"call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation","_id":"260F1432-B435-11E9-9278-68D0E5697425","grant_number":"742573"}],"month":"10","year":"2019","department":[{"_id":"CaHe"},{"_id":"BjHo"}],"article_type":"original","day":"31","publication":"Cell","volume":179,"pmid":1,"intvolume":" 179","has_accepted_license":"1","date_published":"2019-10-31T00:00:00Z","doi":"10.1016/j.cell.2019.10.006","file_date_updated":"2020-10-21T07:09:45Z","ec_funded":1,"article_processing_charge":"No","oa":1,"citation":{"ista":"Schwayer C, Shamipour S, Pranjic-Ferscha K, Schauer A, Balda M, Tada M, Matter K, Heisenberg C-PJ. 2019. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 179(4), 937–952.e18.","short":"C. Schwayer, S. Shamipour, K. Pranjic-Ferscha, A. Schauer, M. Balda, M. Tada, K. Matter, C.-P.J. Heisenberg, Cell 179 (2019) 937–952.e18.","ieee":"C. Schwayer et al., “Mechanosensation of tight junctions depends on ZO-1 phase separation and flow,” Cell, vol. 179, no. 4. Cell Press, p. 937–952.e18, 2019.","ama":"Schwayer C, Shamipour S, Pranjic-Ferscha K, et al. Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. 2019;179(4):937-952.e18. doi:10.1016/j.cell.2019.10.006","chicago":"Schwayer, Cornelia, Shayan Shamipour, Kornelija Pranjic-Ferscha, Alexandra Schauer, M Balda, M Tada, K Matter, and Carl-Philipp J Heisenberg. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell. Cell Press, 2019. https://doi.org/10.1016/j.cell.2019.10.006.","apa":"Schwayer, C., Shamipour, S., Pranjic-Ferscha, K., Schauer, A., Balda, M., Tada, M., … Heisenberg, C.-P. J. (2019). Mechanosensation of tight junctions depends on ZO-1 phase separation and flow. Cell. Cell Press. https://doi.org/10.1016/j.cell.2019.10.006","mla":"Schwayer, Cornelia, et al. “Mechanosensation of Tight Junctions Depends on ZO-1 Phase Separation and Flow.” Cell, vol. 179, no. 4, Cell Press, 2019, p. 937–952.e18, doi:10.1016/j.cell.2019.10.006."},"date_created":"2019-11-12T12:51:06Z","acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"}],"quality_controlled":"1","page":"937-952.e18","title":"Mechanosensation of tight junctions depends on ZO-1 phase separation and flow"},{"oa_version":"None","type":"journal_article","_id":"7002","issue":"4","publication_status":"published","external_id":{"isi":["000475740600011"]},"publisher":"ACM","department":[{"_id":"ChWo"}],"article_type":"original","isi":1,"publication_identifier":{"issn":["0730-0301"]},"year":"2019","month":"07","project":[{"grant_number":"642841","call_identifier":"H2020","name":"Distributed 3D Object Design","_id":"2508E324-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Multiple Importance Sampling (MIS) is a key technique for achieving robustness of Monte Carlo estimators in computer graphics and other fields. We derive optimal weighting functions for MIS that provably minimize the variance of an MIS estimator, given a set of sampling techniques. We show that the resulting variance reduction over the balance heuristic can be higher than predicted by the variance bounds derived by Veach and Guibas, who assumed only non-negative weights in their proof. We theoretically analyze the variance of the optimal MIS weights and show the relation to the variance of the balance heuristic. Furthermore, we establish a connection between the new weighting functions and control variates as previously applied to mixture sampling. We apply the new optimal weights to integration problems in light transport and show that they allow for new design considerations when choosing the appropriate sampling techniques for a given integration problem.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-08-30T07:21:25Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","author":[{"first_name":"Ivo","full_name":"Kondapaneni, Ivo","last_name":"Kondapaneni"},{"first_name":"Petr","full_name":"Vevoda, Petr","last_name":"Vevoda"},{"last_name":"Grittmann","full_name":"Grittmann, Pascal","first_name":"Pascal"},{"last_name":"Skrivan","full_name":"Skrivan, Tomas","first_name":"Tomas","id":"486A5A46-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Slusallek, Philipp","last_name":"Slusallek","first_name":"Philipp"},{"first_name":"Jaroslav","full_name":"Křivánek, Jaroslav","last_name":"Křivánek"}],"status":"public","date_created":"2019-11-12T13:05:40Z","citation":{"short":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, J. Křivánek, ACM Transactions on Graphics 38 (2019).","ieee":"I. Kondapaneni, P. Vevoda, P. Grittmann, T. Skrivan, P. Slusallek, and J. Křivánek, “Optimal multiple importance sampling,” ACM Transactions on Graphics, vol. 38, no. 4. ACM, 2019.","ista":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. 2019. Optimal multiple importance sampling. ACM Transactions on Graphics. 38(4), 37.","ama":"Kondapaneni I, Vevoda P, Grittmann P, Skrivan T, Slusallek P, Křivánek J. Optimal multiple importance sampling. ACM Transactions on Graphics. 2019;38(4). doi:10.1145/3306346.3323009","chicago":"Kondapaneni, Ivo, Petr Vevoda, Pascal Grittmann, Tomas Skrivan, Philipp Slusallek, and Jaroslav Křivánek. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics. ACM, 2019. https://doi.org/10.1145/3306346.3323009.","apa":"Kondapaneni, I., Vevoda, P., Grittmann, P., Skrivan, T., Slusallek, P., & Křivánek, J. (2019). Optimal multiple importance sampling. ACM Transactions on Graphics. ACM. https://doi.org/10.1145/3306346.3323009","mla":"Kondapaneni, Ivo, et al. “Optimal Multiple Importance Sampling.” ACM Transactions on Graphics, vol. 38, no. 4, 37, ACM, 2019, doi:10.1145/3306346.3323009."},"quality_controlled":"1","article_number":"37","title":"Optimal multiple importance sampling","intvolume":" 38","date_published":"2019-07-01T00:00:00Z","volume":38,"day":"01","publication":"ACM Transactions on Graphics","article_processing_charge":"No","ec_funded":1,"doi":"10.1145/3306346.3323009"},{"page":"570-583","title":"Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction","oa":1,"quality_controlled":"1","date_created":"2019-11-12T14:37:08Z","citation":{"ista":"Cheung GT, Cousin MA. 2019. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 151(5), 570–583.","ieee":"G. T. Cheung and M. A. Cousin, “Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction,” Journal of Neurochemistry, vol. 151, no. 5. Wiley, pp. 570–583, 2019.","short":"G.T. Cheung, M.A. Cousin, Journal of Neurochemistry 151 (2019) 570–583.","ama":"Cheung GT, Cousin MA. Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. 2019;151(5):570-583. doi:10.1111/jnc.14862","mla":"Cheung, Giselle T., and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry, vol. 151, no. 5, Wiley, 2019, pp. 570–83, doi:10.1111/jnc.14862.","chicago":"Cheung, Giselle T, and Michael A. Cousin. “Synaptic Vesicle Generation from Activity‐dependent Bulk Endosomes Requires a Dephosphorylation‐dependent Dynamin–Syndapin Interaction.” Journal of Neurochemistry. Wiley, 2019. https://doi.org/10.1111/jnc.14862.","apa":"Cheung, G. T., & Cousin, M. A. (2019). Synaptic vesicle generation from activity‐dependent bulk endosomes requires a dephosphorylation‐dependent dynamin–syndapin interaction. Journal of Neurochemistry. Wiley. https://doi.org/10.1111/jnc.14862"},"file_date_updated":"2020-07-14T12:47:47Z","doi":"10.1111/jnc.14862","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"pmid":1,"volume":151,"day":"01","publication":"Journal of Neurochemistry","date_published":"2019-12-01T00:00:00Z","has_accepted_license":"1","intvolume":" 151","year":"2019","month":"12","isi":1,"publication_identifier":{"issn":["0022-3042"],"eissn":["1471-4159"]},"article_type":"original","department":[{"_id":"SiHi"}],"publisher":"Wiley","issue":"5","_id":"7005","external_id":{"pmid":["31479508"],"isi":["000490703100001"]},"publication_status":"published","file":[{"date_updated":"2020-07-14T12:47:47Z","access_level":"open_access","content_type":"application/pdf","date_created":"2020-02-05T10:30:02Z","checksum":"ec1fb2aebb874009bc309adaada6e1d7","file_size":4334962,"file_name":"2019_JournNeurochemistry_Cheung.pdf","relation":"main_file","file_id":"7452","creator":"dernst"}],"type":"journal_article","ddc":["570"],"oa_version":"Published Version","author":[{"last_name":"Cheung","full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","first_name":"Giselle T","id":"471195F6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cousin, Michael A.","last_name":"Cousin","first_name":"Michael A."}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-30T07:21:50Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Activity-dependent bulk endocytosis generates synaptic vesicles (SVs) during intense neuronal activity via a two-step process. First, bulk endosomes are formed direct from the plasma membrane from which SVs are then generated. SV generation from bulk endosomes requires the efflux of previously accumulated calcium and activation of the protein phosphatase calcineurin. However, it is still unknown how calcineurin mediates SV generation. We addressed this question using a series of acute interventions that decoupled the generation of SVs from bulk endosomes in rat primary neuronal culture. This was achieved by either disruption of protein–protein interactions via delivery of competitive peptides, or inhibition of enzyme activity by known inhibitors. SV generation was monitored using either a morphological horseradish peroxidase assay or an optical assay that monitors the replenishment of the reserve SV pool. We found that SV generation was inhibited by, (i) peptides that disrupt calcineurin interactions, (ii) an inhibitor of dynamin I GTPase activity and (iii) peptides that disrupt the phosphorylation-dependent dynamin I–syndapin I interaction. Peptides that disrupted syndapin I interactions with eps15 homology domain-containing proteins had no effect. This revealed that (i) calcineurin must be localized at bulk endosomes to mediate its effect, (ii) dynamin I GTPase activity is essential for SV fission and (iii) the calcineurin-dependent interaction between dynamin I and syndapin I is essential for SV generation. We therefore propose that a calcineurin-dependent dephosphorylation cascade that requires both dynamin I GTPase and syndapin I lipid-deforming activity is essential for SV generation from bulk endosomes."}]},{"file_date_updated":"2020-07-14T12:47:47Z","doi":"10.3390/a12100218","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":12,"day":"18","publication":"Algorithms","date_published":"2019-10-18T00:00:00Z","intvolume":" 12","has_accepted_license":"1","title":"A new coding paradigm for the primitive relay channel","article_number":"218","oa":1,"arxiv":1,"quality_controlled":"1","date_created":"2019-11-12T14:46:19Z","citation":{"ama":"Mondelli M, Hassani SH, Urbanke R. A new coding paradigm for the primitive relay channel. Algorithms. 2019;12(10). doi:10.3390/a12100218","short":"M. Mondelli, S.H. Hassani, R. Urbanke, Algorithms 12 (2019).","ista":"Mondelli M, Hassani SH, Urbanke R. 2019. A new coding paradigm for the primitive relay channel. Algorithms. 12(10), 218.","ieee":"M. Mondelli, S. H. Hassani, and R. Urbanke, “A new coding paradigm for the primitive relay channel,” Algorithms, vol. 12, no. 10. MDPI, 2019.","apa":"Mondelli, M., Hassani, S. H., & Urbanke, R. (2019). A new coding paradigm for the primitive relay channel. Algorithms. MDPI. https://doi.org/10.3390/a12100218","chicago":"Mondelli, Marco, S. Hamed Hassani, and Rüdiger Urbanke. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms. MDPI, 2019. https://doi.org/10.3390/a12100218.","mla":"Mondelli, Marco, et al. “A New Coding Paradigm for the Primitive Relay Channel.” Algorithms, vol. 12, no. 10, 218, MDPI, 2019, doi:10.3390/a12100218."},"author":[{"orcid":"0000-0002-3242-7020","full_name":"Mondelli, Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","first_name":"Marco"},{"full_name":"Hassani, S. Hamed","last_name":"Hassani","first_name":"S. Hamed"},{"first_name":"Rüdiger","last_name":"Urbanke","full_name":"Urbanke, Rüdiger"}],"status":"public","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-02-23T12:49:28Z","scopus_import":1,"abstract":[{"lang":"eng","text":"We consider the primitive relay channel, where the source sends a message to the relay and to the destination, and the relay helps the communication by transmitting an additional message to the destination via a separate channel. Two well-known coding techniques have been introduced for this setting: decode-and-forward and compress-and-forward. In decode-and-forward, the relay completely decodes the message and sends some information to the destination; in compress-and-forward, the relay does not decode, and it sends a compressed version of the received signal to the destination using Wyner–Ziv coding. In this paper, we present a novel coding paradigm that provides an improved achievable rate for the primitive relay channel. The idea is to combine compress-and-forward and decode-and-forward via a chaining construction. We transmit over pairs of blocks: in the first block, we use compress-and-forward; and, in the second block, we use decode-and-forward. More specifically, in the first block, the relay does not decode, it compresses the received signal via Wyner–Ziv, and it sends only part of the compression to the destination. In the second block, the relay completely decodes the message, it sends some information to the destination, and it also sends the remaining part of the compression coming from the first block. By doing so, we are able to strictly outperform both compress-and-forward and decode-and-forward. Note that the proposed coding scheme can be implemented with polar codes. As such, it has the typical attractive properties of polar coding schemes, namely, quasi-linear encoding and decoding complexity, and error probability that decays at super-polynomial speed. As a running example, we take into account the special case of the erasure relay channel, and we provide a comparison between the rates achievable by our proposed scheme and the existing upper and lower bounds."}],"related_material":{"record":[{"id":"6675","status":"public","relation":"earlier_version"}]},"year":"2019","month":"10","publication_identifier":{"issn":["1999-4893"]},"article_type":"original","department":[{"_id":"MaMo"}],"publisher":"MDPI","_id":"7007","issue":"10","external_id":{"arxiv":["1801.03153"]},"publication_status":"published","ddc":["510"],"oa_version":"Published Version","file":[{"date_created":"2019-11-12T14:48:45Z","file_size":696791,"checksum":"267756d8f9db572f496cd1663c89d59a","date_updated":"2020-07-14T12:47:47Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"7008","creator":"dernst","file_name":"2019_Algorithms_Mondelli.pdf"}],"type":"journal_article"},{"status":"public","author":[{"last_name":"Yamada","full_name":"Yamada, KM","first_name":"KM"},{"orcid":"0000-0002-6620-9179","last_name":"Sixt","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","first_name":"Michael K"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-30T07:22:20Z","scopus_import":"1","abstract":[{"text":"Cell migration is essential for physiological processes as diverse as development, immune defence and wound healing. It is also a hallmark of cancer malignancy. Thousands of publications have elucidated detailed molecular and biophysical mechanisms of cultured cells migrating on flat, 2D substrates of glass and plastic. However, much less is known about how cells successfully navigate the complex 3D environments of living tissues. In these more complex, native environments, cells use multiple modes of migration, including mesenchymal, amoeboid, lobopodial and collective, and these are governed by the local extracellular microenvironment, specific modalities of Rho GTPase signalling and non- muscle myosin contractility. Migration through 3D environments is challenging because it requires the cell to squeeze through complex or dense extracellular structures. Doing so requires specific cellular adaptations to mechanical features of the extracellular matrix (ECM) or its remodelling. In addition, besides navigating through diverse ECM environments and overcoming extracellular barriers, cells often interact with neighbouring cells and tissues through physical and signalling interactions. Accordingly, cells need to call on an impressively wide diversity of mechanisms to meet these challenges. This Review examines how cells use both classical and novel mechanisms of locomotion as they traverse challenging 3D matrices and cellular environments. It focuses on principles rather than details of migratory mechanisms and draws comparisons between 1D, 2D and 3D migration.","lang":"eng"}],"month":"12","year":"2019","publication_identifier":{"eissn":["1471-0080"],"issn":["1471-0072"]},"isi":1,"article_type":"review","department":[{"_id":"MiSi"}],"publisher":"Springer Nature","publication_status":"published","external_id":{"pmid":["31582855"],"isi":["000497966900007"]},"issue":"12","_id":"7009","oa_version":"None","type":"journal_article","doi":"10.1038/s41580-019-0172-9","article_processing_charge":"No","pmid":1,"publication":"Nature Reviews Molecular Cell Biology","day":"01","volume":20,"date_published":"2019-12-01T00:00:00Z","intvolume":" 20","page":"738–752","title":"Mechanisms of 3D cell migration","quality_controlled":"1","citation":{"short":"K. Yamada, M.K. Sixt, Nature Reviews Molecular Cell Biology 20 (2019) 738–752.","ieee":"K. Yamada and M. K. Sixt, “Mechanisms of 3D cell migration,” Nature Reviews Molecular Cell Biology, vol. 20, no. 12. Springer Nature, pp. 738–752, 2019.","ista":"Yamada K, Sixt MK. 2019. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 20(12), 738–752.","ama":"Yamada K, Sixt MK. Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. 2019;20(12):738–752. doi:10.1038/s41580-019-0172-9","mla":"Yamada, KM, and Michael K. Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology, vol. 20, no. 12, Springer Nature, 2019, pp. 738–752, doi:10.1038/s41580-019-0172-9.","chicago":"Yamada, KM, and Michael K Sixt. “Mechanisms of 3D Cell Migration.” Nature Reviews Molecular Cell Biology. Springer Nature, 2019. https://doi.org/10.1038/s41580-019-0172-9.","apa":"Yamada, K., & Sixt, M. K. (2019). Mechanisms of 3D cell migration. Nature Reviews Molecular Cell Biology. Springer Nature. https://doi.org/10.1038/s41580-019-0172-9"},"date_created":"2019-11-12T14:54:42Z"},{"intvolume":" 11076","date_published":"2019-07-22T00:00:00Z","publication":"Advances in Microscopic Imaging II","day":"22","volume":11076,"article_processing_charge":"No","doi":"10.1117/12.2527058","citation":{"ieee":"H. S. Davies et al., “Blood cell-vessel wall interactions probed by reflection interference contrast microscopy,” in Advances in Microscopic Imaging II, Munich, Germany, 2019, vol. 11076.","short":"H.S. Davies, N.S. Baranova, N. El Amri, L. Coche-Guérente, C. Verdier, L. Bureau, R.P. Richter, D. Débarre, in:, Advances in Microscopic Imaging II, SPIE, 2019.","ista":"Davies HS, Baranova NS, El Amri N, Coche-Guérente L, Verdier C, Bureau L, Richter RP, Débarre D. 2019. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. Advances in Microscopic Imaging II. European Conferences on Biomedical Optics vol. 11076, 110760V.","ama":"Davies HS, Baranova NS, El Amri N, et al. Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In: Advances in Microscopic Imaging II. Vol 11076. SPIE; 2019. doi:10.1117/12.2527058","mla":"Davies, Heather S., et al. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” Advances in Microscopic Imaging II, vol. 11076, 110760V, SPIE, 2019, doi:10.1117/12.2527058.","chicago":"Davies, Heather S., Natalia S. Baranova, Nouha El Amri, Liliane Coche-Guérente, Claude Verdier, Lionel Bureau, Ralf P. Richter, and Delphine Débarre. “Blood Cell-Vessel Wall Interactions Probed by Reflection Interference Contrast Microscopy.” In Advances in Microscopic Imaging II, Vol. 11076. SPIE, 2019. https://doi.org/10.1117/12.2527058.","apa":"Davies, H. S., Baranova, N. S., El Amri, N., Coche-Guérente, L., Verdier, C., Bureau, L., … Débarre, D. (2019). Blood cell-vessel wall interactions probed by reflection interference contrast microscopy. In Advances in Microscopic Imaging II (Vol. 11076). Munich, Germany: SPIE. https://doi.org/10.1117/12.2527058"},"date_created":"2019-11-12T15:10:18Z","quality_controlled":"1","conference":{"location":"Munich, Germany","end_date":"2019-06-27","name":"European Conferences on Biomedical Optics","start_date":"2019-06-26"},"oa":1,"article_number":"110760V","title":"Blood cell-vessel wall interactions probed by reflection interference contrast microscopy","main_file_link":[{"open_access":"1","url":"https://hal.archives-ouvertes.fr/hal-02368135/file/110760V.pdf"}],"abstract":[{"lang":"eng","text":"Numerous biophysical questions require the quantification of short-range interactions between (functionalized) surfaces and synthetic or biological objects such as cells. Here, we present an original, custom built setup for reflection interference contrast microscopy that can assess distances between a substrate and a flowing object at high speed with nanometric accuracy. We demonstrate its use to decipher the complex biochemical and mechanical interplay regulating blood cell homing at the vessel wall in the microcirculation using an in vitro approach. We show that in the absence of specific biochemical interactions, flowing cells are repelled from the soft layer lining the vessel wall, contributing to red blood cell repulsion in vivo. In contrast, this so-called glycocalyx stabilizes rolling of cells under flow in the presence of a specific receptor naturally present on activated leucocytes and a number of cancer cell lines."}],"scopus_import":"1","date_updated":"2023-08-29T06:54:38Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","author":[{"first_name":"Heather S.","full_name":"Davies, Heather S.","last_name":"Davies"},{"full_name":"Baranova, Natalia S.","last_name":"Baranova","orcid":"0000-0002-3086-9124","first_name":"Natalia S.","id":"38661662-F248-11E8-B48F-1D18A9856A87"},{"full_name":"El Amri, Nouha","last_name":"El Amri","first_name":"Nouha"},{"last_name":"Coche-Guérente","full_name":"Coche-Guérente, Liliane","first_name":"Liliane"},{"first_name":"Claude","last_name":"Verdier","full_name":"Verdier, Claude"},{"full_name":"Bureau, Lionel","last_name":"Bureau","first_name":"Lionel"},{"full_name":"Richter, Ralf P.","last_name":"Richter","first_name":"Ralf P."},{"first_name":"Delphine","last_name":"Débarre","full_name":"Débarre, Delphine"}],"oa_version":"Published Version","type":"conference","external_id":{"isi":["000535353000023"]},"publication_status":"published","_id":"7010","publisher":"SPIE","department":[{"_id":"MaLo"}],"publication_identifier":{"isbn":["9781510628458"],"issn":["1605-7422"]},"isi":1,"year":"2019","month":"07"},{"title":"Probing the many-body localization phase transition with superconducting circuits","article_number":"134504","oa":1,"citation":{"chicago":"Orell, Tuure, Alexios Michailidis, Maksym Serbyn, and Matti Silveri. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.134504.","apa":"Orell, T., Michailidis, A., Serbyn, M., & Silveri, M. (2019). Probing the many-body localization phase transition with superconducting circuits. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.134504","mla":"Orell, Tuure, et al. “Probing the Many-Body Localization Phase Transition with Superconducting Circuits.” Physical Review B, vol. 100, no. 13, 134504, American Physical Society, 2019, doi:10.1103/physrevb.100.134504.","short":"T. Orell, A. Michailidis, M. Serbyn, M. Silveri, Physical Review B 100 (2019).","ieee":"T. Orell, A. Michailidis, M. Serbyn, and M. Silveri, “Probing the many-body localization phase transition with superconducting circuits,” Physical Review B, vol. 100, no. 13. American Physical Society, 2019.","ista":"Orell T, Michailidis A, Serbyn M, Silveri M. 2019. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 100(13), 134504.","ama":"Orell T, Michailidis A, Serbyn M, Silveri M. Probing the many-body localization phase transition with superconducting circuits. Physical Review B. 2019;100(13). doi:10.1103/physrevb.100.134504"},"date_created":"2019-11-13T08:25:48Z","arxiv":1,"quality_controlled":"1","doi":"10.1103/physrevb.100.134504","article_processing_charge":"No","volume":100,"publication":"Physical Review B","day":"01","intvolume":" 100","date_published":"2019-10-01T00:00:00Z","isi":1,"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"month":"10","year":"2019","department":[{"_id":"MaSe"}],"article_type":"original","publisher":"American Physical Society","type":"journal_article","oa_version":"Preprint","_id":"7013","issue":"13","publication_status":"published","external_id":{"arxiv":["1907.04043"],"isi":["000489036500004"]},"author":[{"full_name":"Orell, Tuure","last_name":"Orell","first_name":"Tuure"},{"first_name":"Alexios","id":"36EBAD38-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8443-1064","full_name":"Michailidis, Alexios","last_name":"Michailidis"},{"id":"47809E7E-F248-11E8-B48F-1D18A9856A87","first_name":"Maksym","full_name":"Serbyn, Maksym","last_name":"Serbyn","orcid":"0000-0002-2399-5827"},{"last_name":"Silveri","full_name":"Silveri, Matti","first_name":"Matti"}],"status":"public","date_updated":"2024-02-28T13:13:13Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"abstract":[{"text":"Chains of superconducting circuit devices provide a natural platform for studies of synthetic bosonic quantum matter. Motivated by the recent experimental progress in realizing disordered and interacting chains of superconducting transmon devices, we study the bosonic many-body localization phase transition using the methods of exact diagonalization as well as matrix product state dynamics. We estimate the location of transition separating the ergodic and the many-body localized phases as a function of the disorder strength and the many-body on-site interaction strength. The main difference between the bosonic model realized by superconducting circuits and similar fermionic model is that the effect of the on-site interaction is stronger due to the possibility of multiple excitations occupying the same site. The phase transition is found to be robust upon including longer-range hopping and interaction terms present in the experiments. Furthermore, we calculate experimentally relevant local observables and show that their temporal fluctuations can be used to distinguish between the dynamics of Anderson insulator, many-body localization, and delocalized phases. While we consider unitary dynamics, neglecting the effects of dissipation, decoherence, and measurement back action, the timescales on which the dynamics is unitary are sufficient for observation of characteristic dynamics in the many-body localized phase. Moreover, the experimentally available disorder strength and interactions allow for tuning the many-body localization phase transition, thus making the arrays of superconducting circuit devices a promising platform for exploring localization physics and phase transition.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1907.04043"}],"scopus_import":"1"},{"title":"Non-polynomial worst-case analysis of recursive programs","article_number":"20","oa":1,"arxiv":1,"quality_controlled":"1","date_created":"2019-11-13T08:33:43Z","citation":{"short":"K. Chatterjee, H. Fu, A.K. Goharshady, ACM Transactions on Programming Languages and Systems 41 (2019).","ieee":"K. Chatterjee, H. Fu, and A. K. Goharshady, “Non-polynomial worst-case analysis of recursive programs,” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4. ACM, 2019.","ista":"Chatterjee K, Fu H, Goharshady AK. 2019. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 41(4), 20.","ama":"Chatterjee K, Fu H, Goharshady AK. Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. 2019;41(4). doi:10.1145/3339984","mla":"Chatterjee, Krishnendu, et al. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems, vol. 41, no. 4, 20, ACM, 2019, doi:10.1145/3339984.","chicago":"Chatterjee, Krishnendu, Hongfei Fu, and Amir Kafshdar Goharshady. “Non-Polynomial Worst-Case Analysis of Recursive Programs.” ACM Transactions on Programming Languages and Systems. ACM, 2019. https://doi.org/10.1145/3339984.","apa":"Chatterjee, K., Fu, H., & Goharshady, A. K. (2019). Non-polynomial worst-case analysis of recursive programs. ACM Transactions on Programming Languages and Systems. ACM. https://doi.org/10.1145/3339984"},"doi":"10.1145/3339984","article_processing_charge":"No","ec_funded":1,"volume":41,"day":"01","publication":"ACM Transactions on Programming Languages and Systems","date_published":"2019-10-01T00:00:00Z","intvolume":" 41","month":"10","year":"2019","project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","name":"Rigorous Systems Engineering","call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7"},{"name":"Quantitative Analysis of Probablistic Systems with a focus on Crypto-currencies","_id":"267066CE-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts","_id":"266EEEC0-B435-11E9-9278-68D0E5697425"}],"isi":1,"article_type":"original","department":[{"_id":"KrCh"}],"publisher":"ACM","_id":"7014","issue":"4","external_id":{"isi":["000564108400001"],"arxiv":["1705.00317"]},"publication_status":"published","type":"journal_article","oa_version":"Preprint","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"first_name":"Hongfei","last_name":"Fu","full_name":"Fu, Hongfei"},{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2025-06-02T08:53:47Z","scopus_import":"1","abstract":[{"lang":"eng","text":"We study the problem of developing efficient approaches for proving\r\nworst-case bounds of non-deterministic recursive programs. Ranking functions\r\nare sound and complete for proving termination and worst-case bounds of\r\nnonrecursive programs. First, we apply ranking functions to recursion,\r\nresulting in measure functions. We show that measure functions provide a sound\r\nand complete approach to prove worst-case bounds of non-deterministic recursive\r\nprograms. Our second contribution is the synthesis of measure functions in\r\nnonpolynomial forms. We show that non-polynomial measure functions with\r\nlogarithm and exponentiation can be synthesized through abstraction of\r\nlogarithmic or exponentiation terms, Farkas' Lemma, and Handelman's Theorem\r\nusing linear programming. While previous methods obtain worst-case polynomial\r\nbounds, our approach can synthesize bounds of the form $\\mathcal{O}(n\\log n)$\r\nas well as $\\mathcal{O}(n^r)$ where $r$ is not an integer. We present\r\nexperimental results to demonstrate that our approach can obtain efficiently\r\nworst-case bounds of classical recursive algorithms such as (i) Merge-Sort, the\r\ndivide-and-conquer algorithm for the Closest-Pair problem, where we obtain\r\n$\\mathcal{O}(n \\log n)$ worst-case bound, and (ii) Karatsuba's algorithm for\r\npolynomial multiplication and Strassen's algorithm for matrix multiplication,\r\nwhere we obtain $\\mathcal{O}(n^r)$ bound such that $r$ is not an integer and\r\nclose to the best-known bounds for the respective algorithms."}],"related_material":{"record":[{"relation":"earlier_version","status":"public","id":"639"},{"relation":"dissertation_contains","status":"public","id":"8934"}]},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1705.00317"}]},{"volume":100,"publication":"Physical Review B","day":"25","date_published":"2019-07-25T00:00:00Z","intvolume":" 100","doi":"10.1103/physrevb.100.035127","ec_funded":1,"article_processing_charge":"No","article_number":"035127","oa":1,"arxiv":1,"quality_controlled":"1","citation":{"ista":"Lewin M, Lieb EH, Seiringer R. 2019. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 100(3), 035127.","short":"M. Lewin, E.H. Lieb, R. Seiringer, Physical Review B 100 (2019).","ieee":"M. Lewin, E. H. Lieb, and R. Seiringer, “Floating Wigner crystal with no boundary charge fluctuations,” Physical Review B, vol. 100, no. 3. American Physical Society, 2019.","ama":"Lewin M, Lieb EH, Seiringer R. Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. 2019;100(3). doi:10.1103/physrevb.100.035127","mla":"Lewin, Mathieu, et al. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B, vol. 100, no. 3, 035127, American Physical Society, 2019, doi:10.1103/physrevb.100.035127.","chicago":"Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Floating Wigner Crystal with No Boundary Charge Fluctuations.” Physical Review B. American Physical Society, 2019. https://doi.org/10.1103/physrevb.100.035127.","apa":"Lewin, M., Lieb, E. H., & Seiringer, R. (2019). Floating Wigner crystal with no boundary charge fluctuations. Physical Review B. American Physical Society. https://doi.org/10.1103/physrevb.100.035127"},"date_created":"2019-11-13T08:41:48Z","title":"Floating Wigner crystal with no boundary charge fluctuations","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-02-28T13:13:23Z","scopus_import":"1","abstract":[{"lang":"eng","text":"We modify the \"floating crystal\" trial state for the classical homogeneous electron gas (also known as jellium), in order to suppress the boundary charge fluctuations that are known to lead to a macroscopic increase of the energy. The argument is to melt a thin layer of the crystal close to the boundary and consequently replace it by an incompressible fluid. With the aid of this trial state we show that three different definitions of the ground-state energy of jellium coincide. In the first point of view the electrons are placed in a neutralizing uniform background. In the second definition there is no background but the electrons are submitted to the constraint that their density is constant, as is appropriate in density functional theory. Finally, in the third system each electron interacts with a periodic image of itself; that is, periodic boundary conditions are imposed on the interaction potential."}],"main_file_link":[{"url":"https://arxiv.org/abs/1905.09138","open_access":"1"}],"author":[{"first_name":"Mathieu","full_name":"Lewin, Mathieu","last_name":"Lewin"},{"last_name":"Lieb","full_name":"Lieb, Elliott H.","first_name":"Elliott H."},{"full_name":"Seiringer, Robert","last_name":"Seiringer","orcid":"0000-0002-6781-0521","first_name":"Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"status":"public","publisher":"American Physical Society","_id":"7015","issue":"3","external_id":{"isi":["000477888200001"],"arxiv":["1905.09138"]},"publication_status":"published","type":"journal_article","oa_version":"Preprint","year":"2019","month":"07","project":[{"grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems"}],"isi":1,"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"article_type":"original","department":[{"_id":"RoSe"}]},{"department":[{"_id":"CaGu"}],"title":"Data for the paper \"Gene amplification as a form of population-level gene expression regulation\"","contributor":[{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_leader","first_name":"Calin C","orcid":"0000-0001-6220-2052","last_name":"Guet"}],"month":"11","year":"2019","ddc":["576"],"oa_version":"Published Version","type":"research_data","file":[{"file_name":"D8_S35_R2_001.fastq","description":"Illumina whole genome sequence data for Locus 1 - amplified.","file_id":"7017","creator":"itomanek","relation":"main_file","title":"Locus1_amplified","access_level":"open_access","content_type":"application/octet-stream","date_updated":"2020-07-14T12:47:47Z","file_size":2456192500,"checksum":"72441055043eda4cbf1398a422e2c118","date_created":"2019-11-13T08:52:21Z"},{"file_size":2833452234,"checksum":"a4ac50bf655d9c751f0305ade5c2ee16","date_created":"2019-11-13T08:52:59Z","access_level":"open_access","content_type":"application/octet-stream","date_updated":"2020-07-14T12:47:47Z","file_id":"7018","creator":"itomanek","relation":"main_file","title":"Locus1_ancestral","file_name":"IT028_S11_R2_001.fastq","description":"Illumina whole genome sequence data for Locus 1 - ancestral."},{"content_type":"application/octet-stream","access_level":"open_access","date_updated":"2020-07-14T12:47:47Z","file_size":2878017264,"checksum":"5b227708ff478ca06e3f0448a4efdc2f","date_created":"2019-11-13T08:54:10Z","file_name":"D8-DOG1_S47_R2_001.fastq","description":"Illumina whole genome sequence data for Locus 1 - amplified, after DOG-selection.","creator":"itomanek","file_id":"7019","title":"Locus1_amplified_DOG","relation":"main_file"},{"file_size":2180826995,"checksum":"d9550a4c044116075fa83f8f2ea31d6f","date_created":"2019-11-13T08:54:27Z","access_level":"open_access","content_type":"application/octet-stream","date_updated":"2020-07-14T12:47:47Z","file_id":"7020","creator":"itomanek","relation":"main_file","title":"Locus2_amplified","file_name":"D4_S71_R2_001.fastq","description":"Illumina whole genome sequence data for Locus 2 - amplified."},{"checksum":"466ceb302c020ac013007a879fcde69d","file_size":2108826444,"date_created":"2019-11-13T08:55:58Z","content_type":"application/octet-stream","access_level":"open_access","date_updated":"2020-07-14T12:47:47Z","creator":"itomanek","file_id":"7021","title":"Locus2_ancestral","relation":"main_file","file_name":"IT030_S23_R2_001.fastq","description":"Illumina whole genome sequence data for Locus 2 - ancestral."},{"title":"Locus2_amplified_DOG","relation":"main_file","creator":"itomanek","file_id":"7092","description":"Illumina whole genome sequence data for Locus 2 - amplified, after DOG-selection.","file_name":"D4-DOG1_S83_R2_001.fastq","date_created":"2019-11-21T12:31:01Z","file_size":3144330494,"checksum":"8aeb1da771713c7baa5a847eff889604","date_updated":"2020-07-14T12:47:47Z","content_type":"application/octet-stream","access_level":"open_access"},{"content_type":"application/zip","access_level":"open_access","date_updated":"2020-07-14T12:47:47Z","file_size":4179,"checksum":"bf7d4b053f14af4655fb5574209fdb2d","date_created":"2020-01-14T11:22:27Z","file_name":"galK_dual_reporter_cassette.gb.zip","description":"Compressed genbank file format containing the sequence of the chromosomal reporter gene cassette.","creator":"itomanek","file_id":"7273","title":"DNA sequence of the chromosomal reporter gene cassette","relation":"main_file"},{"file_size":435,"checksum":"5e91cee2eff6f4a7cde456c6fb07c2ff","date_created":"2020-01-15T14:15:55Z","content_type":"text/plain","access_level":"open_access","date_updated":"2020-07-14T12:47:47Z","creator":"dernst","file_id":"7335","title":"Read_me_sequence_data","relation":"main_file","file_name":"Readme_7016.txt"},{"relation":"main_file","title":"FACS data","file_id":"7351","creator":"itomanek","description":"FACS data associated with Fig. 2c - see read_me_FACS","file_name":"FACS_data.xlsx.zip","date_created":"2020-01-22T15:44:16Z","file_size":3765861,"checksum":"5e6745dcfb9c1b11dd935ac3ee45fe33","date_updated":"2020-07-14T12:47:47Z","access_level":"open_access","content_type":"application/zip"},{"access_level":"open_access","content_type":"text/rtf","date_updated":"2020-07-14T12:47:47Z","checksum":"a85caf092ae4b17668f70af2d93fad00","file_size":4996,"date_created":"2020-01-22T15:44:16Z","file_name":"read_me_FACS.rtf","file_id":"7352","creator":"itomanek","relation":"main_file"},{"access_level":"open_access","content_type":"text/rtf","date_updated":"2020-07-14T12:47:47Z","file_size":868,"checksum":"fd8ba5d75d24e47ddf7e70bfdadb40d4","date_created":"2020-01-22T15:44:16Z","file_name":"read_me_microfluidics.rtf","file_id":"7353","creator":"itomanek","relation":"main_file"},{"creator":"itomanek","file_id":"7354","title":"microfluidics data","relation":"main_file","file_name":"microfuidics_data.zip","description":"microfluidics time trace data - see read_me_microfluidics","checksum":"69c5dc5ca5c069a138183c934acc1778","file_size":8141727,"date_created":"2020-01-22T15:44:17Z","content_type":"application/zip","access_level":"open_access","date_updated":"2020-07-14T12:47:47Z"}],"date_created":"2019-11-13T09:07:31Z","citation":{"apa":"Tomanek, I. (2019). Data for the paper “Gene amplification as a form of population-level gene expression regulation.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:7016","chicago":"Tomanek, Isabella. “Data for the Paper ‘Gene Amplification as a Form of Population-Level Gene Expression Regulation.’” Institute of Science and Technology Austria, 2019. https://doi.org/10.15479/AT:ISTA:7016.","mla":"Tomanek, Isabella. Data for the Paper “Gene Amplification as a Form of Population-Level Gene Expression Regulation.” Institute of Science and Technology Austria, 2019, doi:10.15479/AT:ISTA:7016.","ama":"Tomanek I. Data for the paper “Gene amplification as a form of population-level gene expression regulation.” 2019. doi:10.15479/AT:ISTA:7016","ieee":"I. Tomanek, “Data for the paper ‘Gene amplification as a form of population-level gene expression regulation.’” Institute of Science and Technology Austria, 2019.","ista":"Tomanek I. 2019. Data for the paper ‘Gene amplification as a form of population-level gene expression regulation’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:7016.","short":"I. Tomanek, (2019)."},"_id":"7016","publisher":"Institute of Science and Technology Austria","oa":1,"status":"public","article_processing_charge":"No","author":[{"first_name":"Isabella","id":"3981F020-F248-11E8-B48F-1D18A9856A87","full_name":"Tomanek, Isabella","last_name":"Tomanek","orcid":"0000-0001-6197-363X"}],"doi":"10.15479/AT:ISTA:7016","file_date_updated":"2020-07-14T12:47:47Z","related_material":{"record":[{"id":"7652","status":"public","relation":"used_in_publication"}]},"has_accepted_license":"1","keyword":["Escherichia coli","gene amplification","galactose","DOG","experimental evolution","Illumina sequence data","FACS data","microfluidics data"],"abstract":[{"text":"Organisms cope with change by employing transcriptional regulators. However, when faced with rare environments, the evolution of transcriptional regulators and their promoters may be too slow. We ask whether the intrinsic instability of gene duplication and amplification provides a generic alternative to canonical gene regulation. By real-time monitoring of gene copy number mutations in E. coli, we show that gene duplications and amplifications enable adaptation to fluctuating environments by rapidly generating copy number, and hence expression level, polymorphism. This ‘amplification-mediated gene expression tuning’ occurs on timescales similar to canonical gene regulation and can deal with rapid environmental changes. Mathematical modeling shows that amplifications also tune gene expression in stochastic environments where transcription factor-based schemes are hard to evolve or maintain. The fleeting nature of gene amplifications gives rise to a generic population-level mechanism that relies on genetic heterogeneity to rapidly tune expression of any gene, without leaving any genomic signature.","lang":"eng"}],"date_published":"2019-11-13T00:00:00Z","day":"13","date_updated":"2024-02-21T12:45:25Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"volume":9,"day":"27","publication":"Cell Systems","date_published":"2019-11-27T00:00:00Z","intvolume":" 9","has_accepted_license":"1","file_date_updated":"2020-07-14T12:47:48Z","doi":"10.1016/j.cels.2019.10.004","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"oa":1,"quality_controlled":"1","acknowledged_ssus":[{"_id":"LifeSc"}],"date_created":"2019-11-15T10:51:42Z","citation":{"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.","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.","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","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.","short":"M. Lukacisin, M.T. Bollenbach, Cell Systems 9 (2019) 423-433.e1-e3.","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."},"page":"423-433.e1-e3","title":"Emergent gene expression responses to drug combinations predict higher-order drug interactions","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-30T07:24:58Z","scopus_import":"1","abstract":[{"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.","lang":"eng"}],"author":[{"id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","first_name":"Martin","orcid":"0000-0001-6549-4177","last_name":"Lukacisin","full_name":"Lukacisin, Martin"},{"orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Tobias","last_name":"Bollenbach","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Tobias"}],"status":"public","publisher":"Cell Press","issue":"5","_id":"7026","publication_status":"published","external_id":{"isi":["000499495400003"]},"type":"journal_article","file":[{"file_name":"2019_CellSystems_Lukacisin.pdf","relation":"main_file","file_id":"7027","creator":"dernst","date_updated":"2020-07-14T12:47:48Z","access_level":"open_access","content_type":"application/pdf","date_created":"2019-11-15T10:57:42Z","file_size":4238460,"checksum":"7a11d6c2f9523d65b049512d61733178"}],"ddc":["570"],"oa_version":"Published Version","year":"2019","month":"11","project":[{"grant_number":"P27201-B22","call_identifier":"FWF","name":"Revealing the mechanisms underlying drug interactions","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0042/2013","_id":"25EB3A80-B435-11E9-9278-68D0E5697425","name":"Revealing the fundamental limits of cell growth"}],"isi":1,"publication_identifier":{"issn":["2405-4712"]},"article_type":"original","department":[{"_id":"ToBo"}]},{"status":"public","author":[{"id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","first_name":"Alfredo R","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez","orcid":"0000-0001-6249-5860"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"full_name":"Leuchs, Gerd","last_name":"Leuchs","first_name":"Gerd"},{"first_name":"Madhuri","full_name":"Kuamri, Madhuri","last_name":"Kuamri"},{"first_name":"Harald G. L.","full_name":"Schwefel, Harald G. L.","last_name":"Schwefel"}],"article_processing_charge":"No","doi":"10.1109/cleoe-eqec.2019.8873300","abstract":[{"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].","lang":"eng"}],"scopus_import":"1","date_published":"2019-10-17T00:00:00Z","publication":"2019 Conference on Lasers and Electro-Optics Europe & European Quantum Electronics Conference","day":"17","date_updated":"2023-08-30T07:26:01Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"title":"Electro-optic frequency comb generation in lithium niobate whispering gallery mode resonators","publication_identifier":{"isbn":["9781728104690"]},"isi":1,"month":"10","year":"2019","type":"conference","oa_version":"None","date_created":"2019-11-18T13:58:22Z","citation":{"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.","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","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.","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.","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.","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.","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"},"quality_controlled":"1","publication_status":"published","external_id":{"isi":["000630002701617"]},"_id":"7032","conference":{"location":"Munich, Germany","end_date":"2019-06-27","start_date":"2019-06-23","name":"CLEO: Conference on Lasers and Electro-Optics Europe"},"publisher":"IEEE","article_number":"8873300"},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-30T07:26:25Z","scopus_import":"1","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."}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1709.00508"}],"author":[{"orcid":"0000-0001-8485-1774","full_name":"Fulek, Radoslav","last_name":"Fulek","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","first_name":"Radoslav"},{"first_name":"Jan","full_name":"Kynčl, Jan","last_name":"Kynčl"}],"status":"public","publisher":"Springer Nature","issue":"6","_id":"7034","publication_status":"published","external_id":{"arxiv":["1709.00508"],"isi":["000493267200003"]},"oa_version":"Preprint","type":"journal_article","year":"2019","month":"10","project":[{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"International IST Postdoc Fellowship Programme"},{"grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","name":"Eliminating intersections in drawings of graphs","call_identifier":"FWF"}],"isi":1,"publication_identifier":{"issn":["0209-9683"],"eissn":["1439-6912"]},"article_type":"original","department":[{"_id":"UlWa"}],"volume":39,"day":"29","publication":"Combinatorica","date_published":"2019-10-29T00:00:00Z","intvolume":" 39","doi":"10.1007/s00493-019-3905-7","ec_funded":1,"article_processing_charge":"No","oa":1,"quality_controlled":"1","arxiv":1,"citation":{"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.","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.","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","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.","short":"R. Fulek, J. Kynčl, Combinatorica 39 (2019) 1267–1279.","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."},"date_created":"2019-11-18T14:29:50Z","page":"1267-1279","title":"Counterexample to an extension of the Hanani-Tutte theorem on the surface of genus 4"},{"citation":{"ama":"Geher GP, Titkos T, Virosztek D. Dirac masses and isometric rigidity. In: Kyoto RIMS Kôkyûroku. Vol 2125. Research Institute for Mathematical Sciences, Kyoto University; 2019:34-41.","ista":"Geher GP, Titkos T, Virosztek D. 2019. Dirac masses and isometric rigidity. Kyoto RIMS Kôkyûroku. Research on isometries as preserver problems and related topics vol. 2125, 34–41.","ieee":"G. P. Geher, T. Titkos, and D. Virosztek, “Dirac masses and isometric rigidity,” in Kyoto RIMS Kôkyûroku, Kyoto, Japan, 2019, vol. 2125, pp. 34–41.","short":"G.P. Geher, T. Titkos, D. Virosztek, in:, Kyoto RIMS Kôkyûroku, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.","mla":"Geher, Gyorgy Pal, et al. “Dirac Masses and Isometric Rigidity.” Kyoto RIMS Kôkyûroku, vol. 2125, Research Institute for Mathematical Sciences, Kyoto University, 2019, pp. 34–41.","apa":"Geher, G. P., Titkos, T., & Virosztek, D. (2019). Dirac masses and isometric rigidity. In Kyoto RIMS Kôkyûroku (Vol. 2125, pp. 34–41). Kyoto, Japan: Research Institute for Mathematical Sciences, Kyoto University.","chicago":"Geher, Gyorgy Pal, Tamas Titkos, and Daniel Virosztek. “Dirac Masses and Isometric Rigidity.” In Kyoto RIMS Kôkyûroku, 2125:34–41. Research Institute for Mathematical Sciences, Kyoto University, 2019."},"date_created":"2019-11-18T15:39:53Z","type":"conference","oa_version":"Submitted Version","_id":"7035","conference":{"name":"Research on isometries as preserver problems and related topics","start_date":"2019-01-28","location":"Kyoto, Japan","end_date":"2019-01-30"},"quality_controlled":"1","publication_status":"published","publisher":"Research Institute for Mathematical Sciences, Kyoto University","oa":1,"title":"Dirac masses and isometric rigidity","department":[{"_id":"LaEr"}],"year":"2019","month":"01","page":"34-41","abstract":[{"text":"The aim of this short note is to expound one particular issue that was discussed during the talk [10] given at the symposium ”Researches on isometries as preserver problems and related topics” at Kyoto RIMS. That is, the role of Dirac masses by describing the isometry group of various metric spaces of probability measures. This article is of survey character, and it does not contain any essentially new results.From an isometric point of view, in some cases, metric spaces of measures are similar to C(K)-type function spaces. Similarity means here that their isometries are driven by some nice transformations of the underlying space. Of course, it depends on the particular choice of the metric how nice these transformations should be. Sometimes, as we will see, being a homeomorphism is enough to generate an isometry. But sometimes we need more: the transformation must preserve the underlying distance as well. Statements claiming that isometries in questions are necessarily induced by homeomorphisms are called Banach-Stone-type results, while results asserting that the underlying transformation is necessarily an isometry are termed as isometric rigidity results.As Dirac masses can be considered as building bricks of the set of all Borel measures, a natural question arises:Is it enough to understand how an isometry acts on the set of Dirac masses? Does this action extend uniquely to all measures?In what follows, we will thoroughly investigate this question.","lang":"eng"}],"main_file_link":[{"open_access":"1","url":"http://www.kurims.kyoto-u.ac.jp/~kyodo/kokyuroku/contents/2125.html"}],"intvolume":" 2125","date_published":"2019-01-30T00:00:00Z","volume":2125,"date_updated":"2021-01-12T08:11:33Z","publication":"Kyoto RIMS Kôkyûroku","day":"30","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","language":[{"iso":"eng"}],"author":[{"first_name":"Gyorgy Pal","full_name":"Geher, Gyorgy Pal","last_name":"Geher"},{"first_name":"Tamas","last_name":"Titkos","full_name":"Titkos, Tamas"},{"id":"48DB45DA-F248-11E8-B48F-1D18A9856A87","first_name":"Daniel","orcid":"0000-0003-1109-5511","last_name":"Virosztek","full_name":"Virosztek, Daniel"}],"article_processing_charge":"No","status":"public"},{"oa":1,"arxiv":1,"quality_controlled":"1","citation":{"ama":"Huszár K, Spreer J, Wagner U. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 2019;10(2):70–98. doi:10.20382/JOGC.V10I2A5","ista":"Huszár K, Spreer J, Wagner U. 2019. On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. 10(2), 70–98.","short":"K. Huszár, J. Spreer, U. Wagner, Journal of Computational Geometry 10 (2019) 70–98.","ieee":"K. Huszár, J. Spreer, and U. Wagner, “On the treewidth of triangulated 3-manifolds,” Journal of Computational Geometry, vol. 10, no. 2. Computational Geometry Laborartoy, pp. 70–98, 2019.","apa":"Huszár, K., Spreer, J., & Wagner, U. (2019). On the treewidth of triangulated 3-manifolds. Journal of Computational Geometry. Computational Geometry Laborartoy. https://doi.org/10.20382/JOGC.V10I2A5","chicago":"Huszár, Kristóf, Jonathan Spreer, and Uli Wagner. “On the Treewidth of Triangulated 3-Manifolds.” Journal of Computational Geometry. Computational Geometry Laborartoy, 2019. https://doi.org/10.20382/JOGC.V10I2A5.","mla":"Huszár, Kristóf, et al. “On the Treewidth of Triangulated 3-Manifolds.” Journal of Computational Geometry, vol. 10, no. 2, Computational Geometry Laborartoy, 2019, pp. 70–98, doi:10.20382/JOGC.V10I2A5."},"date_created":"2019-11-23T12:14:09Z","page":"70–98","title":"On the treewidth of triangulated 3-manifolds","volume":10,"day":"01","publication":"Journal of Computational Geometry","date_published":"2019-11-01T00:00:00Z","has_accepted_license":"1","intvolume":" 10","file_date_updated":"2020-07-14T12:47:49Z","doi":"10.20382/JOGC.V10I2A5","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publisher":"Computational Geometry Laborartoy","issue":"2","_id":"7093","publication_status":"published","external_id":{"arxiv":["1712.00434"]},"type":"journal_article","ddc":["514"],"file":[{"file_name":"479-1917-1-PB.pdf","creator":"khuszar","file_id":"7094","relation":"main_file","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:49Z","file_size":857590,"checksum":"c872d590d38d538404782bca20c4c3f5","date_created":"2019-11-23T12:35:16Z"}],"oa_version":"Published Version","month":"11","year":"2019","publication_identifier":{"issn":["1920-180X"]},"article_type":"original","department":[{"_id":"UlWa"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-07T13:18:26Z","abstract":[{"lang":"eng","text":"In graph theory, as well as in 3-manifold topology, there exist several width-type parameters to describe how \"simple\" or \"thin\" a given graph or 3-manifold is. These parameters, such as pathwidth or treewidth for graphs, or the concept of thin position for 3-manifolds, play an important role when studying algorithmic problems; in particular, there is a variety of problems in computational 3-manifold topology - some of them known to be computationally hard in general - that become solvable in polynomial time as soon as the dual graph of the input triangulation has bounded treewidth.\r\nIn view of these algorithmic results, it is natural to ask whether every 3-manifold admits a triangulation of bounded treewidth. We show that this is not the case, i.e., that there exists an infinite family of closed 3-manifolds not admitting triangulations of bounded pathwidth or treewidth (the latter implies the former, but we present two separate proofs).\r\nWe derive these results from work of Agol, of Scharlemann and Thompson, and of Scharlemann, Schultens and Saito by exhibiting explicit connections between the topology of a 3-manifold M on the one hand and width-type parameters of the dual graphs of triangulations of M on the other hand, answering a question that had been raised repeatedly by researchers in computational 3-manifold topology. In particular, we show that if a closed, orientable, irreducible, non-Haken 3-manifold M has a triangulation of treewidth (resp. pathwidth) k then the Heegaard genus of M is at most 18(k+1) (resp. 4(3k+1))."}],"related_material":{"record":[{"id":"285","status":"public","relation":"earlier_version"},{"relation":"part_of_dissertation","status":"public","id":"8032"}]},"author":[{"orcid":"0000-0002-5445-5057","last_name":"Huszár","full_name":"Huszár, Kristóf","id":"33C26278-F248-11E8-B48F-1D18A9856A87","first_name":"Kristóf"},{"last_name":"Spreer","full_name":"Spreer, Jonathan","first_name":"Jonathan"},{"last_name":"Wagner","full_name":"Wagner, Uli","orcid":"0000-0002-1494-0568","first_name":"Uli","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"}],"status":"public"},{"oa":1,"article_number":"16565","citation":{"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.","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.","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","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.","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","quality_controlled":"1","title":"Completion of BAX recruitment correlates with mitochondrial fission during apoptosis","day":"12","publication":"Scientific Reports","volume":9,"pmid":1,"intvolume":" 9","has_accepted_license":"1","date_published":"2019-11-12T00:00:00Z","doi":"10.1038/s41598-019-53049-w","file_date_updated":"2020-07-14T12:47:49Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","publisher":"Springer Nature","ddc":["570"],"type":"journal_article","oa_version":"Published Version","file":[{"relation":"main_file","creator":"dernst","file_id":"7096","file_name":"2019_ScientificReports_Maes.pdf","date_created":"2019-11-25T07:49:52Z","checksum":"9ab397ed9c1c454b34bffb8cc863d734","file_size":6467393,"date_updated":"2020-07-14T12:47:49Z","content_type":"application/pdf","access_level":"open_access"}],"publication_status":"published","external_id":{"pmid":["31719602"],"isi":["000495857600019"]},"_id":"7095","publication_identifier":{"eissn":["2045-2322"]},"isi":1,"month":"11","year":"2019","department":[{"_id":"SaSi"}],"article_type":"original","date_updated":"2023-08-30T07:26:54Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"abstract":[{"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.","lang":"eng"}],"scopus_import":"1","status":"public","author":[{"orcid":"0000-0001-9642-1085","last_name":"Maes","full_name":"Maes, Margaret E","id":"3838F452-F248-11E8-B48F-1D18A9856A87","first_name":"Margaret E"},{"first_name":"J. A.","last_name":"Grosser","full_name":"Grosser, J. A."},{"last_name":"Fehrman","full_name":"Fehrman, R. L.","first_name":"R. L."},{"full_name":"Schlamp, C. L.","last_name":"Schlamp","first_name":"C. L."},{"first_name":"R. W.","last_name":"Nickells","full_name":"Nickells, R. W."}]},{"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"doi":"10.1038/s42003-019-0670-5","file_date_updated":"2020-07-14T12:47:49Z","has_accepted_license":"1","intvolume":" 2","date_published":"2019-11-15T00:00:00Z","volume":2,"publication":"Communications Biology","day":"15","title":"Rab5-mediated endosome formation is regulated at the trans-Golgi network","date_created":"2019-11-25T07:55:01Z","citation":{"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.","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.","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","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.","short":"M. Nagano, J.Y. Toshima, D.E. Siekhaus, J. Toshima, Communications Biology 2 (2019).","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."},"quality_controlled":"1","article_number":"419","oa":1,"author":[{"first_name":"Makoto","full_name":"Nagano, Makoto","last_name":"Nagano"},{"last_name":"Toshima","full_name":"Toshima, Junko Y.","first_name":"Junko Y."},{"orcid":"0000-0001-8323-8353","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","first_name":"Daria E"},{"first_name":"Jiro","full_name":"Toshima, Jiro","last_name":"Toshima"}],"status":"public","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."}],"scopus_import":"1","date_updated":"2023-08-30T07:27:55Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"DaSi"}],"article_type":"original","isi":1,"publication_identifier":{"issn":["2399-3642"]},"year":"2019","month":"11","type":"journal_article","file":[{"date_created":"2019-11-25T07:58:05Z","file_size":2626069,"checksum":"c63c69a264fc8a0e52f2b0d482f3bdae","date_updated":"2020-07-14T12:47:49Z","access_level":"open_access","content_type":"application/pdf","relation":"main_file","file_id":"7098","creator":"dernst","file_name":"2019_CommunicBiology_Nagano.pdf"}],"ddc":["570"],"oa_version":"Published Version","issue":"1","_id":"7097","publication_status":"published","external_id":{"isi":["000496767800005"]},"publisher":"Springer Nature"},{"status":"public","author":[{"first_name":"Yu","full_name":"Kasugai, Yu","last_name":"Kasugai"},{"last_name":"Vogel","full_name":"Vogel, Elisabeth","first_name":"Elisabeth"},{"full_name":"Hörtnagl, Heide","last_name":"Hörtnagl","first_name":"Heide"},{"last_name":"Schönherr","full_name":"Schönherr, Sabine","first_name":"Sabine"},{"full_name":"Paradiso, Enrica","last_name":"Paradiso","first_name":"Enrica"},{"first_name":"Markus","full_name":"Hauschild, Markus","last_name":"Hauschild"},{"first_name":"Georg","last_name":"Göbel","full_name":"Göbel, Georg"},{"first_name":"Ivan","full_name":"Milenkovic, Ivan","last_name":"Milenkovic"},{"full_name":"Peterschmitt, Yvan","last_name":"Peterschmitt","first_name":"Yvan"},{"first_name":"Ramon","full_name":"Tasan, Ramon","last_name":"Tasan"},{"last_name":"Sperk","full_name":"Sperk, Günther","first_name":"Günther"},{"orcid":"0000-0001-8761-9444","last_name":"Shigemoto","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Sieghart","full_name":"Sieghart, Werner","first_name":"Werner"},{"full_name":"Singewald, Nicolas","last_name":"Singewald","first_name":"Nicolas"},{"last_name":"Lüthi","full_name":"Lüthi, Andreas","first_name":"Andreas"},{"last_name":"Ferraguti","full_name":"Ferraguti, Francesco","first_name":"Francesco"}],"main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2019.08.013","open_access":"1"}],"scopus_import":"1","date_updated":"2023-08-30T07:28:22Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"RySh"}],"article_type":"original","publication_identifier":{"issn":["0896-6273"]},"isi":1,"year":"2019","month":"11","oa_version":"Published Version","ddc":["571","599"],"type":"journal_article","publication_status":"published","external_id":{"isi":["000497963500017"],"pmid":["31543297"]},"_id":"7099","issue":"4","publisher":"Elsevier","article_processing_charge":"No","doi":"10.1016/j.neuron.2019.08.013","has_accepted_license":"1","intvolume":" 104","date_published":"2019-11-20T00:00:00Z","publication":"Neuron","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.","day":"20","volume":104,"pmid":1,"title":"Structural and functional remodeling of amygdala GABAergic synapses in associative fear learning","page":"781-794.e4","date_created":"2019-11-25T08:02:39Z","citation":{"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.","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.","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","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.","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.","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."},"quality_controlled":"1","oa":1},{"title":"Derivation of the time dependent Gross–Pitaevskii equation in two dimensions","page":"1-69","citation":{"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.","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.","short":"M. Jeblick, N.K. Leopold, P. Pickl, Communications in Mathematical Physics 372 (2019) 1–69.","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","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.","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","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."},"date_created":"2019-11-25T08:08:02Z","quality_controlled":"1","oa":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","ec_funded":1,"doi":"10.1007/s00220-019-03599-x","file_date_updated":"2020-07-14T12:47:49Z","has_accepted_license":"1","intvolume":" 372","date_published":"2019-11-08T00:00:00Z","acknowledgement":"OA fund by IST Austria","day":"08","publication":"Communications in Mathematical Physics","volume":372,"department":[{"_id":"RoSe"}],"article_type":"original","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"isi":1,"project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"year":"2019","month":"11","ddc":["510"],"oa_version":"Published Version","type":"journal_article","file":[{"creator":"dernst","file_id":"7101","relation":"main_file","file_name":"2019_CommMathPhys_Jeblick.pdf","file_size":884469,"checksum":"cd283b475dd739e04655315abd46f528","date_created":"2019-11-25T08:11:11Z","content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:49Z"}],"external_id":{"isi":["000495193700002"]},"publication_status":"published","issue":"1","_id":"7100","publisher":"Springer Nature","status":"public","author":[{"first_name":"Maximilian","last_name":"Jeblick","full_name":"Jeblick, Maximilian"},{"orcid":"0000-0002-0495-6822","last_name":"Leopold","full_name":"Leopold, Nikolai K","id":"4BC40BEC-F248-11E8-B48F-1D18A9856A87","first_name":"Nikolai K"},{"last_name":"Pickl","full_name":"Pickl, Peter","first_name":"Peter"}],"abstract":[{"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.","lang":"eng"}],"scopus_import":"1","date_updated":"2023-09-06T10:47:43Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}]}]