[{"article_type":"review","type":"journal_article","fulldoi":"https://doi.org/10.3390/cells12121613","project":[{"grant_number":"26130","_id":"62883ed7-2b32-11ec-9570-93580204e56b","name":"Functional asymmetry of medial habenula outputs in mice"}],"year":"2023","license":"https://creativecommons.org/licenses/by/4.0/","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","issue":"12","acknowledgement":"This work was supported by the Austrian Academy of Sciences ÖAW: Doc fellowship (26130) to Stefan Riegler.","has_accepted_license":"1","ddc":["570"],"publisher":"MDPI","corr_author":"1","publication_identifier":{"issn":["2073-4409"]},"abstract":[{"text":"Nitrogen is an important macronutrient required for plant growth and development, thus directly impacting agricultural productivity. In recent years, numerous studies have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen homeostasis and hormonal networks that act both locally and systemically to coordinate growth and development of plant organs. In this review, we will focus on recent advances in understanding the role of the plant hormones auxin and cytokinin and their crosstalk in nitrate-regulated growth and discuss the significance of novel findings and possible missing links.","lang":"eng"}],"scopus_import":"1","day":"13","volume":12,"month":"06","oa":1,"article_processing_charge":"Yes","external_id":{"isi":["001017033600001"],"pmid":["37371083"]},"publication":"Cells","pmid":1,"file":[{"file_size":1066802,"content_type":"application/pdf","date_updated":"2023-07-12T10:01:54Z","checksum":"6dc9df5f4f59fc27c509c275060354a5","relation":"main_file","date_created":"2023-07-12T10:01:54Z","success":1,"creator":"alisjak","file_name":"2023_cells_Abualia.pdf","access_level":"open_access","file_id":"13218"}],"publication_status":"published","author":[{"last_name":"Abualia","first_name":"R","full_name":"Abualia, R"},{"full_name":"Riegler, Stefan","first_name":"Stefan","last_name":"Riegler","orcid":"0000-0003-3413-1343","id":"FF6018E0-D806-11E9-8E43-0B14E6697425"},{"first_name":"Eva","last_name":"Benková","orcid":"0000-0002-8510-9739","id":"38F4F166-F248-11E8-B48F-1D18A9856A87","full_name":"Benková, Eva"}],"date_published":"2023-06-13T00:00:00Z","file_date_updated":"2023-07-12T10:01:54Z","isi":1,"title":"Nitrate, auxin and cytokinin - a trio to tango","doi":"10.3390/cells12121613","intvolume":"        12","date_created":"2023-07-12T07:41:25Z","quality_controlled":"1","article_number":"1613","date_updated":"2025-04-15T06:27:18Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"13214","oa_version":"Published Version","language":[{"iso":"eng"}],"department":[{"_id":"EvBe"}],"citation":{"mla":"Abualia, R., et al. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” <i>Cells</i>, vol. 12, no. 12, 1613, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/cells12121613\">10.3390/cells12121613</a>.","ama":"Abualia R, Riegler S, Benková E. Nitrate, auxin and cytokinin - a trio to tango. <i>Cells</i>. 2023;12(12). doi:<a href=\"https://doi.org/10.3390/cells12121613\">10.3390/cells12121613</a>","ista":"Abualia R, Riegler S, Benková E. 2023. Nitrate, auxin and cytokinin - a trio to tango. Cells. 12(12), 1613.","ieee":"R. Abualia, S. Riegler, and E. Benková, “Nitrate, auxin and cytokinin - a trio to tango,” <i>Cells</i>, vol. 12, no. 12. MDPI, 2023.","chicago":"Abualia, R, Stefan Riegler, and Eva Benková. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” <i>Cells</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/cells12121613\">https://doi.org/10.3390/cells12121613</a>.","apa":"Abualia, R., Riegler, S., &#38; Benková, E. (2023). Nitrate, auxin and cytokinin - a trio to tango. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells12121613\">https://doi.org/10.3390/cells12121613</a>","short":"R. Abualia, S. Riegler, E. Benková, Cells 12 (2023)."},"status":"public"},{"fulldoi":"https://doi.org/10.1007/s00205-023-01893-6","project":[{"_id":"25C6DC12-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227"}],"year":"2023","issue":"4","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","type":"journal_article","month":"08","oa":1,"article_processing_charge":"Yes (via OA deal)","arxiv":1,"external_id":{"isi":["001024369000001"],"arxiv":["2106.13185"]},"publication":"Archive for Rational Mechanics and Analysis","acknowledgement":"RS was supported by the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 694227). MP acknowledges financial support from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (ERC StG MaMBoQ, Grant Agreement No. 802901). BS acknowledges financial support from the NCCR SwissMAP, from the Swiss National Science Foundation through the Grant “Dynamical and energetic properties of Bose-Einstein condensates” and from the European Research Council through the ERC AdG CLaQS (Grant Agreement No. 834782). NB and MP were supported by Gruppo Nazionale per la Fisica Matematica (GNFM) of Italy. NB was supported by the European Research Council’s Starting Grant FERMIMATH (Grant Agreement No. 101040991).\r\nOpen access funding provided by Università degli Studi di Milano within the CRUI-CARE Agreement.","ddc":["510"],"has_accepted_license":"1","publisher":"Springer Nature","publication_identifier":{"eissn":["1432-0673"],"issn":["0003-9527"]},"scopus_import":"1","abstract":[{"text":"Recently the leading order of the correlation energy of a Fermi gas in a coupled mean-field and semiclassical scaling regime has been derived, under the assumption of an interaction potential with a small norm and with compact support in Fourier space. We generalize this result to large interaction potentials, requiring only |⋅|V^∈ℓ1(Z3). Our proof is based on approximate, collective bosonization in three dimensions. Significant improvements compared to recent work include stronger bounds on non-bosonizable terms and more efficient control on the bosonization of the kinetic energy.","lang":"eng"}],"day":"01","volume":247,"publication_status":"published","author":[{"full_name":"Benedikter, Niels P","first_name":"Niels P","id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","last_name":"Benedikter","orcid":"0000-0002-1071-6091"},{"full_name":"Porta, Marcello","first_name":"Marcello","last_name":"Porta"},{"last_name":"Schlein","first_name":"Benjamin","full_name":"Schlein, Benjamin"},{"id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","orcid":"0000-0002-6781-0521","first_name":"Robert","full_name":"Seiringer, Robert"}],"date_published":"2023-08-01T00:00:00Z","file":[{"creator":"dernst","success":1,"date_created":"2023-11-14T13:12:12Z","relation":"main_file","date_updated":"2023-11-14T13:12:12Z","checksum":"2b45828d854a253b14bf7aa196ec55e9","content_type":"application/pdf","file_size":851626,"file_id":"14535","access_level":"open_access","file_name":"2023_ArchiveRationalMechAnalysis_Benedikter.pdf"}],"isi":1,"file_date_updated":"2023-11-14T13:12:12Z","title":"Correlation energy of a weakly interacting Fermi gas with large interaction potential","doi":"10.1007/s00205-023-01893-6","ec_funded":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"department":[{"_id":"RoSe"}],"citation":{"ieee":"N. P. Benedikter, M. Porta, B. Schlein, and R. Seiringer, “Correlation energy of a weakly interacting Fermi gas with large interaction potential,” <i>Archive for Rational Mechanics and Analysis</i>, vol. 247, no. 4. Springer Nature, 2023.","ama":"Benedikter NP, Porta M, Schlein B, Seiringer R. Correlation energy of a weakly interacting Fermi gas with large interaction potential. <i>Archive for Rational Mechanics and Analysis</i>. 2023;247(4). doi:<a href=\"https://doi.org/10.1007/s00205-023-01893-6\">10.1007/s00205-023-01893-6</a>","ista":"Benedikter NP, Porta M, Schlein B, Seiringer R. 2023. Correlation energy of a weakly interacting Fermi gas with large interaction potential. Archive for Rational Mechanics and Analysis. 247(4), 65.","mla":"Benedikter, Niels P., et al. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” <i>Archive for Rational Mechanics and Analysis</i>, vol. 247, no. 4, 65, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s00205-023-01893-6\">10.1007/s00205-023-01893-6</a>.","short":"N.P. Benedikter, M. Porta, B. Schlein, R. Seiringer, Archive for Rational Mechanics and Analysis 247 (2023).","chicago":"Benedikter, Niels P, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Correlation Energy of a Weakly Interacting Fermi Gas with Large Interaction Potential.” <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00205-023-01893-6\">https://doi.org/10.1007/s00205-023-01893-6</a>.","apa":"Benedikter, N. P., Porta, M., Schlein, B., &#38; Seiringer, R. (2023). Correlation energy of a weakly interacting Fermi gas with large interaction potential. <i>Archive for Rational Mechanics and Analysis</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00205-023-01893-6\">https://doi.org/10.1007/s00205-023-01893-6</a>"},"status":"public","intvolume":"       247","date_created":"2023-07-16T22:01:08Z","article_number":"65","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-04-14T07:26:58Z","_id":"13225"},{"language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","status":"public","department":[{"_id":"RoSe"}],"citation":{"short":"L. Bossmann, S.P. Petrat, Letters in Mathematical Physics 113 (2023).","chicago":"Bossmann, Lea, and Sören P Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” <i>Letters in Mathematical Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s11005-023-01698-4\">https://doi.org/10.1007/s11005-023-01698-4</a>.","apa":"Bossmann, L., &#38; Petrat, S. P. (2023). Weak Edgeworth expansion for the mean-field Bose gas. <i>Letters in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s11005-023-01698-4\">https://doi.org/10.1007/s11005-023-01698-4</a>","ieee":"L. Bossmann and S. P. Petrat, “Weak Edgeworth expansion for the mean-field Bose gas,” <i>Letters in Mathematical Physics</i>, vol. 113, no. 4. Springer Nature, 2023.","ama":"Bossmann L, Petrat SP. Weak Edgeworth expansion for the mean-field Bose gas. <i>Letters in Mathematical Physics</i>. 2023;113(4). doi:<a href=\"https://doi.org/10.1007/s11005-023-01698-4\">10.1007/s11005-023-01698-4</a>","ista":"Bossmann L, Petrat SP. 2023. Weak Edgeworth expansion for the mean-field Bose gas. Letters in Mathematical Physics. 113(4), 77.","mla":"Bossmann, Lea, and Sören P. Petrat. “Weak Edgeworth Expansion for the Mean-Field Bose Gas.” <i>Letters in Mathematical Physics</i>, vol. 113, no. 4, 77, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1007/s11005-023-01698-4\">10.1007/s11005-023-01698-4</a>."},"article_number":"77","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-06-25T06:20:15Z","_id":"13226","intvolume":"       113","date_created":"2023-07-16T22:01:08Z","OA_type":"hybrid","file":[{"file_size":586698,"content_type":"application/pdf","date_updated":"2025-06-25T06:20:02Z","checksum":"995c902a989a6769fd3db456cfd41111","relation":"main_file","date_created":"2025-06-25T06:20:02Z","success":1,"creator":"dernst","file_name":"2023_LettersMathPhysics_Bossmann.pdf","access_level":"open_access","file_id":"19898"}],"author":[{"full_name":"Bossmann, Lea","id":"A2E3BCBE-5FCC-11E9-AA4B-76F3E5697425","orcid":"0000-0002-6854-1343","last_name":"Bossmann","first_name":"Lea"},{"last_name":"Petrat","orcid":"0000-0002-9166-5889","id":"40AC02DC-F248-11E8-B48F-1D18A9856A87","first_name":"Sören P","full_name":"Petrat, Sören P"}],"date_published":"2023-07-03T00:00:00Z","publication_status":"published","title":"Weak Edgeworth expansion for the mean-field Bose gas","isi":1,"file_date_updated":"2025-06-25T06:20:02Z","doi":"10.1007/s11005-023-01698-4","month":"07","external_id":{"isi":["001022878900002"],"arxiv":["2208.00199"]},"publication":"Letters in Mathematical Physics","OA_place":"publisher","oa":1,"article_processing_charge":"Yes (via OA deal)","arxiv":1,"publisher":"Springer Nature","corr_author":"1","acknowledgement":"It is a pleasure to thank Martin Kolb, Simone Rademacher, Robert Seiringer and Stefan Teufel for helpful discussions. Moreover, we thank the referee for many constructive comments. L.B. gratefully acknowledges funding from the German Research Foundation within the Munich Center of Quantum Science and Technology (EXC 2111) and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411. We thank the Mathematical Research Institute Oberwolfach, where part of this work was done, for their hospitality.\r\nOpen Access funding enabled and organized by Projekt DEAL.","has_accepted_license":"1","ddc":["510"],"day":"03","volume":113,"publication_identifier":{"issn":["0377-9017"],"eissn":["1573-0530"]},"scopus_import":"1","abstract":[{"text":"We consider the ground state and the low-energy excited states of a system of N identical bosons with interactions in the mean-field scaling regime. For the ground state, we derive a weak Edgeworth expansion for the fluctuations of bounded one-body operators, which yields corrections to a central limit theorem to any order in 1/N−−√. For suitable excited states, we show that the limiting distribution is a polynomial times a normal distribution, and that higher-order corrections are given by an Edgeworth-type expansion.","lang":"eng"}],"fulldoi":"https://doi.org/10.1007/s11005-023-01698-4","project":[{"grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"year":"2023","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"4","article_type":"original","type":"journal_article"},{"quality_controlled":"1","_id":"13229","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-04-14T07:46:59Z","intvolume":"        21","date_created":"2023-07-16T22:01:09Z","language":[{"iso":"eng"}],"ec_funded":1,"oa_version":"Published Version","status":"public","department":[{"_id":"CaHe"}],"citation":{"ista":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. 2023. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. PLoS Biology. 21(6), e3002146.","ama":"Shamipour S, Hofmann L, Steccari I, Kardos R, Heisenberg C-PJ. Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. <i>PLoS Biology</i>. 2023;21(6):e3002146. doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002146\">10.1371/journal.pbio.3002146</a>","mla":"Shamipour, Shayan, et al. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” <i>PLoS Biology</i>, vol. 21, no. 6, Public Library of Science, 2023, p. e3002146, doi:<a href=\"https://doi.org/10.1371/journal.pbio.3002146\">10.1371/journal.pbio.3002146</a>.","ieee":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, and C.-P. J. Heisenberg, “Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes,” <i>PLoS Biology</i>, vol. 21, no. 6. Public Library of Science, p. e3002146, 2023.","apa":"Shamipour, S., Hofmann, L., Steccari, I., Kardos, R., &#38; Heisenberg, C.-P. J. (2023). Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes. <i>PLoS Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pbio.3002146\">https://doi.org/10.1371/journal.pbio.3002146</a>","chicago":"Shamipour, Shayan, Laura Hofmann, Irene Steccari, Roland Kardos, and Carl-Philipp J Heisenberg. “Yolk Granule Fusion and Microtubule Aster Formation Regulate Cortical Granule Translocation and Exocytosis in Zebrafish Oocytes.” <i>PLoS Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pbio.3002146\">https://doi.org/10.1371/journal.pbio.3002146</a>.","short":"S. Shamipour, L. Hofmann, I. Steccari, R. Kardos, C.-P.J. Heisenberg, PLoS Biology 21 (2023) e3002146."},"file":[{"content_type":"application/pdf","file_size":4431723,"relation":"main_file","checksum":"8e88cb0e5a6433a2f1939a9030bed384","date_updated":"2023-07-18T07:59:58Z","creator":"dernst","success":1,"date_created":"2023-07-18T07:59:58Z","file_name":"2023_PloSBiology_Shamipour.pdf","access_level":"open_access","file_id":"13246"}],"publication_status":"published","pmid":1,"author":[{"full_name":"Shamipour, Shayan","last_name":"Shamipour","id":"40B34FE2-F248-11E8-B48F-1D18A9856A87","first_name":"Shayan"},{"full_name":"Hofmann, Laura","first_name":"Laura","last_name":"Hofmann","id":"b88d43f2-dc74-11ea-a0a7-e41b7912e031"},{"full_name":"Steccari, Irene","last_name":"Steccari","id":"2705C766-9FE2-11EA-B224-C6773DDC885E","first_name":"Irene"},{"full_name":"Kardos, Roland","last_name":"Kardos","id":"4039350E-F248-11E8-B48F-1D18A9856A87","first_name":"Roland"},{"last_name":"Heisenberg","orcid":"0000-0002-0912-4566","id":"39427864-F248-11E8-B48F-1D18A9856A87","first_name":"Carl-Philipp J","full_name":"Heisenberg, Carl-Philipp J"}],"date_published":"2023-06-08T00:00:00Z","page":"e3002146","isi":1,"file_date_updated":"2023-07-18T07:59:58Z","title":"Yolk granule fusion and microtubule aster formation regulate cortical granule translocation and exocytosis in zebrafish oocytes","doi":"10.1371/journal.pbio.3002146","corr_author":"1","publisher":"Public Library of Science","acknowledgement":"This work was supported by funding from the European Union (European Research Council Advanced grant 742573) to C.-P.H. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.","has_accepted_license":"1","ddc":["570"],"day":"08","volume":21,"publication_identifier":{"eissn":["1545-7885"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"Dynamic reorganization of the cytoplasm is key to many core cellular processes, such as cell division, cell migration, and cell polarization. Cytoskeletal rearrangements are thought to constitute the main drivers of cytoplasmic flows and reorganization. In contrast, remarkably little is known about how dynamic changes in size and shape of cell organelles affect cytoplasmic organization. Here, we show that within the maturing zebrafish oocyte, the surface localization of exocytosis-competent cortical granules (Cgs) upon germinal vesicle breakdown (GVBD) is achieved by the combined activities of yolk granule (Yg) fusion and microtubule aster formation and translocation. We find that Cgs are moved towards the oocyte surface through radially outward cytoplasmic flows induced by Ygs fusing and compacting towards the oocyte center in response to GVBD. We further show that vesicles decorated with the small Rab GTPase Rab11, a master regulator of vesicular trafficking and exocytosis, accumulate together with Cgs at the oocyte surface. This accumulation is achieved by Rab11-positive vesicles being transported by acentrosomal microtubule asters, the formation of which is induced by the release of CyclinB/Cdk1 upon GVBD, and which display a net movement towards the oocyte surface by preferentially binding to the oocyte actin cortex. We finally demonstrate that the decoration of Cgs by Rab11 at the oocyte surface is needed for Cg exocytosis and subsequent chorion elevation, a process central in egg activation. Collectively, these findings unravel a yet unrecognized role of organelle fusion, functioning together with cytoskeletal rearrangements, in orchestrating cytoplasmic organization during oocyte maturation."}],"month":"06","publication":"PLoS Biology","external_id":{"isi":["001003199100005"],"pmid":["37289834"]},"oa":1,"article_processing_charge":"No","article_type":"original","type":"journal_article","fulldoi":"https://doi.org/10.1371/journal.pbio.3002146","project":[{"grant_number":"742573","_id":"260F1432-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Interaction and feedback between cell mechanics and fate specification in vertebrate gastrulation"}],"year":"2023","issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"status":"public","citation":{"short":"J.A. Charlton, W.F. Mlynarski, Y.H. Bai, A.M. Hermundstad, R.L.T. Goris, PLoS Computational Biology 19 (2023).","apa":"Charlton, J. A., Mlynarski, W. F., Bai, Y. H., Hermundstad, A. M., &#38; Goris, R. L. T. (2023). Environmental dynamics shape perceptual decision bias. <i>PLoS Computational Biology</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">https://doi.org/10.1371/journal.pcbi.1011104</a>","chicago":"Charlton, Julie A., Wiktor F Mlynarski, Yoon H. Bai, Ann M. Hermundstad, and Robbe L.T. Goris. “Environmental Dynamics Shape Perceptual Decision Bias.” <i>PLoS Computational Biology</i>. Public Library of Science, 2023. <a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">https://doi.org/10.1371/journal.pcbi.1011104</a>.","ieee":"J. A. Charlton, W. F. Mlynarski, Y. H. Bai, A. M. Hermundstad, and R. L. T. Goris, “Environmental dynamics shape perceptual decision bias,” <i>PLoS Computational Biology</i>, vol. 19, no. 6. Public Library of Science, 2023.","ista":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. 2023. Environmental dynamics shape perceptual decision bias. PLoS Computational Biology. 19(6), e1011104.","ama":"Charlton JA, Mlynarski WF, Bai YH, Hermundstad AM, Goris RLT. Environmental dynamics shape perceptual decision bias. <i>PLoS Computational Biology</i>. 2023;19(6). doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">10.1371/journal.pcbi.1011104</a>","mla":"Charlton, Julie A., et al. “Environmental Dynamics Shape Perceptual Decision Bias.” <i>PLoS Computational Biology</i>, vol. 19, no. 6, e1011104, Public Library of Science, 2023, doi:<a href=\"https://doi.org/10.1371/journal.pcbi.1011104\">10.1371/journal.pcbi.1011104</a>."},"department":[{"_id":"MaJö"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","_id":"13230","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2023-08-02T06:33:50Z","article_number":"e1011104","quality_controlled":"1","date_created":"2023-07-16T22:01:09Z","intvolume":"        19","doi":"10.1371/journal.pcbi.1011104","isi":1,"file_date_updated":"2023-07-18T08:07:59Z","title":"Environmental dynamics shape perceptual decision bias","author":[{"first_name":"Julie A.","last_name":"Charlton","full_name":"Charlton, Julie A."},{"last_name":"Mlynarski","id":"358A453A-F248-11E8-B48F-1D18A9856A87","first_name":"Wiktor F","full_name":"Mlynarski, Wiktor F"},{"full_name":"Bai, Yoon H.","first_name":"Yoon H.","last_name":"Bai"},{"full_name":"Hermundstad, Ann M.","last_name":"Hermundstad","first_name":"Ann M."},{"last_name":"Goris","first_name":"Robbe L.T.","full_name":"Goris, Robbe L.T."}],"file":[{"file_id":"13247","access_level":"open_access","file_name":"2023_PloSCompBio_Charlton.pdf","creator":"dernst","date_created":"2023-07-18T08:07:59Z","success":1,"relation":"main_file","checksum":"800761fa2c647fabd6ad034589bc526e","date_updated":"2023-07-18T08:07:59Z","content_type":"application/pdf","file_size":2281868}],"pmid":1,"publication_status":"published","date_published":"2023-06-08T00:00:00Z","publication":"PLoS Computational Biology","external_id":{"isi":["001003410200003"],"pmid":["37289753"]},"article_processing_charge":"No","oa":1,"month":"06","volume":19,"day":"08","scopus_import":"1","abstract":[{"lang":"eng","text":"To interpret the sensory environment, the brain combines ambiguous sensory measurements with knowledge that reflects context-specific prior experience. But environmental contexts can change abruptly and unpredictably, resulting in uncertainty about the current context. Here we address two questions: how should context-specific prior knowledge optimally guide the interpretation of sensory stimuli in changing environments, and do human decision-making strategies resemble this optimum? We probe these questions with a task in which subjects report the orientation of ambiguous visual stimuli that were drawn from three dynamically switching distributions, representing different environmental contexts. We derive predictions for an ideal Bayesian observer that leverages knowledge about the statistical structure of the task to maximize decision accuracy, including knowledge about the dynamics of the environment. We show that its decisions are biased by the dynamically changing task context. The magnitude of this decision bias depends on the observer’s continually evolving belief about the current context. The model therefore not only predicts that decision bias will grow as the context is indicated more reliably, but also as the stability of the environment increases, and as the number of trials since the last context switch grows. Analysis of human choice data validates all three predictions, suggesting that the brain leverages knowledge of the statistical structure of environmental change when interpreting ambiguous sensory signals."}],"publication_identifier":{"eissn":["1553-7358"]},"publisher":"Public Library of Science","ddc":["570"],"has_accepted_license":"1","acknowledgement":"The authors thank Corey Ziemba and Zoe Boundy-Singer for valuable discussion and feedback.","issue":"6","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2023","fulldoi":"https://doi.org/10.1371/journal.pcbi.1011104","type":"journal_article","article_type":"original"},{"doi":"10.3390/vaccines11061014","title":"Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein","file_date_updated":"2023-07-18T07:25:43Z","isi":1,"date_published":"2023-06-01T00:00:00Z","file":[{"file_size":2339746,"content_type":"application/pdf","success":1,"date_created":"2023-07-18T07:25:43Z","creator":"dernst","checksum":"8f484c0f30f8699c589b1c29a0fd7d7f","date_updated":"2023-07-18T07:25:43Z","relation":"main_file","file_name":"2023_Vaccines_Dormeshkin.pdf","file_id":"13244","access_level":"open_access"}],"pmid":1,"publication_status":"published","author":[{"first_name":"Dmitri","last_name":"Dormeshkin","full_name":"Dormeshkin, Dmitri"},{"full_name":"Katsin, Mikalai","first_name":"Mikalai","last_name":"Katsin"},{"first_name":"Maria","last_name":"Stegantseva","full_name":"Stegantseva, Maria"},{"full_name":"Golenchenko, Sergey","last_name":"Golenchenko","first_name":"Sergey"},{"full_name":"Shapira, Michail","last_name":"Shapira","first_name":"Michail"},{"full_name":"Dubovik, Simon","first_name":"Simon","last_name":"Dubovik"},{"full_name":"Lutskovich, Dzmitry","first_name":"Dzmitry","last_name":"Lutskovich"},{"last_name":"Kavaleuski","orcid":"0000-0003-2091-526X","id":"62304f89-eb97-11eb-a6c2-8903dd183976","first_name":"Anton","full_name":"Kavaleuski, Anton"},{"last_name":"Meleshko","first_name":"Alexander","full_name":"Meleshko, Alexander"}],"citation":{"apa":"Dormeshkin, D., Katsin, M., Stegantseva, M., Golenchenko, S., Shapira, M., Dubovik, S., … Meleshko, A. (2023). Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. <i>Vaccines</i>. MDPI. <a href=\"https://doi.org/10.3390/vaccines11061014\">https://doi.org/10.3390/vaccines11061014</a>","chicago":"Dormeshkin, Dmitri, Mikalai Katsin, Maria Stegantseva, Sergey Golenchenko, Michail Shapira, Simon Dubovik, Dzmitry Lutskovich, Anton Kavaleuski, and Alexander Meleshko. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” <i>Vaccines</i>. MDPI, 2023. <a href=\"https://doi.org/10.3390/vaccines11061014\">https://doi.org/10.3390/vaccines11061014</a>.","short":"D. Dormeshkin, M. Katsin, M. Stegantseva, S. Golenchenko, M. Shapira, S. Dubovik, D. Lutskovich, A. Kavaleuski, A. Meleshko, Vaccines 11 (2023).","ama":"Dormeshkin D, Katsin M, Stegantseva M, et al. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. <i>Vaccines</i>. 2023;11(6). doi:<a href=\"https://doi.org/10.3390/vaccines11061014\">10.3390/vaccines11061014</a>","ista":"Dormeshkin D, Katsin M, Stegantseva M, Golenchenko S, Shapira M, Dubovik S, Lutskovich D, Kavaleuski A, Meleshko A. 2023. Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein. Vaccines. 11(6), 1014.","mla":"Dormeshkin, Dmitri, et al. “Design and Immunogenicity of SARS-CoV-2 DNA Vaccine Encoding RBD-PVXCP Fusion Protein.” <i>Vaccines</i>, vol. 11, no. 6, 1014, MDPI, 2023, doi:<a href=\"https://doi.org/10.3390/vaccines11061014\">10.3390/vaccines11061014</a>.","ieee":"D. Dormeshkin <i>et al.</i>, “Design and immunogenicity of SARS-CoV-2 DNA vaccine encoding RBD-PVXCP fusion protein,” <i>Vaccines</i>, vol. 11, no. 6. MDPI, 2023."},"department":[{"_id":"LeSa"}],"status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"date_created":"2023-07-16T22:01:10Z","intvolume":"        11","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"13232","date_updated":"2025-04-23T13:01:23Z","article_number":"1014","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6","year":"2023","fulldoi":"https://doi.org/10.3390/vaccines11061014","type":"journal_article","article_type":"original","article_processing_charge":"No","oa":1,"external_id":{"pmid":["37376403"],"isi":["001017740000001"]},"publication":"Vaccines","month":"06","scopus_import":"1","abstract":[{"text":"The potential of immune-evasive mutation accumulation in the SARS-CoV-2 virus has led to its rapid spread, causing over 600 million confirmed cases and more than 6.5 million confirmed deaths. The huge demand for the rapid development and deployment of low-cost and effective vaccines against emerging variants has renewed interest in DNA vaccine technology. Here, we report the rapid generation and immunological evaluation of novel DNA vaccine candidates against the Wuhan-Hu-1 and Omicron variants based on the RBD protein fused with the Potato virus X coat protein (PVXCP). The delivery of DNA vaccines using electroporation in a two-dose regimen induced high-antibody titers and profound cellular responses in mice. The antibody titers induced against the Omicron variant of the vaccine were sufficient for effective protection against both Omicron and Wuhan-Hu-1 virus infections. The PVXCP protein in the vaccine construct shifted the immune response to the favorable Th1-like type and provided the oligomerization of RBD-PVXCP protein. Naked DNA delivery by needle-free injection allowed us to achieve antibody titers comparable with mRNA-LNP delivery in rabbits. These data identify the RBD-PVXCP DNA vaccine platform as a promising solution for robust and effective SARS-CoV-2 protection, supporting further translational study.","lang":"eng"}],"publication_identifier":{"eissn":["2076-393X"]},"volume":11,"day":"01","has_accepted_license":"1","ddc":["570"],"acknowledgement":"The authors declare that this study received funding from Immunofusion. The funder was not involved in the study design, collection, analysis, interpretation of data, the writing of this article, or the decision to submit it for publication. The authors express their gratitude to the Institute of Physiology of the National Academy of Sciences of Belarus for providing assistance in keeping laboratory animals.","publisher":"MDPI"},{"article_processing_charge":"Yes (in subscription journal)","arxiv":1,"oa":1,"publication":"International Journal on Software Tools for Technology Transfer","external_id":{"arxiv":["2009.06429"],"isi":["001020160000001"]},"month":"08","related_material":{"record":[{"id":"10206","status":"public","relation":"shorter_version"}]},"abstract":[{"text":"Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. We consider the problem of monitoring the classification decisions of neural networks in the presence of novel classes. For this purpose, we generalize our recently proposed abstraction-based monitor from binary output to real-valued quantitative output. This quantitative output enables new applications, two of which we investigate in the paper. As our first application, we introduce an algorithmic framework for active monitoring of a neural network, which allows us to learn new classes dynamically and yet maintain high monitoring performance. As our second application, we present an offline procedure to retrain the neural network to improve the monitor’s detection performance without deteriorating the network’s classification accuracy. Our experimental evaluation demonstrates both the benefits of our active monitoring framework in dynamic scenarios and the effectiveness of the retraining procedure.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["1433-2787"],"issn":["1433-2779"]},"volume":25,"day":"01","has_accepted_license":"1","ddc":["000"],"acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, by DIREC - Digital Research Centre Denmark, and by the Villum Investigator Grant S4OS.","corr_author":"1","publisher":"Springer Nature","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","fulldoi":"https://doi.org/10.1007/s10009-023-00711-4","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"}],"type":"journal_article","article_type":"original","citation":{"short":"K. Kueffner, A. Lukina, C. Schilling, T.A. Henzinger, International Journal on Software Tools for Technology Transfer 25 (2023) 575–592.","apa":"Kueffner, K., Lukina, A., Schilling, C., &#38; Henzinger, T. A. (2023). Into the unknown: Active monitoring of neural networks (extended version). <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10009-023-00711-4\">https://doi.org/10.1007/s10009-023-00711-4</a>","chicago":"Kueffner, Konstantin, Anna Lukina, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” <i>International Journal on Software Tools for Technology Transfer</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s10009-023-00711-4\">https://doi.org/10.1007/s10009-023-00711-4</a>.","ieee":"K. Kueffner, A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: Active monitoring of neural networks (extended version),” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 25. Springer Nature, pp. 575–592, 2023.","mla":"Kueffner, Konstantin, et al. “Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” <i>International Journal on Software Tools for Technology Transfer</i>, vol. 25, Springer Nature, 2023, pp. 575–92, doi:<a href=\"https://doi.org/10.1007/s10009-023-00711-4\">10.1007/s10009-023-00711-4</a>.","ista":"Kueffner K, Lukina A, Schilling C, Henzinger TA. 2023. Into the unknown: Active monitoring of neural networks (extended version). International Journal on Software Tools for Technology Transfer. 25, 575–592.","ama":"Kueffner K, Lukina A, Schilling C, Henzinger TA. Into the unknown: Active monitoring of neural networks (extended version). <i>International Journal on Software Tools for Technology Transfer</i>. 2023;25:575-592. doi:<a href=\"https://doi.org/10.1007/s10009-023-00711-4\">10.1007/s10009-023-00711-4</a>"},"department":[{"_id":"ToHe"}],"status":"public","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"date_created":"2023-07-16T22:01:11Z","intvolume":"        25","date_updated":"2025-04-15T06:55:00Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"13234","quality_controlled":"1","doi":"10.1007/s10009-023-00711-4","file_date_updated":"2024-01-30T12:06:07Z","isi":1,"title":"Into the unknown: Active monitoring of neural networks (extended version)","page":"575-592","publication_status":"published","author":[{"full_name":"Kueffner, Konstantin","orcid":"0000-0001-8974-2542","last_name":"Kueffner","id":"8121a2d0-dc85-11ea-9058-af578f3b4515","first_name":"Konstantin"},{"full_name":"Lukina, Anna","last_name":"Lukina","id":"CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425","first_name":"Anna"},{"full_name":"Schilling, Christian","last_name":"Schilling","orcid":"0000-0003-3658-1065","id":"3A2F4DCE-F248-11E8-B48F-1D18A9856A87","first_name":"Christian"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","last_name":"Henzinger","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"}],"file":[{"success":1,"date_created":"2024-01-30T12:06:07Z","creator":"dernst","date_updated":"2024-01-30T12:06:07Z","checksum":"3c4b347f39412a76872f9a6f30101f94","relation":"main_file","content_type":"application/pdf","file_size":13387667,"file_id":"14903","access_level":"open_access","file_name":"2023_JourSoftwareTools_Kueffner.pdf"}],"date_published":"2023-08-01T00:00:00Z"},{"month":"06","publication":"ACS Nano","external_id":{"isi":["001008564800001"],"pmid":["37310395"]},"article_processing_charge":"No","publisher":"American Chemical Society","acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (Grant No. 22208293). Y.Z. acknowledges support from the SBIR program NanoOhmics. J.L. is grateful for the project supported by the Natural Science Foundation of Sichuan (2022NSFSC1229). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.","day":"13","volume":17,"publication_identifier":{"issn":["1936-0851"],"eissn":["1936-086X"]},"abstract":[{"text":"AgSbSe2 is a promising thermoelectric (TE) p-type material for applications in the middle-temperature range. AgSbSe2 is characterized by relatively low thermal conductivities and high Seebeck coefficients, but its main limitation is moderate electrical conductivity. Herein, we detail an efficient and scalable hot-injection synthesis route to produce AgSbSe2 nanocrystals (NCs). To increase the carrier concentration and improve the electrical conductivity, these NCs are doped with Sn2+ on Sb3+ sites. Upon processing, the Sn2+ chemical state is conserved using a reducing NaBH4 solution to displace the organic ligand and anneal the material under a forming gas flow. The TE properties of the dense materials obtained from the consolidation of the NCs using a hot pressing are then characterized. The presence of Sn2+ ions replacing Sb3+ significantly increases the charge carrier concentration and, consequently, the electrical conductivity. Opportunely, the measured Seebeck coefficient varied within a small range upon Sn doping. The excellent performance obtained when Sn2+ ions are prevented from oxidation is rationalized by modeling the system. Calculated band structures disclosed that Sn doping induces convergence of the AgSbSe2 valence bands, accounting for an enhanced electronic effective mass. The dramatically enhanced carrier transport leads to a maximized power factor for AgSb0.98Sn0.02Se2 of 0.63 mW m–1 K–2 at 640 K. Thermally, phonon scattering is significantly enhanced in the NC-based materials, yielding an ultralow thermal conductivity of 0.3 W mK–1 at 666 K. Overall, a record-high figure of merit (zT) is obtained at 666 K for AgSb0.98Sn0.02Se2 at zT = 1.37, well above the values obtained for undoped AgSbSe2, at zT = 0.58 and state-of-art Pb- and Te-free materials, which makes AgSb0.98Sn0.02Se2 an excellent p-type candidate for medium-temperature TE applications.","lang":"eng"}],"scopus_import":"1","fulldoi":"https://doi.org/10.1021/acsnano.3c03541","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"year":"2023","issue":"12","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"None","status":"public","department":[{"_id":"MaIb"}],"citation":{"ieee":"Y. Liu <i>et al.</i>, “Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance,” <i>ACS Nano</i>, vol. 17, no. 12. American Chemical Society, pp. 11923–11934, 2023.","ista":"Liu Y, Li M, Wan S, Lim KH, Zhang Y, Li M, Li J, Ibáñez M, Hong M, Cabot A. 2023. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. ACS Nano. 17(12), 11923–11934.","ama":"Liu Y, Li M, Wan S, et al. Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. <i>ACS Nano</i>. 2023;17(12):11923–11934. doi:<a href=\"https://doi.org/10.1021/acsnano.3c03541\">10.1021/acsnano.3c03541</a>","mla":"Liu, Yu, et al. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” <i>ACS Nano</i>, vol. 17, no. 12, American Chemical Society, 2023, pp. 11923–11934, doi:<a href=\"https://doi.org/10.1021/acsnano.3c03541\">10.1021/acsnano.3c03541</a>.","short":"Y. Liu, M. Li, S. Wan, K.H. Lim, Y. Zhang, M. Li, J. Li, M. Ibáñez, M. Hong, A. Cabot, ACS Nano 17 (2023) 11923–11934.","apa":"Liu, Y., Li, M., Wan, S., Lim, K. H., Zhang, Y., Li, M., … Cabot, A. (2023). Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance. <i>ACS Nano</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acsnano.3c03541\">https://doi.org/10.1021/acsnano.3c03541</a>","chicago":"Liu, Yu, Mingquan Li, Shanhong Wan, Khak Ho Lim, Yu Zhang, Mengyao Li, Junshan Li, Maria Ibáñez, Min Hong, and Andreu Cabot. “Surface Chemistry and Band Engineering in AgSbSe₂: Toward High Thermoelectric Performance.” <i>ACS Nano</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acsnano.3c03541\">https://doi.org/10.1021/acsnano.3c03541</a>."},"quality_controlled":"1","date_updated":"2025-04-15T06:36:40Z","_id":"13235","intvolume":"        17","date_created":"2023-07-16T22:01:11Z","author":[{"full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","last_name":"Liu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87","first_name":"Yu"},{"full_name":"Li, Mingquan","first_name":"Mingquan","last_name":"Li"},{"first_name":"Shanhong","last_name":"Wan","full_name":"Wan, Shanhong"},{"last_name":"Lim","first_name":"Khak Ho","full_name":"Lim, Khak Ho"},{"full_name":"Zhang, Yu","first_name":"Yu","last_name":"Zhang"},{"full_name":"Li, Mengyao","first_name":"Mengyao","last_name":"Li"},{"full_name":"Li, Junshan","last_name":"Li","first_name":"Junshan"},{"full_name":"Ibáñez, Maria","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","orcid":"0000-0001-5013-2843"},{"full_name":"Hong, Min","last_name":"Hong","first_name":"Min"},{"full_name":"Cabot, Andreu","first_name":"Andreu","last_name":"Cabot"}],"date_published":"2023-06-13T00:00:00Z","publication_status":"published","pmid":1,"page":"11923–11934","title":"Surface chemistry and band engineering in AgSbSe₂: Toward high thermoelectric performance","isi":1,"doi":"10.1021/acsnano.3c03541"},{"citation":{"mla":"Michaels, Thomas C. T., et al. “Amyloid Formation as a Protein Phase Transition.” <i>Nature Reviews Physics</i>, vol. 5, Springer Nature, 2023, pp. 379–397, doi:<a href=\"https://doi.org/10.1038/s42254-023-00598-9\">10.1038/s42254-023-00598-9</a>.","ista":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. 2023. Amyloid formation as a protein phase transition. Nature Reviews Physics. 5, 379–397.","ama":"Michaels TCT, Qian D, Šarić A, Vendruscolo M, Linse S, Knowles TPJ. Amyloid formation as a protein phase transition. <i>Nature Reviews Physics</i>. 2023;5:379–397. doi:<a href=\"https://doi.org/10.1038/s42254-023-00598-9\">10.1038/s42254-023-00598-9</a>","ieee":"T. C. T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, and T. P. J. Knowles, “Amyloid formation as a protein phase transition,” <i>Nature Reviews Physics</i>, vol. 5. Springer Nature, pp. 379–397, 2023.","apa":"Michaels, T. C. T., Qian, D., Šarić, A., Vendruscolo, M., Linse, S., &#38; Knowles, T. P. J. (2023). Amyloid formation as a protein phase transition. <i>Nature Reviews Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s42254-023-00598-9\">https://doi.org/10.1038/s42254-023-00598-9</a>","chicago":"Michaels, Thomas C.T., Daoyuan Qian, Anđela Šarić, Michele Vendruscolo, Sara Linse, and Tuomas P.J. Knowles. “Amyloid Formation as a Protein Phase Transition.” <i>Nature Reviews Physics</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s42254-023-00598-9\">https://doi.org/10.1038/s42254-023-00598-9</a>.","short":"T.C.T. Michaels, D. Qian, A. Šarić, M. Vendruscolo, S. Linse, T.P.J. Knowles, Nature Reviews Physics 5 (2023) 379–397."},"department":[{"_id":"AnSa"}],"status":"public","oa_version":"None","language":[{"iso":"eng"}],"date_created":"2023-07-16T22:01:12Z","intvolume":"         5","date_updated":"2023-08-02T06:28:38Z","_id":"13237","quality_controlled":"1","doi":"10.1038/s42254-023-00598-9","isi":1,"title":"Amyloid formation as a protein phase transition","page":"379–397","publication_status":"published","author":[{"last_name":"Michaels","first_name":"Thomas C.T.","full_name":"Michaels, Thomas C.T."},{"full_name":"Qian, Daoyuan","last_name":"Qian","first_name":"Daoyuan"},{"orcid":"0000-0002-7854-2139","last_name":"Šarić","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","first_name":"Anđela","full_name":"Šarić, Anđela"},{"full_name":"Vendruscolo, Michele","first_name":"Michele","last_name":"Vendruscolo"},{"first_name":"Sara","last_name":"Linse","full_name":"Linse, Sara"},{"first_name":"Tuomas P.J.","last_name":"Knowles","full_name":"Knowles, Tuomas P.J."}],"date_published":"2023-07-01T00:00:00Z","article_processing_charge":"No","publication":"Nature Reviews Physics","external_id":{"isi":["001017539800001"]},"month":"07","abstract":[{"text":"The formation of amyloid fibrils is a general class of protein self-assembly behaviour, which is associated with both functional biology and the development of a number of disorders, such as Alzheimer and Parkinson diseases. In this Review, we discuss how general physical concepts from the study of phase transitions can be used to illuminate the fundamental mechanisms of amyloid self-assembly. We summarize progress in the efforts to describe the essential biophysical features of amyloid self-assembly as a nucleation-and-growth process and discuss how master equation approaches can reveal the key molecular pathways underlying this process, including the role of secondary nucleation. Additionally, we outline how non-classical aspects of aggregate formation involving oligomers or biomolecular condensates have emerged, inspiring developments in understanding, modelling and modulating complex protein assembly pathways. Finally, we consider how these concepts can be applied to kinetics-based drug discovery and therapeutic design to develop treatments for protein aggregation diseases.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["2522-5820"]},"volume":5,"day":"01","acknowledgement":"The authors acknowledge support from the Institute for the Physics of Living Systems, University College London (T.C.T.M.), the Swedish Research Council (2015-00143) (S.L.), the European Research Council under the European Union’s Seventh Framework Programme (FP7/2007-2013) through the ERC grant PhysProt (agreement no. 337969) (T.P.J.K.), the BBSRC (T.P.J.K.), the Newman Foundation (T.P.J.K.) and the Wellcome Trust Collaborative Award 203249/Z/16/Z (T.P.J.K.). The authors thank C. Flandoli for help with illustrations.","publisher":"Springer Nature","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","year":"2023","fulldoi":"https://doi.org/10.1038/s42254-023-00598-9","type":"journal_article","article_type":"original"},{"page":"6309-6314","date_published":"2023-07-05T00:00:00Z","file":[{"file_size":2121252,"content_type":"application/pdf","relation":"main_file","date_updated":"2023-07-19T06:55:39Z","checksum":"c0c040063f06a51b9c463adc504f1a23","creator":"dernst","date_created":"2023-07-19T06:55:39Z","success":1,"file_name":"2023_JourPhysChemistry_Wei.pdf","access_level":"open_access","file_id":"13253"}],"pmid":1,"publication_status":"published","author":[{"orcid":"0000-0001-8913-9719","last_name":"Wei","id":"0c5ff007-2600-11ee-b896-98bd8d663294","first_name":"Yujing","full_name":"Wei, Yujing"},{"full_name":"Volosniev, Artem","first_name":"Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","last_name":"Volosniev"},{"full_name":"Lorenc, Dusan","last_name":"Lorenc","id":"40D8A3E6-F248-11E8-B48F-1D18A9856A87","first_name":"Dusan"},{"last_name":"Zhumekenov","first_name":"Ayan A.","full_name":"Zhumekenov, Ayan A."},{"full_name":"Bakr, Osman M.","first_name":"Osman M.","last_name":"Bakr"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail"},{"full_name":"Alpichshev, Zhanybek","id":"45E67A2A-F248-11E8-B48F-1D18A9856A87","last_name":"Alpichshev","orcid":"0000-0002-7183-5203","first_name":"Zhanybek"}],"keyword":["General Materials Science","Physical and Theoretical Chemistry"],"doi":"10.1021/acs.jpclett.3c01158","title":"Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites","isi":1,"file_date_updated":"2023-07-19T06:55:39Z","date_created":"2023-07-18T11:13:17Z","intvolume":"        14","date_updated":"2025-04-23T13:01:50Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"13251","quality_controlled":"1","oa_version":"Published Version","ec_funded":1,"language":[{"iso":"eng"}],"citation":{"apa":"Wei, Y., Volosniev, A., Lorenc, D., Zhumekenov, A. A., Bakr, O. M., Lemeshko, M., &#38; Alpichshev, Z. (2023). Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">https://doi.org/10.1021/acs.jpclett.3c01158</a>","chicago":"Wei, Yujing, Artem Volosniev, Dusan Lorenc, Ayan A. Zhumekenov, Osman M. Bakr, Mikhail Lemeshko, and Zhanybek Alpichshev. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” <i>The Journal of Physical Chemistry Letters</i>. American Chemical Society, 2023. <a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">https://doi.org/10.1021/acs.jpclett.3c01158</a>.","short":"Y. Wei, A. Volosniev, D. Lorenc, A.A. Zhumekenov, O.M. Bakr, M. Lemeshko, Z. Alpichshev, The Journal of Physical Chemistry Letters 14 (2023) 6309–6314.","ista":"Wei Y, Volosniev A, Lorenc D, Zhumekenov AA, Bakr OM, Lemeshko M, Alpichshev Z. 2023. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. The Journal of Physical Chemistry Letters. 14(27), 6309–6314.","ama":"Wei Y, Volosniev A, Lorenc D, et al. Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites. <i>The Journal of Physical Chemistry Letters</i>. 2023;14(27):6309-6314. doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">10.1021/acs.jpclett.3c01158</a>","mla":"Wei, Yujing, et al. “Bond Polarizability as a Probe of Local Crystal Fields in Hybrid Lead-Halide Perovskites.” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 27, American Chemical Society, 2023, pp. 6309–14, doi:<a href=\"https://doi.org/10.1021/acs.jpclett.3c01158\">10.1021/acs.jpclett.3c01158</a>.","ieee":"Y. Wei <i>et al.</i>, “Bond polarizability as a probe of local crystal fields in hybrid lead-halide perovskites,” <i>The Journal of Physical Chemistry Letters</i>, vol. 14, no. 27. American Chemical Society, pp. 6309–6314, 2023."},"department":[{"_id":"MiLe"},{"_id":"ZhAl"}],"status":"public","article_type":"original","type":"journal_article","year":"2023","project":[{"grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"fulldoi":"https://doi.org/10.1021/acs.jpclett.3c01158","issue":"27","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"has_accepted_license":"1","acknowledgement":"We thank Bingqing Cheng and Hong-Zhou Ye for valuable discussions; Y.W.’s work at IST Austria was supported through ISTernship summer internship program funded by OeADGmbH; D.L. and Z.A. acknowledge support by IST Austria (ISTA); M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).\r\nA.A.Z. and O.M.B. acknowledge support by KAUST.","publisher":"American Chemical Society","corr_author":"1","scopus_import":"1","abstract":[{"text":"A rotating organic cation and a dynamically disordered soft inorganic cage are the hallmark features of organic-inorganic lead-halide perovskites. Understanding the interplay between these two subsystems is a challenging problem, but it is this coupling that is widely conjectured to be responsible for the unique behavior of photocarriers in these materials. In this work, we use the fact that the polarizability of the organic cation strongly depends on the ambient electrostatic environment to put the molecule forward as a sensitive probe of the local crystal fields inside the lattice cell. We measure the average polarizability of the C/N–H bond stretching mode by means of infrared spectroscopy, which allows us to deduce the character of the motion of the cation molecule, find the magnitude of the local crystal field, and place an estimate on the strength of the hydrogen bond between the hydrogen and halide atoms. Our results pave the way for understanding electric fields in lead-halide perovskites using infrared bond spectroscopy.","lang":"eng"}],"publication_identifier":{"eissn":["1948-7185"]},"volume":14,"day":"05","month":"07","article_processing_charge":"Yes (via OA deal)","arxiv":1,"oa":1,"external_id":{"pmid":["37405449"],"arxiv":["2304.14198"],"isi":["001022811500001"]},"publication":"The Journal of Physical Chemistry Letters"},{"title":"An assessment of the ENSO-monsoon teleconnection in a warming climate","isi":1,"file_date_updated":"2023-07-31T08:00:01Z","doi":"10.1038/s41612-023-00411-5","file":[{"relation":"main_file","checksum":"e9967d436a83b8ffcc6f58782e1f7500","date_updated":"2023-07-31T08:00:01Z","creator":"dernst","success":1,"date_created":"2023-07-31T08:00:01Z","content_type":"application/pdf","file_size":1750712,"access_level":"open_access","file_id":"13326","file_name":"2023_npjclimate_Goswami.pdf"}],"date_published":"2023-07-08T00:00:00Z","author":[{"first_name":"Bidyut B","last_name":"Goswami","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","full_name":"Goswami, Bidyut B"},{"last_name":"An","first_name":"Soon Il","full_name":"An, Soon Il"}],"publication_status":"published","department":[{"_id":"CaMu"}],"citation":{"ama":"GOSWAMI BB, An SI. An assessment of the ENSO-monsoon teleconnection in a warming climate. <i>npj Climate and Atmospheric Science</i>. 2023;6. doi:<a href=\"https://doi.org/10.1038/s41612-023-00411-5\">10.1038/s41612-023-00411-5</a>","ista":"GOSWAMI BB, An SI. 2023. An assessment of the ENSO-monsoon teleconnection in a warming climate. npj Climate and Atmospheric Science. 6, 82.","mla":"GOSWAMI, BIDYUT B., and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>, vol. 6, 82, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41612-023-00411-5\">10.1038/s41612-023-00411-5</a>.","ieee":"B. B. GOSWAMI and S. I. An, “An assessment of the ENSO-monsoon teleconnection in a warming climate,” <i>npj Climate and Atmospheric Science</i>, vol. 6. Springer Nature, 2023.","apa":"GOSWAMI, B. B., &#38; An, S. I. (2023). An assessment of the ENSO-monsoon teleconnection in a warming climate. <i>Npj Climate and Atmospheric Science</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41612-023-00411-5\">https://doi.org/10.1038/s41612-023-00411-5</a>","chicago":"GOSWAMI, BIDYUT B, and Soon Il An. “An Assessment of the ENSO-Monsoon Teleconnection in a Warming Climate.” <i>Npj Climate and Atmospheric Science</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41612-023-00411-5\">https://doi.org/10.1038/s41612-023-00411-5</a>.","short":"B.B. GOSWAMI, S.I. An, Npj Climate and Atmospheric Science 6 (2023)."},"status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"intvolume":"         6","date_created":"2023-07-23T22:01:10Z","article_number":"82","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"13256","date_updated":"2023-08-02T06:38:07Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","fulldoi":"https://doi.org/10.1038/s41612-023-00411-5","year":"2023","type":"journal_article","article_type":"original","oa":1,"article_processing_charge":"Yes","publication":"npj Climate and Atmospheric Science","external_id":{"isi":["001024920300002"]},"month":"07","publication_identifier":{"eissn":["2397-3722"]},"abstract":[{"text":"The El Niño-Southern Oscillation (ENSO) and the Indian summer monsoon (ISM, or monsoon) are two giants of tropical climate. Here we assess the future evolution of the ENSO-monsoon teleconnection in climate simulations with idealized forcing of CO2 increment at a rate of 1% year-1 starting from a present-day condition (367 p.p.m.) until quadrupling. We find a monotonous weakening of the ENSO-monsoon teleconnection with the increase in CO2. Increased co-occurrences of El Niño and positive Indian Ocean Dipoles (pIODs) in a warmer climate weaken the teleconnection. Co-occurrences of El Niño and pIOD are attributable to mean sea surface temperature (SST) warming that resembles a pIOD-type warming pattern in the Indian Ocean and an El Niño-type warming in the Pacific. Since ENSO is a critical precursor of the strength of the Indian monsoon, a weakening of this relation may mean a less predictable Indian monsoon in a warmer climate.","lang":"eng"}],"scopus_import":"1","day":"08","volume":6,"acknowledgement":"This work was supported by National Research Foundation of Korea (NRF) grants funded by the Korean government (MSIT) (NRF-2018R1A5A1024958, RS-2023-00208000). Model simulation and data transfer were supported by the National Supercomputing Center with supercomputing resources including technical support (KSC-2019-CHA-0005), the National Center for Meteorological Supercomputer of the Korea Meteorological Administration (KMA), and by the Korea Research Environment Open NETwork (KREONET), respectively. We sincerely thank Dr. Jongsoo Shin of Pohang University of Science and Technology, Pohang, South Korea for the model simulations.","ddc":["550"],"has_accepted_license":"1","publisher":"Springer Nature"},{"article_processing_charge":"No","arxiv":1,"oa":1,"publication":"Physical Review B","external_id":{"arxiv":["2208.10038"],"isi":["001062708600002"]},"month":"07","scopus_import":"1","abstract":[{"text":"The magnetotropic susceptibility is the thermodynamic coefficient associated with the rotational anisotropy of the free energy in an external magnetic field and is closely related to the magnetic susceptibility. It emerges naturally in frequency-shift measurements of oscillating mechanical cantilevers, which are becoming an increasingly important tool in the quantitative study of the thermodynamics of modern condensed-matter systems. Here we discuss the basic properties of the magnetotropic susceptibility as they relate to the experimental aspects of frequency-shift measurements, as well as to the interpretation of those experiments in terms of the intrinsic properties of the system under study.","lang":"eng"}],"publication_identifier":{"issn":["2469-9950"],"eissn":["2469-9969"]},"volume":108,"day":"15","acknowledgement":"We thank Aharon Kapitulnik, Philip Moll, and Andreas Rydh for illuminating discussions. The work at the Los Alamos National Laboratory is supported by National Science Foundation Cooperative Agreements No. DMR-1157490 and No. DMR-1644779, the state of Florida, and the U.S. Department of Energy. A.S. acknowledges support from the DOE/BES Science of 100T grant. B.J.R. acknowledges funding from the National Science Foundation under Grant No.\r\nDMR-1752784.","publisher":"American Physical Society","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","year":"2023","fulldoi":"https://doi.org/10.1103/PhysRevB.108.035111","type":"journal_article","article_type":"original","citation":{"chicago":"Shekhter, A., R. D. Mcdonald, B. J. Ramshaw, and Kimberly A Modic. “Magnetotropic Susceptibility.” <i>Physical Review B</i>. American Physical Society, 2023. <a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">https://doi.org/10.1103/PhysRevB.108.035111</a>.","apa":"Shekhter, A., Mcdonald, R. D., Ramshaw, B. J., &#38; Modic, K. A. (2023). Magnetotropic susceptibility. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">https://doi.org/10.1103/PhysRevB.108.035111</a>","short":"A. Shekhter, R.D. Mcdonald, B.J. Ramshaw, K.A. Modic, Physical Review B 108 (2023).","ista":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. 2023. Magnetotropic susceptibility. Physical Review B. 108(3), 035111.","ama":"Shekhter A, Mcdonald RD, Ramshaw BJ, Modic KA. Magnetotropic susceptibility. <i>Physical Review B</i>. 2023;108(3). doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">10.1103/PhysRevB.108.035111</a>","mla":"Shekhter, A., et al. “Magnetotropic Susceptibility.” <i>Physical Review B</i>, vol. 108, no. 3, 035111, American Physical Society, 2023, doi:<a href=\"https://doi.org/10.1103/PhysRevB.108.035111\">10.1103/PhysRevB.108.035111</a>.","ieee":"A. Shekhter, R. D. Mcdonald, B. J. Ramshaw, and K. A. Modic, “Magnetotropic susceptibility,” <i>Physical Review B</i>, vol. 108, no. 3. American Physical Society, 2023."},"department":[{"_id":"KiMo"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.10038"}],"status":"public","oa_version":"Preprint","language":[{"iso":"eng"}],"date_created":"2023-07-23T22:01:10Z","intvolume":"       108","date_updated":"2023-12-13T11:58:57Z","_id":"13257","quality_controlled":"1","article_number":"035111","doi":"10.1103/PhysRevB.108.035111","isi":1,"title":"Magnetotropic susceptibility","publication_status":"published","author":[{"first_name":"A.","last_name":"Shekhter","full_name":"Shekhter, A."},{"first_name":"R. D.","last_name":"Mcdonald","full_name":"Mcdonald, R. D."},{"last_name":"Ramshaw","first_name":"B. J.","full_name":"Ramshaw, B. J."},{"first_name":"Kimberly A","last_name":"Modic","orcid":"0000-0001-9760-3147","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","full_name":"Modic, Kimberly A"}],"date_published":"2023-07-15T00:00:00Z"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications"},{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"fulldoi":"https://doi.org/10.1038/s41467-023-39625-9","year":"2023","type":"journal_article","article_type":"original","oa":1,"article_processing_charge":"Yes","publication":"Nature Communications","external_id":{"pmid":["37438341"],"isi":["001029450400031"]},"related_material":{"record":[{"status":"public","relation":"research_data","id":"13336"}]},"month":"07","publication_identifier":{"eissn":["2041-1723"]},"abstract":[{"text":"Many human interactions feature the characteristics of social dilemmas where individual actions have consequences for the group and the environment. The feedback between behavior and environment can be studied with the framework of stochastic games. In stochastic games, the state of the environment can change, depending on the choices made by group members. Past work suggests that such feedback can reinforce cooperative behaviors. In particular, cooperation can evolve in stochastic games even if it is infeasible in each separate repeated game. In stochastic games, participants have an interest in conditioning their strategies on the state of the environment. Yet in many applications, precise information about the state could be scarce. Here, we study how the availability of information (or lack thereof) shapes evolution of cooperation. Already for simple examples of two state games we find surprising effects. In some cases, cooperation is only possible if there is precise information about the state of the environment. In other cases, cooperation is most abundant when there is no information about the state of the environment. We systematically analyze all stochastic games of a given complexity class, to determine when receiving information about the environment is better, neutral, or worse for evolution of cooperation.","lang":"eng"}],"scopus_import":"1","day":"12","volume":14,"acknowledgement":"This work was supported by the European Research Council CoG 863818 (ForM-SMArt) (to K.C.), the European Research Council Starting Grant 850529: E-DIRECT (to C.H.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement #754411 and the French Agence Nationale de la Recherche (under the Investissement d’Avenir programme, ANR-17-EURE-0010) (to M.K.).","has_accepted_license":"1","ddc":["000"],"publisher":"Springer Nature","corr_author":"1","isi":1,"file_date_updated":"2023-07-31T11:32:36Z","title":"The effect of environmental information on evolution of cooperation in stochastic games","doi":"10.1038/s41467-023-39625-9","file":[{"file_size":1601682,"content_type":"application/pdf","checksum":"5aceefdfe76686267b93ae4fe81899f1","date_updated":"2023-07-31T11:32:36Z","relation":"main_file","date_created":"2023-07-31T11:32:36Z","success":1,"creator":"dernst","file_name":"2023_NatureComm_Kleshnina.pdf","access_level":"open_access","file_id":"13337"}],"author":[{"id":"4E21749C-F248-11E8-B48F-1D18A9856A87","last_name":"Kleshnina","first_name":"Maria","full_name":"Kleshnina, Maria"},{"orcid":"0000-0001-5116-955X","last_name":"Hilbe","id":"2FDF8F3C-F248-11E8-B48F-1D18A9856A87","first_name":"Christian","full_name":"Hilbe, Christian"},{"orcid":"0000-0001-6687-1210","last_name":"Simsa","id":"409d615c-2f95-11ee-b934-90a352102c1e","first_name":"Stepan","full_name":"Simsa, Stepan"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu"},{"last_name":"Nowak","first_name":"Martin A.","full_name":"Nowak, Martin A."}],"pmid":1,"publication_status":"published","date_published":"2023-07-12T00:00:00Z","department":[{"_id":"KrCh"}],"citation":{"chicago":"Kleshnina, Maria, Christian Hilbe, Stepan Simsa, Krishnendu Chatterjee, and Martin A. Nowak. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>.","apa":"Kleshnina, M., Hilbe, C., Simsa, S., Chatterjee, K., &#38; Nowak, M. A. (2023). The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-023-39625-9\">https://doi.org/10.1038/s41467-023-39625-9</a>","short":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, M.A. Nowak, Nature Communications 14 (2023).","mla":"Kleshnina, Maria, et al. “The Effect of Environmental Information on Evolution of Cooperation in Stochastic Games.” <i>Nature Communications</i>, vol. 14, 4153, Springer Nature, 2023, doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>.","ama":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. The effect of environmental information on evolution of cooperation in stochastic games. <i>Nature Communications</i>. 2023;14. doi:<a href=\"https://doi.org/10.1038/s41467-023-39625-9\">10.1038/s41467-023-39625-9</a>","ista":"Kleshnina M, Hilbe C, Simsa S, Chatterjee K, Nowak MA. 2023. The effect of environmental information on evolution of cooperation in stochastic games. Nature Communications. 14, 4153.","ieee":"M. Kleshnina, C. Hilbe, S. Simsa, K. Chatterjee, and M. A. Nowak, “The effect of environmental information on evolution of cooperation in stochastic games,” <i>Nature Communications</i>, vol. 14. Springer Nature, 2023."},"status":"public","ec_funded":1,"oa_version":"Published Version","language":[{"iso":"eng"}],"intvolume":"        14","date_created":"2023-07-23T22:01:11Z","article_number":"4153","quality_controlled":"1","date_updated":"2025-04-14T07:43:55Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"13258"},{"issue":"7","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1093/gbe/evad113","year":"2023","type":"journal_article","article_type":"original","oa":1,"article_processing_charge":"Yes","external_id":{"pmid":["37341535"],"isi":["001023444700003"]},"publication":"Genome biology and evolution","related_material":{"link":[{"url":"https://github.com/carolbarata/dpseudo-n-beyond","relation":"software"}]},"month":"07","publication_identifier":{"eissn":["1759-6653"]},"abstract":[{"lang":"eng","text":"Experimental evolution studies are powerful approaches to examine the evolutionary history of lab populations. Such studies have shed light on how selection changes phenotypes and genotypes. Most of these studies have not examined the time course of adaptation under sexual selection manipulation, by resequencing the populations’ genomes at multiple time points. Here, we analyze allele frequency trajectories in Drosophila pseudoobscura where we altered their sexual selection regime for 200 generations and sequenced pooled populations at 5 time points. The intensity of sexual selection was either relaxed in monogamous populations (M) or elevated in polyandrous lines (E). We present a comprehensive study of how selection alters population genetics parameters at the chromosome and gene level. We investigate differences in the effective population size—Ne—between the treatments, and perform a genome-wide scan to identify signatures of selection from the time-series data. We found genomic signatures of adaptation to both regimes in D. pseudoobscura. There are more significant variants in E lines as expected from stronger sexual selection. However, we found that the response on the X chromosome was substantial in both treatments, more pronounced in E and restricted to the more recently sex-linked chromosome arm XR in M. In the first generations of experimental evolution, we estimate Ne to be lower on the X in E lines, which might indicate a swift adaptive response at the onset of selection. Additionally, the third chromosome was affected by elevated polyandry whereby its distal end harbors a region showing a strong signal of adaptive evolution especially in E lines."}],"scopus_import":"1","day":"01","volume":15,"acknowledgement":"This work was supported by the Vienna Science and Technology Fund (WWTF)(10.47379/MA16061). C.K. received funding from the Royal Society (RG170315) and the Carnegie Trust (RIG007474). M.G.R. and R.R.S. have been supported by NERC (UK) grants NE/I014632/1 and NE/V001566/1. Bioinformatics analyses were performed on the computer cluster at the University of St Andrews Bioinformatics Unit, which is funded by Wellcome Trust ISSF awards 105621/Z/14/Z. Complementary data parsing was carried out with the computational resources provided by the Research/Scientific Computing teams at The James Hutton Institute and the National Institute of Agricultural Botany (NIAB)—UK’s Crop Diversity Bioinformatics HPC, BBSRC grant BB/S019669/1. We are thankful to Paris Veltsos and R. Axel W. Wiberg for useful discussions about the project as well as providing us with the resequencing data they had produced as a result of previous work on this experiment. We are especially grateful to Tanya Sneddon for her help with the DNA extraction process and shipping.","has_accepted_license":"1","ddc":["570"],"publisher":"Oxford University Press","corr_author":"1","isi":1,"file_date_updated":"2023-08-01T06:58:34Z","title":"Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura","doi":"10.1093/gbe/evad113","publication_status":"published","author":[{"orcid":"0000-0003-1945-2245","last_name":"De Castro Barbosa Rodrigues Barata","id":"20565186-803f-11ed-ab7e-96a4ff7694ef","first_name":"Carolina","full_name":"De Castro Barbosa Rodrigues Barata, Carolina"},{"last_name":"Snook","first_name":"Rhonda R.","full_name":"Snook, Rhonda R."},{"first_name":"Michael G.","last_name":"Ritchie","full_name":"Ritchie, Michael G."},{"first_name":"Carolin","last_name":"Kosiol","full_name":"Kosiol, Carolin"}],"pmid":1,"date_published":"2023-07-01T00:00:00Z","file":[{"checksum":"70de3c4878de6efe00dc56de2df8812f","date_updated":"2023-08-01T06:58:34Z","relation":"main_file","date_created":"2023-08-01T06:58:34Z","success":1,"creator":"dernst","file_size":2382587,"content_type":"application/pdf","access_level":"open_access","file_id":"13339","file_name":"2023_GBE_Barata.pdf"}],"department":[{"_id":"BeVi"}],"citation":{"apa":"de Castro Barbosa Rodrigues Barata, C., Snook, R. R., Ritchie, M. G., &#38; Kosiol, C. (2023). Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>","chicago":"Castro Barbosa Rodrigues Barata, Carolina de, Rhonda R. Snook, Michael G. Ritchie, and Carolin Kosiol. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/gbe/evad113\">https://doi.org/10.1093/gbe/evad113</a>.","short":"C. de Castro Barbosa Rodrigues Barata, R.R. Snook, M.G. Ritchie, C. Kosiol, Genome Biology and Evolution 15 (2023).","ista":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. 2023. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. Genome biology and evolution. 15(7), evad113.","ama":"de Castro Barbosa Rodrigues Barata C, Snook RR, Ritchie MG, Kosiol C. Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura. <i>Genome biology and evolution</i>. 2023;15(7). doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>","mla":"de Castro Barbosa Rodrigues Barata, Carolina, et al. “Selection on the Fly: Short-Term Adaptation to an Altered Sexual Selection Regime in Drosophila Pseudoobscura.” <i>Genome Biology and Evolution</i>, vol. 15, no. 7, evad113, Oxford University Press, 2023, doi:<a href=\"https://doi.org/10.1093/gbe/evad113\">10.1093/gbe/evad113</a>.","ieee":"C. de Castro Barbosa Rodrigues Barata, R. R. Snook, M. G. Ritchie, and C. Kosiol, “Selection on the fly: Short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura,” <i>Genome biology and evolution</i>, vol. 15, no. 7. Oxford University Press, 2023."},"status":"public","oa_version":"Published Version","language":[{"iso":"eng"}],"intvolume":"        15","date_created":"2023-07-23T22:01:11Z","quality_controlled":"1","article_number":"evad113","date_updated":"2025-05-14T11:08:37Z","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"13260"},{"article_type":"original","type":"journal_article","fulldoi":"https://doi.org/10.1126/science.adf5568","project":[{"_id":"34e2a5b5-11ca-11ed-8bc3-b2265616ef0b","name":"A mechano-chemical theory for stem cell fate decisions in organoid development","grant_number":"ALTF 343-2022"}],"year":"2023","issue":"6652","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by the U.S. National Science Foundation, the Center for the Physics of Biological Function (grant PHY-1734030), and the National Institutes of Health (grants R01GM097275, U01DA047730, and U01DK127429). D.B.B. was supported by the NOMIS Foundation as a fellow and by an EMBO postdoctoral fellowship (ALTF 343-2022). H.C. was supported by a Charles H. Revson Biomedical Science Fellowship.","publisher":"American Association for the Advancement of Science","publication_identifier":{"eissn":["1095-9203"]},"abstract":[{"text":"Chromosomes in the eukaryotic nucleus are highly compacted. However, for many functional processes, including transcription initiation, the pairwise motion of distal chromosomal elements such as enhancers and promoters is essential and necessitates dynamic fluidity. Here, we used a live-imaging assay to simultaneously measure the positions of pairs of enhancers and promoters and their transcriptional output while systematically varying the genomic separation between these two DNA loci. Our analysis reveals the coexistence of a compact globular organization and fast subdiffusive dynamics. These combined features cause an anomalous scaling of polymer relaxation times with genomic separation leading to long-ranged correlations. Thus, encounter times of DNA loci are much less dependent on genomic distance than predicted by existing polymer models, with potential consequences for eukaryotic gene expression.","lang":"eng"}],"scopus_import":"1","day":"29","volume":380,"month":"06","oa":1,"article_processing_charge":"No","publication":"Science","external_id":{"isi":["001106405600028"]},"date_published":"2023-06-29T00:00:00Z","publication_status":"published","author":[{"id":"e1e86031-6537-11eb-953a-f7ab92be508d","last_name":"Brückner","orcid":"0000-0001-7205-2975","first_name":"David","full_name":"Brückner, David"},{"first_name":"Hongtao","last_name":"Chen","full_name":"Chen, Hongtao"},{"last_name":"Barinov","first_name":"Lev","full_name":"Barinov, Lev"},{"last_name":"Zoller","first_name":"Benjamin","full_name":"Zoller, Benjamin"},{"first_name":"Thomas","last_name":"Gregor","full_name":"Gregor, Thomas"}],"page":"1357-1362","title":"Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome","isi":1,"doi":"10.1126/science.adf5568","intvolume":"       380","date_created":"2023-07-23T22:01:12Z","quality_controlled":"1","date_updated":"2025-04-14T08:55:54Z","_id":"13261","oa_version":"Preprint","language":[{"iso":"eng"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1126/science.adf5568"}],"department":[{"_id":"EdHa"}],"citation":{"chicago":"Brückner, David, Hongtao Chen, Lev Barinov, Benjamin Zoller, and Thomas Gregor. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>. American Association for the Advancement of Science, 2023. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>.","apa":"Brückner, D., Chen, H., Barinov, L., Zoller, B., &#38; Gregor, T. (2023). Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. American Association for the Advancement of Science. <a href=\"https://doi.org/10.1126/science.adf5568\">https://doi.org/10.1126/science.adf5568</a>","short":"D. Brückner, H. Chen, L. Barinov, B. Zoller, T. Gregor, Science 380 (2023) 1357–1362.","ista":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. 2023. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. Science. 380(6652), 1357–1362.","ama":"Brückner D, Chen H, Barinov L, Zoller B, Gregor T. Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome. <i>Science</i>. 2023;380(6652):1357-1362. doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>","mla":"Brückner, David, et al. “Stochastic Motion and Transcriptional Dynamics of Pairs of Distal DNA Loci on a Compacted Chromosome.” <i>Science</i>, vol. 380, no. 6652, American Association for the Advancement of Science, 2023, pp. 1357–62, doi:<a href=\"https://doi.org/10.1126/science.adf5568\">10.1126/science.adf5568</a>.","ieee":"D. Brückner, H. Chen, L. Barinov, B. Zoller, and T. Gregor, “Stochastic motion and transcriptional dynamics of pairs of distal DNA loci on a compacted chromosome,” <i>Science</i>, vol. 380, no. 6652. American Association for the Advancement of Science, pp. 1357–1362, 2023."},"status":"public"},{"month":"06","article_processing_charge":"Yes (via OA deal)","arxiv":1,"oa":1,"publication":"Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures","external_id":{"isi":["001108889000024"],"arxiv":["2304.09331"]},"has_accepted_license":"1","ddc":["000"],"publisher":"Association for Computing Machinery","corr_author":"1","abstract":[{"text":"Determining the degree of inherent parallelism in classical sequential algorithms and leveraging it for fast parallel execution is a key topic in parallel computing, and detailed analyses are known for a wide range of classical algorithms. In this paper, we perform the first such analysis for the fundamental Union-Find problem, in which we are given a graph as a sequence of edges, and must maintain its connectivity structure under edge additions. We prove that classic sequential algorithms for this problem are well-parallelizable under reasonable assumptions, addressing a conjecture by [Blelloch, 2017]. More precisely, we show via a new potential argument that, under uniform random edge ordering, parallel union-find operations are unlikely to interfere: T concurrent threads processing the graph in parallel will encounter memory contention O(T2 · log |V| · log |E|) times in expectation, where |E| and |V| are the number of edges and nodes in the graph, respectively. We leverage this result to design a new parallel Union-Find algorithm that is both internally deterministic, i.e., its results are guaranteed to match those of a sequential execution, but also work-efficient and scalable, as long as the number of threads T is O(|E|1 over 3 - ε), for an arbitrarily small constant ε > 0, which holds for most large real-world graphs. We present lower bounds which show that our analysis is close to optimal, and experimental results suggesting that the performance cost of internal determinism is limited.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"isbn":["9781450395458"]},"day":"17","year":"2023","fulldoi":"https://doi.org/10.1145/3558481.3591082","conference":{"location":"Orlando, FL, United States","name":"SPAA: Symposium on Parallelism in Algorithms and Architectures","end_date":"2023-06-19","start_date":"2023-06-17"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","type":"conference","oa_version":"Published Version","language":[{"iso":"eng"}],"citation":{"short":"A. Fedorov, D. Hashemi, G. Nadiradze, D.-A. Alistarh, in:, Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures, Association for Computing Machinery, 2023, pp. 261–271.","apa":"Fedorov, A., Hashemi, D., Nadiradze, G., &#38; Alistarh, D.-A. (2023). Provably-efficient and internally-deterministic parallel Union-Find. In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i> (pp. 261–271). Orlando, FL, United States: Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>","chicago":"Fedorov, Alexander, Diba Hashemi, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” In <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, 261–71. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3558481.3591082\">https://doi.org/10.1145/3558481.3591082</a>.","ieee":"A. Fedorov, D. Hashemi, G. Nadiradze, and D.-A. Alistarh, “Provably-efficient and internally-deterministic parallel Union-Find,” in <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Orlando, FL, United States, 2023, pp. 261–271.","ama":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. Provably-efficient and internally-deterministic parallel Union-Find. In: <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>. Association for Computing Machinery; 2023:261-271. doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>","ista":"Fedorov A, Hashemi D, Nadiradze G, Alistarh D-A. 2023. Provably-efficient and internally-deterministic parallel Union-Find. Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures. SPAA: Symposium on Parallelism in Algorithms and Architectures, 261–271.","mla":"Fedorov, Alexander, et al. “Provably-Efficient and Internally-Deterministic Parallel Union-Find.” <i>Proceedings of the 35th ACM Symposium on Parallelism in Algorithms and Architectures</i>, Association for Computing Machinery, 2023, pp. 261–71, doi:<a href=\"https://doi.org/10.1145/3558481.3591082\">10.1145/3558481.3591082</a>."},"department":[{"_id":"DaAl"},{"_id":"GradSch"}],"status":"public","date_created":"2023-07-23T22:01:12Z","_id":"13262","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-09-09T12:43:18Z","quality_controlled":"1","page":"261-271","date_published":"2023-06-17T00:00:00Z","file":[{"file_size":2087937,"content_type":"application/pdf","checksum":"72e312aabf0c5248c99b5cd3a88e4c88","date_updated":"2023-07-31T10:53:08Z","relation":"main_file","success":1,"date_created":"2023-07-31T10:53:08Z","creator":"dernst","file_name":"2023_SPAA_Fedorov.pdf","access_level":"open_access","file_id":"13334"}],"publication_status":"published","author":[{"full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","last_name":"Fedorov","first_name":"Alexander"},{"id":"ed9595ea-2f8f-11ee-ba95-d2b546540783","last_name":"Hashemi","first_name":"Diba","full_name":"Hashemi, Diba"},{"last_name":"Nadiradze","orcid":"0000-0001-5634-0731","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","first_name":"Giorgi","full_name":"Nadiradze, Giorgi"},{"first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","full_name":"Alistarh, Dan-Adrian"}],"doi":"10.1145/3558481.3591082","file_date_updated":"2023-07-31T10:53:08Z","title":"Provably-efficient and internally-deterministic parallel Union-Find","isi":1},{"status":"public","citation":{"short":"V.G. Trinh, B. Benhamou, T.A. Henzinger, S. Pastva, Bioinformatics 39 (2023) i513–i522.","chicago":"Trinh, Van Giang, Belaid Benhamou, Thomas A Henzinger, and Samuel Pastva. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>. Oxford University Press, 2023. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>.","apa":"Trinh, V. G., Benhamou, B., Henzinger, T. A., &#38; Pastva, S. (2023). Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/bioinformatics/btad262\">https://doi.org/10.1093/bioinformatics/btad262</a>","ieee":"V. G. Trinh, B. Benhamou, T. A. Henzinger, and S. Pastva, “Trap spaces of multi-valued networks: Definition, computation, and applications,” <i>Bioinformatics</i>, vol. 39, no. Supplement_1. Oxford University Press, pp. i513–i522, 2023.","mla":"Trinh, Van Giang, et al. “Trap Spaces of Multi-Valued Networks: Definition, Computation, and Applications.” <i>Bioinformatics</i>, vol. 39, no. Supplement_1, Oxford University Press, 2023, pp. i513–22, doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>.","ama":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. Trap spaces of multi-valued networks: Definition, computation, and applications. <i>Bioinformatics</i>. 2023;39(Supplement_1):i513-i522. doi:<a href=\"https://doi.org/10.1093/bioinformatics/btad262\">10.1093/bioinformatics/btad262</a>","ista":"Trinh VG, Benhamou B, Henzinger TA, Pastva S. 2023. Trap spaces of multi-valued networks: Definition, computation, and applications. Bioinformatics. 39(Supplement_1), i513–i522."},"department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"oa_version":"Published Version","ec_funded":1,"_id":"13263","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2025-05-14T11:07:28Z","quality_controlled":"1","date_created":"2023-07-23T22:01:12Z","intvolume":"        39","doi":"10.1093/bioinformatics/btad262","title":"Trap spaces of multi-valued networks: Definition, computation, and applications","file_date_updated":"2023-07-31T11:09:05Z","isi":1,"page":"i513-i522","date_published":"2023-06-30T00:00:00Z","pmid":1,"file":[{"access_level":"open_access","file_id":"13335","file_name":"2023_Bioinformatics_Trinh.pdf","relation":"main_file","checksum":"ba3abe1171df1958413b7c7f957f5486","date_updated":"2023-07-31T11:09:05Z","creator":"dernst","date_created":"2023-07-31T11:09:05Z","success":1,"content_type":"application/pdf","file_size":641736}],"publication_status":"published","author":[{"first_name":"Van Giang","last_name":"Trinh","full_name":"Trinh, Van Giang"},{"full_name":"Benhamou, Belaid","first_name":"Belaid","last_name":"Benhamou"},{"first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A"},{"id":"07c5ea74-f61c-11ec-a664-aa7c5d957b2b","last_name":"Pastva","orcid":"0000-0003-1993-0331","first_name":"Samuel","full_name":"Pastva, Samuel"}],"external_id":{"isi":["001027457000060"],"pmid":["37387165"]},"publication":"Bioinformatics","article_processing_charge":"Yes","oa":1,"month":"06","related_material":{"link":[{"relation":"software","url":"https://github.com/giang-trinh/trap-mvn"}]},"volume":39,"day":"30","abstract":[{"lang":"eng","text":"Motivation: Boolean networks are simple but efficient mathematical formalism for modelling complex biological systems. However, having only two levels of activation is sometimes not enough to fully capture the dynamics of real-world biological systems. Hence, the need for multi-valued networks (MVNs), a generalization of Boolean networks. Despite the importance of MVNs for modelling biological systems, only limited progress has been made on developing theories, analysis methods, and tools that can support them. In particular, the recent use of trap spaces in Boolean networks made a great impact on the field of systems biology, but there has been no similar concept defined and studied for MVNs to date.\r\n\r\nResults: In this work, we generalize the concept of trap spaces in Boolean networks to that in MVNs. We then develop the theory and the analysis methods for trap spaces in MVNs. In particular, we implement all proposed methods in a Python package called trapmvn. Not only showing the applicability of our approach via a realistic case study, we also evaluate the time efficiency of the method on a large collection of real-world models. The experimental results confirm the time efficiency, which we believe enables more accurate analysis on larger and more complex multi-valued models."}],"scopus_import":"1","publication_identifier":{"issn":["1367-4803"],"eissn":["1367-4811"]},"publisher":"Oxford University Press","corr_author":"1","ddc":["000"],"has_accepted_license":"1","acknowledgement":"This work was supported by L’Institut Carnot STAR, Marseille, France, and by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. [101034413].","issue":"Supplement_1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"fulldoi":"https://doi.org/10.1093/bioinformatics/btad262","type":"journal_article","article_type":"original"},{"publication_status":"published","author":[{"last_name":"Zhong","first_name":"Fanchao","full_name":"Zhong, Fanchao"},{"last_name":"Xu","first_name":"Yonglai","full_name":"Xu, Yonglai"},{"id":"fb7f793a-80d1-11eb-8869-d56e5b2a8ff4","last_name":"Zhao","orcid":"0000-0002-6389-1045","first_name":"Haisen","full_name":"Zhao, Haisen"},{"last_name":"Lu","first_name":"Lin","full_name":"Lu, Lin"}],"date_published":"2023-03-17T00:00:00Z","isi":1,"title":"As-Continuous-As-Possible extrusion-based fabrication of surface models","doi":"10.1145/3575859","intvolume":"        42","date_created":"2023-07-23T22:01:13Z","article_number":"26","quality_controlled":"1","date_updated":"2023-12-13T11:34:59Z","_id":"13265","oa_version":"Preprint","language":[{"iso":"eng"}],"department":[{"_id":"BeBi"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2201.02374"}],"citation":{"ieee":"F. Zhong, Y. Xu, H. Zhao, and L. Lu, “As-Continuous-As-Possible extrusion-based fabrication of surface models,” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3. Association for Computing Machinery, 2023.","ama":"Zhong F, Xu Y, Zhao H, Lu L. As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. 2023;42(3). doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>","ista":"Zhong F, Xu Y, Zhao H, Lu L. 2023. As-Continuous-As-Possible extrusion-based fabrication of surface models. ACM Transactions on Graphics. 42(3), 26.","mla":"Zhong, Fanchao, et al. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>, vol. 42, no. 3, 26, Association for Computing Machinery, 2023, doi:<a href=\"https://doi.org/10.1145/3575859\">10.1145/3575859</a>.","short":"F. Zhong, Y. Xu, H. Zhao, L. Lu, ACM Transactions on Graphics 42 (2023).","apa":"Zhong, F., Xu, Y., Zhao, H., &#38; Lu, L. (2023). As-Continuous-As-Possible extrusion-based fabrication of surface models. <i>ACM Transactions on Graphics</i>. Association for Computing Machinery. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>","chicago":"Zhong, Fanchao, Yonglai Xu, Haisen Zhao, and Lin Lu. “As-Continuous-As-Possible Extrusion-Based Fabrication of Surface Models.” <i>ACM Transactions on Graphics</i>. Association for Computing Machinery, 2023. <a href=\"https://doi.org/10.1145/3575859\">https://doi.org/10.1145/3575859</a>."},"status":"public","article_type":"original","type":"journal_article","fulldoi":"https://doi.org/10.1145/3575859","year":"2023","issue":"3","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported in part by grants from the NSFC (61972232), Science and Technology Program of Shenzhen, China (CJGJZD20200617102202007). ","publisher":"Association for Computing Machinery","publication_identifier":{"issn":["0730-0301"],"eissn":["1557-7368"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"In this study, we propose a computational framework for optimizing the continuity of the toolpath in fabricating surface models on an extrusion-based 3D printer. Toolpath continuity is a critical issue that influences both the quality and the efficiency of extrusion-based fabrication. Transfer moves lead to rough and bumpy surfaces, where this phenomenon worsens for materials with large viscosity, like clay. The effects of continuity on the surface models are even more severe in terms of the quality of the surface and the stability of the model. We introduce a criterion called the one–path patch (OPP) to represent a patch on the surface of the shell that can be traversed along one path by considering the constraints on fabrication. We study the properties of the OPPs and their merging operations to propose a bottom-up OPP merging procedure to decompose the given shell surface into a minimal number of OPPs, and to generate the “as-continuous-as-possible” (ACAP) toolpath. Furthermore, we augment the path planning algorithm with a curved-layer printing scheme that reduces staircase defects and improves the continuity of the toolpath by connecting multiple segments. We evaluated the ACAP algorithm on ceramic and thermoplastic materials, and the results showed that it improves the fabrication of surface models in terms of both efficiency and surface quality."}],"day":"17","volume":42,"month":"03","oa":1,"article_processing_charge":"No","arxiv":1,"publication":"ACM Transactions on Graphics","external_id":{"arxiv":["2201.02374"],"isi":["001018739600002"]}},{"month":"10","oa":1,"article_processing_charge":"Yes (via OA deal)","publication":"New Phytologist","external_id":{"pmid":["37434303"],"isi":["001026321500001"]},"acknowledgement":"We gratefully acknowledge our brave colleagues, whose excellent efforts kept the plant cAMP research going in the last two decades. The authors were financially supported by the Austrian Science Fund (FWF): I 6123 and P 37051-B.","has_accepted_license":"1","ddc":["580"],"corr_author":"1","publisher":"Wiley","publication_identifier":{"eissn":["1469-8137"],"issn":["0028-646X"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general."}],"day":"01","volume":240,"project":[{"grant_number":"I06123","name":"Peptide receptors for auxin canalization in Arabidopsis","_id":"bd76d395-d553-11ed-ba76-f678c14f9033"},{"name":"Guanylate cyclase activity of TIR1/AFBs auxin receptors","_id":"7bcece63-9f16-11ee-852c-ae94e099eeb6","grant_number":"P37051"}],"fulldoi":"https://doi.org/10.1111/nph.19123","year":"2023","issue":"2","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_type":"original","type":"journal_article","oa_version":"Published Version","language":[{"iso":"eng"}],"department":[{"_id":"JiFr"}],"citation":{"ista":"Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 240(2), 489–495.","ama":"Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond. <i>New Phytologist</i>. 2023;240(2):489-495. doi:<a href=\"https://doi.org/10.1111/nph.19123\">10.1111/nph.19123</a>","mla":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” <i>New Phytologist</i>, vol. 240, no. 2, Wiley, 2023, pp. 489–95, doi:<a href=\"https://doi.org/10.1111/nph.19123\">10.1111/nph.19123</a>.","ieee":"L. Qi and J. Friml, “Tale of cAMP as a second messenger in auxin signaling and beyond,” <i>New Phytologist</i>, vol. 240, no. 2. Wiley, pp. 489–495, 2023.","apa":"Qi, L., &#38; Friml, J. (2023). Tale of cAMP as a second messenger in auxin signaling and beyond. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.19123\">https://doi.org/10.1111/nph.19123</a>","chicago":"Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” <i>New Phytologist</i>. Wiley, 2023. <a href=\"https://doi.org/10.1111/nph.19123\">https://doi.org/10.1111/nph.19123</a>.","short":"L. Qi, J. Friml, New Phytologist 240 (2023) 489–495."},"status":"public","intvolume":"       240","date_created":"2023-07-23T22:01:13Z","quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"_id":"13266","date_updated":"2024-10-22T12:50:00Z","pmid":1,"publication_status":"published","file":[{"content_type":"application/pdf","file_size":974464,"checksum":"6d9bbd45b8e7bb3ceee2586d447bacb2","date_updated":"2024-01-29T11:21:43Z","relation":"main_file","success":1,"date_created":"2024-01-29T11:21:43Z","creator":"dernst","file_name":"2023_NewPhytologist_Qi.pdf","access_level":"open_access","file_id":"14898"}],"author":[{"full_name":"Qi, Linlin","orcid":"0000-0001-5187-8401","last_name":"Qi","id":"44B04502-A9ED-11E9-B6FC-583AE6697425","first_name":"Linlin"},{"full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"}],"date_published":"2023-10-01T00:00:00Z","page":"489-495","file_date_updated":"2024-01-29T11:21:43Z","title":"Tale of cAMP as a second messenger in auxin signaling and beyond","isi":1,"doi":"10.1111/nph.19123"},{"year":"2023","fulldoi":"https://doi.org/10.1007/s00454-023-00500-5","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","article_type":"original","type":"journal_article","month":"07","publication":"Discrete and Computational Geometry","external_id":{"arxiv":["2107.04112"],"isi":["001023742800003"]},"article_processing_charge":"Yes (via OA deal)","arxiv":1,"oa":1,"publisher":"Springer Nature","corr_author":"1","has_accepted_license":"1","ddc":["510"],"acknowledgement":"Open access funding provided by the Institute of Science and Technology (IST Austria).","volume":70,"day":"05","abstract":[{"text":"Consider a geodesic triangle on a surface of constant curvature and subdivide it recursively into four triangles by joining the midpoints of its edges. We show the existence of a uniform δ>0\r\n such that, at any step of the subdivision, all the triangle angles lie in the interval (δ,π−δ)\r\n. Additionally, we exhibit stabilising behaviours for both angles and lengths as this subdivision progresses.","lang":"eng"}],"scopus_import":"1","publication_identifier":{"eissn":["1432-0444"],"issn":["0179-5376"]},"page":"1059-1089","date_published":"2023-07-05T00:00:00Z","file":[{"file_size":1466020,"content_type":"application/pdf","creator":"dernst","date_created":"2024-01-29T11:15:22Z","success":1,"relation":"main_file","checksum":"865e68daafdd4edcfc280172ec50f5ea","date_updated":"2024-01-29T11:15:22Z","file_name":"2023_DiscreteComputGeometry_Brunck.pdf","file_id":"14897","access_level":"open_access"}],"publication_status":"published","author":[{"full_name":"Brunck, Florestan R","id":"6ab6e556-f394-11eb-9cf6-9dfb78f00d8d","last_name":"Brunck","first_name":"Florestan R"}],"doi":"10.1007/s00454-023-00500-5","title":"Iterated medial triangle subdivision in surfaces of constant curvature","file_date_updated":"2024-01-29T11:15:22Z","isi":1,"language":[{"iso":"eng"}],"oa_version":"Published Version","status":"public","citation":{"mla":"Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” <i>Discrete and Computational Geometry</i>, vol. 70, no. 3, Springer Nature, 2023, pp. 1059–89, doi:<a href=\"https://doi.org/10.1007/s00454-023-00500-5\">10.1007/s00454-023-00500-5</a>.","ista":"Brunck FR. 2023. Iterated medial triangle subdivision in surfaces of constant curvature. Discrete and Computational Geometry. 70(3), 1059–1089.","ama":"Brunck FR. Iterated medial triangle subdivision in surfaces of constant curvature. <i>Discrete and Computational Geometry</i>. 2023;70(3):1059-1089. doi:<a href=\"https://doi.org/10.1007/s00454-023-00500-5\">10.1007/s00454-023-00500-5</a>","ieee":"F. R. Brunck, “Iterated medial triangle subdivision in surfaces of constant curvature,” <i>Discrete and Computational Geometry</i>, vol. 70, no. 3. Springer Nature, pp. 1059–1089, 2023.","chicago":"Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2023. <a href=\"https://doi.org/10.1007/s00454-023-00500-5\">https://doi.org/10.1007/s00454-023-00500-5</a>.","apa":"Brunck, F. R. (2023). Iterated medial triangle subdivision in surfaces of constant curvature. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-023-00500-5\">https://doi.org/10.1007/s00454-023-00500-5</a>","short":"F.R. Brunck, Discrete and Computational Geometry 70 (2023) 1059–1089."},"department":[{"_id":"UlWa"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","short":"CC BY (4.0)"},"date_updated":"2024-10-09T21:06:01Z","_id":"13270","quality_controlled":"1","date_created":"2023-07-23T22:01:14Z","intvolume":"        70"}]