[{"ddc":["570"],"title":"Frequent horizontal chromosome transfer between asexual fungal insect pathogens","status":"public","intvolume":" 121","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"14478","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"15124","date_created":"2024-03-19T09:02:57Z","date_updated":"2024-03-19T09:02:57Z","checksum":"f5e871db617b682edc71fcd08670dc81","success":1,"file_name":"2024_PNAS_Habig.pdf","access_level":"open_access","file_size":5750361,"content_type":"application/pdf","creator":"dernst"}],"type":"journal_article","abstract":[{"text":"Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungusMetarhizium robertsiiduring experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome – but no other – was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment betweenM. robertsiiand another congeneric insect pathogen,M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange.Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens.","lang":"eng"}],"issue":"11","article_type":"original","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"apa":"Habig, M., Grasse, A. V., Müller, J., Stukenbrock, E. H., Leitner, H., & Cremer, S. (2024). Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2316284121","ieee":"M. Habig, A. V. Grasse, J. Müller, E. H. Stukenbrock, H. Leitner, and S. Cremer, “Frequent horizontal chromosome transfer between asexual fungal insect pathogens,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.","ista":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. 2024. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2316284121.","ama":"Habig M, Grasse AV, Müller J, Stukenbrock EH, Leitner H, Cremer S. Frequent horizontal chromosome transfer between asexual fungal insect pathogens. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2316284121","chicago":"Habig, Michael, Anna V Grasse, Judith Müller, Eva H. Stukenbrock, Hanna Leitner, and Sylvia Cremer. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2316284121.","short":"M. Habig, A.V. Grasse, J. Müller, E.H. Stukenbrock, H. Leitner, S. Cremer, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","mla":"Habig, Michael, et al. “Frequent Horizontal Chromosome Transfer between Asexual Fungal Insect Pathogens.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2316284121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2316284121."},"date_published":"2024-03-12T00:00:00Z","scopus_import":"1","day":"12","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","publication_status":"published","publisher":"Proceedings of the National Academy of Sciences","department":[{"_id":"SyCr"}],"year":"2024","acknowledgement":"We thank Bernhardt Steinwender, Jorgen Eilenberg, and Nicolai V. Meyling for the fungal strains. We further thank Chengshu Wang for providing the short sequencing reads for M. guizhouense ARESF977 he used for his published genome assembly, and Kristian Ullrich for help in the bioinformatics analysis for methylation pattern in Nanopore reads, and the VBC and the Max Planck Society for the use of their sequencing centers. We thank Barbara Milutinović and Hinrich Schulenburg for discussion, and Tal Dagan and Jens Rolff for comments on a previous version of the manuscript. Fig. 1A was created with BioRender.com. This study received funding by the European Research Council under the European Union’s Horizon 2020 Research and Innovation Programme (No. 771402; EPIDEMICSonCHIP) to S.C. and by the German Research Foundation (DFG grant HA9263/1-1) to M.H.","pmid":1,"date_created":"2023-10-31T13:30:00Z","date_updated":"2024-03-19T09:07:20Z","volume":121,"author":[{"full_name":"Habig, Michael","last_name":"Habig","first_name":"Michael"},{"last_name":"Grasse","first_name":"Anna V","id":"406F989C-F248-11E8-B48F-1D18A9856A87","full_name":"Grasse, Anna V"},{"first_name":"Judith","last_name":"Müller","full_name":"Müller, Judith"},{"full_name":"Stukenbrock, Eva H.","first_name":"Eva H.","last_name":"Stukenbrock"},{"full_name":"Leitner, Hanna","id":"8fc5c6f6-5903-11ec-abad-c83f046253e7","last_name":"Leitner","first_name":"Hanna"},{"full_name":"Cremer, Sylvia","orcid":"0000-0002-2193-3868","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","last_name":"Cremer","first_name":"Sylvia"}],"article_number":"e2316284121","license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2024-03-19T09:02:57Z","ec_funded":1,"quality_controlled":"1","project":[{"grant_number":"771402","_id":"2649B4DE-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Epidemics in ant societies on a chip"}],"external_id":{"pmid":["38442176"]},"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1073/pnas.2316284121","month":"03","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]}},{"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2109.10203"]},"language":[{"iso":"eng"}],"doi":"10.1007/s10107-024-02064-5","month":"03","publication_identifier":{"issn":["0025-5610"],"eissn":["1436-4646"]},"publication_status":"epub_ahead","department":[{"_id":"GradSch"},{"_id":"VlKo"}],"publisher":"Springer Nature","acknowledgement":"We thank the anonymous reviewers for their careful reading of our manuscript and their many insightful comments and suggestions. Open access funding provided by Institute of Science and Technology (IST Austria).","year":"2024","date_updated":"2024-03-19T08:20:31Z","date_created":"2021-09-27T10:48:23Z","author":[{"full_name":"Dvorak, Martin","orcid":"0000-0001-5293-214X","id":"40ED02A8-C8B4-11E9-A9C0-453BE6697425","last_name":"Dvorak","first_name":"Martin"},{"full_name":"Kolmogorov, Vladimir","id":"3D50B0BA-F248-11E8-B48F-1D18A9856A87","first_name":"Vladimir","last_name":"Kolmogorov"}],"article_number":"2109.10203","license":"https://creativecommons.org/licenses/by/4.0/","file_date_updated":"2021-09-27T10:54:51Z","article_type":"original","publication":"Mathematical Programming","citation":{"mla":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming, 2109.10203, Springer Nature, 2024, doi:10.1007/s10107-024-02064-5.","short":"M. Dvorak, V. Kolmogorov, Mathematical Programming (2024).","chicago":"Dvorak, Martin, and Vladimir Kolmogorov. “Generalized Minimum 0-Extension Problem and Discrete Convexity.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02064-5.","ama":"Dvorak M, Kolmogorov V. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. 2024. doi:10.1007/s10107-024-02064-5","ista":"Dvorak M, Kolmogorov V. 2024. Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming., 2109.10203.","ieee":"M. Dvorak and V. Kolmogorov, “Generalized minimum 0-extension problem and discrete convexity,” Mathematical Programming. Springer Nature, 2024.","apa":"Dvorak, M., & Kolmogorov, V. (2024). Generalized minimum 0-extension problem and discrete convexity. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02064-5"},"date_published":"2024-03-07T00:00:00Z","keyword":["minimum 0-extension problem","metric labeling problem","discrete metric spaces","metric extensions","computational complexity","valued constraint satisfaction problems","discrete convex analysis","L-convex functions"],"scopus_import":"1","day":"07","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","ddc":["004"],"status":"public","title":"Generalized minimum 0-extension problem and discrete convexity","_id":"10045","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","file":[{"creator":"mdvorak","content_type":"application/pdf","file_size":603672,"access_level":"open_access","file_name":"Generalized-0-Ext.pdf","success":1,"checksum":"e7e83065f7bc18b9c188bf93b5ca5db6","date_updated":"2021-09-27T10:54:51Z","date_created":"2021-09-27T10:54:51Z","file_id":"10046","relation":"main_file"}],"type":"journal_article","abstract":[{"lang":"eng","text":"Given a fixed finite metric space (V,μ), the {\\em minimum 0-extension problem}, denoted as 0-Ext[μ], is equivalent to the following optimization problem: minimize function of the form minx∈Vn∑ifi(xi)+∑ijcijμ(xi,xj) where cij,cvi are given nonnegative costs and fi:V→R are functions given by fi(xi)=∑v∈Vcviμ(xi,v). The computational complexity of 0-Ext[μ] has been recently established by Karzanov and by Hirai: if metric μ is {\\em orientable modular} then 0-Ext[μ] can be solved in polynomial time, otherwise 0-Ext[μ] is NP-hard. To prove the tractability part, Hirai developed a theory of discrete convex functions on orientable modular graphs generalizing several known classes of functions in discrete convex analysis, such as L♮-convex functions. We consider a more general version of the problem in which unary functions fi(xi) can additionally have terms of the form cuv;iμ(xi,{u,v}) for {u,v}∈F, where set F⊆(V2) is fixed. We extend the complexity classification above by providing an explicit condition on (μ,F) for the problem to be tractable. In order to prove the tractability part, we generalize Hirai's theory and define a larger class of discrete convex functions. It covers, in particular, another well-known class of functions, namely submodular functions on an integer lattice. Finally, we improve the complexity of Hirai's algorithm for solving 0-Ext on orientable modular graphs.\r\n"}]},{"article_type":"original","citation":{"ista":"Zheng DW, Henzinger MH. 2024. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming.","apa":"Zheng, D. W., & Henzinger, M. H. (2024). Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. Springer Nature. https://doi.org/10.1007/s10107-024-02066-3","ieee":"D. W. Zheng and M. H. Henzinger, “Multiplicative auction algorithm for approximate maximum weight bipartite matching,” Mathematical Programming. Springer Nature, 2024.","ama":"Zheng DW, Henzinger MH. Multiplicative auction algorithm for approximate maximum weight bipartite matching. Mathematical Programming. 2024. doi:10.1007/s10107-024-02066-3","chicago":"Zheng, Da Wei, and Monika H Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming. Springer Nature, 2024. https://doi.org/10.1007/s10107-024-02066-3.","mla":"Zheng, Da Wei, and Monika H. Henzinger. “Multiplicative Auction Algorithm for Approximate Maximum Weight Bipartite Matching.” Mathematical Programming, Springer Nature, 2024, doi:10.1007/s10107-024-02066-3.","short":"D.W. Zheng, M.H. Henzinger, Mathematical Programming (2024)."},"publication":"Mathematical Programming","date_published":"2024-03-06T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"06","title":"Multiplicative auction algorithm for approximate maximum weight bipartite matching","status":"public","_id":"15121","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","type":"journal_article","abstract":[{"lang":"eng","text":"We present an auction algorithm using multiplicative instead of constant weight updates to compute a (1-E)-approximate maximum weight matching (MWM) in a bipartite graph with n vertices and m edges in time 0(mE-1), beating the running time of the fastest known approximation algorithm of Duan and Pettie [JACM ’14] that runs in 0(mE-1 log E-1). Our algorithm is very simple and it can be extended to give a dynamic data structure that maintains a (1-E)-approximate maximum weight matching under (1) one-sided vertex deletions (with incident edges) and (2) one-sided vertex insertions (with incident edges sorted by weight) to the other side. The total time time used is 0(mE-1), where m is the sum of the number of initially existing and inserted edges."}],"project":[{"call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","grant_number":"101019564","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"},{"name":"Fast Algorithms for a Reactive Network Layer","grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe"}],"quality_controlled":"1","external_id":{"arxiv":["2301.09217"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.09217","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s10107-024-02066-3","publication_identifier":{"issn":["0025-5610"],"eissn":["1436-4646"]},"month":"03","department":[{"_id":"MoHe"}],"publisher":"Springer Nature","publication_status":"epub_ahead","year":"2024","acknowledgement":"The first author thanks Chandra Chekuri for useful discussions about this paper. This work was done in part at the University of Vienna. This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.","date_created":"2024-03-17T23:00:58Z","date_updated":"2024-03-19T08:32:32Z","related_material":{"record":[{"id":"13236","relation":"earlier_version","status":"public"}]},"author":[{"last_name":"Zheng","first_name":"Da Wei","full_name":"Zheng, Da Wei"},{"orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H","full_name":"Henzinger, Monika H"}],"ec_funded":1},{"_id":"15114","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling","intvolume":" 291","oa_version":"None","type":"journal_article","abstract":[{"text":"As a key liquid organic hydrogen carrier, investigating the decomposition of formic acid (HCOOH) on the Pd (1 1 1) transition metal surface is imperative for harnessing hydrogen energy. Despite a multitude of studies, the major mechanisms and key intermediates involved in the dehydrogenation process of formic acid remain a great topic of debate due to ambiguous adsorbate interactions. In this research, we develop an advanced microkinetic model based on first-principles calculations, accounting for adsorbate–adsorbate interactions. Our study unveils a comprehensive mechanism for the Pd (1 1 1) surface, highlighting the significance of coverage effects in formic acid dehydrogenation. Our findings unequivocally demonstrate that H coverage on the Pd (1 1 1) surface renders formic acid more susceptible to decompose into H2 and CO2 through COOH intermediates. Consistent with experimental results, the selectivity of H2 in the decomposition of formic acid on the Pd (1 1 1) surface approaches 100 %. Considering the influence of H coverage, our kinetic analysis aligns perfectly with experimental values at a temperature of 373 K.","lang":"eng"}],"publication":"Chemical Engineering Science","citation":{"ista":"Yao Z, Liu X, Bunting R, Wang J. 2024. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 291, 119959.","ieee":"Z. Yao, X. Liu, R. Bunting, and J. Wang, “Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling,” Chemical Engineering Science, vol. 291. Elsevier, 2024.","apa":"Yao, Z., Liu, X., Bunting, R., & Wang, J. (2024). Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. Elsevier. https://doi.org/10.1016/j.ces.2024.119959","ama":"Yao Z, Liu X, Bunting R, Wang J. Unravelling the reaction mechanism for H2 production via formic acid decomposition over Pd: Coverage-dependent microkinetic modeling. Chemical Engineering Science. 2024;291. doi:10.1016/j.ces.2024.119959","chicago":"Yao, Zihao, Xu Liu, Rhys Bunting, and Jianguo Wang. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science. Elsevier, 2024. https://doi.org/10.1016/j.ces.2024.119959.","mla":"Yao, Zihao, et al. “Unravelling the Reaction Mechanism for H2 Production via Formic Acid Decomposition over Pd: Coverage-Dependent Microkinetic Modeling.” Chemical Engineering Science, vol. 291, 119959, Elsevier, 2024, doi:10.1016/j.ces.2024.119959.","short":"Z. Yao, X. Liu, R. Bunting, J. Wang, Chemical Engineering Science 291 (2024)."},"article_type":"original","date_published":"2024-03-04T00:00:00Z","scopus_import":"1","day":"04","article_processing_charge":"No","year":"2024","acknowledgement":"The authors acknowledge the financial support from the National Key Research and Development Project of China (2021YFA1500900, 2022YFE0113800), the National Natural Science Foundation of China (22141001, U21A20298), Zhejiang Innovation Team (2017R5203).","publication_status":"epub_ahead","department":[{"_id":"MaIb"}],"publisher":"Elsevier","author":[{"full_name":"Yao, Zihao","first_name":"Zihao","last_name":"Yao"},{"full_name":"Liu, Xu","first_name":"Xu","last_name":"Liu"},{"full_name":"Bunting, Rhys","first_name":"Rhys","last_name":"Bunting","id":"91deeae8-1207-11ec-b130-c194ad5b50c6","orcid":"0000-0001-6928-074X"},{"first_name":"Jianguo","last_name":"Wang","full_name":"Wang, Jianguo"}],"date_updated":"2024-03-19T08:47:42Z","date_created":"2024-03-17T23:00:57Z","volume":291,"article_number":"119959","quality_controlled":"1","doi":"10.1016/j.ces.2024.119959","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0009-2509"]}},{"type":"journal_article","abstract":[{"lang":"eng","text":"Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water–collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H2O/D2O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H2O and D2O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D2O than in H2O, and collagen in D2O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H2O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D2O is less hydrated than in H2O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen–water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly."}],"issue":"11","_id":"15116","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["550"],"title":"Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration","status":"public","intvolume":" 121","oa_version":"Published Version","file":[{"file_id":"15125","relation":"main_file","date_updated":"2024-03-19T10:22:42Z","date_created":"2024-03-19T10:22:42Z","success":1,"checksum":"a3f7fdc29dd9f0a38952ab4e322b3a05","file_name":"2024_PNAS_Giubertoni.pdf","access_level":"open_access","creator":"dernst","file_size":12952586,"content_type":"application/pdf"}],"scopus_import":"1","day":"12","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","publication":"Proceedings of the National Academy of Sciences of the United States of America","citation":{"chicago":"Giubertoni, Giulia, Liru Feng, Kevin Klein, Guido Giannetti, Luco Rutten, Yeji Choi, Anouk Van Der Net, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences, 2024. https://doi.org/10.1073/pnas.2313162121.","mla":"Giubertoni, Giulia, et al. “Elucidating the Role of Water in Collagen Self-Assembly by Isotopically Modulating Collagen Hydration.” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11, e2313162121, Proceedings of the National Academy of Sciences, 2024, doi:10.1073/pnas.2313162121.","short":"G. Giubertoni, L. Feng, K. Klein, G. Giannetti, L. Rutten, Y. Choi, A. Van Der Net, G. Castro-Linares, F. Caporaletti, D. Micha, J. Hunger, A. Deblais, D. Bonn, N. Sommerdijk, A. Šarić, I.M. Ilie, G.H. Koenderink, S. Woutersen, Proceedings of the National Academy of Sciences of the United States of America 121 (2024).","ista":"Giubertoni G, Feng L, Klein K, Giannetti G, Rutten L, Choi Y, Van Der Net A, Castro-Linares G, Caporaletti F, Micha D, Hunger J, Deblais A, Bonn D, Sommerdijk N, Šarić A, Ilie IM, Koenderink GH, Woutersen S. 2024. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 121(11), e2313162121.","apa":"Giubertoni, G., Feng, L., Klein, K., Giannetti, G., Rutten, L., Choi, Y., … Woutersen, S. (2024). Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. Proceedings of the National Academy of Sciences. https://doi.org/10.1073/pnas.2313162121","ieee":"G. Giubertoni et al., “Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration,” Proceedings of the National Academy of Sciences of the United States of America, vol. 121, no. 11. Proceedings of the National Academy of Sciences, 2024.","ama":"Giubertoni G, Feng L, Klein K, et al. Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration. Proceedings of the National Academy of Sciences of the United States of America. 2024;121(11). doi:10.1073/pnas.2313162121"},"article_type":"original","date_published":"2024-03-12T00:00:00Z","article_number":"e2313162121","file_date_updated":"2024-03-19T10:22:42Z","acknowledgement":"We thank Dr. Steven Roeters (Aarhus University), Dr. Federica Burla, and Prof. Dr. Mischa Bonn (Institute for Polymer Research, Mainz, Germany) for the useful discussions. We thank Dr. Wim Roeterdink and Michiel Hilberts for technical support. G.H.K. acknowledges financial support by the “BaSyC Building a Synthetic Cell” Gravitation grant (024.003.019) of The Netherlands Ministry of Education, Culture and Science (OCW) and The Netherlands Organization for Scientific Research and from NWO grant OCENW.GROOT.2019.022. This work has received support from the National Research Foundation of Korea (NRF), funded by the Ministry of Science and ICT, under Grant No. 2022K1A3A1A04062969. This publication is part of the project (with Project Number VI.Veni.212.240) of the research programme NWO Talent Programme Veni 2021, which is financed by the Dutch Research Council (NWO). I.M.I. acknowledges support from the Sectorplan Bèta & Techniek of the Dutch Government and the Dementia Research - Synapsis Foundation Switzerland. A.Š. and K.K. acknowledge support from Royal Society and European Research Council Starting Grant. G. Giubertoni kindly thanks to the Care4Bones community and the Collagen Café community for reminding that we do not own the knowledge we create, but it is, rather, a collective resource intended for the advancement of human progress.","year":"2024","pmid":1,"publication_status":"published","department":[{"_id":"AnSa"}],"publisher":"Proceedings of the National Academy of Sciences","author":[{"last_name":"Giubertoni","first_name":"Giulia","full_name":"Giubertoni, Giulia"},{"first_name":"Liru","last_name":"Feng","full_name":"Feng, Liru"},{"first_name":"Kevin","last_name":"Klein","full_name":"Klein, Kevin"},{"first_name":"Guido","last_name":"Giannetti","full_name":"Giannetti, Guido"},{"full_name":"Rutten, Luco","first_name":"Luco","last_name":"Rutten"},{"first_name":"Yeji","last_name":"Choi","full_name":"Choi, Yeji"},{"first_name":"Anouk","last_name":"Van Der Net","full_name":"Van Der Net, Anouk"},{"full_name":"Castro-Linares, Gerard","last_name":"Castro-Linares","first_name":"Gerard"},{"full_name":"Caporaletti, Federico","first_name":"Federico","last_name":"Caporaletti"},{"first_name":"Dimitra","last_name":"Micha","full_name":"Micha, Dimitra"},{"first_name":"Johannes","last_name":"Hunger","full_name":"Hunger, Johannes"},{"first_name":"Antoine","last_name":"Deblais","full_name":"Deblais, Antoine"},{"full_name":"Bonn, Daniel","last_name":"Bonn","first_name":"Daniel"},{"full_name":"Sommerdijk, Nico","first_name":"Nico","last_name":"Sommerdijk"},{"orcid":"0000-0002-7854-2139","id":"bf63d406-f056-11eb-b41d-f263a6566d8b","last_name":"Šarić","first_name":"Anđela","full_name":"Šarić, Anđela"},{"first_name":"Ioana M.","last_name":"Ilie","full_name":"Ilie, Ioana M."},{"last_name":"Koenderink","first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H."},{"full_name":"Woutersen, Sander","first_name":"Sander","last_name":"Woutersen"}],"related_material":{"record":[{"id":"15126","relation":"research_data","status":"public"}]},"date_created":"2024-03-17T23:00:57Z","date_updated":"2024-03-19T11:41:32Z","volume":121,"month":"03","publication_identifier":{"eissn":["1091-6490"],"issn":["0027-8424"]},"oa":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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38451946"]},"quality_controlled":"1","doi":"10.1073/pnas.2313162121","language":[{"iso":"eng"}]},{"issue":"6687","abstract":[{"text":"The hippocampal mossy fiber synapse, formed between axons of dentate gyrus granule cells and dendrites of CA3 pyramidal neurons, is a key synapse in the trisynaptic circuitry of the hippocampus. Because of its comparatively large size, this synapse is accessible to direct presynaptic recording, allowing a rigorous investigation of the biophysical mechanisms of synaptic transmission and plasticity. Furthermore, because of its placement in the very center of the hippocampal memory circuit, this synapse seems to be critically involved in several higher network functions, such as learning, memory, pattern separation, and pattern completion. Recent work based on new technologies in both nanoanatomy and nanophysiology, including presynaptic patch-clamp recording, paired recording, super-resolution light microscopy, and freeze-fracture and “flash-and-freeze” electron microscopy, has provided new insights into the structure, biophysics, and network function of this intriguing synapse. This brings us one step closer to answering a fundamental question in neuroscience: how basic synaptic properties shape higher network computations.","lang":"eng"}],"type":"journal_article","oa_version":"None","_id":"15117","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 383","status":"public","title":"Structure, biophysics, and circuit function of a \"giant\" cortical presynaptic terminal","article_processing_charge":"No","day":"08","scopus_import":"1","date_published":"2024-03-08T00:00:00Z","citation":{"short":"D.H. Vandael, P.M. Jonas, Science 383 (2024) eadg6757.","mla":"Vandael, David H., and Peter M. Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science, vol. 383, no. 6687, AAAS, 2024, p. eadg6757, doi:10.1126/science.adg6757.","chicago":"Vandael, David H, and Peter M Jonas. “Structure, Biophysics, and Circuit Function of a ‘Giant’ Cortical Presynaptic Terminal.” Science. AAAS, 2024. https://doi.org/10.1126/science.adg6757.","ama":"Vandael DH, Jonas PM. Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. 2024;383(6687):eadg6757. doi:10.1126/science.adg6757","ieee":"D. H. Vandael and P. M. Jonas, “Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal,” Science, vol. 383, no. 6687. AAAS, p. eadg6757, 2024.","apa":"Vandael, D. H., & Jonas, P. M. (2024). Structure, biophysics, and circuit function of a “giant” cortical presynaptic terminal. Science. AAAS. https://doi.org/10.1126/science.adg6757","ista":"Vandael DH, Jonas PM. 2024. Structure, biophysics, and circuit function of a ‘giant’ cortical presynaptic terminal. Science. 383(6687), eadg6757."},"publication":"Science","page":"eadg6757","article_type":"review","ec_funded":1,"author":[{"full_name":"Vandael, David H","last_name":"Vandael","first_name":"David H","orcid":"0000-0001-7577-1676","id":"3AE48E0A-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jonas, Peter M","first_name":"Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804"}],"volume":383,"date_created":"2024-03-17T23:00:57Z","date_updated":"2024-03-20T07:42:52Z","pmid":1,"acknowledgement":"We thank previous students, postdocs, and collaborators, particularly J. Geiger, and (in alphabetical order) H. Alle, J. Bischofberger, C. Borges-Merjane, D. Engel, M. Frotscher, S. Hallermann, M. Heckmann, S. Jamrichova, O. Kim, L. Li, K. Lichter, P. Lin, J. Lübke, Y. Okamoto, C. Pawlu, C. Schmidt-Hieber, N. Spruston, and N. Vyleta for their outstanding experimental contributions. We also thank P. Castillo, J. Geiger, T. Sakaba, S. Siegert, T. Vogels, and J. Watson for critically reading the manuscript, E. Kralli-Beller for text editing, and J. Malikovic and L. Slomianka for useful discussions. We apologize that, due to space constraints, not all relevant papers could be cited.\r\nThis project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (grant agreement 692692, AdG “GIANTSYN”) and the Fonds zur Förderung der Wissenschaftlichen Forschung (Z 312-B27, Wittgenstein Award; P 36232-B, stand-alone grant), both to P.J.","year":"2024","department":[{"_id":"PeJo"}],"publisher":"AAAS","publication_status":"published","publication_identifier":{"eissn":["1095-9203"]},"month":"03","doi":"10.1126/science.adg6757","language":[{"iso":"eng"}],"external_id":{"pmid":["38452088"]},"project":[{"grant_number":"692692","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425","name":"Biophysics and circuit function of a giant cortical glumatergic synapse","call_identifier":"H2020"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25C5A090-B435-11E9-9278-68D0E5697425","grant_number":"Z00312"},{"grant_number":"P36232","_id":"bd88be38-d553-11ed-ba76-81d5a70a6ef5","name":"Mechanisms of GABA release in hippocampal circuits"}],"quality_controlled":"1"},{"ec_funded":1,"file_date_updated":"2024-03-14T14:14:35Z","license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"11660"},{"relation":"part_of_dissertation","status":"public","id":"11658"},{"id":"13182","relation":"part_of_dissertation","status":"public"},{"id":"15090","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"15091"},{"relation":"part_of_dissertation","status":"public","id":"15093"}]},"author":[{"orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","last_name":"Cultrera di Montesano","first_name":"Sebastiano","full_name":"Cultrera di Montesano, Sebastiano"}],"date_created":"2024-03-08T15:28:10Z","date_updated":"2024-03-20T09:36:57Z","year":"2024","publisher":"Institute of Science and Technology Austria","department":[{"_id":"GradSch"},{"_id":"HeEd"}],"publication_status":"published","publication_identifier":{"issn":["2663 - 337X"]},"month":"03","doi":"10.15479/at:ista:15094","language":[{"iso":"eng"}],"degree_awarded":"PhD","supervisor":[{"full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","first_name":"Herbert","last_name":"Edelsbrunner"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","image":"/images/cc_by_nc_sa.png","short":"CC BY-NC-SA (4.0)"},"oa":1,"project":[{"_id":"266A2E9E-B435-11E9-9278-68D0E5697425","grant_number":"788183","name":"Alpha Shape Theory Extended","call_identifier":"H2020"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"Discretization in Geometry and Dynamics","grant_number":"I4887","_id":"0aa4bc98-070f-11eb-9043-e6fff9c6a316"},{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35","name":"Persistence and stability of geometric complexes","call_identifier":"FWF"}],"abstract":[{"text":"Point sets, geometric networks, and arrangements of hyperplanes are fundamental objects in\r\ndiscrete geometry that have captivated mathematicians for centuries, if not millennia. This\r\nthesis seeks to cast new light on these structures by illustrating specific instances where a\r\ntopological perspective, specifically through discrete Morse theory and persistent homology,\r\nprovides valuable insights.\r\n\r\nAt first glance, the topology of these geometric objects might seem uneventful: point sets\r\nessentially lack of topology, arrangements of hyperplanes are a decomposition of Rd, which\r\nis a contractible space, and the topology of a network primarily involves the enumeration\r\nof connected components and cycles within the network. However, beneath this apparent\r\nsimplicity, there lies an array of intriguing structures, a small subset of which will be uncovered\r\nin this thesis.\r\n\r\nFocused on three case studies, each addressing one of the mentioned objects, this work\r\nwill showcase connections that intertwine topology with diverse fields such as combinatorial\r\ngeometry, algorithms and data structures, and emerging applications like spatial biology.\r\n\r\n","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"file_size":4106872,"content_type":"application/pdf","creator":"scultrer","access_level":"open_access","file_name":"Thesis Sebastiano.pdf","checksum":"1e468bfa42a7dcf04d89f4dadc621c87","success":1,"date_created":"2024-03-14T08:55:07Z","date_updated":"2024-03-14T08:55:07Z","relation":"main_file","file_id":"15112"},{"date_created":"2024-03-14T08:56:24Z","date_updated":"2024-03-14T14:14:35Z","checksum":"bcbd213490f5a7e68855a092bbce93f1","file_id":"15113","relation":"source_file","creator":"scultrer","content_type":"application/zip","file_size":4746234,"file_name":"Thesis (1).zip","access_level":"closed"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"15094","ddc":["514","500","516"],"title":"Persistence and Morse theory for discrete geometric structures","status":"public","article_processing_charge":"No","has_accepted_license":"1","day":"08","date_published":"2024-03-08T00:00:00Z","citation":{"ama":"Cultrera di Montesano S. Persistence and Morse theory for discrete geometric structures. 2024. doi:10.15479/at:ista:15094","ista":"Cultrera di Montesano S. 2024. Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria.","apa":"Cultrera di Montesano, S. (2024). Persistence and Morse theory for discrete geometric structures. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:15094","ieee":"S. Cultrera di Montesano, “Persistence and Morse theory for discrete geometric structures,” Institute of Science and Technology Austria, 2024.","mla":"Cultrera di Montesano, Sebastiano. Persistence and Morse Theory for Discrete Geometric Structures. Institute of Science and Technology Austria, 2024, doi:10.15479/at:ista:15094.","short":"S. Cultrera di Montesano, Persistence and Morse Theory for Discrete Geometric Structures, Institute of Science and Technology Austria, 2024.","chicago":"Cultrera di Montesano, Sebastiano. “Persistence and Morse Theory for Discrete Geometric Structures.” Institute of Science and Technology Austria, 2024. https://doi.org/10.15479/at:ista:15094."},"page":"108"},{"article_processing_charge":"No","day":"04","citation":{"short":"S. Cultrera di Montesano, H. Edelsbrunner, M.H. Henzinger, L. Ost, in:, D.P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Society for Industrial and Applied Mathematics, 2024, pp. 243–295.","mla":"Cultrera di Montesano, Sebastiano, et al. “Dynamically Maintaining the Persistent Homology of Time Series.” Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, Society for Industrial and Applied Mathematics, 2024, pp. 243–95, doi:10.1137/1.9781611977912.11.","chicago":"Cultrera di Montesano, Sebastiano, Herbert Edelsbrunner, Monika H Henzinger, and Lara Ost. “Dynamically Maintaining the Persistent Homology of Time Series.” In Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), edited by David P. Woodruff, 243–95. Society for Industrial and Applied Mathematics, 2024. https://doi.org/10.1137/1.9781611977912.11.","ama":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. Dynamically maintaining the persistent homology of time series. In: Woodruff DP, ed. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). Society for Industrial and Applied Mathematics; 2024:243-295. doi:10.1137/1.9781611977912.11","ieee":"S. Cultrera di Montesano, H. Edelsbrunner, M. H. Henzinger, and L. Ost, “Dynamically maintaining the persistent homology of time series,” in Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA), Alexandria, VA, USA, 2024, pp. 243–295.","apa":"Cultrera di Montesano, S., Edelsbrunner, H., Henzinger, M. H., & Ost, L. (2024). Dynamically maintaining the persistent homology of time series. In D. P. Woodruff (Ed.), Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA) (pp. 243–295). Alexandria, VA, USA: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977912.11","ista":"Cultrera di Montesano S, Edelsbrunner H, Henzinger MH, Ost L. 2024. Dynamically maintaining the persistent homology of time series. Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA). SODA: Symposium on Discrete Algorigthms, 243–295."},"publication":"Proceedings of the 2024 Annual ACM-SIAM Symposium on Discrete Algorithms (SODA)","page":"243 - 295","date_published":"2024-01-04T00:00:00Z","type":"conference","abstract":[{"text":"We present a dynamic data structure for maintaining the persistent homology of a time series of real numbers. The data structure supports local operations, including the insertion and deletion of an item and the cutting and concatenating of lists, each in time O(log n + k), in which n counts the critical items and k the changes in the augmented persistence diagram. To achieve this, we design a tailor-made tree structure with an unconventional representation, referred to as banana tree, which may be useful in its own right.","lang":"eng"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"15093","title":"Dynamically maintaining the persistent homology of time series","status":"public","oa_version":"Preprint","publication_identifier":{"eisbn":["9781611977912"]},"month":"01","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2311.01115"}],"external_id":{"arxiv":["2311.01115"]},"project":[{"grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Alpha Shape Theory Extended"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","name":"The Wittgenstein Prize","call_identifier":"FWF"},{"call_identifier":"H2020","name":"The design and evaluation of modern fully dynamic data structures","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62","grant_number":"101019564"},{"_id":"34def286-11ca-11ed-8bc3-da5948e1613c","grant_number":"Z00422","name":"Wittgenstein Award - Monika Henzinger"},{"grant_number":"P33775 ","_id":"bd9e3a2e-d553-11ed-ba76-8aa684ce17fe","name":"Fast Algorithms for a Reactive Network Layer"}],"quality_controlled":"1","doi":"10.1137/1.9781611977912.11","conference":{"location":"Alexandria, VA, USA","start_date":"2024-01-07","end_date":"2024-01-10","name":"SODA: Symposium on Discrete Algorigthms"},"language":[{"iso":"eng"}],"ec_funded":1,"year":"2024","acknowledgement":"The first and second authors are funded by the European Research Council under the European Union’s Horizon 2020 research and innovation programme, ERC grant no. 788183,“Alpha Shape Theory Extended (Alpha)”, by the Wittgenstein Prize, FWF grant no. Z 342-N31, and by the DFG Collaborative Research Center TRR 109, FWF grant no. I 02979-N35.The third author received funding by the European Research Council under the European Union’s Horizon 2020research and innovation programme, ERC grant no. 101019564, “The Design of Modern Fully Dynamic DataStructures (MoDynStruct)”, and by the Austrian Science Fund through the Wittgenstein Prize with FWF grant no. Z 422-N, and also by FWF grant no. I 5982-N, and by FWF grant no. P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024. The fourth author is funded by the Vienna Graduate School on Computational Optimization, FWF project no. W1260-N35.","publisher":"Society for Industrial and Applied Mathematics","editor":[{"full_name":"Woodruff, David P.","last_name":"Woodruff","first_name":"David P."}],"department":[{"_id":"HeEd"},{"_id":"MoHe"}],"publication_status":"published","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15094"}]},"author":[{"full_name":"Cultrera di Montesano, Sebastiano","last_name":"Cultrera di Montesano","first_name":"Sebastiano","orcid":"0000-0001-6249-0832","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"full_name":"Henzinger, Monika H","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","orcid":"0000-0002-5008-6530","first_name":"Monika H","last_name":"Henzinger"},{"first_name":"Lara","last_name":"Ost","full_name":"Ost, Lara"}],"date_created":"2024-03-08T10:27:39Z","date_updated":"2024-03-20T09:36:56Z"},{"language":[{"iso":"eng"}],"date_published":"2024-02-07T00:00:00Z","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2212.03128"}],"external_id":{"arxiv":["2212.03128"]},"oa":1,"citation":{"chicago":"Cultrera di Montesano, Sebastiano, Ondrej Draganov, Herbert Edelsbrunner, and Morteza Saghafian. “Chromatic Alpha Complexes.” ArXiv, n.d.","mla":"Cultrera di Montesano, Sebastiano, et al. “Chromatic Alpha Complexes.” ArXiv, 2212.03128.","short":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, M. Saghafian, ArXiv (n.d.).","ista":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv, 2212.03128.","apa":"Cultrera di Montesano, S., Draganov, O., Edelsbrunner, H., & Saghafian, M. (n.d.). Chromatic alpha complexes. arXiv.","ieee":"S. Cultrera di Montesano, O. Draganov, H. Edelsbrunner, and M. Saghafian, “Chromatic alpha complexes,” arXiv. .","ama":"Cultrera di Montesano S, Draganov O, Edelsbrunner H, Saghafian M. Chromatic alpha complexes. arXiv."},"publication":"arXiv","article_processing_charge":"No","day":"07","month":"02","oa_version":"Preprint","date_created":"2024-03-08T10:13:59Z","date_updated":"2024-03-20T09:36:56Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"15094"}]},"author":[{"first_name":"Sebastiano","last_name":"Cultrera di Montesano","id":"34D2A09C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-0832","full_name":"Cultrera di Montesano, Sebastiano"},{"full_name":"Draganov, Ondrej","id":"2B23F01E-F248-11E8-B48F-1D18A9856A87","first_name":"Ondrej","last_name":"Draganov"},{"full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","first_name":"Herbert","orcid":"0000-0002-9823-6833","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Saghafian","first_name":"Morteza","id":"f86f7148-b140-11ec-9577-95435b8df824","full_name":"Saghafian, Morteza"}],"department":[{"_id":"HeEd"}],"title":"Chromatic alpha complexes","status":"public","publication_status":"submitted","_id":"15091","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","year":"2024","abstract":[{"lang":"eng","text":"Motivated by applications in the medical sciences, we study finite chromatic\r\nsets in Euclidean space from a topological perspective. Based on the persistent\r\nhomology for images, kernels and cokernels, we design provably stable\r\nhomological quantifiers that describe the geometric micro- and macro-structure\r\nof how the color classes mingle. These can be efficiently computed using\r\nchromatic variants of Delaunay and alpha complexes, and code that does these\r\ncomputations is provided."}],"type":"preprint","article_number":"2212.03128"},{"month":"03","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"doi":"10.1038/s41593-024-01597-4","language":[{"iso":"eng"}],"oa":1,"main_file_link":[{"url":"https://doi.org/10.1038/s41593-024-01597-4","open_access":"1"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603"}],"ec_funded":1,"author":[{"full_name":"Agnes, Everton J.","first_name":"Everton J.","last_name":"Agnes"},{"first_name":"Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","orcid":"0000-0003-3295-6181","full_name":"Vogels, Tim P"}],"date_updated":"2024-03-25T07:04:05Z","date_created":"2024-03-24T23:01:00Z","acknowledgement":"We thank C. Currin, B. Podlaski and the members of the Vogels group for fruitful discussions. E.J.A. and T.P.V. were supported by a Research Project Grant from the Leverhulme Trust (RPG-2016-446; TPV), a Sir Henry Dale Fellowship from the Wellcome Trust and the Royal Society (WT100000; T.P.V.), a Wellcome Trust Senior Research Fellowship (214316/Z/18/Z; T.P.V.) and a European Research Council Consolidator Grant (SYNAPSEEK, 819603; T.P.V.). For the purpose of open access, the authors have applied a CC BY public copyright license to any author accepted manuscript version arising from this submission. Open access funding provided by University of Basel.","year":"2024","publication_status":"epub_ahead","department":[{"_id":"TiVo"}],"publisher":"Springer Nature","day":"20","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","date_published":"2024-03-20T00:00:00Z","publication":"Nature Neuroscience","citation":{"ista":"Agnes EJ, Vogels TP. 2024. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience.","ieee":"E. J. Agnes and T. P. Vogels, “Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks,” Nature Neuroscience. Springer Nature, 2024.","apa":"Agnes, E. J., & Vogels, T. P. (2024). Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-024-01597-4","ama":"Agnes EJ, Vogels TP. Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks. Nature Neuroscience. 2024. doi:10.1038/s41593-024-01597-4","chicago":"Agnes, Everton J., and Tim P Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience. Springer Nature, 2024. https://doi.org/10.1038/s41593-024-01597-4.","mla":"Agnes, Everton J., and Tim P. Vogels. “Co-Dependent Excitatory and Inhibitory Plasticity Accounts for Quick, Stable and Long-Lasting Memories in Biological Networks.” Nature Neuroscience, Springer Nature, 2024, doi:10.1038/s41593-024-01597-4.","short":"E.J. Agnes, T.P. Vogels, Nature Neuroscience (2024)."},"article_type":"original","abstract":[{"lang":"eng","text":"The brain’s functionality is developed and maintained through synaptic plasticity. As synapses undergo plasticity, they also affect each other. The nature of such ‘co-dependency’ is difficult to disentangle experimentally, because multiple synapses must be monitored simultaneously. To help understand the experimentally observed phenomena, we introduce a framework that formalizes synaptic co-dependency between different connection types. The resulting model explains how inhibition can gate excitatory plasticity while neighboring excitatory–excitatory interactions determine the strength of long-term potentiation. Furthermore, we show how the interplay between excitatory and inhibitory synapses can account for the quick rise and long-term stability of a variety of synaptic weight profiles, such as orientation tuning and dendritic clustering of co-active synapses. In recurrent neuronal networks, co-dependent plasticity produces rich and stable motor cortex-like dynamics with high input sensitivity. Our results suggest an essential role for the neighborly synaptic interaction during learning, connecting micro-level physiology with network-wide phenomena."}],"type":"journal_article","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15171","status":"public","title":"Co-dependent excitatory and inhibitory plasticity accounts for quick, stable and long-lasting memories in biological networks"},{"type":"journal_article","abstract":[{"lang":"eng","text":"We propose a novel approach to concentration for non-independent random variables. The main idea is to “pretend” that the random variables are independent and pay a multiplicative price measuring how far they are from actually being independent. This price is encapsulated in the Hellinger integral between the joint and the product of the marginals, which is then upper bounded leveraging tensorisation properties. Our bounds represent a natural generalisation of concentration inequalities in the presence of dependence: we recover exactly the classical bounds (McDiarmid’s inequality) when the random variables are independent. Furthermore, in a “large deviations” regime, we obtain the same decay in the probability as for the independent case, even when the random variables display non-trivial dependencies. To show this, we consider a number of applications of interest. First, we provide a bound for Markov chains with finite state space. Then, we consider the Simple Symmetric Random Walk, which is a non-contracting Markov chain, and a non-Markovian setting in which the stochastic process depends on its entire past. To conclude, we propose an application to Markov Chain Monte Carlo methods, where our approach leads to an improved lower bound on the minimum burn-in period required to reach a certain accuracy. In all of these settings, we provide a regime of parameters in which our bound fares better than what the state of the art can provide."}],"year":"2024","_id":"15172","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Concentration without independence via information measures","publication_status":"inpress","status":"public","department":[{"_id":"MaMo"}],"publisher":"IEEE","author":[{"first_name":"Amedeo Roberto","last_name":"Esposito","id":"9583e921-e1ad-11ec-9862-cef099626dc9","full_name":"Esposito, Amedeo Roberto"},{"last_name":"Mondelli","first_name":"Marco","orcid":"0000-0002-3242-7020","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"}],"related_material":{"record":[{"id":"14922","status":"public","relation":"earlier_version"}]},"date_created":"2024-03-24T23:01:00Z","date_updated":"2024-03-25T07:15:51Z","oa_version":"None","scopus_import":"1","month":"02","day":"20","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"article_processing_charge":"No","publication":"IEEE Transactions on Information Theory","external_id":{"arxiv":["2303.07245"]},"citation":{"ama":"Esposito AR, Mondelli M. Concentration without independence via information measures. IEEE Transactions on Information Theory. doi:10.1109/TIT.2024.3367767","ieee":"A. R. Esposito and M. Mondelli, “Concentration without independence via information measures,” IEEE Transactions on Information Theory. IEEE.","apa":"Esposito, A. R., & Mondelli, M. (n.d.). Concentration without independence via information measures. IEEE Transactions on Information Theory. IEEE. https://doi.org/10.1109/TIT.2024.3367767","ista":"Esposito AR, Mondelli M. Concentration without independence via information measures. IEEE Transactions on Information Theory.","short":"A.R. Esposito, M. Mondelli, IEEE Transactions on Information Theory (n.d.).","mla":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” IEEE Transactions on Information Theory, IEEE, doi:10.1109/TIT.2024.3367767.","chicago":"Esposito, Amedeo Roberto, and Marco Mondelli. “Concentration without Independence via Information Measures.” IEEE Transactions on Information Theory. IEEE, n.d. https://doi.org/10.1109/TIT.2024.3367767."},"article_type":"original","quality_controlled":"1","project":[{"name":"Prix Lopez-Loretta 2019 - Marco Mondelli","_id":"059876FA-7A3F-11EA-A408-12923DDC885E"}],"date_published":"2024-02-20T00:00:00Z","doi":"10.1109/TIT.2024.3367767","language":[{"iso":"eng"}]},{"publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"month":"03","doi":"10.3847/1538-4357/ad1e5f","language":[{"iso":"eng"}],"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2309.05714"]},"quality_controlled":"1","file_date_updated":"2024-03-25T08:02:43Z","article_number":"39","author":[{"first_name":"Jenny E.","last_name":"Greene","full_name":"Greene, Jenny E."},{"first_name":"Ivo","last_name":"Labbe","full_name":"Labbe, Ivo"},{"last_name":"Goulding","first_name":"Andy D.","full_name":"Goulding, Andy D."},{"first_name":"Lukas J.","last_name":"Furtak","full_name":"Furtak, Lukas J."},{"full_name":"Chemerynska, Iryna","first_name":"Iryna","last_name":"Chemerynska"},{"last_name":"Kokorev","first_name":"Vasily","full_name":"Kokorev, Vasily"},{"first_name":"Pratika","last_name":"Dayal","full_name":"Dayal, Pratika"},{"full_name":"Volonteri, Marta","first_name":"Marta","last_name":"Volonteri"},{"last_name":"Williams","first_name":"Christina C.","full_name":"Williams, Christina C."},{"last_name":"Wang","first_name":"Bingjie","full_name":"Wang, Bingjie"},{"full_name":"Setton, David J.","first_name":"David J.","last_name":"Setton"},{"first_name":"Adam J.","last_name":"Burgasser","full_name":"Burgasser, Adam J."},{"full_name":"Bezanson, Rachel","first_name":"Rachel","last_name":"Bezanson"},{"last_name":"Atek","first_name":"Hakim","full_name":"Atek, Hakim"},{"last_name":"Brammer","first_name":"Gabriel","full_name":"Brammer, Gabriel"},{"first_name":"Sam E.","last_name":"Cutler","full_name":"Cutler, Sam E."},{"last_name":"Feldmann","first_name":"Robert","full_name":"Feldmann, Robert"},{"full_name":"Fujimoto, Seiji","last_name":"Fujimoto","first_name":"Seiji"},{"first_name":"Karl","last_name":"Glazebrook","full_name":"Glazebrook, Karl"},{"last_name":"De Graaff","first_name":"Anna","full_name":"De Graaff, Anna"},{"full_name":"Khullar, Gourav","first_name":"Gourav","last_name":"Khullar"},{"full_name":"Leja, Joel","last_name":"Leja","first_name":"Joel"},{"full_name":"Marchesini, Danilo","first_name":"Danilo","last_name":"Marchesini"},{"first_name":"Michael V.","last_name":"Maseda","full_name":"Maseda, Michael V."},{"id":"7439a258-f3c0-11ec-9501-9df22fe06720","orcid":"0000-0003-2871-127X","first_name":"Jorryt J","last_name":"Matthee","full_name":"Matthee, Jorryt J"},{"full_name":"Miller, Tim B.","last_name":"Miller","first_name":"Tim B."},{"full_name":"Naidu, Rohan P.","last_name":"Naidu","first_name":"Rohan P."},{"full_name":"Nanayakkara, Themiya","first_name":"Themiya","last_name":"Nanayakkara"},{"last_name":"Oesch","first_name":"Pascal A.","full_name":"Oesch, Pascal A."},{"full_name":"Pan, Richard","first_name":"Richard","last_name":"Pan"},{"full_name":"Papovich, Casey","first_name":"Casey","last_name":"Papovich"},{"last_name":"Price","first_name":"Sedona H.","full_name":"Price, Sedona H."},{"first_name":"Pieter","last_name":"Van Dokkum","full_name":"Van Dokkum, Pieter"},{"last_name":"Weaver","first_name":"John R.","full_name":"Weaver, John R."},{"first_name":"Katherine E.","last_name":"Whitaker","full_name":"Whitaker, Katherine E."},{"first_name":"Adi","last_name":"Zitrin","full_name":"Zitrin, Adi"}],"volume":964,"date_created":"2024-03-24T23:00:59Z","date_updated":"2024-03-25T08:04:13Z","year":"2024","acknowledgement":"J.E.G. and A.D.G acknowledge support from NSF/AAG grant No. 1007094, and J.E.G. also acknowledges support from NSF/AAG grant No. 1007052. A.Z. acknowledges support by grant No. 2020750 from the United States-Israel Binational Science Foundation (BSF) and grant No. 2109066 from the United States National Science Foundation (NSF), and by the Ministry of Science & Technology of Israel. The Cosmic Dawn Center is funded by the Danish National Research Foundation (DNRF) under grant No. 140. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract number MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. P.D. acknowledges support from the NWO grant 016.VIDI.189.162 (\"ODIN\") and from the European Commission's and University of Groningen's CO-FUND Rosalind Franklin program. K.G. and T.N. acknowledge support from Australian Research Council Laureate Fellowship FL180100060. H.A. and I.C. acknowledge support from CNES, focused on the JWST mission, and the Programme National Cosmology and Galaxies (PNCG) of CNRS/INSU with INP and IN2P3, cofunded by CEA and CNES. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. The research of C.C.W. is supported by NOIRLab, which is managed by the Association of Universities for Research in Astronomy (AURA) under a cooperative agreement with the National Science Foundation. B.W. acknowledges support from JWST-GO-02561.022-A. A.J.B. acknowledges funding support from NASA/ADAP grant 21-ADAP21-0187. Support for this work was provided by The Brinson Foundation through a Brinson Prize Fellowship grant. R.P.N. acknowledges support for this work provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. C.P. thanks Marsha and Ralph Schilling for the generous support of this research.","publisher":"IOP Publishing","department":[{"_id":"JoMa"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","scopus_import":"1","date_published":"2024-03-01T00:00:00Z","citation":{"ista":"Greene JE, Labbe I, Goulding AD, Furtak LJ, Chemerynska I, Kokorev V, Dayal P, Volonteri M, Williams CC, Wang B, Setton DJ, Burgasser AJ, Bezanson R, Atek H, Brammer G, Cutler SE, Feldmann R, Fujimoto S, Glazebrook K, De Graaff A, Khullar G, Leja J, Marchesini D, Maseda MV, Matthee JJ, Miller TB, Naidu RP, Nanayakkara T, Oesch PA, Pan R, Papovich C, Price SH, Van Dokkum P, Weaver JR, Whitaker KE, Zitrin A. 2024. UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. 964, 39.","apa":"Greene, J. E., Labbe, I., Goulding, A. D., Furtak, L. J., Chemerynska, I., Kokorev, V., … Zitrin, A. (2024). UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. IOP Publishing. https://doi.org/10.3847/1538-4357/ad1e5f","ieee":"J. E. Greene et al., “UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5,” Astrophysical Journal, vol. 964. IOP Publishing, 2024.","ama":"Greene JE, Labbe I, Goulding AD, et al. UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5. Astrophysical Journal. 2024;964. doi:10.3847/1538-4357/ad1e5f","chicago":"Greene, Jenny E., Ivo Labbe, Andy D. Goulding, Lukas J. Furtak, Iryna Chemerynska, Vasily Kokorev, Pratika Dayal, et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical Journal. IOP Publishing, 2024. https://doi.org/10.3847/1538-4357/ad1e5f.","mla":"Greene, Jenny E., et al. “UNCOVER Spectroscopy Confirms the Surprising Ubiquity of Active Galactic Nuclei in Red Sources at z > 5.” Astrophysical Journal, vol. 964, 39, IOP Publishing, 2024, doi:10.3847/1538-4357/ad1e5f.","short":"J.E. Greene, I. Labbe, A.D. Goulding, L.J. Furtak, I. Chemerynska, V. Kokorev, P. Dayal, M. Volonteri, C.C. Williams, B. Wang, D.J. Setton, A.J. Burgasser, R. Bezanson, H. Atek, G. Brammer, S.E. Cutler, R. Feldmann, S. Fujimoto, K. Glazebrook, A. De Graaff, G. Khullar, J. Leja, D. Marchesini, M.V. Maseda, J.J. Matthee, T.B. Miller, R.P. Naidu, T. Nanayakkara, P.A. Oesch, R. Pan, C. Papovich, S.H. Price, P. Van Dokkum, J.R. Weaver, K.E. Whitaker, A. Zitrin, Astrophysical Journal 964 (2024)."},"publication":"Astrophysical Journal","article_type":"original","abstract":[{"lang":"eng","text":"The James Webb Space Telescope is revealing a new population of dust-reddened broad-line active galactic nuclei (AGN) at redshifts z ≳ 5. Here we present deep NIRSpec/Prism spectroscopy from the Cycle 1 Treasury program Ultradeep NIRSpec and NIRCam ObserVations before the Epoch of Reionization (UNCOVER) of 15 AGN candidates selected to be compact, with red continua in the rest-frame optical but with blue slopes in the UV. From NIRCam photometry alone, they could have been dominated by dusty star formation or an AGN. Here we show that the majority of the compact red sources in UNCOVER are dust-reddened AGN: 60% show definitive evidence for broad-line Hα with a FWHM > 2000 km s −1, 20% of the current data are inconclusive, and 20% are brown dwarf stars. We propose an updated photometric criterion to select red z > 5 AGN that excludes brown dwarfs and is expected to yield >80% AGN. Remarkably, among all zphot > 5 galaxies with F277W – F444W > 1 in UNCOVER at least 33% are AGN regardless of compactness, climbing to at least 80% AGN for sources with F277W – F444W > 1.6. The confirmed AGN have black hole masses of 107–109M⊙. While their UV luminosities (−16 > MUV > −20 AB mag) are low compared to UV-selected AGN at these epochs, consistent with percent-level scattered AGN light or low levels of unobscured star formation, the inferred bolometric luminosities are typical of 107–109M⊙ black holes radiating at ∼10%–40% the Eddington limit. The number densities are surprisingly high at ∼10−5 Mpc−3 mag−1, 100 times more common than the faintest UV-selected quasars, while accounting for ∼1% of the UV-selected galaxies. While their UV faintness suggests they may not contribute strongly to reionization, their ubiquity poses challenges to models of black hole growth."}],"type":"journal_article","oa_version":"Published Version","file":[{"creator":"dernst","file_size":2700137,"content_type":"application/pdf","access_level":"open_access","file_name":"2024_AstrophysicalJourn_Greene.pdf","success":1,"checksum":"389a880e176799d5c062ea7cb82d08c9","date_updated":"2024-03-25T08:02:43Z","date_created":"2024-03-25T08:02:43Z","file_id":"15176","relation":"main_file"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15170","intvolume":" 964","status":"public","ddc":["550"],"title":"UNCOVER spectroscopy confirms the surprising ubiquity of active galactic nuclei in red sources at z > 5"},{"date_published":"2024-03-01T00:00:00Z","citation":{"ama":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In: 41st International Symposium on Theoretical Aspects of Computer Science. Vol 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2024. doi:10.4230/LIPIcs.STACS.2024.34","ista":"Filakovský M, Nakajima TV, Opršal J, Tasinato G, Wagner U. 2024. Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. 41st International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 289, 34.","apa":"Filakovský, M., Nakajima, T. V., Opršal, J., Tasinato, G., & Wagner, U. (2024). Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs. In 41st International Symposium on Theoretical Aspects of Computer Science (Vol. 289). Clermont-Ferrand, France: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2024.34","ieee":"M. Filakovský, T. V. Nakajima, J. Opršal, G. Tasinato, and U. Wagner, “Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs,” in 41st International Symposium on Theoretical Aspects of Computer Science, Clermont-Ferrand, France, 2024, vol. 289.","mla":"Filakovský, Marek, et al. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” 41st International Symposium on Theoretical Aspects of Computer Science, vol. 289, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024, doi:10.4230/LIPIcs.STACS.2024.34.","short":"M. Filakovský, T.V. Nakajima, J. Opršal, G. Tasinato, U. Wagner, in:, 41st International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024.","chicago":"Filakovský, Marek, Tamio Vesa Nakajima, Jakub Opršal, Gianluca Tasinato, and Uli Wagner. “Hardness of Linearly Ordered 4-Colouring of 3-Colourable 3-Uniform Hypergraphs.” In 41st International Symposium on Theoretical Aspects of Computer Science, Vol. 289. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2024. https://doi.org/10.4230/LIPIcs.STACS.2024.34."},"publication":"41st International Symposium on Theoretical Aspects of Computer Science","article_processing_charge":"No","has_accepted_license":"1","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"15175","date_updated":"2024-03-25T07:44:30Z","date_created":"2024-03-25T07:44:30Z","checksum":"0524d4189fd1ed08989546511343edf3","success":1,"file_name":"2024_LIPICs_Filakovsky.pdf","access_level":"open_access","file_size":927290,"content_type":"application/pdf","creator":"dernst"}],"_id":"15168","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 289","title":"Hardness of linearly ordered 4-colouring of 3-colourable 3-uniform hypergraphs","status":"public","ddc":["510"],"abstract":[{"text":"A linearly ordered (LO) k-colouring of a hypergraph is a colouring of its vertices with colours 1, … , k such that each edge contains a unique maximal colour. Deciding whether an input hypergraph admits LO k-colouring with a fixed number of colours is NP-complete (and in the special case of graphs, LO colouring coincides with the usual graph colouring). Here, we investigate the complexity of approximating the \"linearly ordered chromatic number\" of a hypergraph. We prove that the following promise problem is NP-complete: Given a 3-uniform hypergraph, distinguish between the case that it is LO 3-colourable, and the case that it is not even LO 4-colourable. We prove this result by a combination of algebraic, topological, and combinatorial methods, building on and extending a topological approach for studying approximate graph colouring introduced by Krokhin, Opršal, Wrochna, and Živný (2023).","lang":"eng"}],"type":"conference","alternative_title":["LIPIcs"],"doi":"10.4230/LIPIcs.STACS.2024.34","conference":{"name":"STACS: Symposium on Theoretical Aspects of Computer Science","end_date":"2024-03-14","location":"Clermont-Ferrand, France","start_date":"2024-03-12"},"language":[{"iso":"eng"}],"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2312.12981"]},"oa":1,"project":[{"grant_number":"P31312","_id":"26611F5C-B435-11E9-9278-68D0E5697425","name":"Algorithms for Embeddings and Homotopy Theory","call_identifier":"FWF"},{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"quality_controlled":"1","publication_identifier":{"eissn":["1868-8969"],"isbn":["9783959773119"]},"month":"03","author":[{"full_name":"Filakovský, Marek","id":"3E8AF77E-F248-11E8-B48F-1D18A9856A87","first_name":"Marek","last_name":"Filakovský"},{"full_name":"Nakajima, Tamio Vesa","first_name":"Tamio Vesa","last_name":"Nakajima"},{"full_name":"Opršal, Jakub","id":"ec596741-c539-11ec-b829-c79322a91242","orcid":"0000-0003-1245-3456","first_name":"Jakub","last_name":"Opršal"},{"first_name":"Gianluca","last_name":"Tasinato","id":"0433290C-AF8F-11E9-A4C7-F729E6697425","full_name":"Tasinato, Gianluca"},{"first_name":"Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli"}],"volume":289,"date_created":"2024-03-24T23:00:59Z","date_updated":"2024-03-25T07:45:54Z","acknowledgement":"Marek Filakovský: This research was supported by Charles University (project PRIMUS/\r\n21/SCI/014), the Austrian Science Fund (FWF project P31312-N35), and MSCAfellow5_MUNI\r\n(CZ.02.01.01/00/22_010/0003229). Tamio-Vesa Nakajima: This research was funded by UKRI EP/X024431/1 and by a Clarendon Fund Scholarship. All data is provided in full in the results section of this paper. Jakub Opršal: This project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No 101034413. Uli Wagner: This research was supported by the Austrian Science Fund (FWF project P31312-N35).","year":"2024","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"UlWa"}],"publication_status":"published","ec_funded":1,"file_date_updated":"2024-03-25T07:44:30Z","article_number":"34"},{"file":[{"access_level":"open_access","file_name":"2024_MedEngineeringPhysics_SilvaHenao.pdf","creator":"dernst","file_size":10039402,"content_type":"application/pdf","file_id":"15177","relation":"main_file","success":1,"checksum":"974acbf2731e7382dcf5920ac762e551","date_updated":"2024-03-25T08:29:52Z","date_created":"2024-03-25T08:29:52Z"}],"oa_version":"Published Version","intvolume":" 126","title":"Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading","ddc":["610"],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15164","abstract":[{"text":"Primary implant stability, which refers to the stability of the implant during the initial healing period is a crucial factor in determining the long-term success of the implant and lays the foundation for secondary implant stability achieved through osseointegration. Factors affecting primary stability include implant design, surgical technique, and patient-specific factors like bone quality and morphology. In vivo, the cyclic nature of anatomical loading puts osteosynthesis locking screws under dynamic loads, which can lead to the formation of micro cracks and defects that slowly degrade the mechanical connection between the bone and screw, thus compromising the initial stability and secondary stability of the implant. Monotonic quasi-static loading used for testing the holding capacity of implanted screws is not well suited to capture this behavior since it cannot capture the progressive deterioration of peri‑implant bone at small displacements. In order to address this issue, this study aims to determine a critical point of loss of primary implant stability in osteosynthesis locking screws under cyclic overloading by investigating the evolution of damage, dissipated energy, and permanent deformation. A custom-made test setup was used to test implanted 2.5 mm locking screws under cyclic overloading test. For each loading cycle, maximum forces and displacement were recorded as well as initial and final cycle displacements and used to calculate damage and energy dissipation evolution. The results of this study demonstrate that for axial, shear, and mixed loading significant damage and energy dissipation can be observed at approximately 20 % of the failure force. Additionally, at this load level, permanent deformations on the screw-bone interface were found to be in the range of 50 to 150 mm which promotes osseointegration and secondary implant stability. This research can assist surgeons in making informed preoperative decisions by providing a better understanding of the critical point of loss of primary implant stability, thus improving the long-term success of the implant and overall patient satisfaction.","lang":"eng"}],"type":"journal_article","date_published":"2024-04-01T00:00:00Z","article_type":"original","citation":{"mla":"Silva-Henao, Juan D., et al. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics, vol. 126, 104143, Elsevier, 2024, doi:10.1016/j.medengphy.2024.104143.","short":"J.D. Silva-Henao, S. Schober, D.H. Pahr, A.G. Reisinger, Medical Engineering and Physics 126 (2024).","chicago":"Silva-Henao, Juan D., Sophie Schober, Dieter H. Pahr, and Andreas G. Reisinger. “Critical Loss of Primary Implant Stability in Osteosynthesis Locking Screws under Cyclic Overloading.” Medical Engineering and Physics. Elsevier, 2024. https://doi.org/10.1016/j.medengphy.2024.104143.","ama":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 2024;126. doi:10.1016/j.medengphy.2024.104143","ista":"Silva-Henao JD, Schober S, Pahr DH, Reisinger AG. 2024. Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. 126, 104143.","apa":"Silva-Henao, J. D., Schober, S., Pahr, D. H., & Reisinger, A. G. (2024). Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading. Medical Engineering and Physics. Elsevier. https://doi.org/10.1016/j.medengphy.2024.104143","ieee":"J. D. Silva-Henao, S. Schober, D. H. Pahr, and A. G. Reisinger, “Critical loss of primary implant stability in osteosynthesis locking screws under cyclic overloading,” Medical Engineering and Physics, vol. 126. Elsevier, 2024."},"publication":"Medical Engineering and Physics","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","day":"01","scopus_import":"1","volume":126,"date_created":"2024-03-24T23:00:58Z","date_updated":"2024-03-25T08:31:01Z","author":[{"first_name":"Juan D.","last_name":"Silva-Henao","full_name":"Silva-Henao, Juan D."},{"id":"80b0a0ef-4b9f-11ec-b119-8d9d94c4a1d8","first_name":"Sophie","last_name":"Schober","full_name":"Schober, Sophie"},{"first_name":"Dieter H.","last_name":"Pahr","full_name":"Pahr, Dieter H."},{"full_name":"Reisinger, Andreas G.","first_name":"Andreas G.","last_name":"Reisinger"}],"publisher":"Elsevier","department":[{"_id":"PreCl"}],"publication_status":"published","acknowledgement":"The authors declare no conflict of interest related to this study. This project was funded by the Gesellschaft fuer Forschungsfoerderung Niederoesterreich m.b.H. Life Science Call 2017 Grant No. LS17004 and Science call 2019 Dissertationen Grant No. SC19014. No ethical approval was required for this study.","year":"2024","file_date_updated":"2024-03-25T08:29:52Z","article_number":"104143","language":[{"iso":"eng"}],"doi":"10.1016/j.medengphy.2024.104143","quality_controlled":"1","oa":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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"publication_identifier":{"eissn":["1873-4030"],"issn":["1350-4533"]},"month":"04"},{"oa_version":"Published Version","intvolume":" 20","status":"public","title":"kCSD-python, reliable current source density estimation with quality control","_id":"15169","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"3","abstract":[{"text":"Interpretation of extracellular recordings can be challenging due to the long range of electric field. This challenge can be mitigated by estimating the current source density (CSD). Here we introduce kCSD-python, an open Python package implementing Kernel Current Source Density (kCSD) method and related tools to facilitate CSD analysis of experimental data and the interpretation of results. We show how to counter the limitations imposed by noise and assumptions in the method itself. kCSD-python allows CSD estimation for an arbitrary distribution of electrodes in 1D, 2D, and 3D, assuming distributions of sources in tissue, a slice, or in a single cell, and includes a range of diagnostic aids. We demonstrate its features in a Jupyter Notebook tutorial which illustrates a typical analytical workflow and main functionalities useful in validating analysis results.","lang":"eng"}],"type":"journal_article","date_published":"2024-03-14T00:00:00Z","article_type":"original","citation":{"ieee":"C. Chintaluri et al., “kCSD-python, reliable current source density estimation with quality control,” PLoS Computational Biology, vol. 20, no. 3. Public Library of Science, 2024.","apa":"Chintaluri, C., Bejtka, M., Sredniawa, W., Czerwinski, M., Dzik, J. M., Jedrzejewska-Szmek, J., & Wojciki, D. K. (2024). kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1011941","ista":"Chintaluri C, Bejtka M, Sredniawa W, Czerwinski M, Dzik JM, Jedrzejewska-Szmek J, Wojciki DK. 2024. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 20(3), e1011941.","ama":"Chintaluri C, Bejtka M, Sredniawa W, et al. kCSD-python, reliable current source density estimation with quality control. PLoS Computational Biology. 2024;20(3). doi:10.1371/journal.pcbi.1011941","chicago":"Chintaluri, Chaitanya, Marta Bejtka, Wladyslaw Sredniawa, Michal Czerwinski, Jakub M. Dzik, Joanna Jedrzejewska-Szmek, and Daniel K. Wojciki. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” PLoS Computational Biology. Public Library of Science, 2024. https://doi.org/10.1371/journal.pcbi.1011941.","short":"C. Chintaluri, M. Bejtka, W. Sredniawa, M. Czerwinski, J.M. Dzik, J. Jedrzejewska-Szmek, D.K. Wojciki, PLoS Computational Biology 20 (2024).","mla":"Chintaluri, Chaitanya, et al. “KCSD-Python, Reliable Current Source Density Estimation with Quality Control.” PLoS Computational Biology, vol. 20, no. 3, e1011941, Public Library of Science, 2024, doi:10.1371/journal.pcbi.1011941."},"publication":"PLoS Computational Biology","article_processing_charge":"Yes","day":"14","scopus_import":"1","volume":20,"date_created":"2024-03-24T23:00:59Z","date_updated":"2024-03-25T07:54:23Z","related_material":{"link":[{"url":"https://github.com/Neuroinflab/kCSD-python","relation":"software"}]},"author":[{"first_name":"Chaitanya","last_name":"Chintaluri","id":"E4EDB536-3485-11EA-98D2-20AF3DDC885E","full_name":"Chintaluri, Chaitanya"},{"full_name":"Bejtka, Marta","first_name":"Marta","last_name":"Bejtka"},{"last_name":"Sredniawa","first_name":"Wladyslaw","full_name":"Sredniawa, Wladyslaw"},{"full_name":"Czerwinski, Michal","first_name":"Michal","last_name":"Czerwinski"},{"first_name":"Jakub M.","last_name":"Dzik","full_name":"Dzik, Jakub M."},{"full_name":"Jedrzejewska-Szmek, Joanna","last_name":"Jedrzejewska-Szmek","first_name":"Joanna"},{"full_name":"Wojciki, Daniel K.","last_name":"Wojciki","first_name":"Daniel K."}],"department":[{"_id":"TiVo"}],"publisher":"Public Library of Science","publication_status":"published","acknowledgement":"The Python implementation of kCSD was started by Grzegorz Parka during Google Summer of Code project through the International Neuroinformatics Coordinating Facility. Jan Mąka implemented the first Python version of skCSD class. This work was supported by the Polish National Science Centre (2013/08/W/NZ4/00691 to DKW; 2015/17/B/ST7/04123 to DKW). ","year":"2024","article_number":"e1011941","language":[{"iso":"eng"}],"doi":"10.1371/journal.pcbi.1011941","quality_controlled":"1","publication_identifier":{"issn":["1553-734X"],"eissn":["1553-7358"]},"month":"03"},{"publisher":"American Physical Society","department":[{"_id":"MiLe"}],"publication_status":"published","acknowledgement":"We thank Félix Werner and Kris Van Houcke for interesting discussions.","year":"2024","volume":109,"date_updated":"2024-03-25T07:36:55Z","date_created":"2024-03-24T23:00:59Z","author":[{"id":"d1c405be-ae15-11ed-8510-ccf53278162e","first_name":"Ragheed","last_name":"Al Hyder","full_name":"Al Hyder, Ragheed"},{"full_name":"Chevy, F.","first_name":"F.","last_name":"Chevy"},{"full_name":"Leyronas, X.","first_name":"X.","last_name":"Leyronas"}],"article_number":"033315","quality_controlled":"1","oa":1,"external_id":{"arxiv":["2311.14536"]},"main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2311.14536","open_access":"1"}],"language":[{"iso":"eng"}],"doi":"10.1103/PhysRevA.109.033315","publication_identifier":{"issn":["2469-9926"],"eissn":["2469-9934"]},"month":"03","intvolume":" 109","status":"public","title":"Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15167","oa_version":"Preprint","type":"journal_article","issue":"3","abstract":[{"text":"We perform a diagrammatic analysis of the energy of a mobile impurity immersed in a strongly interacting two-component Fermi gas to second order in the impurity-bath interaction. These corrections demonstrate divergent behavior in the limit of large impurity momentum. We show the fundamental processes responsible for these logarithmically divergent terms. We study the problem in the general case without any assumptions regarding the fermion-fermion interactions in the bath. We show that the divergent term can be summed up to all orders in the Fermi-Fermi interaction and that the resulting expression is equivalent to the one obtained in the few-body calculation. Finally, we provide a perturbative calculation to the second order in the Fermi-Fermi interaction, and we show the diagrams responsible for these terms.","lang":"eng"}],"article_type":"original","citation":{"short":"R. Al Hyder, F. Chevy, X. Leyronas, Physical Review A 109 (2024).","mla":"Al Hyder, Ragheed, et al. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” Physical Review A, vol. 109, no. 3, 033315, American Physical Society, 2024, doi:10.1103/PhysRevA.109.033315.","chicago":"Al Hyder, Ragheed, F. Chevy, and X. Leyronas. “Exploring Beyond-Mean-Field Logarithmic Divergences in Fermi-Polaron Energy.” Physical Review A. American Physical Society, 2024. https://doi.org/10.1103/PhysRevA.109.033315.","ama":"Al Hyder R, Chevy F, Leyronas X. Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. 2024;109(3). doi:10.1103/PhysRevA.109.033315","ieee":"R. Al Hyder, F. Chevy, and X. Leyronas, “Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy,” Physical Review A, vol. 109, no. 3. American Physical Society, 2024.","apa":"Al Hyder, R., Chevy, F., & Leyronas, X. (2024). Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. American Physical Society. https://doi.org/10.1103/PhysRevA.109.033315","ista":"Al Hyder R, Chevy F, Leyronas X. 2024. Exploring beyond-mean-field logarithmic divergences in Fermi-polaron energy. Physical Review A. 109(3), 033315."},"publication":"Physical Review A","date_published":"2024-03-19T00:00:00Z","scopus_import":"1","article_processing_charge":"No","day":"19"},{"publication":"Discrete Mathematics","citation":{"chicago":"Campbell, Rutger, Florian Hörsch, and Benjamin Moore. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics. Elsevier, 2024. https://doi.org/10.1016/j.disc.2024.113962.","short":"R. Campbell, F. Hörsch, B. Moore, Discrete Mathematics 347 (2024).","mla":"Campbell, Rutger, et al. “Decompositions into Two Linear Forests of Bounded Lengths.” Discrete Mathematics, vol. 347, no. 6, 113962, Elsevier, 2024, doi:10.1016/j.disc.2024.113962.","ieee":"R. Campbell, F. Hörsch, and B. Moore, “Decompositions into two linear forests of bounded lengths,” Discrete Mathematics, vol. 347, no. 6. Elsevier, 2024.","apa":"Campbell, R., Hörsch, F., & Moore, B. (2024). Decompositions into two linear forests of bounded lengths. Discrete Mathematics. Elsevier. https://doi.org/10.1016/j.disc.2024.113962","ista":"Campbell R, Hörsch F, Moore B. 2024. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 347(6), 113962.","ama":"Campbell R, Hörsch F, Moore B. Decompositions into two linear forests of bounded lengths. Discrete Mathematics. 2024;347(6). doi:10.1016/j.disc.2024.113962"},"article_type":"original","date_published":"2024-03-19T00:00:00Z","scopus_import":"1","day":"19","article_processing_charge":"No","_id":"15163","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Decompositions into two linear forests of bounded lengths","intvolume":" 347","oa_version":"Preprint","type":"journal_article","abstract":[{"text":"For some k∈Z≥0∪{∞}, we call a linear forest k-bounded if each of its components has at most k edges. We will say a (k,ℓ)-bounded linear forest decomposition of a graph G is a partition of E(G) into the edge sets of two linear forests Fk,Fℓ where Fk is k-bounded and Fℓ is ℓ-bounded. We show that the problem of deciding whether a given graph has such a decomposition is NP-complete if both k and ℓ are at least 2, NP-complete if k≥9 and ℓ=1, and is in P for (k,ℓ)=(2,1). Before this, the only known NP-complete cases were the (2,2) and (3,3) cases. Our hardness result answers a question of Bermond et al. from 1984. We also show that planar graphs of girth at least nine decompose into a linear forest and a matching, which in particular is stronger than 3-edge-colouring such graphs.","lang":"eng"}],"issue":"6","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2301.11615","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2301.11615"]},"quality_controlled":"1","doi":"10.1016/j.disc.2024.113962","language":[{"iso":"eng"}],"month":"03","publication_identifier":{"issn":["0012-365X"]},"acknowledgement":"We wish to thank Dániel Marx and András Sebő for making us aware of the results in [8] and some clarifications on them.","year":"2024","publication_status":"epub_ahead","department":[{"_id":"MaKw"}],"publisher":"Elsevier","author":[{"full_name":"Campbell, Rutger","last_name":"Campbell","first_name":"Rutger"},{"full_name":"Hörsch, Florian","first_name":"Florian","last_name":"Hörsch"},{"full_name":"Moore, Benjamin","id":"6dc1a1be-bf1c-11ed-8d2b-d044840f49d6","first_name":"Benjamin","last_name":"Moore"}],"date_created":"2024-03-24T23:00:58Z","date_updated":"2024-03-25T08:09:43Z","volume":347,"article_number":"113962"},{"date_published":"2024-03-07T00:00:00Z","article_type":"original","publication":"The Astrophysical Journal","citation":{"ista":"Matthee JJ, Naidu RP, Brammer G, Chisholm J, Eilers A-C, Goulding A, Greene J, Kashino D, Labbe I, Lilly SJ, Mackenzie R, Oesch PA, Weibel A, Wuyts S, Xiao M, Bordoloi R, Bouwens R, van Dokkum P, Illingworth G, Kramarenko I, Maseda MV, Mason C, Meyer RA, Nelson EJ, Reddy NA, Shivaei I, Simcoe RA, Yue M. 2024. Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. 963(2), 129.","ieee":"J. J. Matthee et al., “Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys,” The Astrophysical Journal, vol. 963, no. 2. American Astronomical Society, 2024.","apa":"Matthee, J. J., Naidu, R. P., Brammer, G., Chisholm, J., Eilers, A.-C., Goulding, A., … Yue, M. (2024). Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. American Astronomical Society. https://doi.org/10.3847/1538-4357/ad2345","ama":"Matthee JJ, Naidu RP, Brammer G, et al. Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys. The Astrophysical Journal. 2024;963(2). doi:10.3847/1538-4357/ad2345","chicago":"Matthee, Jorryt J, Rohan P. Naidu, Gabriel Brammer, John Chisholm, Anna-Christina Eilers, Andy Goulding, Jenny Greene, et al. “Little Red Dots: An Abundant Population of Faint Active Galactic Nuclei at z ∼ 5 Revealed by the EIGER and FRESCO JWST Surveys.” The Astrophysical Journal. American Astronomical Society, 2024. https://doi.org/10.3847/1538-4357/ad2345.","mla":"Matthee, Jorryt J., et al. “Little Red Dots: An Abundant Population of Faint Active Galactic Nuclei at z ∼ 5 Revealed by the EIGER and FRESCO JWST Surveys.” The Astrophysical Journal, vol. 963, no. 2, 129, American Astronomical Society, 2024, doi:10.3847/1538-4357/ad2345.","short":"J.J. Matthee, R.P. Naidu, G. Brammer, J. Chisholm, A.-C. Eilers, A. Goulding, J. Greene, D. Kashino, I. Labbe, S.J. Lilly, R. Mackenzie, P.A. Oesch, A. Weibel, S. Wuyts, M. Xiao, R. Bordoloi, R. Bouwens, P. van Dokkum, G. Illingworth, I. Kramarenko, M.V. Maseda, C. Mason, R.A. Meyer, E.J. Nelson, N.A. Reddy, I. Shivaei, R.A. Simcoe, M. Yue, The Astrophysical Journal 963 (2024)."},"day":"07","article_processing_charge":"Yes","has_accepted_license":"1","keyword":["Space and Planetary Science","Astronomy and Astrophysics"],"scopus_import":"1","oa_version":"Published Version","file":[{"date_updated":"2024-03-25T09:31:58Z","date_created":"2024-03-25T09:31:58Z","success":1,"checksum":"dc7af4694f9f94a551417ab49fa43edf","file_id":"15184","relation":"main_file","creator":"dernst","content_type":"application/pdf","file_size":6047536,"file_name":"2024_AstrophysicalJourn_Matthee.pdf","access_level":"open_access"}],"ddc":["550"],"title":"Little Red Dots: An abundant population of faint active galactic nuclei at z ∼ 5 revealed by the EIGER and FRESCO JWST surveys","status":"public","intvolume":" 963","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15180","abstract":[{"text":"Characterizing the prevalence and properties of faint active galactic nuclei (AGNs) in the early Universe is key for understanding the formation of supermassive black holes (SMBHs) and determining their role in cosmic reionization. We perform a spectroscopic search for broad Hα emitters at z ≈ 4–6 using deep JWST/NIRCam imaging and wide field slitless spectroscopy from the EIGER and FRESCO surveys. We identify 20 Hα lines at z = 4.2–5.5 that have broad components with line widths from ∼1200–3700 km s−1, contributing ∼30%–90% of the total line flux. We interpret these broad components as being powered by accretion onto SMBHs with implied masses ∼107–8M⊙. In the UV luminosity range MUV,AGN+host = −21 to −18, we measure number densities of ≈10−5 cMpc−3. This is an order of magnitude higher than expected from extrapolating quasar UV luminosity functions (LFs). Yet, such AGN are found in only <1% of star-forming galaxies at z ∼ 5. The number density discrepancy is much lower when compared to the broad Hα LF. The SMBH mass function agrees with large cosmological simulations. In two objects, we detect complex Hα profiles that we tentatively interpret as caused by absorption signatures from dense gas fueling SMBH growth and outflows. We may be witnessing early AGN feedback that will clear dust-free pathways through which more massive blue quasars are seen. We uncover a strong correlation between reddening and the fraction of total galaxy luminosity arising from faint AGN. This implies that early SMBH growth is highly obscured and that faint AGN are only minor contributors to cosmic reionization.","lang":"eng"}],"issue":"2","type":"journal_article","language":[{"iso":"eng"}],"doi":"10.3847/1538-4357/ad2345","quality_controlled":"1","project":[{"name":"Young galaxies as tracers and agents of cosmic reionization","grant_number":"101076224","_id":"bd9b2118-d553-11ed-ba76-db24564edfea"}],"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"month":"03","publication_identifier":{"issn":["0004-637X"],"eissn":["1538-4357"]},"date_created":"2024-03-25T08:54:47Z","date_updated":"2024-03-25T09:37:27Z","volume":963,"author":[{"orcid":"0000-0003-2871-127X","id":"7439a258-f3c0-11ec-9501-9df22fe06720","last_name":"Matthee","first_name":"Jorryt J","full_name":"Matthee, Jorryt J"},{"first_name":"Rohan P.","last_name":"Naidu","full_name":"Naidu, Rohan P."},{"first_name":"Gabriel","last_name":"Brammer","full_name":"Brammer, Gabriel"},{"last_name":"Chisholm","first_name":"John","full_name":"Chisholm, John"},{"full_name":"Eilers, Anna-Christina","first_name":"Anna-Christina","last_name":"Eilers"},{"first_name":"Andy","last_name":"Goulding","full_name":"Goulding, Andy"},{"first_name":"Jenny","last_name":"Greene","full_name":"Greene, Jenny"},{"last_name":"Kashino","first_name":"Daichi","full_name":"Kashino, Daichi"},{"last_name":"Labbe","first_name":"Ivo","full_name":"Labbe, Ivo"},{"first_name":"Simon J.","last_name":"Lilly","full_name":"Lilly, Simon J."},{"last_name":"Mackenzie","first_name":"Ruari","full_name":"Mackenzie, Ruari"},{"first_name":"Pascal A.","last_name":"Oesch","full_name":"Oesch, Pascal A."},{"first_name":"Andrea","last_name":"Weibel","full_name":"Weibel, Andrea"},{"full_name":"Wuyts, Stijn","first_name":"Stijn","last_name":"Wuyts"},{"last_name":"Xiao","first_name":"Mengyuan","full_name":"Xiao, Mengyuan"},{"full_name":"Bordoloi, Rongmon","first_name":"Rongmon","last_name":"Bordoloi"},{"full_name":"Bouwens, Rychard","first_name":"Rychard","last_name":"Bouwens"},{"first_name":"Pieter","last_name":"van Dokkum","full_name":"van Dokkum, Pieter"},{"full_name":"Illingworth, Garth","last_name":"Illingworth","first_name":"Garth"},{"last_name":"Kramarenko","first_name":"Ivan","full_name":"Kramarenko, Ivan"},{"full_name":"Maseda, Michael V.","first_name":"Michael V.","last_name":"Maseda"},{"first_name":"Charlotte","last_name":"Mason","full_name":"Mason, Charlotte"},{"last_name":"Meyer","first_name":"Romain A.","full_name":"Meyer, Romain A."},{"last_name":"Nelson","first_name":"Erica J.","full_name":"Nelson, Erica J."},{"last_name":"Reddy","first_name":"Naveen A.","full_name":"Reddy, Naveen A."},{"last_name":"Shivaei","first_name":"Irene","full_name":"Shivaei, Irene"},{"last_name":"Simcoe","first_name":"Robert A.","full_name":"Simcoe, Robert A."},{"first_name":"Minghao","last_name":"Yue","full_name":"Yue, Minghao"}],"publication_status":"published","publisher":"American Astronomical Society","department":[{"_id":"JoMa"}],"acknowledgement":"We thank the anonymous referee for constructive comments that helped improve the manuscript. This work is based on observations made with the NASA/ESA/CSA James Webb Space Telescope. The data were obtained from the Mikulski Archive for Space Telescopes at the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-03127 for JWST. These observations are associated with program Nos. 1243 and 1895. The specific observations analyzed can be accessed via doi:10.17909/4xx0-zj76. Funded by the European Union (ERC, AGENTS, 101076224). Views and opinions expressed are however those of the author(s) only and do not necessarily reflect those of the European Union or the European Research Council. Neither the European Union nor the granting authority can be held responsible for them. R.P.N. acknowledges funding from JWST programs GO-1933 and GO-2279. Support for this work for R.P.N. was provided by NASA through the NASA Hubble Fellowship grant HST-HF2-51515.001-A awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Incorporated, under NASA contract NAS5-26555. Support for this work for G.I. was provided by NASA through grant JWST-GO-01895 awarded by the Space Telescope Science Institute, which is operated by the Association of Universities for Research in Astronomy, Inc., under NASA contract NAS 5-26555. This work has received funding from the Swiss State Secretariat for Education, Research and Innovation (SERI) under contract No. MB22.00072, as well as from the Swiss National Science Foundation (SNSF) through project grant 200020_207349. The Cosmic Dawn Center (DAWN) is funded by the Danish National Research Foundation under grant No. 140.\r\nFacility: JWST - James Webb Space Telescope, HST - Hubble Space Telescope satellite\r\nSoftware: Python, matplotlib (Hunter 2007), numpy (Harris et al. 2020), scipy (Virtanen et al. 2020), Astropy (Astropy Collaboration et al. 2013, 2018), Imfit (Erwin 2015).","year":"2024","file_date_updated":"2024-03-25T09:31:58Z","article_number":"129"},{"date_published":"2024-03-01T00:00:00Z","citation":{"ista":"Palkina KA, Karataeva TA, Perfilov MM, Fakhranurova LI, Markina NM, Gonzalez Somermeyer L, Garcia-Perez E, Vazquez-Vilar M, Rodriguez-Rodriguez M, Vazquez-Vilriales V, Shakhova ES, Mitiouchkina T, Belozerova OA, Kovalchuk SI, Alekberova A, Malyshevskaia AK, Bugaeva EN, Guglya EB, Balakireva A, Sytov N, Bezlikhotnova A, Boldyreva DI, Babenko VV, Kondrashov F, Choob VV, Orzaez D, Yampolsky IV, Mishin AS, Sarkisyan KS. 2024. A hybrid pathway for self-sustained luminescence. Science Advances. 10(10), adk1992.","ieee":"K. A. Palkina et al., “A hybrid pathway for self-sustained luminescence,” Science Advances, vol. 10, no. 10. American Association for the Advancement of Science, 2024.","apa":"Palkina, K. A., Karataeva, T. A., Perfilov, M. M., Fakhranurova, L. I., Markina, N. M., Gonzalez Somermeyer, L., … Sarkisyan, K. S. (2024). A hybrid pathway for self-sustained luminescence. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adk1992","ama":"Palkina KA, Karataeva TA, Perfilov MM, et al. A hybrid pathway for self-sustained luminescence. Science Advances. 2024;10(10). doi:10.1126/sciadv.adk1992","chicago":"Palkina, Kseniia A., Tatiana A. Karataeva, Maxim M. Perfilov, Liliia I. Fakhranurova, Nadezhda M. Markina, Louisa Gonzalez Somermeyer, Elena Garcia-Perez, et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/sciadv.adk1992.","mla":"Palkina, Kseniia A., et al. “A Hybrid Pathway for Self-Sustained Luminescence.” Science Advances, vol. 10, no. 10, adk1992, American Association for the Advancement of Science, 2024, doi:10.1126/sciadv.adk1992.","short":"K.A. Palkina, T.A. Karataeva, M.M. Perfilov, L.I. Fakhranurova, N.M. Markina, L. Gonzalez Somermeyer, E. Garcia-Perez, M. Vazquez-Vilar, M. Rodriguez-Rodriguez, V. Vazquez-Vilriales, E.S. Shakhova, T. Mitiouchkina, O.A. Belozerova, S.I. Kovalchuk, A. Alekberova, A.K. Malyshevskaia, E.N. Bugaeva, E.B. Guglya, A. Balakireva, N. Sytov, A. Bezlikhotnova, D.I. Boldyreva, V.V. Babenko, F. Kondrashov, V.V. Choob, D. Orzaez, I.V. Yampolsky, A.S. Mishin, K.S. Sarkisyan, Science Advances 10 (2024)."},"publication":"Science Advances","article_type":"original","has_accepted_license":"1","article_processing_charge":"Yes","day":"01","scopus_import":"1","oa_version":"Published Version","file":[{"creator":"dernst","content_type":"application/pdf","file_size":1499302,"access_level":"open_access","file_name":"2024_ScienceAdv_Palkina.pdf","success":1,"checksum":"a19c43b260ea0bbaf895a29712e3153c","date_created":"2024-03-25T09:42:10Z","date_updated":"2024-03-25T09:42:10Z","file_id":"15185","relation":"main_file"}],"_id":"15179","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 10","title":"A hybrid pathway for self-sustained luminescence","status":"public","ddc":["580"],"issue":"10","abstract":[{"lang":"eng","text":"The fungal bioluminescence pathway can be reconstituted in other organisms allowing luminescence imaging without exogenously supplied substrate. The pathway starts from hispidin biosynthesis—a step catalyzed by a large fungal polyketide synthase that requires a posttranslational modification for activity. Here, we report identification of alternative compact hispidin synthases encoded by a phylogenetically diverse group of plants. A hybrid bioluminescence pathway that combines plant and fungal genes is more compact, not dependent on availability of machinery for posttranslational modifications, and confers autonomous bioluminescence in yeast, mammalian, and plant hosts. The compact size of plant hispidin synthases enables additional modes of delivery of autoluminescence, such as delivery with viral vectors."}],"type":"journal_article","doi":"10.1126/sciadv.adk1992","language":[{"iso":"eng"}],"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","publication_identifier":{"issn":["2375-2548"]},"month":"03","author":[{"full_name":"Palkina, Kseniia A.","first_name":"Kseniia A.","last_name":"Palkina"},{"last_name":"Karataeva","first_name":"Tatiana A.","full_name":"Karataeva, Tatiana A."},{"full_name":"Perfilov, Maxim M.","last_name":"Perfilov","first_name":"Maxim M."},{"full_name":"Fakhranurova, Liliia I.","first_name":"Liliia I.","last_name":"Fakhranurova"},{"full_name":"Markina, Nadezhda M.","first_name":"Nadezhda M.","last_name":"Markina"},{"full_name":"Gonzalez Somermeyer, Louisa","orcid":"0000-0001-9139-5383","id":"4720D23C-F248-11E8-B48F-1D18A9856A87","last_name":"Gonzalez Somermeyer","first_name":"Louisa"},{"full_name":"Garcia-Perez, Elena","first_name":"Elena","last_name":"Garcia-Perez"},{"last_name":"Vazquez-Vilar","first_name":"Marta","full_name":"Vazquez-Vilar, Marta"},{"full_name":"Rodriguez-Rodriguez, Marta","last_name":"Rodriguez-Rodriguez","first_name":"Marta"},{"first_name":"Victor","last_name":"Vazquez-Vilriales","full_name":"Vazquez-Vilriales, Victor"},{"full_name":"Shakhova, Ekaterina S.","first_name":"Ekaterina S.","last_name":"Shakhova"},{"last_name":"Mitiouchkina","first_name":"Tatiana","full_name":"Mitiouchkina, Tatiana"},{"full_name":"Belozerova, Olga A.","last_name":"Belozerova","first_name":"Olga A."},{"first_name":"Sergey I.","last_name":"Kovalchuk","full_name":"Kovalchuk, Sergey I."},{"last_name":"Alekberova","first_name":"Anna","full_name":"Alekberova, Anna"},{"first_name":"Alena K.","last_name":"Malyshevskaia","full_name":"Malyshevskaia, Alena K."},{"full_name":"Bugaeva, Evgenia N.","last_name":"Bugaeva","first_name":"Evgenia N."},{"first_name":"Elena B.","last_name":"Guglya","full_name":"Guglya, Elena B."},{"full_name":"Balakireva, Anastasia","first_name":"Anastasia","last_name":"Balakireva"},{"last_name":"Sytov","first_name":"Nikita","full_name":"Sytov, Nikita"},{"last_name":"Bezlikhotnova","first_name":"Anastasia","full_name":"Bezlikhotnova, Anastasia"},{"full_name":"Boldyreva, Daria I.","first_name":"Daria I.","last_name":"Boldyreva"},{"full_name":"Babenko, Vladislav V.","first_name":"Vladislav V.","last_name":"Babenko"},{"full_name":"Kondrashov, Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8243-4694","first_name":"Fyodor","last_name":"Kondrashov"},{"last_name":"Choob","first_name":"Vladimir V.","full_name":"Choob, Vladimir V."},{"full_name":"Orzaez, Diego","first_name":"Diego","last_name":"Orzaez"},{"full_name":"Yampolsky, Ilia V.","first_name":"Ilia V.","last_name":"Yampolsky"},{"full_name":"Mishin, Alexander S.","first_name":"Alexander S.","last_name":"Mishin"},{"full_name":"Sarkisyan, Karen S.","first_name":"Karen S.","last_name":"Sarkisyan"}],"volume":10,"date_updated":"2024-03-25T09:44:53Z","date_created":"2024-03-25T08:54:33Z","acknowledgement":"We thank Milaboratory (milaboratory.com) for the access to computing and storage infrastructure. We thank J. Petrasek for providing the BY-2 cell culture line. We thank Konstantin Lukyanov laboratory and Sergey Deyev laboratory for assistance with experiments.\r\nThis study was partially funded by Light Bio and Planta. The Synthetic biology Group is funded by the MRC London Institute of Medical Sciences (UKRI MC-A658-5QEA0). Cloning and luminescent assays performed in BY-2 were partially supported by RSF, project number 22-14-00400, https://rscf.ru/project/22-14-00400/. Plant transformations were funded by RFBR and MOST, project number 21-54-52004. Plant imaging experiments were funded by RSF, project number 22-74-00124, https://rscf.ru/project/22-74-00124/. Viral delivery experiments were funded by the grant PID2019-108203RB-I00 Plan Nacional I + D from the Ministerio de Ciencia e Innovación (Spain) through the Agencia Estatal de Investigación (cofinanced by the European Regional Development Fund).","year":"2024","department":[{"_id":"FyKo"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","file_date_updated":"2024-03-25T09:42:10Z","article_number":"adk1992"},{"file":[{"date_updated":"2024-03-25T11:28:25Z","date_created":"2024-03-25T11:28:25Z","checksum":"eacb011091a503b9e7b748fef639ba4c","success":1,"relation":"main_file","file_id":"15187","content_type":"application/pdf","file_size":1280108,"creator":"dernst","file_name":"2024_GeophysResLetters_Hwong.pdf","access_level":"open_access"}],"oa_version":"Published Version","title":"The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation","ddc":["550"],"status":"public","intvolume":" 51","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15186","abstract":[{"text":"The elimination of rain evaporation in the planetary boundary layer (PBL) has been found to lead to convective self‐aggregation (CSA) even without radiative feedback, but the precise mechanisms underlying this phenomenon remain unclear. We conducted cloud‐resolving simulations with two domain sizes and progressively reduced rain evaporation in the PBL. Surprisingly, CSA only occurred when rain evaporation was almost completely removed. The additional convective heating resulting from the reduction of evaporative cooling in the moist patch was found to be the trigger, thereafter a dry subsidence intrusion into the PBL in the dry patch takes over and sets CSA in motion. Temperature and moisture anomalies oppose each other in their buoyancy effects, hence explaining the need for almost total rain evaporation removal. We also found radiative cooling and not cold pools to be the leading cause for the comparative ease of CSA to take place in the larger domain.","lang":"eng"}],"issue":"6","type":"journal_article","date_published":"2024-03-19T00:00:00Z","article_type":"original","publication":"Geophysical Research Letters","citation":{"chicago":"Hwong, Yi-Ling, and Caroline J Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical Research Letters. American Geophysical Union, 2024. https://doi.org/10.1029/2023gl106523.","mla":"Hwong, Yi-Ling, and Caroline J. Muller. “The Unreasonable Efficiency of Total Rain Evaporation Removal in Triggering Convective Self‐aggregation.” Geophysical Research Letters, vol. 51, no. 6, e2023GL106523, American Geophysical Union, 2024, doi:10.1029/2023gl106523.","short":"Y.-L. Hwong, C.J. Muller, Geophysical Research Letters 51 (2024).","ista":"Hwong Y-L, Muller CJ. 2024. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. 51(6), e2023GL106523.","ieee":"Y.-L. Hwong and C. J. Muller, “The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation,” Geophysical Research Letters, vol. 51, no. 6. American Geophysical Union, 2024.","apa":"Hwong, Y.-L., & Muller, C. J. (2024). The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2023gl106523","ama":"Hwong Y-L, Muller CJ. The unreasonable efficiency of total rain evaporation removal in triggering convective self‐aggregation. Geophysical Research Letters. 2024;51(6). doi:10.1029/2023gl106523"},"day":"19","has_accepted_license":"1","article_processing_charge":"Yes (in subscription journal)","keyword":["General Earth and Planetary Sciences","Geophysics"],"date_updated":"2024-03-25T11:32:06Z","date_created":"2024-03-25T10:27:30Z","volume":51,"author":[{"first_name":"Yi-Ling","last_name":"Hwong","id":"1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22","orcid":"0000-0001-9281-3479","full_name":"Hwong, Yi-Ling"},{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","orcid":"0000-0001-5836-5350","first_name":"Caroline J","last_name":"Muller","full_name":"Muller, Caroline J"}],"publication_status":"published","publisher":"American Geophysical Union","department":[{"_id":"CaMu"}],"year":"2024","acknowledgement":"YLH is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant 101034413. CM gratefully acknowledges funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant 805041). The authors warmly thank Steven Sherwood, Jiawei Bao, Bidyut Goswami, and Martin Janssens for stimulating and helpful discussions. They also thank Christopher Holloway and an anonymous reviewer for providing helpful feedback that greatly improved this manuscript.\r\n","file_date_updated":"2024-03-25T11:28:25Z","ec_funded":1,"article_number":" e2023GL106523","language":[{"iso":"eng"}],"doi":"10.1029/2023gl106523","quality_controlled":"1","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413","name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020"},{"_id":"629205d8-2b32-11ec-9570-e1356ff73576","grant_number":"805041","call_identifier":"H2020","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"month":"03","publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]}},{"month":"03","publication_identifier":{"issn":["2643-1564"]},"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"arxiv":["2310.17995"]},"oa":1,"quality_controlled":"1","project":[{"name":"IST-BRIDGE: International postdoctoral program","call_identifier":"H2020","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","grant_number":"101034413"}],"doi":"10.1103/physrevresearch.6.013257","language":[{"iso":"eng"}],"article_number":"013257","file_date_updated":"2024-03-25T09:24:55Z","ec_funded":1,"acknowledgement":"This work has been funded by the Cluster of Excellence “Advanced Imaging of Matter” of the Deutsche Forschungsgemeinschaft (DFG) - EXC 2056 - Project ID 390715994.\r\nG.M.K. gratefully acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413.","year":"2024","publication_status":"published","department":[{"_id":"MiLe"}],"publisher":"American Physical Society","author":[{"first_name":"A.","last_name":"Becker","full_name":"Becker, A."},{"full_name":"Koutentakis, Georgios","id":"d7b23d3a-9e21-11ec-b482-f76739596b95","first_name":"Georgios","last_name":"Koutentakis"},{"full_name":"Schmelcher, P.","last_name":"Schmelcher","first_name":"P."}],"date_updated":"2024-03-25T09:27:37Z","date_created":"2024-03-25T08:57:07Z","volume":6,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes","publication":"Physical Review Research","citation":{"ama":"Becker A, Koutentakis G, Schmelcher P. Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 2024;6(1). doi:10.1103/physrevresearch.6.013257","ista":"Becker A, Koutentakis G, Schmelcher P. 2024. Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. 6(1), 013257.","ieee":"A. Becker, G. Koutentakis, and P. Schmelcher, “Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions,” Physical Review Research, vol. 6, no. 1. American Physical Society, 2024.","apa":"Becker, A., Koutentakis, G., & Schmelcher, P. (2024). Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.6.013257","mla":"Becker, A., et al. “Synthetic Dimension-Induced Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research, vol. 6, no. 1, 013257, American Physical Society, 2024, doi:10.1103/physrevresearch.6.013257.","short":"A. Becker, G. Koutentakis, P. Schmelcher, Physical Review Research 6 (2024).","chicago":"Becker, A., Georgios Koutentakis, and P. Schmelcher. “Synthetic Dimension-Induced Pseudo Jahn-Teller Effect in One-Dimensional Confined Fermions.” Physical Review Research. American Physical Society, 2024. https://doi.org/10.1103/physrevresearch.6.013257."},"article_type":"original","date_published":"2024-03-01T00:00:00Z","type":"journal_article","abstract":[{"text":"We demonstrate the failure of the adiabatic Born-Oppenheimer approximation to describe the ground state of a quantum impurity within an ultracold Fermi gas despite substantial mass differences between the bath and impurity species. Increasing repulsion leads to the appearance of nonadiabatic couplings between the fast bath and slow impurity degrees of freedom, which reduce the parity symmetry of the latter according to the pseudo Jahn-Teller effect. The presence of this mechanism is associated to a conical intersection involving the impurity position and the inverse of the interaction strength, which acts as a synthetic dimension. We elucidate the presence of these effects via a detailed ground-state analysis involving the comparison of ab initio fully correlated simulations with effective models. Our study suggests ultracold atomic ensembles as potent emulators of complex molecular phenomena.","lang":"eng"}],"issue":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15181","ddc":["530"],"status":"public","title":"Synthetic dimension-induced pseudo Jahn-Teller effect in one-dimensional confined fermions","intvolume":" 6","file":[{"date_created":"2024-03-25T09:24:55Z","date_updated":"2024-03-25T09:24:55Z","checksum":"4e0e58d1f58386fb016284c84db2a300","success":1,"relation":"main_file","file_id":"15183","file_size":2207067,"content_type":"application/pdf","creator":"dernst","file_name":"2024_PhysicalReviewResearch_Becker.pdf","access_level":"open_access"}],"oa_version":"Published Version"},{"article_number":"2400408","date_created":"2024-03-25T08:57:40Z","date_updated":"2024-03-25T09:21:05Z","author":[{"id":"8BD9DE16-AB3C-11E9-9C8C-2A03E6697425","first_name":"Tobias","last_name":"Kleinhanns","full_name":"Kleinhanns, Tobias"},{"full_name":"Milillo, Francesco","last_name":"Milillo","first_name":"Francesco","id":"38b830db-ea88-11ee-bf9b-929beaf79054"},{"id":"45D7531A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4566-5877","first_name":"Mariano","last_name":"Calcabrini","full_name":"Calcabrini, Mariano"},{"first_name":"Christine","last_name":"Fiedler","id":"bd3fceba-dc74-11ea-a0a7-c17f71817366","full_name":"Fiedler, Christine"},{"full_name":"Horta, Sharona","first_name":"Sharona","last_name":"Horta","id":"03a7e858-01b1-11ec-8b71-99ae6c4a05bc"},{"orcid":"0000-0001-7597-043X","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs","first_name":"Daniel","full_name":"Balazs, Daniel"},{"first_name":"Marissa J.","last_name":"Strumolo","full_name":"Strumolo, Marissa J."},{"first_name":"Roger","last_name":"Hasler","full_name":"Hasler, Roger"},{"first_name":"Jordi","last_name":"Llorca","full_name":"Llorca, Jordi"},{"full_name":"Tkadletz, Michael","last_name":"Tkadletz","first_name":"Michael"},{"full_name":"Brutchey, Richard L.","last_name":"Brutchey","first_name":"Richard L."},{"full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5013-2843","first_name":"Maria","last_name":"Ibáñez"}],"publisher":"Wiley","department":[{"_id":"MaIb"},{"_id":"LifeSc"}],"publication_status":"epub_ahead","year":"2024","acknowledgement":"This work was supported by the Scientific Service Units (SSU) of ISTA through resources provided by the Electron Microscopy Facility (EMF), the Lab Support Facility (LSF), and the Nanofabrication Facility (NNF). This work was financially supported by ISTA and the Werner Siemens Foundation. The USTEM Service Unit of the Technical University of Vienna is acknowledged for EBSD sample preparation and analysis. R.L.B. acknowledges the National Science Foundation for funding the mass spectrometry analysis under award DMR 1904719. J.L. is a Serra Húnter Fellow and is grateful to the ICREA Academia program and projects MICINN/FEDER PID2021-124572OB-C31 and GC 2021 SGR 01061.","publication_identifier":{"issn":["1614-6832"],"eissn":["1614-6840"]},"month":"03","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"LifeSc"},{"_id":"NanoFab"}],"doi":"10.1002/aenm.202400408","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"quality_controlled":"1","oa":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1002/aenm.202400408"}],"abstract":[{"lang":"eng","text":"Thermoelectric materials convert heat into electricity, with a broad range of applications near room temperature (RT). However, the library of RT high-performance materials is limited. Traditional high-temperature synthetic methods constrain the range of materials achievable, hindering the ability to surpass crystal structure limitations and engineer defects. Here, a solution-based synthetic approach is introduced, enabling RT synthesis of powders and exploration of densification at lower temperatures to influence the material's microstructure. The approach is exemplified by Ag2Se, an n-type alternative to bismuth telluride. It is demonstrated that the concentration of Ag interstitials, grain boundaries, and dislocations are directly correlated to the sintering temperature, and achieve a figure of merit of 1.1 from RT to 100 °C after optimization. Moreover, insights into and resolve Ag2Se's challenges are provided, including stoichiometry issues leading to irreproducible performances. This work highlights the potential of RT solution synthesis in expanding the repertoire of high-performance thermoelectric materials for practical applications."}],"type":"journal_article","oa_version":"Published Version","title":"A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15182","article_processing_charge":"Yes (via OA deal)","day":"13","scopus_import":"1","date_published":"2024-03-13T00:00:00Z","article_type":"original","citation":{"ama":"Kleinhanns T, Milillo F, Calcabrini M, et al. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. 2024. doi:10.1002/aenm.202400408","apa":"Kleinhanns, T., Milillo, F., Calcabrini, M., Fiedler, C., Horta, S., Balazs, D., … Ibáñez, M. (2024). A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials. Wiley. https://doi.org/10.1002/aenm.202400408","ieee":"T. Kleinhanns et al., “A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se,” Advanced Energy Materials. Wiley, 2024.","ista":"Kleinhanns T, Milillo F, Calcabrini M, Fiedler C, Horta S, Balazs D, Strumolo MJ, Hasler R, Llorca J, Tkadletz M, Brutchey RL, Ibáñez M. 2024. A route to high thermoelectric performance: Solution‐based control of microstructure and composition in Ag2Se. Advanced Energy Materials., 2400408.","short":"T. Kleinhanns, F. Milillo, M. Calcabrini, C. Fiedler, S. Horta, D. Balazs, M.J. Strumolo, R. Hasler, J. Llorca, M. Tkadletz, R.L. Brutchey, M. Ibáñez, Advanced Energy Materials (2024).","mla":"Kleinhanns, Tobias, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials, 2400408, Wiley, 2024, doi:10.1002/aenm.202400408.","chicago":"Kleinhanns, Tobias, Francesco Milillo, Mariano Calcabrini, Christine Fiedler, Sharona Horta, Daniel Balazs, Marissa J. Strumolo, et al. “A Route to High Thermoelectric Performance: Solution‐based Control of Microstructure and Composition in Ag2Se.” Advanced Energy Materials. Wiley, 2024. https://doi.org/10.1002/aenm.202400408."},"publication":"Advanced Energy Materials"},{"publication_identifier":{"issn":["0094-8276"],"eissn":["1944-8007"]},"month":"03","doi":"10.1029/2023GL106569","language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"oa":1,"project":[{"call_identifier":"H2020","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","grant_number":"805041","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"quality_controlled":"1","ec_funded":1,"file_date_updated":"2024-03-25T08:36:00Z","article_number":"e2023GL106569","author":[{"first_name":"Bidyut B","last_name":"Goswami","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","orcid":"0000-0001-8602-3083","full_name":"Goswami, Bidyut B"}],"volume":51,"date_updated":"2024-03-25T10:00:57Z","date_created":"2024-03-24T23:00:58Z","year":"2024","acknowledgement":"The author gratefully acknowledges ISTA for supporting this research through funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (Project CLUSTER, grant agreement No. 805041).","publisher":"Wiley","department":[{"_id":"CaMu"}],"publication_status":"published","has_accepted_license":"1","article_processing_charge":"Yes","day":"16","scopus_import":"1","date_published":"2024-03-16T00:00:00Z","citation":{"chicago":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” Geophysical Research Letters. Wiley, 2024. https://doi.org/10.1029/2023GL106569.","mla":"GOSWAMI, BIDYUT B. “A Pre-Monsoon Signal of False Alarms of Indian Monsoon Droughts.” Geophysical Research Letters, vol. 51, no. 5, e2023GL106569, Wiley, 2024, doi:10.1029/2023GL106569.","short":"B.B. GOSWAMI, Geophysical Research Letters 51 (2024).","ista":"GOSWAMI BB. 2024. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 51(5), e2023GL106569.","apa":"GOSWAMI, B. B. (2024). A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. Wiley. https://doi.org/10.1029/2023GL106569","ieee":"B. B. GOSWAMI, “A pre-monsoon signal of false alarms of Indian monsoon droughts,” Geophysical Research Letters, vol. 51, no. 5. Wiley, 2024.","ama":"GOSWAMI BB. A pre-monsoon signal of false alarms of Indian monsoon droughts. Geophysical Research Letters. 2024;51(5). doi:10.1029/2023GL106569"},"publication":"Geophysical Research Letters","article_type":"original","issue":"5","abstract":[{"text":"Current knowledge suggests a drought Indian monsoon (perhaps a severe one) when the El Nino Southern Oscillation and Pacific Decadal Oscillation each exhibit positive phases (a joint positive phase). For the monsoons, which are exceptions in this regard, we found northeast India often gets excess pre-monsoon rainfall. Further investigation reveals that this excess pre-monsoon rainfall is produced by the interaction of the large-scale circulation associated with the joint phase with the mountains in northeast India. We posit that a warmer troposphere, a consequence of excess rainfall over northeast India, drives a stronger monsoon circulation and enhances monsoon rainfall over central India. Hence, we argue that pre-monsoon rainfall over northeast India can be used for seasonal monsoon rainfall prediction over central India. Most importantly, its predictive value is at its peak when the Pacific Ocean exhibits a joint positive phase and the threat of extreme drought monsoon looms over India.","lang":"eng"}],"type":"journal_article","file":[{"file_id":"15178","relation":"main_file","date_created":"2024-03-25T08:36:00Z","date_updated":"2024-03-25T08:36:00Z","success":1,"checksum":"243bd966aca968ec7d9e474af8639f8d","file_name":"2024_GeophysResLetters_Goswami.pdf","access_level":"open_access","creator":"dernst","file_size":2887134,"content_type":"application/pdf"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"15165","intvolume":" 51","status":"public","title":"A pre-monsoon signal of false alarms of Indian monsoon droughts","ddc":["550"]},{"date_published":"2024-03-14T00:00:00Z","page":"1184","article_type":"letter_note","citation":{"ama":"Jakhar N, Ibáñez M. Electron highways are cooler. Science. 2024;383(6688):1184. doi:10.1126/science.ado4077","ista":"Jakhar N, Ibáñez M. 2024. Electron highways are cooler. Science. 383(6688), 1184.","ieee":"N. Jakhar and M. Ibáñez, “Electron highways are cooler,” Science, vol. 383, no. 6688. American Association for the Advancement of Science, p. 1184, 2024.","apa":"Jakhar, N., & Ibáñez, M. (2024). Electron highways are cooler. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.ado4077","mla":"Jakhar, Navita, and Maria Ibáñez. “Electron Highways Are Cooler.” Science, vol. 383, no. 6688, American Association for the Advancement of Science, 2024, p. 1184, doi:10.1126/science.ado4077.","short":"N. Jakhar, M. Ibáñez, Science 383 (2024) 1184.","chicago":"Jakhar, Navita, and Maria Ibáñez. “Electron Highways Are Cooler.” Science. American Association for the Advancement of Science, 2024. https://doi.org/10.1126/science.ado4077."},"publication":"Science","article_processing_charge":"No","day":"14","scopus_import":"1","oa_version":"None","intvolume":" 383","title":"Electron highways are cooler","status":"public","_id":"15166","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"6688","abstract":[{"text":"Reducing defects boosts room-temperature performance of a thermoelectric device","lang":"eng"}],"type":"journal_article","language":[{"iso":"eng"}],"doi":"10.1126/science.ado4077","project":[{"_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A","name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery"}],"quality_controlled":"1","publication_identifier":{"issn":["0036-8075"],"eissn":["1095-9203"]},"month":"03","volume":383,"date_created":"2024-03-24T23:00:58Z","date_updated":"2024-03-25T10:31:20Z","author":[{"id":"6ebe278d-ba0b-11ee-8184-f34cdc671de4","first_name":"Navita","last_name":"Navita","full_name":"Navita, Navita"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","id":"43C61214-F248-11E8-B48F-1D18A9856A87","last_name":"Ibáñez","first_name":"Maria"}],"department":[{"_id":"MaIb"}],"publisher":"American Association for the Advancement of Science","publication_status":"published","year":"2024","acknowledgement":"The authors thank the Werner-Siemens-Stiftung and the Institute of Science and Technology Austria for financial support."},{"article_number":"e202309125","ec_funded":1,"file_date_updated":"2024-03-25T12:52:04Z","pmid":1,"acknowledgement":"Open Access funding provided by IST Austria. We thank Armel Nicolas and his team at the ISTA proteomics facility, Alois Schloegl, Stefano Elefante, and colleagues at the ISTA Scientific Computing facility, Tommaso Constanzo and Ludek Lovicar at the Electron Microsocpy Facility (EMF), and Thomas Menner at the Miba Machine shop for their support. We also thank Wanda Kukulski (University of Bern) as well as Darío Porley, Andreas Thader, and other members of the Schur group for helpful discussions. Matt Swulius and Jessica Heebner provided great support in using Dragonfly. We thank Dorotea Fracciolla (Art & Science) for support in figure illustration.\r\n\r\nThis research was supported by the Scientific Service Units of ISTA through resources provided by Scientific Computing, the Lab Support Facility, and the Electron Microscopy Facility. We acknowledge funding support from the following sources: Austrian Science Fund (FWF) grant P33367 (to F.K.M. Schur), the Federation of European Biochemical Societies (to F.K.M. Schur), Niederösterreich (NÖ) Fonds (to B. Zens), FWF grant E435 (to J.M. Hansen), European Research Council under the European Union’s Horizon 2020 research (grant agreement No. 724373) (to M. Sixt), and Jenny and Antti Wihuri Foundation (to J. Alanko). This publication has been made possible in part by CZI grant DAF2021-234754 and grant DOI https://doi.org/10.37921/812628ebpcwg from the Chan Zuckerberg Initiative DAF, an advised fund of Silicon Valley Community Foundation (to F.K.M. Schur).","year":"2024","publisher":"Rockefeller University Press","department":[{"_id":"FlSc"},{"_id":"MiSi"},{"_id":"Bio"},{"_id":"EM-Fac"}],"publication_status":"published","author":[{"last_name":"Zens","first_name":"Bettina","id":"45FD126C-F248-11E8-B48F-1D18A9856A87","full_name":"Zens, Bettina"},{"orcid":"0000-0001-7149-769X","id":"404F5528-F248-11E8-B48F-1D18A9856A87","last_name":"Fäßler","first_name":"Florian","full_name":"Fäßler, Florian"},{"id":"1063c618-6f9b-11ec-9123-f912fccded63","last_name":"Hansen","first_name":"Jesse","full_name":"Hansen, Jesse"},{"last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","full_name":"Hauschild, Robert"},{"full_name":"Datler, Julia","first_name":"Julia","last_name":"Datler","id":"3B12E2E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3616-8580"},{"full_name":"Hodirnau, Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","last_name":"Hodirnau","first_name":"Victor-Valentin"},{"last_name":"Zheden","first_name":"Vanessa","orcid":"0000-0002-9438-4783","id":"39C5A68A-F248-11E8-B48F-1D18A9856A87","full_name":"Zheden, Vanessa"},{"full_name":"Alanko, Jonna H","last_name":"Alanko","first_name":"Jonna H","orcid":"0000-0002-7698-3061","id":"2CC12E8C-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6620-9179","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"},{"full_name":"Schur, Florian KM","orcid":"0000-0003-4790-8078","id":"48AD8942-F248-11E8-B48F-1D18A9856A87","last_name":"Schur","first_name":"Florian KM"}],"volume":223,"date_updated":"2024-03-25T13:03:57Z","date_created":"2024-03-21T06:45:51Z","publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"month":"03","oa":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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["38506714"]},"project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"grant_number":"E435","_id":"7bd318a1-9f16-11ee-852c-cc9217763180","name":"In Situ Actin Structures via Hybrid Cryo-electron Microscopy"},{"call_identifier":"H2020","name":"Cellular navigation along spatial gradients","grant_number":"724373","_id":"25FE9508-B435-11E9-9278-68D0E5697425"},{"name":"NÖ-Fonds Preis für die Jungforscherin des Jahres am IST Austria","_id":"059B463C-7A3F-11EA-A408-12923DDC885E"},{"_id":"2615199A-B435-11E9-9278-68D0E5697425","grant_number":"21317","name":"Spatiotemporal regulation of chemokine-induced signalling in leukocyte chemotaxis"},{"_id":"62909c6f-2b32-11ec-9570-e1476aab5308","grant_number":"CZI01","name":"CryoMinflux-guided in-situ visual proteomics and structure determination"}],"quality_controlled":"1","doi":"10.1083/jcb.202309125","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"ScienComp"},{"_id":"EM-Fac"},{"_id":"M-Shop"}],"type":"journal_article","issue":"6","abstract":[{"text":"The extracellular matrix (ECM) serves as a scaffold for cells and plays an essential role in regulating numerous cellular processes, including cell migration and proliferation. Due to limitations in specimen preparation for conventional room-temperature electron microscopy, we lack structural knowledge on how ECM components are secreted, remodeled, and interact with surrounding cells. We have developed a 3D-ECM platform compatible with sample thinning by cryo-focused ion beam milling, the lift-out extraction procedure, and cryo-electron tomography. Our workflow implements cell-derived matrices (CDMs) grown on EM grids, resulting in a versatile tool closely mimicking ECM environments. This allows us to visualize ECM for the first time in its hydrated, native context. Our data reveal an intricate network of extracellular fibers, their positioning relative to matrix-secreting cells, and previously unresolved structural entities. Our workflow and results add to the structural atlas of the ECM, providing novel insights into its secretion and assembly.","lang":"eng"}],"_id":"15146","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 223","ddc":["570"],"title":"Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix","status":"public","file":[{"file_name":"2024_JCB_Zens.pdf","access_level":"open_access","creator":"dernst","file_size":11907016,"content_type":"application/pdf","file_id":"15188","relation":"main_file","date_created":"2024-03-25T12:52:04Z","date_updated":"2024-03-25T12:52:04Z","success":1,"checksum":"90d1984a93660735e506c2a304bc3f73"}],"oa_version":"Published Version","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","day":"20","citation":{"chicago":"Zens, Bettina, Florian Fäßler, Jesse Hansen, Robert Hauschild, Julia Datler, Victor-Valentin Hodirnau, Vanessa Zheden, Jonna H Alanko, Michael K Sixt, and Florian KM Schur. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology. Rockefeller University Press, 2024. https://doi.org/10.1083/jcb.202309125.","short":"B. Zens, F. Fäßler, J. Hansen, R. Hauschild, J. Datler, V.-V. Hodirnau, V. Zheden, J.H. Alanko, M.K. Sixt, F.K. Schur, Journal of Cell Biology 223 (2024).","mla":"Zens, Bettina, et al. “Lift-out Cryo-FIBSEM and Cryo-ET Reveal the Ultrastructural Landscape of Extracellular Matrix.” Journal of Cell Biology, vol. 223, no. 6, e202309125, Rockefeller University Press, 2024, doi:10.1083/jcb.202309125.","apa":"Zens, B., Fäßler, F., Hansen, J., Hauschild, R., Datler, J., Hodirnau, V.-V., … Schur, F. K. (2024). Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202309125","ieee":"B. Zens et al., “Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix,” Journal of Cell Biology, vol. 223, no. 6. Rockefeller University Press, 2024.","ista":"Zens B, Fäßler F, Hansen J, Hauschild R, Datler J, Hodirnau V-V, Zheden V, Alanko JH, Sixt MK, Schur FK. 2024. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 223(6), e202309125.","ama":"Zens B, Fäßler F, Hansen J, et al. Lift-out cryo-FIBSEM and cryo-ET reveal the ultrastructural landscape of extracellular matrix. Journal of Cell Biology. 2024;223(6). doi:10.1083/jcb.202309125"},"publication":"Journal of Cell Biology","article_type":"original","date_published":"2024-03-20T00:00:00Z"},{"oa_version":"Published Version","_id":"14931","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","status":"public","title":"Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion","intvolume":" 286","abstract":[{"text":"We prove an upper bound on the ground state energy of the dilute spin-polarized Fermi gas capturing the leading correction to the kinetic energy resulting from repulsive interactions. One of the main ingredients in the proof is a rigorous implementation of the fermionic cluster expansion of Gaudin et al. (1971) [15].","lang":"eng"}],"issue":"7","type":"journal_article","date_published":"2024-01-24T00:00:00Z","publication":"Journal of Functional Analysis","citation":{"chicago":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis. Elsevier, 2024. https://doi.org/10.1016/j.jfa.2024.110320.","mla":"Lauritsen, Asbjørn Bækgaard, and Robert Seiringer. “Ground State Energy of the Dilute Spin-Polarized Fermi Gas: Upper Bound via Cluster Expansion.” Journal of Functional Analysis, vol. 286, no. 7, 110320, Elsevier, 2024, doi:10.1016/j.jfa.2024.110320.","short":"A.B. Lauritsen, R. Seiringer, Journal of Functional Analysis 286 (2024).","ista":"Lauritsen AB, Seiringer R. 2024. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 286(7), 110320.","apa":"Lauritsen, A. B., & Seiringer, R. (2024). Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2024.110320","ieee":"A. B. Lauritsen and R. Seiringer, “Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion,” Journal of Functional Analysis, vol. 286, no. 7. Elsevier, 2024.","ama":"Lauritsen AB, Seiringer R. Ground state energy of the dilute spin-polarized Fermi gas: Upper bound via cluster expansion. Journal of Functional Analysis. 2024;286(7). doi:10.1016/j.jfa.2024.110320"},"article_type":"original","day":"24","article_processing_charge":"Yes (via OA deal)","scopus_import":"1","author":[{"orcid":"0000-0003-4476-2288","id":"e1a2682f-dc8d-11ea-abe3-81da9ac728f1","last_name":"Lauritsen","first_name":"Asbjørn Bækgaard","full_name":"Lauritsen, Asbjørn Bækgaard"},{"orcid":"0000-0002-6781-0521","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87","last_name":"Seiringer","first_name":"Robert","full_name":"Seiringer, Robert"}],"date_updated":"2024-03-28T10:54:02Z","date_created":"2024-02-04T23:00:53Z","volume":286,"acknowledgement":"A.B.L. would like to thank Johannes Agerskov and Jan Philip Solovej for valuable discussions. We thank Alessandro Giuliani for helpful discussions and for pointing out the reference [18]. Funding from the European Union's Horizon 2020 research and innovation programme under the ERC grant agreement No 694227 is acknowledged. Financial support by the Austrian Science Fund (FWF) through project number I 6427-N (as part of the SFB/TRR 352) is gratefully acknowledged.","year":"2024","publication_status":"epub_ahead","publisher":"Elsevier","department":[{"_id":"RoSe"}],"ec_funded":1,"article_number":"110320","doi":"10.1016/j.jfa.2024.110320","language":[{"iso":"eng"}],"oa":1,"external_id":{"arxiv":["2301.04894"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.jfa.2024.110320"}],"quality_controlled":"1","project":[{"call_identifier":"H2020","name":"Analysis of quantum many-body systems","grant_number":"694227","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"},{"name":"Mathematical Challenges in BCS Theory of Superconductivity","grant_number":"I06427","_id":"bda63fe5-d553-11ed-ba76-a16e3d2f256b"}],"month":"01","publication_identifier":{"issn":["0022-1236"],"eissn":["1096--0783"]}},{"pmid":1,"year":"2023","editor":[{"last_name":"Margadant","first_name":"Coert","full_name":"Margadant, Coert"}],"department":[{"_id":"EdHa"}],"publisher":"Springer Nature","publication_status":"published","author":[{"full_name":"Hannezo, Edouard B","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6005-1561","first_name":"Edouard B","last_name":"Hannezo"},{"last_name":"Scheele","first_name":"Colinda L.G.J.","full_name":"Scheele, Colinda L.G.J."}],"volume":2608,"date_updated":"2023-02-03T10:58:56Z","date_created":"2023-01-29T23:00:58Z","file_date_updated":"2023-02-03T10:56:39Z","external_id":{"pmid":["36653709"]},"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","doi":"10.1007/978-1-0716-2887-4_12","language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9781071628874"],"isbn":["9781071628867"],"eissn":["1940-6029"]},"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12428","intvolume":" 2608","title":"A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland","ddc":["570"],"status":"public","file":[{"date_created":"2023-02-03T10:56:39Z","date_updated":"2023-02-03T10:56:39Z","checksum":"aec1b8d3ba938ddf9d8fcb777f3c38ee","success":1,"relation":"main_file","file_id":"12500","content_type":"application/pdf","file_size":826598,"creator":"dernst","file_name":"2023_MIMB_Hannezo.pdf","access_level":"open_access"}],"oa_version":"Published Version","type":"book_chapter","alternative_title":["Methods in Molecular Biology"],"abstract":[{"text":"The mammary gland consists of a bilayered epithelial structure with an extensively branched morphology. The majority of this epithelial tree is laid down during puberty, during which actively proliferating terminal end buds repeatedly elongate and bifurcate to form the basic structure of the ductal tree. Mammary ducts consist of a basal and luminal cell layer with a multitude of identified sub-lineages within both layers. The understanding of how these different cell lineages are cooperatively driving branching morphogenesis is a problem of crossing multiple scales, as this requires information on the macroscopic branched structure of the gland, as well as data on single-cell dynamics driving the morphogenic program. Here we describe a method to combine genetic lineage tracing with whole-gland branching analysis. Quantitative data on the global organ structure can be used to derive a model for mammary gland branching morphogenesis and provide a backbone on which the dynamics of individual cell lineages can be simulated and compared to lineage-tracing approaches. Eventually, these quantitative models and experiments allow to understand the couplings between the macroscopic shape of the mammary gland and the underlying single-cell dynamics driving branching morphogenesis.","lang":"eng"}],"citation":{"mla":"Hannezo, Edouard B., and Colinda L. G. J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” Cell Migration in Three Dimensions, edited by Coert Margadant, vol. 2608, Springer Nature, 2023, pp. 183–205, doi:10.1007/978-1-0716-2887-4_12.","short":"E.B. Hannezo, C.L.G.J. Scheele, in:, C. Margadant (Ed.), Cell Migration in Three Dimensions, Springer Nature, 2023, pp. 183–205.","chicago":"Hannezo, Edouard B, and Colinda L.G.J. Scheele. “A Guide Toward Multi-Scale and Quantitative Branching Analysis in the Mammary Gland.” In Cell Migration in Three Dimensions, edited by Coert Margadant, 2608:183–205. MIMB. Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-2887-4_12.","ama":"Hannezo EB, Scheele CLGJ. A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Margadant C, ed. Cell Migration in Three Dimensions. Vol 2608. MIMB. Springer Nature; 2023:183-205. doi:10.1007/978-1-0716-2887-4_12","ista":"Hannezo EB, Scheele CLGJ. 2023.A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In: Cell Migration in Three Dimensions. Methods in Molecular Biology, vol. 2608, 183–205.","apa":"Hannezo, E. B., & Scheele, C. L. G. J. (2023). A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland. In C. Margadant (Ed.), Cell Migration in Three Dimensions (Vol. 2608, pp. 183–205). Springer Nature. https://doi.org/10.1007/978-1-0716-2887-4_12","ieee":"E. B. Hannezo and C. L. G. J. Scheele, “A Guide Toward Multi-scale and Quantitative Branching Analysis in the Mammary Gland,” in Cell Migration in Three Dimensions, vol. 2608, C. Margadant, Ed. Springer Nature, 2023, pp. 183–205."},"publication":"Cell Migration in Three Dimensions","page":"183-205","date_published":"2023-01-19T00:00:00Z","scopus_import":"1","series_title":"MIMB","article_processing_charge":"No","has_accepted_license":"1","day":"19"},{"department":[{"_id":"MiLe"}],"publisher":"American Physical Society","publication_status":"published","acknowledgement":"We thank Rafael Barfknecht for help at the initial stages of this project; Fabian Brauneis for useful discussions; Miguel A. Garcia-March, Georgios Koutentakis, and Simeon Mistakidis\r\nfor comments on the paper. M.L. acknowledges support by the European Research Council (ERC) Starting Grant No. 801770 (ANGULON).","year":"2023","volume":5,"date_created":"2023-02-10T09:02:26Z","date_updated":"2023-02-20T07:02:00Z","author":[{"full_name":"Ghazaryan, Areg","last_name":"Ghazaryan","first_name":"Areg","orcid":"0000-0001-9666-3543","id":"4AF46FD6-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Cappellaro, Alberto","id":"9d13b3cb-30a2-11eb-80dc-f772505e8660","orcid":"0000-0001-6110-2359","first_name":"Alberto","last_name":"Cappellaro"},{"full_name":"Lemeshko, Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"},{"id":"37D278BC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0393-5525","first_name":"Artem","last_name":"Volosniev","full_name":"Volosniev, Artem"}],"article_number":"013029","ec_funded":1,"file_date_updated":"2023-02-13T10:38:10Z","project":[{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","grant_number":"801770","name":"Angulon: physics and applications of a new quasiparticle","call_identifier":"H2020"}],"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1103/physrevresearch.5.013029","publication_identifier":{"issn":["2643-1564"]},"month":"01","intvolume":" 5","status":"public","title":"Dissipative dynamics of an impurity with spin-orbit coupling","ddc":["530"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12534","file":[{"file_size":865150,"content_type":"application/pdf","creator":"dernst","access_level":"open_access","file_name":"2023_PhysicalReviewResearch_Ghazaryan.pdf","checksum":"6068b62874c0099628a108bb9c5c6bd2","success":1,"date_created":"2023-02-13T10:38:10Z","date_updated":"2023-02-13T10:38:10Z","relation":"main_file","file_id":"12546"}],"oa_version":"Published Version","type":"journal_article","issue":"1","abstract":[{"text":"Brownian motion of a mobile impurity in a bath is affected by spin-orbit coupling (SOC). Here, we discuss a Caldeira-Leggett-type model that can be used to propose and interpret quantum simulators of this problem in cold Bose gases. First, we derive a master equation that describes the model and explore it in a one-dimensional (1D) setting. To validate the standard assumptions needed for our derivation, we analyze available experimental data without SOC; as a byproduct, this analysis suggests that the quench dynamics of the impurity is beyond the 1D Bose-polaron approach at temperatures currently accessible in a cold-atom laboratory—motion of the impurity is mainly driven by dissipation. For systems with SOC, we demonstrate that 1D spin-orbit coupling can be gauged out even in the presence of dissipation—the information about SOC is incorporated in the initial conditions. Observables sensitive to this information (such as spin densities) can be used to study formation of steady spin polarization domains during quench dynamics.","lang":"eng"}],"article_type":"original","citation":{"ama":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 2023;5(1). doi:10.1103/physrevresearch.5.013029","ista":"Ghazaryan A, Cappellaro A, Lemeshko M, Volosniev A. 2023. Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. 5(1), 013029.","ieee":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, and A. Volosniev, “Dissipative dynamics of an impurity with spin-orbit coupling,” Physical Review Research, vol. 5, no. 1. American Physical Society, 2023.","apa":"Ghazaryan, A., Cappellaro, A., Lemeshko, M., & Volosniev, A. (2023). Dissipative dynamics of an impurity with spin-orbit coupling. Physical Review Research. American Physical Society. https://doi.org/10.1103/physrevresearch.5.013029","mla":"Ghazaryan, Areg, et al. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research, vol. 5, no. 1, 013029, American Physical Society, 2023, doi:10.1103/physrevresearch.5.013029.","short":"A. Ghazaryan, A. Cappellaro, M. Lemeshko, A. Volosniev, Physical Review Research 5 (2023).","chicago":"Ghazaryan, Areg, Alberto Cappellaro, Mikhail Lemeshko, and Artem Volosniev. “Dissipative Dynamics of an Impurity with Spin-Orbit Coupling.” Physical Review Research. American Physical Society, 2023. https://doi.org/10.1103/physrevresearch.5.013029."},"publication":"Physical Review Research","date_published":"2023-01-20T00:00:00Z","scopus_import":"1","has_accepted_license":"1","article_processing_charge":"No","day":"20"},{"publication_identifier":{"issn":["1061-4036"],"eissn":["1546-1718"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1038/s41588-022-01260-3","quality_controlled":"1","oa":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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2023-02-27T07:46:45Z","volume":55,"date_updated":"2023-02-27T07:48:24Z","date_created":"2023-01-12T12:09:09Z","author":[{"last_name":"Zeller","first_name":"Peter","full_name":"Zeller, Peter"},{"first_name":"Jake","last_name":"Yeung","id":"123012b2-db30-11eb-b4d8-a35840c0551b","orcid":"0000-0003-1732-1559","full_name":"Yeung, Jake"},{"full_name":"Viñas Gaza, Helena","first_name":"Helena","last_name":"Viñas Gaza"},{"full_name":"de Barbanson, Buys Anton","last_name":"de Barbanson","first_name":"Buys Anton"},{"full_name":"Bhardwaj, Vivek","last_name":"Bhardwaj","first_name":"Vivek"},{"full_name":"Florescu, Maria","first_name":"Maria","last_name":"Florescu"},{"full_name":"van der Linden, Reinier","first_name":"Reinier","last_name":"van der Linden"},{"full_name":"van Oudenaarden, Alexander","first_name":"Alexander","last_name":"van Oudenaarden"}],"publisher":"Springer Nature","department":[{"_id":"ScienComp"}],"publication_status":"published","acknowledgement":"We thank A. Giladi for sharing mRNA abundance tables of cell types together with J. van den Berg for critical reading of the manuscript. We thank M. Bartosovic for sharing method comparison data. pK19pA-MN was a gift from Ulrich Laemmli (Addgene plasmid 86973, http://n2t.net/addgene:86973; RRID:Addgene_86973). Figure 8 is adopted from Hematopoiesis (human) diagram by A. Rad and M. Häggström under CC-BY-SA 3.0 license. This work was supported by European Research Council Advanced under grant ERC-AdG 742225-IntScOmics and Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO) TOP award NWO-CW 714.016.001. The SNF (P2BSP3-174991), HFSP (LT000209/2018-L) and Marie Skłodowska-Curie Actions (798573) supported P.Z. The SNF (P2ELP3_184488) and HFSP (LT000097/2019-L) supported J.Y. and the EMBO LTF (ALTF 1197–2019) supported V.B. This work is part of the Oncode Institute, which is partly financed by the Dutch Cancer Society. The funders had no role in study design, data collection and analysis, decision to publish or preparation of the manuscript.","year":"2023","article_processing_charge":"No","has_accepted_license":"1","day":"01","keyword":["Genetics"],"scopus_import":"1","date_published":"2023-02-01T00:00:00Z","page":"333-345","article_type":"review","citation":{"short":"P. Zeller, J. Yeung, H. Viñas Gaza, B.A. de Barbanson, V. Bhardwaj, M. Florescu, R. van der Linden, A. van Oudenaarden, Nature Genetics 55 (2023) 333–345.","mla":"Zeller, Peter, et al. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics, vol. 55, Springer Nature, 2023, pp. 333–45, doi:10.1038/s41588-022-01260-3.","chicago":"Zeller, Peter, Jake Yeung, Helena Viñas Gaza, Buys Anton de Barbanson, Vivek Bhardwaj, Maria Florescu, Reinier van der Linden, and Alexander van Oudenaarden. “Single-Cell SortChIC Identifies Hierarchical Chromatin Dynamics during Hematopoiesis.” Nature Genetics. Springer Nature, 2023. https://doi.org/10.1038/s41588-022-01260-3.","ama":"Zeller P, Yeung J, Viñas Gaza H, et al. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 2023;55:333-345. doi:10.1038/s41588-022-01260-3","ieee":"P. Zeller et al., “Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis,” Nature Genetics, vol. 55. Springer Nature, pp. 333–345, 2023.","apa":"Zeller, P., Yeung, J., Viñas Gaza, H., de Barbanson, B. A., Bhardwaj, V., Florescu, M., … van Oudenaarden, A. (2023). Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. Springer Nature. https://doi.org/10.1038/s41588-022-01260-3","ista":"Zeller P, Yeung J, Viñas Gaza H, de Barbanson BA, Bhardwaj V, Florescu M, van der Linden R, van Oudenaarden A. 2023. Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis. Nature Genetics. 55, 333–345."},"publication":"Nature Genetics","abstract":[{"lang":"eng","text":"Post-translational histone modifications modulate chromatin activity to affect gene expression. How chromatin states underlie lineage choice in single cells is relatively unexplored. We develop sort-assisted single-cell chromatin immunocleavage (sortChIC) and map active (H3K4me1 and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in the mouse bone marrow. During differentiation, hematopoietic stem and progenitor cells (HSPCs) acquire active chromatin states mediated by cell-type-specifying transcription factors, which are unique for each lineage. By contrast, most alterations in repressive marks during differentiation occur independent of the final cell type. Chromatin trajectory analysis shows that lineage choice at the chromatin level occurs at the progenitor stage. Joint profiling of H3K4me1 and H3K9me3 demonstrates that cell types within the myeloid lineage have distinct active chromatin but share similar myeloid-specific heterochromatin states. This implies a hierarchical regulation of chromatin during hematopoiesis: heterochromatin dynamics distinguish differentiation trajectories and lineages, while euchromatin dynamics reflect cell types within lineages."}],"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2023_NatureGenetics_Zeller.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":21484855,"file_id":"12688","relation":"main_file","date_created":"2023-02-27T07:46:45Z","date_updated":"2023-02-27T07:46:45Z","success":1,"checksum":"6fdb8e34fbeea63edd0f2c6c2cc5823e"}],"intvolume":" 55","status":"public","title":"Single-cell sortChIC identifies hierarchical chromatin dynamics during hematopoiesis","ddc":["570","000"],"_id":"12158","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"title":"Faster algorithm for turn-based stochastic games with bounded treewidth","status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12676","oa_version":"Published Version","type":"conference","abstract":[{"text":"Turn-based stochastic games (aka simple stochastic games) are two-player zero-sum games played on directed graphs with probabilistic transitions. The goal of player-max is to maximize the probability to reach a target state against the adversarial player-min. These games lie in NP ∩ coNP and are among the rare combinatorial problems that belong to this complexity class for which the existence of polynomial-time algorithm is a major open question. While randomized sub-exponential time algorithm exists, all known deterministic algorithms require exponential time in the worst-case. An important open question has been whether faster algorithms can be obtained parametrized by the treewidth of the game graph. Even deterministic sub-exponential time algorithm for constant treewidth turn-based stochastic games has remain elusive. In this work our main result is a deterministic algorithm to solve turn-based stochastic games that, given a game with n states, treewidth at most t, and the bit-complexity of the probabilistic transition function log D, has running time O ((tn2 log D)t log n). In particular, our algorithm is quasi-polynomial time for games with constant or poly-logarithmic treewidth.","lang":"eng"}],"page":"4590-4605","publication":"Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms","citation":{"ista":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. 2023. Faster algorithm for turn-based stochastic games with bounded treewidth. Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. SODA: Symposium on Discrete Algorithms, 4590–4605.","apa":"Chatterjee, K., Meggendorfer, T., Saona Urmeneta, R. J., & Svoboda, J. (2023). Faster algorithm for turn-based stochastic games with bounded treewidth. In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms (pp. 4590–4605). Florence, Italy: Society for Industrial and Applied Mathematics. https://doi.org/10.1137/1.9781611977554.ch173","ieee":"K. Chatterjee, T. Meggendorfer, R. J. Saona Urmeneta, and J. Svoboda, “Faster algorithm for turn-based stochastic games with bounded treewidth,” in Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Florence, Italy, 2023, pp. 4590–4605.","ama":"Chatterjee K, Meggendorfer T, Saona Urmeneta RJ, Svoboda J. Faster algorithm for turn-based stochastic games with bounded treewidth. In: Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms. Society for Industrial and Applied Mathematics; 2023:4590-4605. doi:10.1137/1.9781611977554.ch173","chicago":"Chatterjee, Krishnendu, Tobias Meggendorfer, Raimundo J Saona Urmeneta, and Jakub Svoboda. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” In Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, 4590–4605. Society for Industrial and Applied Mathematics, 2023. https://doi.org/10.1137/1.9781611977554.ch173.","mla":"Chatterjee, Krishnendu, et al. “Faster Algorithm for Turn-Based Stochastic Games with Bounded Treewidth.” Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–605, doi:10.1137/1.9781611977554.ch173.","short":"K. Chatterjee, T. Meggendorfer, R.J. Saona Urmeneta, J. Svoboda, in:, Proceedings of the 2023 Annual ACM-SIAM Symposium on Discrete Algorithms, Society for Industrial and Applied Mathematics, 2023, pp. 4590–4605."},"date_published":"2023-02-01T00:00:00Z","day":"01","article_processing_charge":"No","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"KrCh"}],"publisher":"Society for Industrial and Applied Mathematics","acknowledgement":"This research was partially supported by the ERC CoG 863818 (ForM-SMArt) grant.","year":"2023","date_updated":"2023-02-27T09:01:16Z","date_created":"2023-02-24T12:20:47Z","author":[{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","first_name":"Krishnendu"},{"orcid":"0000-0002-1712-2165","id":"b21b0c15-30a2-11eb-80dc-f13ca25802e1","last_name":"Meggendorfer","first_name":"Tobias","full_name":"Meggendorfer, Tobias"},{"full_name":"Saona Urmeneta, Raimundo J","last_name":"Saona Urmeneta","first_name":"Raimundo J","orcid":"0000-0001-5103-038X","id":"BD1DF4C4-D767-11E9-B658-BC13E6697425"},{"full_name":"Svoboda, Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","last_name":"Svoboda","first_name":"Jakub"}],"ec_funded":1,"quality_controlled":"1","project":[{"grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020"}],"main_file_link":[{"url":"https://doi.org/10.1137/1.9781611977554.ch173","open_access":"1"}],"oa":1,"language":[{"iso":"eng"}],"conference":{"name":"SODA: Symposium on Discrete Algorithms","location":"Florence, Italy","start_date":"2023-01-22","end_date":"2023-01-25"},"doi":"10.1137/1.9781611977554.ch173","month":"02","publication_identifier":{"isbn":["9781611977554"]}},{"abstract":[{"text":"Here we describe the in vivo DNA assembly approach, where molecular cloning procedures are performed using an E. coli recA-independent recombination pathway, which assembles linear fragments of DNA with short homologous termini. This pathway is present in all standard laboratory E. coli strains and, by bypassing the need for in vitro DNA assembly, allows simplified molecular cloning to be performed without the plasmid instability issues associated with specialized recombination-cloning bacterial strains. The methodology requires specific primer design and can perform all standard plasmid modifications (insertions, deletions, mutagenesis, and sub-cloning) in a rapid, simple, and cost-efficient manner, as it does not require commercial kits or specialized bacterial strains. Additionally, this approach can be used to perform complex procedures such as multiple modifications to a plasmid, as up to 6 linear fragments can be assembled in vivo by this recombination pathway. Procedures generally require less than 3 h, involving PCR amplification, DpnI digestion of template DNA, and transformation, upon which circular plasmids are assembled. In this chapter we describe the requirements, procedure, and potential pitfalls when using this technique, as well as protocol variations to overcome the most common issues.","lang":"eng"}],"alternative_title":["Methods in Molecular Biology"],"type":"book_chapter","oa_version":"None","title":"Molecular Cloning Using In Vivo DNA Assembly","status":"public","intvolume":" 2633","_id":"12720","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","day":"01","article_processing_charge":"No","series_title":"MIMB","scopus_import":"1","date_published":"2023-03-01T00:00:00Z","page":"33-44","publication":"DNA Manipulation and Analysis","citation":{"chicago":"Arroyo-Urea, Sandra, Jake Watson, and Javier García-Nafría. “Molecular Cloning Using In Vivo DNA Assembly.” In DNA Manipulation and Analysis, edited by Garry Scarlett, 2633:33–44. MIMB. New York, NY, United States: Springer Nature, 2023. https://doi.org/10.1007/978-1-0716-3004-4_3.","mla":"Arroyo-Urea, Sandra, et al. “Molecular Cloning Using In Vivo DNA Assembly.” DNA Manipulation and Analysis, edited by Garry Scarlett, vol. 2633, Springer Nature, 2023, pp. 33–44, doi:10.1007/978-1-0716-3004-4_3.","short":"S. Arroyo-Urea, J. Watson, J. García-Nafría, in:, G. Scarlett (Ed.), DNA Manipulation and Analysis, Springer Nature, New York, NY, United States, 2023, pp. 33–44.","ista":"Arroyo-Urea S, Watson J, García-Nafría J. 2023.Molecular Cloning Using In Vivo DNA Assembly. In: DNA Manipulation and Analysis. Methods in Molecular Biology, vol. 2633, 33–44.","ieee":"S. Arroyo-Urea, J. Watson, and J. García-Nafría, “Molecular Cloning Using In Vivo DNA Assembly,” in DNA Manipulation and Analysis, vol. 2633, G. Scarlett, Ed. New York, NY, United States: Springer Nature, 2023, pp. 33–44.","apa":"Arroyo-Urea, S., Watson, J., & García-Nafría, J. (2023). Molecular Cloning Using In Vivo DNA Assembly. In G. Scarlett (Ed.), DNA Manipulation and Analysis (Vol. 2633, pp. 33–44). New York, NY, United States: Springer Nature. https://doi.org/10.1007/978-1-0716-3004-4_3","ama":"Arroyo-Urea S, Watson J, García-Nafría J. Molecular Cloning Using In Vivo DNA Assembly. In: Scarlett G, ed. DNA Manipulation and Analysis. Vol 2633. MIMB. New York, NY, United States: Springer Nature; 2023:33-44. doi:10.1007/978-1-0716-3004-4_3"},"place":"New York, NY, United States","date_created":"2023-03-12T23:01:02Z","date_updated":"2023-03-16T08:34:24Z","volume":2633,"author":[{"first_name":"Sandra","last_name":"Arroyo-Urea","full_name":"Arroyo-Urea, Sandra"},{"full_name":"Watson, Jake","orcid":"0000-0002-8698-3823","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","first_name":"Jake"},{"first_name":"Javier","last_name":"García-Nafría","full_name":"García-Nafría, Javier"}],"publication_status":"published","publisher":"Springer Nature","editor":[{"full_name":"Scarlett, Garry","first_name":"Garry","last_name":"Scarlett"}],"department":[{"_id":"PeJo"}],"year":"2023","pmid":1,"month":"03","publication_identifier":{"eissn":["1940-6029"],"isbn":["978-1-0716-3003-7"],"issn":["1064-3745"],"eisbn":["978-1-0716-3004-4"]},"language":[{"iso":"eng"}],"doi":"10.1007/978-1-0716-3004-4_3","quality_controlled":"1","external_id":{"pmid":["36853454"]}},{"abstract":[{"lang":"eng","text":"Asynchronous programming has gained significant popularity over the last decade: support for this programming pattern is available in many popular languages via libraries and native language implementations, typically in the form of coroutines or the async/await construct. Instead of programming via shared memory, this concept assumes implicit synchronization through message passing. The key data structure enabling such communication is the rendezvous channel. Roughly, a rendezvous channel is a blocking queue of size zero, so both send(e) and receive() operations wait for each other, performing a rendezvous when they meet. To optimize the message passing pattern, channels are usually equipped with a fixed-size buffer, so sends do not suspend and put elements into the buffer until its capacity is exceeded. This primitive is known as a buffered channel.\r\n\r\nThis paper presents a fast and scalable algorithm for both rendezvous and buffered channels. Similarly to modern queues, our solution is based on an infinite array with two positional counters for send(e) and receive() operations, leveraging the unconditional Fetch-And-Add instruction to update them. Yet, the algorithm requires non-trivial modifications of this classic pattern, in order to support the full channel semantics, such as buffering and cancellation of waiting requests. We compare the performance of our solution to that of the Kotlin implementation, as well as against other academic proposals, showing up to 9.8× speedup. To showcase its expressiveness and performance, we also integrated the proposed algorithm into the standard Kotlin Coroutines library, replacing the previous channel implementations."}],"type":"conference","author":[{"full_name":"Koval, Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","first_name":"Nikita","last_name":"Koval"},{"full_name":"Alistarh, Dan-Adrian","first_name":"Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-3650-940X"},{"first_name":"Roman","last_name":"Elizarov","full_name":"Elizarov, Roman"}],"oa_version":"Preprint","date_updated":"2023-03-20T07:29:28Z","date_created":"2023-03-19T23:00:58Z","year":"2023","_id":"12735","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"DaAl"}],"publisher":"Association for Computing Machinery","publication_status":"published","title":"Fast and scalable channels in Kotlin Coroutines","status":"public","article_processing_charge":"No","publication_identifier":{"isbn":["9798400700156"]},"day":"25","month":"02","scopus_import":"1","date_published":"2023-02-25T00:00:00Z","doi":"10.1145/3572848.3577481","conference":{"name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","end_date":"2023-03-01","location":"Montreal, QC, Canada","start_date":"2023-02-25"},"language":[{"iso":"eng"}],"citation":{"mla":"Koval, Nikita, et al. “Fast and Scalable Channels in Kotlin Coroutines.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–18, doi:10.1145/3572848.3577481.","short":"N. Koval, D.-A. Alistarh, R. Elizarov, in:, Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 107–118.","chicago":"Koval, Nikita, Dan-Adrian Alistarh, and Roman Elizarov. “Fast and Scalable Channels in Kotlin Coroutines.” In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, 107–18. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577481.","ama":"Koval N, Alistarh D-A, Elizarov R. Fast and scalable channels in Kotlin Coroutines. In: Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery; 2023:107-118. doi:10.1145/3572848.3577481","ista":"Koval N, Alistarh D-A, Elizarov R. 2023. Fast and scalable channels in Kotlin Coroutines. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. PPoPP: Sympopsium on Principles and Practice of Parallel Programming, 107–118.","apa":"Koval, N., Alistarh, D.-A., & Elizarov, R. (2023). Fast and scalable channels in Kotlin Coroutines. In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 107–118). Montreal, QC, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577481","ieee":"N. Koval, D.-A. Alistarh, and R. Elizarov, “Fast and scalable channels in Kotlin Coroutines,” in Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Montreal, QC, Canada, 2023, pp. 107–118."},"external_id":{"arxiv":["2211.04986"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2211.04986"}],"oa":1,"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","page":"107-118","quality_controlled":"1"},{"publication_identifier":{"isbn":["9798400700156"]},"article_processing_charge":"No","day":"25","month":"02","language":[{"iso":"eng"}],"date_published":"2023-02-25T00:00:00Z","doi":"10.1145/3572848.3577512","conference":{"name":"PPoPP: Sympopsium on Principles and Practice of Parallel Programming","end_date":"2023-03-01","location":"Montreal, QB, Canada","start_date":"2023-02-25"},"page":"438-440","quality_controlled":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1145/3572848.3577512"}],"oa":1,"citation":{"chicago":"Aksenov, Vitaly, Trevor A Brown, Alexander Fedorov, and Ilya Kokorin. Unexpected Scaling in Path Copying Trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming. Association for Computing Machinery, 2023. https://doi.org/10.1145/3572848.3577512.","mla":"Aksenov, Vitaly, et al. “Unexpected Scaling in Path Copying Trees.” Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Association for Computing Machinery, 2023, pp. 438–40, doi:10.1145/3572848.3577512.","short":"V. Aksenov, T.A. Brown, A. Fedorov, I. Kokorin, Unexpected Scaling in Path Copying Trees, Association for Computing Machinery, 2023.","ista":"Aksenov V, Brown TA, Fedorov A, Kokorin I. 2023. Unexpected scaling in path copying trees, Association for Computing Machinery,p.","apa":"Aksenov, V., Brown, T. A., Fedorov, A., & Kokorin, I. (2023). Unexpected scaling in path copying trees. Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming (pp. 438–440). Montreal, QB, Canada: Association for Computing Machinery. https://doi.org/10.1145/3572848.3577512","ieee":"V. Aksenov, T. A. Brown, A. Fedorov, and I. Kokorin, Unexpected scaling in path copying trees. Association for Computing Machinery, 2023, pp. 438–440.","ama":"Aksenov V, Brown TA, Fedorov A, Kokorin I. Unexpected Scaling in Path Copying Trees. Association for Computing Machinery; 2023:438-440. doi:10.1145/3572848.3577512"},"publication":"Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming","abstract":[{"lang":"eng","text":"Although a wide variety of handcrafted concurrent data structures have been proposed, there is considerable interest in universal approaches (Universal Constructions or UCs) for building concurrent data structures. UCs (semi-)automatically convert a sequential data structure into a concurrent one. The simplest approach uses locks [3, 6] that protect a sequential data structure and allow only one process to access it at a time. However, the resulting data structure is blocking. Most work on UCs instead focuses on obtaining non-blocking progress guarantees such as obstruction-freedom, lock-freedom or wait-freedom. Many non-blocking UCs have appeared. Key examples include the seminal wait-free UC [2] by Herlihy, a NUMA-aware UC [10] by Yi et al., and an efficient UC for large objects [1] by Fatourou et al."}],"type":"conference_poster","oa_version":"Published Version","date_created":"2023-03-19T23:00:58Z","date_updated":"2023-03-20T07:57:27Z","author":[{"last_name":"Aksenov","first_name":"Vitaly","full_name":"Aksenov, Vitaly"},{"id":"3569F0A0-F248-11E8-B48F-1D18A9856A87","last_name":"Brown","first_name":"Trevor A","full_name":"Brown, Trevor A"},{"full_name":"Fedorov, Alexander","id":"2e711909-896a-11ed-bdf8-eb0f5a2984c6","first_name":"Alexander","last_name":"Fedorov"},{"first_name":"Ilya","last_name":"Kokorin","full_name":"Kokorin, Ilya"}],"publisher":"Association for Computing Machinery","department":[{"_id":"DaAl"},{"_id":"GradSch"}],"status":"public","publication_status":"published","title":"Unexpected scaling in path copying trees","_id":"12736","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"This work was supported by: the Natural Sciences and Engineering Research Council of Canada (NSERC) Discovery Program grant: RGPIN-2019-04227, and the Canada Foundation for Innovation John R. Evans Leaders Fund (CFI-JELF) with equal support from the Ontario Research Fund CFI Leaders Opportunity Fund: 38512.","year":"2023"},{"publication_status":"published","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","department":[{"_id":"MoHe"}],"year":"2023","acknowledgement":"Monika Henzinger: This project has received funding from the European Research Council\r\n(ERC) under the European Union’s Horizon 2020 research and innovation programme (Grant\r\nagreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)” and from the Austrian Science Fund (FWF) project “Fast Algorithms for a Reactive Network Layer (ReactNet)”, P 33775-N, with additional funding from the netidee SCIENCE Stiftung, 2020–2024.\r\nStefan Neumann: This research is supported by the the ERC Advanced Grant REBOUND (834862) and the EC H2020 RIA project SoBigData++ (871042).\r\nStefan Schmid: Research supported by Austrian Science Fund (FWF) project I 5025-N (DELTA), 2020-2024.","date_created":"2023-03-26T22:01:07Z","date_updated":"2023-03-27T06:46:27Z","volume":254,"author":[{"full_name":"Henzinger, Monika H","orcid":"0000-0002-5008-6530","id":"540c9bbd-f2de-11ec-812d-d04a5be85630","last_name":"Henzinger","first_name":"Monika H"},{"full_name":"Neumann, Stefan","first_name":"Stefan","last_name":"Neumann"},{"last_name":"Räcke","first_name":"Harald","full_name":"Räcke, Harald"},{"full_name":"Schmid, Stefan","first_name":"Stefan","last_name":"Schmid"}],"article_number":"36","file_date_updated":"2023-03-27T06:37:22Z","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"external_id":{"arxiv":["2301.01744"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2023-03-09","location":"Hamburg, Germany","start_date":"2023-03-07","name":"STACS: Symposium on Theoretical Aspects of Computer Science"},"doi":"10.4230/LIPIcs.STACS.2023.36","month":"03","publication_identifier":{"isbn":["9783959772662"],"issn":["1868-8969"]},"status":"public","title":"Dynamic maintenance of monotone dynamic programs and applications","ddc":["000"],"intvolume":" 254","_id":"12760","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"checksum":"22141ab8bc55188e2dfff665e5daecbd","success":1,"date_updated":"2023-03-27T06:37:22Z","date_created":"2023-03-27T06:37:22Z","relation":"main_file","file_id":"12769","content_type":"application/pdf","file_size":872706,"creator":"dernst","access_level":"open_access","file_name":"2023_LIPICS_HenzingerM.pdf"}],"oa_version":"Published Version","alternative_title":["LIPIcs"],"type":"conference","abstract":[{"text":"Dynamic programming (DP) is one of the fundamental paradigms in algorithm design. However,\r\nmany DP algorithms have to fill in large DP tables, represented by two-dimensional arrays, which causes at least quadratic running times and space usages. This has led to the development of improved algorithms for special cases when the DPs satisfy additional properties like, e.g., the Monge property or total monotonicity.\r\nIn this paper, we consider a new condition which assumes (among some other technical assumptions) that the rows of the DP table are monotone. Under this assumption, we introduce\r\na novel data structure for computing (1 + ϵ)-approximate DP solutions in near-linear time and\r\nspace in the static setting, and with polylogarithmic update times when the DP entries change\r\ndynamically. To the best of our knowledge, our new condition is incomparable to previous conditions and is the first which allows to derive dynamic algorithms based on existing DPs. Instead of using two-dimensional arrays to store the DP tables, we store the rows of the DP tables using monotone piecewise constant functions. This allows us to store length-n DP table rows with entries in [0, W] using only polylog(n, W) bits, and to perform operations, such as (min, +)-convolution or rounding, on these functions in polylogarithmic time.\r\nWe further present several applications of our data structure. For bicriteria versions of k-balanced graph partitioning and simultaneous source location, we obtain the first dynamic algorithms with subpolynomial update times, as well as the first static algorithms using only near-linear time and space. Additionally, we obtain the currently fastest algorithm for fully dynamic knapsack.","lang":"eng"}],"publication":"40th International Symposium on Theoretical Aspects of Computer Science","citation":{"mla":"Henzinger, Monika H., et al. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” 40th International Symposium on Theoretical Aspects of Computer Science, vol. 254, 36, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023, doi:10.4230/LIPIcs.STACS.2023.36.","short":"M.H. Henzinger, S. Neumann, H. Räcke, S. Schmid, in:, 40th International Symposium on Theoretical Aspects of Computer Science, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023.","chicago":"Henzinger, Monika H, Stefan Neumann, Harald Räcke, and Stefan Schmid. “Dynamic Maintenance of Monotone Dynamic Programs and Applications.” In 40th International Symposium on Theoretical Aspects of Computer Science, Vol. 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2023. https://doi.org/10.4230/LIPIcs.STACS.2023.36.","ama":"Henzinger MH, Neumann S, Räcke H, Schmid S. Dynamic maintenance of monotone dynamic programs and applications. In: 40th International Symposium on Theoretical Aspects of Computer Science. Vol 254. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2023. doi:10.4230/LIPIcs.STACS.2023.36","ista":"Henzinger MH, Neumann S, Räcke H, Schmid S. 2023. Dynamic maintenance of monotone dynamic programs and applications. 40th International Symposium on Theoretical Aspects of Computer Science. STACS: Symposium on Theoretical Aspects of Computer Science, LIPIcs, vol. 254, 36.","ieee":"M. H. Henzinger, S. Neumann, H. Räcke, and S. Schmid, “Dynamic maintenance of monotone dynamic programs and applications,” in 40th International Symposium on Theoretical Aspects of Computer Science, Hamburg, Germany, 2023, vol. 254.","apa":"Henzinger, M. H., Neumann, S., Räcke, H., & Schmid, S. (2023). Dynamic maintenance of monotone dynamic programs and applications. In 40th International Symposium on Theoretical Aspects of Computer Science (Vol. 254). Hamburg, Germany: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. https://doi.org/10.4230/LIPIcs.STACS.2023.36"},"date_published":"2023-03-01T00:00:00Z","scopus_import":"1","day":"01","article_processing_charge":"No","has_accepted_license":"1"},{"oa_version":"Published Version","file":[{"file_name":"Burnett_Thesis_2023.docx","access_level":"closed","file_size":23029260,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"lburnett","relation":"source_file","file_id":"12717","date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z","checksum":"6c6d9cc2c4cdacb74e6b1047a34d7332"},{"file_size":11959869,"content_type":"application/pdf","creator":"lburnett","file_name":"Burnett_Thesis_2023_pdfA.pdf","access_level":"open_access","date_updated":"2023-03-08T15:08:46Z","date_created":"2023-03-08T15:08:46Z","checksum":"cebc77705288bf4382db9b3541483cd0","success":1,"relation":"main_file","file_id":"12718"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12716","ddc":["599","573"],"status":"public","title":"To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism","abstract":[{"text":"The process of detecting and evaluating sensory information to guide behaviour is termed perceptual decision-making (PDM), and is critical for the ability of an organism to interact with its external world. Individuals with autism, a neurodevelopmental condition primarily characterised by social and communication difficulties, frequently exhibit altered sensory processing and PDM difficulties are widely reported. Recent technological advancements have pushed forward our understanding of the genetic changes accompanying this condition, however our understanding of how these mutations affect the function of specific neuronal circuits and bring about the corresponding behavioural changes remains limited. Here, we use an innate PDM task, the looming avoidance response (LAR) paradigm, to identify a convergent behavioural abnormality across three molecularly distinct genetic mouse models of autism (Cul3, Setd5 and Ptchd1). Although mutant mice can rapidly detect threatening visual stimuli, their responses are consistently delayed, requiring longer to initiate an appropriate response than their wild-type siblings. Mutant animals show abnormal adaptation in both their stimulus- evoked escape responses and exploratory dynamics following repeated stimulus presentations. Similarly delayed behavioural responses are observed in wild-type animals when faced with more ambiguous threats, suggesting the mutant phenotype could arise from a dysfunction in the flexible control of this PDM process.\r\nOur knowledge of the core neuronal circuitry mediating the LAR facilitated a detailed dissection of the neuronal mechanisms underlying the behavioural impairment. In vivo extracellular recording revealed that visual responses were unaffected within a key brain region for the rapid processing of visual threats, the superior colliculus (SC), indicating that the behavioural delay was unlikely to originate from sensory impairments. Delayed behavioural responses were recapitulated in the Setd5 model following optogenetic stimulation of the excitatory output neurons of the SC, which are known to mediate escape initiation through the activation of cells in the underlying dorsal periaqueductal grey (dPAG). In vitro patch-clamp recordings of dPAG cells uncovered a stark hypoexcitability phenotype in two out of the three genetic models investigated (Setd5 and Ptchd1), that in Setd5, is mediated by the misregulation of voltage-gated potassium channels. Overall, our results show that the ability to use visual information to drive efficient escape responses is impaired in three diverse genetic mouse models of autism and that, in one of the models studied, this behavioural delay likely originates from differences in the intrinsic excitability of a key subcortical node, the dPAG. Furthermore, this work showcases the use of an innate behavioural paradigm to mechanistically dissect PDM processes in autism.","lang":"eng"}],"type":"dissertation","alternative_title":["ISTA Thesis"],"date_published":"2023-03-10T00:00:00Z","citation":{"ama":"Burnett L. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. 2023. doi:10.15479/at:ista:12716","ieee":"L. Burnett, “To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism,” Institute of Science and Technology Austria, 2023.","apa":"Burnett, L. (2023). To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12716","ista":"Burnett L. 2023. To flee, or not to flee? Using innate defensive behaviours to investigate rapid perceptual decision-making through subcortical circuits in mouse models of autism. Institute of Science and Technology Austria.","short":"L. Burnett, To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism, Institute of Science and Technology Austria, 2023.","mla":"Burnett, Laura. To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12716.","chicago":"Burnett, Laura. “To Flee, or Not to Flee? Using Innate Defensive Behaviours to Investigate Rapid Perceptual Decision-Making through Subcortical Circuits in Mouse Models of Autism.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12716."},"page":"178","day":"10","has_accepted_license":"1","article_processing_charge":"No","author":[{"first_name":"Laura","last_name":"Burnett","id":"3B717F68-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8937-410X","full_name":"Burnett, Laura"}],"date_created":"2023-03-08T15:19:45Z","date_updated":"2023-04-05T10:59:04Z","year":"2023","publication_status":"published","department":[{"_id":"GradSch"},{"_id":"MaJö"}],"publisher":"Institute of Science and Technology Austria","file_date_updated":"2023-03-08T15:08:46Z","ec_funded":1,"doi":"10.15479/at:ista:12716","supervisor":[{"id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3937-1330","first_name":"Maximilian A","last_name":"Jösch","full_name":"Jösch, Maximilian A"}],"acknowledged_ssus":[{"_id":"PreCl"},{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"CampIT"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"oa":1,"project":[{"grant_number":"756502","_id":"2634E9D2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Circuits of Visual Attention"}],"month":"03","publication_identifier":{"issn":["2663-337X"]}},{"publication_identifier":{"isbn":["9783031308192"],"eissn":["1611-3349"],"eisbn":["9783031308208"],"issn":["0302-9743"]},"month":"04","language":[{"iso":"eng"}],"doi":"10.1007/978-3-031-30820-8_32","conference":{"location":"Paris, France","start_date":"2023-04-22","end_date":"2023-04-27","name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems"},"project":[{"name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020","grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d"}],"quality_controlled":"1","oa":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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"ec_funded":1,"file_date_updated":"2023-04-25T06:58:36Z","volume":13994,"date_updated":"2023-04-25T07:02:43Z","date_created":"2023-04-20T08:22:53Z","author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"department":[{"_id":"ToHe"}],"publisher":"Springer Nature","publication_status":"published","year":"2023","acknowledgement":"This work was supported by the ERC-2020-AdG 10102009 grant.","article_processing_charge":"No","has_accepted_license":"1","day":"20","date_published":"2023-04-20T00:00:00Z","page":"535-540","citation":{"ieee":"M. Chalupa and T. A. Henzinger, “Bubaak: Runtime monitoring of program verifiers,” in Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 535–540.","apa":"Chalupa, M., & Henzinger, T. A. (2023). Bubaak: Runtime monitoring of program verifiers. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 535–540). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_32","ista":"Chalupa M, Henzinger TA. 2023. Bubaak: Runtime monitoring of program verifiers. Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 535–540.","ama":"Chalupa M, Henzinger TA. Bubaak: Runtime monitoring of program verifiers. In: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:535-540. doi:10.1007/978-3-031-30820-8_32","chicago":"Chalupa, Marek, and Thomas A Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” In Tools and Algorithms for the Construction and Analysis of Systems, 13994:535–40. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_32.","short":"M. Chalupa, T.A. Henzinger, in:, Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 535–540.","mla":"Chalupa, Marek, and Thomas A. Henzinger. “Bubaak: Runtime Monitoring of Program Verifiers.” Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 535–40, doi:10.1007/978-3-031-30820-8_32."},"publication":"Tools and Algorithms for the Construction and Analysis of Systems","abstract":[{"text":"The main idea behind BUBAAK is to run multiple program analyses in parallel and use runtime monitoring and enforcement to observe and control their progress in real time. The analyses send information about (un)explored states of the program and discovered invariants to a monitor. The monitor processes the received data and can force an analysis to stop the search of certain program parts (which have already been analyzed by other analyses), or to make it utilize a program invariant found by another analysis.\r\nAt SV-COMP 2023, the implementation of data exchange between the monitor and the analyses was not yet completed, which is why BUBAAK only ran several analyses in parallel, without any coordination. Still, BUBAAK won the meta-category FalsificationOverall and placed very well in several other (sub)-categories of the competition.","lang":"eng"}],"alternative_title":["LNCS"],"type":"conference","file":[{"creator":"dernst","content_type":"application/pdf","file_size":16096413,"access_level":"open_access","file_name":"2023_LNCS_Chalupa.pdf","success":1,"checksum":"120d2c2a38384058ad0630fdf8288312","date_updated":"2023-04-25T06:58:36Z","date_created":"2023-04-25T06:58:36Z","file_id":"12864","relation":"main_file"}],"oa_version":"Published Version","intvolume":" 13994","status":"public","ddc":["000"],"title":"Bubaak: Runtime monitoring of program verifiers","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12854"},{"article_processing_charge":"No","day":"25","month":"03","project":[{"grant_number":"101045083","_id":"34bc2376-11ca-11ed-8bc3-9a3b3961a088","name":"Computational Discovery of Numerical Algorithms for Animation and Simulation of Natural Phenomena"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2303.14555"}],"citation":{"mla":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, 2303.14555, doi:10.48550/arXiv.2303.14555.","short":"A. Chern, S. Ishida, ArXiv (n.d.).","chicago":"Chern, Albert, and Sadashige Ishida. “Area Formula for Spherical Polygons via Prequantization.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2303.14555.","ama":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv. doi:10.48550/arXiv.2303.14555","ista":"Chern A, Ishida S. Area formula for spherical polygons via prequantization. arXiv, 2303.14555.","apa":"Chern, A., & Ishida, S. (n.d.). Area formula for spherical polygons via prequantization. arXiv. https://doi.org/10.48550/arXiv.2303.14555","ieee":"A. Chern and S. Ishida, “Area formula for spherical polygons via prequantization,” arXiv. ."},"external_id":{"arxiv":["2303.14555"]},"oa":1,"publication":"arXiv","language":[{"iso":"eng"}],"date_published":"2023-03-25T00:00:00Z","doi":"10.48550/arXiv.2303.14555","type":"preprint","article_number":"2303.14555","abstract":[{"lang":"eng","text":"We present a formula for the signed area of a spherical polygon via prequantization. In contrast to the traditional formula based on the Gauss-Bonnet theorem that requires measuring angles, the new formula mimics Green's theorem and is applicable to a wider range of degenerate spherical curves and polygons."}],"department":[{"_id":"GradSch"},{"_id":"ChWo"}],"title":"Area formula for spherical polygons via prequantization","publication_status":"submitted","status":"public","_id":"12846","acknowledgement":"The authors acknowledge Chris Wojtan for his continuous support to the present work through discussions and advice. The second author thanks Anna Sisak for a fruitful discussion on prequantum bundles. This project was funded in part by the European Research Council (ERC Consolidator Grant 101045083 CoDiNA).","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023","oa_version":"Preprint","date_updated":"2023-04-25T06:51:21Z","date_created":"2023-04-18T19:16:06Z","author":[{"last_name":"Chern","first_name":"Albert","full_name":"Chern, Albert"},{"full_name":"Ishida, Sadashige","first_name":"Sadashige","last_name":"Ishida","id":"6F7C4B96-A8E9-11E9-A7CA-09ECE5697425"}]},{"month":"04","publication_identifier":{"issn":["0302-9743"],"eisbn":["9783031308260"],"isbn":["9783031308253"],"eissn":["1611-3349"]},"language":[{"iso":"eng"}],"conference":{"end_date":"2023-04-27","start_date":"2023-04-22","location":"Paris, France","name":"FASE: Fundamental Approaches to Software Engineering"},"doi":"10.1007/978-3-031-30826-0_15","quality_controlled":"1","project":[{"_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093","name":"Vigilant Algorithmic Monitoring of Software","call_identifier":"H2020"}],"oa":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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"file_date_updated":"2023-04-25T07:16:36Z","ec_funded":1,"date_updated":"2023-04-25T07:19:07Z","date_created":"2023-04-20T08:29:42Z","volume":13991,"author":[{"full_name":"Chalupa, Marek","last_name":"Chalupa","first_name":"Marek","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"full_name":"Mühlböck, Fabian","id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177","first_name":"Fabian","last_name":"Mühlböck"},{"id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","last_name":"Muroya Lei","first_name":"Stefanie","full_name":"Muroya Lei, Stefanie"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"related_material":{"record":[{"id":"12407","relation":"earlier_version","status":"public"}]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","day":"20","article_processing_charge":"No","has_accepted_license":"1","date_published":"2023-04-20T00:00:00Z","page":"260-281","publication":"Fundamental Approaches to Software Engineering","citation":{"ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. Vamos: Middleware for best-effort third-party monitoring. In: Fundamental Approaches to Software Engineering. Vol 13991. Springer Nature; 2023:260-281. doi:10.1007/978-3-031-30826-0_15","ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, “Vamos: Middleware for best-effort third-party monitoring,” in Fundamental Approaches to Software Engineering, Paris, France, 2023, vol. 13991, pp. 260–281.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). Vamos: Middleware for best-effort third-party monitoring. In Fundamental Approaches to Software Engineering (Vol. 13991, pp. 260–281). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30826-0_15","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. Vamos: Middleware for best-effort third-party monitoring. Fundamental Approaches to Software Engineering. FASE: Fundamental Approaches to Software Engineering, LNCS, vol. 13991, 260–281.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, in:, Fundamental Approaches to Software Engineering, Springer Nature, 2023, pp. 260–281.","mla":"Chalupa, Marek, et al. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” Fundamental Approaches to Software Engineering, vol. 13991, Springer Nature, 2023, pp. 260–81, doi:10.1007/978-3-031-30826-0_15.","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. “Vamos: Middleware for Best-Effort Third-Party Monitoring.” In Fundamental Approaches to Software Engineering, 13991:260–81. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30826-0_15."},"abstract":[{"lang":"eng","text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch."}],"alternative_title":["LNCS"],"type":"conference","oa_version":"Published Version","file":[{"date_updated":"2023-04-25T07:16:36Z","date_created":"2023-04-25T07:16:36Z","checksum":"17a7c8e08be609cf2408d37ea55e322c","success":1,"relation":"main_file","file_id":"12865","file_size":580828,"content_type":"application/pdf","creator":"dernst","file_name":"2023_LNCS_ChalupaM.pdf","access_level":"open_access"}],"status":"public","ddc":["000"],"title":"Vamos: Middleware for best-effort third-party monitoring","intvolume":" 13991","_id":"12856","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"month":"01","publication_identifier":{"eissn":["2664-1690"]},"project":[{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"}],"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"language":[{"iso":"eng"}],"doi":"10.15479/AT:ISTA:12407","file_date_updated":"2023-01-27T03:18:34Z","ec_funded":1,"publication_status":"published","publisher":"Institute of Science and Technology Austria","department":[{"_id":"ToHe"}],"year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093. \r\nThe authors would like to thank the anonymous FASE reviewers for their valuable feedback and suggestions.","date_created":"2023-01-27T03:18:08Z","date_updated":"2023-04-25T07:19:06Z","author":[{"full_name":"Chalupa, Marek","first_name":"Marek","last_name":"Chalupa","id":"87e34708-d6c6-11ec-9f5b-9391e7be2463"},{"id":"6395C5F6-89DF-11E9-9C97-6BDFE5697425","orcid":"0000-0003-1548-0177","first_name":"Fabian","last_name":"Mühlböck","full_name":"Mühlböck, Fabian"},{"full_name":"Muroya Lei, Stefanie","id":"a376de31-8972-11ed-ae7b-d0251c13c8ff","first_name":"Stefanie","last_name":"Muroya Lei"},{"full_name":"Henzinger, Thomas A","first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724"}],"related_material":{"record":[{"relation":"later_version","status":"public","id":"12856"}]},"keyword":["runtime monitoring","best effort","third party"],"day":"27","has_accepted_license":"1","article_processing_charge":"No","page":"38","citation":{"ieee":"M. Chalupa, F. Mühlböck, S. Muroya Lei, and T. A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023.","apa":"Chalupa, M., Mühlböck, F., Muroya Lei, S., & Henzinger, T. A. (2023). VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12407","ista":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. 2023. VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 38p.","ama":"Chalupa M, Mühlböck F, Muroya Lei S, Henzinger TA. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria; 2023. doi:10.15479/AT:ISTA:12407","chicago":"Chalupa, Marek, Fabian Mühlböck, Stefanie Muroya Lei, and Thomas A Henzinger. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12407.","short":"M. Chalupa, F. Mühlböck, S. Muroya Lei, T.A. Henzinger, VAMOS: Middleware for Best-Effort Third-Party Monitoring, Institute of Science and Technology Austria, 2023.","mla":"Chalupa, Marek, et al. VAMOS: Middleware for Best-Effort Third-Party Monitoring. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12407."},"date_published":"2023-01-27T00:00:00Z","alternative_title":["IST Austria Technical Report"],"type":"technical_report","abstract":[{"text":"As the complexity and criticality of software increase every year, so does the importance of run-time monitoring. Third-party monitoring, with limited knowledge of the monitored software, and best-effort monitoring, which keeps pace with the monitored software, are especially valuable, yet underexplored areas of run-time monitoring. Most existing monitoring frameworks do not support their combination because they either require access to the monitored code for instrumentation purposes or the processing of all observed events, or both.\r\n\r\nWe present a middleware framework, VAMOS, for the run-time monitoring of software which is explicitly designed to support third-party and best-effort scenarios. The design goals of VAMOS are (i) efficiency (keeping pace at low overhead), (ii) flexibility (the ability to monitor black-box code through a variety of different event channels, and the connectability to monitors written in different specification languages), and (iii) ease-of-use. To achieve its goals, VAMOS combines aspects of event broker and event recognition systems with aspects of stream processing systems.\r\n\r\nWe implemented a prototype toolchain for VAMOS and conducted experiments including a case study of monitoring for data races. The results indicate that VAMOS enables writing useful yet efficient monitors, is compatible with a variety of event sources and monitor specifications, and simplifies key aspects of setting up a monitoring system from scratch.","lang":"eng"}],"status":"public","title":"VAMOS: Middleware for Best-Effort Third-Party Monitoring","ddc":["005"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"12407","file":[{"file_name":"main.pdf","access_level":"open_access","creator":"fmuehlbo","file_size":662409,"content_type":"application/pdf","file_id":"12408","relation":"main_file","date_created":"2023-01-27T03:18:34Z","date_updated":"2023-01-27T03:18:34Z","success":1,"checksum":"55426e463fdeafe9777fc3ff635154c7"}],"oa_version":"Published Version"},{"month":"02","day":"01","article_processing_charge":"No","publication_identifier":{"isbn":["9780128188736"]},"language":[{"iso":"eng"}],"date_published":"2023-02-01T00:00:00Z","doi":"10.1016/b978-0-12-818872-9.00129-1","quality_controlled":"1","page":"86-98","publication":"Encyclopedia of Child and Adolescent Health","citation":{"short":"C. Currin, C. Beyer, in:, B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health, 1st ed., Elsevier, 2023, pp. 86–98.","mla":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., Elsevier, 2023, pp. 86–98, doi:10.1016/b978-0-12-818872-9.00129-1.","chicago":"Currin, Christopher, and Chad Beyer. “Altered Childhood Brain Development in Autism and Epilepsy.” In Encyclopedia of Child and Adolescent Health, edited by Bonnie Halpern-Felsher, 1st ed., 86–98. Elsevier, 2023. https://doi.org/10.1016/b978-0-12-818872-9.00129-1.","ama":"Currin C, Beyer C. Altered childhood brain development in autism and epilepsy. In: Halpern-Felsher B, ed. Encyclopedia of Child and Adolescent Health. 1st ed. Elsevier; 2023:86-98. doi:10.1016/b978-0-12-818872-9.00129-1","ieee":"C. Currin and C. Beyer, “Altered childhood brain development in autism and epilepsy,” in Encyclopedia of Child and Adolescent Health, 1st ed., B. Halpern-Felsher, Ed. Elsevier, 2023, pp. 86–98.","apa":"Currin, C., & Beyer, C. (2023). Altered childhood brain development in autism and epilepsy. In B. Halpern-Felsher (Ed.), Encyclopedia of Child and Adolescent Health (1st ed., pp. 86–98). Elsevier. https://doi.org/10.1016/b978-0-12-818872-9.00129-1","ista":"Currin C, Beyer C. 2023.Altered childhood brain development in autism and epilepsy. In: Encyclopedia of Child and Adolescent Health. Vol. 1: Biological Development and Physical Health, , 86–98."},"abstract":[{"text":"Autism spectrum disorder (ASD) and epilepsy are frequently comorbid neurodevelopmental disorders. Extensive research has demonstrated shared pathological pathways, etiologies, and phenotypes. Many risk factors for these disorders, like genetic mutations and environmental pressures, are linked to changes in childhood brain development, which is a critical period for their manifestation.\r\nDecades of research have yielded many signatures for ASD and epilepsy, some shared and others unique or opposing. The anatomical, physiological, and behavioral correlates of these disorders are discussed in this chapter in the context of understanding shared pathological pathways. We end with important takeaways on the presentation, prevention, intervention, and policy changes for ASD and epilepsy. This chapter aims to explore the complexity of these disorders, both in etiology and phenotypes, with the further goal of appreciating the expanse of unknowns still to explore about the brain.","lang":"eng"}],"alternative_title":["Vol. 1: Biological Development and Physical Health"],"type":"book_chapter","date_created":"2023-04-25T07:52:43Z","date_updated":"2023-04-25T09:25:40Z","oa_version":"None","author":[{"last_name":"Currin","first_name":"Christopher","orcid":"0000-0002-4809-5059","id":"e8321fc5-3091-11eb-8a53-83f309a11ac9","full_name":"Currin, Christopher"},{"first_name":"Chad","last_name":"Beyer","full_name":"Beyer, Chad"}],"edition":"1","status":"public","title":"Altered childhood brain development in autism and epilepsy","publication_status":"published","department":[{"_id":"TiVo"}],"editor":[{"full_name":"Halpern-Felsher, Bonnie","last_name":"Halpern-Felsher","first_name":"Bonnie"}],"publisher":"Elsevier","_id":"12866","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","year":"2023"},{"file_date_updated":"2023-04-07T06:18:05Z","date_created":"2023-04-06T07:54:09Z","date_updated":"2023-04-26T12:16:56Z","author":[{"full_name":"Alcarva, Catarina","id":"3A96634C-F248-11E8-B48F-1D18A9856A87","last_name":"Alcarva","first_name":"Catarina"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"RySh"}],"publisher":"Institute of Science and Technology Austria","year":"2023","month":"04","publication_identifier":{"issn":["2663 - 337X"]},"supervisor":[{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8761-9444","first_name":"Ryuichi","last_name":"Shigemoto"}],"acknowledged_ssus":[{"_id":"EM-Fac"},{"_id":"Bio"},{"_id":"PreCl"}],"degree_awarded":"PhD","language":[{"iso":"eng"}],"doi":"10.15479/at:ista:12809","project":[{"name":"Plasticity in the cerebellum: Which molecular mechanisms are behind physiological learning?","_id":"267DFB90-B435-11E9-9278-68D0E5697425"}],"abstract":[{"text":"Understanding the mechanisms of learning and memory formation has always been one of\r\nthe main goals in neuroscience. Already Pavlov (1927) in his early days has used his classic\r\nconditioning experiments to study the neural mechanisms governing behavioral adaptation.\r\nWhat was not known back then was that the part of the brain that is largely responsible for\r\nthis type of associative learning is the cerebellum.\r\nSince then, plenty of theories on cerebellar learning have emerged. Despite their differences,\r\none thing they all have in common is that learning relies on synaptic and intrinsic plasticity.\r\nThe goal of my PhD project was to unravel the molecular mechanisms underlying synaptic\r\nplasticity in two synapses that have been shown to be implicated in motor learning, in an\r\neffort to understand how learning and memory formation are processed in the cerebellum.\r\nOne of the earliest and most well-known cerebellar theories postulates that motor learning\r\nlargely depends on long-term depression at the parallel fiber-Purkinje cell (PC-PC) synapse.\r\nHowever, the discovery of other types of plasticity in the cerebellar circuitry, like long-term\r\npotentiation (LTP) at the PC-PC synapse, potentiation of molecular layer interneurons (MLIs),\r\nand plasticity transfer from the cortex to the cerebellar/ vestibular nuclei has increased the\r\npopularity of the idea that multiple sites of plasticity might be involved in learning.\r\nStill a lot remains unknown about the molecular mechanisms responsible for these types of\r\nplasticity and whether they occur during physiological learning.\r\nIn the first part of this thesis we have analyzed the variation and nanodistribution of voltagegated calcium channels (VGCCs) and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid\r\ntype glutamate receptors (AMPARs) on the parallel fiber-Purkinje cell synapse after vestibuloocular reflex phase reversal adaptation, a behavior that has been suggested to rely on PF-PC\r\nLTP. We have found that on the last day of adaptation there is no learning trace in form of\r\nVGCCs nor AMPARs variation at the PF-PC synapse, but instead a decrease in the number of\r\nPF-PC synapses. These data seem to support the view that learning is only stored in the\r\ncerebellar cortex in an initial learning phase, being transferred later to the vestibular nuclei.\r\nNext, we have studied the role of MLIs in motor learning using a relatively simple and well characterized behavioral paradigm – horizontal optokinetic reflex (HOKR) adaptation. We\r\nhave found behavior-induced MLI potentiation in form of release probability increase that\r\ncould be explained by the increase of VGCCs at the presynaptic side. Our results strengthen\r\nthe idea of distributed cerebellar plasticity contributing to learning and provide a novel\r\nmechanism for release probability increase. ","lang":"eng"}],"alternative_title":["ISTA Thesis"],"type":"dissertation","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"12814","embargo":"2024-04-07","date_created":"2023-04-07T06:16:06Z","date_updated":"2023-04-07T06:16:06Z","checksum":"35b5997d2b0acb461f9d33d073da0df5","embargo_to":"open_access","file_name":"Thesis_CatarinaAlcarva_final pdfA.pdf","access_level":"closed","content_type":"application/pdf","file_size":9881969,"creator":"cchlebak"},{"relation":"source_file","file_id":"12815","date_created":"2023-04-07T06:17:11Z","date_updated":"2023-04-07T06:17:11Z","checksum":"81198f63c294890f6d58e8b29782efdc","file_name":"Thesis_CatarinaAlcarva_final_for printing.pdf","access_level":"closed","content_type":"application/pdf","file_size":44201583,"creator":"cchlebak"},{"checksum":"0317bf7f457bb585f99d453ffa69eb53","date_updated":"2023-04-07T06:18:05Z","date_created":"2023-04-07T06:18:05Z","file_id":"12816","relation":"source_file","creator":"cchlebak","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","file_size":84731244,"access_level":"closed","file_name":"Thesis_CatarinaAlcarva_final.docx"}],"title":"Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning","status":"public","ddc":["570"],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12809","day":"06","article_processing_charge":"No","has_accepted_license":"1","date_published":"2023-04-06T00:00:00Z","page":"115","citation":{"chicago":"Alcarva, Catarina. “Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12809.","mla":"Alcarva, Catarina. Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12809.","short":"C. Alcarva, Plasticity in the Cerebellum: What Molecular Mechanisms Are behind Physiological Learning, Institute of Science and Technology Austria, 2023.","ista":"Alcarva C. 2023. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria.","ieee":"C. Alcarva, “Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning,” Institute of Science and Technology Austria, 2023.","apa":"Alcarva, C. (2023). Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12809","ama":"Alcarva C. Plasticity in the cerebellum: What molecular mechanisms are behind physiological learning. 2023. doi:10.15479/at:ista:12809"}},{"publication_identifier":{"isbn":["9781450399135"]},"month":"06","language":[{"iso":"eng"}],"doi":"10.1145/3564246.3585113","conference":{"name":"STOC: Symposium on Theory of Computing","location":"Orlando, FL, United States","start_date":"2023-06-20","end_date":"2023-06-23"},"project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"},{"grant_number":"M03073","_id":"fc390959-9c52-11eb-aca3-afa58bd282b2","name":"Learning and triangulating manifolds via collapses"}],"quality_controlled":"1","main_file_link":[{"url":"https://arxiv.org/abs/2303.04014","open_access":"1"}],"external_id":{"arxiv":["2303.04014"]},"oa":1,"ec_funded":1,"date_created":"2023-05-22T08:02:02Z","date_updated":"2023-05-22T08:15:19Z","author":[{"full_name":"Lieutier, André","last_name":"Lieutier","first_name":"André"},{"full_name":"Wintraecken, Mathijs","id":"307CFBC8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7472-2220","first_name":"Mathijs","last_name":"Wintraecken"}],"publisher":"Association for Computing Machinery","department":[{"_id":"HeEd"}],"publication_status":"published","acknowledgement":"We are greatly indebted to Erin Chambers for posing a number of questions that eventually led to this paper. We would also like to thank the other organizers of the workshop on ‘Algorithms\r\nfor the medial axis’. We are also indebted to Tatiana Ezubova for helping with the search for and translation of Russian literature. The second author thanks all members of the Edelsbrunner and Datashape groups for the atmosphere in which the research was conducted.\r\nThe research leading to these results has received funding from the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) / ERC Grant Agreement No. 339025 GUDHI (Algorithmic Foundations of Geometry Understanding in Higher Dimensions). Supported by the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No. 754411. The Austrian science fund (FWF) M-3073.","year":"2023","article_processing_charge":"No","day":"02","date_published":"2023-06-02T00:00:00Z","page":"1768-1776","citation":{"chicago":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” In Proceedings of the 55th Annual ACM Symposium on Theory of Computing, 1768–76. Association for Computing Machinery, 2023. https://doi.org/10.1145/3564246.3585113.","mla":"Lieutier, André, and Mathijs Wintraecken. “Hausdorff and Gromov-Hausdorff Stable Subsets of the Medial Axis.” Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–76, doi:10.1145/3564246.3585113.","short":"A. Lieutier, M. Wintraecken, in:, Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Association for Computing Machinery, 2023, pp. 1768–1776.","ista":"Lieutier A, Wintraecken M. 2023. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. Proceedings of the 55th Annual ACM Symposium on Theory of Computing. STOC: Symposium on Theory of Computing, 1768–1776.","apa":"Lieutier, A., & Wintraecken, M. (2023). Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In Proceedings of the 55th Annual ACM Symposium on Theory of Computing (pp. 1768–1776). Orlando, FL, United States: Association for Computing Machinery. https://doi.org/10.1145/3564246.3585113","ieee":"A. Lieutier and M. Wintraecken, “Hausdorff and Gromov-Hausdorff stable subsets of the medial axis,” in Proceedings of the 55th Annual ACM Symposium on Theory of Computing, Orlando, FL, United States, 2023, pp. 1768–1776.","ama":"Lieutier A, Wintraecken M. Hausdorff and Gromov-Hausdorff stable subsets of the medial axis. In: Proceedings of the 55th Annual ACM Symposium on Theory of Computing. Association for Computing Machinery; 2023:1768-1776. doi:10.1145/3564246.3585113"},"publication":"Proceedings of the 55th Annual ACM Symposium on Theory of Computing","abstract":[{"lang":"eng","text":"In this paper we introduce a pruning of the medial axis called the (λ,α)-medial axis (axλα). We prove that the (λ,α)-medial axis of a set K is stable in a Gromov-Hausdorff sense under weak assumptions. More formally we prove that if K and K′ are close in the Hausdorff (dH) sense then the (λ,α)-medial axes of K and K′ are close as metric spaces, that is the Gromov-Hausdorff distance (dGH) between the two is 1/4-Hölder in the sense that dGH (axλα(K),axλα(K′)) ≲ dH(K,K′)1/4. The Hausdorff distance between the two medial axes is also bounded, by dH (axλα(K),λα(K′)) ≲ dH(K,K′)1/2. These quantified stability results provide guarantees for practical computations of medial axes from approximations. Moreover, they provide key ingredients for studying the computability of the medial axis in the context of computable analysis."}],"type":"conference","oa_version":"Preprint","title":"Hausdorff and Gromov-Hausdorff stable subsets of the medial axis","status":"public","_id":"13048","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"article_processing_charge":"No","month":"05","project":[{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","grant_number":"805223","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning"}],"quality_controlled":"1","main_file_link":[{"url":"https://openreview.net/pdf?id=_eTZBs-yedr","open_access":"1"}],"oa":1,"external_id":{"arxiv":["2207.14200"]},"citation":{"short":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, D.-A. Alistarh, in:, 11th International Conference on Learning Representations , n.d.","mla":"Peste, Elena-Alexandra, et al. “CrAM: A Compression-Aware Minimizer.” 11th International Conference on Learning Representations .","chicago":"Peste, Elena-Alexandra, Adrian Vladu, Eldar Kurtic, Christoph Lampert, and Dan-Adrian Alistarh. “CrAM: A Compression-Aware Minimizer.” In 11th International Conference on Learning Representations , n.d.","ama":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. In: 11th International Conference on Learning Representations .","apa":"Peste, E.-A., Vladu, A., Kurtic, E., Lampert, C., & Alistarh, D.-A. (n.d.). CrAM: A Compression-Aware Minimizer. In 11th International Conference on Learning Representations . Kigali, Rwanda .","ieee":"E.-A. Peste, A. Vladu, E. Kurtic, C. Lampert, and D.-A. Alistarh, “CrAM: A Compression-Aware Minimizer,” in 11th International Conference on Learning Representations , Kigali, Rwanda .","ista":"Peste E-A, Vladu A, Kurtic E, Lampert C, Alistarh D-A. CrAM: A Compression-Aware Minimizer. 11th International Conference on Learning Representations . ICLR: International Conference on Learning Representations."},"publication":"11th International Conference on Learning Representations ","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"ScienComp"}],"date_published":"2023-05-01T00:00:00Z","conference":{"end_date":"2023-05-05","start_date":"2023-05-01","location":"Kigali, Rwanda ","name":"ICLR: International Conference on Learning Representations"},"type":"conference","ec_funded":1,"abstract":[{"lang":"eng","text":"Deep neural networks (DNNs) often have to be compressed, via pruning and/or quantization, before they can be deployed in practical settings. In this work we propose a new compression-aware minimizer dubbed CrAM that modifies the optimization step in a principled way, in order to produce models whose local loss behavior is stable under compression operations such as pruning. Thus, dense models trained via CrAM should be compressible post-training, in a single step, without significant accuracy loss. Experimental results on standard benchmarks, such as residual networks for ImageNet classification and BERT models for language modelling, show that CrAM produces dense models that can be more accurate than the standard SGD/Adam-based baselines, but which are stable under weight pruning: specifically, we can prune models in one-shot to 70-80% sparsity with almost no accuracy loss, and to 90% with reasonable (∼1%) accuracy loss, which is competitive with gradual compression methods. Additionally, CrAM can produce sparse models which perform well for transfer learning, and it also works for semi-structured 2:4 pruning patterns supported by GPU hardware. The code for reproducing the results is available at this https URL ."}],"department":[{"_id":"GradSch"},{"_id":"DaAl"},{"_id":"ChLa"}],"title":"CrAM: A Compression-Aware Minimizer","publication_status":"accepted","status":"public","year":"2023","_id":"13053","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","acknowledgement":"AP, EK, DA received funding from the European Research Council (ERC) under the European\r\nUnion’s Horizon 2020 research and innovation programme (grant agreement No 805223 ScaleML). AV acknowledges the support of the French Agence Nationale de la Recherche (ANR), under grant ANR-21-CE48-0016 (project COMCOPT). We further acknowledge the support from the Scientific Service Units (SSU) of ISTA through resources provided by Scientific Computing (SciComp)-","oa_version":"Preprint","date_created":"2023-05-23T11:36:18Z","date_updated":"2023-06-01T12:54:45Z","related_material":{"record":[{"id":"13074","relation":"dissertation_contains","status":"public"}]},"author":[{"first_name":"Elena-Alexandra","last_name":"Peste","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra"},{"last_name":"Vladu","first_name":"Adrian","full_name":"Vladu, Adrian"},{"full_name":"Kurtic, Eldar","last_name":"Kurtic","first_name":"Eldar","id":"47beb3a5-07b5-11eb-9b87-b108ec578218"},{"full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","first_name":"Christoph","last_name":"Lampert"},{"full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","first_name":"Dan-Adrian","orcid":"0000-0003-3650-940X","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}]},{"scopus_import":"1","day":"02","article_processing_charge":"No","publication":"Public-Key Cryptography - PKC 2023","citation":{"ama":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. Certifying giant nonprimes. In: Public-Key Cryptography - PKC 2023. Vol 13940. Springer Nature; 2023:530-553. doi:10.1007/978-3-031-31368-4_19","ista":"Hoffmann C, Hubáček P, Kamath C, Pietrzak KZ. 2023. Certifying giant nonprimes. Public-Key Cryptography - PKC 2023. PKC: Public-Key Cryptography, LNCS, vol. 13940, 530–553.","ieee":"C. Hoffmann, P. Hubáček, C. Kamath, and K. Z. Pietrzak, “Certifying giant nonprimes,” in Public-Key Cryptography - PKC 2023, Atlanta, GA, United States, 2023, vol. 13940, pp. 530–553.","apa":"Hoffmann, C., Hubáček, P., Kamath, C., & Pietrzak, K. Z. (2023). Certifying giant nonprimes. In Public-Key Cryptography - PKC 2023 (Vol. 13940, pp. 530–553). Atlanta, GA, United States: Springer Nature. https://doi.org/10.1007/978-3-031-31368-4_19","mla":"Hoffmann, Charlotte, et al. “Certifying Giant Nonprimes.” Public-Key Cryptography - PKC 2023, vol. 13940, Springer Nature, 2023, pp. 530–53, doi:10.1007/978-3-031-31368-4_19.","short":"C. Hoffmann, P. Hubáček, C. Kamath, K.Z. Pietrzak, in:, Public-Key Cryptography - PKC 2023, Springer Nature, 2023, pp. 530–553.","chicago":"Hoffmann, Charlotte, Pavel Hubáček, Chethan Kamath, and Krzysztof Z Pietrzak. “Certifying Giant Nonprimes.” In Public-Key Cryptography - PKC 2023, 13940:530–53. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-31368-4_19."},"page":"530-553","date_published":"2023-05-02T00:00:00Z","type":"conference","alternative_title":["LNCS"],"abstract":[{"lang":"eng","text":"GIMPS and PrimeGrid are large-scale distributed projects dedicated to searching giant prime numbers, usually of special forms like Mersenne and Proth primes. The numbers in the current search-space are millions of digits large and the participating volunteers need to run resource-consuming primality tests. Once a candidate prime N has been found, the only way for another party to independently verify the primality of N used to be by repeating the expensive primality test. To avoid the need for second recomputation of each primality test, these projects have recently adopted certifying mechanisms that enable efficient verification of performed tests. However, the mechanisms presently in place only detect benign errors and there is no guarantee against adversarial behavior: a malicious volunteer can mislead the project to reject a giant prime as being non-prime.\r\nIn this paper, we propose a practical, cryptographically-sound mechanism for certifying the non-primality of Proth numbers. That is, a volunteer can – parallel to running the primality test for N – generate an efficiently verifiable proof at a little extra cost certifying that N is not prime. The interactive protocol has statistical soundness and can be made non-interactive using the Fiat-Shamir heuristic.\r\nOur approach is based on a cryptographic primitive called Proof of Exponentiation (PoE) which, for a group G, certifies that a tuple (x,y,T)∈G2×N satisfies x2T=y (Pietrzak, ITCS 2019 and Wesolowski, J. Cryptol. 2020). In particular, we show how to adapt Pietrzak’s PoE at a moderate additional cost to make it a cryptographically-sound certificate of non-primality."}],"_id":"13143","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Certifying giant nonprimes","status":"public","intvolume":" 13940","oa_version":"Submitted Version","month":"05","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031313677"],"eissn":["1611-3349"]},"oa":1,"main_file_link":[{"url":"https://eprint.iacr.org/2023/238","open_access":"1"}],"quality_controlled":"1","conference":{"name":"PKC: Public-Key Cryptography","start_date":"2023-05-07","location":"Atlanta, GA, United States","end_date":"2023-05-10"},"doi":"10.1007/978-3-031-31368-4_19","language":[{"iso":"eng"}],"acknowledgement":"We are grateful to Pavel Atnashev for clarifying via e-mail several aspects of the primality tests implementated in the PrimeGrid project. Pavel Hubáček is supported by the Czech Academy of Sciences (RVO 67985840), the Grant Agency of the Czech Republic under the grant agreement no. 19-27871X, and by the Charles University project UNCE/SCI/004. Chethan Kamath is supported by Azrieli International Postdoctoral Fellowship, ISF grants 484/18 and 1789/19, and ERC StG project SPP: Secrecy Preserving Proofs.","year":"2023","publication_status":"published","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","author":[{"full_name":"Hoffmann, Charlotte","first_name":"Charlotte","last_name":"Hoffmann","id":"0f78d746-dc7d-11ea-9b2f-83f92091afe7"},{"full_name":"Hubáček, Pavel","first_name":"Pavel","last_name":"Hubáček"},{"full_name":"Kamath, Chethan","last_name":"Kamath","first_name":"Chethan"},{"full_name":"Pietrzak, Krzysztof Z","orcid":"0000-0002-9139-1654","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z"}],"date_created":"2023-06-18T22:00:47Z","date_updated":"2023-06-19T08:03:37Z","volume":13940},{"ec_funded":1,"file_date_updated":"2023-06-19T08:29:30Z","author":[{"full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X"},{"first_name":"Thomas A","last_name":"Henzinger","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2985-7724","full_name":"Henzinger, Thomas A"},{"full_name":"Lechner, Mathias","last_name":"Lechner","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zikelic, Dorde","last_name":"Zikelic","first_name":"Dorde","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87"}],"volume":13993,"date_created":"2023-06-18T22:00:47Z","date_updated":"2023-06-19T08:30:54Z","year":"2023","acknowledgement":"This work was supported in part by the ERC-2020-AdG 101020093, ERC CoG 863818 (FoRM-SMArt) and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 665385.","publisher":"Springer Nature","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"publication_status":"published","publication_identifier":{"issn":["0302-9743"],"eissn":["1611-3349"],"isbn":["9783031308222"]},"month":"04","doi":"10.1007/978-3-031-30823-9_1","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22"},"language":[{"iso":"eng"}],"oa":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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020"}],"quality_controlled":"1","abstract":[{"text":"Reinforcement learning has received much attention for learning controllers of deterministic systems. We consider a learner-verifier framework for stochastic control systems and survey recent methods that formally guarantee a conjunction of reachability and safety properties. Given a property and a lower bound on the probability of the property being satisfied, our framework jointly learns a control policy and a formal certificate to ensure the satisfaction of the property with a desired probability threshold. Both the control policy and the formal certificate are continuous functions from states to reals, which are learned as parameterized neural networks. While in the deterministic case, the certificates are invariant and barrier functions for safety, or Lyapunov and ranking functions for liveness, in the stochastic case the certificates are supermartingales. For certificate verification, we use interval arithmetic abstract interpretation to bound the expected values of neural network functions.","lang":"eng"}],"type":"conference","alternative_title":["LNCS"],"file":[{"content_type":"application/pdf","file_size":528455,"creator":"dernst","access_level":"open_access","file_name":"2023_LNCS_Chatterjee.pdf","checksum":"3d8a8bb24d211bc83360dfc2fd744307","success":1,"date_created":"2023-06-19T08:29:30Z","date_updated":"2023-06-19T08:29:30Z","relation":"main_file","file_id":"13150"}],"oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","_id":"13142","intvolume":" 13993","title":"A learner-verifier framework for neural network controllers and certificates of stochastic systems","status":"public","ddc":["000"],"article_processing_charge":"No","has_accepted_license":"1","day":"22","scopus_import":"1","date_published":"2023-04-22T00:00:00Z","citation":{"short":"K. Chatterjee, T.A. Henzinger, M. Lechner, D. Zikelic, in:, Tools and Algorithms for the Construction and Analysis of Systems , Springer Nature, 2023, pp. 3–25.","mla":"Chatterjee, Krishnendu, et al. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” Tools and Algorithms for the Construction and Analysis of Systems , vol. 13993, Springer Nature, 2023, pp. 3–25, doi:10.1007/978-3-031-30823-9_1.","chicago":"Chatterjee, Krishnendu, Thomas A Henzinger, Mathias Lechner, and Dorde Zikelic. “A Learner-Verifier Framework for Neural Network Controllers and Certificates of Stochastic Systems.” In Tools and Algorithms for the Construction and Analysis of Systems , 13993:3–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30823-9_1.","ama":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. A learner-verifier framework for neural network controllers and certificates of stochastic systems. In: Tools and Algorithms for the Construction and Analysis of Systems . Vol 13993. Springer Nature; 2023:3-25. doi:10.1007/978-3-031-30823-9_1","apa":"Chatterjee, K., Henzinger, T. A., Lechner, M., & Zikelic, D. (2023). A learner-verifier framework for neural network controllers and certificates of stochastic systems. In Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13993, pp. 3–25). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30823-9_1","ieee":"K. Chatterjee, T. A. Henzinger, M. Lechner, and D. Zikelic, “A learner-verifier framework for neural network controllers and certificates of stochastic systems,” in Tools and Algorithms for the Construction and Analysis of Systems , Paris, France, 2023, vol. 13993, pp. 3–25.","ista":"Chatterjee K, Henzinger TA, Lechner M, Zikelic D. 2023. A learner-verifier framework for neural network controllers and certificates of stochastic systems. Tools and Algorithms for the Construction and Analysis of Systems . TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13993, 3–25."},"publication":"Tools and Algorithms for the Construction and Analysis of Systems ","page":"3-25"},{"_id":"13141","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","ddc":["000"],"title":"Computing adequately permissive assumptions for synthesis","intvolume":" 13994","oa_version":"Published Version","file":[{"relation":"main_file","file_id":"13151","checksum":"60dcafc1b4f6f070be43bad3fe877974","success":1,"date_created":"2023-06-19T08:43:21Z","date_updated":"2023-06-19T08:43:21Z","access_level":"open_access","file_name":"2023_LNCS_Anand.pdf","content_type":"application/pdf","file_size":521425,"creator":"dernst"}],"type":"conference","alternative_title":["LNCS"],"abstract":[{"text":"We automatically compute a new class of environment assumptions in two-player turn-based finite graph games which characterize an “adequate cooperation” needed from the environment to allow the system player to win. Given an ω-regular winning condition Φ for the system player, we compute an ω-regular assumption Ψ for the environment player, such that (i) every environment strategy compliant with Ψ allows the system to fulfill Φ (sufficiency), (ii) Ψ\r\n can be fulfilled by the environment for every strategy of the system (implementability), and (iii) Ψ does not prevent any cooperative strategy choice (permissiveness).\r\nFor parity games, which are canonical representations of ω-regular games, we present a polynomial-time algorithm for the symbolic computation of adequately permissive assumptions and show that our algorithm runs faster and produces better assumptions than existing approaches—both theoretically and empirically. To the best of our knowledge, for ω\r\n-regular games, we provide the first algorithm to compute sufficient and implementable environment assumptions that are also permissive.","lang":"eng"}],"publication":"TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems","citation":{"short":"A. Anand, K. Mallik, S.P. Nayak, A.K. Schmuck, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 211–228.","mla":"Anand, Ashwani, et al. “Computing Adequately Permissive Assumptions for Synthesis.” TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, vol. 13994, Springer Nature, 2023, pp. 211–28, doi:10.1007/978-3-031-30820-8_15.","chicago":"Anand, Ashwani, Kaushik Mallik, Satya Prakash Nayak, and Anne Kathrin Schmuck. “Computing Adequately Permissive Assumptions for Synthesis.” In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, 13994:211–28. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30820-8_15.","ama":"Anand A, Mallik K, Nayak SP, Schmuck AK. Computing adequately permissive assumptions for synthesis. In: TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13994. Springer Nature; 2023:211-228. doi:10.1007/978-3-031-30820-8_15","ieee":"A. Anand, K. Mallik, S. P. Nayak, and A. K. Schmuck, “Computing adequately permissive assumptions for synthesis,” in TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13994, pp. 211–228.","apa":"Anand, A., Mallik, K., Nayak, S. P., & Schmuck, A. K. (2023). Computing adequately permissive assumptions for synthesis. In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13994, pp. 211–228). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30820-8_15","ista":"Anand A, Mallik K, Nayak SP, Schmuck AK. 2023. Computing adequately permissive assumptions for synthesis. TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. TACAS: Tools and Algorithms for the Construction and Analysis of Systems, LNCS, vol. 13994, 211–228."},"page":"211-228","date_published":"2023-04-20T00:00:00Z","scopus_import":"1","day":"20","article_processing_charge":"No","has_accepted_license":"1","year":"2023","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"ToHe"}],"author":[{"full_name":"Anand, Ashwani","last_name":"Anand","first_name":"Ashwani"},{"full_name":"Mallik, Kaushik","id":"0834ff3c-6d72-11ec-94e0-b5b0a4fb8598","orcid":"0000-0001-9864-7475","first_name":"Kaushik","last_name":"Mallik"},{"last_name":"Nayak","first_name":"Satya Prakash","full_name":"Nayak, Satya Prakash"},{"full_name":"Schmuck, Anne Kathrin","first_name":"Anne Kathrin","last_name":"Schmuck"}],"date_created":"2023-06-18T22:00:47Z","date_updated":"2023-06-19T08:49:46Z","volume":13994,"file_date_updated":"2023-06-19T08:43:21Z","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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","conference":{"name":"TACAS: Tools and Algorithms for the Construction and Analysis of Systems","end_date":"2023-04-27","location":"Paris, France","start_date":"2023-04-22"},"doi":"10.1007/978-3-031-30820-8_15","language":[{"iso":"eng"}],"month":"04","publication_identifier":{"issn":["0302-9743"],"isbn":["9783031308192"],"eissn":["1611-3349"]}},{"publication_identifier":{"issn":["2663 - 337X"]},"month":"04","doi":"10.15479/at:ista:12826","language":[{"iso":"eng"}],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"}],"supervisor":[{"orcid":"0000-0002-3937-1330","id":"2BD278E6-F248-11E8-B48F-1D18A9856A87","last_name":"Jösch","first_name":"Maximilian A","full_name":"Jösch, Maximilian A"}],"degree_awarded":"PhD","oa":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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"ec_funded":1,"file_date_updated":"2023-04-20T09:26:51Z","author":[{"first_name":"Victoria","last_name":"Pokusaeva","id":"3184041C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7660-444X","full_name":"Pokusaeva, Victoria"}],"date_updated":"2023-06-23T09:47:36Z","date_created":"2023-04-14T14:56:04Z","year":"2023","department":[{"_id":"MaJö"},{"_id":"GradSch"}],"publisher":"Institute of Science and Technology Austria","publication_status":"published","article_processing_charge":"No","has_accepted_license":"1","day":"18","date_published":"2023-04-18T00:00:00Z","citation":{"mla":"Pokusaeva, Victoria. Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:12826.","short":"V. Pokusaeva, Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster, Institute of Science and Technology Austria, 2023.","chicago":"Pokusaeva, Victoria. “Neural Control of Optic Flow-Based Navigation in Drosophila Melanogaster.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:12826.","ama":"Pokusaeva V. Neural control of optic flow-based navigation in Drosophila melanogaster. 2023. doi:10.15479/at:ista:12826","ista":"Pokusaeva V. 2023. Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria.","ieee":"V. Pokusaeva, “Neural control of optic flow-based navigation in Drosophila melanogaster,” Institute of Science and Technology Austria, 2023.","apa":"Pokusaeva, V. (2023). Neural control of optic flow-based navigation in Drosophila melanogaster. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:12826"},"page":"106","abstract":[{"lang":"eng","text":"During navigation, animals can infer the structure of the environment by computing the optic flow cues elicited by their own movements, and subsequently use this information to instruct proper locomotor actions. These computations require a panoramic assessment of the visual environment in order to disambiguate similar sensory experiences that may require distinct behavioral responses. The estimation of the global motion patterns is therefore essential for successful navigation. Yet, our understanding of the algorithms and implementations that enable coherent panoramic visual perception remains scarce. Here I pursue this problem by dissecting the functional aspects of interneuronal communication in the lobula plate tangential cell network in Drosophila melanogaster. The results presented in the thesis demonstrate that the basis for effective interpretation of the optic flow in this circuit are stereotyped synaptic connections that mediate the formation of distinct subnetworks, each extracting a particular pattern of global motion. \r\nFirstly, I show that gap junctions are essential for a correct interpretation of binocular motion cues by horizontal motion-sensitive cells. HS cells form electrical synapses with contralateral H2 neurons that are involved in detecting yaw rotation and translation. I developed an FlpStop-mediated mutant of a gap junction protein ShakB that disrupts these electrical synapses. While the loss of electrical synapses does not affect the tuning of the direction selectivity in HS neurons, it severely alters their sensitivity to horizontal motion in the contralateral side. These physiological changes result in an inappropriate integration of binocular motion cues in walking animals. While wild-type flies form a binocular perception of visual motion by non-linear integration of monocular optic flow cues, the mutant flies sum the monocular inputs linearly. These results indicate that rather than averaging signals in neighboring neurons, gap-junctions operate in conjunction with chemical synapses to mediate complex non-linear optic flow computations.\r\nSecondly, I show that stochastic manipulation of neuronal activity in the lobula plate tangential cell network is a powerful approach to study the neuronal implementation of optic flow-based navigation in flies. Tangential neurons form multiple subnetworks, each mediating course-stabilizing response to a particular global pattern of visual motion. Application of genetic mosaic techniques can provide sparse optogenetic activation of HS cells in numerous combinations. These distinct combinations of activated neurons drive an array of distinct behavioral responses, providing important insights into how visuomotor transformation is performed in the lobula plate tangential cell network. This approach can be complemented by stochastic silencing of tangential neurons, enabling direct assessment of the functional role of individual tangential neurons in the processing of specific visual motion patterns.\r\n\tTaken together, the findings presented in this thesis suggest that establishing specific activity patterns of tangential cells via stereotyped synaptic connectivity is a key to efficient optic flow-based navigation in Drosophila melanogaster."}],"type":"dissertation","alternative_title":["ISTA Thesis"],"file":[{"relation":"source_file","file_id":"12857","checksum":"5f589a9af025f7eeebfd0c186209913e","date_created":"2023-04-20T09:14:38Z","date_updated":"2023-04-20T09:26:51Z","access_level":"closed","file_name":"Thesis_Pokusaeva.docx","file_size":14507243,"content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","creator":"vpokusae"},{"content_type":"application/pdf","file_size":10090711,"creator":"vpokusae","access_level":"open_access","file_name":"Thesis_Pokusaeva.pdf","checksum":"bbeed76db45a996b4c91a9abe12ce0ec","success":1,"date_updated":"2023-04-20T09:14:44Z","date_created":"2023-04-20T09:14:44Z","relation":"main_file","file_id":"12858"}],"oa_version":"Published Version","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","_id":"12826","title":"Neural control of optic flow-based navigation in Drosophila melanogaster","ddc":["570","571"],"status":"public"},{"isi":1,"quality_controlled":"1","project":[{"name":"Alpha Shape Theory Extended","call_identifier":"H2020","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"Z00342","_id":"268116B8-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"The Wittgenstein Prize"},{"name":"Persistence and stability of geometric complexes","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","grant_number":"I02979-N35"}],"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"isi":["000846967100001"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1007/s00453-022-01027-6","month":"01","publication_identifier":{"issn":["0178-4617"],"eissn":["1432-0541"]},"publication_status":"published","publisher":"Springer Nature","department":[{"_id":"HeEd"}],"year":"2023","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). This project has received funding from the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme, Grant No. 788183, from the Wittgenstein Prize, Austrian Science Fund (FWF), Grant No. Z 342-N31, and from the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, Austrian Science Fund (FWF), Grant No. I 02979-N35.","date_updated":"2023-06-27T12:53:43Z","date_created":"2022-09-11T22:01:57Z","volume":85,"author":[{"first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert"},{"full_name":"Osang, Georg F","first_name":"Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2023-01-20T10:02:48Z","ec_funded":1,"article_type":"original","page":"277-295","publication":"Algorithmica","citation":{"ista":"Edelsbrunner H, Osang GF. 2023. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 85, 277–295.","apa":"Edelsbrunner, H., & Osang, G. F. (2023). A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-022-01027-6","ieee":"H. Edelsbrunner and G. F. Osang, “A simple algorithm for higher-order Delaunay mosaics and alpha shapes,” Algorithmica, vol. 85. Springer Nature, pp. 277–295, 2023.","ama":"Edelsbrunner H, Osang GF. A simple algorithm for higher-order Delaunay mosaics and alpha shapes. Algorithmica. 2023;85:277-295. doi:10.1007/s00453-022-01027-6","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-022-01027-6.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. “A Simple Algorithm for Higher-Order Delaunay Mosaics and Alpha Shapes.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 277–95, doi:10.1007/s00453-022-01027-6.","short":"H. Edelsbrunner, G.F. Osang, Algorithmica 85 (2023) 277–295."},"date_published":"2023-01-01T00:00:00Z","scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","title":"A simple algorithm for higher-order Delaunay mosaics and alpha shapes","status":"public","ddc":["510"],"intvolume":" 85","_id":"12086","user_id":"2EBD1598-F248-11E8-B48F-1D18A9856A87","oa_version":"Published Version","file":[{"content_type":"application/pdf","file_size":911017,"creator":"dernst","access_level":"open_access","file_name":"2023_Algorithmica_Edelsbrunner.pdf","checksum":"71685ca5121f4c837f40c3f8eb50c915","success":1,"date_updated":"2023-01-20T10:02:48Z","date_created":"2023-01-20T10:02:48Z","relation":"main_file","file_id":"12322"}],"type":"journal_article","abstract":[{"lang":"eng","text":"We present a simple algorithm for computing higher-order Delaunay mosaics that works in Euclidean spaces of any finite dimensions. The algorithm selects the vertices of the order-k mosaic from incrementally constructed lower-order mosaics and uses an algorithm for weighted first-order Delaunay mosaics as a black-box to construct the order-k mosaic from its vertices. Beyond this black-box, the algorithm uses only combinatorial operations, thus facilitating easy implementation. We extend this algorithm to compute higher-order α-shapes and provide open-source implementations. We present experimental results for properties of higher-order Delaunay mosaics of random point sets."}]},{"month":"01","publication_identifier":{"eissn":["1424-3202"],"issn":["1424-3199"]},"external_id":{"isi":["000906214600004"]},"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","short":"CC BY (4.0)","image":"/images/cc_by.png"},"oa":1,"quality_controlled":"1","isi":1,"project":[{"grant_number":"F6504","_id":"fc31cba2-9c52-11eb-aca3-ff467d239cd2","name":"Taming Complexity in Partial Differential Systems"},{"call_identifier":"H2020","name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425"},{"name":"Configuration Spaces over Non-Smooth Spaces","_id":"34dbf174-11ca-11ed-8bc3-afe9d43d4b9c","grant_number":"E208"},{"_id":"34c6ea2d-11ca-11ed-8bc3-c04f3c502833","grant_number":"ESP156_N","name":"Gradient flow techniques for quantum Markov semigroups"}],"doi":"10.1007/s00028-022-00859-7","language":[{"iso":"eng"}],"article_number":"9","file_date_updated":"2023-01-20T10:45:06Z","ec_funded":1,"year":"2023","acknowledgement":"Research supported by the Austrian Science Fund (FWF) grant F65 at the Institute of Science and Technology Austria and by the European Research Council (ERC) (Grant agreement No. 716117 awarded to Prof. Dr. Jan Maas). L.D.S. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 208). M.W. gratefully acknowledges funding of his current position by the Austrian Science Fund (FWF) through the ESPRIT Programme (Grant No. 156).","publication_status":"published","publisher":"Springer Nature","department":[{"_id":"JaMa"}],"author":[{"orcid":"0000-0002-9881-6870","id":"ECEBF480-9E4F-11EA-B557-B0823DDC885E","last_name":"Dello Schiavo","first_name":"Lorenzo","full_name":"Dello Schiavo, Lorenzo"},{"orcid":"0000-0002-0519-4241","id":"88644358-0A0E-11EA-8FA5-49A33DDC885E","last_name":"Wirth","first_name":"Melchior","full_name":"Wirth, Melchior"}],"date_updated":"2023-06-28T11:54:35Z","date_created":"2023-01-08T23:00:53Z","volume":23,"scopus_import":"1","day":"01","has_accepted_license":"1","article_processing_charge":"Yes (via OA deal)","publication":"Journal of Evolution Equations","citation":{"ama":"Dello Schiavo L, Wirth M. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 2023;23(1). doi:10.1007/s00028-022-00859-7","ista":"Dello Schiavo L, Wirth M. 2023. Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. 23(1), 9.","ieee":"L. Dello Schiavo and M. Wirth, “Ergodic decompositions of Dirichlet forms under order isomorphisms,” Journal of Evolution Equations, vol. 23, no. 1. Springer Nature, 2023.","apa":"Dello Schiavo, L., & Wirth, M. (2023). Ergodic decompositions of Dirichlet forms under order isomorphisms. Journal of Evolution Equations. Springer Nature. https://doi.org/10.1007/s00028-022-00859-7","mla":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations, vol. 23, no. 1, 9, Springer Nature, 2023, doi:10.1007/s00028-022-00859-7.","short":"L. Dello Schiavo, M. Wirth, Journal of Evolution Equations 23 (2023).","chicago":"Dello Schiavo, Lorenzo, and Melchior Wirth. “Ergodic Decompositions of Dirichlet Forms under Order Isomorphisms.” Journal of Evolution Equations. Springer Nature, 2023. https://doi.org/10.1007/s00028-022-00859-7."},"article_type":"original","date_published":"2023-01-01T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"We study ergodic decompositions of Dirichlet spaces under intertwining via unitary order isomorphisms. We show that the ergodic decomposition of a quasi-regular Dirichlet space is unique up to a unique isomorphism of the indexing space. Furthermore, every unitary order isomorphism intertwining two quasi-regular Dirichlet spaces is decomposable over their ergodic decompositions up to conjugation via an isomorphism of the corresponding indexing spaces."}],"issue":"1","_id":"12104","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"title":"Ergodic decompositions of Dirichlet forms under order isomorphisms","status":"public","intvolume":" 23","oa_version":"Published Version","file":[{"file_name":"2023_JourEvolutionEquations_DelloSchiavo.pdf","access_level":"open_access","creator":"dernst","content_type":"application/pdf","file_size":422612,"file_id":"12325","relation":"main_file","date_created":"2023-01-20T10:45:06Z","date_updated":"2023-01-20T10:45:06Z","success":1,"checksum":"1f34f3e2cb521033de6154f274ea3a4e"}]},{"volume":60,"date_updated":"2023-06-28T11:49:58Z","date_created":"2022-06-05T22:01:50Z","related_material":{"link":[{"url":" https://doi.org/10.1007/s00382-022-06401-2","relation":"erratum"}]},"author":[{"full_name":"Goswami, Bidyut B","id":"3a4ac09c-6d61-11ec-bf66-884cde66b64b","last_name":"Goswami","first_name":"Bidyut B"}],"department":[{"_id":"CaMu"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"This work was supported by the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (NRF-2018R1A5A1024958). 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 Korea Meteorological Administration, and by the Korea Research Environment Open NETwork (KREONET), respectively. The authors declare no conflicts of interest.","year":"2023","publication_identifier":{"eissn":["1432-0894"],"issn":["0930-7575"]},"month":"01","language":[{"iso":"eng"}],"doi":"10.1007/s00382-022-06337-7","isi":1,"quality_controlled":"1","external_id":{"isi":["000803119400002"]},"abstract":[{"text":"The Indian summer monsoon rainfall (ISMR) has been declining since the 1950s. However, since 2002 it is reported to have revived. For these observed changes in the ISMR, several explanations have been reported. Among these explanations, however, the role of the eastern equatorial Indian Ocean (EEIO) is missing despite being one of the warmest regions in the Indian Ocean, and monotonously warming. A recent study reported that EEIO warming impacts the rainfall over northern India. Here we report that warming in the EEIO weakens the low-level Indian summer monsoon circulation and reduces ISMR. A warm EEIO drives easterly winds in the Indo–Pacific sector as a Gill response. The warm EEIO also enhances nocturnal convection offshore the western coast of Sumatra. The latent heating associated with the increased convection augments the Gill response and the resultant circulation opposes the monsoon low-level circulation and weakens the seasonal rainfall.","lang":"eng"}],"type":"journal_article","oa_version":"None","intvolume":" 60","title":"Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend","status":"public","_id":"11434","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2023-01-01T00:00:00Z","page":"427-442","article_type":"original","citation":{"chicago":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics. Springer Nature, 2023. https://doi.org/10.1007/s00382-022-06337-7.","mla":"GOSWAMI, BIDYUT B. “Role of the Eastern Equatorial Indian Ocean Warming in the Indian Summer Monsoon Rainfall Trend.” Climate Dynamics, vol. 60, Springer Nature, 2023, pp. 427–42, doi:10.1007/s00382-022-06337-7.","short":"B.B. GOSWAMI, Climate Dynamics 60 (2023) 427–442.","ista":"GOSWAMI BB. 2023. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 60, 427–442.","ieee":"B. B. GOSWAMI, “Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend,” Climate Dynamics, vol. 60. Springer Nature, pp. 427–442, 2023.","apa":"GOSWAMI, B. B. (2023). Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. Springer Nature. https://doi.org/10.1007/s00382-022-06337-7","ama":"GOSWAMI BB. Role of the eastern equatorial Indian Ocean warming in the Indian summer monsoon rainfall trend. Climate Dynamics. 2023;60:427-442. doi:10.1007/s00382-022-06337-7"},"publication":"Climate Dynamics"}]