--- _id: '14798' abstract: - lang: eng text: 'A faithful reproduction of gloss is inherently difficult because of the limited dynamic range, peak luminance, and 3D capabilities of display devices. This work investigates how the display capabilities affect gloss appearance with respect to a real-world reference object. To this end, we employ an accurate imaging pipeline to achieve a perceptual gloss match between a virtual and real object presented side-by-side on an augmented-reality high-dynamic-range (HDR) stereoscopic display, which has not been previously attained to this extent. Based on this precise gloss reproduction, we conduct a series of gloss matching experiments to study how gloss perception degrades based on individual factors: object albedo, display luminance, dynamic range, stereopsis, and tone mapping. We support the study with a detailed analysis of individual factors, followed by an in-depth discussion on the observed perceptual effects. Our experiments demonstrate that stereoscopic presentation has a limited effect on the gloss matching task on our HDR display. However, both reduced luminance and dynamic range of the display reduce the perceived gloss. This means that the visual system cannot compensate for the changes in gloss appearance across luminance (lack of gloss constancy), and the tone mapping operator should be carefully selected when reproducing gloss on a low dynamic range (LDR) display.' acknowledgement: "This work is supported by FWF Lise Meitner (Grant M 3319), Spanish Agencia Estatal de Investigación (project PID2022-141539NBI00), European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement\r\nN◦ 725253–EyeCode), Swiss National Science Foundation (Grant no. 200502), and academic gifts from Meta. We thank Dmitry Lubyako and Ali Özgür Yöntem for building the turntable for our experiment." article_number: '90' article_processing_charge: Yes (in subscription journal) author: - first_name: Bin full_name: Chen, Bin last_name: Chen - first_name: Akshay full_name: Jindal, Akshay last_name: Jindal - first_name: Michael full_name: Piovarci, Michael id: 62E473F4-5C99-11EA-A40E-AF823DDC885E last_name: Piovarci orcid: 0000-0002-5062-4474 - first_name: Chao full_name: Wang, Chao last_name: Wang - first_name: Hans Peter full_name: Seidel, Hans Peter last_name: Seidel - first_name: Piotr full_name: Didyk, Piotr last_name: Didyk - first_name: Karol full_name: Myszkowski, Karol last_name: Myszkowski - first_name: Ana full_name: Serrano, Ana last_name: Serrano - first_name: Rafał K. full_name: Mantiuk, Rafał K. last_name: Mantiuk citation: ama: 'Chen B, Jindal A, Piovarci M, et al. The effect of display capabilities on the gloss consistency between real and virtual objects. In: Proceedings of the SIGGRAPH Asia 2023 Conference. Association for Computing Machinery; 2023. doi:10.1145/3610548.3618226' apa: 'Chen, B., Jindal, A., Piovarci, M., Wang, C., Seidel, H. P., Didyk, P., … Mantiuk, R. K. (2023). The effect of display capabilities on the gloss consistency between real and virtual objects. In Proceedings of the SIGGRAPH Asia 2023 Conference. Sydney, Australia: Association for Computing Machinery. https://doi.org/10.1145/3610548.3618226' chicago: Chen, Bin, Akshay Jindal, Michael Piovarci, Chao Wang, Hans Peter Seidel, Piotr Didyk, Karol Myszkowski, Ana Serrano, and Rafał K. Mantiuk. “The Effect of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.” In Proceedings of the SIGGRAPH Asia 2023 Conference. Association for Computing Machinery, 2023. https://doi.org/10.1145/3610548.3618226. ieee: B. Chen et al., “The effect of display capabilities on the gloss consistency between real and virtual objects,” in Proceedings of the SIGGRAPH Asia 2023 Conference, Sydney, Australia, 2023. ista: 'Chen B, Jindal A, Piovarci M, Wang C, Seidel HP, Didyk P, Myszkowski K, Serrano A, Mantiuk RK. 2023. The effect of display capabilities on the gloss consistency between real and virtual objects. Proceedings of the SIGGRAPH Asia 2023 Conference. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 90.' mla: Chen, Bin, et al. “The Effect of Display Capabilities on the Gloss Consistency between Real and Virtual Objects.” Proceedings of the SIGGRAPH Asia 2023 Conference, 90, Association for Computing Machinery, 2023, doi:10.1145/3610548.3618226. short: B. Chen, A. Jindal, M. Piovarci, C. Wang, H.P. Seidel, P. Didyk, K. Myszkowski, A. Serrano, R.K. Mantiuk, in:, Proceedings of the SIGGRAPH Asia 2023 Conference, Association for Computing Machinery, 2023. conference: end_date: 2023-12-15 location: Sydney, Australia name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2023-12-12 date_created: 2024-01-14T23:00:57Z date_published: 2023-12-10T00:00:00Z date_updated: 2024-01-17T08:38:35Z day: '10' ddc: - '000' department: - _id: BeBi doi: 10.1145/3610548.3618226 file: - access_level: open_access checksum: 8abe27432ed222b50d1af9b3388db1b0 content_type: application/pdf creator: dernst date_created: 2024-01-17T08:33:06Z date_updated: 2024-01-17T08:33:06Z file_id: '14823' file_name: 2023_SA_Chen.pdf file_size: 95967451 relation: main_file success: 1 file_date_updated: 2024-01-17T08:33:06Z has_accepted_license: '1' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: eb901961-77a9-11ec-83b8-f5c883a62027 grant_number: M03319 name: Perception-Aware Appearance Fabrication publication: Proceedings of the SIGGRAPH Asia 2023 Conference publication_identifier: isbn: - '9798400703157' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: The effect of display capabilities on the gloss consistency between real and virtual objects tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14815' abstract: - lang: eng text: In the last few years, various communication compression techniques have emerged as an indispensable tool helping to alleviate the communication bottleneck in distributed learning. However, despite the fact biased compressors often show superior performance in practice when compared to the much more studied and understood unbiased compressors, very little is known about them. In this work we study three classes of biased compression operators, two of which are new, and their performance when applied to (stochastic) gradient descent and distributed (stochastic) gradient descent. We show for the first time that biased compressors can lead to linear convergence rates both in the single node and distributed settings. We prove that distributed compressed SGD method, employed with error feedback mechanism, enjoys the ergodic rate O(δLexp[−μKδL]+(C+δD)Kμ), where δ≥1 is a compression parameter which grows when more compression is applied, L and μ are the smoothness and strong convexity constants, C captures stochastic gradient noise (C=0 if full gradients are computed on each node) and D captures the variance of the gradients at the optimum (D=0 for over-parameterized models). Further, via a theoretical study of several synthetic and empirical distributions of communicated gradients, we shed light on why and by how much biased compressors outperform their unbiased variants. Finally, we propose several new biased compressors with promising theoretical guarantees and practical performance. acknowledgement: 'The work in Sections 1-5 was conducted while A. Beznosikov was a research intern in the Optimizationand Machine Learning Lab of Peter Richtárik at KAUST; this visit was funded by the KAUST Baseline Research Funding Scheme. The work of A. Beznosikov in Section 6 was conducted in Skoltech and was supported by Ministry of Science and Higher Education grant No. 075-10-2021-068. ' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Aleksandr full_name: Beznosikov, Aleksandr last_name: Beznosikov - first_name: Samuel full_name: Horvath, Samuel last_name: Horvath - first_name: Peter full_name: Richtarik, Peter last_name: Richtarik - first_name: Mher full_name: Safaryan, Mher id: dd546b39-0804-11ed-9c55-ef075c39778d last_name: Safaryan citation: ama: Beznosikov A, Horvath S, Richtarik P, Safaryan M. On biased compression for distributed learning. Journal of Machine Learning Research. 2023;24:1-50. apa: Beznosikov, A., Horvath, S., Richtarik, P., & Safaryan, M. (2023). On biased compression for distributed learning. Journal of Machine Learning Research. Journal of Machine Learning Research. chicago: Beznosikov, Aleksandr, Samuel Horvath, Peter Richtarik, and Mher Safaryan. “On Biased Compression for Distributed Learning.” Journal of Machine Learning Research. Journal of Machine Learning Research, 2023. ieee: A. Beznosikov, S. Horvath, P. Richtarik, and M. Safaryan, “On biased compression for distributed learning,” Journal of Machine Learning Research, vol. 24. Journal of Machine Learning Research, pp. 1–50, 2023. ista: Beznosikov A, Horvath S, Richtarik P, Safaryan M. 2023. On biased compression for distributed learning. Journal of Machine Learning Research. 24, 1–50. mla: Beznosikov, Aleksandr, et al. “On Biased Compression for Distributed Learning.” Journal of Machine Learning Research, vol. 24, Journal of Machine Learning Research, 2023, pp. 1–50. short: A. Beznosikov, S. Horvath, P. Richtarik, M. Safaryan, Journal of Machine Learning Research 24 (2023) 1–50. date_created: 2024-01-16T12:13:36Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-17T09:14:13Z day: '01' ddc: - '000' department: - _id: DaAl external_id: arxiv: - '2002.12410' isi: - '001111578500001' file: - access_level: open_access checksum: c50f2b9db53938b755e30a085f464059 content_type: application/pdf creator: dernst date_created: 2024-01-16T12:13:27Z date_updated: 2024-01-16T12:13:27Z file_id: '14816' file_name: 2023_JMLR_Beznosikov.pdf file_size: 1510993 relation: main_file success: 1 file_date_updated: 2024-01-16T12:13:27Z has_accepted_license: '1' intvolume: ' 24' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 1-50 publication: Journal of Machine Learning Research publication_identifier: eissn: - 1533-7928 publication_status: published publisher: Journal of Machine Learning Research quality_controlled: '1' status: public title: On biased compression for distributed learning tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 24 year: '2023' ... --- _id: '14456' abstract: - lang: eng text: In this paper, we present novel algorithms that efficiently compute a shortest reconfiguration sequence between two given dominating sets in trees and interval graphs under the TOKEN SLIDING model. In this problem, a graph is provided along with its two dominating sets, which can be imagined as tokens placed on vertices. The objective is to find a shortest sequence of dominating sets that transforms one set into the other, with each set in the sequence resulting from sliding a single token in the previous set. While identifying any sequence has been well studied, our work presents the first polynomial algorithms for this optimization variant in the context of dominating sets. alternative_title: - LNCS article_processing_charge: No author: - first_name: Jan Matyáš full_name: Křišťan, Jan Matyáš last_name: Křišťan - first_name: Jakub full_name: Svoboda, Jakub id: 130759D2-D7DD-11E9-87D2-DE0DE6697425 last_name: Svoboda orcid: 0000-0002-1419-3267 citation: ama: 'Křišťan JM, Svoboda J. Shortest dominating set reconfiguration under token sliding. In: 24th International Symposium on Fundamentals of Computation Theory. Vol 14292. Springer Nature; 2023:333-347. doi:10.1007/978-3-031-43587-4_24' apa: 'Křišťan, J. M., & Svoboda, J. (2023). Shortest dominating set reconfiguration under token sliding. In 24th International Symposium on Fundamentals of Computation Theory (Vol. 14292, pp. 333–347). Trier, Germany: Springer Nature. https://doi.org/10.1007/978-3-031-43587-4_24' chicago: Křišťan, Jan Matyáš, and Jakub Svoboda. “Shortest Dominating Set Reconfiguration under Token Sliding.” In 24th International Symposium on Fundamentals of Computation Theory, 14292:333–47. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-43587-4_24. ieee: J. M. Křišťan and J. Svoboda, “Shortest dominating set reconfiguration under token sliding,” in 24th International Symposium on Fundamentals of Computation Theory, Trier, Germany, 2023, vol. 14292, pp. 333–347. ista: 'Křišťan JM, Svoboda J. 2023. Shortest dominating set reconfiguration under token sliding. 24th International Symposium on Fundamentals of Computation Theory. FCT: Fundamentals of Computation Theory, LNCS, vol. 14292, 333–347.' mla: Křišťan, Jan Matyáš, and Jakub Svoboda. “Shortest Dominating Set Reconfiguration under Token Sliding.” 24th International Symposium on Fundamentals of Computation Theory, vol. 14292, Springer Nature, 2023, pp. 333–47, doi:10.1007/978-3-031-43587-4_24. short: J.M. Křišťan, J. Svoboda, in:, 24th International Symposium on Fundamentals of Computation Theory, Springer Nature, 2023, pp. 333–347. conference: end_date: 2023-09-21 location: Trier, Germany name: 'FCT: Fundamentals of Computation Theory' start_date: 2023-09-18 date_created: 2023-10-29T23:01:16Z date_published: 2023-09-21T00:00:00Z date_updated: 2024-01-22T08:10:49Z day: '21' department: - _id: KrCh doi: 10.1007/978-3-031-43587-4_24 external_id: arxiv: - '2307.10847' intvolume: ' 14292' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2307.10847 month: '09' oa: 1 oa_version: Preprint page: 333-347 publication: 24th International Symposium on Fundamentals of Computation Theory publication_identifier: eissn: - 1611-3349 isbn: - '9783031435867' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: erratum url: https://doi.org/10.1007/978-3-031-43587-4_31 scopus_import: '1' status: public title: Shortest dominating set reconfiguration under token sliding type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14292 year: '2023' ... --- _id: '14829' abstract: - lang: eng text: 'This paper explores a modular design architecture aimed at helping blockchains (and other SMR implementation) to scale to a very large number of processes. This comes in contrast to existing monolithic architectures that interleave transaction dissemination, ordering, and execution in a single functionality. To achieve this we first split the monolith to multiple layers which can use existing distributed computing primitives. The exact specifications of the data dissemination part are formally defined by the Proof of Availability & Retrieval (PoA &R) abstraction. Solutions to the PoA &R problem contain two related sub-protocols: one that “pushes” information into the network and another that “pulls” this information. Regarding the latter, there is a dearth of research literature which is rectified in this paper. We present a family of pulling sub-protocols and rigorously analyze them. Extensive simulations support the theoretical claims of efficiency and robustness in case of a very large number of players. Finally, actual implementation and deployment on a small number of machines (roughly the size of several industrial systems) demonstrates the viability of the architecture’s paradigm.' acknowledgement: 'This work is partially supported by Meta. Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N. Shir Cohen is supported by the Adams Fellowship Program of the Israel Academy of Sciences and Humanities.' alternative_title: - LNCS article_processing_charge: No author: - first_name: Shir full_name: Cohen, Shir last_name: Cohen - first_name: Guy full_name: Goren, Guy last_name: Goren - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Alberto full_name: Sonnino, Alberto last_name: Sonnino - first_name: Alexander full_name: Spiegelman, Alexander last_name: Spiegelman citation: ama: 'Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. Proof of availability and retrieval in a modular blockchain architecture. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13951. Springer Nature; 2023:36-53. doi:10.1007/978-3-031-47751-5_3' apa: 'Cohen, S., Goren, G., Kokoris Kogias, E., Sonnino, A., & Spiegelman, A. (2023). Proof of availability and retrieval in a modular blockchain architecture. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13951, pp. 36–53). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47751-5_3' chicago: Cohen, Shir, Guy Goren, Eleftherios Kokoris Kogias, Alberto Sonnino, and Alexander Spiegelman. “Proof of Availability and Retrieval in a Modular Blockchain Architecture.” In 27th International Conference on Financial Cryptography and Data Security, 13951:36–53. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47751-5_3. ieee: S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, and A. Spiegelman, “Proof of availability and retrieval in a modular blockchain architecture,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13951, pp. 36–53. ista: 'Cohen S, Goren G, Kokoris Kogias E, Sonnino A, Spiegelman A. 2023. Proof of availability and retrieval in a modular blockchain architecture. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13951, 36–53.' mla: Cohen, Shir, et al. “Proof of Availability and Retrieval in a Modular Blockchain Architecture.” 27th International Conference on Financial Cryptography and Data Security, vol. 13951, Springer Nature, 2023, pp. 36–53, doi:10.1007/978-3-031-47751-5_3. short: S. Cohen, G. Goren, E. Kokoris Kogias, A. Sonnino, A. Spiegelman, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 36–53. conference: end_date: 2023-05-05 location: Bol, Brac, Croatia name: 'FC: Financial Cryptography and Data Security' start_date: 2023-05-01 date_created: 2024-01-18T07:41:12Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-22T13:58:07Z day: '01' department: - _id: ElKo doi: 10.1007/978-3-031-47751-5_3 intvolume: ' 13951' language: - iso: eng main_file_link: - open_access: '1' url: https://fc23.ifca.ai/preproceedings/150.pdf month: '12' oa: 1 oa_version: Submitted Version page: 36-53 project: - _id: 34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f grant_number: F8512 name: Secure Network and Hardware for Efficient Blockchains publication: 27th International Conference on Financial Cryptography and Data Security publication_identifier: eisbn: - '9783031477515' eissn: - 1611-3349 isbn: - '9783031477508' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Proof of availability and retrieval in a modular blockchain architecture type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13951 year: '2023' ... --- _id: '14833' abstract: - lang: eng text: Understanding the factors that have shaped the current distributions and diversity of species is a central and longstanding aim of evolutionary biology. The recent inclusion of genomic data into phylogeographic studies has dramatically improved our understanding in organisms where evolutionary relationships have been challenging to infer. We used whole-genome sequences to study the phylogeography of the intertidal snail Littorina saxatilis, which has successfully colonized and diversified across a broad range of coastal environments in the Northern Hemisphere amid repeated cycles of glaciation. Building on past studies based on short DNA sequences, we used genome-wide data to provide a clearer picture of the relationships among samples spanning most of the species natural range. Our results confirm the trans-Atlantic colonization of North America from Europe, and have allowed us to identify rough locations of glacial refugia and to infer likely routes of colonization within Europe. We also investigated the signals in different datasets to account for the effects of genomic architecture and non-neutral evolution, which provides new insights about diversification of four ecotypes of L. saxatilis (the crab, wave, barnacle, and brackish ecotypes) at different spatial scales. Overall, we provide a much clearer picture of the biogeography of L. saxatilis, providing a foundation for more detailed phylogenomic and demographic studies. acknowledgement: Isobel Eyres, Richard Turney, Graciela Sotelo, Jenny Larson, and Stéphane Loisel helped with the collection and processing of samples. Petri Kemppainen kindly provided samples from Trondheim Fjord. Mark Dunning helped with the development of bioinformatic pipelines. The analysis of genomic data was conducted on the University of Sheffield high-performance computing cluster, ShARC. Funding was provided by the Natural Environment Research Council (NERC) and the European Research Council (ERC). J.G. was funded by a Juntas Industriales y Navales (JIN) project (Ministerio de Ciencia, Innovación y Universidades, code RTI2018-101274-J-I00). article_number: kzad002 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski - first_name: Zuzanna B full_name: Zagrodzka, Zuzanna B last_name: Zagrodzka - first_name: Juan full_name: Galindo, Juan last_name: Galindo - first_name: Mauricio full_name: Montaño-Rendón, Mauricio last_name: Montaño-Rendón - first_name: Rui full_name: Faria, Rui last_name: Faria - first_name: Natalia full_name: Mikhailova, Natalia last_name: Mikhailova - first_name: April M H full_name: Blakeslee, April M H last_name: Blakeslee - first_name: Einar full_name: Arnason, Einar last_name: Arnason - first_name: Thomas full_name: Broquet, Thomas last_name: Broquet - first_name: Hernán E full_name: Morales, Hernán E last_name: Morales - first_name: John W full_name: Grahame, John W last_name: Grahame - first_name: Anja M full_name: Westram, Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Kerstin full_name: Johannesson, Kerstin last_name: Johannesson - first_name: Roger K full_name: Butlin, Roger K last_name: Butlin citation: ama: Stankowski S, Zagrodzka ZB, Galindo J, et al. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2023;2(1). doi:10.1093/evolinnean/kzad002 apa: Stankowski, S., Zagrodzka, Z. B., Galindo, J., Montaño-Rendón, M., Faria, R., Mikhailova, N., … Butlin, R. K. (2023). Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. Oxford University Press. https://doi.org/10.1093/evolinnean/kzad002 chicago: Stankowski, Sean, Zuzanna B Zagrodzka, Juan Galindo, Mauricio Montaño-Rendón, Rui Faria, Natalia Mikhailova, April M H Blakeslee, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society. Oxford University Press, 2023. https://doi.org/10.1093/evolinnean/kzad002. ieee: S. Stankowski et al., “Whole-genome phylogeography of the intertidal snail Littorina saxatilis,” Evolutionary Journal of the Linnean Society, vol. 2, no. 1. Oxford University Press, 2023. ista: Stankowski S, Zagrodzka ZB, Galindo J, Montaño-Rendón M, Faria R, Mikhailova N, Blakeslee AMH, Arnason E, Broquet T, Morales HE, Grahame JW, Westram AM, Johannesson K, Butlin RK. 2023. Whole-genome phylogeography of the intertidal snail Littorina saxatilis. Evolutionary Journal of the Linnean Society. 2(1), kzad002. mla: Stankowski, Sean, et al. “Whole-Genome Phylogeography of the Intertidal Snail Littorina Saxatilis.” Evolutionary Journal of the Linnean Society, vol. 2, no. 1, kzad002, Oxford University Press, 2023, doi:10.1093/evolinnean/kzad002. short: S. Stankowski, Z.B. Zagrodzka, J. Galindo, M. Montaño-Rendón, R. Faria, N. Mikhailova, A.M.H. Blakeslee, E. Arnason, T. Broquet, H.E. Morales, J.W. Grahame, A.M. Westram, K. Johannesson, R.K. Butlin, Evolutionary Journal of the Linnean Society 2 (2023). date_created: 2024-01-18T07:54:10Z date_published: 2023-08-17T00:00:00Z date_updated: 2024-01-23T08:13:43Z day: '17' ddc: - '570' department: - _id: NiBa doi: 10.1093/evolinnean/kzad002 file: - access_level: open_access checksum: ba6f9102d3a9fe6631c4fa398c5e4313 content_type: application/pdf creator: dernst date_created: 2024-01-23T08:10:00Z date_updated: 2024-01-23T08:10:00Z file_id: '14875' file_name: 2023_EvolJourLinneanSociety_Stankowski.pdf file_size: 3408944 relation: main_file success: 1 file_date_updated: 2024-01-23T08:10:00Z has_accepted_license: '1' intvolume: ' 2' issue: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version publication: Evolutionary Journal of the Linnean Society publication_identifier: eissn: - 2752-938X publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Whole-genome phylogeography of the intertidal snail Littorina saxatilis tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2023' ... --- _id: '14831' abstract: - lang: eng text: Catalysis, the acceleration of product formation by a substance that is left unchanged, typically results from multiple elementary processes, including diffusion of the reactants toward the catalyst, chemical steps, and release of the products. While efforts to design catalysts are often focused on accelerating the chemical reaction on the catalyst, catalysis is a global property of the catalytic cycle that involves all processes. These are controlled by both intrinsic parameters such as the composition and shape of the catalyst and extrinsic parameters such as the concentration of the chemical species at play. We examine here the conditions that catalysis imposes on the different steps of a reaction cycle and the respective role of intrinsic and extrinsic parameters of the system on the emergence of catalysis by using an approach based on first-passage times. We illustrate this approach for various decompositions of a catalytic cycle into elementary steps, including non-Markovian decompositions, which are useful when the presence and nature of intermediate states are a priori unknown. Our examples cover different types of reactions and clarify the constraints on elementary steps and the impact of species concentrations on catalysis. acknowledgement: We acknowledge funding from ANR-22-CE06-0037-02. This work has received funding from the European Unions Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement No. 754387. article_processing_charge: No article_type: original author: - first_name: Yann full_name: Sakref, Yann last_name: Sakref - first_name: Maitane full_name: Muñoz Basagoiti, Maitane id: 1a8a7950-82cd-11ed-bd4f-9624c913a607 last_name: Muñoz Basagoiti orcid: 0000-0003-1483-1457 - first_name: Zorana full_name: Zeravcic, Zorana last_name: Zeravcic - first_name: Olivier full_name: Rivoire, Olivier last_name: Rivoire citation: ama: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. 2023;127(51):10950-10959. doi:10.1021/acs.jpcb.3c04627 apa: Sakref, Y., Muñoz Basagoiti, M., Zeravcic, Z., & Rivoire, O. (2023). On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. American Chemical Society. https://doi.org/10.1021/acs.jpcb.3c04627 chicago: Sakref, Yann, Maitane Muñoz Basagoiti, Zorana Zeravcic, and Olivier Rivoire. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” The Journal of Physical Chemistry B. American Chemical Society, 2023. https://doi.org/10.1021/acs.jpcb.3c04627. ieee: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, and O. Rivoire, “On kinetic constraints that catalysis imposes on elementary processes,” The Journal of Physical Chemistry B, vol. 127, no. 51. American Chemical Society, pp. 10950–10959, 2023. ista: Sakref Y, Muñoz Basagoiti M, Zeravcic Z, Rivoire O. 2023. On kinetic constraints that catalysis imposes on elementary processes. The Journal of Physical Chemistry B. 127(51), 10950–10959. mla: Sakref, Yann, et al. “On Kinetic Constraints That Catalysis Imposes on Elementary Processes.” The Journal of Physical Chemistry B, vol. 127, no. 51, American Chemical Society, 2023, pp. 10950–59, doi:10.1021/acs.jpcb.3c04627. short: Y. Sakref, M. Muñoz Basagoiti, Z. Zeravcic, O. Rivoire, The Journal of Physical Chemistry B 127 (2023) 10950–10959. date_created: 2024-01-18T07:47:11Z date_published: 2023-12-13T00:00:00Z date_updated: 2024-01-23T07:58:27Z day: '13' department: - _id: AnSa doi: 10.1021/acs.jpcb.3c04627 external_id: arxiv: - '2312.15940' isi: - '001134068000001' intvolume: ' 127' isi: 1 issue: '51' keyword: - Materials Chemistry - Surfaces - Coatings and Films - Physical and Theoretical Chemistry language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2312.15940 month: '12' oa: 1 oa_version: Preprint page: 10950-10959 publication: The Journal of Physical Chemistry B publication_identifier: eissn: - 1520-5207 issn: - 1520-6106 publication_status: published publisher: American Chemical Society quality_controlled: '1' status: public title: On kinetic constraints that catalysis imposes on elementary processes type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 127 year: '2023' ... --- _id: '14844' abstract: - lang: eng text: 'Many cell functions require a concerted effort from multiple membrane proteins, for example, for signaling, cell division, and endocytosis. One contribution to their successful self-organization stems from the membrane deformations that these proteins induce. While the pairwise interaction potential of two membrane-deforming spheres has recently been measured, membrane-deformation-induced interactions have been predicted to be nonadditive, and hence their collective behavior cannot be deduced from this measurement. We here employ a colloidal model system consisting of adhesive spheres and giant unilamellar vesicles to test these predictions by measuring the interaction potential of the simplest case of three membrane-deforming, spherical particles. We quantify their interactions and arrangements and, for the first time, experimentally confirm and quantify the nonadditive nature of membrane-deformation-induced interactions. We furthermore conclude that there exist two favorable configurations on the membrane: (1) a linear and (2) a triangular arrangement of the three spheres. Using Monte Carlo simulations, we corroborate the experimentally observed energy minima and identify a lowering of the membrane deformation as the cause for the observed configurations. The high symmetry of the preferred arrangements for three particles suggests that arrangements of many membrane-deforming objects might follow simple rules.' acknowledgement: We gratefully acknowledge useful discussions with Casper van der Wel, help by Yogesh Shelke with PAA coverslip preparation, and support by Rachel Doherty with particle functionalization. A.A. and D.J.K. would like to thank Timon Idema and George Dadunashvili for initial attempts to simulate the experimental system. D.J.K. would like to thank the physics department at Leiden University for funding the PhD position of A.A. B.M. and A.Š. acknowledge funding by the European Union’s Horizon 2020 research and innovation programme (ERC starting grant no. 802960). article_processing_charge: No article_type: original author: - first_name: Ali full_name: Azadbakht, Ali last_name: Azadbakht - first_name: Billie full_name: Meadowcroft, Billie id: a4725fd6-932b-11ed-81e2-c098c7f37ae1 last_name: Meadowcroft orcid: 0000-0003-3441-1337 - first_name: Juraj full_name: Majek, Juraj id: 3e6d9473-f38e-11ec-8ae0-c4e05a8aa9e1 last_name: Majek - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Daniela J. full_name: Kraft, Daniela J. last_name: Kraft citation: ama: Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. doi:10.1016/j.bpj.2023.12.020 apa: Azadbakht, A., Meadowcroft, B., Majek, J., Šarić, A., & Kraft, D. J. (n.d.). Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.12.020 chicago: Azadbakht, Ali, Billie Meadowcroft, Juraj Majek, Anđela Šarić, and Daniela J. Kraft. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” Biophysical Journal. Elsevier, n.d. https://doi.org/10.1016/j.bpj.2023.12.020. ieee: A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, and D. J. Kraft, “Nonadditivity in interactions between three membrane-wrapped colloidal spheres,” Biophysical Journal. Elsevier. ista: Azadbakht A, Meadowcroft B, Majek J, Šarić A, Kraft DJ. Nonadditivity in interactions between three membrane-wrapped colloidal spheres. Biophysical Journal. mla: Azadbakht, Ali, et al. “Nonadditivity in Interactions between Three Membrane-Wrapped Colloidal Spheres.” Biophysical Journal, Elsevier, doi:10.1016/j.bpj.2023.12.020. short: A. Azadbakht, B. Meadowcroft, J. Majek, A. Šarić, D.J. Kraft, Biophysical Journal (n.d.). date_created: 2024-01-21T23:00:56Z date_published: 2023-12-29T00:00:00Z date_updated: 2024-01-23T09:26:35Z day: '29' ddc: - '570' department: - _id: AnSa doi: 10.1016/j.bpj.2023.12.020 ec_funded: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1016/j.bpj.2023.12.020 month: '12' oa: 1 oa_version: Published Version project: - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' publication: Biophysical Journal publication_identifier: eissn: - 1542-0086 issn: - 0006-3495 publication_status: inpress publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Nonadditivity in interactions between three membrane-wrapped colloidal spheres tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14861' abstract: - lang: eng text: Cover Page article_number: ' e202304138' article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Mélanie full_name: Berbon, Mélanie last_name: Berbon - first_name: Alicia full_name: Vallet, Alicia last_name: Vallet - first_name: Axelle full_name: Grelard, Axelle last_name: Grelard - first_name: Estelle full_name: Morvan, Estelle last_name: Morvan - first_name: Benjamin full_name: Bardiaux, Benjamin last_name: Bardiaux - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Antoine full_name: Loquet, Antoine last_name: Loquet - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Becker LM, Berbon M, Vallet A, et al. Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues. Vol 62. Wiley; 2023. doi:10.1002/anie.202304138' apa: 'Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues. Angewandte Chemie International Edition (Vol. 62). Wiley. https://doi.org/10.1002/anie.202304138' chicago: 'Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues. Angewandte Chemie International Edition. Vol. 62. Wiley, 2023. https://doi.org/10.1002/anie.202304138.' ieee: 'L. M. Becker et al., Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues, vol. 62, no. 19. Wiley, 2023.' ista: 'Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues, Wiley,p.' mla: 'Becker, Lea Marie, et al. “Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues.” Angewandte Chemie International Edition, vol. 62, no. 19, e202304138, Wiley, 2023, doi:10.1002/anie.202304138.' short: 'L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Cover Picture: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle‐Spinning NMR Spectroscopy of Aromatic Residues, Wiley, 2023.' date_created: 2024-01-22T11:54:34Z date_published: 2023-05-02T00:00:00Z date_updated: 2024-01-23T08:48:14Z day: '02' department: - _id: PaSc doi: 10.1002/anie.202304138 intvolume: ' 62' issue: '19' keyword: - General Chemistry - Catalysis language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1002/anie.202304138 month: '05' oa: 1 oa_version: Published Version publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley related_material: link: - relation: translation url: https://doi.org/10.1002/ange.202304138 record: - id: '12675' relation: other status: public status: public title: 'Cover Picture: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle‐Spinning NMR spectroscopy of aromatic residues' type: other_academic_publication user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2023' ... --- _id: '14849' abstract: - lang: eng text: We establish a precise three-term asymptotic expansion, with an optimal estimate of the error term, for the rightmost eigenvalue of an n×n random matrix with independent identically distributed complex entries as n tends to infinity. All terms in the expansion are universal. acknowledgement: "The second and the fourth author were supported by the ERC Advanced Grant\r\n“RMTBeyond” No. 101020331. The third author was supported by Dr. Max Rössler, the\r\nWalter Haefner Foundation and the ETH Zürich Foundation." article_processing_charge: No article_type: original author: - first_name: Giorgio full_name: Cipolloni, Giorgio id: 42198EFA-F248-11E8-B48F-1D18A9856A87 last_name: Cipolloni orcid: 0000-0002-4901-7992 - first_name: László full_name: Erdös, László id: 4DBD5372-F248-11E8-B48F-1D18A9856A87 last_name: Erdös orcid: 0000-0001-5366-9603 - first_name: Dominik J full_name: Schröder, Dominik J id: 408ED176-F248-11E8-B48F-1D18A9856A87 last_name: Schröder orcid: 0000-0002-2904-1856 - first_name: Yuanyuan full_name: Xu, Yuanyuan last_name: Xu citation: ama: Cipolloni G, Erdös L, Schröder DJ, Xu Y. On the rightmost eigenvalue of non-Hermitian random matrices. The Annals of Probability. 2023;51(6):2192-2242. doi:10.1214/23-aop1643 apa: Cipolloni, G., Erdös, L., Schröder, D. J., & Xu, Y. (2023). On the rightmost eigenvalue of non-Hermitian random matrices. The Annals of Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/23-aop1643 chicago: Cipolloni, Giorgio, László Erdös, Dominik J Schröder, and Yuanyuan Xu. “On the Rightmost Eigenvalue of Non-Hermitian Random Matrices.” The Annals of Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/23-aop1643. ieee: G. Cipolloni, L. Erdös, D. J. Schröder, and Y. Xu, “On the rightmost eigenvalue of non-Hermitian random matrices,” The Annals of Probability, vol. 51, no. 6. Institute of Mathematical Statistics, pp. 2192–2242, 2023. ista: Cipolloni G, Erdös L, Schröder DJ, Xu Y. 2023. On the rightmost eigenvalue of non-Hermitian random matrices. The Annals of Probability. 51(6), 2192–2242. mla: Cipolloni, Giorgio, et al. “On the Rightmost Eigenvalue of Non-Hermitian Random Matrices.” The Annals of Probability, vol. 51, no. 6, Institute of Mathematical Statistics, 2023, pp. 2192–242, doi:10.1214/23-aop1643. short: G. Cipolloni, L. Erdös, D.J. Schröder, Y. Xu, The Annals of Probability 51 (2023) 2192–2242. date_created: 2024-01-22T08:08:41Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-23T10:56:30Z day: '01' department: - _id: LaEr doi: 10.1214/23-aop1643 ec_funded: 1 external_id: arxiv: - '2206.04448' intvolume: ' 51' issue: '6' keyword: - Statistics - Probability and Uncertainty - Statistics and Probability language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2206.04448 month: '11' oa: 1 oa_version: Preprint page: 2192-2242 project: - _id: 62796744-2b32-11ec-9570-940b20777f1d call_identifier: H2020 grant_number: '101020331' name: Random matrices beyond Wigner-Dyson-Mehta publication: The Annals of Probability publication_identifier: issn: - 0091-1798 publication_status: published publisher: Institute of Mathematical Statistics quality_controlled: '1' status: public title: On the rightmost eigenvalue of non-Hermitian random matrices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 51 year: '2023' ... --- _id: '14835' abstract: - lang: ger text: Aromatische Seitenketten sind wichtige Indikatoren für die Plastizität von Proteinen und bilden oft entscheidende Kontakte bei Protein‐Protein‐Wechselwirkungen. Wir untersuchten aromatische Reste in den beiden strukturell homologen cross‐β Amyloidfibrillen HET‐s und HELLF mit Hilfe eines spezifischen Ansatzes zur Isotopenmarkierung und Festkörper NMR mit Drehung am magischen Winkel. Das dynamische Verhalten der aromatischen Reste Phe und Tyr deutet darauf hin, dass der hydrophobe Amyloidkern starr ist und keine Anzeichen von “atmenden Bewegungen” auf einer Zeitskala von Hunderten von Millisekunden zeigt. Aromatische Reste, die exponiert an der Fibrillenoberfläche sitzen, haben zwar eine starre Ringachse, weisen aber Ringflips auf verschiedenen Zeitskalen von Nanosekunden bis Mikrosekunden auf. Unser Ansatz bietet einen direkten Einblick in die Bewegungen des hydrophoben Kerns und ermöglicht eine bessere Bewertung der Konformationsheterogenität, die aus einem NMR‐Strukturensemble einer solchen Cross‐β‐Amyloidstruktur hervorgeht. acknowledgement: Wir danken Albert A. Smith (Leipzig) für aufschlussreiche Diskussionen. Diese Arbeit wurde mit Mitteln des Europäischen Forschungsrats (StG-2012-311318 an P.S.) unterstützt und nutzte die Plattformen des Grenoble Instruct-ERIC Center (ISBG; UMS 3518 CNRS-CEA-UJF-EMBL) im Rahmen der Grenoble Partnership for Structural Biology (PSB) sowie die Einrichtungen und das Fachwissen der Biophysical and Structural Chemistry Platform (BPCS) am IECB, CNRS UAR3033, INSERM US001 und der Universität Bordeaux. article_number: e202219314 article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Mélanie full_name: Berbon, Mélanie last_name: Berbon - first_name: Alicia full_name: Vallet, Alicia last_name: Vallet - first_name: Axelle full_name: Grelard, Axelle last_name: Grelard - first_name: Estelle full_name: Morvan, Estelle last_name: Morvan - first_name: Benjamin full_name: Bardiaux, Benjamin last_name: Bardiaux - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Antoine full_name: Loquet, Antoine last_name: Loquet - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Becker LM, Berbon M, Vallet A, et al. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. 2023;135(19). doi:10.1002/ange.202219314 apa: Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. Wiley. https://doi.org/10.1002/ange.202219314 chicago: Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” Angewandte Chemie. Wiley, 2023. https://doi.org/10.1002/ange.202219314. ieee: L. M. Becker et al., “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten,” Angewandte Chemie, vol. 135, no. 19. Wiley, 2023. ista: Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten. Angewandte Chemie. 135(19), e202219314. mla: Becker, Lea Marie, et al. “Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten.” Angewandte Chemie, vol. 135, no. 19, e202219314, Wiley, 2023, doi:10.1002/ange.202219314. short: L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie 135 (2023). date_created: 2024-01-18T10:01:01Z date_published: 2023-05-02T00:00:00Z date_updated: 2024-01-23T12:23:35Z day: '02' ddc: - '540' department: - _id: PaSc doi: 10.1002/ange.202219314 file: - access_level: open_access checksum: 98e68d370159f7be52a3d7c8a8ee1198 content_type: application/pdf creator: dernst date_created: 2024-01-23T08:57:01Z date_updated: 2024-01-23T08:57:01Z file_id: '14876' file_name: 2023_AngewChem_Becker.pdf file_size: 1004676 relation: main_file success: 1 file_date_updated: 2024-01-23T08:57:01Z has_accepted_license: '1' intvolume: ' 135' issue: '19' keyword: - General Medicine language: - iso: ger month: '05' oa: 1 oa_version: Published Version publication: Angewandte Chemie publication_identifier: eissn: - 1521-3757 issn: - 0044-8249 publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Der starre Kern und die flexible Oberfläche von Amyloidfibrillen – Magic‐Angle‐Spinning NMR Spektroskopie von aromatischen Resten tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 135 year: '2023' ... --- _id: '14847' abstract: - lang: eng text: Understanding the mechanisms of chaperones at the atomic level generally requires producing chaperone–client complexes in vitro. This task comes with significant challenges, because one needs to find conditions in which the client protein is presented to the chaperone in a state that binds and at the same time avoid the pitfalls of protein aggregation that are often inherent to such states. The strategy differs significantly for different client proteins and chaperones, but there are common underlying principles. Here, we discuss these principles and deduce the strategies that can be successfully applied for different chaperone–client complexes. We review successful biochemical strategies applied to making the client protein “binding competent” and illustrate the different strategies with examples of recent biophysical and biochemical studies. alternative_title: - New Developments in NMR article_processing_charge: No author: - first_name: I. full_name: Sučec, I. last_name: Sučec - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Sučec I, Schanda P. Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Hiller S, Liu M, He L, eds. Biophysics of Molecular Chaperones. Vol 29. Royal Society of Chemistry; 2023:136-161. doi:10.1039/bk9781839165986-00136' apa: Sučec, I., & Schanda, P. (2023). Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In S. Hiller, M. Liu, & L. He (Eds.), Biophysics of Molecular Chaperones (Vol. 29, pp. 136–161). Royal Society of Chemistry. https://doi.org/10.1039/bk9781839165986-00136 chicago: Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” In Biophysics of Molecular Chaperones, edited by Sebastian Hiller, Maili Liu, and Lichun He, 29:136–61. Royal Society of Chemistry, 2023. https://doi.org/10.1039/bk9781839165986-00136. ieee: I. Sučec and P. Schanda, “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies,” in Biophysics of Molecular Chaperones, vol. 29, S. Hiller, M. Liu, and L. He, Eds. Royal Society of Chemistry, 2023, pp. 136–161. ista: 'Sučec I, Schanda P. 2023.Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies. In: Biophysics of Molecular Chaperones. New Developments in NMR, vol. 29, 136–161.' mla: Sučec, I., and Paul Schanda. “Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies.” Biophysics of Molecular Chaperones, edited by Sebastian Hiller et al., vol. 29, Royal Society of Chemistry, 2023, pp. 136–61, doi:10.1039/bk9781839165986-00136. short: I. Sučec, P. Schanda, in:, S. Hiller, M. Liu, L. He (Eds.), Biophysics of Molecular Chaperones, Royal Society of Chemistry, 2023, pp. 136–161. date_created: 2024-01-22T08:04:57Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-23T11:50:10Z day: '01' department: - _id: PaSc doi: 10.1039/bk9781839165986-00136 editor: - first_name: Sebastian full_name: Hiller, Sebastian last_name: Hiller - first_name: Maili full_name: Liu, Maili last_name: Liu - first_name: Lichun full_name: He, Lichun last_name: He intvolume: ' 29' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.26434/chemrxiv-2023-rpn28 month: '11' oa: 1 oa_version: Preprint page: 136-161 publication: Biophysics of Molecular Chaperones publication_identifier: eisbn: - '9781839165993' isbn: - '9781839162824' publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' status: public title: Preparing Chaperone–Client Protein Complexes for Biophysical and Structural Studies type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2023' ... --- _id: '14867' abstract: - lang: eng text: Starting with the empty graph on $[n]$, at each round, a set of $K=K(n)$ edges is presented chosen uniformly at random from the ones that have not been presented yet. We are then asked to choose at most one of the presented edges and add it to the current graph. Our goal is to construct a Hamiltonian graph with $(1+o(1))n$ edges within as few rounds as possible. We show that in this process, one can build a Hamiltonian graph of size $(1+o(1))n$ in $(1+o(1))(1+(\log n)/2K) n$ rounds w.h.p. The case $K=1$ implies that w.h.p. one can build a Hamiltonian graph by choosing $(1+o(1))n$ edges in an online fashion as they appear along the first $(0.5+o(1))n\log n$ rounds of the random graph process. This answers a question of Frieze, Krivelevich and Michaeli. Observe that the number of rounds is asymptotically optimal as the first $0.5n\log n$ edges do not span a Hamilton cycle w.h.p. The case $K=\Theta(\log n)$ implies that the Hamiltonicity threshold of the corresponding Achlioptas process is at most $(1+o(1))(1+(\log n)/2K) n$. This matches the $(1-o(1))(1+(\log n)/2K) n$ lower bound due to Krivelevich, Lubetzky and Sudakov and resolves the problem of determining the Hamiltonicity threshold of the Achlioptas process with $K=\Theta(\log n)$. We also show that in the above process one can construct a graph $G$ that spans a matching of size $\lfloor V(G)/2) \rfloor$ and $(0.5+o(1))n$ edges within $(1+o(1))(0.5+(\log n)/2K) n$ rounds w.h.p. Our proof relies on a robust Hamiltonicity property of the strong $4$-core of the binomial random graph which we use as a black-box. This property allows it to absorb paths covering vertices outside the strong $4$-core into a cycle. acknowledgement: "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.\r\n" article_processing_charge: No author: - first_name: Michael full_name: Anastos, Michael id: 0b2a4358-bb35-11ec-b7b9-e3279b593dbb last_name: Anastos citation: ama: 'Anastos M. Constructing Hamilton cycles and perfect matchings efficiently. In: Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications. Masaryk University Press; 2023:36-41. doi:10.5817/cz.muni.eurocomb23-005' apa: 'Anastos, M. (2023). Constructing Hamilton cycles and perfect matchings efficiently. In Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications (pp. 36–41). Prague, Czech Republic: Masaryk University Press. https://doi.org/10.5817/cz.muni.eurocomb23-005' chicago: Anastos, Michael. “Constructing Hamilton Cycles and Perfect Matchings Efficiently.” In Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications, 36–41. Masaryk University Press, 2023. https://doi.org/10.5817/cz.muni.eurocomb23-005. ieee: M. Anastos, “Constructing Hamilton cycles and perfect matchings efficiently,” in Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications, Prague, Czech Republic, 2023, pp. 36–41. ista: 'Anastos M. 2023. Constructing Hamilton cycles and perfect matchings efficiently. Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications. EUROCOMB: European Conference on Combinatorics, Graph Theory and Applications, 36–41.' mla: Anastos, Michael. “Constructing Hamilton Cycles and Perfect Matchings Efficiently.” Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications, Masaryk University Press, 2023, pp. 36–41, doi:10.5817/cz.muni.eurocomb23-005. short: M. Anastos, in:, Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications, Masaryk University Press, 2023, pp. 36–41. conference: end_date: 2023-09-01 location: Prague, Czech Republic name: 'EUROCOMB: European Conference on Combinatorics, Graph Theory and Applications' start_date: 2023-08-28 date_created: 2024-01-22T12:20:15Z date_published: 2023-09-01T00:00:00Z date_updated: 2024-01-24T09:38:44Z day: '01' ddc: - '510' department: - _id: MaKw doi: 10.5817/cz.muni.eurocomb23-005 ec_funded: 1 external_id: arxiv: - '2209.09860' file: - access_level: open_access checksum: fb1d9a1e7389d90ec0e5e76934373cf8 content_type: application/pdf creator: dernst date_created: 2024-01-24T09:34:43Z date_updated: 2024-01-24T09:34:43Z file_id: '14881' file_name: 2023_Eurocomb_Anastos.pdf file_size: 464230 relation: main_file success: 1 file_date_updated: 2024-01-24T09:34:43Z has_accepted_license: '1' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 36-41 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: Proceedings of the 12th European Conference on Combinatorics, Graph Theory and Applications publication_identifier: eissn: - 2788-3116 publication_status: published publisher: Masaryk University Press quality_controlled: '1' status: public title: Constructing Hamilton cycles and perfect matchings efficiently tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14864' acknowledgement: This project has received funding from the European Research Council (ERC) under the European Union’s Starting Grant (No. 949120). article_number: '6166' article_processing_charge: No author: - first_name: Andrea full_name: Stöllner, Andrea id: 4bdcf7f6-eb97-11eb-a6c2-9981bbdc3bed last_name: Stöllner orcid: 0000-0002-0464-8440 - first_name: Isaac C full_name: Lenton, Isaac C id: a550210f-223c-11ec-8182-e2d45e817efb last_name: Lenton orcid: 0000-0002-5010-6984 - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Scott R full_name: Waitukaitis, Scott R id: 3A1FFC16-F248-11E8-B48F-1D18A9856A87 last_name: Waitukaitis orcid: 0000-0002-2299-3176 citation: ama: 'Stöllner A, Lenton IC, Muller CJ, Waitukaitis SR. Measuring spontaneous charging of single aerosol particles. In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-6166' apa: 'Stöllner, A., Lenton, I. C., Muller, C. J., & Waitukaitis, S. R. (2023). Measuring spontaneous charging of single aerosol particles. In EGU General Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-6166' chicago: Stöllner, Andrea, Isaac C Lenton, Caroline J Muller, and Scott R Waitukaitis. “Measuring Spontaneous Charging of Single Aerosol Particles.” In EGU General Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-6166. ieee: A. Stöllner, I. C. Lenton, C. J. Muller, and S. R. Waitukaitis, “Measuring spontaneous charging of single aerosol particles,” in EGU General Assembly 2023, Vienna, Austria & Virtual, 2023. ista: Stöllner A, Lenton IC, Muller CJ, Waitukaitis SR. 2023. Measuring spontaneous charging of single aerosol particles. EGU General Assembly 2023. EGU General Assembly, 6166. mla: Stöllner, Andrea, et al. “Measuring Spontaneous Charging of Single Aerosol Particles.” EGU General Assembly 2023, 6166, European Geosciences Union, 2023, doi:10.5194/egusphere-egu23-6166. short: A. Stöllner, I.C. Lenton, C.J. Muller, S.R. Waitukaitis, in:, EGU General Assembly 2023, European Geosciences Union, 2023. conference: end_date: 2023-04-28 location: Vienna, Austria & Virtual name: EGU General Assembly start_date: 2023-04-23 date_created: 2024-01-22T12:09:07Z date_published: 2023-04-23T00:00:00Z date_updated: 2024-01-24T11:21:42Z day: '23' ddc: - '530' department: - _id: CaMu - _id: ScWa doi: 10.5194/egusphere-egu23-6166 ec_funded: 1 file: - access_level: open_access checksum: 8d6ddbb359e584b156f991f00196d86b content_type: application/pdf creator: dernst date_created: 2024-01-23T13:00:26Z date_updated: 2024-01-23T13:00:26Z file_id: '14880' file_name: 2023_EGU_Stoellner.pdf file_size: 419736 relation: main_file success: 1 file_date_updated: 2024-01-23T13:00:26Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version project: - _id: 0aa60e99-070f-11eb-9043-a6de6bdc3afa call_identifier: H2020 grant_number: '949120' name: 'Tribocharge: a multi-scale approach to an enduring problem in physics' publication: EGU General Assembly 2023 publication_status: published publisher: European Geosciences Union status: public title: Measuring spontaneous charging of single aerosol particles tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14862' article_number: ckad160.597 article_processing_charge: No author: - first_name: Simon full_name: Rella, Simon id: B4765ACA-AA38-11E9-AC9A-0930E6697425 last_name: Rella - first_name: Y full_name: Kulikova, Y last_name: Kulikova - first_name: Aygul full_name: Minnegalieva, Aygul id: 87DF77F0-1D9A-11EA-B6AE-CE443DDC885E last_name: Minnegalieva - first_name: Fyodor full_name: Kondrashov, Fyodor id: 44FDEF62-F248-11E8-B48F-1D18A9856A87 last_name: Kondrashov orcid: 0000-0001-8243-4694 citation: ama: 'Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. Complex vaccination strategies prevent the emergence of vaccine resistance. In: European Journal of Public Health. Vol 33. Oxford University Press; 2023. doi:10.1093/eurpub/ckad160.597' apa: Rella, S., Kulikova, Y., Minnegalieva, A., & Kondrashov, F. (2023). Complex vaccination strategies prevent the emergence of vaccine resistance. In European Journal of Public Health (Vol. 33). Oxford University Press. https://doi.org/10.1093/eurpub/ckad160.597 chicago: Rella, Simon, Y Kulikova, Aygul Minnegalieva, and Fyodor Kondrashov. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” In European Journal of Public Health, Vol. 33. Oxford University Press, 2023. https://doi.org/10.1093/eurpub/ckad160.597. ieee: S. Rella, Y. Kulikova, A. Minnegalieva, and F. Kondrashov, “Complex vaccination strategies prevent the emergence of vaccine resistance,” in European Journal of Public Health, 2023, vol. 33, no. Supplement_2. ista: Rella S, Kulikova Y, Minnegalieva A, Kondrashov F. 2023. Complex vaccination strategies prevent the emergence of vaccine resistance. European Journal of Public Health. vol. 33, ckad160.597. mla: Rella, Simon, et al. “Complex Vaccination Strategies Prevent the Emergence of Vaccine Resistance.” European Journal of Public Health, vol. 33, no. Supplement_2, ckad160.597, Oxford University Press, 2023, doi:10.1093/eurpub/ckad160.597. short: S. Rella, Y. Kulikova, A. Minnegalieva, F. Kondrashov, in:, European Journal of Public Health, Oxford University Press, 2023. date_created: 2024-01-22T12:02:28Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-24T11:16:09Z day: '01' ddc: - '570' department: - _id: GaTk doi: 10.1093/eurpub/ckad160.597 file: - access_level: open_access checksum: 98706755bb4cc5d553818ade7660a7d2 content_type: application/pdf creator: dernst date_created: 2024-01-24T11:12:33Z date_updated: 2024-01-24T11:12:33Z file_id: '14882' file_name: 2023_EurJourPublicHealth_Rella.pdf file_size: 71057 relation: main_file success: 1 file_date_updated: 2024-01-24T11:12:33Z has_accepted_license: '1' intvolume: ' 33' issue: Supplement_2 keyword: - Public Health - Environmental and Occupational Health language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: European Journal of Public Health publication_identifier: eissn: - 1464-360X issn: - 1101-1262 publication_status: published publisher: Oxford University Press quality_controlled: '1' status: public title: Complex vaccination strategies prevent the emergence of vaccine resistance tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 33 year: '2023' ... --- _id: '14863' article_number: EGU23-6157 article_processing_charge: No author: - first_name: Andrea full_name: Polesello, Andrea id: 74c777f4-32da-11ee-b498-874db0835561 last_name: Polesello - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Claudia full_name: Pasquero, Claudia last_name: Pasquero - first_name: Agostino N. full_name: Meroni, Agostino N. last_name: Meroni citation: ama: 'Polesello A, Muller CJ, Pasquero C, Meroni AN. Intensification mechanisms of tropical cyclones. In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-6157' apa: 'Polesello, A., Muller, C. J., Pasquero, C., & Meroni, A. N. (2023). Intensification mechanisms of tropical cyclones. In EGU General Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-6157' chicago: Polesello, Andrea, Caroline J Muller, Claudia Pasquero, and Agostino N. Meroni. “Intensification Mechanisms of Tropical Cyclones.” In EGU General Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-6157. ieee: A. Polesello, C. J. Muller, C. Pasquero, and A. N. Meroni, “Intensification mechanisms of tropical cyclones,” in EGU General Assembly 2023, Vienna, Austria & Virtual, 2023. ista: Polesello A, Muller CJ, Pasquero C, Meroni AN. 2023. Intensification mechanisms of tropical cyclones. EGU General Assembly 2023. EGU General Assembly, EGU23-6157. mla: Polesello, Andrea, et al. “Intensification Mechanisms of Tropical Cyclones.” EGU General Assembly 2023, EGU23-6157, European Geosciences Union, 2023, doi:10.5194/egusphere-egu23-6157. short: A. Polesello, C.J. Muller, C. Pasquero, A.N. Meroni, in:, EGU General Assembly 2023, European Geosciences Union, 2023. conference: end_date: 2023-04-28 location: Vienna, Austria & Virtual name: EGU General Assembly start_date: 2023-04-23 date_created: 2024-01-22T12:08:12Z date_published: 2023-04-13T00:00:00Z date_updated: 2024-01-24T11:25:07Z day: '13' ddc: - '550' department: - _id: CaMu - _id: GradSch doi: 10.5194/egusphere-egu23-6157 file: - access_level: open_access checksum: 8cb88c1bc80ccee328478a62064d98f7 content_type: application/pdf creator: dernst date_created: 2024-01-24T11:19:54Z date_updated: 2024-01-24T11:19:54Z file_id: '14883' file_name: 2023_EGU_Polesello.pdf file_size: 296769 relation: main_file success: 1 file_date_updated: 2024-01-24T11:19:54Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: EGU General Assembly 2023 publication_status: published publisher: European Geosciences Union status: public title: Intensification mechanisms of tropical cyclones tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14732' abstract: - lang: eng text: 'Fragmented landscapes pose a significant threat to the persistence of species as they are highly susceptible to heightened risk of extinction due to the combined effects of genetic and demographic factors such as genetic drift and demographic stochasticity. This paper explores the intricate interplay between genetic load and extinction risk within metapopulations with a focus on understanding the impact of eco-evolutionary feedback mechanisms. We distinguish between two models of selection: soft selection, characterised by subpopulations maintaining carrying capacity despite load, and hard selection, where load can significantly affect population size. Within the soft selection framework, we investigate the impact of gene flow on genetic load at a single locus, while also considering the effect of selection strength and dominance coefficient. We subsequently build on this to examine how gene flow influences both population size and load under hard selection as well as identify critical thresholds for metapopulation persistence. Our analysis employs the diffusion, semi-deterministic and effective migration approximations. Our findings reveal that under soft selection, even modest levels of migration can significantly alleviate the burden of load. In sharp contrast, with hard selection, a much higher degree of gene flow is required to mitigate load and prevent the collapse of the metapopulation. Overall, this study sheds light into the crucial role migration plays in shaping the dynamics of genetic load and extinction risk in fragmented landscapes, offering valuable insights for conservation strategies and the preservation of diversity in a changing world.' article_processing_charge: No author: - first_name: Oluwafunmilola O full_name: Olusanya, Oluwafunmilola O id: 41AD96DC-F248-11E8-B48F-1D18A9856A87 last_name: Olusanya orcid: 0000-0003-1971-8314 - first_name: Kseniia full_name: Khudiakova, Kseniia id: 4E6DC800-AE37-11E9-AC72-31CAE5697425 last_name: Khudiakova orcid: 0000-0002-6246-1465 - first_name: Himani full_name: Sachdeva, Himani id: 42377A0A-F248-11E8-B48F-1D18A9856A87 last_name: Sachdeva citation: ama: Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. doi:10.1101/2023.12.02.569702 apa: Olusanya, O. O., Khudiakova, K., & Sachdeva, H. (n.d.). Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv. https://doi.org/10.1101/2023.12.02.569702 chicago: Olusanya, Oluwafunmilola O, Kseniia Khudiakova, and Himani Sachdeva. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, n.d. https://doi.org/10.1101/2023.12.02.569702. ieee: O. O. Olusanya, K. Khudiakova, and H. Sachdeva, “Genetic load, eco-evolutionary feedback and extinction in a metapopulation,” bioRxiv. . ista: Olusanya OO, Khudiakova K, Sachdeva H. Genetic load, eco-evolutionary feedback and extinction in a metapopulation. bioRxiv, 10.1101/2023.12.02.569702. mla: Olusanya, Oluwafunmilola O., et al. “Genetic Load, Eco-Evolutionary Feedback and Extinction in a Metapopulation.” BioRxiv, doi:10.1101/2023.12.02.569702. short: O.O. Olusanya, K. Khudiakova, H. Sachdeva, BioRxiv (n.d.). date_created: 2024-01-04T09:35:54Z date_published: 2023-12-04T00:00:00Z date_updated: 2024-01-26T12:00:53Z day: '04' department: - _id: NiBa - _id: JaMa doi: 10.1101/2023.12.02.569702 language: - iso: eng main_file_link: - open_access: '1' url: https://www.biorxiv.org/content/10.1101/2023.12.02.569702v1 month: '12' oa: 1 oa_version: Preprint project: - _id: c08d3278-5a5b-11eb-8a69-fdb09b55f4b8 grant_number: P32896 name: Causes and consequences of population fragmentation - _id: 34d33d68-11ca-11ed-8bc3-ec13763c0ca8 grant_number: '26293' name: The impact of deleterious mutations on small populations - _id: 34c872fe-11ca-11ed-8bc3-8534b82131e6 grant_number: '26380' name: Polygenic Adaptation in a Metapopulation publication: bioRxiv publication_status: submitted related_material: record: - id: '14711' relation: dissertation_contains status: public status: public title: Genetic load, eco-evolutionary feedback and extinction in a metapopulation tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '13049' abstract: - lang: eng text: "We propose a computational design approach for covering a surface with individually addressable RGB LEDs, effectively forming a low-resolution surface screen. To achieve a low-cost and scalable approach, we propose creating designs from flat PCB panels bent in-place along the surface of a 3D printed core. Working with standard rigid PCBs enables the use of\r\nestablished PCB manufacturing services, allowing the fabrication of designs with several hundred LEDs. \r\nOur approach optimizes the PCB geometry for folding, and then jointly optimizes the LED packing, circuit and routing, solving a challenging layout problem under strict manufacturing requirements. Unlike paper, PCBs cannot bend beyond a certain point without breaking. Therefore, we introduce parametric cut patterns acting as hinges, designed to allow bending while remaining compact. To tackle the joint optimization of placement, circuit and routing, we propose a specialized algorithm that splits the global problem into one sub-problem per triangle, which is then individually solved.\r\nOur technique generates PCB blueprints in a completely automated way. After being fabricated by a PCB manufacturing service, the boards are bent and glued by the user onto the 3D printed support. We demonstrate our technique on a range of physical models and virtual examples, creating intricate surface light patterns from hundreds of LEDs." acknowledged_ssus: - _id: M-Shop acknowledgement: We thank the reviewers for the valuable feedback. We also thank the Miba Machine Shop at ISTA, PCBWay, and PragoBoard for helping us with fabrication and assembly. This project was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation program (Grant Agreement No. 715767 – MATERIALIZABLE). article_number: '142' article_processing_charge: No article_type: original author: - first_name: Marco full_name: Freire, Marco last_name: Freire - first_name: Manas full_name: Bhargava, Manas id: FF8FA64C-AA6A-11E9-99AD-50D4E5697425 last_name: Bhargava orcid: 0009-0007-6138-6890 - first_name: Camille full_name: Schreck, Camille id: 2B14B676-F248-11E8-B48F-1D18A9856A87 last_name: Schreck - first_name: Pierre-Alexandre full_name: Hugron, Pierre-Alexandre last_name: Hugron - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Sylvain full_name: Lefebvre, Sylvain last_name: Lefebvre citation: ama: 'Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. 2023;42(4). doi:10.1145/3592411' apa: 'Freire, M., Bhargava, M., Schreck, C., Hugron, P.-A., Bickel, B., & Lefebvre, S. (2023). PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3592411' chicago: 'Freire, Marco, Manas Bhargava, Camille Schreck, Pierre-Alexandre Hugron, Bernd Bickel, and Sylvain Lefebvre. “PCBend: Light up Your 3D Shapes with Foldable Circuit Boards.” Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3592411.' ieee: 'M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, and S. Lefebvre, “PCBend: Light up your 3D shapes with foldable circuit boards,” Transactions on Graphics, vol. 42, no. 4. Association for Computing Machinery, 2023.' ista: 'Freire M, Bhargava M, Schreck C, Hugron P-A, Bickel B, Lefebvre S. 2023. PCBend: Light up your 3D shapes with foldable circuit boards. Transactions on Graphics. 42(4), 142.' mla: 'Freire, Marco, et al. “PCBend: Light up Your 3D Shapes with Foldable Circuit Boards.” Transactions on Graphics, vol. 42, no. 4, 142, Association for Computing Machinery, 2023, doi:10.1145/3592411.' short: M. Freire, M. Bhargava, C. Schreck, P.-A. Hugron, B. Bickel, S. Lefebvre, Transactions on Graphics 42 (2023). conference: end_date: 2023-08-10 location: Los Angeles, CA, United States name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2023-08-06 date_created: 2023-05-22T08:37:04Z date_published: 2023-07-26T00:00:00Z date_updated: 2024-01-29T10:30:49Z day: '26' ddc: - '006' department: - _id: GradSch - _id: BeBi doi: 10.1145/3592411 ec_funded: 1 external_id: isi: - '001044671300108' file: - access_level: open_access checksum: a0b0ba3b36f43a94388e8824613d812a content_type: application/pdf creator: dernst date_created: 2023-06-19T11:02:23Z date_updated: 2023-06-19T11:02:23Z file_id: '13156' file_name: 2023_ACMToG_Freire.pdf file_size: 78940724 relation: main_file success: 1 - access_level: open_access checksum: b9206bbb67af82df49b7e7cdbde3410c content_type: application/pdf creator: dernst date_created: 2023-06-20T12:20:51Z date_updated: 2023-06-20T12:20:51Z file_id: '13157' file_name: 2023_ACMToG_SuppMaterial_Freire.pdf file_size: 34345905 relation: main_file success: 1 file_date_updated: 2023-06-20T12:20:51Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '4' keyword: - PCB design and layout - Mesh geometry models language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: 24F9549A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715767' name: 'MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling' publication: Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: 'PCBend: Light up your 3D shapes with foldable circuit boards' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2023' ... --- _id: '13212' abstract: - lang: eng text: Auxin is the major plant hormone regulating growth and development (Friml, 2022). Forward genetic approaches in the model plant Arabidopsis thaliana have identified major components of auxin signalling and established the canonical mechanism mediating transcriptional and thus developmental reprogramming. In this textbook view, TRANSPORT INHIBITOR RESPONSE 1 (TIR1)/AUXIN-SIGNALING F-BOX (AFBs) are auxin receptors, which act as F-box subunits determining the substrate specificity of the Skp1-Cullin1-F box protein (SCF) type E3 ubiquitin ligase complex. Auxin acts as a “molecular glue” increasing the affinity between TIR1/AFBs and the Aux/IAA repressors. Subsequently, Aux/IAAs are ubiquitinated and degraded, thus releasing auxin transcription factors from their repression making them free to mediate transcription of auxin response genes (Yu et al., 2022). Nonetheless, accumulating evidence suggests existence of rapid, non-transcriptional responses downstream of TIR1/AFBs such as auxin-induced cytosolic calcium (Ca2+) transients, plasma membrane depolarization and apoplast alkalinisation, all converging on the process of root growth inhibition and root gravitropism (Li et al., 2022). Particularly, these rapid responses are mostly contributed by predominantly cytosolic AFB1, while the long-term growth responses are mediated by mainly nuclear TIR1 and AFB2-AFB5 (Li et al., 2021; Prigge et al., 2020; Serre et al., 2021). How AFB1 conducts auxin-triggered rapid responses and how it is different from TIR1 and AFB2-AFB5 remains elusive. Here, we compare the roles of TIR1 and AFB1 in transcriptional and rapid responses by modulating their subcellular localization in Arabidopsis and by testing their ability to mediate transcriptional responses when part of the minimal auxin circuit reconstituted in yeast. acknowledged_ssus: - _id: LifeSc - _id: Bio acknowledgement: We thank all the authors for sharing the published materials. This research was supported by the Lab Support Facility and the Imaging and Optics Facility of ISTA. We thank Lukáš Fiedler (ISTA) for critical reading of the manuscript. This project was funded by the European Research Council Advanced Grant (ETAP-742985). article_processing_charge: Yes (via OA deal) article_type: letter_note author: - first_name: Huihuang full_name: Chen, Huihuang id: 83c96512-15b2-11ec-abd3-b7eede36184f last_name: Chen - first_name: Lanxin full_name: Li, Lanxin id: 367EF8FA-F248-11E8-B48F-1D18A9856A87 last_name: Li orcid: 0000-0002-5607-272X - first_name: Minxia full_name: Zou, Minxia id: 5c243f41-03f3-11ec-841c-96faf48a7ef9 last_name: Zou - first_name: Linlin full_name: Qi, Linlin id: 44B04502-A9ED-11E9-B6FC-583AE6697425 last_name: Qi orcid: 0000-0001-5187-8401 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Chen H, Li L, Zou M, Qi L, Friml J. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 2023;16(7):1117-1119. doi:10.1016/j.molp.2023.06.007 apa: Chen, H., Li, L., Zou, M., Qi, L., & Friml, J. (2023). Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. Elsevier . https://doi.org/10.1016/j.molp.2023.06.007 chicago: Chen, Huihuang, Lanxin Li, Minxia Zou, Linlin Qi, and Jiří Friml. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant. Elsevier , 2023. https://doi.org/10.1016/j.molp.2023.06.007. ieee: H. Chen, L. Li, M. Zou, L. Qi, and J. Friml, “Distinct functions of TIR1 and AFB1 receptors in auxin signalling.,” Molecular Plant, vol. 16, no. 7. Elsevier , pp. 1117–1119, 2023. ista: Chen H, Li L, Zou M, Qi L, Friml J. 2023. Distinct functions of TIR1 and AFB1 receptors in auxin signalling. Molecular Plant. 16(7), 1117–1119. mla: Chen, Huihuang, et al. “Distinct Functions of TIR1 and AFB1 Receptors in Auxin Signalling.” Molecular Plant, vol. 16, no. 7, Elsevier , 2023, pp. 1117–19, doi:10.1016/j.molp.2023.06.007. short: H. Chen, L. Li, M. Zou, L. Qi, J. Friml, Molecular Plant 16 (2023) 1117–1119. date_created: 2023-07-12T07:32:46Z date_published: 2023-07-01T00:00:00Z date_updated: 2024-01-29T10:38:57Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.molp.2023.06.007 ec_funded: 1 external_id: isi: - '001044410900001' pmid: - '37393433' file: - access_level: open_access checksum: 6012b7e4a2f680ee6c1f84001e2b945f content_type: application/pdf creator: dernst date_created: 2024-01-29T10:37:05Z date_updated: 2024-01-29T10:37:05Z file_id: '14894' file_name: 2023_MolecularPlant_Chen.pdf file_size: 1000871 relation: main_file success: 1 file_date_updated: 2024-01-29T10:37:05Z has_accepted_license: '1' intvolume: ' 16' isi: 1 issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1117-1119 pmid: 1 project: - _id: 261099A6-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '742985' name: Tracing Evolution of Auxin Transport and Polarity in Plants publication: Molecular Plant publication_identifier: eissn: - 1674-2052 issn: - 1752-9867 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' scopus_import: '1' status: public title: Distinct functions of TIR1 and AFB1 receptors in auxin signalling. tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 16 year: '2023' ... --- _id: '12984' abstract: - lang: eng text: Tattoos are a highly popular medium, with both artistic and medical applications. Although the mechanical process of tattoo application has evolved historically, the results are reliant on the artisanal skill of the artist. This can be especially challenging for some skin tones, or in cases where artists lack experience. We provide the first systematic overview of tattooing as a computational fabrication technique. We built an automated tattooing rig and a recipe for the creation of silicone sheets mimicking realistic skin tones, which allowed us to create an accurate model predicting tattoo appearance. This enables several exciting applications including tattoo previewing, color retargeting, novel ink spectra optimization, color-accurate prosthetics, and more. acknowledged_ssus: - _id: M-Shop acknowledgement: We thank Todor Asenov and the Miba Machine Shop for their help in assembling the tattoo machine and manufacturing the substrates. We thank Geysler Rodrigues for the insightful discussions on tattooing practices from a professional artist's perspective. We thank Maria Fernanda Portugal for sharing a doctor's perspective on medical applications of tattoos. This work is graciously supported by the FWF Lise Meitner (Grant M 3319). article_number: '67' article_processing_charge: No article_type: original author: - first_name: Michael full_name: Piovarci, Michael id: 62E473F4-5C99-11EA-A40E-AF823DDC885E last_name: Piovarci orcid: 0000-0002-5062-4474 - first_name: Alexandre full_name: Chapiro, Alexandre last_name: Chapiro - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 citation: ama: 'Piovarci M, Chapiro A, Bickel B. Skin-Screen: A computational fabrication framework for color tattoos. Transactions on Graphics. 2023;42(4). doi:10.1145/3592432' apa: 'Piovarci, M., Chapiro, A., & Bickel, B. (2023). Skin-Screen: A computational fabrication framework for color tattoos. Transactions on Graphics. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3592432' chicago: 'Piovarci, Michael, Alexandre Chapiro, and Bernd Bickel. “Skin-Screen: A Computational Fabrication Framework for Color Tattoos.” Transactions on Graphics. Association for Computing Machinery, 2023. https://doi.org/10.1145/3592432.' ieee: 'M. Piovarci, A. Chapiro, and B. Bickel, “Skin-Screen: A computational fabrication framework for color tattoos,” Transactions on Graphics, vol. 42, no. 4. Association for Computing Machinery, 2023.' ista: 'Piovarci M, Chapiro A, Bickel B. 2023. Skin-Screen: A computational fabrication framework for color tattoos. Transactions on Graphics. 42(4), 67.' mla: 'Piovarci, Michael, et al. “Skin-Screen: A Computational Fabrication Framework for Color Tattoos.” Transactions on Graphics, vol. 42, no. 4, 67, Association for Computing Machinery, 2023, doi:10.1145/3592432.' short: M. Piovarci, A. Chapiro, B. Bickel, Transactions on Graphics 42 (2023). conference: end_date: 2023-08-10 location: Los Angeles, CA, United States name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2023-08-06 date_created: 2023-05-16T09:39:14Z date_published: 2023-07-26T00:00:00Z date_updated: 2024-01-29T10:27:23Z day: '26' ddc: - '004' department: - _id: BeBi doi: 10.1145/3592432 external_id: isi: - '001044671300033' file: - access_level: open_access checksum: 5f0a6867689e025a661bd0b4fd90b821 content_type: application/pdf creator: mpiovarc date_created: 2023-05-16T09:38:25Z date_updated: 2023-05-16T09:38:25Z file_id: '12985' file_name: Piovarci2023.pdf file_size: 30817343 relation: main_file success: 1 file_date_updated: 2023-05-16T09:38:25Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '4' keyword: - appearance - modeling - reproduction - tattoo - skin color - gamut mapping - ink-optimization - prosthetic language: - iso: eng month: '07' oa: 1 oa_version: Submitted Version project: - _id: eb901961-77a9-11ec-83b8-f5c883a62027 grant_number: M03319 name: Perception-Aware Appearance Fabrication publication: Transactions on Graphics publication_identifier: eissn: - 1557-7368 issn: - 0730-0301 publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: 'Skin-Screen: A computational fabrication framework for color tattoos' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2023' ... --- _id: '14892' abstract: - lang: eng text: 'Code and data necessary to reproduce the simulations and data analyses reported in our manuscript: Tomé, D.F., Zhang, Y., Aida, T., Mosto, O., Lu, Y., Chen, M., Sadeh, S., Roy, D. S., Clopath, C. Dynamic and selective engrams emerge with memory consolidation. 2023.' article_processing_charge: No author: - first_name: Douglas full_name: Feitosa Tomé, Douglas id: 0eed2d40-3d48-11ec-8d38-f789cc2e40b2 last_name: Feitosa Tomé citation: ama: 'Feitosa Tomé D. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation. 2023. doi:10.5281/ZENODO.10251087' apa: 'Feitosa Tomé, D. (2023). douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation. Zenodo. https://doi.org/10.5281/ZENODO.10251087' chicago: 'Feitosa Tomé, Douglas. “Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.10251087.' ieee: 'D. Feitosa Tomé, “douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation.” Zenodo, 2023.' ista: 'Feitosa Tomé D. 2023. douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation, Zenodo, 10.5281/ZENODO.10251087.' mla: 'Feitosa Tomé, Douglas. Douglastome/Dynamic-Engrams: Dynamic and Selective Engrams Emerge with Memory Consolidation. Zenodo, 2023, doi:10.5281/ZENODO.10251087.' short: D. Feitosa Tomé, (2023). date_created: 2024-01-29T09:06:43Z date_published: 2023-12-02T00:00:00Z date_updated: 2024-01-29T09:22:01Z day: '02' ddc: - '570' department: - _id: TiVo doi: 10.5281/ZENODO.10251087 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.10251087 month: '12' oa: 1 oa_version: None publisher: Zenodo related_material: record: - id: '14887' relation: used_in_publication status: public status: public title: 'douglastome/dynamic-engrams: Dynamic and selective engrams emerge with memory consolidation' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14032' abstract: - lang: eng text: Arrays of Josephson junctions are governed by a competition between superconductivity and repulsive Coulomb interactions, and are expected to exhibit diverging low-temperature resistance when interactions exceed a critical level. Here we report a study of the transport and microwave response of Josephson arrays with interactions exceeding this level. Contrary to expectations, we observe that the array resistance drops dramatically as the temperature is decreased—reminiscent of superconducting behaviour—and then saturates at low temperature. Applying a magnetic field, we eventually observe a transition to a highly resistive regime. These observations can be understood within a theoretical picture that accounts for the effect of thermal fluctuations on the insulating phase. On the basis of the agreement between experiment and theory, we suggest that apparent superconductivity in our Josephson arrays arises from melting the zero-temperature insulator. acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: We thank D. Haviland, J. Pekola, C. Ciuti, A. Bubis and A. Shnirman for helpful feedback on the paper. This research was supported by the Scientific Service Units of IST Austria through resources provided by the MIBA Machine Shop and the Nanofabrication Facility. Work supported by the Austrian FWF grant P33692-N (S.M., J.S. and A.P.H.), the European Union’s Horizon 2020 Research and Innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411 (J.S.) and a NOMIS foundation research grant (J.M.F. and A.P.H.). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Soham full_name: Mukhopadhyay, Soham id: FDE60288-A89D-11E9-947F-1AF6E5697425 last_name: Mukhopadhyay - first_name: Jorden L full_name: Senior, Jorden L id: 5479D234-2D30-11EA-89CC-40953DDC885E last_name: Senior orcid: 0000-0002-0672-9295 - first_name: Jaime full_name: Saez Mollejo, Jaime id: e0390f72-f6e0-11ea-865d-862393336714 last_name: Saez Mollejo - first_name: Denise full_name: Puglia, Denise id: 4D495994-AE37-11E9-AC72-31CAE5697425 last_name: Puglia orcid: 0000-0003-1144-2763 - first_name: Martin full_name: Zemlicka, Martin id: 2DCF8DE6-F248-11E8-B48F-1D18A9856A87 last_name: Zemlicka - first_name: Johannes M full_name: Fink, Johannes M id: 4B591CBA-F248-11E8-B48F-1D18A9856A87 last_name: Fink orcid: 0000-0001-8112-028X - first_name: Andrew P full_name: Higginbotham, Andrew P id: 4AD6785A-F248-11E8-B48F-1D18A9856A87 last_name: Higginbotham orcid: 0000-0003-2607-2363 citation: ama: Mukhopadhyay S, Senior JL, Saez Mollejo J, et al. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 2023;19:1630-1635. doi:10.1038/s41567-023-02161-w apa: Mukhopadhyay, S., Senior, J. L., Saez Mollejo, J., Puglia, D., Zemlicka, M., Fink, J. M., & Higginbotham, A. P. (2023). Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02161-w chicago: Mukhopadhyay, Soham, Jorden L Senior, Jaime Saez Mollejo, Denise Puglia, Martin Zemlicka, Johannes M Fink, and Andrew P Higginbotham. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02161-w. ieee: S. Mukhopadhyay et al., “Superconductivity from a melted insulator in Josephson junction arrays,” Nature Physics, vol. 19. Springer Nature, pp. 1630–1635, 2023. ista: Mukhopadhyay S, Senior JL, Saez Mollejo J, Puglia D, Zemlicka M, Fink JM, Higginbotham AP. 2023. Superconductivity from a melted insulator in Josephson junction arrays. Nature Physics. 19, 1630–1635. mla: Mukhopadhyay, Soham, et al. “Superconductivity from a Melted Insulator in Josephson Junction Arrays.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1630–35, doi:10.1038/s41567-023-02161-w. short: S. Mukhopadhyay, J.L. Senior, J. Saez Mollejo, D. Puglia, M. Zemlicka, J.M. Fink, A.P. Higginbotham, Nature Physics 19 (2023) 1630–1635. date_created: 2023-08-11T07:41:17Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-29T11:27:49Z day: '01' ddc: - '530' department: - _id: GradSch - _id: AnHi - _id: JoFi doi: 10.1038/s41567-023-02161-w ec_funded: 1 external_id: isi: - '001054563800006' file: - access_level: open_access checksum: 1fc86d71bfbf836e221c1e925343adc5 content_type: application/pdf creator: dernst date_created: 2024-01-29T11:25:38Z date_updated: 2024-01-29T11:25:38Z file_id: '14899' file_name: 2023_NaturePhysics_Mukhopadhyay.pdf file_size: 1977706 relation: main_file success: 1 file_date_updated: 2024-01-29T11:25:38Z has_accepted_license: '1' intvolume: ' 19' isi: 1 keyword: - General Physics and Astronomy language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1630-1635 project: - _id: 0aa3608a-070f-11eb-9043-e9cd8a2bd931 grant_number: P33692 name: Cavity electromechanics across a quantum phase transition - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: eb9b30ac-77a9-11ec-83b8-871f581d53d2 name: Protected states of quantum matter - _id: bd5b4ec5-d553-11ed-ba76-a6eedb083344 name: Protected states of quantum matter publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Superconductivity from a melted insulator in Josephson junction arrays tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2023' ... --- _id: '13266' abstract: - lang: eng text: The 3′,5′-cyclic adenosine monophosphate (cAMP) is a versatile second messenger in many mammalian signaling pathways. However, its role in plants remains not well-recognized. Recent discovery of adenylate cyclase (AC) activity for transport inhibitor response 1/auxin-signaling F-box proteins (TIR1/AFB) auxin receptors and the demonstration of its importance for canonical auxin signaling put plant cAMP research back into spotlight. This insight briefly summarizes the well-established cAMP signaling pathways in mammalian cells and describes the turbulent and controversial history of plant cAMP research highlighting the major progress and the unresolved points. We also briefly review the current paradigm of auxin signaling to provide a background for the discussion on the AC activity of TIR1/AFB auxin receptors and its potential role in transcriptional auxin signaling as well as impact of these discoveries on plant cAMP research in general. acknowledgement: 'We gratefully acknowledge our brave colleagues, whose excellent efforts kept the plant cAMP research going in the last two decades. The authors were financially supported by the Austrian Science Fund (FWF): I 6123 and P 37051-B.' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Linlin full_name: Qi, Linlin id: 44B04502-A9ED-11E9-B6FC-583AE6697425 last_name: Qi orcid: 0000-0001-5187-8401 - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 citation: ama: Qi L, Friml J. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 2023;240(2):489-495. doi:10.1111/nph.19123 apa: Qi, L., & Friml, J. (2023). Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. Wiley. https://doi.org/10.1111/nph.19123 chicago: Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” New Phytologist. Wiley, 2023. https://doi.org/10.1111/nph.19123. ieee: L. Qi and J. Friml, “Tale of cAMP as a second messenger in auxin signaling and beyond,” New Phytologist, vol. 240, no. 2. Wiley, pp. 489–495, 2023. ista: Qi L, Friml J. 2023. Tale of cAMP as a second messenger in auxin signaling and beyond. New Phytologist. 240(2), 489–495. mla: Qi, Linlin, and Jiří Friml. “Tale of CAMP as a Second Messenger in Auxin Signaling and Beyond.” New Phytologist, vol. 240, no. 2, Wiley, 2023, pp. 489–95, doi:10.1111/nph.19123. short: L. Qi, J. Friml, New Phytologist 240 (2023) 489–495. date_created: 2023-07-23T22:01:13Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-29T11:21:55Z day: '01' ddc: - '580' department: - _id: JiFr doi: 10.1111/nph.19123 external_id: isi: - '001026321500001' pmid: - '37434303' file: - access_level: open_access checksum: 6d9bbd45b8e7bb3ceee2586d447bacb2 content_type: application/pdf creator: dernst date_created: 2024-01-29T11:21:43Z date_updated: 2024-01-29T11:21:43Z file_id: '14898' file_name: 2023_NewPhytologist_Qi.pdf file_size: 974464 relation: main_file success: 1 file_date_updated: 2024-01-29T11:21:43Z has_accepted_license: '1' intvolume: ' 240' isi: 1 issue: '2' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 489-495 pmid: 1 project: - _id: bd76d395-d553-11ed-ba76-f678c14f9033 grant_number: I06123 name: Peptide receptor complexes for auxin canalization and regeneration in Arabidopsis - _id: 7bcece63-9f16-11ee-852c-ae94e099eeb6 grant_number: P37051 name: Guanylate cyclase activity of TIR1/AFBs auxin receptors publication: New Phytologist publication_identifier: eissn: - 1469-8137 issn: - 0028-646X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Tale of cAMP as a second messenger in auxin signaling and beyond tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 240 year: '2023' ... --- _id: '13136' abstract: - lang: eng text: Despite its fundamental importance for development, the question of how organs achieve their correct size and shape is poorly understood. This complex process requires coordination between the generation of cell mass and the morphogenetic mechanisms that sculpt tissues. These processes are regulated by morphogen signalling pathways and mechanical forces. Yet, in many systems, it is unclear how biochemical and mechanical signalling are quantitatively interpreted to determine the behaviours of individual cells and how they contribute to growth and morphogenesis at the tissue scale. In this review, we discuss the development of the vertebrate neural tube and somites as an example of the state of knowledge, as well as the challenges in understanding the mechanisms of tissue size control in vertebrate organogenesis. We highlight how the recent advances in stem cell differentiation and organoid approaches can be harnessed to provide new insights into this question. acknowledgement: 'We thank J. Briscoe for comments on the manuscript. Work in the AK lab is supported by ISTA, the European Research Council under Horizon Europe: grant 101044579, and Austrian Science Fund (FWF): F78 (Stem Cell Modulation). SR is supported by Gesellschaft für Forschungsförderung Niederösterreich m.b.H. fellowship SC19-011.' article_number: '100459' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Thomas full_name: Minchington, Thomas id: 7d1648cb-19e9-11eb-8e7a-f8c037fb3e3f last_name: Minchington - first_name: Stefanie full_name: Rus, Stefanie id: 4D9EC9B6-F248-11E8-B48F-1D18A9856A87 last_name: Rus orcid: 0000-0001-8703-1093 - first_name: Anna full_name: Kicheva, Anna id: 3959A2A0-F248-11E8-B48F-1D18A9856A87 last_name: Kicheva orcid: 0000-0003-4509-4998 citation: ama: Minchington T, Rus S, Kicheva A. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 2023;35. doi:10.1016/j.coisb.2023.100459 apa: Minchington, T., Rus, S., & Kicheva, A. (2023). Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. Elsevier. https://doi.org/10.1016/j.coisb.2023.100459 chicago: Minchington, Thomas, Stefanie Rus, and Anna Kicheva. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems Biology. Elsevier, 2023. https://doi.org/10.1016/j.coisb.2023.100459. ieee: T. Minchington, S. Rus, and A. Kicheva, “Control of tissue dimensions in the developing neural tube and somites,” Current Opinion in Systems Biology, vol. 35. Elsevier, 2023. ista: Minchington T, Rus S, Kicheva A. 2023. Control of tissue dimensions in the developing neural tube and somites. Current Opinion in Systems Biology. 35, 100459. mla: Minchington, Thomas, et al. “Control of Tissue Dimensions in the Developing Neural Tube and Somites.” Current Opinion in Systems Biology, vol. 35, 100459, Elsevier, 2023, doi:10.1016/j.coisb.2023.100459. short: T. Minchington, S. Rus, A. Kicheva, Current Opinion in Systems Biology 35 (2023). date_created: 2023-06-18T22:00:46Z date_published: 2023-09-01T00:00:00Z date_updated: 2024-01-29T11:07:47Z day: '01' ddc: - '570' department: - _id: AnKi doi: 10.1016/j.coisb.2023.100459 file: - access_level: open_access checksum: 8a75c4e29fd9b62e3c50663c2265b173 content_type: application/pdf creator: dernst date_created: 2024-01-29T11:06:45Z date_updated: 2024-01-29T11:06:45Z file_id: '14896' file_name: 2023_CurrOpSystBioloy_Minchington.pdf file_size: 598842 relation: main_file success: 1 file_date_updated: 2024-01-29T11:06:45Z has_accepted_license: '1' intvolume: ' 35' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: bd7e737f-d553-11ed-ba76-d69ffb5ee3aa grant_number: '101044579' name: Mechanisms of tissue size regulation in spinal cord development - _id: 059DF620-7A3F-11EA-A408-12923DDC885E grant_number: F07802 name: Morphogen control of growth and pattern in the spinal cord - _id: 9B9B39FA-BA93-11EA-9121-9846C619BF3A grant_number: SC19-011 name: The regulatory logic of pattern formation in the vertebrate dorsal neural tube publication: Current Opinion in Systems Biology publication_identifier: eissn: - 2452-3100 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Control of tissue dimensions in the developing neural tube and somites tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 35 year: '2023' ... --- _id: '13135' abstract: - lang: eng text: In this paper we consider a class of stochastic reaction-diffusion equations. We provide local well-posedness, regularity, blow-up criteria and positivity of solutions. The key novelties of this work are related to the use transport noise, critical spaces and the proof of higher order regularity of solutions – even in case of non-smooth initial data. Crucial tools are Lp(Lp)-theory, maximal regularity estimates and sharp blow-up criteria. We view the results of this paper as a general toolbox for establishing global well-posedness for a large class of reaction-diffusion systems of practical interest, of which many are completely open. In our follow-up work [8], the results of this paper are applied in the specific cases of the Lotka-Volterra equations and the Brusselator model. acknowledgement: The first author has received funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation programme (grant agreement No. 948819) Image 1. The second author is supported by the VICI subsidy VI.C.212.027 of the Netherlands Organisation for Scientific Research (NWO). article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Antonio full_name: Agresti, Antonio id: 673cd0cc-9b9a-11eb-b144-88f30e1fbb72 last_name: Agresti orcid: 0000-0002-9573-2962 - first_name: Mark full_name: Veraar, Mark last_name: Veraar citation: ama: 'Agresti A, Veraar M. Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. Journal of Differential Equations. 2023;368(9):247-300. doi:10.1016/j.jde.2023.05.038' apa: 'Agresti, A., & Veraar, M. (2023). Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. Journal of Differential Equations. Elsevier. https://doi.org/10.1016/j.jde.2023.05.038' chicago: 'Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with Transport Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.” Journal of Differential Equations. Elsevier, 2023. https://doi.org/10.1016/j.jde.2023.05.038.' ieee: 'A. Agresti and M. Veraar, “Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity,” Journal of Differential Equations, vol. 368, no. 9. Elsevier, pp. 247–300, 2023.' ista: 'Agresti A, Veraar M. 2023. Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity. Journal of Differential Equations. 368(9), 247–300.' mla: 'Agresti, Antonio, and Mark Veraar. “Reaction-Diffusion Equations with Transport Noise and Critical Superlinear Diffusion: Local Well-Posedness and Positivity.” Journal of Differential Equations, vol. 368, no. 9, Elsevier, 2023, pp. 247–300, doi:10.1016/j.jde.2023.05.038.' short: A. Agresti, M. Veraar, Journal of Differential Equations 368 (2023) 247–300. date_created: 2023-06-18T22:00:45Z date_published: 2023-09-25T00:00:00Z date_updated: 2024-01-29T11:04:41Z day: '25' ddc: - '510' department: - _id: JuFi doi: 10.1016/j.jde.2023.05.038 ec_funded: 1 external_id: isi: - '001019018700001' file: - access_level: open_access checksum: 246b703b091dfe047bfc79abf0891a63 content_type: application/pdf creator: dernst date_created: 2024-01-29T11:03:09Z date_updated: 2024-01-29T11:03:09Z file_id: '14895' file_name: 2023_JourDifferentialEquations_Agresti.pdf file_size: 834638 relation: main_file success: 1 file_date_updated: 2024-01-29T11:03:09Z has_accepted_license: '1' intvolume: ' 368' isi: 1 issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 247-300 project: - _id: 0aa76401-070f-11eb-9043-b5bb049fa26d call_identifier: H2020 grant_number: '948819' name: Bridging Scales in Random Materials publication: Journal of Differential Equations publication_identifier: eissn: - 1090-2732 issn: - 0022-0396 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Reaction-diffusion equations with transport noise and critical superlinear diffusion: Local well-posedness and positivity' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 368 year: '2023' ... --- _id: '13270' abstract: - lang: eng text: "Consider a geodesic triangle on a surface of constant curvature and subdivide it recursively into four triangles by joining the midpoints of its edges. We show the existence of a uniform δ>0\r\n such that, at any step of the subdivision, all the triangle angles lie in the interval (δ,π−δ)\r\n. Additionally, we exhibit stabilising behaviours for both angles and lengths as this subdivision progresses." acknowledgement: Open access funding provided by the Institute of Science and Technology (IST Austria). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Florestan R full_name: Brunck, Florestan R id: 6ab6e556-f394-11eb-9cf6-9dfb78f00d8d last_name: Brunck citation: ama: Brunck FR. Iterated medial triangle subdivision in surfaces of constant curvature. Discrete and Computational Geometry. 2023;70(3):1059-1089. doi:10.1007/s00454-023-00500-5 apa: Brunck, F. R. (2023). Iterated medial triangle subdivision in surfaces of constant curvature. Discrete and Computational Geometry. Springer Nature. https://doi.org/10.1007/s00454-023-00500-5 chicago: Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” Discrete and Computational Geometry. Springer Nature, 2023. https://doi.org/10.1007/s00454-023-00500-5. ieee: F. R. Brunck, “Iterated medial triangle subdivision in surfaces of constant curvature,” Discrete and Computational Geometry, vol. 70, no. 3. Springer Nature, pp. 1059–1089, 2023. ista: Brunck FR. 2023. Iterated medial triangle subdivision in surfaces of constant curvature. Discrete and Computational Geometry. 70(3), 1059–1089. mla: Brunck, Florestan R. “Iterated Medial Triangle Subdivision in Surfaces of Constant Curvature.” Discrete and Computational Geometry, vol. 70, no. 3, Springer Nature, 2023, pp. 1059–89, doi:10.1007/s00454-023-00500-5. short: F.R. Brunck, Discrete and Computational Geometry 70 (2023) 1059–1089. date_created: 2023-07-23T22:01:14Z date_published: 2023-07-05T00:00:00Z date_updated: 2024-01-29T11:16:16Z day: '05' ddc: - '510' department: - _id: UlWa doi: 10.1007/s00454-023-00500-5 external_id: arxiv: - '2107.04112' isi: - '001023742800003' file: - access_level: open_access checksum: 865e68daafdd4edcfc280172ec50f5ea content_type: application/pdf creator: dernst date_created: 2024-01-29T11:15:22Z date_updated: 2024-01-29T11:15:22Z file_id: '14897' file_name: 2023_DiscreteComputGeometry_Brunck.pdf file_size: 1466020 relation: main_file success: 1 file_date_updated: 2024-01-29T11:15:22Z has_accepted_license: '1' intvolume: ' 70' isi: 1 issue: '3' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 1059-1089 publication: Discrete and Computational Geometry publication_identifier: eissn: - 1432-0444 issn: - 0179-5376 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Iterated medial triangle subdivision in surfaces of constant curvature tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 70 year: '2023' ... --- _id: '13269' abstract: - lang: eng text: This paper is a collection of results on combinatorial properties of codes for the Z-channel . A Z-channel with error fraction τ takes as input a length- n binary codeword and injects in an adversarial manner up to n τ asymmetric errors, i.e., errors that only zero out bits but do not flip 0’s to 1’s. It is known that the largest ( L - 1)-list-decodable code for the Z-channel with error fraction τ has exponential size (in n ) if τ is less than a critical value that we call the ( L - 1)- list-decoding Plotkin point and has constant size if τ is larger than the threshold. The ( L -1)-list-decoding Plotkin point is known to be L -1/L-1 – L -L/ L-1 , which equals 1/4 for unique-decoding with L -1 = 1. In this paper, we derive various results for the size of the largest codes above and below the list-decoding Plotkin point. In particular, we show that the largest ( L -1)-list-decodable code ε-above the Plotkin point, for any given sufficiently small positive constant ε > 0, has size Θ L (ε -3/2 ) for any L - 1 ≥ 1. We also devise upper and lower bounds on the exponential size of codes below the list-decoding Plotkin point. acknowledgement: "Nikita Polyanskii’s research was conducted in part during October 2020 - December 2021 with the Technical University of Munich and the Skolkovo Institute of Science and Technology. His work was supported by the German Research Foundation (Deutsche Forschungsgemeinschaft, DFG) under Grant No. WA3907/1-1 and the Russian Foundation for Basic Research (RFBR)\r\nunder Grant No. 20-01-00559.\r\nYihan Zhang is supported by funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 682203-ERC-[Inf-Speed-Tradeoff]." article_processing_charge: No article_type: original author: - first_name: Nikita full_name: Polyanskii, Nikita last_name: Polyanskii - first_name: Yihan full_name: Zhang, Yihan id: 2ce5da42-b2ea-11eb-bba5-9f264e9d002c last_name: Zhang orcid: 0000-0002-6465-6258 citation: ama: Polyanskii N, Zhang Y. Codes for the Z-channel. IEEE Transactions on Information Theory. 2023;69(10):6340-6357. doi:10.1109/TIT.2023.3292219 apa: Polyanskii, N., & Zhang, Y. (2023). Codes for the Z-channel. IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TIT.2023.3292219 chicago: Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/TIT.2023.3292219. ieee: N. Polyanskii and Y. Zhang, “Codes for the Z-channel,” IEEE Transactions on Information Theory, vol. 69, no. 10. Institute of Electrical and Electronics Engineers, pp. 6340–6357, 2023. ista: Polyanskii N, Zhang Y. 2023. Codes for the Z-channel. IEEE Transactions on Information Theory. 69(10), 6340–6357. mla: Polyanskii, Nikita, and Yihan Zhang. “Codes for the Z-Channel.” IEEE Transactions on Information Theory, vol. 69, no. 10, Institute of Electrical and Electronics Engineers, 2023, pp. 6340–57, doi:10.1109/TIT.2023.3292219. short: N. Polyanskii, Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 6340–6357. date_created: 2023-07-23T22:01:14Z date_published: 2023-07-04T00:00:00Z date_updated: 2024-01-29T11:10:54Z day: '04' department: - _id: MaMo doi: 10.1109/TIT.2023.3292219 external_id: arxiv: - '2105.01427' isi: - '001069680100011' intvolume: ' 69' isi: 1 issue: '10' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2105.01427 month: '07' oa: 1 oa_version: Preprint page: 6340-6357 publication: IEEE Transactions on Information Theory publication_identifier: eissn: - 1557-9654 issn: - 0018-9448 publication_status: published publisher: Institute of Electrical and Electronics Engineers quality_controlled: '1' scopus_import: '1' status: public title: Codes for the Z-channel type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 69 year: '2023' ... --- _id: '13128' abstract: - lang: eng text: "Given A⊆GL2(Fq), we prove that there exist disjoint subsets B,C⊆A such that A=B⊔C and their additive and multiplicative energies satisfying max{E+(B),E×(C)}≪|A|3/M(|A|), where\r\nM(|A|)=min{q4/3/|A|1/3(log|A|)2/3,|A|4/5/q13/5(log|A|)27/10}.\r\n We also study some related questions on moderate expanders over matrix rings, namely, for A,B,C⊆GL2(Fq), we have |AB+C|, |(A+B)C|≫q4, whenever |A||B||C|≫q10+1/2. These improve earlier results due to Karabulut, Koh, Pham, Shen, and Vinh ([2019], Expanding phenomena over matrix rings, ForumMath., 31, 951–970).\r\n" article_processing_charge: No article_type: original author: - first_name: Ali full_name: Mohammadi, Ali last_name: Mohammadi - first_name: Thang full_name: Pham, Thang last_name: Pham - first_name: Yiting full_name: Wang, Yiting id: 1917d194-076e-11ed-97cd-837255f88785 last_name: Wang orcid: 0000-0002-2856-767X citation: ama: Mohammadi A, Pham T, Wang Y. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 2023;66(4):1280-1295. doi:10.4153/S000843952300036X apa: Mohammadi, A., Pham, T., & Wang, Y. (2023). An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. Cambridge University Press. https://doi.org/10.4153/S000843952300036X chicago: Mohammadi, Ali, Thang Pham, and Yiting Wang. “An Energy Decomposition Theorem for Matrices and Related Questions.” Canadian Mathematical Bulletin. Cambridge University Press, 2023. https://doi.org/10.4153/S000843952300036X. ieee: A. Mohammadi, T. Pham, and Y. Wang, “An energy decomposition theorem for matrices and related questions,” Canadian Mathematical Bulletin, vol. 66, no. 4. Cambridge University Press, pp. 1280–1295, 2023. ista: Mohammadi A, Pham T, Wang Y. 2023. An energy decomposition theorem for matrices and related questions. Canadian Mathematical Bulletin. 66(4), 1280–1295. mla: Mohammadi, Ali, et al. “An Energy Decomposition Theorem for Matrices and Related Questions.” Canadian Mathematical Bulletin, vol. 66, no. 4, Cambridge University Press, 2023, pp. 1280–95, doi:10.4153/S000843952300036X. short: A. Mohammadi, T. Pham, Y. Wang, Canadian Mathematical Bulletin 66 (2023) 1280–1295. date_created: 2023-06-11T22:00:40Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-29T11:00:46Z day: '01' department: - _id: GradSch doi: 10.4153/S000843952300036X external_id: arxiv: - '2106.07328' isi: - '001011963000001' intvolume: ' 66' isi: 1 issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2106.07328 month: '12' oa: 1 oa_version: Preprint page: 1280-1295 publication: Canadian Mathematical Bulletin publication_identifier: eissn: - 1496-4287 issn: - 0008-4395 publication_status: published publisher: Cambridge University Press quality_controlled: '1' scopus_import: '1' status: public title: An energy decomposition theorem for matrices and related questions type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 66 year: '2023' ... --- _id: '13209' abstract: - lang: eng text: The phytohormone auxin plays central roles in many growth and developmental processes in plants. Development of chemical tools targeting the auxin pathway is useful for both plant biology and agriculture. Here we reveal that naproxen, a synthetic compound with anti-inflammatory activity in humans, acts as an auxin transport inhibitor targeting PIN-FORMED (PIN) transporters in plants. Physiological experiments indicate that exogenous naproxen treatment affects pleiotropic auxin-regulated developmental processes. Additional cellular and biochemical evidence indicates that naproxen suppresses auxin transport, specifically PIN-mediated auxin efflux. Moreover, biochemical and structural analyses confirm that naproxen binds directly to PIN1 protein via the same binding cavity as the indole-3-acetic acid substrate. Thus, by combining cellular, biochemical, and structural approaches, this study clearly establishes that naproxen is a PIN inhibitor and elucidates the underlying mechanisms. Further use of this compound may advance our understanding of the molecular mechanisms of PIN-mediated auxin transport and expand our toolkit in auxin biology and agriculture. acknowledgement: "This work was supported by the Strategic Priority Research Program of the Chinese Academy of Sciences (XDB37020103 to Linfeng Sun); research funds from the Center for Advanced Interdisciplinary Science\r\nand Biomedicine of IHM, Division of Life Sciences and Medicine, University of Science and Technology of China (QYPY20220012 to S.T.); start-up funding from the University of Science and Technology of China and the\r\nChinese Academy of Sciences (GG9100007007, KY9100000026,KY9100000051, and KJ2070000079 to S.T.); the National Natural Science Foundation of China (31900885 to X.L. and 31870732 to Linfeng Sun); the Natural Science Foundation of Anhui Province (2008085MC90 to X.L. and 2008085J15 to Linfeng Sun); the Fundamental Research Funds for the Central Universities (WK9100000021 to S.T. and WK9100000031 to Linfeng Sun); and the USTC Research Funds of the Double First-Class Initiative (YD9100002016 to S.T. and YD9100002004 to Linfeng Sun). Linfeng Sun is supported by an Outstanding Young Scholar Award from the Qiu Shi Science and Technologies Foundation and a Young Scholar Award from the Cyrus Tang Foundation.We thank Dr. Yang Zhao for sharing published materials (Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences) and the Cryo-EM Center of the University of Science and Technology of China for the EM facility support. We are grateful to Y. Gao and all other staff members for their technical support on cryo-EM data collection. " article_number: '100632' article_processing_charge: Yes article_type: original author: - first_name: Jing full_name: Xia, Jing last_name: Xia - first_name: Mengjuan full_name: Kong, Mengjuan last_name: Kong - first_name: Zhisen full_name: Yang, Zhisen last_name: Yang - first_name: Lianghanxiao full_name: Sun, Lianghanxiao last_name: Sun - first_name: Yakun full_name: Peng, Yakun last_name: Peng - first_name: Yanbo full_name: Mao, Yanbo last_name: Mao - first_name: Hong full_name: Wei, Hong last_name: Wei - first_name: Wei full_name: Ying, Wei last_name: Ying - first_name: Yongxiao full_name: Gao, Yongxiao last_name: Gao - first_name: Jiří full_name: Friml, Jiří id: 4159519E-F248-11E8-B48F-1D18A9856A87 last_name: Friml orcid: 0000-0002-8302-7596 - first_name: Jianping full_name: Weng, Jianping last_name: Weng - first_name: Xin full_name: Liu, Xin last_name: Liu - first_name: Linfeng full_name: Sun, Linfeng last_name: Sun - first_name: Shutang full_name: Tan, Shutang last_name: Tan citation: ama: Xia J, Kong M, Yang Z, et al. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. 2023;4(6). doi:10.1016/j.xplc.2023.100632 apa: Xia, J., Kong, M., Yang, Z., Sun, L., Peng, Y., Mao, Y., … Tan, S. (2023). Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. Elsevier . https://doi.org/10.1016/j.xplc.2023.100632 chicago: Xia, Jing, Mengjuan Kong, Zhisen Yang, Lianghanxiao Sun, Yakun Peng, Yanbo Mao, Hong Wei, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” Plant Communications. Elsevier , 2023. https://doi.org/10.1016/j.xplc.2023.100632. ieee: J. Xia et al., “Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen,” Plant Communications, vol. 4, no. 6. Elsevier , 2023. ista: Xia J, Kong M, Yang Z, Sun L, Peng Y, Mao Y, Wei H, Ying W, Gao Y, Friml J, Weng J, Liu X, Sun L, Tan S. 2023. Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen. Plant Communications. 4(6), 100632. mla: Xia, Jing, et al. “Chemical Inhibition of Arabidopsis PIN-FORMED Auxin Transporters by the Anti-Inflammatory Drug Naproxen.” Plant Communications, vol. 4, no. 6, 100632, Elsevier , 2023, doi:10.1016/j.xplc.2023.100632. short: J. Xia, M. Kong, Z. Yang, L. Sun, Y. Peng, Y. Mao, H. Wei, W. Ying, Y. Gao, J. Friml, J. Weng, X. Liu, L. Sun, S. Tan, Plant Communications 4 (2023). date_created: 2023-07-12T07:32:00Z date_published: 2023-11-13T00:00:00Z date_updated: 2024-01-30T10:55:34Z day: '13' ddc: - '580' department: - _id: JiFr doi: 10.1016/j.xplc.2023.100632 external_id: isi: - '001113003000001' pmid: - '37254481' file: - access_level: open_access checksum: f8ef92af6096834f91ce38587fb1db9f content_type: application/pdf creator: dernst date_created: 2024-01-30T10:54:40Z date_updated: 2024-01-30T10:54:40Z file_id: '14900' file_name: 2023_PlantCommunications_Xia.pdf file_size: 1434862 relation: main_file success: 1 file_date_updated: 2024-01-30T10:54:40Z has_accepted_license: '1' intvolume: ' 4' isi: 1 issue: '6' language: - iso: eng month: '11' oa: 1 oa_version: Published Version pmid: 1 publication: Plant Communications publication_identifier: eissn: - 2590-3462 publication_status: published publisher: 'Elsevier ' quality_controlled: '1' status: public title: Chemical inhibition of Arabidopsis PIN-FORMED auxin transporters by the anti-inflammatory drug naproxen tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 4 year: '2023' ... --- _id: '13971' abstract: - lang: eng text: When in equilibrium, thermal forces agitate molecules, which then diffuse, collide and bind to form materials. However, the space of accessible structures in which micron-scale particles can be organized by thermal forces is limited, owing to the slow dynamics and metastable states. Active agents in a passive fluid generate forces and flows, forming a bath with active fluctuations. Two unanswered questions are whether those active agents can drive the assembly of passive components into unconventional states and which material properties they will exhibit. Here we show that passive, sticky beads immersed in a bath of swimming Escherichia coli bacteria aggregate into unconventional clusters and gels that are controlled by the activity of the bath. We observe a slow but persistent rotation of the aggregates that originates in the chirality of the E. coli flagella and directs aggregation into structures that are not accessible thermally. We elucidate the aggregation mechanism with a numerical model of spinning, sticky beads and reproduce quantitatively the experimental results. We show that internal activity controls the phase diagram and the structure of the aggregates. Overall, our results highlight the promising role of active baths in designing the structural and mechanical properties of materials with unconventional phases. acknowledgement: D.G. and J.P. thank E. Krasnopeeva, C. Guet, G. Guessous and T. Hwa for providing the E. coli strains. This material is based upon work supported by the US Department of Energy under award DE-SC0019769. I.P. acknowledges funding by the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 101034413. A.Š. acknowledges funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant No. 802960). M.C.U. acknowledges funding from the European Union’s Horizon 2020 research and innovation programme under Marie Skłodowska-Curie Grant Agreement No. 754411. article_processing_charge: Yes article_type: original author: - first_name: Daniel full_name: Grober, Daniel id: abdfc56f-34fb-11ee-bd33-fd766fce5a99 last_name: Grober - first_name: Ivan full_name: Palaia, Ivan id: 9c805cd2-4b75-11ec-a374-db6dd0ed57fa last_name: Palaia orcid: ' 0000-0002-8843-9485 ' - first_name: Mehmet C full_name: Ucar, Mehmet C id: 50B2A802-6007-11E9-A42B-EB23E6697425 last_name: Ucar orcid: 0000-0003-0506-4217 - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Anđela full_name: Šarić, Anđela id: bf63d406-f056-11eb-b41d-f263a6566d8b last_name: Šarić orcid: 0000-0002-7854-2139 - first_name: Jérémie A full_name: Palacci, Jérémie A id: 8fb92548-2b22-11eb-b7c1-a3f0d08d7c7d last_name: Palacci orcid: 0000-0002-7253-9465 citation: ama: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. 2023;19:1680-1688. doi:10.1038/s41567-023-02136-x apa: Grober, D., Palaia, I., Ucar, M. C., Hannezo, E. B., Šarić, A., & Palacci, J. A. (2023). Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02136-x chicago: Grober, Daniel, Ivan Palaia, Mehmet C Ucar, Edouard B Hannezo, Anđela Šarić, and Jérémie A Palacci. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02136-x. ieee: D. Grober, I. Palaia, M. C. Ucar, E. B. Hannezo, A. Šarić, and J. A. Palacci, “Unconventional colloidal aggregation in chiral bacterial baths,” Nature Physics, vol. 19. Springer Nature, pp. 1680–1688, 2023. ista: Grober D, Palaia I, Ucar MC, Hannezo EB, Šarić A, Palacci JA. 2023. Unconventional colloidal aggregation in chiral bacterial baths. Nature Physics. 19, 1680–1688. mla: Grober, Daniel, et al. “Unconventional Colloidal Aggregation in Chiral Bacterial Baths.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1680–88, doi:10.1038/s41567-023-02136-x. short: D. Grober, I. Palaia, M.C. Ucar, E.B. Hannezo, A. Šarić, J.A. Palacci, Nature Physics 19 (2023) 1680–1688. date_created: 2023-08-06T22:01:11Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-01-30T12:26:55Z day: '01' ddc: - '530' department: - _id: EdHa - _id: AnSa - _id: JePa doi: 10.1038/s41567-023-02136-x ec_funded: 1 external_id: isi: - '001037346400005' file: - access_level: open_access checksum: 7e282c2ebc0ac82125a04f6b4742d4c1 content_type: application/pdf creator: dernst date_created: 2024-01-30T12:26:08Z date_updated: 2024-01-30T12:26:08Z file_id: '14906' file_name: 2023_NaturePhysics_Grober.pdf file_size: 6365607 relation: main_file success: 1 file_date_updated: 2024-01-30T12:26:08Z has_accepted_license: '1' intvolume: ' 19' isi: 1 language: - iso: eng month: '11' oa: 1 oa_version: Published Version page: 1680-1688 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' - _id: eba2549b-77a9-11ec-83b8-a81e493eae4e call_identifier: H2020 grant_number: '802960' name: 'Non-Equilibrium Protein Assembly: from Building Blocks to Biological Machines' - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Unconventional colloidal aggregation in chiral bacterial baths tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2023' ... --- _id: '10551' abstract: - lang: eng text: 'The Dean–Kawasaki equation—a strongly singular SPDE—is a basic equation of fluctuating hydrodynamics; it has been proposed in the physics literature to describe the fluctuations of the density of N independent diffusing particles in the regime of large particle numbers N≫1. The singular nature of the Dean–Kawasaki equation presents a substantial challenge for both its analysis and its rigorous mathematical justification. Besides being non-renormalisable by the theory of regularity structures by Hairer et al., it has recently been shown to not even admit nontrivial martingale solutions. In the present work, we give a rigorous and fully quantitative justification of the Dean–Kawasaki equation by considering the natural regularisation provided by standard numerical discretisations: We show that structure-preserving discretisations of the Dean–Kawasaki equation may approximate the density fluctuations of N non-interacting diffusing particles to arbitrary order in N−1 (in suitable weak metrics). In other words, the Dean–Kawasaki equation may be interpreted as a “recipe” for accurate and efficient numerical simulations of the density fluctuations of independent diffusing particles.' acknowledgement: "We thank the anonymous referee for his/her careful reading of the manuscript and valuable suggestions. FC gratefully acknowledges funding from the Austrian Science Fund (FWF) through the project F65, and from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.\r\nOpen access funding provided by Austrian Science Fund (FWF)." article_number: '76' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Federico full_name: Cornalba, Federico id: 2CEB641C-A400-11E9-A717-D712E6697425 last_name: Cornalba orcid: 0000-0002-6269-5149 - first_name: Julian L full_name: Fischer, Julian L id: 2C12A0B0-F248-11E8-B48F-1D18A9856A87 last_name: Fischer orcid: 0000-0002-0479-558X citation: ama: Cornalba F, Fischer JL. The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. 2023;247(5). doi:10.1007/s00205-023-01903-7 apa: Cornalba, F., & Fischer, J. L. (2023). The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. Springer Nature. https://doi.org/10.1007/s00205-023-01903-7 chicago: Cornalba, Federico, and Julian L Fischer. “The Dean-Kawasaki Equation and the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive for Rational Mechanics and Analysis. Springer Nature, 2023. https://doi.org/10.1007/s00205-023-01903-7. ieee: F. Cornalba and J. L. Fischer, “The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles,” Archive for Rational Mechanics and Analysis, vol. 247, no. 5. Springer Nature, 2023. ista: Cornalba F, Fischer JL. 2023. The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles. Archive for Rational Mechanics and Analysis. 247(5), 76. mla: Cornalba, Federico, and Julian L. Fischer. “The Dean-Kawasaki Equation and the Structure of Density Fluctuations in Systems of Diffusing Particles.” Archive for Rational Mechanics and Analysis, vol. 247, no. 5, 76, Springer Nature, 2023, doi:10.1007/s00205-023-01903-7. short: F. Cornalba, J.L. Fischer, Archive for Rational Mechanics and Analysis 247 (2023). date_created: 2021-12-16T12:16:03Z date_published: 2023-08-04T00:00:00Z date_updated: 2024-01-30T12:10:10Z day: '04' ddc: - '510' department: - _id: JuFi doi: 10.1007/s00205-023-01903-7 ec_funded: 1 external_id: arxiv: - '2109.06500' isi: - '001043086800001' file: - access_level: open_access checksum: 4529eeff170b6745a461d397ee611b5a content_type: application/pdf creator: dernst date_created: 2024-01-30T12:09:34Z date_updated: 2024-01-30T12:09:34Z file_id: '14904' file_name: 2023_ArchiveRationalMech_Cornalba.pdf file_size: 1851185 relation: main_file success: 1 file_date_updated: 2024-01-30T12:09:34Z has_accepted_license: '1' intvolume: ' 247' isi: 1 issue: '5' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships - _id: fc31cba2-9c52-11eb-aca3-ff467d239cd2 grant_number: F6504 name: Taming Complexity in Partial Differential Systems publication: Archive for Rational Mechanics and Analysis publication_identifier: eissn: - 1432-0673 issn: - 0003-9527 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: The Dean-Kawasaki equation and the structure of density fluctuations in systems of diffusing particles tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 247 year: '2023' ... --- _id: '13234' abstract: - lang: eng text: Neural-network classifiers achieve high accuracy when predicting the class of an input that they were trained to identify. Maintaining this accuracy in dynamic environments, where inputs frequently fall outside the fixed set of initially known classes, remains a challenge. We consider the problem of monitoring the classification decisions of neural networks in the presence of novel classes. For this purpose, we generalize our recently proposed abstraction-based monitor from binary output to real-valued quantitative output. This quantitative output enables new applications, two of which we investigate in the paper. As our first application, we introduce an algorithmic framework for active monitoring of a neural network, which allows us to learn new classes dynamically and yet maintain high monitoring performance. As our second application, we present an offline procedure to retrain the neural network to improve the monitor’s detection performance without deteriorating the network’s classification accuracy. Our experimental evaluation demonstrates both the benefits of our active monitoring framework in dynamic scenarios and the effectiveness of the retraining procedure. acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093, by DIREC - Digital Research Centre Denmark, and by the Villum Investigator Grant S4OS. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Konstantin full_name: Kueffner, Konstantin id: 8121a2d0-dc85-11ea-9058-af578f3b4515 last_name: Kueffner orcid: 0000-0001-8974-2542 - first_name: Anna full_name: Lukina, Anna id: CBA4D1A8-0FE8-11E9-BDE6-07BFE5697425 last_name: Lukina - first_name: Christian full_name: Schilling, Christian id: 3A2F4DCE-F248-11E8-B48F-1D18A9856A87 last_name: Schilling orcid: 0000-0003-3658-1065 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: 'Kueffner K, Lukina A, Schilling C, Henzinger TA. Into the unknown: Active monitoring of neural networks (extended version). International Journal on Software Tools for Technology Transfer. 2023;25:575-592. doi:10.1007/s10009-023-00711-4' apa: 'Kueffner, K., Lukina, A., Schilling, C., & Henzinger, T. A. (2023). Into the unknown: Active monitoring of neural networks (extended version). International Journal on Software Tools for Technology Transfer. Springer Nature. https://doi.org/10.1007/s10009-023-00711-4' chicago: 'Kueffner, Konstantin, Anna Lukina, Christian Schilling, and Thomas A Henzinger. “Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” International Journal on Software Tools for Technology Transfer. Springer Nature, 2023. https://doi.org/10.1007/s10009-023-00711-4.' ieee: 'K. Kueffner, A. Lukina, C. Schilling, and T. A. Henzinger, “Into the unknown: Active monitoring of neural networks (extended version),” International Journal on Software Tools for Technology Transfer, vol. 25. Springer Nature, pp. 575–592, 2023.' ista: 'Kueffner K, Lukina A, Schilling C, Henzinger TA. 2023. Into the unknown: Active monitoring of neural networks (extended version). International Journal on Software Tools for Technology Transfer. 25, 575–592.' mla: 'Kueffner, Konstantin, et al. “Into the Unknown: Active Monitoring of Neural Networks (Extended Version).” International Journal on Software Tools for Technology Transfer, vol. 25, Springer Nature, 2023, pp. 575–92, doi:10.1007/s10009-023-00711-4.' short: K. Kueffner, A. Lukina, C. Schilling, T.A. Henzinger, International Journal on Software Tools for Technology Transfer 25 (2023) 575–592. date_created: 2023-07-16T22:01:11Z date_published: 2023-08-01T00:00:00Z date_updated: 2024-01-30T12:06:57Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/s10009-023-00711-4 ec_funded: 1 external_id: arxiv: - '2009.06429' isi: - '001020160000001' file: - access_level: open_access checksum: 3c4b347f39412a76872f9a6f30101f94 content_type: application/pdf creator: dernst date_created: 2024-01-30T12:06:07Z date_updated: 2024-01-30T12:06:07Z file_id: '14903' file_name: 2023_JourSoftwareTools_Kueffner.pdf file_size: 13387667 relation: main_file success: 1 file_date_updated: 2024-01-30T12:06:07Z has_accepted_license: '1' intvolume: ' 25' isi: 1 language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: 575-592 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: International Journal on Software Tools for Technology Transfer publication_identifier: eissn: - 1433-2787 issn: - 1433-2779 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '10206' relation: shorter_version status: public scopus_import: '1' status: public title: 'Into the unknown: Active monitoring of neural networks (extended version)' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2023' ... --- _id: '14036' abstract: - lang: eng text: Magic-angle spinning (MAS) nuclear magnetic resonance (NMR) is establishing itself as a powerful method for the characterization of protein dynamics at the atomic scale. We discuss here how R1ρ MAS relaxation dispersion NMR can explore microsecond-to-millisecond motions. Progress in instrumentation, isotope labeling, and pulse sequence design has paved the way for quantitative analyses of even rare structural fluctuations. In addition to isotropic chemical-shift fluctuations exploited in solution-state NMR relaxation dispersion experiments, MAS NMR has a wider arsenal of observables, allowing to see motions even if the exchanging states do not differ in their chemical shifts. We demonstrate the potential of the technique for probing motions in challenging large enzymes, membrane proteins, and protein assemblies. acknowledgement: We thank Petra Rovó for critical reading of this manuscript. We acknowledge the Austrian Science Foundation FWF (project AlloSpace, number I5812–B) and funding by the Institute of Science and Technology Austria. article_number: '102660' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Federico full_name: Napoli, Federico id: d42e08e7-f4fc-11eb-af0a-d71e26138f1b last_name: Napoli orcid: 0000-0002-9043-136X - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Napoli F, Becker LM, Schanda P. Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural Biology. 2023;82(10). doi:10.1016/j.sbi.2023.102660 apa: Napoli, F., Becker, L. M., & Schanda, P. (2023). Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural Biology. Elsevier. https://doi.org/10.1016/j.sbi.2023.102660 chicago: Napoli, Federico, Lea Marie Becker, and Paul Schanda. “Protein Dynamics Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” Current Opinion in Structural Biology. Elsevier, 2023. https://doi.org/10.1016/j.sbi.2023.102660. ieee: F. Napoli, L. M. Becker, and P. Schanda, “Protein dynamics detected by magic-angle spinning relaxation dispersion NMR,” Current Opinion in Structural Biology, vol. 82, no. 10. Elsevier, 2023. ista: Napoli F, Becker LM, Schanda P. 2023. Protein dynamics detected by magic-angle spinning relaxation dispersion NMR. Current Opinion in Structural Biology. 82(10), 102660. mla: Napoli, Federico, et al. “Protein Dynamics Detected by Magic-Angle Spinning Relaxation Dispersion NMR.” Current Opinion in Structural Biology, vol. 82, no. 10, 102660, Elsevier, 2023, doi:10.1016/j.sbi.2023.102660. short: F. Napoli, L.M. Becker, P. Schanda, Current Opinion in Structural Biology 82 (2023). date_created: 2023-08-13T22:01:11Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-30T12:37:36Z day: '01' ddc: - '570' department: - _id: PaSc doi: 10.1016/j.sbi.2023.102660 external_id: isi: - '001053616200001' pmid: - '37536064' file: - access_level: open_access checksum: c850f7ac8a4234319755b672c1df69ae content_type: application/pdf creator: dernst date_created: 2024-01-30T12:36:39Z date_updated: 2024-01-30T12:36:39Z file_id: '14907' file_name: 2023_CurrentOpinionStrucBio_Napoli.pdf file_size: 1231998 relation: main_file success: 1 file_date_updated: 2024-01-30T12:36:39Z intvolume: ' 82' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: eb9c82eb-77a9-11ec-83b8-aadd536561cf grant_number: I05812 name: AlloSpace. The emergence and mechanisms of allostery publication: Current Opinion in Structural Biology publication_identifier: eissn: - 1879-033X issn: - 0959-440X publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Protein dynamics detected by magic-angle spinning relaxation dispersion NMR tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 82 year: '2023' ... --- _id: '14043' abstract: - lang: eng text: 'Over the last two decades, a significant line of work in theoretical algorithms has made progress in solving linear systems of the form Lx=b, where L is the Laplacian matrix of a weighted graph with weights w(i,j)>0 on the edges. The solution x of the linear system can be interpreted as the potentials of an electrical flow in which the resistance on edge (i, j) is 1/w(i, j). Kelner et al. (in: Proceedings of the 45th Annual ACM Symposium on the Theory of Computing, pp 911–920, 2013. https://doi.org/10.1145/2488608.2488724) give a combinatorial, near-linear time algorithm that maintains the Kirchoff Current Law, and gradually enforces the Kirchoff Potential Law by updating flows around cycles (cycle toggling). In this paper, we consider a dual version of the algorithm that maintains the Kirchoff Potential Law, and gradually enforces the Kirchoff Current Law by cut toggling: each iteration updates all potentials on one side of a fundamental cut of a spanning tree by the same amount. We prove that this dual algorithm also runs in a near-linear number of iterations. We show, however, that if we abstract cut toggling as a natural data structure problem, this problem can be reduced to the online vector–matrix-vector problem, which has been conjectured to be difficult for dynamic algorithms (Henzinger et al., in: Proceedings of the 47th Annual ACM Symposium on the Theory of Computing, pp 21–30, 2015. https://doi.org/10.1145/2746539.2746609). The conjecture implies that the data structure does not have an O(n1−ϵ) time algorithm for any ϵ>0, and thus a straightforward implementation of the cut-toggling algorithm requires essentially linear time per iteration. To circumvent the lower bound, we batch update steps, and perform them simultaneously instead of sequentially. An appropriate choice of batching leads to an O˜(m1.5) time cut-toggling algorithm for solving Laplacian systems. Furthermore, we show that if we sparsify the graph and call our algorithm recursively on the Laplacian system implied by batching and sparsifying, we can reduce the running time to O(m1+ϵ) for any ϵ>0. Thus, the dual cut-toggling algorithm can achieve (almost) the same running time as its primal cycle-toggling counterpart.' acknowledgement: Monika Henzinger was supported by 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. Billy Jin was Supported in part by NSERC fellowship PGSD3-532673-2019 and NSF grant CCF-2007009. Richard Peng was supported in part by an NSERC Discovery Grant and NSF grant CCF-1846218. David P. Williamson was supported in part by NSF grant CCF-2007009. article_processing_charge: No article_type: original author: - first_name: Monika H full_name: Henzinger, Monika H id: 540c9bbd-f2de-11ec-812d-d04a5be85630 last_name: Henzinger orcid: 0000-0002-5008-6530 - first_name: Billy full_name: Jin, Billy last_name: Jin - first_name: Richard full_name: Peng, Richard last_name: Peng - first_name: David P. full_name: Williamson, David P. last_name: Williamson citation: ama: Henzinger MH, Jin B, Peng R, Williamson DP. A combinatorial cut-toggling algorithm for solving Laplacian linear systems. Algorithmica. 2023;85:2680-3716. doi:10.1007/s00453-023-01154-8 apa: Henzinger, M. H., Jin, B., Peng, R., & Williamson, D. P. (2023). A combinatorial cut-toggling algorithm for solving Laplacian linear systems. Algorithmica. Springer Nature. https://doi.org/10.1007/s00453-023-01154-8 chicago: Henzinger, Monika H, Billy Jin, Richard Peng, and David P. Williamson. “A Combinatorial Cut-Toggling Algorithm for Solving Laplacian Linear Systems.” Algorithmica. Springer Nature, 2023. https://doi.org/10.1007/s00453-023-01154-8. ieee: M. H. Henzinger, B. Jin, R. Peng, and D. P. Williamson, “A combinatorial cut-toggling algorithm for solving Laplacian linear systems,” Algorithmica, vol. 85. Springer Nature, pp. 2680–3716, 2023. ista: Henzinger MH, Jin B, Peng R, Williamson DP. 2023. A combinatorial cut-toggling algorithm for solving Laplacian linear systems. Algorithmica. 85, 2680–3716. mla: Henzinger, Monika H., et al. “A Combinatorial Cut-Toggling Algorithm for Solving Laplacian Linear Systems.” Algorithmica, vol. 85, Springer Nature, 2023, pp. 2680–3716, doi:10.1007/s00453-023-01154-8. short: M.H. Henzinger, B. Jin, R. Peng, D.P. Williamson, Algorithmica 85 (2023) 2680–3716. date_created: 2023-08-13T22:01:13Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-30T12:33:10Z day: '01' department: - _id: MoHe doi: 10.1007/s00453-023-01154-8 ec_funded: 1 external_id: arxiv: - '2010.16316' isi: - '001041254900002' intvolume: ' 85' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2010.16316 month: '12' oa: 1 oa_version: Preprint page: 2680-3716 project: - _id: bd9ca328-d553-11ed-ba76-dc4f890cfe62 call_identifier: H2020 grant_number: '101019564' name: The design and evaluation of modern fully dynamic data structures - _id: bd9e3a2e-d553-11ed-ba76-8aa684ce17fe grant_number: 'P33775 ' name: Fast Algorithms for a Reactive Network Layer publication: Algorithmica publication_identifier: eissn: - 1432-0541 issn: - 0178-4617 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: A combinatorial cut-toggling algorithm for solving Laplacian linear systems type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 85 year: '2023' ... --- _id: '14087' abstract: - lang: eng text: Polar active matter of self-propelled particles sustain spontaneous flows through the full-integer topological defects. We study theoretically the incompressible flow profiles around ±1 defects induced by polar and dipolar active forces. We show that dipolar forces induce vortical flows around the +1 defect, while the flow around the −1 defect has an 8-fold rotational symmetry. The vortical flow changes its chirality near the +1 defect core in the absence of the friction with a substrate. We show analytically that the flow induced by polar active forces is vortical near the +1 defect and is 4-fold symmetric near the −1 defect, while it becomes uniform in the far-field. For a pair of oppositely charged defects, this polar flow contributes to a mutual interaction force that depends only on the orientation of the defect pair relative to the background polarization, and that enhances defect pair annihilation. This is in contradiction with the effect of dipolar active forces which decay inversely proportional with the defect separation distance. As such, our analyses reveals a long-ranged mechanism for the pairwise interaction between topological defects in polar active matter. acknowledgement: J. Rø and L. A. acknowledge support from the Research Council of Norway through the Center of Excellence funding scheme, Project No. 262644 (PoreLab). A. D. acknowledges funding from the Novo Nordisk Foundation (grant No. NNF18SA0035142 and NERD grant No. NNF21OC0068687), Villum Fonden Grant no. 29476, and the European Union via the ERC-Starting Grant PhysCoMeT. Views and opinions expressed are however those of the authors 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. article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Jonas full_name: Rønning, Jonas last_name: Rønning - first_name: Julian B full_name: Renaud, Julian B id: 7af6767d-14eb-11ed-b536-a32449ae867c last_name: Renaud - first_name: Amin full_name: Doostmohammadi, Amin last_name: Doostmohammadi - first_name: Luiza full_name: Angheluta, Luiza last_name: Angheluta citation: ama: Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. Soft Matter. 2023;39:7513-7527. doi:10.1039/d3sm00316g apa: Rønning, J., Renaud, J. B., Doostmohammadi, A., & Angheluta, L. (2023). Spontaneous flows and dynamics of full-integer topological defects in polar active matter. Soft Matter. Royal Society of Chemistry. https://doi.org/10.1039/d3sm00316g chicago: Rønning, Jonas, Julian B Renaud, Amin Doostmohammadi, and Luiza Angheluta. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” Soft Matter. Royal Society of Chemistry, 2023. https://doi.org/10.1039/d3sm00316g. ieee: J. Rønning, J. B. Renaud, A. Doostmohammadi, and L. Angheluta, “Spontaneous flows and dynamics of full-integer topological defects in polar active matter,” Soft Matter, vol. 39. Royal Society of Chemistry, pp. 7513–7527, 2023. ista: Rønning J, Renaud JB, Doostmohammadi A, Angheluta L. 2023. Spontaneous flows and dynamics of full-integer topological defects in polar active matter. Soft Matter. 39, 7513–7527. mla: Rønning, Jonas, et al. “Spontaneous Flows and Dynamics of Full-Integer Topological Defects in Polar Active Matter.” Soft Matter, vol. 39, Royal Society of Chemistry, 2023, pp. 7513–27, doi:10.1039/d3sm00316g. short: J. Rønning, J.B. Renaud, A. Doostmohammadi, L. Angheluta, Soft Matter 39 (2023) 7513–7527. date_created: 2023-08-20T22:01:15Z date_published: 2023-09-01T00:00:00Z date_updated: 2024-01-30T12:49:24Z day: '01' ddc: - '540' department: - _id: GradSch doi: 10.1039/d3sm00316g external_id: arxiv: - '2303.07063' isi: - '001035766100001' file: - access_level: open_access checksum: b936747170d0b708172b518078c4081a content_type: application/pdf creator: dernst date_created: 2024-01-30T12:48:24Z date_updated: 2024-01-30T12:48:24Z file_id: '14908' file_name: 2023_SoftMatter_Ronning.pdf file_size: 7660662 relation: main_file success: 1 file_date_updated: 2024-01-30T12:48:24Z has_accepted_license: '1' intvolume: ' 39' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 7513-7527 publication: Soft Matter publication_identifier: eissn: - 1744-6848 issn: - 1744-683X publication_status: published publisher: Royal Society of Chemistry quality_controlled: '1' scopus_import: '1' status: public title: Spontaneous flows and dynamics of full-integer topological defects in polar active matter tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 39 year: '2023' ... --- _id: '13319' abstract: - lang: eng text: We prove that the generator of the L2 implementation of a KMS-symmetric quantum Markov semigroup can be expressed as the square of a derivation with values in a Hilbert bimodule, extending earlier results by Cipriani and Sauvageot for tracially symmetric semigroups and the second-named author for GNS-symmetric semigroups. This result hinges on the introduction of a new completely positive map on the algebra of bounded operators on the GNS Hilbert space. This transformation maps symmetric Markov operators to symmetric Markov operators and is essential to obtain the required inner product on the Hilbert bimodule. acknowledgement: The authors are grateful to Martijn Caspers for helpful comments on a preliminary version of this manuscript. M. V. was supported by the NWO Vidi grant VI.Vidi.192.018 ‘Non-commutative harmonic analysis and rigidity of operator algebras’. M. W. was funded by the Austrian Science Fund (FWF) under the Esprit Programme [ESP 156]. For the purpose of Open Access, the authors have applied a CC BY public copyright licence to any Author Accepted Manuscript (AAM) version arising from this submission. Open access funding provided by Austrian Science Fund (FWF). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Matthijs full_name: Vernooij, Matthijs last_name: Vernooij - first_name: Melchior full_name: Wirth, Melchior id: 88644358-0A0E-11EA-8FA5-49A33DDC885E last_name: Wirth orcid: 0000-0002-0519-4241 citation: ama: Vernooij M, Wirth M. Derivations and KMS-symmetric quantum Markov semigroups. Communications in Mathematical Physics. 2023;403:381-416. doi:10.1007/s00220-023-04795-6 apa: Vernooij, M., & Wirth, M. (2023). Derivations and KMS-symmetric quantum Markov semigroups. Communications in Mathematical Physics. Springer Nature. https://doi.org/10.1007/s00220-023-04795-6 chicago: Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric Quantum Markov Semigroups.” Communications in Mathematical Physics. Springer Nature, 2023. https://doi.org/10.1007/s00220-023-04795-6. ieee: M. Vernooij and M. Wirth, “Derivations and KMS-symmetric quantum Markov semigroups,” Communications in Mathematical Physics, vol. 403. Springer Nature, pp. 381–416, 2023. ista: Vernooij M, Wirth M. 2023. Derivations and KMS-symmetric quantum Markov semigroups. Communications in Mathematical Physics. 403, 381–416. mla: Vernooij, Matthijs, and Melchior Wirth. “Derivations and KMS-Symmetric Quantum Markov Semigroups.” Communications in Mathematical Physics, vol. 403, Springer Nature, 2023, pp. 381–416, doi:10.1007/s00220-023-04795-6. short: M. Vernooij, M. Wirth, Communications in Mathematical Physics 403 (2023) 381–416. date_created: 2023-07-30T22:01:03Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-30T12:16:32Z day: '01' ddc: - '510' department: - _id: JaMa doi: 10.1007/s00220-023-04795-6 external_id: arxiv: - '2303.15949' isi: - '001033655400002' file: - access_level: open_access checksum: cca204e81891270216a0c84eb8bcd398 content_type: application/pdf creator: dernst date_created: 2024-01-30T12:15:11Z date_updated: 2024-01-30T12:15:11Z file_id: '14905' file_name: 2023_CommMathPhysics_Vernooij.pdf file_size: 481209 relation: main_file success: 1 file_date_updated: 2024-01-30T12:15:11Z has_accepted_license: '1' intvolume: ' 403' isi: 1 language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 381-416 project: - _id: 34c6ea2d-11ca-11ed-8bc3-c04f3c502833 grant_number: ESP156_N name: Gradient flow techniques for quantum Markov semigroups publication: Communications in Mathematical Physics publication_identifier: eissn: - 1432-0916 issn: - 0010-3616 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Derivations and KMS-symmetric quantum Markov semigroups tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 403 year: '2023' ... --- _id: '14402' abstract: - lang: eng text: Alpha oscillations are a distinctive feature of the awake resting state of the human brain. However, their functional role in resting-state neuronal dynamics remains poorly understood. Here we show that, during resting wakefulness, alpha oscillations drive an alternation of attenuation and amplification bouts in neural activity. Our analysis indicates that inhibition is activated in pulses that last for a single alpha cycle and gradually suppress neural activity, while excitation is successively enhanced over a few alpha cycles to amplify neural activity. Furthermore, we show that long-term alpha amplitude fluctuations—the “waxing and waning” phenomenon—are an attenuation-amplification mechanism described by a power-law decay of the activity rate in the “waning” phase. Importantly, we do not observe such dynamics during non-rapid eye movement (NREM) sleep with marginal alpha oscillations. The results suggest that alpha oscillations modulate neural activity not only through pulses of inhibition (pulsed inhibition hypothesis) but also by timely enhancement of excitation (or disinhibition). acknowledgement: This research was funded in whole or in part by the Austrian Science Fund (FWF) (grant PT1013M03318 to F.L.). For the purpose of open access, the author has applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission. The study was supported by the European Union Horizon 2020 Research and Innovation Program under the Marie Sklodowska-Curie action (grant agreement 754411 to F.L.) and in part by the NextGenerationEU through the grant TAlent in ReSearch@University of Padua – STARS@UNIPD (to F.L.) (project BRAINCIP [brain criticality and information processing]). L.d.A. acknowledges support from the Italian MIUR project PRIN2017WZFTZP and partial support from NEXTGENERATIONEU (NGEU) funded by the Ministry of University and Research (MUR), National Recovery and Resilience Plan (NRRP), and project MNESYS (PE0000006)—a multiscale integrated approach to the study of the nervous system in health and disease (DN. 1553 11.10.2022). O.S. acknowledges support from the Israel Science Foundation, grant 504/17. The work was supported in part by DIRP ZIAMH02797 (to D.P.). article_number: '113162' article_processing_charge: Yes article_type: original author: - first_name: Fabrizio full_name: Lombardi, Fabrizio id: A057D288-3E88-11E9-986D-0CF4E5697425 last_name: Lombardi orcid: 0000-0003-2623-5249 - first_name: Hans J. full_name: Herrmann, Hans J. last_name: Herrmann - first_name: Liborio full_name: Parrino, Liborio last_name: Parrino - first_name: Dietmar full_name: Plenz, Dietmar last_name: Plenz - first_name: Silvia full_name: Scarpetta, Silvia last_name: Scarpetta - first_name: Anna Elisabetta full_name: Vaudano, Anna Elisabetta last_name: Vaudano - first_name: Lucilla full_name: De Arcangelis, Lucilla last_name: De Arcangelis - first_name: Oren full_name: Shriki, Oren last_name: Shriki citation: ama: 'Lombardi F, Herrmann HJ, Parrino L, et al. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. 2023;42(10). doi:10.1016/j.celrep.2023.113162' apa: 'Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2023). Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. Elsevier. https://doi.org/10.1016/j.celrep.2023.113162' chicago: 'Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla De Arcangelis, and Oren Shriki. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” Cell Reports. Elsevier, 2023. https://doi.org/10.1016/j.celrep.2023.113162.' ieee: 'F. Lombardi et al., “Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state,” Cell Reports, vol. 42, no. 10. Elsevier, 2023.' ista: 'Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, De Arcangelis L, Shriki O. 2023. Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state. Cell Reports. 42(10), 113162.' mla: 'Lombardi, Fabrizio, et al. “Beyond Pulsed Inhibition: Alpha Oscillations Modulate Attenuation and Amplification of Neural Activity in the Awake Resting State.” Cell Reports, vol. 42, no. 10, 113162, Elsevier, 2023, doi:10.1016/j.celrep.2023.113162.' short: F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. De Arcangelis, O. Shriki, Cell Reports 42 (2023). date_created: 2023-10-08T22:01:15Z date_published: 2023-10-31T00:00:00Z date_updated: 2024-01-30T14:07:40Z day: '31' ddc: - '570' department: - _id: GaTk doi: 10.1016/j.celrep.2023.113162 ec_funded: 1 external_id: isi: - '001086695500001' pmid: - '37777965' file: - access_level: open_access checksum: 9c71eb2a03aa160415f01ad95f49ceb5 content_type: application/pdf creator: dernst date_created: 2024-01-30T14:07:08Z date_updated: 2024-01-30T14:07:08Z file_id: '14914' file_name: 2023_CellReports_Lombardi.pdf file_size: 5599007 relation: main_file success: 1 file_date_updated: 2024-01-30T14:07:08Z has_accepted_license: '1' intvolume: ' 42' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 project: - _id: eb943429-77a9-11ec-83b8-9f471cdf5c67 grant_number: M03318 name: Functional Advantages of Critical Brain Dynamics - _id: 260C2330-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '754411' name: ISTplus - Postdoctoral Fellowships publication: Cell Reports publication_identifier: eissn: - 2211-1247 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: 'Beyond pulsed inhibition: Alpha oscillations modulate attenuation and amplification of neural activity in the awake resting state' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 42 year: '2023' ... --- _id: '14258' abstract: - lang: eng text: There is currently little evidence that the genetic basis of human phenotype varies significantly across the lifespan. However, time-to-event phenotypes are understudied and can be thought of as reflecting an underlying hazard, which is unlikely to be constant through life when values take a broad range. Here, we find that 74% of 245 genome-wide significant genetic associations with age at natural menopause (ANM) in the UK Biobank show a form of age-specific effect. Nineteen of these replicated discoveries are identified only by our modeling framework, which determines the time dependency of DNA-variant age-at-onset associations without a significant multiple-testing burden. Across the range of early to late menopause, we find evidence for significantly different underlying biological pathways, changes in the signs of genetic correlations of ANM to health indicators and outcomes, and differences in inferred causal relationships. We find that DNA damage response processes only act to shape ovarian reserve and depletion for women of early ANM. Genetically mediated delays in ANM were associated with increased relative risk of breast cancer and leiomyoma at all ages and with high cholesterol and heart failure for late-ANM women. These findings suggest that a better understanding of the age dependency of genetic risk factor relationships among health indicators and outcomes is achievable through appropriate statistical modeling of large-scale biobank data. acknowledgement: This project was funded by an SNSF Eccellenza grant to M.R.R. (PCEGP3-181181) and by core funding from the Institute of Science and Technology Austria. K.L. and R.M. were supported by the Estonian Research Council grant 1911. Estonian Biobank computations were performed in the High-Performance Computing Center, University of Tartu. We thank Triin Laisk for her valuable insights and comments that helped greatly. We would like to acknowledge the participants and investigators of UK Biobank and Estonian Biobank studies. This project uses UK Biobank data under project number 35520. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Sven E. full_name: Ojavee, Sven E. last_name: Ojavee - first_name: Liza full_name: Darrous, Liza last_name: Darrous - first_name: Marion full_name: Patxot, Marion last_name: Patxot - first_name: Kristi full_name: Läll, Kristi last_name: Läll - first_name: Krista full_name: Fischer, Krista last_name: Fischer - first_name: Reedik full_name: Mägi, Reedik last_name: Mägi - first_name: Zoltan full_name: Kutalik, Zoltan last_name: Kutalik - first_name: Matthew Richard full_name: Robinson, Matthew Richard id: E5D42276-F5DA-11E9-8E24-6303E6697425 last_name: Robinson orcid: 0000-0001-8982-8813 citation: ama: Ojavee SE, Darrous L, Patxot M, et al. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. American Journal of Human Genetics. 2023;110(9):1549-1563. doi:10.1016/j.ajhg.2023.07.006 apa: Ojavee, S. E., Darrous, L., Patxot, M., Läll, K., Fischer, K., Mägi, R., … Robinson, M. R. (2023). Genetic insights into the age-specific biological mechanisms governing human ovarian aging. American Journal of Human Genetics. Elsevier. https://doi.org/10.1016/j.ajhg.2023.07.006 chicago: Ojavee, Sven E., Liza Darrous, Marion Patxot, Kristi Läll, Krista Fischer, Reedik Mägi, Zoltan Kutalik, and Matthew Richard Robinson. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” American Journal of Human Genetics. Elsevier, 2023. https://doi.org/10.1016/j.ajhg.2023.07.006. ieee: S. E. Ojavee et al., “Genetic insights into the age-specific biological mechanisms governing human ovarian aging,” American Journal of Human Genetics, vol. 110, no. 9. Elsevier, pp. 1549–1563, 2023. ista: Ojavee SE, Darrous L, Patxot M, Läll K, Fischer K, Mägi R, Kutalik Z, Robinson MR. 2023. Genetic insights into the age-specific biological mechanisms governing human ovarian aging. American Journal of Human Genetics. 110(9), 1549–1563. mla: Ojavee, Sven E., et al. “Genetic Insights into the Age-Specific Biological Mechanisms Governing Human Ovarian Aging.” American Journal of Human Genetics, vol. 110, no. 9, Elsevier, 2023, pp. 1549–63, doi:10.1016/j.ajhg.2023.07.006. short: S.E. Ojavee, L. Darrous, M. Patxot, K. Läll, K. Fischer, R. Mägi, Z. Kutalik, M.R. Robinson, American Journal of Human Genetics 110 (2023) 1549–1563. date_created: 2023-09-03T22:01:15Z date_published: 2023-09-07T00:00:00Z date_updated: 2024-01-30T13:21:05Z day: '07' ddc: - '570' department: - _id: MaRo doi: 10.1016/j.ajhg.2023.07.006 external_id: pmid: - '37543033' file: - access_level: open_access checksum: 4108b031dc726ae6b4a5ae7e021ba188 content_type: application/pdf creator: dernst date_created: 2024-01-30T13:20:35Z date_updated: 2024-01-30T13:20:35Z file_id: '14912' file_name: 2023_AJHG_Ojavee.pdf file_size: 2551276 relation: main_file success: 1 file_date_updated: 2024-01-30T13:20:35Z has_accepted_license: '1' intvolume: ' 110' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 1549-1563 pmid: 1 publication: American Journal of Human Genetics publication_identifier: eissn: - 1537-6605 issn: - 0002-9297 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Genetic insights into the age-specific biological mechanisms governing human ovarian aging tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 110 year: '2023' ... --- _id: '14244' abstract: - lang: eng text: "In this paper, we determine the motivic class — in particular, the weight polynomial and conjecturally the Poincaré polynomial — of the open de Rham space, defined and studied by Boalch, of certain moduli spaces of irregular meromorphic connections on the trivial rank \r\n bundle on P1. The computation is by motivic Fourier transform. We show that the result satisfies the purity conjecture, that is, it agrees with the pure part of the conjectured mixed Hodge polynomial of the corresponding wild character variety. We also identify the open de Rham spaces with quiver varieties with multiplicities of Yamakawa and Geiss–Leclerc–Schröer. We finish with constructing natural complete hyperkähler metrics on them, which in the four-dimensional cases are expected to be of type ALF." acknowledgement: We would like to thank Gergely Bérczy, Roger Bielawski, Philip Boalch, Sergey Cherkis, Andrew Dancer, Brent Doran, Eloïse Hamilton, Frances Kirwan, Bernard Leclerc, Emmanuel Letellier, Alessia Mandini, Maxence Mayrand, András Némethi, Szilárd Szabó, and Daisuke Yamakawa for discussions related to the paper. We especially thank the referee for an extensive list of very careful comments. At various stages of this project, the authors were supported by the Advanced Grant “Arithmetic and physics of Higgs moduli spaces” no. 320593 of the European Research Council, by grant no. 153627 and NCCR SwissMAP, both funded by the Swiss National Science Foundation as well as by EPF Lausanne and IST Austria. In the final stages of this project, MLW was supported by SFB/TR 45 “Periods, moduli and arithmetic of algebraic varieties,” subproject M08-10 “Moduli of vector bundles on higher-dimensional varieties.” DW was also supported by the Fondation Sciences Mathématiques de Paris, as well as public grants overseen by the Agence national de la recherche (ANR) of France as part of the Investissements d'avenir program, under reference numbers ANR-10-LABX-0098 and ANR-15-CE40-0008 (Défigéo). article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Tamás full_name: Hausel, Tamás id: 4A0666D8-F248-11E8-B48F-1D18A9856A87 last_name: Hausel - first_name: Michael Lennox full_name: Wong, Michael Lennox last_name: Wong - first_name: Dimitri full_name: Wyss, Dimitri last_name: Wyss citation: ama: Hausel T, Wong ML, Wyss D. Arithmetic and metric aspects of open de Rham spaces. Proceedings of the London Mathematical Society. 2023;127(4):958-1027. doi:10.1112/plms.12555 apa: Hausel, T., Wong, M. L., & Wyss, D. (2023). Arithmetic and metric aspects of open de Rham spaces. Proceedings of the London Mathematical Society. Wiley. https://doi.org/10.1112/plms.12555 chicago: Hausel, Tamás, Michael Lennox Wong, and Dimitri Wyss. “Arithmetic and Metric Aspects of Open de Rham Spaces.” Proceedings of the London Mathematical Society. Wiley, 2023. https://doi.org/10.1112/plms.12555. ieee: T. Hausel, M. L. Wong, and D. Wyss, “Arithmetic and metric aspects of open de Rham spaces,” Proceedings of the London Mathematical Society, vol. 127, no. 4. Wiley, pp. 958–1027, 2023. ista: Hausel T, Wong ML, Wyss D. 2023. Arithmetic and metric aspects of open de Rham spaces. Proceedings of the London Mathematical Society. 127(4), 958–1027. mla: Hausel, Tamás, et al. “Arithmetic and Metric Aspects of Open de Rham Spaces.” Proceedings of the London Mathematical Society, vol. 127, no. 4, Wiley, 2023, pp. 958–1027, doi:10.1112/plms.12555. short: T. Hausel, M.L. Wong, D. Wyss, Proceedings of the London Mathematical Society 127 (2023) 958–1027. date_created: 2023-08-27T22:01:18Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-30T12:56:10Z day: '01' ddc: - '510' department: - _id: TaHa doi: 10.1112/plms.12555 ec_funded: 1 external_id: arxiv: - '1807.04057' isi: - '001049312700001' file: - access_level: open_access checksum: 2af4d2d6a8ae42f7d3fba0188e79ae82 content_type: application/pdf creator: dernst date_created: 2024-01-30T12:56:00Z date_updated: 2024-01-30T12:56:00Z file_id: '14910' file_name: 2023_ProcLondonMathSoc_Hausel.pdf file_size: 651335 relation: main_file success: 1 file_date_updated: 2024-01-30T12:56:00Z has_accepted_license: '1' intvolume: ' 127' isi: 1 issue: '4' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 958-1027 project: - _id: 25E549F4-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '320593' name: Arithmetic and physics of Higgs moduli spaces - _id: 25E6C798-B435-11E9-9278-68D0E5697425 grant_number: '153627' name: Arithmetic quantization of character and quiver varities publication: Proceedings of the London Mathematical Society publication_identifier: eissn: - 1460-244X issn: - 0024-6115 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Arithmetic and metric aspects of open de Rham spaces tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 127 year: '2023' ... --- _id: '14080' abstract: - lang: eng text: Extracellular signal-regulated kinase (ERK) has been recognized as a critical regulator in various physiological and pathological processes. Extensive research has elucidated the signaling mechanisms governing ERK activation via biochemical regulations with upstream molecules, particularly receptor tyrosine kinases (RTKs). However, recent advances have highlighted the role of mechanical forces in activating the RTK–ERK signaling pathways, thereby opening new avenues of research into mechanochemical interplay in multicellular tissues. Here, we review the force-induced ERK activation in cells and propose possible mechanosensing mechanisms underlying the mechanoresponsive ERK activation. We conclude that mechanical forces are not merely passive factors shaping cells and tissues but also active regulators of cellular signaling pathways controlling collective cell behaviors. acknowledgement: TH was supported by JSPS KAKENHI Grant (no. 21H05290) and the Ministry of Education under the Research Centres of Excellence programme through the Mechanobiology Institute at National University of Singapore and by Department of Physiology at National University of Singapore. NH was supported by JSPS KAKENHI Grant (no. 20K22653). KA was supported by JSPS KAKENHI Grants (no. 19H05798 and no. 22H02625). MM was supported by JSPS KAKENHI Grants (no. 19H00993 and no. 20H05898) and JST Moonshot R&D Grant JPMJPS2022. We appreciate Virgile Viasnoff and the lab members for their valuable comments on the manuscript. We apologize to authors whose work could not be highlighted due to space limitations. article_number: '102217' article_processing_charge: Yes (in subscription journal) article_type: review author: - first_name: Tsuyoshi full_name: Hirashima, Tsuyoshi last_name: Hirashima - first_name: Naoya full_name: Hino, Naoya id: 5299a9ce-7679-11eb-a7bc-d1e62b936307 last_name: Hino - first_name: Kazuhiro full_name: Aoki, Kazuhiro last_name: Aoki - first_name: Michiyuki full_name: Matsuda, Michiyuki last_name: Matsuda citation: ama: Hirashima T, Hino N, Aoki K, Matsuda M. Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation. Current Opinion in Cell Biology. 2023;84(10). doi:10.1016/j.ceb.2023.102217 apa: Hirashima, T., Hino, N., Aoki, K., & Matsuda, M. (2023). Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation. Current Opinion in Cell Biology. Elsevier. https://doi.org/10.1016/j.ceb.2023.102217 chicago: Hirashima, Tsuyoshi, Naoya Hino, Kazuhiro Aoki, and Michiyuki Matsuda. “Stretching the Limits of Extracellular Signal-Related Kinase (ERK) Signaling — Cell Mechanosensing to ERK Activation.” Current Opinion in Cell Biology. Elsevier, 2023. https://doi.org/10.1016/j.ceb.2023.102217. ieee: T. Hirashima, N. Hino, K. Aoki, and M. Matsuda, “Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation,” Current Opinion in Cell Biology, vol. 84, no. 10. Elsevier, 2023. ista: Hirashima T, Hino N, Aoki K, Matsuda M. 2023. Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation. Current Opinion in Cell Biology. 84(10), 102217. mla: Hirashima, Tsuyoshi, et al. “Stretching the Limits of Extracellular Signal-Related Kinase (ERK) Signaling — Cell Mechanosensing to ERK Activation.” Current Opinion in Cell Biology, vol. 84, no. 10, 102217, Elsevier, 2023, doi:10.1016/j.ceb.2023.102217. short: T. Hirashima, N. Hino, K. Aoki, M. Matsuda, Current Opinion in Cell Biology 84 (2023). date_created: 2023-08-20T22:01:12Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-30T12:52:42Z day: '01' ddc: - '570' department: - _id: CaHe doi: 10.1016/j.ceb.2023.102217 external_id: isi: - '001054692200001' pmid: - '37574635' file: - access_level: open_access checksum: 25923f8ae71344e8974530dd23c71bdc content_type: application/pdf creator: dernst date_created: 2024-01-30T12:52:12Z date_updated: 2024-01-30T12:52:12Z file_id: '14909' file_name: 2023_CurrentOpinionCellBio_Hirashima.pdf file_size: 1173762 relation: main_file success: 1 file_date_updated: 2024-01-30T12:52:12Z has_accepted_license: '1' intvolume: ' 84' isi: 1 issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version pmid: 1 publication: Current Opinion in Cell Biology publication_identifier: eissn: - 1879-0410 issn: - 0955-0674 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Stretching the limits of extracellular signal-related kinase (ERK) signaling — Cell mechanosensing to ERK activation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 84 year: '2023' ... --- _id: '13165' abstract: - lang: eng text: "A graph G=(V, E) is called fully regular if for every independent set I c V, the number of vertices in V\\I that are not connected to any element of I depends only on the size of I. A linear ordering of the vertices of G is called successive if for every i, the first i vertices induce a connected subgraph of G. We give an explicit formula for the number of successive vertex orderings of a fully regular graph.\r\nAs an application of our results, we give alternative proofs of two theorems of Stanley and Gao & Peng, determining the number of linear edge orderings of complete graphs and complete bipartite graphs, respectively, with the property that the first i edges induce a connected subgraph.\r\nAs another application, we give a simple product formula for the number of linear orderings of the hyperedges of a complete 3-partite 3-uniform hypergraph such that, for every i, the first i hyperedges induce a connected subgraph. We found similar formulas for complete (non-partite) 3-uniform hypergraphs and in another closely related case, but we managed to verify them only when the number of vertices is small." article_number: '105776' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Lixing full_name: Fang, Lixing last_name: Fang - first_name: Hao full_name: Huang, Hao last_name: Huang - first_name: János full_name: Pach, János id: E62E3130-B088-11EA-B919-BF823C25FEA4 last_name: Pach - first_name: Gábor full_name: Tardos, Gábor last_name: Tardos - first_name: Junchi full_name: Zuo, Junchi last_name: Zuo citation: ama: Fang L, Huang H, Pach J, Tardos G, Zuo J. Successive vertex orderings of fully regular graphs. Journal of Combinatorial Theory Series A. 2023;199(10). doi:10.1016/j.jcta.2023.105776 apa: Fang, L., Huang, H., Pach, J., Tardos, G., & Zuo, J. (2023). Successive vertex orderings of fully regular graphs. Journal of Combinatorial Theory. Series A. Elsevier. https://doi.org/10.1016/j.jcta.2023.105776 chicago: Fang, Lixing, Hao Huang, János Pach, Gábor Tardos, and Junchi Zuo. “Successive Vertex Orderings of Fully Regular Graphs.” Journal of Combinatorial Theory. Series A. Elsevier, 2023. https://doi.org/10.1016/j.jcta.2023.105776. ieee: L. Fang, H. Huang, J. Pach, G. Tardos, and J. Zuo, “Successive vertex orderings of fully regular graphs,” Journal of Combinatorial Theory. Series A, vol. 199, no. 10. Elsevier, 2023. ista: Fang L, Huang H, Pach J, Tardos G, Zuo J. 2023. Successive vertex orderings of fully regular graphs. Journal of Combinatorial Theory. Series A. 199(10), 105776. mla: Fang, Lixing, et al. “Successive Vertex Orderings of Fully Regular Graphs.” Journal of Combinatorial Theory. Series A, vol. 199, no. 10, 105776, Elsevier, 2023, doi:10.1016/j.jcta.2023.105776. short: L. Fang, H. Huang, J. Pach, G. Tardos, J. Zuo, Journal of Combinatorial Theory. Series A 199 (2023). date_created: 2023-06-25T22:00:45Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-01-30T12:03:51Z day: '01' ddc: - '510' department: - _id: HeEd doi: 10.1016/j.jcta.2023.105776 external_id: arxiv: - '2206.13592' file: - access_level: open_access checksum: 9eebc213b4182a66063a99083ff5bd04 content_type: application/pdf creator: dernst date_created: 2024-01-30T12:03:10Z date_updated: 2024-01-30T12:03:10Z file_id: '14902' file_name: 2023_JourCombinatiorialTheory_Fang.pdf file_size: 352555 relation: main_file success: 1 file_date_updated: 2024-01-30T12:03:10Z has_accepted_license: '1' intvolume: ' 199' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version publication: Journal of Combinatorial Theory. Series A publication_identifier: eissn: - 1096-0899 issn: - 0097-3165 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Successive vertex orderings of fully regular graphs tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 199 year: '2023' ... --- _id: '14409' abstract: - lang: eng text: We present a photon- and metal-free approach for the radical fluorination of aliphatic oxalate-activated alcohols. The method relies on the spontaneous generation of the N-(chloromethyl)triethylenediamine radical dication, a potent single electron oxidant, from Selectfluor and 4-(dimethylamino)pyridine. The protocol is easily scalable and provides the desired fluorinated products within only a few minutes reaction time. acknowledgement: We gratefully acknowledge the Max-Planck Society and the Institute of Science and Technology Austria (ISTA) for generous financial support. We also thank the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy – EXC 2008 – 390540038 – UniSysCat for funding. B.P. thanks the Boehringer Ingelheim Foundation for funding through the Plus 3 Perspectives Programme. article_number: e202300769 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Haralds full_name: Baunis, Haralds id: 2eea55ec-e8ec-11ed-86cb-d9c76787acfe last_name: Baunis - first_name: Bartholomäus full_name: Pieber, Bartholomäus id: 93e5e5b2-0da6-11ed-8a41-af589a024726 last_name: Pieber orcid: 0000-0001-8689-388X citation: ama: Baunis H, Pieber B. Formal radical deoxyfluorination of oxalate-activated alcohols triggered by the selectfluor-DMAP charge-transfer complex. European Journal of Organic Chemistry. 2023;26(42). doi:10.1002/ejoc.202300769 apa: Baunis, H., & Pieber, B. (2023). Formal radical deoxyfluorination of oxalate-activated alcohols triggered by the selectfluor-DMAP charge-transfer complex. European Journal of Organic Chemistry. Wiley. https://doi.org/10.1002/ejoc.202300769 chicago: Baunis, Haralds, and Bartholomäus Pieber. “Formal Radical Deoxyfluorination of Oxalate-Activated Alcohols Triggered by the Selectfluor-DMAP Charge-Transfer Complex.” European Journal of Organic Chemistry. Wiley, 2023. https://doi.org/10.1002/ejoc.202300769. ieee: H. Baunis and B. Pieber, “Formal radical deoxyfluorination of oxalate-activated alcohols triggered by the selectfluor-DMAP charge-transfer complex,” European Journal of Organic Chemistry, vol. 26, no. 42. Wiley, 2023. ista: Baunis H, Pieber B. 2023. Formal radical deoxyfluorination of oxalate-activated alcohols triggered by the selectfluor-DMAP charge-transfer complex. European Journal of Organic Chemistry. 26(42), e202300769. mla: Baunis, Haralds, and Bartholomäus Pieber. “Formal Radical Deoxyfluorination of Oxalate-Activated Alcohols Triggered by the Selectfluor-DMAP Charge-Transfer Complex.” European Journal of Organic Chemistry, vol. 26, no. 42, e202300769, Wiley, 2023, doi:10.1002/ejoc.202300769. short: H. Baunis, B. Pieber, European Journal of Organic Chemistry 26 (2023). date_created: 2023-10-08T22:01:18Z date_published: 2023-11-07T00:00:00Z date_updated: 2024-01-30T14:05:14Z day: '07' ddc: - '540' department: - _id: BaPi doi: 10.1002/ejoc.202300769 external_id: isi: - '001072666500001' file: - access_level: open_access checksum: e8ad7865acd94672e476f273ccf3d542 content_type: application/pdf creator: dernst date_created: 2024-01-30T14:04:44Z date_updated: 2024-01-30T14:04:44Z file_id: '14913' file_name: 2023_EurJOrgChem_Baunis.pdf file_size: 3277622 relation: main_file success: 1 file_date_updated: 2024-01-30T14:04:44Z has_accepted_license: '1' intvolume: ' 26' isi: 1 issue: '42' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: European Journal of Organic Chemistry publication_identifier: eissn: - 1099-0690 issn: - 1434-193X publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Formal radical deoxyfluorination of oxalate-activated alcohols triggered by the selectfluor-DMAP charge-transfer complex tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 26 year: '2023' ... --- _id: '14254' abstract: - lang: eng text: In [10] Nam proved a Lieb–Thirring Inequality for the kinetic energy of a fermionic quantum system, with almost optimal (semi-classical) constant and a gradient correction term. We present a stronger version of this inequality, with a much simplified proof. As a corollary we obtain a simple proof of the original Lieb–Thirring inequality. acknowledgement: J.P.S. thanks the Institute of Science and Technology Austria for the hospitality and support during a visit where this work was done. J.P.S. was also partially supported by the VILLUM Centre of Excellence for the Mathematics of Quantum Theory (QMATH) (grant No. 10059). article_number: '110129' article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 - first_name: Jan Philip full_name: Solovej, Jan Philip last_name: Solovej citation: ama: Seiringer R, Solovej JP. A simple approach to Lieb-Thirring type inequalities. Journal of Functional Analysis. 2023;285(10). doi:10.1016/j.jfa.2023.110129 apa: Seiringer, R., & Solovej, J. P. (2023). A simple approach to Lieb-Thirring type inequalities. Journal of Functional Analysis. Elsevier. https://doi.org/10.1016/j.jfa.2023.110129 chicago: Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring Type Inequalities.” Journal of Functional Analysis. Elsevier, 2023. https://doi.org/10.1016/j.jfa.2023.110129. ieee: R. Seiringer and J. P. Solovej, “A simple approach to Lieb-Thirring type inequalities,” Journal of Functional Analysis, vol. 285, no. 10. Elsevier, 2023. ista: Seiringer R, Solovej JP. 2023. A simple approach to Lieb-Thirring type inequalities. Journal of Functional Analysis. 285(10), 110129. mla: Seiringer, Robert, and Jan Philip Solovej. “A Simple Approach to Lieb-Thirring Type Inequalities.” Journal of Functional Analysis, vol. 285, no. 10, 110129, Elsevier, 2023, doi:10.1016/j.jfa.2023.110129. short: R. Seiringer, J.P. Solovej, Journal of Functional Analysis 285 (2023). date_created: 2023-09-03T22:01:14Z date_published: 2023-11-15T00:00:00Z date_updated: 2024-01-30T14:17:23Z day: '15' ddc: - '510' department: - _id: RoSe doi: 10.1016/j.jfa.2023.110129 external_id: arxiv: - '2303.04504' isi: - '001071552300001' file: - access_level: open_access checksum: 28e424ad91be6219e9d321054ce3a412 content_type: application/pdf creator: dernst date_created: 2024-01-30T14:15:16Z date_updated: 2024-01-30T14:15:16Z file_id: '14915' file_name: 2023_JourFunctionalAnalysis_Seiringer.pdf file_size: 232934 relation: main_file success: 1 file_date_updated: 2024-01-30T14:15:16Z has_accepted_license: '1' intvolume: ' 285' isi: 1 issue: '10' language: - iso: eng month: '11' oa: 1 oa_version: Published Version publication: Journal of Functional Analysis publication_identifier: eissn: - 1096-0783 issn: - 0022-1236 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: A simple approach to Lieb-Thirring type inequalities tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 285 year: '2023' ... --- _id: '14362' abstract: - lang: eng text: "Motivated by recent applications to entropy theory in dynamical systems, we generalise notions introduced by Matthews and define weakly weighted and componentwise weakly weighted (generalised) quasi-metrics. We then systematise and extend to full generality the correspondences between these objects and other structures arising in theoretical computer science and dynamics. In particular, we study the correspondences with weak partial metrics and, if the underlying space is a semilattice, with invariant (generalised) quasi-metrics satisfying the descending path condition, and with strictly monotone semi(-co-)valuations.\r\nWe conclude discussing, for endomorphisms of generalised quasi-metric semilattices, a generalisation of both the known intrinsic semilattice entropy and the semigroup entropy." article_number: '114129' article_processing_charge: No article_type: original author: - first_name: Ilaria full_name: Castellano, Ilaria last_name: Castellano - first_name: Anna full_name: Giordano Bruno, Anna last_name: Giordano Bruno - first_name: Nicolò full_name: Zava, Nicolò id: c8b3499c-7a77-11eb-b046-aa368cbbf2ad last_name: Zava orcid: 0000-0001-8686-1888 citation: ama: Castellano I, Giordano Bruno A, Zava N. Weakly weighted generalised quasi-metric spaces and semilattices. Theoretical Computer Science. 2023;977. doi:10.1016/j.tcs.2023.114129 apa: Castellano, I., Giordano Bruno, A., & Zava, N. (2023). Weakly weighted generalised quasi-metric spaces and semilattices. Theoretical Computer Science. Elsevier. https://doi.org/10.1016/j.tcs.2023.114129 chicago: Castellano, Ilaria, Anna Giordano Bruno, and Nicolò Zava. “Weakly Weighted Generalised Quasi-Metric Spaces and Semilattices.” Theoretical Computer Science. Elsevier, 2023. https://doi.org/10.1016/j.tcs.2023.114129. ieee: I. Castellano, A. Giordano Bruno, and N. Zava, “Weakly weighted generalised quasi-metric spaces and semilattices,” Theoretical Computer Science, vol. 977. Elsevier, 2023. ista: Castellano I, Giordano Bruno A, Zava N. 2023. Weakly weighted generalised quasi-metric spaces and semilattices. Theoretical Computer Science. 977, 114129. mla: Castellano, Ilaria, et al. “Weakly Weighted Generalised Quasi-Metric Spaces and Semilattices.” Theoretical Computer Science, vol. 977, 114129, Elsevier, 2023, doi:10.1016/j.tcs.2023.114129. short: I. Castellano, A. Giordano Bruno, N. Zava, Theoretical Computer Science 977 (2023). date_created: 2023-09-24T22:01:11Z date_published: 2023-10-25T00:00:00Z date_updated: 2024-01-30T13:22:04Z day: '25' department: - _id: HeEd doi: 10.1016/j.tcs.2023.114129 external_id: arxiv: - '2212.08424' isi: - '001076934000001' intvolume: ' 977' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: 'https://doi.org/10.48550/arXiv.2212.08424 ' month: '10' oa: 1 oa_version: Preprint publication: Theoretical Computer Science publication_identifier: issn: - 0304-3975 publication_status: published publisher: Elsevier quality_controlled: '1' scopus_import: '1' status: public title: Weakly weighted generalised quasi-metric spaces and semilattices type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 977 year: '2023' ... --- _id: '14401' abstract: - lang: eng text: "Background: \r\nPro-apoptotic BAX is a central mediator of retinal ganglion cell (RGC) death after optic nerve damage. BAX activation occurs in two stages including translocation of latent BAX to the mitochondrial outer membrane (MOM) and then permeabilization of the MOM to facilitate the release of apoptotic signaling molecules. As a critical component of RGC death, BAX is an attractive target for neuroprotective therapies and an understanding of the kinetics of BAX activation and the mechanisms controlling the two stages of this process in RGCs is potentially valuable in informing the development of a neuroprotective strategy.\r\nMethods:\r\nThe kinetics of BAX translocation were assessed by both static and live-cell imaging of a GFP-BAX fusion protein introduced into RGCs using AAV2-mediated gene transfer in mice. Activation of BAX was achieved using an acute optic nerve crush (ONC) protocol. Live-cell imaging of GFP-BAX was achieved using explants of mouse retina harvested 7 days after ONC. Kinetics of translocation in RGCs were compared to GFP-BAX translocation in 661W tissue culture cells. Permeabilization of GFP-BAX was assessed by staining with the 6A7 monoclonal antibody, which recognizes a conformational change in this protein after MOM insertion. Assessment of individual kinases associated with both stages of activation was made using small molecule inhibitors injected into the vitreous either independently or in concert with ONC surgery. The contribution of the Dual Leucine Zipper-JUN-N-Terminal Kinase cascade was evaluated using mice with a double conditional knock-out of both Mkk4 and Mkk7.\r\nResults:\r\nONC induces the translocation of GFP-BAX in RGCs at a slower rate and with less intracellular synchronicity than 661W cells, but exhibits less variability among mitochondrial foci within a single cell. GFP-BAX was also found to translocate in all compartments of an RGC including the dendritic arbor and axon. Approximately 6% of translocating RGCs exhibited retrotranslocation of BAX immediately following translocation. Unlike tissue culture cells, which exhibit simultaneous translocation and permeabilization, RGCs exhibited a significant delay between these two stages, similar to detached cells undergoing anoikis. Translocation, with minimal permeabilization could be induced in a subset of RGCs using an inhibitor of Focal Adhesion Kinase (PF573228). Permeabilization after ONC, in a majority of RGCs, could be inhibited with a broad spectrum kinase inhibitor (sunitinib) or a selective inhibitor for p38/MAPK14 (SB203580). Intervention of DLK-JNK axis signaling abrogated GFP-BAX translocation after ONC.\r\nConclusions:\r\nA comparison between BAX activation kinetics in tissue culture cells and in cells of a complex tissue environment shows distinct differences indicating that caution should be used when translating findings from one condition to the other. RGCs exhibit both a delay between translocation and permeabilization and the ability for translocated BAX to be retrotranslocated, suggesting several stages at which intervention of the activation process could be exploited in the design of a therapeutic strategy." acknowledgement: "The authors would like to thank Mr. Joel Dietz for management of the mouse colony and helpful advice for conducting quantitative PCR studies and Mr. Santoshi Kinoshita at the Translational Research Initiative in Pathology laboratory at the University of Wisconsin-Madison for cutting sections analyzed in this study.\r\nThis work was supported by National Eye Institute grants R01 EY030123 (RWN), R01 EY018606 (RTL), P30 EY016665 (Department of Ophthalmology and Visual Sciences, University of Wisconsin-Madison), T32 EY027721 (RJD) and F31 EY030739 (OJM). Additional funding was provided by the BrightFocus Foundation (RWN) and unrestricted grants from Research to Prevent Blindness, Inc to the Department of Ophthalmology and Visual Sciences (University of Wisconsin-Madison) and to the Department of Ophthalmology (University of Rochester)." article_number: '67' article_processing_charge: Yes article_type: original author: - first_name: Margaret E full_name: Maes, Margaret E id: 3838F452-F248-11E8-B48F-1D18A9856A87 last_name: Maes orcid: 0000-0001-9642-1085 - first_name: Ryan J. full_name: Donahue, Ryan J. last_name: Donahue - first_name: Cassandra L. full_name: Schlamp, Cassandra L. last_name: Schlamp - first_name: Olivia J. full_name: Marola, Olivia J. last_name: Marola - first_name: Richard T. full_name: Libby, Richard T. last_name: Libby - first_name: Robert W. full_name: Nickells, Robert W. last_name: Nickells citation: ama: Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. Molecular Neurodegeneration. 2023;18. doi:10.1186/s13024-023-00659-8 apa: Maes, M. E., Donahue, R. J., Schlamp, C. L., Marola, O. J., Libby, R. T., & Nickells, R. W. (2023). BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. Molecular Neurodegeneration. Springer Nature. https://doi.org/10.1186/s13024-023-00659-8 chicago: Maes, Margaret E, Ryan J. Donahue, Cassandra L. Schlamp, Olivia J. Marola, Richard T. Libby, and Robert W. Nickells. “BAX Activation in Mouse Retinal Ganglion Cells Occurs in Two Temporally and Mechanistically Distinct Steps.” Molecular Neurodegeneration. Springer Nature, 2023. https://doi.org/10.1186/s13024-023-00659-8. ieee: M. E. Maes, R. J. Donahue, C. L. Schlamp, O. J. Marola, R. T. Libby, and R. W. Nickells, “BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps,” Molecular Neurodegeneration, vol. 18. Springer Nature, 2023. ista: Maes ME, Donahue RJ, Schlamp CL, Marola OJ, Libby RT, Nickells RW. 2023. BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps. Molecular Neurodegeneration. 18, 67. mla: Maes, Margaret E., et al. “BAX Activation in Mouse Retinal Ganglion Cells Occurs in Two Temporally and Mechanistically Distinct Steps.” Molecular Neurodegeneration, vol. 18, 67, Springer Nature, 2023, doi:10.1186/s13024-023-00659-8. short: M.E. Maes, R.J. Donahue, C.L. Schlamp, O.J. Marola, R.T. Libby, R.W. Nickells, Molecular Neurodegeneration 18 (2023). date_created: 2023-10-08T22:01:15Z date_published: 2023-09-26T00:00:00Z date_updated: 2024-01-30T14:34:21Z day: '26' ddc: - '570' department: - _id: SaSi doi: 10.1186/s13024-023-00659-8 external_id: isi: - '001071403800001' pmid: - '37292963' file: - access_level: open_access checksum: 3aa218ddea4a082d8fd5e196ae55ca06 content_type: application/pdf creator: dernst date_created: 2024-01-30T14:33:31Z date_updated: 2024-01-30T14:33:31Z file_id: '14917' file_name: 2023_MolecularNeurodegeneration_Maes.pdf file_size: 11568350 relation: main_file success: 1 file_date_updated: 2024-01-30T14:33:31Z has_accepted_license: '1' intvolume: ' 18' isi: 1 language: - iso: eng month: '09' oa: 1 oa_version: Published Version pmid: 1 publication: Molecular Neurodegeneration publication_identifier: eissn: - 1750-1326 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: BAX activation in mouse retinal ganglion cells occurs in two temporally and mechanistically distinct steps tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 18 year: '2023' ... --- _id: '14489' abstract: - lang: eng text: Microwave-optics entanglement is a vital component for building hybrid quantum networks. Here, a new mechanism for preparing stationary entanglement between microwave and optical cavity fields in a cavity optomagnomechanical system is proposed. It consists of a magnon mode in a ferrimagnetic crystal that couples directly to a microwave cavity mode via the magnetic dipole interaction and indirectly to an optical cavity through the deformation displacement of the crystal. The mechanical displacement is induced by the magnetostrictive force and coupled to the optical cavity via radiation pressure. Both the opto- and magnomechanical couplings are dispersive. Magnon–phonon entanglement is created via magnomechanical parametric down-conversion, which is further distributed to optical and microwave photons via simultaneous optomechanical beamsplitter interaction and electromagnonic state-swap interaction, yielding stationary microwave-optics entanglement. The microwave-optics entanglement is robust against thermal noise, which will find broad potential applications in quantum networks and quantum information processing with hybrid quantum systems. acknowledgement: This work was supported by the National Key Research and Development Program of China (Grant no. 2022YFA1405200), the National Natural Science Foundation of China (Nos. 92265202), and the European Research Council (ERC CoG Q-ECHOS, 101001005). article_number: '2200866' article_processing_charge: No article_type: original author: - first_name: Zhi Yuan full_name: Fan, Zhi Yuan last_name: Fan - first_name: Liu full_name: Qiu, Liu id: 45e99c0d-1eb1-11eb-9b96-ed8ab2983cac last_name: Qiu orcid: 0000-0003-4345-4267 - first_name: Simon full_name: Gröblacher, Simon last_name: Gröblacher - first_name: Jie full_name: Li, Jie last_name: Li citation: ama: Fan ZY, Qiu L, Gröblacher S, Li J. Microwave-optics entanglement via cavity optomagnomechanics. Laser and Photonics Reviews. 2023;17(12). doi:10.1002/lpor.202200866 apa: Fan, Z. Y., Qiu, L., Gröblacher, S., & Li, J. (2023). Microwave-optics entanglement via cavity optomagnomechanics. Laser and Photonics Reviews. Wiley. https://doi.org/10.1002/lpor.202200866 chicago: Fan, Zhi Yuan, Liu Qiu, Simon Gröblacher, and Jie Li. “Microwave-Optics Entanglement via Cavity Optomagnomechanics.” Laser and Photonics Reviews. Wiley, 2023. https://doi.org/10.1002/lpor.202200866. ieee: Z. Y. Fan, L. Qiu, S. Gröblacher, and J. Li, “Microwave-optics entanglement via cavity optomagnomechanics,” Laser and Photonics Reviews, vol. 17, no. 12. Wiley, 2023. ista: Fan ZY, Qiu L, Gröblacher S, Li J. 2023. Microwave-optics entanglement via cavity optomagnomechanics. Laser and Photonics Reviews. 17(12), 2200866. mla: Fan, Zhi Yuan, et al. “Microwave-Optics Entanglement via Cavity Optomagnomechanics.” Laser and Photonics Reviews, vol. 17, no. 12, 2200866, Wiley, 2023, doi:10.1002/lpor.202200866. short: Z.Y. Fan, L. Qiu, S. Gröblacher, J. Li, Laser and Photonics Reviews 17 (2023). date_created: 2023-11-05T23:00:54Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-01-30T14:36:42Z day: '01' department: - _id: JoFi doi: 10.1002/lpor.202200866 external_id: arxiv: - '2208.10703' intvolume: ' 17' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2208.10703 month: '12' oa: 1 oa_version: Preprint publication: Laser and Photonics Reviews publication_identifier: eissn: - 1863-8899 issn: - 1863-8880 publication_status: published publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: Microwave-optics entanglement via cavity optomagnomechanics type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2023' ... --- _id: '13097' abstract: - lang: eng text: 'Vertebrate movement is orchestrated by spinal inter- and motor neurons that, together with sensory and cognitive input, produce dynamic motor behaviors. These behaviors vary from the simple undulatory swimming of fish and larval aquatic species to the highly coordinated running, reaching and grasping of mice, humans and other mammals. This variation raises the fundamental question of how spinal circuits have changed in register with motor behavior. In simple, undulatory fish, exemplified by the lamprey, two broad classes of interneurons shape motor neuron output: ipsilateral-projecting excitatory neurons, and commissural-projecting inhibitory neurons. An additional class of ipsilateral inhibitory neurons is required to generate escape swim behavior in larval zebrafish and tadpoles. In limbed vertebrates, a more complex spinal neuron composition is observed. In this review, we provide evidence that movement elaboration correlates with an increase and specialization of these three basic interneuron types into molecularly, anatomically, and functionally distinct subpopulations. We summarize recent work linking neuron types to movement-pattern generation across fish, amphibians, reptiles, birds and mammals.' acknowledgement: 'This work was supported by the ERC Starting grant, ERC-2021-STG #101041551.' article_number: '1146449' article_processing_charge: Yes article_type: original author: - first_name: Alexia C full_name: Wilson, Alexia C id: 5230e794-15b2-11ec-abd3-e2d5335ebd1d last_name: Wilson - first_name: Lora Beatrice Jaeger full_name: Sweeney, Lora Beatrice Jaeger id: 56BE8254-C4F0-11E9-8E45-0B23E6697425 last_name: Sweeney orcid: 0000-0001-9242-5601 citation: ama: 'Wilson AC, Sweeney LB. Spinal cords: Symphonies of interneurons across species. Frontiers in Neural Circuits. 2023;17. doi:10.3389/fncir.2023.1146449' apa: 'Wilson, A. C., & Sweeney, L. B. (2023). Spinal cords: Symphonies of interneurons across species. Frontiers in Neural Circuits. Frontiers. https://doi.org/10.3389/fncir.2023.1146449' chicago: 'Wilson, Alexia C, and Lora B. Sweeney. “Spinal Cords: Symphonies of Interneurons across Species.” Frontiers in Neural Circuits. Frontiers, 2023. https://doi.org/10.3389/fncir.2023.1146449.' ieee: 'A. C. Wilson and L. B. Sweeney, “Spinal cords: Symphonies of interneurons across species,” Frontiers in Neural Circuits, vol. 17. Frontiers, 2023.' ista: 'Wilson AC, Sweeney LB. 2023. Spinal cords: Symphonies of interneurons across species. Frontiers in Neural Circuits. 17, 1146449.' mla: 'Wilson, Alexia C., and Lora B. Sweeney. “Spinal Cords: Symphonies of Interneurons across Species.” Frontiers in Neural Circuits, vol. 17, 1146449, Frontiers, 2023, doi:10.3389/fncir.2023.1146449.' short: A.C. Wilson, L.B. Sweeney, Frontiers in Neural Circuits 17 (2023). date_created: 2023-05-28T22:01:04Z date_published: 2023-04-26T00:00:00Z date_updated: 2024-01-31T10:15:53Z day: '26' ddc: - '570' department: - _id: LoSw doi: 10.3389/fncir.2023.1146449 external_id: isi: - '000984606200001' pmid: - '37180760' file: - access_level: open_access checksum: 7efd06de284a28e91e97127611a9c3fd content_type: application/pdf creator: dernst date_created: 2024-01-03T13:33:21Z date_updated: 2024-01-03T13:33:21Z file_id: '14729' file_name: 2023_FrontiersNeuralCircuits_Wilson.pdf file_size: 6667157 relation: main_file success: 1 file_date_updated: 2024-01-03T13:33:21Z has_accepted_license: '1' intvolume: ' 17' isi: 1 language: - iso: eng month: '04' oa: 1 oa_version: Published Version pmid: 1 project: - _id: ebb66355-77a9-11ec-83b8-b8ac210a4dae grant_number: '101041551' name: Development and Evolution of Tetrapod Motor Circuits publication: Frontiers in Neural Circuits publication_identifier: issn: - 1662-5110 publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: 'Spinal cords: Symphonies of interneurons across species' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2023' ... --- _id: '14865' article_number: EGU23-4968 article_processing_charge: No author: - first_name: Yi-Ling full_name: Hwong, Yi-Ling id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22 last_name: Hwong orcid: 0000-0001-9281-3479 - first_name: Maxime full_name: Colin, Maxime last_name: Colin - first_name: Philipp full_name: Aglas, Philipp id: 02eace56-97fc-11ee-b81a-f0939ca85a77 last_name: Aglas - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Steven full_name: Sherwood, Steven last_name: Sherwood citation: ama: 'Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood S. Evaluating memory properties in convection schemes using idealised tests. In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-4968' apa: 'Hwong, Y.-L., Colin, M., Aglas, P., Muller, C. J., & Sherwood, S. (2023). Evaluating memory properties in convection schemes using idealised tests. In EGU General Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-4968' chicago: Hwong, Yi-Ling, Maxime Colin, Philipp Aglas, Caroline J Muller, and Steven Sherwood. “Evaluating Memory Properties in Convection Schemes Using Idealised Tests.” In EGU General Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-4968. ieee: Y.-L. Hwong, M. Colin, P. Aglas, C. J. Muller, and S. Sherwood, “Evaluating memory properties in convection schemes using idealised tests,” in EGU General Assembly 2023, Vienna, Austria & Virtual, 2023. ista: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood S. 2023. Evaluating memory properties in convection schemes using idealised tests. EGU General Assembly 2023. EGU General Assembly, EGU23-4968. mla: Hwong, Yi-Ling, et al. “Evaluating Memory Properties in Convection Schemes Using Idealised Tests.” EGU General Assembly 2023, EGU23-4968, European Geosciences Union, 2023, doi:10.5194/egusphere-egu23-4968. short: Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S. Sherwood, in:, EGU General Assembly 2023, European Geosciences Union, 2023. conference: end_date: 2023-04-28 location: Vienna, Austria & Virtual name: EGU General Assembly start_date: 2023-04-23 date_created: 2024-01-22T12:10:32Z date_published: 2023-04-23T00:00:00Z date_updated: 2024-02-05T08:49:49Z day: '23' ddc: - '550' department: - _id: CaMu doi: 10.5194/egusphere-egu23-4968 file: - access_level: open_access checksum: 628a27caff437855ab320be46b9e8dcc content_type: application/pdf creator: dernst date_created: 2024-02-05T08:48:41Z date_updated: 2024-02-05T08:48:41Z file_id: '14936' file_name: 2023_EGU_Hwong.pdf file_size: 317541 relation: main_file success: 1 file_date_updated: 2024-02-05T08:48:41Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: EGU General Assembly 2023 publication_status: published publisher: European Geosciences Union status: public title: Evaluating memory properties in convection schemes using idealised tests tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14866' article_number: EGU23-15870 article_processing_charge: No author: - first_name: Sophie full_name: Abramian, Sophie last_name: Abramian - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Camille full_name: Risi, Camille last_name: Risi citation: ama: 'Abramian S, Muller CJ, Risi C. Extreme precipitation in tropical squall lines. In: EGU General Assembly 2023. European Geosciences Union; 2023. doi:10.5194/egusphere-egu23-15870' apa: 'Abramian, S., Muller, C. J., & Risi, C. (2023). Extreme precipitation in tropical squall lines. In EGU General Assembly 2023. Vienna, Austria & Virtual: European Geosciences Union. https://doi.org/10.5194/egusphere-egu23-15870' chicago: Abramian, Sophie, Caroline J Muller, and Camille Risi. “Extreme Precipitation in Tropical Squall Lines.” In EGU General Assembly 2023. European Geosciences Union, 2023. https://doi.org/10.5194/egusphere-egu23-15870. ieee: S. Abramian, C. J. Muller, and C. Risi, “Extreme precipitation in tropical squall lines,” in EGU General Assembly 2023, Vienna, Austria & Virtual, 2023. ista: Abramian S, Muller CJ, Risi C. 2023. Extreme precipitation in tropical squall lines. EGU General Assembly 2023. EGU General Assembly, EGU23-15870. mla: Abramian, Sophie, et al. “Extreme Precipitation in Tropical Squall Lines.” EGU General Assembly 2023, EGU23-15870, European Geosciences Union, 2023, doi:10.5194/egusphere-egu23-15870. short: S. Abramian, C.J. Muller, C. Risi, in:, EGU General Assembly 2023, European Geosciences Union, 2023. conference: end_date: 2023-04-28 location: Vienna, Austria & Virtual name: EGU General Assembly start_date: 2023-04-23 date_created: 2024-01-22T12:10:52Z date_published: 2023-04-23T00:00:00Z date_updated: 2024-02-05T08:13:12Z day: '23' ddc: - '550' department: - _id: CaMu doi: 10.5194/egusphere-egu23-15870 file: - access_level: open_access checksum: 8cd5bb8bf3d48ceefb395b6875819147 content_type: application/pdf creator: dernst date_created: 2024-02-05T08:10:43Z date_updated: 2024-02-05T08:10:43Z file_id: '14935' file_name: 2023_EGU_Abramian.pdf file_size: 294690 relation: main_file success: 1 file_date_updated: 2024-02-05T08:10:43Z has_accepted_license: '1' language: - iso: eng month: '04' oa: 1 oa_version: Published Version publication: EGU General Assembly 2023 publication_status: published publisher: European Geosciences Union status: public title: Extreme precipitation in tropical squall lines tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference_abstract user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14920' abstract: - lang: eng text: "We consider fixpoint algorithms for two-player games on graphs with $\\omega$-regular winning conditions, where the environment is constrained by a strong transition fairness assumption. Strong transition fairness is a widely occurring special case of strong fairness, which requires that any execution is strongly fair with respect to a specified set of live edges: whenever the\r\nsource vertex of a live edge is visited infinitely often along a play, the edge itself is traversed infinitely often along the play as well. We show that, surprisingly, strong transition fairness retains the algorithmic characteristics of the fixpoint algorithms for $\\omega$-regular games -- the new algorithms have the same alternation depth as the classical algorithms but invoke a new type of predecessor operator. For Rabin games with $k$ pairs, the complexity of the new algorithm is $O(n^{k+2}k!)$ symbolic steps, which is independent of the number of live edges in the strong transition fairness assumption. Further, we show that GR(1) specifications with strong transition fairness assumptions can be solved with a 3-nested fixpoint algorithm, same as the usual algorithm. In contrast, strong fairness necessarily requires increasing the alternation depth depending on the number of fairness assumptions. We get symbolic algorithms for (generalized) Rabin, parity and GR(1) objectives under strong transition fairness assumptions as well as a direct symbolic algorithm for qualitative winning in stochastic\r\n$\\omega$-regular games that runs in $O(n^{k+2}k!)$ symbolic steps, improving the state of the art. Finally, we have implemented a BDD-based synthesis engine based on our algorithm. We show on a set of synthetic and real benchmarks that our algorithm is scalable, parallelizable, and outperforms previous algorithms by orders of magnitude." acknowledgement: A previous version of this paper has appeared in TACAS 2022. Authors ordered alphabetically. T. Banerjee was interning with MPI-SWS when this research was conducted. R. Majumdar and A.-K. Schmuck are partially supported by DFG project 389792660 TRR 248–CPEC. A.-K. Schmuck is additionally funded through DFG project (SCHM 3541/1-1). K. Mallik is supported by the ERC project ERC-2020-AdG 101020093. article_number: '4' article_processing_charge: Yes article_type: original author: - first_name: Tamajit full_name: Banerjee, Tamajit last_name: Banerjee - first_name: Rupak full_name: Majumdar, Rupak last_name: Majumdar - first_name: Kaushik full_name: Mallik, Kaushik id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598 last_name: Mallik orcid: 0000-0001-9864-7475 - first_name: Anne-Kathrin full_name: Schmuck, Anne-Kathrin last_name: Schmuck - first_name: Sadegh full_name: Soudjani, Sadegh last_name: Soudjani citation: ama: Banerjee T, Majumdar R, Mallik K, Schmuck A-K, Soudjani S. Fast symbolic algorithms for mega-regular games under strong transition fairness. TheoretiCS. 2023;2. doi:10.46298/theoretics.23.4 apa: Banerjee, T., Majumdar, R., Mallik, K., Schmuck, A.-K., & Soudjani, S. (2023). Fast symbolic algorithms for mega-regular games under strong transition fairness. TheoretiCS. EPI Sciences. https://doi.org/10.46298/theoretics.23.4 chicago: Banerjee, Tamajit, Rupak Majumdar, Kaushik Mallik, Anne-Kathrin Schmuck, and Sadegh Soudjani. “Fast Symbolic Algorithms for Mega-Regular Games under Strong Transition Fairness.” TheoretiCS. EPI Sciences, 2023. https://doi.org/10.46298/theoretics.23.4. ieee: T. Banerjee, R. Majumdar, K. Mallik, A.-K. Schmuck, and S. Soudjani, “Fast symbolic algorithms for mega-regular games under strong transition fairness,” TheoretiCS, vol. 2. EPI Sciences, 2023. ista: Banerjee T, Majumdar R, Mallik K, Schmuck A-K, Soudjani S. 2023. Fast symbolic algorithms for mega-regular games under strong transition fairness. TheoretiCS. 2, 4. mla: Banerjee, Tamajit, et al. “Fast Symbolic Algorithms for Mega-Regular Games under Strong Transition Fairness.” TheoretiCS, vol. 2, 4, EPI Sciences, 2023, doi:10.46298/theoretics.23.4. short: T. Banerjee, R. Majumdar, K. Mallik, A.-K. Schmuck, S. Soudjani, TheoretiCS 2 (2023). date_created: 2024-01-31T13:40:49Z date_published: 2023-02-24T00:00:00Z date_updated: 2024-02-05T10:21:51Z day: '24' ddc: - '000' department: - _id: ToHe doi: 10.46298/theoretics.23.4 ec_funded: 1 external_id: arxiv: - '2202.07480' file: - access_level: open_access checksum: 2972d531122a6f15727b396110fb3f5c content_type: application/pdf creator: dernst date_created: 2024-02-05T10:19:35Z date_updated: 2024-02-05T10:19:35Z file_id: '14940' file_name: 2023_TheoretiCS_Banerjee.pdf file_size: 917076 relation: main_file success: 1 file_date_updated: 2024-02-05T10:19:35Z has_accepted_license: '1' intvolume: ' 2' language: - iso: eng month: '02' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: TheoretiCS publication_identifier: issn: - 2751-4838 publication_status: published publisher: EPI Sciences quality_controlled: '1' status: public title: Fast symbolic algorithms for mega-regular games under strong transition fairness tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2023' ... --- _id: '12859' abstract: - lang: eng text: 'Machine learning models are vulnerable to adversarial perturbations, and a thought-provoking paper by Bubeck and Sellke has analyzed this phenomenon through the lens of over-parameterization: interpolating smoothly the data requires significantly more parameters than simply memorizing it. However, this "universal" law provides only a necessary condition for robustness, and it is unable to discriminate between models. In this paper, we address these gaps by focusing on empirical risk minimization in two prototypical settings, namely, random features and the neural tangent kernel (NTK). We prove that, for random features, the model is not robust for any degree of over-parameterization, even when the necessary condition coming from the universal law of robustness is satisfied. In contrast, for even activations, the NTK model meets the universal lower bound, and it is robust as soon as the necessary condition on over-parameterization is fulfilled. This also addresses a conjecture in prior work by Bubeck, Li and Nagaraj. Our analysis decouples the effect of the kernel of the model from an "interaction matrix", which describes the interaction with the test data and captures the effect of the activation. Our theoretical results are corroborated by numerical evidence on both synthetic and standard datasets (MNIST, CIFAR-10).' acknowledgement: "Simone Bombari and Marco Mondelli were partially supported by the 2019 Lopez-Loreta prize, and\r\nthe authors would like to thank Hamed Hassani for helpful discussions.\r\n" alternative_title: - PMLR article_processing_charge: No author: - first_name: Simone full_name: Bombari, Simone id: ca726dda-de17-11ea-bc14-f9da834f63aa last_name: Bombari - first_name: Shayan full_name: Kiyani, Shayan id: f5a2b424-e339-11ed-8435-ff3b4fe70cf8 last_name: Kiyani - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Bombari S, Kiyani S, Mondelli M. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In: Proceedings of the 40th International Conference on Machine Learning. Vol 202. ML Research Press; 2023:2738-2776.' apa: 'Bombari, S., Kiyani, S., & Mondelli, M. (2023). Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. In Proceedings of the 40th International Conference on Machine Learning (Vol. 202, pp. 2738–2776). Honolulu, HI, United States: ML Research Press.' chicago: 'Bombari, Simone, Shayan Kiyani, and Marco Mondelli. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” In Proceedings of the 40th International Conference on Machine Learning, 202:2738–76. ML Research Press, 2023.' ieee: 'S. Bombari, S. Kiyani, and M. Mondelli, “Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels,” in Proceedings of the 40th International Conference on Machine Learning, Honolulu, HI, United States, 2023, vol. 202, pp. 2738–2776.' ista: 'Bombari S, Kiyani S, Mondelli M. 2023. Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels. Proceedings of the 40th International Conference on Machine Learning. ICML: International Conference on Machine Learning, PMLR, vol. 202, 2738–2776.' mla: 'Bombari, Simone, et al. “Beyond the Universal Law of Robustness: Sharper Laws for Random Features and Neural Tangent Kernels.” Proceedings of the 40th International Conference on Machine Learning, vol. 202, ML Research Press, 2023, pp. 2738–76.' short: S. Bombari, S. Kiyani, M. Mondelli, in:, Proceedings of the 40th International Conference on Machine Learning, ML Research Press, 2023, pp. 2738–2776. conference: end_date: 2023-07-29 location: Honolulu, HI, United States name: 'ICML: International Conference on Machine Learning' start_date: 2023-07-23 date_created: 2023-04-23T16:11:03Z date_published: 2023-10-27T00:00:00Z date_updated: 2024-02-06T07:42:00Z day: '27' department: - _id: GradSch - _id: MaMo external_id: arxiv: - '2302.01629' intvolume: ' 202' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2302.01629 month: '10' oa: 1 oa_version: Preprint page: 2738-2776 project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Proceedings of the 40th International Conference on Machine Learning publication_status: published publisher: ML Research Press quality_controlled: '1' related_material: link: - relation: software url: https://github.com/simone-bombari/beyond-universal-robustness status: public title: 'Beyond the universal law of robustness: Sharper laws for random features and neural tangent kernels' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2023' ... --- _id: '14921' abstract: - lang: eng text: Neural collapse (NC) refers to the surprising structure of the last layer of deep neural networks in the terminal phase of gradient descent training. Recently, an increasing amount of experimental evidence has pointed to the propagation of NC to earlier layers of neural networks. However, while the NC in the last layer is well studied theoretically, much less is known about its multi-layered counterpart - deep neural collapse (DNC). In particular, existing work focuses either on linear layers or only on the last two layers at the price of an extra assumption. Our paper fills this gap by generalizing the established analytical framework for NC - the unconstrained features model - to multiple non-linear layers. Our key technical contribution is to show that, in a deep unconstrained features model, the unique global optimum for binary classification exhibits all the properties typical of DNC. This explains the existing experimental evidence of DNC. We also empirically show that (i) by optimizing deep unconstrained features models via gradient descent, the resulting solution agrees well with our theory, and (ii) trained networks recover the unconstrained features suitable for the occurrence of DNC, thus supporting the validity of this modeling principle. acknowledgement: M. M. is partially supported by the 2019 Lopez-Loreta Prize. The authors would like to thank Eugenia Iofinova, Bernd Prach and Simone Bombari for valuable feedback on the manuscript. alternative_title: - NeurIPS article_processing_charge: No author: - first_name: Peter full_name: Súkeník, Peter id: d64d6a8d-eb8e-11eb-b029-96fd216dec3c last_name: Súkeník - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: 'Súkeník P, Mondelli M, Lampert C. Deep neural collapse is provably optimal for the deep unconstrained features model. In: 37th Annual Conference on Neural Information Processing Systems.' apa: Súkeník, P., Mondelli, M., & Lampert, C. (n.d.). Deep neural collapse is provably optimal for the deep unconstrained features model. In 37th Annual Conference on Neural Information Processing Systems. New Orleans, LA, United States. chicago: Súkeník, Peter, Marco Mondelli, and Christoph Lampert. “Deep Neural Collapse Is Provably Optimal for the Deep Unconstrained Features Model.” In 37th Annual Conference on Neural Information Processing Systems, n.d. ieee: P. Súkeník, M. Mondelli, and C. Lampert, “Deep neural collapse is provably optimal for the deep unconstrained features model,” in 37th Annual Conference on Neural Information Processing Systems, New Orleans, LA, United States. ista: 'Súkeník P, Mondelli M, Lampert C. Deep neural collapse is provably optimal for the deep unconstrained features model. 37th Annual Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems, NeurIPS, .' mla: Súkeník, Peter, et al. “Deep Neural Collapse Is Provably Optimal for the Deep Unconstrained Features Model.” 37th Annual Conference on Neural Information Processing Systems. short: P. Súkeník, M. Mondelli, C. Lampert, in:, 37th Annual Conference on Neural Information Processing Systems, n.d. conference: end_date: 2023-12-16 location: New Orleans, LA, United States name: 'NeurIPS: Neural Information Processing Systems' start_date: 2023-12-10 date_created: 2024-02-02T11:17:41Z date_published: 2023-12-15T00:00:00Z date_updated: 2024-02-06T07:53:26Z day: '15' department: - _id: MaMo - _id: ChLa external_id: arxiv: - '2305.13165' language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.48550/arXiv.2305.13165' month: '12' oa: 1 oa_version: Preprint project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: 37th Annual Conference on Neural Information Processing Systems publication_status: inpress quality_controlled: '1' status: public title: Deep neural collapse is provably optimal for the deep unconstrained features model type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14924' abstract: - lang: eng text: "The stochastic heavy ball method (SHB), also known as stochastic gradient descent (SGD) with Polyak's momentum, is widely used in training neural networks. However, despite the remarkable success of such algorithm in practice, its theoretical characterization remains limited. In this paper, we focus on neural networks with two and three layers and provide a rigorous understanding of the properties of the solutions found by SHB: \\emph{(i)} stability after dropping out part of the neurons, \\emph{(ii)} connectivity along a low-loss path, and \\emph{(iii)} convergence to the global optimum.\r\nTo achieve this goal, we take a mean-field view and relate the SHB dynamics to a certain partial differential equation in the limit of large network widths. This mean-field perspective has inspired a recent line of work focusing on SGD while, in contrast, our paper considers an algorithm with momentum. More specifically, after proving existence and uniqueness of the limit differential equations, we show convergence to the global optimum and give a quantitative bound between the mean-field limit and the SHB dynamics of a finite-width network. Armed with this last bound, we are able to establish the dropout-stability and connectivity of SHB solutions." acknowledgement: D. Wu and M. Mondelli are partially supported by the 2019 Lopez-Loreta Prize. V. Kungurtsev was supported by the OP VVV project CZ.02.1.01/0.0/0.0/16_019/0000765 "Research Center for Informatics". alternative_title: - TMLR article_processing_charge: No author: - first_name: Diyuan full_name: Wu, Diyuan id: 1a5914c2-896a-11ed-bdf8-fb80621a0635 last_name: Wu - first_name: Vyacheslav full_name: Kungurtsev, Vyacheslav last_name: Kungurtsev - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 citation: ama: 'Wu D, Kungurtsev V, Mondelli M. Mean-field analysis for heavy ball methods: Dropout-stability, connectivity, and global convergence. In: Transactions on Machine Learning Research. ML Research Press; 2023.' apa: 'Wu, D., Kungurtsev, V., & Mondelli, M. (2023). Mean-field analysis for heavy ball methods: Dropout-stability, connectivity, and global convergence. In Transactions on Machine Learning Research. ML Research Press.' chicago: 'Wu, Diyuan, Vyacheslav Kungurtsev, and Marco Mondelli. “Mean-Field Analysis for Heavy Ball Methods: Dropout-Stability, Connectivity, and Global Convergence.” In Transactions on Machine Learning Research. ML Research Press, 2023.' ieee: 'D. Wu, V. Kungurtsev, and M. Mondelli, “Mean-field analysis for heavy ball methods: Dropout-stability, connectivity, and global convergence,” in Transactions on Machine Learning Research, 2023.' ista: 'Wu D, Kungurtsev V, Mondelli M. 2023. Mean-field analysis for heavy ball methods: Dropout-stability, connectivity, and global convergence. Transactions on Machine Learning Research. , TMLR, .' mla: 'Wu, Diyuan, et al. “Mean-Field Analysis for Heavy Ball Methods: Dropout-Stability, Connectivity, and Global Convergence.” Transactions on Machine Learning Research, ML Research Press, 2023.' short: D. Wu, V. Kungurtsev, M. Mondelli, in:, Transactions on Machine Learning Research, ML Research Press, 2023. date_created: 2024-02-02T11:21:56Z date_published: 2023-02-28T00:00:00Z date_updated: 2024-02-06T08:53:15Z day: '28' department: - _id: MaMo external_id: arxiv: - '2210.06819' has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2210.06819 month: '02' oa: 1 oa_version: Published Version project: - _id: 059876FA-7A3F-11EA-A408-12923DDC885E name: Prix Lopez-Loretta 2019 - Marco Mondelli publication: Transactions on Machine Learning Research publication_status: published publisher: ML Research Press quality_controlled: '1' status: public title: 'Mean-field analysis for heavy ball methods: Dropout-stability, connectivity, and global convergence' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14919' abstract: - lang: eng text: "GLACIER METEOROLOGICAL DATA SWISS ALPS -2022\r\n" article_processing_charge: No author: - first_name: Thomas full_name: Shaw, Thomas id: 3caa3f91-1f03-11ee-96ce-e0e553054d6e last_name: Shaw orcid: 0000-0001-7640-6152 - first_name: Pascal full_name: Buri, Pascal id: 317987aa-9421-11ee-ac5a-b941b041abba last_name: Buri - first_name: Michael full_name: McCarthy, Michael last_name: McCarthy - first_name: Evan full_name: Miles, Evan last_name: Miles - first_name: Francesca full_name: Pellicciotti, Francesca id: b28f055a-81ea-11ed-b70c-a9fe7f7b0e70 last_name: Pellicciotti orcid: 0000-0002-5554-8087 citation: ama: Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. 2023. doi:10.5281/ZENODO.8277285 apa: Shaw, T., Buri, P., McCarthy, M., Miles, E., & Pellicciotti, F. (2023). Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer. Zenodo. https://doi.org/10.5281/ZENODO.8277285 chicago: Shaw, Thomas, Pascal Buri, Michael McCarthy, Evan Miles, and Francesca Pellicciotti. “Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8277285. ieee: T. Shaw, P. Buri, M. McCarthy, E. Miles, and F. Pellicciotti, “Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer.” Zenodo, 2023. ista: Shaw T, Buri P, McCarthy M, Miles E, Pellicciotti F. 2023. Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer, Zenodo, 10.5281/ZENODO.8277285. mla: Shaw, Thomas, et al. Air Temperature and Near-Surface Meteorology Datasets on Three Swiss Glaciers - Extreme 2022 Summer. Zenodo, 2023, doi:10.5281/ZENODO.8277285. short: T. Shaw, P. Buri, M. McCarthy, E. Miles, F. Pellicciotti, (2023). date_created: 2024-01-31T12:08:26Z date_published: 2023-08-23T00:00:00Z date_updated: 2024-02-06T08:44:01Z day: '23' ddc: - '550' department: - _id: FrPe doi: 10.5281/ZENODO.8277285 main_file_link: - open_access: '1' url: https://doi.org/10.5281/ZENODO.8277285 month: '08' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14885' relation: used_in_publication status: public status: public title: Air temperature and near-surface meteorology datasets on three Swiss glaciers - Extreme 2022 Summer type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13107' abstract: - lang: eng text: "Within the human body, the brain exhibits the highest rate of energy consumption amongst all organs, with the majority of generated ATP being utilized to sustain neuronal activity. Therefore, the metabolism of the mature cerebral cortex is geared towards preserving metabolic homeostasis whilst generating significant amounts of energy. This requires a precise interplay between diverse metabolic pathways, spanning from a tissue-wide scale to the level of individual neurons. Disturbances to this delicate metabolic equilibrium, such as those resulting from maternal malnutrition\r\nor mutations affecting metabolic enzymes, often result in neuropathological variants of neurodevelopment. For instance, mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), have been associated with autism and microcephaly. However, despite recent progress in the field, the extent of metabolic restructuring that occurs within the developing brain and the corresponding alterations in nutrient demands during various critical periods remain largely unknown. To investigate this, we performed metabolomic profiling of the murine cerebral cortex to characterize the metabolic state of the forebrain at different developmental stages. We found that the developing cortex undergoes substantial metabolic reprogramming, with specific sets of metabolites displaying stage-specific changes. According to our observations, we determined a distinct temporal period in postnatal development during which the cortex displays heightened reliance on LNAAs. Hence, using a conditional knock-out mouse model, we deleted Slc7a5 in neural cells, allowing us to monitor the impact of a perturbed neuronal metabolic state across multiple developmental stages of corticogenesis. We found that manipulating the levels of essential LNAAs in cortical neurons in vivo affects one particular perinatal developmental period critical for cortical network refinement. Abnormally low intracellular LNAA levels result in cell-autonomous alterations in neuronal lipid metabolism, excitability, and survival during this particular time window. Although most of the effects of Slc7a5 deletion on neuronal physiology are transient, derailment of these processes during this brief but crucial window leads to long-term circuit dysfunction in mice. In conclusion, out data indicate that the cerebral cortex undergoes significant metabolic reorganization during development. This process involves the intricate integration of multiple metabolic pathways to ensure optimal neuronal function throughout different developmental stages. Our findings offer a paradigm for understanding how neurons synchronize the expression of nutrient-related genes with their activity to allow proper brain maturation. Further, our results demonstrate that disruptions in these precisely calibrated metabolic processes during critical periods of brain development may result in neuropathological outcomes in mice and in humans." acknowledged_ssus: - _id: PreCl - _id: Bio - _id: EM-Fac alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Lisa full_name: Knaus, Lisa id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87 last_name: Knaus citation: ama: 'Knaus L. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. 2023. doi:10.15479/at:ista:13107' apa: 'Knaus, L. (2023). The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13107' chicago: 'Knaus, Lisa. “The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13107.' ieee: 'L. Knaus, “The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival,” Institute of Science and Technology Austria, 2023.' ista: 'Knaus L. 2023. The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival. Institute of Science and Technology Austria.' mla: 'Knaus, Lisa. The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13107.' short: 'L. Knaus, The Metabolism of the Developing Brain : How Large Neutral Amino Acids Modulate Perinatal Neuronal Excitability and Survival, Institute of Science and Technology Austria, 2023.' date_created: 2023-06-01T09:05:24Z date_published: 2023-05-31T00:00:00Z date_updated: 2024-02-07T08:03:33Z day: '31' ddc: - '570' degree_awarded: PhD department: - _id: GradSch - _id: GaNo doi: 10.15479/at:ista:13107 ec_funded: 1 file: - access_level: closed checksum: 4b69a4ac0bbf4163d59c0b58dcb4f2c3 content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: lknaus date_created: 2023-06-01T13:48:41Z date_updated: 2023-06-01T13:48:41Z file_id: '13112' file_name: Thesis_Lisa Knaus_approved_final.docx file_size: 12991551 relation: source_file - access_level: open_access checksum: 6903d152aa01181d87a696085af31c83 content_type: application/pdf creator: lknaus date_created: 2023-06-02T09:47:29Z date_updated: 2023-06-07T08:41:49Z file_id: '13114' file_name: Thesis_Lisa Knaus_approved_final_pdfa2b.pdf file_size: 9309015 relation: main_file file_date_updated: 2023-06-07T08:41:49Z has_accepted_license: '1' language: - iso: eng month: '05' oa: 1 oa_version: Published Version page: '147' project: - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '12802' relation: part_of_dissertation status: public status: public supervisor: - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 title: 'The metabolism of the developing brain : How large neutral amino acids modulate perinatal neuronal excitability and survival' type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '12802' abstract: - lang: eng text: Little is known about the critical metabolic changes that neural cells have to undergo during development and how temporary shifts in this program can influence brain circuitries and behavior. Inspired by the discovery that mutations in SLC7A5, a transporter of metabolically essential large neutral amino acids (LNAAs), lead to autism, we employed metabolomic profiling to study the metabolic states of the cerebral cortex across different developmental stages. We found that the forebrain undergoes significant metabolic remodeling throughout development, with certain groups of metabolites showing stage-specific changes, but what are the consequences of perturbing this metabolic program? By manipulating Slc7a5 expression in neural cells, we found that the metabolism of LNAAs and lipids are interconnected in the cortex. Deletion of Slc7a5 in neurons affects the postnatal metabolic state, leading to a shift in lipid metabolism. Additionally, it causes stage- and cell-type-specific alterations in neuronal activity patterns, resulting in a long-term circuit dysfunction. acknowledged_ssus: - _id: PreCl - _id: EM-Fac - _id: Bio - _id: LifeSc acknowledgement: We thank A. Freeman and V. Voronin for technical assistance, S. Deixler, A. Stichelberger, M. Schunn, and the Preclinical Facility for managing our animal colony. We thank L. Andersen and J. Sonntag, who were involved in generating the MADM lines. We thank the ISTA LSF Mass Spectrometry Core Facility for assistance with the proteomic analysis, as well as the ISTA electron microscopy and Imaging and Optics facility for technical support. Metabolomics LC-MS/MS analysis was performed by the Metabolomics Facility at Vienna BioCenter Core Facilities (VBCF). We acknowledge the support of the EMBL Metabolomics Core Facility (MCF) for lipidomics and intracellular metabolomics mass spectrometry data acquisition and analysis. RNA sequencing was performed by the Next Generation Sequencing Facility at VBCF. Schematics were generated using Biorender.com. This work was supported by the Austrian Science Fund (FWF, DK W1232-B24) and by the European Union’s Horizon 2020 research and innovation program (ERC) grant 725780 (LinPro) to S.H. and 715508 (REVERSEAUTISM) to G.N. article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lisa full_name: Knaus, Lisa id: 3B2ABCF4-F248-11E8-B48F-1D18A9856A87 last_name: Knaus - first_name: Bernadette full_name: Basilico, Bernadette id: 36035796-5ACA-11E9-A75E-7AF2E5697425 last_name: Basilico orcid: 0000-0003-1843-3173 - first_name: Daniel full_name: Malzl, Daniel last_name: Malzl - first_name: Maria full_name: Gerykova Bujalkova, Maria last_name: Gerykova Bujalkova - first_name: Mateja full_name: Smogavec, Mateja last_name: Smogavec - first_name: Lena A. full_name: Schwarz, Lena A. last_name: Schwarz - first_name: Sarah full_name: Gorkiewicz, Sarah id: f141a35d-15a9-11ec-9fb2-fef6becc7b6f last_name: Gorkiewicz - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Florian full_name: Pauler, Florian id: 48EA0138-F248-11E8-B48F-1D18A9856A87 last_name: Pauler orcid: 0000-0002-7462-0048 - first_name: Christian full_name: Knittl-Frank, Christian last_name: Knittl-Frank - first_name: Marianna full_name: Tassinari, Marianna id: 7af593f1-d44a-11ed-bf94-a3646a6bb35e last_name: Tassinari - first_name: Nuno full_name: Maulide, Nuno last_name: Maulide - first_name: Thomas full_name: Rülicke, Thomas last_name: Rülicke - first_name: Jörg full_name: Menche, Jörg last_name: Menche - first_name: Simon full_name: Hippenmeyer, Simon id: 37B36620-F248-11E8-B48F-1D18A9856A87 last_name: Hippenmeyer orcid: 0000-0003-2279-1061 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 citation: ama: Knaus L, Basilico B, Malzl D, et al. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 2023;186(9):1950-1967.e25. doi:10.1016/j.cell.2023.02.037 apa: Knaus, L., Basilico, B., Malzl, D., Gerykova Bujalkova, M., Smogavec, M., Schwarz, L. A., … Novarino, G. (2023). Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. Elsevier. https://doi.org/10.1016/j.cell.2023.02.037 chicago: Knaus, Lisa, Bernadette Basilico, Daniel Malzl, Maria Gerykova Bujalkova, Mateja Smogavec, Lena A. Schwarz, Sarah Gorkiewicz, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell. Elsevier, 2023. https://doi.org/10.1016/j.cell.2023.02.037. ieee: L. Knaus et al., “Large neutral amino acid levels tune perinatal neuronal excitability and survival,” Cell, vol. 186, no. 9. Elsevier, p. 1950–1967.e25, 2023. ista: Knaus L, Basilico B, Malzl D, Gerykova Bujalkova M, Smogavec M, Schwarz LA, Gorkiewicz S, Amberg N, Pauler F, Knittl-Frank C, Tassinari M, Maulide N, Rülicke T, Menche J, Hippenmeyer S, Novarino G. 2023. Large neutral amino acid levels tune perinatal neuronal excitability and survival. Cell. 186(9), 1950–1967.e25. mla: Knaus, Lisa, et al. “Large Neutral Amino Acid Levels Tune Perinatal Neuronal Excitability and Survival.” Cell, vol. 186, no. 9, Elsevier, 2023, p. 1950–1967.e25, doi:10.1016/j.cell.2023.02.037. short: L. Knaus, B. Basilico, D. Malzl, M. Gerykova Bujalkova, M. Smogavec, L.A. Schwarz, S. Gorkiewicz, N. Amberg, F. Pauler, C. Knittl-Frank, M. Tassinari, N. Maulide, T. Rülicke, J. Menche, S. Hippenmeyer, G. Novarino, Cell 186 (2023) 1950–1967.e25. date_created: 2023-04-05T08:15:40Z date_published: 2023-04-27T00:00:00Z date_updated: 2024-02-07T08:03:32Z day: '27' ddc: - '570' department: - _id: SiHi - _id: GaNo doi: 10.1016/j.cell.2023.02.037 ec_funded: 1 external_id: isi: - '000991468700001' file: - access_level: open_access checksum: 47e94fbe19e86505b429cb7a5b503ce6 content_type: application/pdf creator: dernst date_created: 2023-05-02T09:26:21Z date_updated: 2023-05-02T09:26:21Z file_id: '12889' file_name: 2023_Cell_Knaus.pdf file_size: 15712841 relation: main_file success: 1 file_date_updated: 2023-05-02T09:26:21Z has_accepted_license: '1' intvolume: ' 186' isi: 1 issue: '9' keyword: - General Biochemistry - Genetics and Molecular Biology language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 1950-1967.e25 project: - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 260018B0-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '725780' name: Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models publication: Cell publication_identifier: issn: - 0092-8674 publication_status: published publisher: Elsevier quality_controlled: '1' related_material: link: - description: News on ISTA Website relation: press_release url: https://ista.ac.at/en/news/feed-them-or-lose-them/ record: - id: '13107' relation: dissertation_contains status: public scopus_import: '1' status: public title: Large neutral amino acid levels tune perinatal neuronal excitability and survival tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4359f0d1-fa6c-11eb-b949-802e58b17ae8 volume: 186 year: '2023' ... --- _id: '13312' abstract: - lang: eng text: "Superconductor/semiconductor hybrid devices have attracted increasing\r\ninterest in the past years. Superconducting electronics aims to complement\r\nsemiconductor technology, while hybrid architectures are at the forefront of\r\nnew ideas such as topological superconductivity and protected qubits. In this\r\nwork, we engineer the induced superconductivity in two-dimensional germanium\r\nhole gas by varying the distance between the quantum well and the aluminum. We\r\ndemonstrate a hard superconducting gap and realize an electrically and flux\r\ntunable superconducting diode using a superconducting quantum interference\r\ndevice (SQUID). This allows to tune the current phase relation (CPR), to a\r\nregime where single Cooper pair tunneling is suppressed, creating a $ \\sin\r\n\\left( 2 \\varphi \\right)$ CPR. Shapiro experiments complement this\r\ninterpretation and the microwave drive allows to create a diode with $ \\approx\r\n100 \\%$ efficiency. The reported results open up the path towards monolithic\r\nintegration of spin qubit devices, microwave resonators and (protected)\r\nsuperconducting qubits on a silicon technology compatible platform." acknowledged_ssus: - _id: M-Shop - _id: NanoFab acknowledgement: "The authors acknowledge Alexander Brinkmann, Alessandro Crippa, Andrew Higginbotham, Andrea Iorio, Giordano\r\nScappucci and Christian Schonenberger for helpful discussions. We thank Marcel Verheijen for the support in the\r\nTEM analysis. This research and related results were made\r\npossible with the support of the NOMIS Foundation. It was\r\nsupported by the Scientific Service Units of ISTA through resources provided by the MIBA Machine Shop and the\r\nnanofabrication facility, the European Union’s Horizon 2020\r\nresearch and innovation programme under Grant Agreement\r\nNo 862046, the HORIZON-RIA 101069515 project and the\r\nFWF Projects #P-32235, #P-36507 and #F-8606. R.S.S.\r\nacknowledges Spanish CM “Talento Program” Project No.\r\n2022-T1/IND-24070." article_number: '2306.07109' article_processing_charge: No author: - first_name: Marco full_name: Valentini, Marco id: C0BB2FAC-D767-11E9-B658-BC13E6697425 last_name: Valentini - first_name: Oliver full_name: Sagi, Oliver id: 71616374-A8E9-11E9-A7CA-09ECE5697425 last_name: Sagi - first_name: Levon full_name: Baghumyan, Levon last_name: Baghumyan - first_name: Thijs de full_name: Gijsel, Thijs de last_name: Gijsel - first_name: Jason full_name: Jung, Jason id: 4C9ACE7A-F248-11E8-B48F-1D18A9856A87 last_name: Jung - first_name: Stefano full_name: Calcaterra, Stefano last_name: Calcaterra - first_name: Andrea full_name: Ballabio, Andrea last_name: Ballabio - first_name: Juan Aguilera full_name: Servin, Juan Aguilera last_name: Servin - first_name: Kushagra full_name: Aggarwal, Kushagra id: b22ab905-3539-11eb-84c3-fc159dcd79cb last_name: Aggarwal orcid: 0000-0001-9985-9293 - first_name: Marian full_name: Janik, Marian id: 396A1950-F248-11E8-B48F-1D18A9856A87 last_name: Janik - first_name: Thomas full_name: Adletzberger, Thomas id: 38756BB2-F248-11E8-B48F-1D18A9856A87 last_name: Adletzberger - first_name: Rubén Seoane full_name: Souto, Rubén Seoane last_name: Souto - first_name: Martin full_name: Leijnse, Martin last_name: Leijnse - first_name: Jeroen full_name: Danon, Jeroen last_name: Danon - first_name: Constantin full_name: Schrade, Constantin last_name: Schrade - first_name: Erik full_name: Bakkers, Erik last_name: Bakkers - first_name: Daniel full_name: Chrastina, Daniel last_name: Chrastina - first_name: Giovanni full_name: Isella, Giovanni last_name: Isella - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X citation: ama: Valentini M, Sagi O, Baghumyan L, et al. Radio frequency driven superconducting diode and parity conserving  Cooper pair transport in a two-dimensional germanium hole gas. arXiv. doi:10.48550/arXiv.2306.07109 apa: Valentini, M., Sagi, O., Baghumyan, L., Gijsel, T. de, Jung, J., Calcaterra, S., … Katsaros, G. (n.d.). Radio frequency driven superconducting diode and parity conserving  Cooper pair transport in a two-dimensional germanium hole gas. arXiv. https://doi.org/10.48550/arXiv.2306.07109 chicago: Valentini, Marco, Oliver Sagi, Levon Baghumyan, Thijs de Gijsel, Jason Jung, Stefano Calcaterra, Andrea Ballabio, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving  Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.07109. ieee: M. Valentini et al., “Radio frequency driven superconducting diode and parity conserving  Cooper pair transport in a two-dimensional germanium hole gas,” arXiv. . ista: Valentini M, Sagi O, Baghumyan L, Gijsel T de, Jung J, Calcaterra S, Ballabio A, Servin JA, Aggarwal K, Janik M, Adletzberger T, Souto RS, Leijnse M, Danon J, Schrade C, Bakkers E, Chrastina D, Isella G, Katsaros G. Radio frequency driven superconducting diode and parity conserving  Cooper pair transport in a two-dimensional germanium hole gas. arXiv, 2306.07109. mla: Valentini, Marco, et al. “Radio Frequency Driven Superconducting Diode and Parity Conserving  Cooper Pair Transport in a Two-Dimensional Germanium Hole Gas.” ArXiv, 2306.07109, doi:10.48550/arXiv.2306.07109. short: M. Valentini, O. Sagi, L. Baghumyan, T. de Gijsel, J. Jung, S. Calcaterra, A. Ballabio, J.A. Servin, K. Aggarwal, M. Janik, T. Adletzberger, R.S. Souto, M. Leijnse, J. Danon, C. Schrade, E. Bakkers, D. Chrastina, G. Isella, G. Katsaros, ArXiv (n.d.). date_created: 2023-07-26T11:17:20Z date_published: 2023-06-13T00:00:00Z date_updated: 2024-02-07T07:52:32Z day: '13' ddc: - '530' department: - _id: GeKa - _id: M-Shop doi: 10.48550/arXiv.2306.07109 ec_funded: 1 external_id: arxiv: - '2306.07109' keyword: - Mesoscale and Nanoscale Physics language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2306.07109 month: '06' oa: 1 oa_version: Preprint project: - _id: 237E5020-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862046' name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS - _id: 237B3DA4-32DE-11EA-91FC-C7463DDC885E call_identifier: FWF grant_number: P32235 name: Towards scalable hut wire quantum devices - _id: bd8bd29e-d553-11ed-ba76-f0070d4b237a grant_number: P36507 name: Merging spin and superconducting qubits in planar Ge - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: Conventional and unconventional topological superconductors - _id: bd5b4ec5-d553-11ed-ba76-a6eedb083344 name: Protected states of quantum matter publication: arXiv publication_status: submitted related_material: record: - id: '13286' relation: dissertation_contains status: public status: public title: Radio frequency driven superconducting diode and parity conserving Cooper pair transport in a two-dimensional germanium hole gas tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: preprint user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '14949' abstract: - lang: eng text: Many approaches have been proposed to use diffusion models to augment training datasets for downstream tasks, such as classification. However, diffusion models are themselves trained on large datasets, often with noisy annotations, and it remains an open question to which extent these models contribute to downstream classification performance. In particular, it remains unclear if they generalize enough to improve over directly using the additional data of their pre-training process for augmentation. We systematically evaluate a range of existing methods to generate images from diffusion models and study new extensions to assess their benefit for data augmentation. Personalizing diffusion models towards the target data outperforms simpler prompting strategies. However, using the pre-training data of the diffusion model alone, via a simple nearest-neighbor retrieval procedure, leads to even stronger downstream performance. Our study explores the potential of diffusion models in generating new training data, and surprisingly finds that these sophisticated models are not yet able to beat a simple and strong image retrieval baseline on simple downstream vision tasks. acknowledgement: The authors would like to thank Varad Gunjal and Vishaal Udandarao. MFB thanks the International Max Planck Research School for Intelligent Systems (IMPRS-IS). alternative_title: - TMLR article_processing_charge: No article_type: original author: - first_name: Max full_name: Burg, Max last_name: Burg - first_name: Florian full_name: Wenzel, Florian last_name: Wenzel - first_name: Dominik full_name: Zietlow, Dominik last_name: Zietlow - first_name: Max full_name: Horn, Max last_name: Horn - first_name: Osama full_name: Makansi, Osama last_name: Makansi - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Chris full_name: Russell, Chris last_name: Russell citation: ama: Burg M, Wenzel F, Zietlow D, et al. Image retrieval outperforms diffusion models on data augmentation. Journal of Machine Learning Research. 2023. apa: Burg, M., Wenzel, F., Zietlow, D., Horn, M., Makansi, O., Locatello, F., & Russell, C. (2023). Image retrieval outperforms diffusion models on data augmentation. Journal of Machine Learning Research. ML Research Press. chicago: Burg, Max, Florian Wenzel, Dominik Zietlow, Max Horn, Osama Makansi, Francesco Locatello, and Chris Russell. “Image Retrieval Outperforms Diffusion Models on Data Augmentation.” Journal of Machine Learning Research. ML Research Press, 2023. ieee: M. Burg et al., “Image retrieval outperforms diffusion models on data augmentation,” Journal of Machine Learning Research. ML Research Press, 2023. ista: Burg M, Wenzel F, Zietlow D, Horn M, Makansi O, Locatello F, Russell C. 2023. Image retrieval outperforms diffusion models on data augmentation. Journal of Machine Learning Research. mla: Burg, Max, et al. “Image Retrieval Outperforms Diffusion Models on Data Augmentation.” Journal of Machine Learning Research, ML Research Press, 2023. short: M. Burg, F. Wenzel, D. Zietlow, M. Horn, O. Makansi, F. Locatello, C. Russell, Journal of Machine Learning Research (2023). date_created: 2024-02-07T14:57:39Z date_published: 2023-12-10T00:00:00Z date_updated: 2024-02-12T08:30:21Z day: '10' ddc: - '000' department: - _id: FrLo file: - access_level: open_access checksum: af87ddea7908923426365347b9c87ba7 content_type: application/pdf creator: ptazenko date_created: 2024-02-07T14:57:32Z date_updated: 2024-02-07T14:57:32Z file_id: '14950' file_name: Burg_et_al_2023_Image_retrieval_outperforms.pdf file_size: 27325153 relation: main_file file_date_updated: 2024-02-07T14:57:32Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://openreview.net/forum?id=xflYdGZMpv month: '12' oa: 1 oa_version: Published Version publication: Journal of Machine Learning Research publication_identifier: eissn: - 2835-8856 publication_status: published publisher: ML Research Press quality_controlled: '1' status: public title: Image retrieval outperforms diffusion models on data augmentation tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14946' abstract: - lang: eng text: "We present a unified framework for studying the identifiability of\r\nrepresentations learned from simultaneously observed views, such as different\r\ndata modalities. We allow a partially observed setting in which each view\r\nconstitutes a nonlinear mixture of a subset of underlying latent variables,\r\nwhich can be causally related. We prove that the information shared across all\r\nsubsets of any number of views can be learned up to a smooth bijection using\r\ncontrastive learning and a single encoder per view. We also provide graphical\r\ncriteria indicating which latent variables can be identified through a simple\r\nset of rules, which we refer to as identifiability algebra. Our general\r\nframework and theoretical results unify and extend several previous works on\r\nmulti-view nonlinear ICA, disentanglement, and causal representation learning.\r\nWe experimentally validate our claims on numerical, image, and multi-modal data\r\nsets. Further, we demonstrate that the performance of prior methods is\r\nrecovered in different special cases of our setup. Overall, we find that access\r\nto multiple partial views enables us to identify a more fine-grained\r\nrepresentation, under the generally milder assumption of partial observability." acknowledgement: "This work was initiated at the Second Bellairs Workshop on Causality held at the Bellairs Research Institute, January 6–13, 2022; we thank all workshop participants for providing a stimulating research environment. Further, we thank Cian Eastwood, Luigi Gresele, Stefano Soatto, Marco Bagatella, and A. René Geist for helpful discussion. GM is a member of the Machine Learning Cluster of Excellence, EXC number 2064/1 – Project number 390727645. JvK and GM acknowledge support from the German Federal Ministry of Education and Research (BMBF) through the Tübingen AI Center (FKZ: 01IS18039B). The research of DX and SM was supported by the Air Force Office of Scientific Research under award number FA8655-22-1-7155. Any opinions, findings, and conclusions or recommendations expressed in\r\nthis material are those of the author(s) and do not necessarily reflect the views of the United States Air Force. We also thank SURF for the support in using the Dutch National Supercomputer Snellius. DY was supported by an Amazon fellowship and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). Work done outside of Amazon. SL was supported by an IVADO excellence PhD scholarship and by Samsung Electronics Co., Ldt." article_number: '2311.04056' article_processing_charge: No author: - first_name: Dingling full_name: Yao, Dingling id: d3e02e50-48a8-11ee-8f62-c108061797fa last_name: Yao - first_name: Danru full_name: Xu, Danru last_name: Xu - first_name: Sébastien full_name: Lachapelle, Sébastien last_name: Lachapelle - first_name: Sara full_name: Magliacane, Sara last_name: Magliacane - first_name: Perouz full_name: Taslakian, Perouz last_name: Taslakian - first_name: Georg full_name: Martius, Georg last_name: Martius - first_name: Julius von full_name: Kügelgen, Julius von last_name: Kügelgen - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: Yao D, Xu D, Lachapelle S, et al. Multi-view causal representation learning with partial observability. arXiv. doi:10.48550/arXiv.2311.04056 apa: Yao, D., Xu, D., Lachapelle, S., Magliacane, S., Taslakian, P., Martius, G., … Locatello, F. (n.d.). Multi-view causal representation learning with partial observability. arXiv. https://doi.org/10.48550/arXiv.2311.04056 chicago: Yao, Dingling, Danru Xu, Sébastien Lachapelle, Sara Magliacane, Perouz Taslakian, Georg Martius, Julius von Kügelgen, and Francesco Locatello. “Multi-View Causal Representation Learning with Partial Observability.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2311.04056. ieee: D. Yao et al., “Multi-view causal representation learning with partial observability,” arXiv. . ista: Yao D, Xu D, Lachapelle S, Magliacane S, Taslakian P, Martius G, Kügelgen J von, Locatello F. Multi-view causal representation learning with partial observability. arXiv, 2311.04056. mla: Yao, Dingling, et al. “Multi-View Causal Representation Learning with Partial Observability.” ArXiv, 2311.04056, doi:10.48550/arXiv.2311.04056. short: D. Yao, D. Xu, S. Lachapelle, S. Magliacane, P. Taslakian, G. Martius, J. von Kügelgen, F. Locatello, ArXiv (n.d.). date_created: 2024-02-07T14:28:34Z date_published: 2023-11-07T00:00:00Z date_updated: 2024-02-12T08:07:33Z day: '07' department: - _id: FrLo doi: 10.48550/arXiv.2311.04056 external_id: arxiv: - '2311.04056' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2311.04056 month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Multi-view causal representation learning with partial observability type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14952' abstract: - lang: eng text: "While different neural models often exhibit latent spaces that are alike when exposed to semantically related data, this intrinsic similarity is not always immediately discernible. Towards a better understanding of this phenomenon, our work shows how representations learned from these neural modules can be translated between different pre-trained networks via simpler transformations than previously thought. An advantage of this approach is the ability to\r\nestimate these transformations using standard, well-understood algebraic procedures that have closed-form solutions. Our method directly estimates a transformation between two given latent spaces, thereby enabling effective stitching of encoders and decoders without additional training. We extensively validate the adaptability of this translation procedure in different\r\nexperimental settings: across various trainings, domains, architectures (e.g., ResNet, CNN, ViT), and in multiple downstream tasks (classification, reconstruction). Notably, we show how it is possible to zero-shot stitch text encoders and vision decoders, or vice-versa, yielding surprisingly good classification performance in this multimodal setting." acknowledgement: "This work is supported by the ERC grant no.802554 (SPECGEO), PRIN 2020 project no.2020TA3K9N (LEGO.AI), and PNRR MUR project PE0000013-FAIR. Francesco\r\nLocatello did not contribute to this work at Amazon." article_number: '2311.00664' article_processing_charge: No author: - first_name: Valentino full_name: Maiorca, Valentino last_name: Maiorca - first_name: Luca full_name: Moschella, Luca last_name: Moschella - first_name: Antonio full_name: Norelli, Antonio last_name: Norelli - first_name: Marco full_name: Fumero, Marco last_name: Fumero - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Emanuele full_name: Rodolà, Emanuele last_name: Rodolà citation: ama: Maiorca V, Moschella L, Norelli A, Fumero M, Locatello F, Rodolà E. Latent space translation via semantic alignment. arXiv. doi:10.48550/arXiv.2311.00664 apa: Maiorca, V., Moschella, L., Norelli, A., Fumero, M., Locatello, F., & Rodolà, E. (n.d.). Latent space translation via semantic alignment. arXiv. https://doi.org/10.48550/arXiv.2311.00664 chicago: Maiorca, Valentino, Luca Moschella, Antonio Norelli, Marco Fumero, Francesco Locatello, and Emanuele Rodolà. “Latent Space Translation via Semantic Alignment.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2311.00664. ieee: V. Maiorca, L. Moschella, A. Norelli, M. Fumero, F. Locatello, and E. Rodolà, “Latent space translation via semantic alignment,” arXiv. . ista: Maiorca V, Moschella L, Norelli A, Fumero M, Locatello F, Rodolà E. Latent space translation via semantic alignment. arXiv, 2311.00664. mla: Maiorca, Valentino, et al. “Latent Space Translation via Semantic Alignment.” ArXiv, 2311.00664, doi:10.48550/arXiv.2311.00664. short: V. Maiorca, L. Moschella, A. Norelli, M. Fumero, F. Locatello, E. Rodolà, ArXiv (n.d.). date_created: 2024-02-07T15:08:55Z date_published: 2023-11-01T00:00:00Z date_updated: 2024-02-12T09:40:23Z day: '01' department: - _id: FrLo doi: 10.48550/arXiv.2311.00664 external_id: arxiv: - '2311.00664' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2311.00664 month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Latent space translation via semantic alignment type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14948' abstract: - lang: eng text: "The extraction of modular object-centric representations for downstream tasks\r\nis an emerging area of research. Learning grounded representations of objects\r\nthat are guaranteed to be stable and invariant promises robust performance\r\nacross different tasks and environments. Slot Attention (SA) learns\r\nobject-centric representations by assigning objects to \\textit{slots}, but\r\npresupposes a \\textit{single} distribution from which all slots are randomly\r\ninitialised. This results in an inability to learn \\textit{specialized} slots\r\nwhich bind to specific object types and remain invariant to identity-preserving\r\nchanges in object appearance. To address this, we present\r\n\\emph{\\textsc{Co}nditional \\textsc{S}lot \\textsc{A}ttention} (\\textsc{CoSA})\r\nusing a novel concept of \\emph{Grounded Slot Dictionary} (GSD) inspired by\r\nvector quantization. Our proposed GSD comprises (i) canonical object-level\r\nproperty vectors and (ii) parametric Gaussian distributions, which define a\r\nprior over the slots. We demonstrate the benefits of our method in multiple\r\ndownstream tasks such as scene generation, composition, and task adaptation,\r\nwhilst remaining competitive with SA in popular object discovery benchmarks." acknowledgement: "This work was supported by supported by UKRI (grant agreement no. EP/S023356/1), in the UKRI\r\nCentre for Doctoral Training in Safe and Trusted AI via A. Kori." article_number: '2307.09437' article_processing_charge: No author: - first_name: Avinash full_name: Kori, Avinash last_name: Kori - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Fabio De Sousa full_name: Ribeiro, Fabio De Sousa last_name: Ribeiro - first_name: Francesca full_name: Toni, Francesca last_name: Toni - first_name: Ben full_name: Glocker, Ben last_name: Glocker citation: ama: Kori A, Locatello F, Ribeiro FDS, Toni F, Glocker B. Grounded object centric learning. arXiv. doi:10.48550/arXiv.2307.09437 apa: Kori, A., Locatello, F., Ribeiro, F. D. S., Toni, F., & Glocker, B. (n.d.). Grounded object centric learning. arXiv. https://doi.org/10.48550/arXiv.2307.09437 chicago: Kori, Avinash, Francesco Locatello, Fabio De Sousa Ribeiro, Francesca Toni, and Ben Glocker. “Grounded Object Centric Learning.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2307.09437. ieee: A. Kori, F. Locatello, F. D. S. Ribeiro, F. Toni, and B. Glocker, “Grounded object centric learning,” arXiv. . ista: Kori A, Locatello F, Ribeiro FDS, Toni F, Glocker B. Grounded object centric learning. arXiv, 2307.09437. mla: Kori, Avinash, et al. “Grounded Object Centric Learning.” ArXiv, 2307.09437, doi:10.48550/arXiv.2307.09437. short: A. Kori, F. Locatello, F.D.S. Ribeiro, F. Toni, B. Glocker, ArXiv (n.d.). date_created: 2024-02-07T14:47:04Z date_published: 2023-07-18T00:00:00Z date_updated: 2024-02-12T08:13:12Z day: '18' department: - _id: FrLo doi: 10.48550/arXiv.2307.09437 external_id: arxiv: - '2307.09437' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2307.09437 month: '07' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Grounded object centric learning type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14953' abstract: - lang: eng text: This paper provides statistical sample complexity bounds for score-matching and its applications in causal discovery. We demonstrate that accurate estimation of the score function is achievable by training a standard deep ReLU neural network using stochastic gradient descent. We establish bounds on the error rate of recovering causal relationships using the score-matching-based causal discovery method of Rolland et al. [2022], assuming a sufficiently good estimation of the score function. Finally, we analyze the upper bound of score-matching estimation within the score-based generative modeling, which has been applied for causal discovery but is also of independent interest within the domain of generative models. acknowledgement: 'We are thankful to the reviewers for providing constructive feedback and Kun Zhang and Dominik Janzing for helpful discussion on the special case of deterministic children. This work was supported by Hasler Foundation Program: Hasler Responsible AI (project number 21043). This work was supported by the Swiss National Science Foundation (SNSF) under grant number 200021_205011. Francesco Locatello did not contribute to this work at Amazon. ' article_number: '2310.18123' article_processing_charge: No author: - first_name: Zhenyu full_name: Zhu, Zhenyu last_name: Zhu - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Volkan full_name: Cevher, Volkan last_name: Cevher citation: ama: 'Zhu Z, Locatello F, Cevher V. Sample complexity bounds for score-matching: Causal discovery and generative modeling. arXiv. doi:10.48550/arXiv.2310.18123' apa: 'Zhu, Z., Locatello, F., & Cevher, V. (n.d.). Sample complexity bounds for score-matching: Causal discovery and generative modeling. arXiv. https://doi.org/10.48550/arXiv.2310.18123' chicago: 'Zhu, Zhenyu, Francesco Locatello, and Volkan Cevher. “Sample Complexity Bounds for Score-Matching: Causal Discovery and Generative Modeling.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2310.18123.' ieee: 'Z. Zhu, F. Locatello, and V. Cevher, “Sample complexity bounds for score-matching: Causal discovery and generative modeling,” arXiv. .' ista: 'Zhu Z, Locatello F, Cevher V. Sample complexity bounds for score-matching: Causal discovery and generative modeling. arXiv, 2310.18123.' mla: 'Zhu, Zhenyu, et al. “Sample Complexity Bounds for Score-Matching: Causal Discovery and Generative Modeling.” ArXiv, 2310.18123, doi:10.48550/arXiv.2310.18123.' short: Z. Zhu, F. Locatello, V. Cevher, ArXiv (n.d.). date_created: 2024-02-07T15:11:11Z date_published: 2023-10-27T00:00:00Z date_updated: 2024-02-12T09:45:58Z day: '27' department: - _id: FrLo doi: 10.48550/arXiv.2310.18123 external_id: arxiv: - '2310.18123' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2310.18123 month: '10' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 'Sample complexity bounds for score-matching: Causal discovery and generative modeling' type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14954' abstract: - lang: eng text: "When domain knowledge is limited and experimentation is restricted by ethical, financial, or time constraints, practitioners turn to observational causal discovery methods to recover the causal structure, exploiting the statistical properties of their data. Because causal discovery without further assumptions is an ill-posed problem, each algorithm comes with its own set of\r\nusually untestable assumptions, some of which are hard to meet in real datasets. Motivated by these considerations, this paper extensively benchmarks the empirical performance of recent causal discovery methods on observational i.i.d. data generated under different background conditions, allowing for violations of the critical assumptions required by each selected approach. Our experimental findings show that score matching-based methods demonstrate\r\nsurprising performance in the false positive and false negative rate of the inferred graph in these challenging scenarios, and we provide theoretical insights into their performance. This work is also the first effort to benchmark the stability of causal discovery algorithms with respect to the values of their hyperparameters. Finally, we hope this paper will set a new standard for the evaluation of causal discovery methods and can serve as an accessible entry point for practitioners interested in the field, highlighting the empirical implications of different algorithm choices." acknowledgement: "We thank Kun Zhang and Carl-Johann Simon-Gabriel for the insightful discussions. This work\r\nhas been supported by AFOSR, grant n. FA8655-20-1-7035. FM is supported by Programma\r\nOperativo Nazionale ricerca e innovazione 2014-2020. FM partially contributed to this work during an internship at Amazon Web Services with FL. FL partially contributed while at AWS." article_number: '2310.13387' article_processing_charge: No author: - first_name: Francesco full_name: Montagna, Francesco last_name: Montagna - first_name: Atalanti A. full_name: Mastakouri, Atalanti A. last_name: Mastakouri - first_name: Elias full_name: Eulig, Elias last_name: Eulig - first_name: Nicoletta full_name: Noceti, Nicoletta last_name: Noceti - first_name: Lorenzo full_name: Rosasco, Lorenzo last_name: Rosasco - first_name: Dominik full_name: Janzing, Dominik last_name: Janzing - first_name: Bryon full_name: Aragam, Bryon last_name: Aragam - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: Montagna F, Mastakouri AA, Eulig E, et al. Assumption violations in causal discovery and the robustness of score matching. arXiv. doi:10.48550/arXiv.2310.13387 apa: Montagna, F., Mastakouri, A. A., Eulig, E., Noceti, N., Rosasco, L., Janzing, D., … Locatello, F. (n.d.). Assumption violations in causal discovery and the robustness of score matching. arXiv. https://doi.org/10.48550/arXiv.2310.13387 chicago: Montagna, Francesco, Atalanti A. Mastakouri, Elias Eulig, Nicoletta Noceti, Lorenzo Rosasco, Dominik Janzing, Bryon Aragam, and Francesco Locatello. “Assumption Violations in Causal Discovery and the Robustness of Score Matching.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2310.13387. ieee: F. Montagna et al., “Assumption violations in causal discovery and the robustness of score matching,” arXiv. . ista: Montagna F, Mastakouri AA, Eulig E, Noceti N, Rosasco L, Janzing D, Aragam B, Locatello F. Assumption violations in causal discovery and the robustness of score matching. arXiv, 2310.13387. mla: Montagna, Francesco, et al. “Assumption Violations in Causal Discovery and the Robustness of Score Matching.” ArXiv, 2310.13387, doi:10.48550/arXiv.2310.13387. short: F. Montagna, A.A. Mastakouri, E. Eulig, N. Noceti, L. Rosasco, D. Janzing, B. Aragam, F. Locatello, ArXiv (n.d.). date_created: 2024-02-07T15:11:56Z date_published: 2023-10-20T00:00:00Z date_updated: 2024-02-12T09:51:15Z day: '20' department: - _id: FrLo doi: 10.48550/arXiv.2310.13387 external_id: arxiv: - '2310.13387' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2310.13387 month: '10' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Assumption violations in causal discovery and the robustness of score matching type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14210' abstract: - lang: eng text: Recovering the latent factors of variation of high dimensional data has so far focused on simple synthetic settings. Mostly building on unsupervised and weakly-supervised objectives, prior work missed out on the positive implications for representation learning on real world data. In this work, we propose to leverage knowledge extracted from a diversified set of supervised tasks to learn a common disentangled representation. Assuming each supervised task only depends on an unknown subset of the factors of variation, we disentangle the feature space of a supervised multi-task model, with features activating sparsely across different tasks and information being shared as appropriate. Importantly, we never directly observe the factors of variations but establish that access to multiple tasks is sufficient for identifiability under sufficiency and minimality assumptions. We validate our approach on six real world distribution shift benchmarks, and different data modalities (images, text), demonstrating how disentangled representations can be transferred to real settings. article_number: '2304.07939' article_processing_charge: No author: - first_name: Marco full_name: Fumero, Marco last_name: Fumero - first_name: Florian full_name: Wenzel, Florian last_name: Wenzel - first_name: Luca full_name: Zancato, Luca last_name: Zancato - first_name: Alessandro full_name: Achille, Alessandro last_name: Achille - first_name: Emanuele full_name: Rodolà, Emanuele last_name: Rodolà - first_name: Stefano full_name: Soatto, Stefano last_name: Soatto - first_name: Bernhard full_name: Schölkopf, Bernhard last_name: Schölkopf - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: Fumero M, Wenzel F, Zancato L, et al. Leveraging sparse and shared feature activations for disentangled representation learning. arXiv. doi:10.48550/arXiv.2304.07939 apa: Fumero, M., Wenzel, F., Zancato, L., Achille, A., Rodolà, E., Soatto, S., … Locatello, F. (n.d.). Leveraging sparse and shared feature activations for disentangled representation learning. arXiv. https://doi.org/10.48550/arXiv.2304.07939 chicago: Fumero, Marco, Florian Wenzel, Luca Zancato, Alessandro Achille, Emanuele Rodolà, Stefano Soatto, Bernhard Schölkopf, and Francesco Locatello. “Leveraging Sparse and Shared Feature Activations for Disentangled Representation Learning.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2304.07939. ieee: M. Fumero et al., “Leveraging sparse and shared feature activations for disentangled representation learning,” arXiv. . ista: Fumero M, Wenzel F, Zancato L, Achille A, Rodolà E, Soatto S, Schölkopf B, Locatello F. Leveraging sparse and shared feature activations for disentangled representation learning. arXiv, 2304.07939. mla: Fumero, Marco, et al. “Leveraging Sparse and Shared Feature Activations for Disentangled Representation Learning.” ArXiv, 2304.07939, doi:10.48550/arXiv.2304.07939. short: M. Fumero, F. Wenzel, L. Zancato, A. Achille, E. Rodolà, S. Soatto, B. Schölkopf, F. Locatello, ArXiv (n.d.). date_created: 2023-08-22T14:19:03Z date_published: 2023-04-17T00:00:00Z date_updated: 2024-02-12T09:55:48Z day: '17' department: - _id: FrLo doi: 10.48550/arXiv.2304.07939 external_id: arxiv: - '2304.07939' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2304.07939 month: '04' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Leveraging sparse and shared feature activations for disentangled representation learning type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14207' abstract: - lang: eng text: The binding problem in human cognition, concerning how the brain represents and connects objects within a fixed network of neural connections, remains a subject of intense debate. Most machine learning efforts addressing this issue in an unsupervised setting have focused on slot-based methods, which may be limiting due to their discrete nature and difficulty to express uncertainty. Recently, the Complex AutoEncoder was proposed as an alternative that learns continuous and distributed object-centric representations. However, it is only applicable to simple toy data. In this paper, we present Rotating Features, a generalization of complex-valued features to higher dimensions, and a new evaluation procedure for extracting objects from distributed representations. Additionally, we show the applicability of our approach to pre-trained features. Together, these advancements enable us to scale distributed object-centric representations from simple toy to real-world data. We believe this work advances a new paradigm for addressing the binding problem in machine learning and has the potential to inspire further innovation in the field. article_number: '2306.00600' article_processing_charge: No author: - first_name: Sindy full_name: Löwe, Sindy last_name: Löwe - first_name: Phillip full_name: Lippe, Phillip last_name: Lippe - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Max full_name: Welling, Max last_name: Welling citation: ama: Löwe S, Lippe P, Locatello F, Welling M. Rotating features for object discovery. arXiv. doi:10.48550/arXiv.2306.00600 apa: Löwe, S., Lippe, P., Locatello, F., & Welling, M. (n.d.). Rotating features for object discovery. arXiv. https://doi.org/10.48550/arXiv.2306.00600 chicago: Löwe, Sindy, Phillip Lippe, Francesco Locatello, and Max Welling. “Rotating Features for Object Discovery.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2306.00600. ieee: S. Löwe, P. Lippe, F. Locatello, and M. Welling, “Rotating features for object discovery,” arXiv. . ista: Löwe S, Lippe P, Locatello F, Welling M. Rotating features for object discovery. arXiv, 2306.00600. mla: Löwe, Sindy, et al. “Rotating Features for Object Discovery.” ArXiv, 2306.00600, doi:10.48550/arXiv.2306.00600. short: S. Löwe, P. Lippe, F. Locatello, M. Welling, ArXiv (n.d.). date_created: 2023-08-22T14:18:00Z date_published: 2023-06-01T00:00:00Z date_updated: 2024-02-12T09:53:44Z day: '01' department: - _id: FrLo doi: 10.48550/arXiv.2306.00600 external_id: arxiv: - '2306.00600' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/2306.00600 month: '06' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Rotating features for object discovery type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14961' abstract: - lang: eng text: "The use of simulated data in the field of causal discovery is ubiquitous due to the scarcity of annotated real data. Recently, Reisach et al., 2021 highlighted the emergence of patterns in simulated linear data, which displays increasing marginal variance in the casual direction. As an ablation in their experiments, Montagna et al., 2023 found that similar patterns may emerge in\r\nnonlinear models for the variance of the score vector $\\nabla \\log p_{\\mathbf{X}}$, and introduced the ScoreSort algorithm. In this work, we formally define and characterize this score-sortability pattern of nonlinear additive noise models. We find that it defines a class of identifiable (bivariate) causal models overlapping with nonlinear additive noise models. We\r\ntheoretically demonstrate the advantages of ScoreSort in terms of statistical efficiency compared to prior state-of-the-art score matching-based methods and empirically show the score-sortability of the most common synthetic benchmarks in the literature. Our findings remark (1) the lack of diversity in the data as an important limitation in the evaluation of nonlinear causal discovery approaches, (2) the importance of thoroughly testing different settings within a problem class, and (3) the importance of analyzing statistical properties in\r\ncausal discovery, where research is often limited to defining identifiability conditions of the model. " article_number: '2310.14246' article_processing_charge: No author: - first_name: Francesco full_name: Montagna, Francesco last_name: Montagna - first_name: Nicoletta full_name: Noceti, Nicoletta last_name: Noceti - first_name: Lorenzo full_name: Rosasco, Lorenzo last_name: Rosasco - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 citation: ama: Montagna F, Noceti N, Rosasco L, Locatello F. Shortcuts for causal discovery of nonlinear models by score matching. arXiv. doi:10.48550/arXiv.2310.14246 apa: Montagna, F., Noceti, N., Rosasco, L., & Locatello, F. (n.d.). Shortcuts for causal discovery of nonlinear models by score matching. arXiv. https://doi.org/10.48550/arXiv.2310.14246 chicago: Montagna, Francesco, Nicoletta Noceti, Lorenzo Rosasco, and Francesco Locatello. “Shortcuts for Causal Discovery of Nonlinear Models by Score Matching.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2310.14246. ieee: F. Montagna, N. Noceti, L. Rosasco, and F. Locatello, “Shortcuts for causal discovery of nonlinear models by score matching,” arXiv. . ista: Montagna F, Noceti N, Rosasco L, Locatello F. Shortcuts for causal discovery of nonlinear models by score matching. arXiv, 2310.14246. mla: Montagna, Francesco, et al. “Shortcuts for Causal Discovery of Nonlinear Models by Score Matching.” ArXiv, 2310.14246, doi:10.48550/arXiv.2310.14246. short: F. Montagna, N. Noceti, L. Rosasco, F. Locatello, ArXiv (n.d.). date_created: 2024-02-08T15:31:46Z date_published: 2023-10-22T00:00:00Z date_updated: 2024-02-12T10:03:33Z day: '22' department: - _id: FrLo doi: 10.48550/arXiv.2310.14246 external_id: arxiv: - '2310.14246' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2310.14246 month: '10' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: Shortcuts for causal discovery of nonlinear models by score matching type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14958' abstract: - lang: eng text: Causal representation learning (CRL) aims at identifying high-level causal variables from low-level data, e.g. images. Current methods usually assume that all causal variables are captured in the high-dimensional observations. In this work, we focus on learning causal representations from data under partial observability, i.e., when some of the causal variables are not observed in the measurements, and the set of masked variables changes across the different samples. We introduce some initial theoretical results for identifying causal variables under partial observability by exploiting a sparsity regularizer, focusing in particular on the linear and piecewise linear mixing function case. We provide a theorem that allows us to identify the causal variables up to permutation and element-wise linear transformations in the linear case and a lemma that allows us to identify causal variables up to linear transformation in the piecewise case. Finally, we provide a conjecture that would allow us to identify the causal variables up to permutation and element-wise linear transformations also in the piecewise linear case. We test the theorem and conjecture on simulated data, showing the effectiveness of our method. acknowledgement: "This work was initiated at the Second Bellairs Workshop on Causality held at the Bellairs Research Institute, January 6–13, 2022; we thank all workshop participants for providing a stimulating research environment. The research of DX and SM was supported by the Air Force Office of Scientific Research under award number FA8655-22-1-7155. Any opinions, findings, and conclusions or recommendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the United States Air Force. We also thank SURF for the support in using the Dutch National Supercomputer Snellius. DY was supported by an Amazon fellowship and the International Max Planck Research School for Intelligent Systems (IMPRS-IS). Work done outside of Amazon. SL was supported by an IVADO excellence PhD scholarship and by Samsung Electronics Co., Ldt. JvK acknowledges support from the German Federal Ministry of Education and Research (BMBF)\r\nthrough the Tübingen AI Center (FKZ: 01IS18039B).\r\n" article_number: '54' article_processing_charge: No author: - first_name: Danru full_name: Xu, Danru last_name: Xu - first_name: Dingling full_name: Yao, Dingling id: d3e02e50-48a8-11ee-8f62-c108061797fa last_name: Yao - first_name: Sebastien full_name: Lachapelle, Sebastien last_name: Lachapelle - first_name: Perouz full_name: Taslakian, Perouz last_name: Taslakian - first_name: Julius full_name: von Kügelgen, Julius last_name: von Kügelgen - first_name: Francesco full_name: Locatello, Francesco id: 26cfd52f-2483-11ee-8040-88983bcc06d4 last_name: Locatello orcid: 0000-0002-4850-0683 - first_name: Sara full_name: Magliacane, Sara last_name: Magliacane citation: ama: 'Xu D, Yao D, Lachapelle S, et al. A sparsity principle for partially observable causal representation learning. In: Causal Representation Learning Workshop at NeurIPS 2023. OpenReview; 2023.' apa: 'Xu, D., Yao, D., Lachapelle, S., Taslakian, P., von Kügelgen, J., Locatello, F., & Magliacane, S. (2023). A sparsity principle for partially observable causal representation learning. In Causal Representation Learning Workshop at NeurIPS 2023. New Orleans, LA, United States: OpenReview.' chicago: Xu, Danru, Dingling Yao, Sebastien Lachapelle, Perouz Taslakian, Julius von Kügelgen, Francesco Locatello, and Sara Magliacane. “A Sparsity Principle for Partially Observable Causal Representation Learning.” In Causal Representation Learning Workshop at NeurIPS 2023. OpenReview, 2023. ieee: D. Xu et al., “A sparsity principle for partially observable causal representation learning,” in Causal Representation Learning Workshop at NeurIPS 2023, New Orleans, LA, United States, 2023. ista: 'Xu D, Yao D, Lachapelle S, Taslakian P, von Kügelgen J, Locatello F, Magliacane S. 2023. A sparsity principle for partially observable causal representation learning. Causal Representation Learning Workshop at NeurIPS 2023. CRL: Causal Representation Learning Workshop at NeurIPS, 54.' mla: Xu, Danru, et al. “A Sparsity Principle for Partially Observable Causal Representation Learning.” Causal Representation Learning Workshop at NeurIPS 2023, 54, OpenReview, 2023. short: D. Xu, D. Yao, S. Lachapelle, P. Taslakian, J. von Kügelgen, F. Locatello, S. Magliacane, in:, Causal Representation Learning Workshop at NeurIPS 2023, OpenReview, 2023. conference: end_date: 2023-12-15 location: New Orleans, LA, United States name: 'CRL: Causal Representation Learning Workshop at NeurIPS' start_date: 2023-12-15 date_created: 2024-02-07T15:17:51Z date_published: 2023-12-05T00:00:00Z date_updated: 2024-02-13T08:59:27Z day: '05' ddc: - '000' department: - _id: FrLo file: - access_level: open_access checksum: 484efc27bda75ed6666044989695d9b6 content_type: application/pdf creator: dernst date_created: 2024-02-13T08:50:53Z date_updated: 2024-02-13T08:50:53Z file_id: '14982' file_name: 2023_CRL_Xu.pdf file_size: 552357 relation: main_file success: 1 file_date_updated: 2024-02-13T08:50:53Z has_accepted_license: '1' language: - iso: eng main_file_link: - open_access: '1' url: https://openreview.net/forum?id=Whr6uobelR month: '12' oa: 1 oa_version: Published Version publication: Causal Representation Learning Workshop at NeurIPS 2023 publication_status: published publisher: OpenReview quality_controlled: '1' status: public title: A sparsity principle for partially observable causal representation learning tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14923' abstract: - lang: eng text: We study the performance of a Bayesian statistician who estimates a rank-one signal corrupted by non-symmetric rotationally invariant noise with a generic distribution of singular values. As the signal-to-noise ratio and the noise structure are unknown, a Gaussian setup is incorrectly assumed. We derive the exact analytic expression for the error of the mismatched Bayes estimator and also provide the analysis of an approximate message passing (AMP) algorithm. The first result exploits the asymptotic behavior of spherical integrals for rectangular matrices and of low-rank matrix perturbations; the second one relies on the design and analysis of an auxiliary AMP. The numerical experiments show that there is a performance gap between the AMP and Bayes estimators, which is due to the incorrect estimation of the signal norm. article_processing_charge: No author: - first_name: Teng full_name: Fu, Teng last_name: Fu - first_name: YuHao full_name: Liu, YuHao last_name: Liu - first_name: Jean full_name: Barbier, Jean last_name: Barbier - first_name: Marco full_name: Mondelli, Marco id: 27EB676C-8706-11E9-9510-7717E6697425 last_name: Mondelli orcid: 0000-0002-3242-7020 - first_name: ShanSuo full_name: Liang, ShanSuo last_name: Liang - first_name: TianQi full_name: Hou, TianQi last_name: Hou citation: ama: 'Fu T, Liu Y, Barbier J, Mondelli M, Liang S, Hou T. Mismatched estimation of non-symmetric rank-one matrices corrupted by structured noise. In: Proceedings of 2023 IEEE International Symposium on Information Theory. IEEE. doi:10.1109/isit54713.2023.10206671' apa: 'Fu, T., Liu, Y., Barbier, J., Mondelli, M., Liang, S., & Hou, T. (n.d.). Mismatched estimation of non-symmetric rank-one matrices corrupted by structured noise. In Proceedings of 2023 IEEE International Symposium on Information Theory. Taipei, Taiwan: IEEE. https://doi.org/10.1109/isit54713.2023.10206671' chicago: Fu, Teng, YuHao Liu, Jean Barbier, Marco Mondelli, ShanSuo Liang, and TianQi Hou. “Mismatched Estimation of Non-Symmetric Rank-One Matrices Corrupted by Structured Noise.” In Proceedings of 2023 IEEE International Symposium on Information Theory. IEEE, n.d. https://doi.org/10.1109/isit54713.2023.10206671. ieee: T. Fu, Y. Liu, J. Barbier, M. Mondelli, S. Liang, and T. Hou, “Mismatched estimation of non-symmetric rank-one matrices corrupted by structured noise,” in Proceedings of 2023 IEEE International Symposium on Information Theory, Taipei, Taiwan. ista: 'Fu T, Liu Y, Barbier J, Mondelli M, Liang S, Hou T. Mismatched estimation of non-symmetric rank-one matrices corrupted by structured noise. Proceedings of 2023 IEEE International Symposium on Information Theory. ISIT: IEEE International Symposium on Information Theory.' mla: Fu, Teng, et al. “Mismatched Estimation of Non-Symmetric Rank-One Matrices Corrupted by Structured Noise.” Proceedings of 2023 IEEE International Symposium on Information Theory, IEEE, doi:10.1109/isit54713.2023.10206671. short: T. Fu, Y. Liu, J. Barbier, M. Mondelli, S. Liang, T. Hou, in:, Proceedings of 2023 IEEE International Symposium on Information Theory, IEEE, n.d. conference: end_date: 2023-06-30 location: Taipei, Taiwan name: 'ISIT: IEEE International Symposium on Information Theory' start_date: 2023-06-25 date_created: 2024-02-02T11:20:39Z date_published: 2023-06-30T00:00:00Z date_updated: 2024-02-14T14:34:03Z day: '30' department: - _id: MaMo doi: 10.1109/isit54713.2023.10206671 external_id: arxiv: - '2302.03306' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2302.03306 month: '06' oa: 1 oa_version: Preprint publication: Proceedings of 2023 IEEE International Symposium on Information Theory publication_status: inpress publisher: IEEE quality_controlled: '1' status: public title: Mismatched estimation of non-symmetric rank-one matrices corrupted by structured noise type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14466' abstract: - lang: eng text: The first long-lived turbulent structures observable in planar shear flows take the form of localized stripes, inclined with respect to the mean flow direction. The dynamics of these stripes is central to transition, and recent studies proposed an analogy to directed percolation where the stripes’ proliferation is ultimately responsible for the turbulence becoming sustained. In the present study we focus on the internal stripe dynamics as well as on the eventual stripe expansion, and we compare the underlying mechanisms in pressure- and shear-driven planar flows, respectively, plane-Poiseuille and plane-Couette flow. Despite the similarities of the overall laminar–turbulence patterns, the stripe proliferation processes in the two cases are fundamentally different. Starting from the growth and sustenance of individual stripes, we find that in plane-Couette flow new streaks are created stochastically throughout the stripe whereas in plane-Poiseuille flow streak creation is deterministic and occurs locally at the downstream tip. Because of the up/downstream symmetry, Couette stripes, in contrast to Poiseuille stripes, have two weak and two strong laminar turbulent interfaces. These differences in symmetry as well as in internal growth give rise to two fundamentally different stripe splitting mechanisms. In plane-Poiseuille flow splitting is connected to the elongational growth of the original stripe, and it results from a break-off/shedding of the stripe's tail. In plane-Couette flow splitting follows from a broadening of the original stripe and a division along the stripe into two slimmer stripes. acknowledgement: E.M. acknowledges funding from the ISTplus fellowship programme. G.Y. and B.H. acknowledge a grant from the Simons Foundation (662960, BH). article_number: A21 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Elena full_name: Marensi, Elena id: 0BE7553A-1004-11EA-B805-18983DDC885E last_name: Marensi orcid: 0000-0001-7173-4923 - first_name: Gökhan full_name: Yalniz, Gökhan id: 66E74FA2-D8BF-11E9-8249-8DE2E5697425 last_name: Yalniz orcid: 0000-0002-8490-9312 - first_name: Björn full_name: Hof, Björn id: 3A374330-F248-11E8-B48F-1D18A9856A87 last_name: Hof orcid: 0000-0003-2057-2754 citation: ama: Marensi E, Yalniz G, Hof B. Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics. 2023;974. doi:10.1017/jfm.2023.780 apa: Marensi, E., Yalniz, G., & Hof, B. (2023). Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics. Cambridge University Press. https://doi.org/10.1017/jfm.2023.780 chicago: Marensi, Elena, Gökhan Yalniz, and Björn Hof. “Dynamics and Proliferation of Turbulent Stripes in Plane-Poiseuille and Plane-Couette Flows.” Journal of Fluid Mechanics. Cambridge University Press, 2023. https://doi.org/10.1017/jfm.2023.780. ieee: E. Marensi, G. Yalniz, and B. Hof, “Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows,” Journal of Fluid Mechanics, vol. 974. Cambridge University Press, 2023. ista: Marensi E, Yalniz G, Hof B. 2023. Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows. Journal of Fluid Mechanics. 974, A21. mla: Marensi, Elena, et al. “Dynamics and Proliferation of Turbulent Stripes in Plane-Poiseuille and Plane-Couette Flows.” Journal of Fluid Mechanics, vol. 974, A21, Cambridge University Press, 2023, doi:10.1017/jfm.2023.780. short: E. Marensi, G. Yalniz, B. Hof, Journal of Fluid Mechanics 974 (2023). date_created: 2023-10-30T09:32:28Z date_published: 2023-11-10T00:00:00Z date_updated: 2024-02-15T09:06:23Z day: '10' ddc: - '530' department: - _id: GradSch - _id: BjHo doi: 10.1017/jfm.2023.780 external_id: arxiv: - '2212.12406' isi: - '001088363700001' file: - access_level: open_access checksum: 17c64c1fb0d5f73252364bf98b0b9e1a content_type: application/pdf creator: dernst date_created: 2024-02-15T09:05:21Z date_updated: 2024-02-15T09:05:21Z file_id: '14996' file_name: 2023_JourFluidMechanics_Marensi.pdf file_size: 2804641 relation: main_file success: 1 file_date_updated: 2024-02-15T09:05:21Z has_accepted_license: '1' intvolume: ' 974' isi: 1 keyword: - turbulence - transition to turbulence - patterns language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 238598C6-32DE-11EA-91FC-C7463DDC885E grant_number: '662960' name: 'Revisiting the Turbulence Problem Using Statistical Mechanics: Experimental Studies on Transitional and Turbulent Flows' publication: Journal of Fluid Mechanics publication_identifier: eissn: - 1469-7645 issn: - 0022-1120 publication_status: published publisher: Cambridge University Press quality_controlled: '1' status: public title: Dynamics and proliferation of turbulent stripes in plane-Poiseuille and plane-Couette flows tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 974 year: '2023' ... --- _id: '14687' abstract: - lang: eng text: The short history of research on Li-O2 batteries has seen a remarkable number of mechanistic U-turns over the years. From the initial use of carbonate electrolytes, that were then found to be entirely unsuitable, to the belief that (su)peroxide was solely responsible for degradation, before the more reactive singlet oxygen was found to form, to the hypothesis that capacity depends on a competing surface/solution mechanism before a practically exclusive solution mechanism was identified. Herein, we argue for an ever-fresh look at the reported data without bias towards supposedly established explanations. We explain how the latest findings on rate and capacity limits, as well as the origin of side reactions, are connected via the disproportionation (DISP) step in the (dis)charge mechanism. Therefrom, directions emerge for the design of electrolytes and mediators on how to suppress side reactions and to enable high rate and high reversible capacity. article_number: e202316476 article_processing_charge: Yes (via OA deal) article_type: review author: - first_name: Rajesh B full_name: Jethwa, Rajesh B id: 4cc538d5-803f-11ed-ab7e-8139573aad8f last_name: Jethwa orcid: 0000-0002-0404-4356 - first_name: Soumyadip full_name: Mondal, Soumyadip id: d25d21ef-dc8d-11ea-abe3-ec4576307f48 last_name: Mondal - first_name: Bhargavi full_name: Pant, Bhargavi id: 50c64d4d-eb97-11eb-a6c2-d33e5e14f112 last_name: Pant - first_name: Stefan Alexander full_name: Freunberger, Stefan Alexander id: A8CA28E6-CE23-11E9-AD2D-EC27E6697425 last_name: Freunberger orcid: 0000-0003-2902-5319 citation: ama: Jethwa RB, Mondal S, Pant B, Freunberger SA. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. 2023. doi:10.1002/anie.202316476 apa: Jethwa, R. B., Mondal, S., Pant, B., & Freunberger, S. A. (2023). To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202316476 chicago: Jethwa, Rajesh B, Soumyadip Mondal, Bhargavi Pant, and Stefan Alexander Freunberger. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” Angewandte Chemie International Edition. Wiley, 2023. https://doi.org/10.1002/anie.202316476. ieee: R. B. Jethwa, S. Mondal, B. Pant, and S. A. Freunberger, “To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries,” Angewandte Chemie International Edition. Wiley, 2023. ista: Jethwa RB, Mondal S, Pant B, Freunberger SA. 2023. To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries. Angewandte Chemie International Edition., e202316476. mla: Jethwa, Rajesh B., et al. “To DISP or Not? The Far‐reaching Reaction Mechanisms Underpinning Lithium‐air Batteries.” Angewandte Chemie International Edition, e202316476, Wiley, 2023, doi:10.1002/anie.202316476. short: R.B. Jethwa, S. Mondal, B. Pant, S.A. Freunberger, Angewandte Chemie International Edition (2023). date_created: 2023-12-15T16:10:13Z date_published: 2023-12-14T00:00:00Z date_updated: 2024-02-15T14:43:05Z day: '14' department: - _id: StFr - _id: GradSch doi: 10.1002/anie.202316476 keyword: - General Chemistry - Catalysis language: - iso: eng main_file_link: - open_access: '1' url: ' https://doi.org/10.1002/anie.202316476' month: '12' oa: 1 oa_version: Published Version publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: epub_ahead publisher: Wiley quality_controlled: '1' scopus_import: '1' status: public title: To DISP or not? The far‐reaching reaction mechanisms underpinning Lithium‐air batteries type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14985' abstract: - lang: eng text: Lead sulfide (PbS) presents large potential in thermoelectric application due to its earth-abundant S element. However, its inferior average ZT (ZTave) value makes PbS less competitive with its analogs PbTe and PbSe. To promote its thermoelectric performance, this study implements strategies of continuous Se alloying and Cu interstitial doping to synergistically tune thermal and electrical transport properties in n-type PbS. First, the lattice parameter of 5.93 Å in PbS is linearly expanded to 6.03 Å in PbS0.5Se0.5 with increasing Se alloying content. This expanded lattice in Se-alloyed PbS not only intensifies phonon scattering but also facilitates the formation of Cu interstitials. Based on the PbS0.6Se0.4 content with the minimal lattice thermal conductivity, Cu interstitials are introduced to improve the electron density, thus boosting the peak power factor, from 3.88 μW cm−1 K−2 in PbS0.6Se0.4 to 20.58 μW cm−1 K−2 in PbS0.6Se0.4−1%Cu. Meanwhile, the lattice thermal conductivity in PbS0.6Se0.4−x%Cu (x = 0–2) is further suppressed due to the strong strain field caused by Cu interstitials. Finally, with the lowered thermal conductivity and high electrical transport properties, a peak ZT ~1.1 and ZTave ~0.82 can be achieved in PbS0.6Se0.4 − 1%Cu at 300–773K, which outperforms previously reported n-type PbS. acknowledgement: 'The authors would like to acknowledge the strong supportof microstructure observation from Center for HighPressure Science and Technology Advanced Research(HPSTAR). We acknowledge the financial support fromthe National Natural Science Foundation of China:52172236, the Fundamental Research Funds for theCentral Universities: xtr042021007, Top Young TalentsProgramme of Xi''an Jiaotong University and NationalScience Fund for Distinguished Young Scholars: 51925101.' article_processing_charge: Yes article_type: original author: - first_name: Zhengtao full_name: Liu, Zhengtao last_name: Liu - first_name: Tao full_name: Hong, Tao last_name: Hong - first_name: Liqing full_name: Xu, Liqing last_name: Xu - first_name: Sining full_name: Wang, Sining last_name: Wang - first_name: Xiang full_name: Gao, Xiang last_name: Gao - first_name: Cheng full_name: Chang, Cheng id: 9E331C2E-9F27-11E9-AE48-5033E6697425 last_name: Chang orcid: 0000-0002-9515-4277 - first_name: Xiangdong full_name: Ding, Xiangdong last_name: Ding - first_name: Yu full_name: Xiao, Yu last_name: Xiao - first_name: Li‐Dong full_name: Zhao, Li‐Dong last_name: Zhao citation: ama: Liu Z, Hong T, Xu L, et al. Lattice expansion enables interstitial doping to achieve a high average ZT in n‐type PbS. Interdisciplinary Materials. 2023;2(1):161-170. doi:10.1002/idm2.12056 apa: Liu, Z., Hong, T., Xu, L., Wang, S., Gao, X., Chang, C., … Zhao, L. (2023). Lattice expansion enables interstitial doping to achieve a high average ZT in n‐type PbS. Interdisciplinary Materials. Wiley. https://doi.org/10.1002/idm2.12056 chicago: Liu, Zhengtao, Tao Hong, Liqing Xu, Sining Wang, Xiang Gao, Cheng Chang, Xiangdong Ding, Yu Xiao, and Li‐Dong Zhao. “Lattice Expansion Enables Interstitial Doping to Achieve a High Average ZT in N‐type PbS.” Interdisciplinary Materials. Wiley, 2023. https://doi.org/10.1002/idm2.12056. ieee: Z. Liu et al., “Lattice expansion enables interstitial doping to achieve a high average ZT in n‐type PbS,” Interdisciplinary Materials, vol. 2, no. 1. Wiley, pp. 161–170, 2023. ista: Liu Z, Hong T, Xu L, Wang S, Gao X, Chang C, Ding X, Xiao Y, Zhao L. 2023. Lattice expansion enables interstitial doping to achieve a high average ZT in n‐type PbS. Interdisciplinary Materials. 2(1), 161–170. mla: Liu, Zhengtao, et al. “Lattice Expansion Enables Interstitial Doping to Achieve a High Average ZT in N‐type PbS.” Interdisciplinary Materials, vol. 2, no. 1, Wiley, 2023, pp. 161–70, doi:10.1002/idm2.12056. short: Z. Liu, T. Hong, L. Xu, S. Wang, X. Gao, C. Chang, X. Ding, Y. Xiao, L. Zhao, Interdisciplinary Materials 2 (2023) 161–170. date_created: 2024-02-14T12:12:17Z date_published: 2023-01-01T00:00:00Z date_updated: 2024-02-19T10:01:26Z day: '01' ddc: - '540' department: - _id: MaIb doi: 10.1002/idm2.12056 file: - access_level: open_access checksum: 7b5e8210ef1434feb173022c6dbbee0c content_type: application/pdf creator: dernst date_created: 2024-02-19T09:58:32Z date_updated: 2024-02-19T09:58:32Z file_id: '15015' file_name: 2023_InterdiscMaterials_Liu.pdf file_size: 4675941 relation: main_file success: 1 file_date_updated: 2024-02-19T09:58:32Z has_accepted_license: '1' intvolume: ' 2' issue: '1' language: - iso: eng month: '01' oa: 1 oa_version: Published Version page: 161-170 publication: Interdisciplinary Materials publication_identifier: eissn: - 2767-441X publication_status: published publisher: Wiley quality_controlled: '1' status: public title: Lattice expansion enables interstitial doping to achieve a high average ZT in n‐type PbS tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 2 year: '2023' ... --- _id: '14989' abstract: - lang: eng text: "Encryption alone is not enough for secure end-to end encrypted messaging: a server must also honestly serve public keys to users. Key transparency has been presented as an efficient\r\nsolution for detecting (and hence deterring) a server that attempts to dishonestly serve keys. Key transparency involves two major components: (1) a username to public key mapping, stored and cryptographically committed to by the server, and, (2) an outof-band consistency protocol for serving short commitments to users. In the setting of real-world deployments and supporting production scale, new challenges must be considered for both of these components. We enumerate these challenges and provide solutions to address them. In particular, we design and implement a memory-optimized and privacy-preserving verifiable data structure for committing to the username to public key store.\r\nTo make this implementation viable for production, we also integrate support for persistent and distributed storage. We also propose a future-facing solution, termed “compaction”, as\r\na mechanism for mitigating practical issues that arise from dealing with infinitely growing server data structures. Finally, we implement a consensusless solution that achieves the minimum requirements for a service that consistently distributes commitments for a transparency application, providing a much more efficient protocol for distributing small and consistent\r\ncommitments to users. This culminates in our production-grade implementation of a key transparency system (Parakeet) which we have open-sourced, along with a demonstration of feasibility through our benchmarks." acknowledgement: This work is supported by the Novi team at Meta and funded in part by IC3 industry partners and NSF grant 1943499. article_processing_charge: No author: - first_name: Harjasleen full_name: Malvai, Harjasleen last_name: Malvai - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Alberto full_name: Sonnino, Alberto last_name: Sonnino - first_name: Esha full_name: Ghosh, Esha last_name: Ghosh - first_name: Ercan full_name: Oztürk, Ercan last_name: Oztürk - first_name: Kevin full_name: Lewi, Kevin last_name: Lewi - first_name: Sean full_name: Lawlor, Sean last_name: Lawlor citation: ama: 'Malvai H, Kokoris Kogias E, Sonnino A, et al. Parakeet: Practical key transparency for end-to-end eEncrypted messaging. In: Proceedings of the 2023 Network and Distributed System Security Symposium. Internet Society; 2023. doi:10.14722/ndss.2023.24545' apa: 'Malvai, H., Kokoris Kogias, E., Sonnino, A., Ghosh, E., Oztürk, E., Lewi, K., & Lawlor, S. (2023). Parakeet: Practical key transparency for end-to-end eEncrypted messaging. In Proceedings of the 2023 Network and Distributed System Security Symposium. San Diego, CA, United States: Internet Society. https://doi.org/10.14722/ndss.2023.24545' chicago: 'Malvai, Harjasleen, Eleftherios Kokoris Kogias, Alberto Sonnino, Esha Ghosh, Ercan Oztürk, Kevin Lewi, and Sean Lawlor. “Parakeet: Practical Key Transparency for End-to-End EEncrypted Messaging.” In Proceedings of the 2023 Network and Distributed System Security Symposium. Internet Society, 2023. https://doi.org/10.14722/ndss.2023.24545.' ieee: 'H. Malvai et al., “Parakeet: Practical key transparency for end-to-end eEncrypted messaging,” in Proceedings of the 2023 Network and Distributed System Security Symposium, San Diego, CA, United States, 2023.' ista: 'Malvai H, Kokoris Kogias E, Sonnino A, Ghosh E, Oztürk E, Lewi K, Lawlor S. 2023. Parakeet: Practical key transparency for end-to-end eEncrypted messaging. Proceedings of the 2023 Network and Distributed System Security Symposium. NDSS: Network and Distributed Systems Security.' mla: 'Malvai, Harjasleen, et al. “Parakeet: Practical Key Transparency for End-to-End EEncrypted Messaging.” Proceedings of the 2023 Network and Distributed System Security Symposium, Internet Society, 2023, doi:10.14722/ndss.2023.24545.' short: H. Malvai, E. Kokoris Kogias, A. Sonnino, E. Ghosh, E. Oztürk, K. Lewi, S. Lawlor, in:, Proceedings of the 2023 Network and Distributed System Security Symposium, Internet Society, 2023. conference: end_date: 2023-03-03 location: San Diego, CA, United States name: 'NDSS: Network and Distributed Systems Security' start_date: 2023-02-27 date_created: 2024-02-14T14:20:40Z date_published: 2023-03-01T00:00:00Z date_updated: 2024-02-19T12:11:15Z day: '01' department: - _id: ElKo doi: 10.14722/ndss.2023.24545 language: - iso: eng main_file_link: - open_access: '1' url: https://eprint.iacr.org/2023/081 month: '03' oa: 1 oa_version: Published Version publication: Proceedings of the 2023 Network and Distributed System Security Symposium publication_identifier: isbn: - '1891562835' publication_status: published publisher: Internet Society quality_controlled: '1' status: public title: 'Parakeet: Practical key transparency for end-to-end eEncrypted messaging' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14411' abstract: - lang: eng text: "Partially specified Boolean networks (PSBNs) represent a promising framework for the qualitative modelling of biological systems in which the logic of interactions is not completely known. Phenotype control aims to stabilise the network in states exhibiting specific traits.\r\nIn this paper, we define the phenotype control problem in the context of asynchronous PSBNs and propose a novel semi-symbolic algorithm for solving this problem with permanent variable perturbations." acknowledgement: This work was supported by the Czech Foundation grant No. GA22-10845S, Grant Agency of Masaryk University grant No. MUNI/G/1771/2020, and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. alternative_title: - LNBI article_processing_charge: No author: - first_name: Nikola full_name: Beneš, Nikola last_name: Beneš - first_name: Luboš full_name: Brim, Luboš last_name: Brim - first_name: Samuel full_name: Pastva, Samuel id: 07c5ea74-f61c-11ec-a664-aa7c5d957b2b last_name: Pastva orcid: 0000-0003-1993-0331 - first_name: David full_name: Šafránek, David last_name: Šafránek - first_name: Eva full_name: Šmijáková, Eva last_name: Šmijáková citation: ama: 'Beneš N, Brim L, Pastva S, Šafránek D, Šmijáková E. Phenotype control of partially specified boolean networks. In: 21st International Conference on Computational Methods in Systems Biology. Vol 14137. Springer Nature; 2023:18-35. doi:10.1007/978-3-031-42697-1_2' apa: 'Beneš, N., Brim, L., Pastva, S., Šafránek, D., & Šmijáková, E. (2023). Phenotype control of partially specified boolean networks. In 21st International Conference on Computational Methods in Systems Biology (Vol. 14137, pp. 18–35). Luxembourg City, Luxembourg: Springer Nature. https://doi.org/10.1007/978-3-031-42697-1_2' chicago: Beneš, Nikola, Luboš Brim, Samuel Pastva, David Šafránek, and Eva Šmijáková. “Phenotype Control of Partially Specified Boolean Networks.” In 21st International Conference on Computational Methods in Systems Biology, 14137:18–35. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-42697-1_2. ieee: N. Beneš, L. Brim, S. Pastva, D. Šafránek, and E. Šmijáková, “Phenotype control of partially specified boolean networks,” in 21st International Conference on Computational Methods in Systems Biology, Luxembourg City, Luxembourg, 2023, vol. 14137, pp. 18–35. ista: 'Beneš N, Brim L, Pastva S, Šafránek D, Šmijáková E. 2023. Phenotype control of partially specified boolean networks. 21st International Conference on Computational Methods in Systems Biology. CMSB: Computational Methods in Systems Biology, LNBI, vol. 14137, 18–35.' mla: Beneš, Nikola, et al. “Phenotype Control of Partially Specified Boolean Networks.” 21st International Conference on Computational Methods in Systems Biology, vol. 14137, Springer Nature, 2023, pp. 18–35, doi:10.1007/978-3-031-42697-1_2. short: N. Beneš, L. Brim, S. Pastva, D. Šafránek, E. Šmijáková, in:, 21st International Conference on Computational Methods in Systems Biology, Springer Nature, 2023, pp. 18–35. conference: end_date: 2023-09-15 location: Luxembourg City, Luxembourg name: 'CMSB: Computational Methods in Systems Biology' start_date: 2023-09-13 date_created: 2023-10-08T22:01:18Z date_published: 2023-09-09T00:00:00Z date_updated: 2024-02-20T09:02:04Z day: '09' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-031-42697-1_2 ec_funded: 1 file: - access_level: open_access checksum: 6f71bdaedb770b52380222fd9f4d7937 content_type: application/pdf creator: spastva date_created: 2024-02-16T08:26:32Z date_updated: 2024-02-16T08:26:32Z file_id: '14997' file_name: cmsb2023.pdf file_size: 691582 relation: main_file success: 1 file_date_updated: 2024-02-16T08:26:32Z has_accepted_license: '1' intvolume: ' 14137' language: - iso: eng month: '09' oa: 1 oa_version: Submitted Version page: 18-35 project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publication: 21st International Conference on Computational Methods in Systems Biology publication_identifier: eissn: - 1611-3349 isbn: - '9783031426964' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' scopus_import: '1' status: public title: Phenotype control of partially specified boolean networks tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14137 year: '2023' ... --- _id: '14992' abstract: - lang: eng text: In this chapter we first review the Levy–Lieb functional, which gives the lowest kinetic and interaction energy that can be reached with all possible quantum states having a given density. We discuss two possible convex generalizations of this functional, corresponding to using mixed canonical and grand-canonical states, respectively. We present some recent works about the local density approximation, in which the functionals get replaced by purely local functionals constructed using the uniform electron gas energy per unit volume. We then review the known upper and lower bounds on the Levy–Lieb functionals. We start with the kinetic energy alone, then turn to the classical interaction alone, before we are able to put everything together. A later section is devoted to the Hohenberg–Kohn theorem and the role of many-body unique continuation in its proof. alternative_title: - Mathematics and Molecular Modeling article_processing_charge: No author: - first_name: Mathieu full_name: Lewin, Mathieu last_name: Lewin - first_name: Elliott H. full_name: Lieb, Elliott H. last_name: Lieb - first_name: Robert full_name: Seiringer, Robert id: 4AFD0470-F248-11E8-B48F-1D18A9856A87 last_name: Seiringer orcid: 0000-0002-6781-0521 citation: ama: 'Lewin M, Lieb EH, Seiringer R. Universal Functionals in Density Functional Theory. In: Cances E, Friesecke G, eds. Density Functional Theory. 1st ed. MAMOMO. Springer; 2023:115-182. doi:10.1007/978-3-031-22340-2_3' apa: Lewin, M., Lieb, E. H., & Seiringer, R. (2023). Universal Functionals in Density Functional Theory. In E. Cances & G. Friesecke (Eds.), Density Functional Theory (1st ed., pp. 115–182). Springer. https://doi.org/10.1007/978-3-031-22340-2_3 chicago: Lewin, Mathieu, Elliott H. Lieb, and Robert Seiringer. “Universal Functionals in Density Functional Theory.” In Density Functional Theory, edited by Eric Cances and Gero Friesecke, 1st ed., 115–82. MAMOMO. Springer, 2023. https://doi.org/10.1007/978-3-031-22340-2_3. ieee: M. Lewin, E. H. Lieb, and R. Seiringer, “Universal Functionals in Density Functional Theory,” in Density Functional Theory, 1st ed., E. Cances and G. Friesecke, Eds. Springer, 2023, pp. 115–182. ista: 'Lewin M, Lieb EH, Seiringer R. 2023.Universal Functionals in Density Functional Theory. In: Density Functional Theory. Mathematics and Molecular Modeling, , 115–182.' mla: Lewin, Mathieu, et al. “Universal Functionals in Density Functional Theory.” Density Functional Theory, edited by Eric Cances and Gero Friesecke, 1st ed., Springer, 2023, pp. 115–82, doi:10.1007/978-3-031-22340-2_3. short: M. Lewin, E.H. Lieb, R. Seiringer, in:, E. Cances, G. Friesecke (Eds.), Density Functional Theory, 1st ed., Springer, 2023, pp. 115–182. date_created: 2024-02-14T14:44:33Z date_published: 2023-07-19T00:00:00Z date_updated: 2024-02-20T08:33:06Z day: '19' department: - _id: RoSe doi: 10.1007/978-3-031-22340-2_3 edition: '1' editor: - first_name: Eric full_name: Cances, Eric last_name: Cances - first_name: Gero full_name: Friesecke, Gero last_name: Friesecke external_id: arxiv: - '1912.10424' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.1912.10424 month: '07' oa: 1 oa_version: Preprint page: 115-182 publication: Density Functional Theory publication_identifier: eisbn: - '9783031223402' isbn: - '9783031223396' issn: - 3005-0286 publication_status: published publisher: Springer quality_controlled: '1' series_title: MAMOMO status: public title: Universal Functionals in Density Functional Theory type: book_chapter user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12675' abstract: - lang: eng text: Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein--protein interactions. By studying a pair of structurally homologous cross-β amyloid fibrils, HET-s and HELLF, with a specific isotope-labeling approach and magic-angle-spinning (MAS) NMR, we have characterized the dynamic behavior of Phe and Tyr aromatic rings to show that the hydrophobic amyloid core is rigid, without any sign of "breathing motions" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips, on a variety of time scales from ns to µs. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from a NMR structural ensemble of such amyloid cross-β architecture. acknowledgement: We thank AlbertA. Smith (Leipzig)for insightful discussions. This work was supported by funding from the European Research Council (StG-2012-311318 to P.S.) and used the platforms of the Grenoble Instruct-ERIC center (ISBG;UMS 3518 CNRS-CEA-UJF-EMBL) within the Grenoble Partnership for Structural Biology(PSB) and facilities and expertiseof the Biophysical and Structural Chemistry platform (BPCS) at IECB,CNRSUAR3033,INSERMUS001 and Bordeaux University. article_number: e202219314 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Mélanie full_name: Berbon, Mélanie last_name: Berbon - first_name: Alicia full_name: Vallet, Alicia last_name: Vallet - first_name: Axelle full_name: Grelard, Axelle last_name: Grelard - first_name: Estelle full_name: Morvan, Estelle last_name: Morvan - first_name: Benjamin full_name: Bardiaux, Benjamin last_name: Bardiaux - first_name: Roman full_name: Lichtenecker, Roman last_name: Lichtenecker - first_name: Matthias full_name: Ernst, Matthias last_name: Ernst - first_name: Antoine full_name: Loquet, Antoine last_name: Loquet - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: Becker LM, Berbon M, Vallet A, et al. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 2023;62(19). doi:10.1002/anie.202219314 apa: Becker, L. M., Berbon, M., Vallet, A., Grelard, A., Morvan, E., Bardiaux, B., … Schanda, P. (2023). The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. Wiley. https://doi.org/10.1002/anie.202219314 chicago: Becker, Lea Marie, Mélanie Berbon, Alicia Vallet, Axelle Grelard, Estelle Morvan, Benjamin Bardiaux, Roman Lichtenecker, Matthias Ernst, Antoine Loquet, and Paul Schanda. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie International Edition. Wiley, 2023. https://doi.org/10.1002/anie.202219314. ieee: L. M. Becker et al., “The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues,” Angewandte Chemie International Edition, vol. 62, no. 19. Wiley, 2023. ista: Becker LM, Berbon M, Vallet A, Grelard A, Morvan E, Bardiaux B, Lichtenecker R, Ernst M, Loquet A, Schanda P. 2023. The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues. Angewandte Chemie International Edition. 62(19), e202219314. mla: Becker, Lea Marie, et al. “The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic‐Angle Spinning NMR of Aromatic Residues.” Angewandte Chemie International Edition, vol. 62, no. 19, e202219314, Wiley, 2023, doi:10.1002/anie.202219314. short: L.M. Becker, M. Berbon, A. Vallet, A. Grelard, E. Morvan, B. Bardiaux, R. Lichtenecker, M. Ernst, A. Loquet, P. Schanda, Angewandte Chemie International Edition 62 (2023). date_created: 2023-02-24T10:45:01Z date_published: 2023-05-01T00:00:00Z date_updated: 2024-02-21T12:14:06Z day: '01' ddc: - '540' department: - _id: GradSch - _id: PaSc doi: 10.1002/anie.202219314 external_id: isi: - '000956919900001' pmid: - '36738230' file: - access_level: open_access checksum: 7dd083ed8850faa55c34e411ed390de9 content_type: application/pdf creator: dernst date_created: 2023-08-16T12:33:31Z date_updated: 2023-08-16T12:33:31Z file_id: '14072' file_name: 2023_AngewChemInt_Becker.pdf file_size: 1422445 relation: main_file success: 1 file_date_updated: 2023-08-16T12:33:31Z has_accepted_license: '1' intvolume: ' 62' isi: 1 issue: '19' keyword: - General Chemistry - Catalysis language: - iso: eng month: '05' oa: 1 oa_version: Published Version pmid: 1 publication: Angewandte Chemie International Edition publication_identifier: eissn: - 1521-3773 issn: - 1433-7851 publication_status: published publisher: Wiley quality_controlled: '1' related_material: link: - description: News on ISTA website relation: press_release url: https://ista.ac.at/en/news/dancing-styles-of-atoms/ record: - id: '14861' relation: other status: public - id: '12497' relation: research_data status: public status: public title: The rigid core and flexible surface of amyloid fibrils probed by Magic‐Angle Spinning NMR of aromatic residues tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 62 year: '2023' ... --- _id: '12497' abstract: - lang: eng text: Aromatic side chains are important reporters of the plasticity of proteins, and often form important contacts in protein–protein interactions. We studied aromatic residues in the two structurally homologous cross-β amyloid fibrils HET-s, and HELLF by employing a specific isotope-labeling approach and magic-angle-spinning NMR. The dynamic behavior of the aromatic residues Phe and Tyr indicates that the hydrophobic amyloid core is rigid, without any sign of "breathing motions" over hundreds of milliseconds at least. Aromatic residues exposed at the fibril surface have a rigid ring axis but undergo ring flips on a variety of time scales from nanoseconds to microseconds. Our approach provides direct insight into hydrophobic-core motions, enabling a better evaluation of the conformational heterogeneity generated from an NMR structural ensemble of such amyloid cross-β architecture. article_processing_charge: No author: - first_name: Lea Marie full_name: Becker, Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 - first_name: Paul full_name: Schanda, Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 citation: ama: 'Becker LM, Schanda P. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. 2023. doi:10.15479/AT:ISTA:12497' apa: 'Becker, L. M., & Schanda, P. (2023). Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:12497' chicago: 'Becker, Lea Marie, and Paul Schanda. “Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12497.' ieee: 'L. M. Becker and P. Schanda, “Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues.” Institute of Science and Technology Austria, 2023.' ista: 'Becker LM, Schanda P. 2023. Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12497.' mla: 'Becker, Lea Marie, and Paul Schanda. Research Data to: The Rigid Core and Flexible Surface of Amyloid Fibrils Probed by Magic-Angle-Spinning NMR Spectroscopy of Aromatic Residues. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:12497.' short: L.M. Becker, P. Schanda, (2023). contributor: - contributor_type: researcher first_name: Mélanie last_name: Berbon - contributor_type: researcher first_name: Alicia last_name: Vallet - contributor_type: researcher first_name: Axelle last_name: Grelard - contributor_type: researcher first_name: Estelle last_name: Morvan - contributor_type: researcher first_name: Benjamin last_name: Bardiaux - contributor_type: researcher first_name: Roman last_name: Lichtenecker - contributor_type: researcher first_name: Matthias last_name: Ernst - contributor_type: researcher first_name: Antoine last_name: Loquet - contributor_type: contact_person first_name: Paul id: 7B541462-FAF6-11E9-A490-E8DFE5697425 last_name: Schanda orcid: 0000-0002-9350-7606 - contributor_type: researcher first_name: Lea Marie id: 36336939-eb97-11eb-a6c2-c83f1214ca79 last_name: Becker orcid: 0000-0002-6401-5151 date_created: 2023-02-03T08:08:02Z date_published: 2023-03-23T00:00:00Z date_updated: 2024-02-21T12:14:06Z day: '23' ddc: - '572' department: - _id: GradSch - _id: PaSc doi: 10.15479/AT:ISTA:12497 file: - access_level: open_access checksum: fd9a28620a81a82991fb70f4fd6591d9 content_type: application/zip creator: lbecker date_created: 2023-03-23T10:03:16Z date_updated: 2023-03-24T09:34:20Z file_id: '12743' file_name: Research_Data.zip file_size: 87018103 relation: main_file - access_level: open_access checksum: 30ebdfb600af118fcf8518b6efe0b7e9 content_type: text/plain creator: dernst date_created: 2023-03-24T07:13:55Z date_updated: 2023-03-24T09:42:03Z file_id: '12755' file_name: README.txt file_size: 747 relation: main_file file_date_updated: 2023-03-24T09:42:03Z has_accepted_license: '1' keyword: - aromatic side chains - isotopic labeling - protein dynamics - ring flips - spin relaxation month: '03' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '12675' relation: used_in_publication status: public status: public title: 'Research data to: The rigid core and flexible surface of amyloid fibrils probed by magic-angle-spinning NMR spectroscopy of aromatic residues' tmp: image: /images/cc_by_nc.png legal_code_url: https://creativecommons.org/licenses/by-nc/4.0/legalcode name: Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0) short: CC BY-NC (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13126' abstract: - lang: eng text: Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here, we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease. acknowledged_ssus: - _id: ScienComp - _id: Bio - _id: PreCl - _id: LifeSc - _id: M-Shop - _id: E-Lib acknowledgement: "We thank Jakob Vorlaufer, Nathalie Agudelo-Dueñas, Wiebke Jahr, Andreas Wartak for microscope maintenance and troubleshooting, Caroline Kreuzinger, Anna Freeman, and Irene Erber for technical assistance and Matthias Tomschik for support with obtaining human samples. We gratefully acknowledge Eder Miguel for setting up webKnossos and Marek Šuplata for computational support and hardware control. We are grateful to Ryuichi Shigemoto and Bernd Bickel for generous support, and Michael Sixt and Scott Boyd (Stanford University) for discussions and critical reading of the manuscript. PSD95-HaloTag mice were kindly provided by Seth Grant (University of Edinburgh). We acknowledge expert support by IST Austria’s scientific computing, imaging and optics, preclinical, and lab support facilities, and by the Library and Miba machine shop.\r\nWe gratefully acknowledge funding by the following sources: \r\nAustrian Science Fund (FWF) grant I3600-B27 (JGD)\r\nAustrian Science Fund (FWF) grant DK W1232 (JGD, JMM)\r\nAustrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (PJ)\r\nAustrian Science Funds (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (RH)\r\nGesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (JGD)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (GN)\r\nEuropean Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (PJ)\r\nMarie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (JMM, JL)\r\nMarie Skłodowska-Curie Actions Individual Fellowship 101026635 under the EU Horizon 2020 program (JFW)" article_processing_charge: No author: - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Danzl JG. Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” 2023. doi:10.15479/AT:ISTA:13126 apa: Danzl, J. G. (2023). Research data for the publication “Imaging brain tissue architecture across millimeter to nanometer scales.” Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13126 chicago: Danzl, Johann G. “Research Data for the Publication ‘Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13126. ieee: J. G. Danzl, “Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales.’” Institute of Science and Technology Austria, 2023. ista: Danzl JG. 2023. Research data for the publication ‘Imaging brain tissue architecture across millimeter to nanometer scales’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13126. mla: Danzl, Johann G. Research Data for the Publication “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13126. short: J.G. Danzl, (2023). contributor: - first_name: Julia M id: 443DB6DE-F248-11E8-B48F-1D18A9856A87 last_name: Michalska - first_name: Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Hana id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed last_name: Stefanickova - first_name: Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Alban id: 9ac8f577-2357-11eb-997a-e566c5550886 last_name: Cenameri - first_name: Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Alessandro id: 41CB84B2-F248-11E8-B48F-1D18A9856A87 last_name: Venturino orcid: 0000-0003-2356-9403 - first_name: Karl last_name: Roessler - first_name: Thomas last_name: Czech - first_name: Romana last_name: Höftberger - first_name: Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 - first_name: Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 date_created: 2023-06-07T07:15:12Z date_published: 2023-08-04T00:00:00Z date_updated: 2024-02-21T12:18:19Z day: '04' ddc: - '610' department: - _id: JoDa - _id: SaSi - _id: GaNo - _id: PeJo - _id: Bio - _id: RySh doi: 10.15479/AT:ISTA:13126 ec_funded: 1 file: - access_level: open_access checksum: 6f18ce9b89b47ce5abeb379869ff5c49 content_type: text/plain creator: jdanzl date_created: 2023-08-04T13:19:47Z date_updated: 2023-08-04T13:19:47Z file_id: '13961' file_name: Readme_Michalska_2023.txt file_size: 541 relation: main_file success: 1 - access_level: open_access checksum: 2098e8c5285c5e86cb69075e1b5dcf39 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:29:29Z date_updated: 2023-08-03T11:29:29Z file_id: '13482' file_name: Fig1_b_top-left.tif file_size: 64582744 relation: main_file success: 1 - access_level: open_access checksum: 9affab3dacf847096cc8e8d5ff99467e content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:29:28Z date_updated: 2023-08-03T11:29:28Z file_id: '13483' file_name: Fig1_b_top-right.tif file_size: 1442113 relation: main_file success: 1 - access_level: open_access checksum: d7fec0296123a17f6bcdbfee17411424 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:29:29Z date_updated: 2023-08-03T11:29:29Z file_id: '13484' file_name: Fig1_c_1.tif file_size: 40078276 relation: main_file success: 1 - access_level: open_access checksum: 5195a180c4f26a7adc994bad0b3c53c7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:29:29Z date_updated: 2023-08-03T11:29:29Z file_id: '13485' file_name: Fig1_c_2.tif file_size: 7984315 relation: main_file success: 1 - access_level: open_access checksum: df1105d8f41ebd5373cacc597ffa91f3 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:29:29Z date_updated: 2023-08-03T11:29:29Z file_id: '13486' file_name: Fig1_c_3.tif file_size: 8693320 relation: main_file success: 1 - access_level: open_access checksum: 00edbb0c9f42032c830d2291ec55c4c0 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:29:30Z date_updated: 2023-08-03T11:29:30Z file_id: '13487' file_name: Fig1_c_4.tif file_size: 6003063 relation: main_file success: 1 - access_level: open_access checksum: a58399e98ec4b6506a5dae13e387f391 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:29:30Z date_updated: 2023-08-03T11:29:30Z file_id: '13488' file_name: Fig1_d.tif file_size: 24003063 relation: main_file success: 1 - access_level: open_access checksum: 699df4bc104df14607359678963b3d2d content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:29:30Z date_updated: 2023-08-03T11:29:30Z file_id: '13489' file_name: Fig1_e_zoom.tif file_size: 18063 relation: main_file success: 1 - access_level: open_access checksum: ea7b1278da490d221fc7698fd6bc39a4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:29:30Z date_updated: 2023-08-03T11:29:30Z file_id: '13490' file_name: Fig1_e.tif file_size: 186813 relation: main_file success: 1 - access_level: open_access checksum: 37b05ef3a36b9f6bf4ec46199230874a content_type: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet creator: jdanzl date_created: 2023-08-03T11:29:30Z date_updated: 2023-08-03T11:29:30Z file_id: '13491' file_name: Fig1_f.xlsx file_size: 17494 relation: main_file success: 1 - access_level: open_access checksum: 872eb3dc1a94afb26947a365bfae581a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:40:43Z date_updated: 2023-08-03T11:40:43Z file_id: '13492' file_name: Fig2_a_1.tif file_size: 816786862 relation: main_file success: 1 - access_level: open_access checksum: cab6f72d7d546a81c105c229747949ef content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:40:13Z date_updated: 2023-08-03T11:40:13Z file_id: '13493' file_name: Fig2_a_2.tif file_size: 8654692 relation: main_file success: 1 - access_level: open_access checksum: c85bc3ffe7f6bdf16a81290761ed6253 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:40:14Z date_updated: 2023-08-03T11:40:14Z file_id: '13494' file_name: Fig2_a_3.tif file_size: 8654692 relation: main_file success: 1 - access_level: open_access checksum: 5a3fd5484e566c34e210a4acb2b97791 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:40:24Z date_updated: 2023-08-03T11:40:24Z file_id: '13495' file_name: Fig2_a_4.tif file_size: 272262438 relation: main_file success: 1 - access_level: open_access checksum: ae5cbacf56e3fdf934a6d6fd489f5fe0 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:40:37Z date_updated: 2023-08-03T11:40:37Z file_id: '13496' file_name: Fig2_a_5.tif file_size: 272262438 relation: main_file success: 1 - access_level: open_access checksum: e6da436b83bbe3a34138b52e5de49d69 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:40:44Z date_updated: 2023-08-03T11:40:44Z file_id: '13497' file_name: Fig2_a_6.tif file_size: 204301228 relation: main_file success: 1 - access_level: open_access checksum: 855f0a0bcf5b3d7cc7d50561f2c8f625 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:40:49Z date_updated: 2023-08-03T11:40:49Z file_id: '13498' file_name: Fig2_a_7-8.tif file_size: 68094350 relation: main_file success: 1 - access_level: open_access checksum: ff709f9f8ebaa8cf50a4b2fca5ce9813 content_type: application/octet-stream creator: jdanzl date_created: 2023-08-03T11:40:48Z date_updated: 2023-08-03T11:40:48Z file_id: '13499' file_name: Fig2_a_roi.roi file_size: 156 relation: main_file success: 1 - access_level: open_access checksum: ce9b774ff5163ebfa4e3fb162f4cfffe content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:41:37Z date_updated: 2023-08-03T11:41:37Z file_id: '13500' file_name: Fig2_c-i_1_n2v.tif file_size: 1036927887 relation: main_file success: 1 - access_level: open_access checksum: 21f1bb8d2a00c88bdd6febe6285acc2a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:41:25Z date_updated: 2023-08-03T11:41:25Z file_id: '13501' file_name: Fig2_c-i_1.tif file_size: 518519275 relation: main_file success: 1 - access_level: open_access checksum: 9af5b66b74c2ff4b2b99b0d94f2864e6 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:42:48Z date_updated: 2023-08-03T11:42:48Z file_id: '13502' file_name: Fig2_c-i_3_n2v.tif file_size: 1444202302 relation: main_file success: 1 - access_level: open_access checksum: c83261e88821747b301197314d92f2b2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:42:57Z date_updated: 2023-08-03T11:42:57Z file_id: '13503' file_name: Fig2_c-i_3.tif file_size: 1075338708 relation: main_file success: 1 - access_level: open_access checksum: 5d1278ba4b7e085c0c186ea49fce535b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:44:05Z date_updated: 2023-08-03T11:44:05Z file_id: '13504' file_name: Fig2_c-i_2_n2v.tif file_size: 851145493 relation: main_file success: 1 - access_level: open_access checksum: 5aaf1eba65582cf437ff3ce753eba4d7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:43:47Z date_updated: 2023-08-03T11:43:47Z file_id: '13505' file_name: Fig2_c-i_2.tif file_size: 432099834 relation: main_file success: 1 - access_level: open_access checksum: ce9b774ff5163ebfa4e3fb162f4cfffe content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:44:41Z date_updated: 2023-08-03T11:44:41Z file_id: '13506' file_name: Fig2_h_n2v.tif file_size: 1036927887 relation: main_file success: 1 - access_level: open_access checksum: 21f1bb8d2a00c88bdd6febe6285acc2a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:44:36Z date_updated: 2023-08-03T11:44:36Z file_id: '13507' file_name: Fig2_h.tif file_size: 518519275 relation: main_file success: 1 - access_level: open_access checksum: b37f25a90ef42fa4358649fdd6b41f35 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:44:40Z date_updated: 2023-08-03T11:44:40Z file_id: '13508' file_name: Fig2_j_1.tif file_size: 19287397 relation: main_file success: 1 - access_level: open_access checksum: 50f0969c6c2c1209ff776bec4861030a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:44:41Z date_updated: 2023-08-03T11:44:41Z file_id: '13509' file_name: Fig2_j_2.tif file_size: 617552 relation: main_file success: 1 - access_level: open_access checksum: 2a8cc93471378ac4c3b640e4318d89eb content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:44:41Z date_updated: 2023-08-03T11:44:41Z file_id: '13510' file_name: Fig2_j_3.tif file_size: 19287392 relation: main_file success: 1 - access_level: open_access checksum: b90965d20133fea73c99050c32eb7695 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:44:42Z date_updated: 2023-08-03T11:44:42Z file_id: '13511' file_name: Fig2_j_4.tif file_size: 617552 relation: main_file success: 1 - access_level: open_access checksum: 568a1e0efaa62527b51e66a7aabfd05c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:44:43Z date_updated: 2023-08-03T11:44:43Z file_id: '13512' file_name: Fig2_j_coCATS_N2V.tif file_size: 19287339 relation: main_file success: 1 - access_level: open_access checksum: c70447cebe073dd78e0ac34ecc36ad85 content_type: application/octet-stream creator: jdanzl date_created: 2023-08-03T11:44:44Z date_updated: 2023-08-03T11:44:44Z file_id: '13513' file_name: Fig2_j_roi.roi file_size: 148 relation: main_file success: 1 - access_level: open_access checksum: 505252cc4b443b76c2e41ecf5879a542 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:44:52Z date_updated: 2023-08-03T11:44:52Z file_id: '13514' file_name: Fig3_a_n2v.tif file_size: 316842690 relation: main_file success: 1 - access_level: open_access checksum: 35463183611e8ee4fba2025772c40eb2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:45:01Z date_updated: 2023-08-03T11:45:01Z file_id: '13515' file_name: Fig3_a.tif file_size: 172839057 relation: main_file success: 1 - access_level: open_access checksum: e0469102a87332b46904b4ba35b8fb2f content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:45:05Z date_updated: 2023-08-03T11:45:05Z file_id: '13516' file_name: Fig3_g_n2v.tif file_size: 309407894 relation: main_file success: 1 - access_level: open_access checksum: 854c8fe02acd920f8e8f6a3173458e86 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:15Z date_updated: 2023-08-03T11:51:15Z file_id: '13517' file_name: Fig4_a_MIP.tif file_size: 11327792 relation: main_file success: 1 - access_level: open_access checksum: ab35811ffbe3f40733d0e054d9d6c4e6 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:18Z date_updated: 2023-08-03T11:51:18Z file_id: '13518' file_name: Fig4_c_dghilus_bouton2_n2v.tif file_size: 106696700 relation: main_file success: 1 - access_level: open_access checksum: e3b6410d68e42004ef3857967707aeb3 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:17Z date_updated: 2023-08-03T11:51:17Z file_id: '13519' file_name: Fig4_c_dghilus_bouton2.tif file_size: 53367287 relation: main_file success: 1 - access_level: open_access checksum: 9ef0e3f3ec6f0b7b2666e3a0d7e6f355 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:20Z date_updated: 2023-08-03T11:51:20Z file_id: '13520' file_name: Fig4_c_dghilus_bouton5_n2v.tif file_size: 103816699 relation: main_file success: 1 - access_level: open_access checksum: d5d846a4edaf0168ca6cc53d8cc39dde content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:21Z date_updated: 2023-08-03T11:51:21Z file_id: '13521' file_name: Fig4_c_dghilus_bouton5.tif file_size: 51927287 relation: main_file success: 1 - access_level: open_access checksum: 690a87182441c9742da2550189641e5a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:24Z date_updated: 2023-08-03T11:51:24Z file_id: '13522' file_name: Fig4_c_stratum_bouton11_n2v.tif file_size: 76391971 relation: main_file success: 1 - access_level: open_access checksum: 4dc575424729c5ba181bd9a3962d4781 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:23Z date_updated: 2023-08-03T11:51:23Z file_id: '13523' file_name: Fig4_c_stratum_bouton11.tif file_size: 38217920 relation: main_file success: 1 - access_level: open_access checksum: 9fdd51636928f45e8e534cc5a37a48ff content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:29Z date_updated: 2023-08-03T11:51:29Z file_id: '13524' file_name: Fig4_c_stratum_bouton13_n2v.tif file_size: 154149020 relation: main_file success: 1 - access_level: open_access checksum: 643169464252d67753ac6f8493668f34 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:28Z date_updated: 2023-08-03T11:51:28Z file_id: '13525' file_name: Fig4_c_stratum_bouton13.tif file_size: 77099447 relation: main_file success: 1 - access_level: open_access checksum: ab35811ffbe3f40733d0e054d9d6c4e6 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:32Z date_updated: 2023-08-03T11:51:32Z file_id: '13526' file_name: Fig4_d.tif file_size: 106696700 relation: main_file success: 1 - access_level: open_access checksum: 9fdd51636928f45e8e534cc5a37a48ff content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:35Z date_updated: 2023-08-03T11:51:35Z file_id: '13527' file_name: Fig4_e.tif file_size: 154149020 relation: main_file success: 1 - access_level: open_access checksum: 5380d0a98e97d7d8462b38bd0a96644c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:32Z date_updated: 2023-08-03T11:51:32Z file_id: '13528' file_name: Fig4_f_1_top.tif file_size: 5986760 relation: main_file success: 1 - access_level: open_access checksum: 7d1309e806eb31588ebafcf40388e13f content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:33Z date_updated: 2023-08-03T11:51:33Z file_id: '13529' file_name: Fig4_f_2_top.tif file_size: 6001178 relation: main_file success: 1 - access_level: open_access checksum: a71c80207655d508cbc7626bc144d7a1 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:33Z date_updated: 2023-08-03T11:51:33Z file_id: '13530' file_name: Fig4_f_3_top.tif file_size: 6023318 relation: main_file success: 1 - access_level: open_access checksum: 5d76b2ad7d7acbb1afa27cf52194b1cb content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:34Z date_updated: 2023-08-03T11:51:34Z file_id: '13531' file_name: Fig4_f_4_top.tif file_size: 6038186 relation: main_file success: 1 - access_level: open_access checksum: 9cee6b3387bd880843f2c6cdfa0d4a8d content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:51:34Z date_updated: 2023-08-03T11:51:34Z file_id: '13532' file_name: Fig4_f_5_top.tif file_size: 2324158 relation: main_file success: 1 - access_level: open_access checksum: a48fc9e1bb2710cf28466ae6d2a20c19 content_type: image/png creator: jdanzl date_created: 2023-08-03T11:51:34Z date_updated: 2023-08-03T11:51:34Z file_id: '13533' file_name: Fig4_f_1_bottom.png file_size: 1150264 relation: main_file success: 1 - access_level: open_access checksum: ff47ca30f814e17561974b73b0913a1a content_type: image/png creator: jdanzl date_created: 2023-08-03T11:51:34Z date_updated: 2023-08-03T11:51:34Z file_id: '13534' file_name: Fig4_f_2_bottom.png file_size: 1157424 relation: main_file success: 1 - access_level: open_access checksum: 2ea3fb8d79cee8ae9de7ca31d003910f content_type: image/png creator: jdanzl date_created: 2023-08-03T11:51:34Z date_updated: 2023-08-03T11:51:34Z file_id: '13535' file_name: Fig4_f_3_bottom.png file_size: 1152715 relation: main_file success: 1 - access_level: open_access checksum: d25e5ecf2f0c3be7c20a7e25a7a334b8 content_type: image/png creator: jdanzl date_created: 2023-08-03T11:51:34Z date_updated: 2023-08-03T11:51:34Z file_id: '13536' file_name: Fig4_f_4_bottom.png file_size: 1105240 relation: main_file success: 1 - access_level: open_access checksum: 76535f569a57b967e378df89b7d2982a content_type: image/png creator: jdanzl date_created: 2023-08-03T11:51:35Z date_updated: 2023-08-03T11:51:35Z file_id: '13537' file_name: Fig4_f_5_bottom.png file_size: 1228157 relation: main_file success: 1 - access_level: open_access checksum: d46fefe73daa3ec08b847631e9de6828 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:52Z date_updated: 2023-08-03T11:53:52Z file_id: '13538' file_name: Fig5_a_1.tif file_size: 91181184 relation: main_file success: 1 - access_level: open_access checksum: 354c0ba876a33672eca37cd61dac7073 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:54Z date_updated: 2023-08-03T11:53:54Z file_id: '13539' file_name: Fig5_a_2.tif file_size: 176024124 relation: main_file success: 1 - access_level: open_access checksum: d07925040ef0c3c51edbdca8cf3ec1fa content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:53Z date_updated: 2023-08-03T11:53:53Z file_id: '13540' file_name: Fig5_a_3.tif file_size: 15812494 relation: main_file success: 1 - access_level: open_access checksum: 7c34b19a1764e2f501f11dcabd442ce2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:53Z date_updated: 2023-08-03T11:53:53Z file_id: '13541' file_name: Fig5_a_4.tif file_size: 11117689 relation: main_file success: 1 - access_level: open_access checksum: c49af4b96532e00b3a51574a2a94decb content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:53Z date_updated: 2023-08-03T11:53:53Z file_id: '13542' file_name: Fig5_a_5.tif file_size: 111665 relation: main_file success: 1 - access_level: open_access checksum: 1b42eadcdd71f2dc00d82784673aa577 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:54Z date_updated: 2023-08-03T11:53:54Z file_id: '13543' file_name: Fig5_b_1.tif file_size: 16676449 relation: main_file success: 1 - access_level: open_access checksum: 0d27266bf216f71fcb5496731ce76dd5 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:54Z date_updated: 2023-08-03T11:53:54Z file_id: '13544' file_name: Fig5_b_2-4.tif file_size: 427651 relation: main_file success: 1 - access_level: open_access checksum: c4232930068a0a8f7c8a70ce0ea48dc2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:55Z date_updated: 2023-08-03T11:53:55Z file_id: '13545' file_name: Fig5_c_1-3.tif file_size: 11117705 relation: main_file success: 1 - access_level: open_access checksum: c9caad749be0ef04ef8013cfdb69f8fc content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:55Z date_updated: 2023-08-03T11:53:55Z file_id: '13546' file_name: Fig5_c_2-4.tif file_size: 254153 relation: main_file success: 1 - access_level: open_access checksum: 5c6d36b96bde1e090cc428b269aba6ec content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:54:14Z date_updated: 2023-08-03T11:54:14Z file_id: '13547' file_name: Fig5_e_1.tif file_size: 737290746 relation: main_file success: 1 - access_level: open_access checksum: f97632984b6a73e06cc0c8c947cdcc71 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:57Z date_updated: 2023-08-03T11:53:57Z file_id: '13548' file_name: Fig5_e_2.tif file_size: 31366288 relation: main_file success: 1 - access_level: open_access checksum: 8c471eeaa59008eed9e91afe5e1f1698 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:57Z date_updated: 2023-08-03T11:53:57Z file_id: '13549' file_name: Fig5_e_3.tif file_size: 1216304 relation: main_file success: 1 - access_level: open_access checksum: 31c10c3a1d874b5028e35e2dd8800a68 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:59Z date_updated: 2023-08-03T11:53:59Z file_id: '13550' file_name: Fig5_g.tif file_size: 35669193 relation: main_file success: 1 - access_level: open_access checksum: 0e9fe7b7ee06a630837e9d3c41b80e01 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:53:59Z date_updated: 2023-08-03T11:53:59Z file_id: '13551' file_name: Fig5_h.tif file_size: 7492349 relation: main_file success: 1 - access_level: open_access checksum: d25b3d04bb8364089cafdf8deb6846b6 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:18Z date_updated: 2023-08-03T11:59:18Z file_id: '13552' file_name: Fig6_a_1.tif file_size: 121446390 relation: main_file success: 1 - access_level: open_access checksum: 4361e10db6ec48c2d4579ac089ff3ca3 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:22Z date_updated: 2023-08-03T11:59:22Z file_id: '13553' file_name: Fig6_a_2.tif file_size: 264412158 relation: main_file success: 1 - access_level: open_access checksum: fe3a00ae75fb3388438e53ced92a9498 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:21Z date_updated: 2023-08-03T11:59:21Z file_id: '13554' file_name: Fig6_a_3.tif file_size: 57399051 relation: main_file success: 1 - access_level: open_access checksum: 4372c13d6dd2274aa749799b8e96bf06 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:21Z date_updated: 2023-08-03T11:59:21Z file_id: '13555' file_name: Fig6_b_left.tif file_size: 6003163 relation: main_file success: 1 - access_level: open_access checksum: f7ae4e50f2f4d414c598bddd691b722a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:21Z date_updated: 2023-08-03T11:59:21Z file_id: '13556' file_name: Fig6_b_right.tif file_size: 511265 relation: main_file success: 1 - access_level: open_access checksum: cde658a9ca666bdef1b29613ab72092d content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:39Z date_updated: 2023-08-03T11:59:39Z file_id: '13557' file_name: Fig6_c_n2v.tif file_size: 467125933 relation: main_file success: 1 - access_level: open_access checksum: 57e73c1fedcee4bd8ab62518baa0e0e5 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:36Z date_updated: 2023-08-03T11:59:36Z file_id: '13558' file_name: Fig6_c.tif file_size: 322251440 relation: main_file success: 1 - access_level: open_access checksum: 53175073b83ab569241ae64ef7f180b3 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:38Z date_updated: 2023-08-03T11:59:38Z file_id: '13559' file_name: Fig6_d_1.tif file_size: 37641738 relation: main_file success: 1 - access_level: open_access checksum: af97423e1077af85465a5e39fa25d1e4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:40Z date_updated: 2023-08-03T11:59:40Z file_id: '13560' file_name: Fig6_d_2.tif file_size: 70596929 relation: main_file success: 1 - access_level: open_access checksum: f1fd7a9fa2a12a930fe35bdf53ba3ff7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:42Z date_updated: 2023-08-03T11:59:42Z file_id: '13561' file_name: Fig6_d_3.tif file_size: 15303146 relation: main_file success: 1 - access_level: open_access checksum: 95655df5cdb05f09912298de9a3711b4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:41Z date_updated: 2023-08-03T11:59:41Z file_id: '13562' file_name: Fig6_d_4.tif file_size: 893051 relation: main_file success: 1 - access_level: open_access checksum: 4d722b4e09ce617252d284f78ea2ee30 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:58Z date_updated: 2023-08-03T11:59:58Z file_id: '13563' file_name: Fig6_e.tif file_size: 381232200 relation: main_file success: 1 - access_level: open_access checksum: d1eda9599f422a614404dd112f0c3185 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T11:59:58Z date_updated: 2023-08-03T11:59:58Z file_id: '13564' file_name: Fig6_f.tif file_size: 345804470 relation: main_file success: 1 - access_level: open_access checksum: 1cd202570f964b78e1f55c987d5d5de1 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:00:08Z date_updated: 2023-08-03T12:00:08Z file_id: '13565' file_name: Fig6_g.tif file_size: 346119927 relation: main_file success: 1 - access_level: open_access checksum: 78cbf1906ff8746ed524c62f8f580f52 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:00:02Z date_updated: 2023-08-03T12:00:02Z file_id: '13566' file_name: Fig6_h.tif file_size: 7064977 relation: main_file success: 1 - access_level: open_access checksum: 21635ce59f1ae5a334aaad3f4c0b171c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:00:03Z date_updated: 2023-08-03T12:00:03Z file_id: '13567' file_name: Fig6_i.tif file_size: 7110129 relation: main_file success: 1 - access_level: open_access checksum: 704962856f2a024ce1f321a1785556e3 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:00:07Z date_updated: 2023-08-03T12:00:07Z file_id: '13568' file_name: Fig6_j.tif file_size: 110297540 relation: main_file success: 1 - access_level: open_access checksum: 4b74ba5ae1e2bb2201bf51c74d733268 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:00:07Z date_updated: 2023-08-03T12:00:07Z file_id: '13569' file_name: Fig6_k.tif file_size: 11117689 relation: main_file success: 1 - access_level: open_access checksum: a8efa3007df4e9e0f80c7a2bbc451178 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13570' file_name: Extdata_01_a_1.tif file_size: 1287107 relation: main_file success: 1 - access_level: open_access checksum: 7f24b6c84ce96a67347eb5ef4c43fac1 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13571' file_name: Extdata_01_a_2.tif file_size: 58307 relation: main_file success: 1 - access_level: open_access checksum: fa7ae4eefc11b9b60c4ab80f6e839b73 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13572' file_name: Extdata_01_a_3.tif file_size: 1283209 relation: main_file success: 1 - access_level: open_access checksum: cec9a5eb87f1b56e64626a00c6d0e53d content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13573' file_name: Extdata_01_a_4.tif file_size: 54409 relation: main_file success: 1 - access_level: open_access checksum: 450e4786d66d5059028420153908a4dc content_type: image/png creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13574' file_name: Extdata_01_c_1.png file_size: 2431 relation: main_file success: 1 - access_level: open_access checksum: feb758609b399cf644dd3ae7cd75fb96 content_type: image/png creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13575' file_name: Extdata_01_c_2.png file_size: 612 relation: main_file success: 1 - access_level: open_access checksum: 52f43300a50f83f9a6ff1409324086ee content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13576' file_name: Extdata_01_d_1.tif file_size: 433981 relation: main_file success: 1 - access_level: open_access checksum: 28925dcf8792f524e286beb16b0c532c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13577' file_name: Extdata_01_d_2.tif file_size: 19649 relation: main_file success: 1 - access_level: open_access checksum: c93b2f0426c80d18e252435f1e146568 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13578' file_name: Extdata_01_d_3.tif file_size: 433981 relation: main_file success: 1 - access_level: open_access checksum: c0ed722a768001431f47646ef98c44da content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13579' file_name: Extdata_01_d_4.tif file_size: 19649 relation: main_file success: 1 - access_level: open_access checksum: db9d386276b985b8e702f797e910bd0b content_type: image/png creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13580' file_name: Extdata_01_f_1.png file_size: 4752 relation: main_file success: 1 - access_level: open_access checksum: 244f6645d191c50d997c0dc6a15535ec content_type: image/png creator: jdanzl date_created: 2023-08-03T12:05:41Z date_updated: 2023-08-03T12:05:41Z file_id: '13581' file_name: Extdata_01_f_2.png file_size: 2698 relation: main_file success: 1 - access_level: open_access checksum: 3d6100b836d850b38e66e0f5a7919495 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:07:27Z date_updated: 2023-08-03T12:07:27Z file_id: '13582' file_name: Extdata_02_a.tif file_size: 24003247 relation: main_file success: 1 - access_level: open_access checksum: 3cd6a3b7bf2061cf5c7810c0001236e5 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:07:27Z date_updated: 2023-08-03T12:07:27Z file_id: '13583' file_name: Extdata_02_b.tif file_size: 1164723 relation: main_file success: 1 - access_level: open_access checksum: d87c82d663ffea379cc86c56981e2e16 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:10:32Z date_updated: 2023-08-03T12:10:32Z file_id: '13584' file_name: Extdata_03_SYPH1_xy_1.tif file_size: 7109763 relation: main_file success: 1 - access_level: open_access checksum: a3703d0d26393578d4ba466681fc6be8 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:10:32Z date_updated: 2023-08-03T12:10:32Z file_id: '13585' file_name: Extdata_03_SYPH1_xz_1-2.tif file_size: 27791 relation: main_file success: 1 - access_level: open_access checksum: f653ac7d531cf9896cbd6a9edf2a7759 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:10:32Z date_updated: 2023-08-03T12:10:32Z file_id: '13586' file_name: Extdata_03_SYPH1_xz_3-4.tif file_size: 27721 relation: main_file success: 1 - access_level: open_access checksum: 04edbb337df4d5470e033a4f53c07300 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:10:33Z date_updated: 2023-08-03T12:10:33Z file_id: '13587' file_name: Extdata_03_SYPH1_xz_n2v.tif file_size: 57657482 relation: main_file success: 1 - access_level: open_access checksum: 09e1fe2dd3a1e8349693fda55d0985ca content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:10:34Z date_updated: 2023-08-03T12:10:34Z file_id: '13588' file_name: Extdata_03_SYPH1_xz.tif file_size: 57657527 relation: main_file success: 1 - access_level: open_access checksum: 458f8d486cb63876c6664cde4a9be27c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:12:25Z date_updated: 2023-08-03T12:12:25Z file_id: '13589' file_name: Extdata_03_SYP1_xy_1.tif file_size: 7109763 relation: main_file success: 1 - access_level: open_access checksum: e2dfccc882d85b660d65a596e1a8cbac content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:12:25Z date_updated: 2023-08-03T12:12:25Z file_id: '13590' file_name: Extdata_03_SYP1_xy_2-3.tif file_size: 72963 relation: main_file success: 1 - access_level: open_access checksum: a331be6052c68cc027cdb79f15447d9a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:12:25Z date_updated: 2023-08-03T12:12:25Z file_id: '13591' file_name: Extdata_03_SYP1_xz_1-2.tif file_size: 27724 relation: main_file success: 1 - access_level: open_access checksum: 4de626b035b43feaacd923fca411e6a2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:12:25Z date_updated: 2023-08-03T12:12:25Z file_id: '13592' file_name: Extdata_03_SYP1_xz_3-4.tif file_size: 27724 relation: main_file success: 1 - access_level: open_access checksum: d8076e927a074f024924d9bdb6fdd5e6 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:12:30Z date_updated: 2023-08-03T12:12:30Z file_id: '13593' file_name: Extdata_03_SYP1_xz_n2v.tif file_size: 214613644 relation: main_file success: 1 - access_level: open_access checksum: 79cf7d0f450c397caa877dd06b52f8df content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:12:30Z date_updated: 2023-08-03T12:12:30Z file_id: '13594' file_name: Extdata_03_SYP1_xz.tif file_size: 214613687 relation: main_file success: 1 - access_level: open_access checksum: 60ac6ea988d9b8bdaba2f09e0e1ef370 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:14:29Z date_updated: 2023-08-03T12:14:29Z file_id: '13595' file_name: Extdata03_VAMP2_xy_1.tif file_size: 7109747 relation: main_file success: 1 - access_level: open_access checksum: 92bf312da2dd356aa4fc9a0e7d811af2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:14:29Z date_updated: 2023-08-03T12:14:29Z file_id: '13596' file_name: Extdata03_VAMP2_xy_2-3.tif file_size: 72947 relation: main_file success: 1 - access_level: open_access checksum: 9319e293092eeee24e3c658fc178af1a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:14:29Z date_updated: 2023-08-03T12:14:29Z file_id: '13597' file_name: Extdata03_VAMP2_xz_1-2.tif file_size: 27724 relation: main_file success: 1 - access_level: open_access checksum: a627d7fd9a89bdde968e6d9bff846254 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:14:29Z date_updated: 2023-08-03T12:14:29Z file_id: '13598' file_name: Extdata03_VAMP2_xz_3-4.tif file_size: 27708 relation: main_file success: 1 - access_level: open_access checksum: 7a5363a185edce59ce57535f7d855092 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:14:32Z date_updated: 2023-08-03T12:14:32Z file_id: '13599' file_name: Extdata03_VAMP2_xz_n2v.tif file_size: 102457485 relation: main_file success: 1 - access_level: open_access checksum: 8e7fc4d00fff8ec6d9340e969f37e176 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:14:32Z date_updated: 2023-08-03T12:14:32Z file_id: '13600' file_name: Extdata03_VAMP2_xz.tif file_size: 102457527 relation: main_file success: 1 - access_level: open_access checksum: be17472f73ed8cd02a700b861f1dbac0 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:16:08Z date_updated: 2023-08-03T12:16:08Z file_id: '13601' file_name: Extdata04_VGLUT_xy_1.tif file_size: 11117763 relation: main_file success: 1 - access_level: open_access checksum: dbc3ec477f491ce3e98ab40475bd90ca content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:16:08Z date_updated: 2023-08-03T12:16:08Z file_id: '13602' file_name: Extdata04_VGLUT_xy_2-3.tif file_size: 72947 relation: main_file success: 1 - access_level: open_access checksum: 8ee877e6b843bb0e38febb0481962d69 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:16:08Z date_updated: 2023-08-03T12:16:08Z file_id: '13603' file_name: Extdata04_VGLUT_xz_1-2.tif file_size: 53367 relation: main_file success: 1 - access_level: open_access checksum: 9873f54d50955a2c204d0559c87aa13d content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:16:08Z date_updated: 2023-08-03T12:16:08Z file_id: '13604' file_name: Extdata04_VGLUT_xz_3-4.tif file_size: 53358 relation: main_file success: 1 - access_level: open_access checksum: 8eda08ae5981fcfa3758d0320b1923af content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:16:11Z date_updated: 2023-08-03T12:16:11Z file_id: '13605' file_name: Extdata04_VGLUT_xz_n2v.tif file_size: 144076208 relation: main_file success: 1 - access_level: open_access checksum: bc0b10229d498f60996a5b05cb87c428 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:16:10Z date_updated: 2023-08-03T12:16:10Z file_id: '13606' file_name: Extdata04_VGLUT_xz.tif file_size: 72071440 relation: main_file success: 1 - access_level: open_access checksum: e8d093ce7d98ea5647d8a80e3084c40b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:32:32Z date_updated: 2023-08-03T12:32:32Z file_id: '13607' file_name: Extdata03_VGAT_xy_1.tif file_size: 7109763 relation: main_file success: 1 - access_level: open_access checksum: 36590ca7a586de7ad76d3ad659c38995 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:32:32Z date_updated: 2023-08-03T12:32:32Z file_id: '13608' file_name: Extdata03_VGAT_xy_2-3.tif file_size: 72947 relation: main_file success: 1 - access_level: open_access checksum: 3914c7709f69d4d18f23a9fb6dc64572 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:32:32Z date_updated: 2023-08-03T12:32:32Z file_id: '13609' file_name: Extdata03_VGAT_xz_1-2.tif file_size: 53355 relation: main_file success: 1 - access_level: open_access checksum: fa98aa521adaefb9e4476fe519e88e59 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:32:32Z date_updated: 2023-08-03T12:32:32Z file_id: '13610' file_name: Extdata03_VGAT_xz_3-4.tif file_size: 53339 relation: main_file success: 1 - access_level: open_access checksum: cd6f384c51756977e37f45043c913252 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:32:36Z date_updated: 2023-08-03T12:32:36Z file_id: '13611' file_name: Extdata03_VGAT_xz_n2v.tif file_size: 204861338 relation: main_file success: 1 - access_level: open_access checksum: fb7e46feda5ac07877a91ad963da0e31 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:32:35Z date_updated: 2023-08-03T12:32:35Z file_id: '13612' file_name: Extdata03_VGAT_xz.tif file_size: 102457527 relation: main_file success: 1 - access_level: open_access checksum: fe033e0a377d391cd8e4af04987d9900 content_type: image/png creator: jdanzl date_created: 2023-08-03T12:36:46Z date_updated: 2023-08-03T12:36:46Z file_id: '13613' file_name: Extdata04_MUNC_xy_1.png file_size: 4348932 relation: main_file success: 1 - access_level: open_access checksum: 771d8e2b9192b6620f54ab30e4fad594 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:35:58Z date_updated: 2023-08-03T12:35:58Z file_id: '13614' file_name: Extdata04_MUNC_xy_2-3.tif file_size: 72947 relation: main_file success: 1 - access_level: open_access checksum: 4256d8f06fa2077b352776cf76b46618 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:35:58Z date_updated: 2023-08-03T12:35:58Z file_id: '13615' file_name: Extdata04_MUNC_xz_1-2.tif file_size: 53435 relation: main_file success: 1 - access_level: open_access checksum: 0b9365638c81d545e773170cf04b04b8 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:35:58Z date_updated: 2023-08-03T12:35:58Z file_id: '13616' file_name: Extdata04_MUNC_xz_3-4.tif file_size: 55941 relation: main_file success: 1 - access_level: open_access checksum: 9fa62688dab03c592cec47bf5d1c304d content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:36:04Z date_updated: 2023-08-03T12:36:04Z file_id: '13617' file_name: Extdata04_MUNC_xz_n2v.tif file_size: 204861404 relation: main_file success: 1 - access_level: open_access checksum: 39f710080a26136dbbe4c8916b434c65 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:36:02Z date_updated: 2023-08-03T12:36:02Z file_id: '13618' file_name: Extdata04_MUNC_xz.tif file_size: 102457527 relation: main_file success: 1 - access_level: open_access checksum: eaabc8112645a73f4326e621b4e6ad0a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:38:39Z date_updated: 2023-08-03T12:38:39Z file_id: '13619' file_name: Extdata04_BASSOON_xy_1.tif file_size: 11117757 relation: main_file success: 1 - access_level: open_access checksum: 15f624d29c473ce6e0ae7e466efc059a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:38:39Z date_updated: 2023-08-03T12:38:39Z file_id: '13620' file_name: Extdata04_BASSOON_xy_2-3.tif file_size: 74041 relation: main_file success: 1 - access_level: open_access checksum: 1cb4b4d219767a30072c804a07140240 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:38:39Z date_updated: 2023-08-03T12:38:39Z file_id: '13621' file_name: Extdata04_BASSOON_xz_1-2.tif file_size: 53435 relation: main_file success: 1 - access_level: open_access checksum: 1bac9c192da9375d81cb3747f48c9be4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:38:39Z date_updated: 2023-08-03T12:38:39Z file_id: '13622' file_name: Extdata04_BASSOON_xz_3-4.tif file_size: 53362 relation: main_file success: 1 - access_level: open_access checksum: 57fa91bfb1e2937e3449e57096b6fc74 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:38:50Z date_updated: 2023-08-03T12:38:50Z file_id: '13623' file_name: Extdata04_BASSOON_xz_n2v.tif file_size: 576071410 relation: main_file success: 1 - access_level: open_access checksum: ac51a734dcf7d1b94afcd4a471f10626 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:38:46Z date_updated: 2023-08-03T12:38:46Z file_id: '13624' file_name: Extdata04_BASSOON_xz.tif file_size: 288066640 relation: main_file success: 1 - access_level: open_access checksum: 244043f7acba250d560e29123702dcd7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:40:57Z date_updated: 2023-08-03T12:40:57Z file_id: '13625' file_name: Extdata04_HOMER1_xy_1.tif file_size: 7109763 relation: main_file success: 1 - access_level: open_access checksum: eff51ff97539f6491989bfc3d3f88860 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:40:57Z date_updated: 2023-08-03T12:40:57Z file_id: '13626' file_name: Extdata04_HOMER1_xy_2-3.tif file_size: 72963 relation: main_file success: 1 - access_level: open_access checksum: df35046d9bca4e97a5625c5a55218cfb content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:40:57Z date_updated: 2023-08-03T12:40:57Z file_id: '13627' file_name: Extdata04_HOMER1_xz_1-2.tif file_size: 53375 relation: main_file success: 1 - access_level: open_access checksum: 5dc7536f7aaea084dfc329537d8412ce content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:40:57Z date_updated: 2023-08-03T12:40:57Z file_id: '13628' file_name: Extdata04_HOMER1_xz_3-4.tif file_size: 53359 relation: main_file success: 1 - access_level: open_access checksum: 0b407669a26b9d7730a41361ceffda9a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:41:00Z date_updated: 2023-08-03T12:41:00Z file_id: '13629' file_name: Extdata04_HOMER1_xz_n2v.tif file_size: 204861339 relation: main_file success: 1 - access_level: open_access checksum: f95a0da9bea8b605fc2ed310190836b3 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:40:59Z date_updated: 2023-08-03T12:40:59Z file_id: '13630' file_name: Extdata04_HOMER1_xz.tif file_size: 102457527 relation: main_file success: 1 - access_level: open_access checksum: cf74307696548e7aa90e59a0935a74a1 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:45:08Z date_updated: 2023-08-03T12:45:08Z file_id: '13631' file_name: Extdata04_SHANK2_xy_1.tif file_size: 7120361 relation: main_file success: 1 - access_level: open_access checksum: 7b3490246df4f5bb68d0df682161820f content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:45:08Z date_updated: 2023-08-03T12:45:08Z file_id: '13632' file_name: Extdata04_SHANK2_xy_2-3.tif file_size: 72973 relation: main_file success: 1 - access_level: open_access checksum: c599d6830e61c386219e266f4717fe7c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:45:08Z date_updated: 2023-08-03T12:45:08Z file_id: '13633' file_name: Extdata04_SHANK2_xz_1-2.tif file_size: 53443 relation: main_file success: 1 - access_level: open_access checksum: 5b9912b2a408d224ad669f39dc8d5bc6 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:45:08Z date_updated: 2023-08-03T12:45:08Z file_id: '13634' file_name: Extdata04_SHANK2_xz_3-4.tif file_size: 53362 relation: main_file success: 1 - access_level: open_access checksum: 17f2064ceeb99cbb51208c27b1961ed5 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:45:30Z date_updated: 2023-08-03T12:45:30Z file_id: '13635' file_name: Extdata04_SHANK2_xz_n2v.tif file_size: 691291157 relation: main_file success: 1 - access_level: open_access checksum: 21f1bb8d2a00c88bdd6febe6285acc2a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:45:26Z date_updated: 2023-08-03T12:45:26Z file_id: '13636' file_name: Extdata04_SHANK2_xz.tif file_size: 518519275 relation: main_file success: 1 - access_level: open_access checksum: 47597ca873f1ea81cd4f7e9bfbb34aa4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:46:25Z date_updated: 2023-08-03T12:46:25Z file_id: '13637' file_name: Extdata04_GEPHYRIN_xy_1.tif file_size: 752109 relation: main_file success: 1 - access_level: open_access checksum: 14ed7ae64eb783e6b30f824f21959d0f content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:46:25Z date_updated: 2023-08-03T12:46:25Z file_id: '13638' file_name: Extdata04_GEPHYRIN_xy_2-3.tif file_size: 72909 relation: main_file success: 1 - access_level: open_access checksum: e361e226428d7b23618eed35b1cad080 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:46:25Z date_updated: 2023-08-03T12:46:25Z file_id: '13639' file_name: Extdata04_GEPHYRIN_xz_1-2.tif file_size: 53375 relation: main_file success: 1 - access_level: open_access checksum: abe7cee22f69fc2bf1a3ff9955ccf45a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:46:25Z date_updated: 2023-08-03T12:46:25Z file_id: '13640' file_name: Extdata04_GEPHYRIN_xz_3-4.tif file_size: 53360 relation: main_file success: 1 - access_level: open_access checksum: 59b49b451a63c5ac06fa31a17640c1a2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:46:27Z date_updated: 2023-08-03T12:46:27Z file_id: '13641' file_name: Extdata04_GEPHYRIN_xz_n2v.tif file_size: 73174939 relation: main_file success: 1 - access_level: open_access checksum: 1ee1feea85c8319ebc6c49147502e412 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:46:26Z date_updated: 2023-08-03T12:46:26Z file_id: '13642' file_name: Extdata04_GEPHYRIN_xz.tif file_size: 36614327 relation: main_file success: 1 - access_level: open_access checksum: 64d9d868ef89c5cfc65cb199aff831b4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:52:23Z date_updated: 2023-08-03T12:52:23Z file_id: '13643' file_name: Extdata06_a-b_n2v.tif file_size: 2195652677 relation: main_file success: 1 - access_level: open_access checksum: df41d97987798715b1f66e6e72be169b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:51:41Z date_updated: 2023-08-03T12:51:41Z file_id: '13644' file_name: Extdata06_a-b.tif file_size: 1097875840 relation: main_file success: 1 - access_level: open_access checksum: 95a3eaa3b70e964f6871a5765a53659b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:52:57Z date_updated: 2023-08-03T12:52:57Z file_id: '13645' file_name: Extdata07_01_bottom.tif file_size: 3564577 relation: main_file success: 1 - access_level: open_access checksum: 80b41ad0de73fd61eb67a35262627fac content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:52:57Z date_updated: 2023-08-03T12:52:57Z file_id: '13646' file_name: Extdata07_01_top.tif file_size: 11958844 relation: main_file success: 1 - access_level: open_access checksum: f694a0f11e2f782702cb4c411941873a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:27Z date_updated: 2023-08-03T12:54:27Z file_id: '13647' file_name: Extdata07_2_bottom.tif file_size: 3564581 relation: main_file success: 1 - access_level: open_access checksum: b8b1a1339a25806615c0aa7906a032ff content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:27Z date_updated: 2023-08-03T12:54:27Z file_id: '13648' file_name: Extdata07_2_top.tif file_size: 11973592 relation: main_file success: 1 - access_level: open_access checksum: 8a24eb623d65d809fe8afbd527528a77 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:27Z date_updated: 2023-08-03T12:54:27Z file_id: '13649' file_name: Extdata07_3_bottom.tif file_size: 1281901 relation: main_file success: 1 - access_level: open_access checksum: 816b35def703bc48d55b0293fcd8212f content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:27Z date_updated: 2023-08-03T12:54:27Z file_id: '13650' file_name: Extdata07_3_top.tif file_size: 16569776 relation: main_file success: 1 - access_level: open_access checksum: 7f1375ab8cf28cd136e2e44d1fdfd87d content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:27Z date_updated: 2023-08-03T12:54:27Z file_id: '13651' file_name: Extdata07_04_bottom.tif file_size: 3564595 relation: main_file success: 1 - access_level: open_access checksum: b1dbda28e2a010968716c0411568f139 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:27Z date_updated: 2023-08-03T12:54:27Z file_id: '13652' file_name: Extdata07_04_top.tif file_size: 5896404 relation: main_file success: 1 - access_level: open_access checksum: d6e96b7c8e6a7084c14eda83a4dd778a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:28Z date_updated: 2023-08-03T12:54:28Z file_id: '13653' file_name: Extdata07_5_bottom.tif file_size: 3564609 relation: main_file success: 1 - access_level: open_access checksum: a647f89a3048f71512cc58c9e53ec022 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:28Z date_updated: 2023-08-03T12:54:28Z file_id: '13654' file_name: Extdata07_5_top.tif file_size: 15555618 relation: main_file success: 1 - access_level: open_access checksum: 66becb046fe591914df572617d720202 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:28Z date_updated: 2023-08-03T12:54:28Z file_id: '13655' file_name: Extdata07_6_bottom.tif file_size: 3564577 relation: main_file success: 1 - access_level: open_access checksum: 5d76b2ad7d7acbb1afa27cf52194b1cb content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:28Z date_updated: 2023-08-03T12:54:28Z file_id: '13656' file_name: Extdata07_6_top.tif file_size: 6038186 relation: main_file success: 1 - access_level: open_access checksum: 7f137bdea0f0acb3db75c983ce44ab44 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:28Z date_updated: 2023-08-03T12:54:28Z file_id: '13657' file_name: Extdata07_7_bottom.tif file_size: 3560937 relation: main_file success: 1 - access_level: open_access checksum: 479e26106280eb61a2d74e29137a2e43 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:28Z date_updated: 2023-08-03T12:54:28Z file_id: '13658' file_name: Extdata07_7_top.tif file_size: 12031850 relation: main_file success: 1 - access_level: open_access checksum: 8426197ad283c1bc83e3193f323d5f5a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:28Z date_updated: 2023-08-03T12:54:28Z file_id: '13659' file_name: Extdata07_8_bottom.tif file_size: 3560937 relation: main_file success: 1 - access_level: open_access checksum: b9f75a82b564e1c5c363a495d078f6b7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:28Z date_updated: 2023-08-03T12:54:28Z file_id: '13660' file_name: Extdata07_8_top.tif file_size: 22877176 relation: main_file success: 1 - access_level: open_access checksum: 7f1a9f3bb9611362995ae832b2607f4d content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:28Z date_updated: 2023-08-03T12:54:28Z file_id: '13661' file_name: Extdata07_9_bottom.tif file_size: 3564605 relation: main_file success: 1 - access_level: open_access checksum: 40286bcb876b655d7421534d0215e86b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T12:54:28Z date_updated: 2023-08-03T12:54:28Z file_id: '13662' file_name: Extdata07_9_top.tif file_size: 2744190 relation: main_file success: 1 - access_level: open_access checksum: 4af220986cc94d412c2354aa7e6c8cce content_type: image/png creator: jdanzl date_created: 2023-08-03T13:00:03Z date_updated: 2023-08-03T13:00:03Z file_id: '13663' file_name: Extdata08_6_left.png file_size: 7243611 relation: main_file success: 1 - access_level: open_access checksum: af9c2299f1005a3ccc39f41082cea642 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:00:03Z date_updated: 2023-08-03T13:00:03Z file_id: '13664' file_name: Extdata08_6_right.tif file_size: 5562487 relation: main_file success: 1 - access_level: open_access checksum: 63ef28a174215c70e31d2cabf67d90fc content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:00:04Z date_updated: 2023-08-03T13:00:04Z file_id: '13665' file_name: Extdata08_7_left.tif file_size: 34745956 relation: main_file success: 1 - access_level: open_access checksum: 46de918dfe5f3c23e497ee3daa608dd9 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:00:03Z date_updated: 2023-08-03T13:00:03Z file_id: '13666' file_name: Extdata08_7_right.tif file_size: 5562483 relation: main_file success: 1 - access_level: open_access checksum: 8243a7985d2902446183adc35519a0c8 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:00:04Z date_updated: 2023-08-03T13:00:04Z file_id: '13667' file_name: Extdata08_b_1_left.tif file_size: 31506150 relation: main_file success: 1 - access_level: open_access checksum: 857cffa31569efcd5917f9802a106d58 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:00:04Z date_updated: 2023-08-03T13:00:04Z file_id: '13668' file_name: Extdata08_b_1_right.tif file_size: 11117705 relation: main_file success: 1 - access_level: open_access checksum: e34902de9119d2cd9f1910f610627c5f content_type: image/png creator: jdanzl date_created: 2023-08-03T13:00:04Z date_updated: 2023-08-03T13:00:04Z file_id: '13669' file_name: Extdata08_b_2_left.png file_size: 3540493 relation: main_file success: 1 - access_level: open_access checksum: 1247d636ac5af22e8950ffd2ff213fea content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:00:05Z date_updated: 2023-08-03T13:00:05Z file_id: '13670' file_name: Extdata08_b_2_right.tif file_size: 5562553 relation: main_file success: 1 - access_level: open_access checksum: f47c2d3f6824e08853ae2631f6ee7c5f content_type: image/png creator: jdanzl date_created: 2023-08-03T13:00:05Z date_updated: 2023-08-03T13:00:05Z file_id: '13671' file_name: Extdata08_b_3_left.png file_size: 3541547 relation: main_file success: 1 - access_level: open_access checksum: 1247d636ac5af22e8950ffd2ff213fea content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:00:05Z date_updated: 2023-08-03T13:00:05Z file_id: '13672' file_name: Extdata08_b_3_right.tif file_size: 5562553 relation: main_file success: 1 - access_level: open_access checksum: e90a95ec902a683678acd70336852fd9 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:00:05Z date_updated: 2023-08-03T13:00:05Z file_id: '13673' file_name: Extdata08_b_4_left.tif file_size: 25819844 relation: main_file success: 1 - access_level: open_access checksum: 94cd44cd1c8c7a87ffd5861bf88561a1 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:00:05Z date_updated: 2023-08-03T13:00:05Z file_id: '13674' file_name: Extdata08_b_4_right.tif file_size: 5561131 relation: main_file success: 1 - access_level: open_access checksum: fd4ca56dc5c48ad4546df22daef04efc content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:00:06Z date_updated: 2023-08-03T13:00:06Z file_id: '13675' file_name: Extdata08_b_5_left.tif file_size: 38786287 relation: main_file success: 1 - access_level: open_access checksum: 52c04890160c4e0f23d3fe2d3ed0c8e7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:00:06Z date_updated: 2023-08-03T13:00:06Z file_id: '13676' file_name: Extdata08_b_5_right.tif file_size: 5562487 relation: main_file success: 1 - access_level: open_access checksum: 47ee6f4b083130d5bb720bcf8a832443 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:04:52Z date_updated: 2023-08-03T13:04:52Z file_id: '13677' file_name: Extdata08_a_1-1.png file_size: 2133527 relation: main_file success: 1 - access_level: open_access checksum: 5ca2279c372b3b7dbce3ea5658a68399 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:04:52Z date_updated: 2023-08-03T13:04:52Z file_id: '13678' file_name: Extdata08_a_1-2.png file_size: 1782607 relation: main_file success: 1 - access_level: open_access checksum: 34b7781e3e4abf9f30a0c85db156b6d5 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:04:52Z date_updated: 2023-08-03T13:04:52Z file_id: '13679' file_name: Extdata08_a_2.png file_size: 5117469 relation: main_file success: 1 - access_level: open_access checksum: 25717007393682098d2208bd0676a0f7 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:04:52Z date_updated: 2023-08-03T13:04:52Z file_id: '13680' file_name: Extdata08_a_3.png file_size: 6911658 relation: main_file success: 1 - access_level: open_access checksum: b4b003809acec33c71628066744c7ea9 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:04:53Z date_updated: 2023-08-03T13:04:53Z file_id: '13681' file_name: Extdata08_a_4.png file_size: 8579427 relation: main_file success: 1 - access_level: open_access checksum: 4410976cf867ecacf8f197dbd28cc5a0 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:04:53Z date_updated: 2023-08-03T13:04:53Z file_id: '13682' file_name: Extdata08_a_5.png file_size: 9675065 relation: main_file success: 1 - access_level: open_access checksum: a235dd204f28d3323883e044b031b984 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:04:53Z date_updated: 2023-08-03T13:04:53Z file_id: '13683' file_name: Extdata08_a_6.png file_size: 9769588 relation: main_file success: 1 - access_level: open_access checksum: 0e2b768e4eb7200cf6fe28ba511a5ef6 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:04:53Z date_updated: 2023-08-03T13:04:53Z file_id: '13684' file_name: Extdata08_a_7.png file_size: 9114791 relation: main_file success: 1 - access_level: open_access checksum: df4a01c62233ee8ed601c4b90d7780d0 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:04:57Z date_updated: 2023-08-03T13:04:57Z file_id: '13685' file_name: Extdata08_a_8.png file_size: 124540688 relation: main_file success: 1 - access_level: open_access checksum: 1f407c7915e2717a56fec258708e7b7a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:11:30Z date_updated: 2023-08-03T13:11:30Z file_id: '13686' file_name: Exdata09_c_n2v.tif file_size: 204861336 relation: main_file success: 1 - access_level: open_access checksum: 9089dc7c9914edf9750eebd65819708d content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:11:26Z date_updated: 2023-08-03T13:11:26Z file_id: '13687' file_name: Extdata09_a_zoom.tif file_size: 252149 relation: main_file success: 1 - access_level: open_access checksum: 62d295a62cb8dd36c268b28cf0251322 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:11:26Z date_updated: 2023-08-03T13:11:26Z file_id: '13688' file_name: Extdata09_a.tif file_size: 11117705 relation: main_file success: 1 - access_level: open_access checksum: e874d8ee287f924c1076134b5b06bdb2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:11:31Z date_updated: 2023-08-03T13:11:31Z file_id: '13689' file_name: Extdata09_b_n2v.tif file_size: 256074660 relation: main_file success: 1 - access_level: open_access checksum: 488068fff7b42bcf5728739e2a06d742 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:12:53Z date_updated: 2023-08-03T13:12:53Z file_id: '13690' file_name: Extdata10_n2v_CLAHE.tif file_size: 127914854 relation: main_file success: 1 - access_level: open_access checksum: 35351f5af21ce854d41577813a7bdb57 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13691' file_name: Supplfig01_a_1.png file_size: 430878 relation: main_file success: 1 - access_level: open_access checksum: 36204e9e604206366ffc6f61ec91915b content_type: image/png creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13692' file_name: Supplfig01_a_2.png file_size: 438843 relation: main_file success: 1 - access_level: open_access checksum: 92ccc934c4603b29f4f7a96573e49c83 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13693' file_name: Supplfig01_a_3.png file_size: 426713 relation: main_file success: 1 - access_level: open_access checksum: e71faa54934bee8ac3e66ce692f542ab content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13694' file_name: Supplfig01_a_4.tif file_size: 723221 relation: main_file success: 1 - access_level: open_access checksum: 95dc33563f48b650e5ac020bdfd10c48 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13695' file_name: Supplfig01_a_5.tif file_size: 723235 relation: main_file success: 1 - access_level: open_access checksum: c62df0a9faf1c47af121d77eb1582edd content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13696' file_name: Supplfig01_b_1.tif file_size: 1442129 relation: main_file success: 1 - access_level: open_access checksum: 8ae157c5a4a543da1193cb8ca12b1919 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13697' file_name: Supplfig01_b_2.tif file_size: 725407 relation: main_file success: 1 - access_level: open_access checksum: 388370d954ce842781c0d62edfb448a7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13698' file_name: Supplfig01_c_1.tif file_size: 721641 relation: main_file success: 1 - access_level: open_access checksum: 6cae58ba3c98bc8253e1c769e93657a7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13699' file_name: Supplfig01_c_2.tif file_size: 6003079 relation: main_file success: 1 - access_level: open_access checksum: 85cf013232c72895aefc07f5411a765a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13700' file_name: Supplfig01_c_3.tif file_size: 2003311 relation: main_file success: 1 - access_level: open_access checksum: dfb33b91066e3f34d3803f59a4105aba content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13701' file_name: Supplfig01_c_4.tif file_size: 723271 relation: main_file success: 1 - access_level: open_access checksum: 8b899826fe48d7e7536b0b02a2645e87 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13702' file_name: Supplfig01_d_1.tif file_size: 721901 relation: main_file success: 1 - access_level: open_access checksum: 67529fa6e0f12c272275e823f6045f6d content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13703' file_name: Supplfig01_d_2.tif file_size: 721901 relation: main_file success: 1 - access_level: open_access checksum: 111a9231f63c775340d3356109715cb0 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13704' file_name: Supplfig01_e_1.tif file_size: 723223 relation: main_file success: 1 - access_level: open_access checksum: 7685bf02408dcb095a00854ff22763ed content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:21:35Z date_updated: 2023-08-03T13:21:35Z file_id: '13705' file_name: Supplfig01_e_2.tif file_size: 723223 relation: main_file success: 1 - access_level: open_access checksum: 455f5cb9aa8a87b91586a27aca122610 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:00Z date_updated: 2023-08-03T13:26:00Z file_id: '13706' file_name: Supplfig02_b_01.tif file_size: 34821298 relation: main_file success: 1 - access_level: open_access checksum: 311545b39aaa2c72755fd8ae190803a5 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:00Z date_updated: 2023-08-03T13:26:00Z file_id: '13707' file_name: Supplfig02_b_02.tif file_size: 32131123 relation: main_file success: 1 - access_level: open_access checksum: 682deb61f57d9ca54716160ddd52a6cf content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:01Z date_updated: 2023-08-03T13:26:01Z file_id: '13708' file_name: Supplfig02_b_03.tif file_size: 36872674 relation: main_file success: 1 - access_level: open_access checksum: 4f9579c91b2a3f36ff6e66b592907973 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:01Z date_updated: 2023-08-03T13:26:01Z file_id: '13709' file_name: Supplfig02_b_04.tif file_size: 39964115 relation: main_file success: 1 - access_level: open_access checksum: 7ae7053673b53dbed59ffb92618f969a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:02Z date_updated: 2023-08-03T13:26:02Z file_id: '13710' file_name: Supplfig02_b_05.tif file_size: 43053091 relation: main_file success: 1 - access_level: open_access checksum: 827b26d3d2b6ddc9bced9d6113023ced content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:02Z date_updated: 2023-08-03T13:26:02Z file_id: '13711' file_name: Supplfig02_b_06.tif file_size: 46998147 relation: main_file success: 1 - access_level: open_access checksum: bc2e7e8badb42f8e1facc8b7bc96fdda content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:03Z date_updated: 2023-08-03T13:26:03Z file_id: '13712' file_name: Supplfig02_b_07.tif file_size: 45179219 relation: main_file success: 1 - access_level: open_access checksum: c2b78aa0f433928afa10a743c5fb73b8 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:03Z date_updated: 2023-08-03T13:26:03Z file_id: '13713' file_name: Supplfig02_b_08.tif file_size: 46978802 relation: main_file success: 1 - access_level: open_access checksum: 9cd1ab61cced2c0981e813aeae930855 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:04Z date_updated: 2023-08-03T13:26:04Z file_id: '13714' file_name: Supplfig02_b_09.tif file_size: 48840915 relation: main_file success: 1 - access_level: open_access checksum: 3086126338aee6ec4ebc1d3350551197 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:04Z date_updated: 2023-08-03T13:26:04Z file_id: '13715' file_name: Supplfig02_b_10.tif file_size: 45907059 relation: main_file success: 1 - access_level: open_access checksum: 69f52c2b3bb5b5f9fef057860b3386fa content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:05Z date_updated: 2023-08-03T13:26:05Z file_id: '13716' file_name: Supplfig02_b_11.tif file_size: 32231538 relation: main_file success: 1 - access_level: open_access checksum: defdbeab1e672456bfeafdd1983e779e content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:26:05Z date_updated: 2023-08-03T13:26:05Z file_id: '13717' file_name: Supplfig02_b_12.tif file_size: 35264963 relation: main_file success: 1 - access_level: open_access checksum: 02c566f781b9ad44f04ce0088a1fa27a content_type: image/png creator: jdanzl date_created: 2023-08-03T13:28:40Z date_updated: 2023-08-03T13:28:40Z file_id: '13718' file_name: Supplfig03_a_std_xy.png file_size: 63326 relation: main_file success: 1 - access_level: open_access checksum: c6c3630ee9a6ed5d207cb68e330da566 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:28:40Z date_updated: 2023-08-03T13:28:40Z file_id: '13719' file_name: Supplfig03_a_std_xz.png file_size: 50211 relation: main_file success: 1 - access_level: open_access checksum: 0dcd4d19e83a7ff259d6aa04d746cd90 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:28:41Z date_updated: 2023-08-03T13:28:41Z file_id: '13720' file_name: Supplfig03_b_std_xy.png file_size: 52629 relation: main_file success: 1 - access_level: open_access checksum: 4785de4a6dcb23b25a06b0da29df5bb5 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:28:41Z date_updated: 2023-08-03T13:28:41Z file_id: '13721' file_name: Supplfig03_b_std_xz.png file_size: 72245 relation: main_file success: 1 - access_level: open_access checksum: 19d0f198bd8a25073e45e7950d7a78c2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:28:45Z date_updated: 2023-08-03T13:28:45Z file_id: '13722' file_name: Supplfig03_model1.tif file_size: 98570368 relation: main_file success: 1 - access_level: open_access checksum: 51ff687df4a0867f39b69c2c7a4ee3ca content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:28:45Z date_updated: 2023-08-03T13:28:45Z file_id: '13723' file_name: Supplfig03_model2.tif file_size: 98570367 relation: main_file success: 1 - access_level: open_access checksum: ec9d9a041ca85fe632c612baf981fcc5 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:28:49Z date_updated: 2023-08-03T13:28:49Z file_id: '13724' file_name: Supplfig03_model3.tif file_size: 98570365 relation: main_file success: 1 - access_level: open_access checksum: a988b15a9529094f1b5519a72871e98e content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:28:49Z date_updated: 2023-08-03T13:28:49Z file_id: '13725' file_name: Supplfig03_model4.tif file_size: 98570365 relation: main_file success: 1 - access_level: open_access checksum: 4a4fe88fcfd87fcfe118a5a73d81d6b0 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:28:52Z date_updated: 2023-08-03T13:28:52Z file_id: '13726' file_name: Supplfig03_model5.tif file_size: 98570369 relation: main_file success: 1 - access_level: open_access checksum: ce9b774ff5163ebfa4e3fb162f4cfffe content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:34:27Z date_updated: 2023-08-03T13:34:27Z file_id: '13727' file_name: Supplfig04_a_n2v.tif file_size: 1036927887 relation: main_file success: 1 - access_level: open_access checksum: 21f1bb8d2a00c88bdd6febe6285acc2a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:34:13Z date_updated: 2023-08-03T13:34:13Z file_id: '13728' file_name: Supplfig04_a.tif file_size: 518519275 relation: main_file success: 1 - access_level: open_access checksum: 503820214ab994c01b18a241f3b62434 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:34:22Z date_updated: 2023-08-03T13:34:22Z file_id: '13729' file_name: Supplfig04_b.tif file_size: 158440069 relation: main_file success: 1 - access_level: open_access checksum: e0469102a87332b46904b4ba35b8fb2f content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:34:37Z date_updated: 2023-08-03T13:34:37Z file_id: '13730' file_name: Supplfig04_c_n2v.tif file_size: 309407894 relation: main_file success: 1 - access_level: open_access checksum: c30a0d18c43045a8fbc5501a37061bd2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:34:38Z date_updated: 2023-08-03T13:34:38Z file_id: '13731' file_name: Supplfig04_c.tif file_size: 154728887 relation: main_file success: 1 - access_level: open_access checksum: 69c706710d642b30cda6951494702139 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:34:43Z date_updated: 2023-08-03T13:34:43Z file_id: '13732' file_name: Supplfig04_d_n2v.tif file_size: 106696749 relation: main_file success: 1 - access_level: open_access checksum: 7dbd2e881ebf049352913188fa10224a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:34:41Z date_updated: 2023-08-03T13:34:41Z file_id: '13733' file_name: Supplfig04_d.tif file_size: 53367343 relation: main_file success: 1 - access_level: open_access checksum: fd0d1ec674dabbb499fab383b7eb4d58 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:34:46Z date_updated: 2023-08-03T13:34:46Z file_id: '13734' file_name: Supplfig04_e_n2v.tiff file_size: 127917734 relation: main_file success: 1 - access_level: open_access checksum: 86de309d9cd434afbe371da283d8adb6 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:34:46Z date_updated: 2023-08-03T13:34:46Z file_id: '13735' file_name: Supplfig04_e.tif file_size: 63974204 relation: main_file success: 1 - access_level: open_access checksum: ada99b2b5900cb198d1de3cc9e37ebd1 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13736' file_name: Supplfig05_a_xy_1.png file_size: 8403 relation: main_file success: 1 - access_level: open_access checksum: f2e382925a972b98560614016ae3bc55 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13737' file_name: Supplfig05_a_xy_2.png file_size: 10087 relation: main_file success: 1 - access_level: open_access checksum: ef22b640f33d677add1a7b5153f95420 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13738' file_name: Supplfig05_a_xy_3.png file_size: 24561 relation: main_file success: 1 - access_level: open_access checksum: b854cc4a5224b8a6f5d59c74f5740ccd content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13739' file_name: Supplfig05_a_xy_4.png file_size: 8353 relation: main_file success: 1 - access_level: open_access checksum: 446b0362c5ea6e2a5f0e1f8359422358 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13740' file_name: Supplfig05_a_xy_5.png file_size: 8337 relation: main_file success: 1 - access_level: open_access checksum: 5585f7b62fa09ed5a63090b679383601 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13741' file_name: Supplfig05_a_xz_1.png file_size: 7399 relation: main_file success: 1 - access_level: open_access checksum: 190d88bcacbd11d41f4a0e2bbd140862 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13742' file_name: Supplfig05_a_xz_2.png file_size: 10887 relation: main_file success: 1 - access_level: open_access checksum: 0c89010651862f21032a303e159b7a1c content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13743' file_name: Supplfig05_a_xz_3.png file_size: 21654 relation: main_file success: 1 - access_level: open_access checksum: 94e61e553aa2280721acce7d407ff24a content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13744' file_name: Supplfig05_a_xz_4.png file_size: 7248 relation: main_file success: 1 - access_level: open_access checksum: ef9157274686ff5d7056f5a519d413dd content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13745' file_name: Supplfig05_a_xz_5.png file_size: 7214 relation: main_file success: 1 - access_level: open_access checksum: 4b389473cbf769e6e34670dae2224af1 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13746' file_name: Supplfig05_b_xy_1.png file_size: 8544 relation: main_file success: 1 - access_level: open_access checksum: b05aa1e201758a5d55e35d719452fafc content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13747' file_name: Supplfig05_b_xy_2.png file_size: 11135 relation: main_file success: 1 - access_level: open_access checksum: 890f3516930251a367066c049141d6bb content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13748' file_name: Supplfig05_b_xy_3.png file_size: 26762 relation: main_file success: 1 - access_level: open_access checksum: 36345c1d582758ff463072fd04578c0c content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13749' file_name: Supplfig05_b_xy_4.png file_size: 8438 relation: main_file success: 1 - access_level: open_access checksum: c9499ad8914c405a07fc4469b19e8987 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13750' file_name: Supplfig05_b_xy_5.png file_size: 8434 relation: main_file success: 1 - access_level: open_access checksum: 7e7a7c900ce1fc3187ab648f207f9425 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13751' file_name: Supplfig05_b_xz_1.png file_size: 8269 relation: main_file success: 1 - access_level: open_access checksum: b645d1e2422ef3f05344ccd3f955468d content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13752' file_name: Supplfig05_b_xz_2.png file_size: 12762 relation: main_file success: 1 - access_level: open_access checksum: ef0b83b49cf47ca7d8ffe3bdc609fe38 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13753' file_name: Supplfig05_b_xz_3.png file_size: 24819 relation: main_file success: 1 - access_level: open_access checksum: 68719d4d464a2ffc198cb6ad070c4579 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:37Z date_updated: 2023-08-03T13:35:37Z file_id: '13754' file_name: Supplfig05_b_xz_4.png file_size: 8126 relation: main_file success: 1 - access_level: open_access checksum: 18370f47177ef37a477c6fd7bda3fea0 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13755' file_name: Supplfig05_b_xz_5.png file_size: 8114 relation: main_file success: 1 - access_level: open_access checksum: 013d4bd9704ace490810b9ef21b12454 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13756' file_name: Supplfig05_c_xy_1.png file_size: 8273 relation: main_file success: 1 - access_level: open_access checksum: bb431f827386e79c54452d6284f501b9 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13757' file_name: Supplfig05_c_xy_2.png file_size: 12639 relation: main_file success: 1 - access_level: open_access checksum: 4cd54f58c5afff88832a508655f913bb content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13758' file_name: Supplfig05_c_xy_3.png file_size: 25288 relation: main_file success: 1 - access_level: open_access checksum: 07f86f98f6a65eac8608cec8c567309e content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13759' file_name: Supplfig05_c_xz_1.png file_size: 6786 relation: main_file success: 1 - access_level: open_access checksum: 492f699b71761214272b17432e3a54fa content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13760' file_name: Supplfig05_c_xz_2.png file_size: 9781 relation: main_file success: 1 - access_level: open_access checksum: af617da5638db849bea6ff51a08227c6 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13761' file_name: Supplfig05_c_xz_3.png file_size: 20728 relation: main_file success: 1 - access_level: open_access checksum: 5e5d5694af4a22297046d697a01fa4d6 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13762' file_name: Supplfig05_d_xy_1.png file_size: 8428 relation: main_file success: 1 - access_level: open_access checksum: 38bf7b75f3dedd0a3722faae05aa0233 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13763' file_name: Supplfig05_d_xy_2.png file_size: 10813 relation: main_file success: 1 - access_level: open_access checksum: e4ea966553f158ec2cfbdc696780390e content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13764' file_name: Supplfig05_d_xy_3.png file_size: 26552 relation: main_file success: 1 - access_level: open_access checksum: 356f424d9f5f608e9aea962bb63672f1 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13765' file_name: Supplfig05_d_xz_1.png file_size: 7876 relation: main_file success: 1 - access_level: open_access checksum: 05068476beee0f394e28b98209686394 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13766' file_name: Supplfig05_d_xz_2.png file_size: 11634 relation: main_file success: 1 - access_level: open_access checksum: 78b3a0d93df22383a384a2f3acc80401 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13767' file_name: Supplfig05_d_xz_3.png file_size: 25006 relation: main_file success: 1 - access_level: open_access checksum: f5ee6a817f11a42c9db82ad6325f58b9 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13768' file_name: Supplfig05_e_xy_1.png file_size: 7895 relation: main_file success: 1 - access_level: open_access checksum: 019ca89e892d6e19589609bc99eab331 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13769' file_name: Supplfig05_e_xy_2.png file_size: 6180 relation: main_file success: 1 - access_level: open_access checksum: 0e1a5cbbd70dc245edaecaca70d974cb content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13770' file_name: Supplfig05_e_xy_3.png file_size: 18326 relation: main_file success: 1 - access_level: open_access checksum: 4d4d64a5bb7b096aaf8130ece4512bc2 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13771' file_name: Supplfig05_e_xz_1.png file_size: 6295 relation: main_file success: 1 - access_level: open_access checksum: 607302aec5ec2a14a271dbffd3465261 content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13772' file_name: Supplfig05_e_xz_2.png file_size: 4335 relation: main_file success: 1 - access_level: open_access checksum: a673e17ead1fd2e776b9a5f560a289ab content_type: image/png creator: jdanzl date_created: 2023-08-03T13:35:38Z date_updated: 2023-08-03T13:35:38Z file_id: '13773' file_name: Supplfig05_e_xz_3.png file_size: 23243 relation: main_file success: 1 - access_level: open_access checksum: 4349e511fc86a8bddb790a7be7175c75 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:13Z date_updated: 2023-08-03T13:46:13Z file_id: '13774' file_name: Supplfig06_a_1.tif file_size: 4002153 relation: main_file success: 1 - access_level: open_access checksum: cd12977e4c1a472d80193be01f69a895 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:13Z date_updated: 2023-08-03T13:46:13Z file_id: '13775' file_name: Supplfig06_a_2.tif file_size: 2252137 relation: main_file success: 1 - access_level: open_access checksum: 575e32b8c25ce658e20f0c86a5f1b9b7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:13Z date_updated: 2023-08-03T13:46:13Z file_id: '13776' file_name: Supplfig06_a_3.tif file_size: 2252137 relation: main_file success: 1 - access_level: open_access checksum: b06f775e0210e7a16cb4b58aed32118c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:13Z date_updated: 2023-08-03T13:46:13Z file_id: '13777' file_name: Supplfig06_a_i.tif file_size: 78329 relation: main_file success: 1 - access_level: open_access checksum: 56854c1a05c721c36877fe7c7454b7d7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:13Z date_updated: 2023-08-03T13:46:13Z file_id: '13778' file_name: Supplfig06_a_ii.tif file_size: 78329 relation: main_file success: 1 - access_level: open_access checksum: 9aff42ea5138931fedb5a00643ae7a22 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:13Z date_updated: 2023-08-03T13:46:13Z file_id: '13779' file_name: Supplfig06_a_iii.tif file_size: 78329 relation: main_file success: 1 - access_level: open_access checksum: 9474b7d00d4dee46659afedef75dc095 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:13Z date_updated: 2023-08-03T13:46:13Z file_id: '13780' file_name: Supplfig06_d_1.tif file_size: 501149 relation: main_file success: 1 - access_level: open_access checksum: 53df41dd968b04b4657cd2b91870d636 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:13Z date_updated: 2023-08-03T13:46:13Z file_id: '13781' file_name: Supplfig06_d_2.tif file_size: 500153 relation: main_file success: 1 - access_level: open_access checksum: 1a39b8310598dd25d97f848b682b8de0 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:14Z date_updated: 2023-08-03T13:46:14Z file_id: '13782' file_name: Supplfig06_d_3.tif file_size: 500153 relation: main_file success: 1 - access_level: open_access checksum: 6d9b496be6aecedbb2cb4cbf68f02872 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:14Z date_updated: 2023-08-03T13:46:14Z file_id: '13783' file_name: Supplfig06_d_i.tif file_size: 78329 relation: main_file success: 1 - access_level: open_access checksum: bc034b1636c2db8b9d9e7bd131b9780a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:14Z date_updated: 2023-08-03T13:46:14Z file_id: '13784' file_name: Supplfig06_d_ii.tif file_size: 78329 relation: main_file success: 1 - access_level: open_access checksum: 54f6e55e30a2aeea6c82eb6dbd376240 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:14Z date_updated: 2023-08-03T13:46:14Z file_id: '13785' file_name: Supplfig06_d_iii.tif file_size: 78329 relation: main_file success: 1 - access_level: open_access checksum: 446da3cc16897277890f23f966c2bf52 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:14Z date_updated: 2023-08-03T13:46:14Z file_id: '13786' file_name: Supplfig06_g_1.tif file_size: 960011 relation: main_file success: 1 - access_level: open_access checksum: 71192d0ec592a33195f2386a5f95aa86 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:14Z date_updated: 2023-08-03T13:46:14Z file_id: '13787' file_name: Supplfig06_g_2.tif file_size: 960011 relation: main_file success: 1 - access_level: open_access checksum: 246782dbe8ff525aea360efc72e65f07 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:14Z date_updated: 2023-08-03T13:46:14Z file_id: '13788' file_name: Supplfig06_g_3.tif file_size: 960041 relation: main_file success: 1 - access_level: open_access checksum: d49b12fec5508aa8d72587757cccc0a4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:14Z date_updated: 2023-08-03T13:46:14Z file_id: '13789' file_name: Supplfig06_g_4.tif file_size: 960041 relation: main_file success: 1 - access_level: open_access checksum: 27b11b1d4fc784a49ffd7660624d00b6 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:46:14Z date_updated: 2023-08-03T13:46:14Z file_id: '13790' file_name: Supplfig06_g_5.tif file_size: 963241 relation: main_file success: 1 - access_level: open_access checksum: 9ce944049c1b88fadbf43609385f9e2f content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:38Z date_updated: 2023-08-03T13:51:38Z file_id: '13791' file_name: Suppl08_a_1.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 06265515f06688843a415362f7b2c485 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:38Z date_updated: 2023-08-03T13:51:38Z file_id: '13792' file_name: Suppl08_a_2.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 50f0969c6c2c1209ff776bec4861030a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:38Z date_updated: 2023-08-03T13:51:38Z file_id: '13793' file_name: Suppl08_a_3.tif file_size: 617552 relation: main_file success: 1 - access_level: open_access checksum: b90965d20133fea73c99050c32eb7695 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:38Z date_updated: 2023-08-03T13:51:38Z file_id: '13794' file_name: Suppl08_a_4.tif file_size: 617552 relation: main_file success: 1 - access_level: open_access checksum: 568a1e0efaa62527b51e66a7aabfd05c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:40Z date_updated: 2023-08-03T13:51:40Z file_id: '13795' file_name: Suppl08_a_coCATS_N2V.tif file_size: 19287339 relation: main_file success: 1 - access_level: open_access checksum: 06265515f06688843a415362f7b2c485 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:40Z date_updated: 2023-08-03T13:51:40Z file_id: '13796' file_name: Suppl08_c_1_4_predictedBASSOON.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 568a1e0efaa62527b51e66a7aabfd05c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:43Z date_updated: 2023-08-03T13:51:43Z file_id: '13797' file_name: Suppl08_c_1_coCATS.tif file_size: 19287339 relation: main_file success: 1 - access_level: open_access checksum: feae08c38b1d9c540b697977cd7f2666 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T15:36:47Z date_updated: 2023-08-03T15:36:47Z file_id: '13798' file_name: Suppl08_c_2_coCATS.tif file_size: 19287340 relation: main_file success: 1 - access_level: open_access checksum: af2c1199fdcaecfec76189dae86cc12e content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:44Z date_updated: 2023-08-03T13:51:44Z file_id: '13799' file_name: Suppl08_c_2-3_predictedBASSOON.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 1f92db47605959d0db01f612f7c9c034 content_type: application/octet-stream creator: jdanzl date_created: 2023-08-03T13:51:43Z date_updated: 2023-08-03T13:51:43Z file_id: '13800' file_name: Suppl08_c_3-6_roi.roi file_size: 156 relation: main_file success: 1 - access_level: open_access checksum: 4fc4f8803adcfacd53a41b91f4699dc5 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:45Z date_updated: 2023-08-03T13:51:45Z file_id: '13801' file_name: Suppl08_e_1_3.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 459551aae114daa4f5ca5d06fcd6b203 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:45Z date_updated: 2023-08-03T13:51:45Z file_id: '13802' file_name: Suppl08_e_1-2.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 032cbace7ec436f7b62478c0ffd35e5e content_type: application/octet-stream creator: jdanzl date_created: 2023-08-03T13:51:45Z date_updated: 2023-08-03T13:51:45Z file_id: '13803' file_name: Suppl08_e_2-5_roi.roi file_size: 152 relation: main_file success: 1 - access_level: open_access checksum: 7379168be281ef618b8cecd8efd31ed5 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:46Z date_updated: 2023-08-03T13:51:46Z file_id: '13804' file_name: Suppl08_e_4-5_coCATS.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 5c4c092f608f4c10bb422c9e08b5955b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:46Z date_updated: 2023-08-03T13:51:46Z file_id: '13805' file_name: Suppl08_e_4.tif file_size: 617552 relation: main_file success: 1 - access_level: open_access checksum: 903e31be124f6e4ec1c2e7ab7db80e6b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:46Z date_updated: 2023-08-03T13:51:46Z file_id: '13806' file_name: Suppl08_e_5.tif file_size: 617552 relation: main_file success: 1 - access_level: open_access checksum: 173d956392d67b0a7e544629b51881e4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:48Z date_updated: 2023-08-03T13:51:48Z file_id: '13807' file_name: Suppl08_e_6_8.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 2a4cea867a253a6af7e9b0d2e100de14 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:48Z date_updated: 2023-08-03T13:51:48Z file_id: '13808' file_name: Suppl08_e_6-7.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 6b40f99fddfa26f0a9713000769741b7 content_type: application/octet-stream creator: jdanzl date_created: 2023-08-03T13:51:48Z date_updated: 2023-08-03T13:51:48Z file_id: '13809' file_name: Suppl08_e_7-10_roi.roi file_size: 174 relation: main_file success: 1 - access_level: open_access checksum: 82f7013959df99c27366886de9b38ba2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:49Z date_updated: 2023-08-03T13:51:49Z file_id: '13810' file_name: Suppl08_e_9-10_coCATS.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 50f0969c6c2c1209ff776bec4861030a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:48Z date_updated: 2023-08-03T13:51:48Z file_id: '13811' file_name: Suppl08_e_9.tif file_size: 617552 relation: main_file success: 1 - access_level: open_access checksum: 569f599d7f2be49d4dcf7cb385f428c4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:49Z date_updated: 2023-08-03T13:51:49Z file_id: '13812' file_name: Suppl08_e_10.tif file_size: 617552 relation: main_file success: 1 - access_level: open_access checksum: 50f0969c6c2c1209ff776bec4861030a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:49Z date_updated: 2023-08-03T13:51:49Z file_id: '13813' file_name: Suppl08_g_1.tif file_size: 617552 relation: main_file success: 1 - access_level: open_access checksum: 62797fc860176197142a47e831eaf1f6 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:49Z date_updated: 2023-08-03T13:51:49Z file_id: '13814' file_name: Suppl08_g_2.tif file_size: 617552 relation: main_file success: 1 - access_level: open_access checksum: b90965d20133fea73c99050c32eb7695 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:49Z date_updated: 2023-08-03T13:51:49Z file_id: '13815' file_name: Suppl08_g_3.tif file_size: 617552 relation: main_file success: 1 - access_level: open_access checksum: a96dc9f38c6a1d3c959771a649a42748 content_type: application/octet-stream creator: jdanzl date_created: 2023-08-03T13:51:49Z date_updated: 2023-08-03T13:51:49Z file_id: '13816' file_name: Suppl08_i_add_roi.roi file_size: 160 relation: main_file success: 1 - access_level: open_access checksum: f2135207ebbc4bdc014763ba852a5cf0 content_type: application/octet-stream creator: jdanzl date_created: 2023-08-03T13:51:50Z date_updated: 2023-08-03T13:51:50Z file_id: '13817' file_name: Suppl08_i_shape_roi.roi file_size: 160 relation: main_file success: 1 - access_level: open_access checksum: f6f31fe2d87cf7208387f98ce1e37b04 content_type: application/octet-stream creator: jdanzl date_created: 2023-08-03T13:51:50Z date_updated: 2023-08-03T13:51:50Z file_id: '13818' file_name: Suppl08_i_split_roi.roi file_size: 158 relation: main_file success: 1 - access_level: open_access checksum: 71590db0ad391e0c5baf03024981b1d9 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:51Z date_updated: 2023-08-03T13:51:51Z file_id: '13819' file_name: Suppl08_i_1.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 9ce944049c1b88fadbf43609385f9e2f content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:51Z date_updated: 2023-08-03T13:51:51Z file_id: '13820' file_name: Suppl08_i_2.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 06265515f06688843a415362f7b2c485 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:52Z date_updated: 2023-08-03T13:51:52Z file_id: '13821' file_name: Suppl08_i_3.tiff file_size: 19286002 relation: main_file success: 1 - access_level: open_access checksum: 16c628c160fb81e40df0ad1eb134e92b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:52Z date_updated: 2023-08-03T13:51:52Z file_id: '13822' file_name: Suppl08_i_4.tif file_size: 19284766 relation: main_file success: 1 - access_level: open_access checksum: b06e62c3a9834a40002d7aad3eaacc3f content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:53Z date_updated: 2023-08-03T13:51:53Z file_id: '13823' file_name: Suppl08_i_5.tif file_size: 9649818 relation: main_file success: 1 - access_level: open_access checksum: 41ef98c7f01755b43cf6e77fff287732 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:51:53Z date_updated: 2023-08-03T13:51:53Z file_id: '13824' file_name: Suppl08_i_6.tif file_size: 19284766 relation: main_file success: 1 - access_level: open_access checksum: feae08c38b1d9c540b697977cd7f2666 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:53:29Z date_updated: 2023-08-03T13:53:29Z file_id: '13825' file_name: Suppl08_c_2_coCATS.tif file_size: 19287340 relation: main_file success: 1 - access_level: open_access checksum: c01509a1c657fbbbfdbbd484c298b6e3 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:58:08Z date_updated: 2023-08-03T13:58:08Z file_id: '13826' file_name: Supplfig09_b_1_n2v.tiff file_size: 179788642 relation: main_file success: 1 - access_level: open_access checksum: 64a7f270274ff3480b18d690087016e2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:58:20Z date_updated: 2023-08-03T13:58:20Z file_id: '13827' file_name: Supplfig09_b_2_n2v.tif file_size: 742420240 relation: main_file success: 1 - access_level: open_access checksum: b34a6beaaf13698f421df961e009efeb content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:58:20Z date_updated: 2023-08-03T13:58:20Z file_id: '13828' file_name: Supplfig09_b_3_n2v.tif file_size: 478900363 relation: main_file success: 1 - access_level: open_access checksum: ec04501f234b5e4fd91f9eac0e585395 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:58:25Z date_updated: 2023-08-03T13:58:25Z file_id: '13829' file_name: Supplfig09_b_4_n2v.tif file_size: 191873159 relation: main_file success: 1 - access_level: open_access checksum: 3a1b313298da35c97550abf0d245b4a7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:59:27Z date_updated: 2023-08-03T13:59:27Z file_id: '13830' file_name: Supplfig11_i.tif file_size: 55286 relation: main_file success: 1 - access_level: open_access checksum: 9cf00c0252f0a2efe1994c83c224389a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:59:27Z date_updated: 2023-08-03T13:59:27Z file_id: '13831' file_name: Supplfig11_ii.tif file_size: 55286 relation: main_file success: 1 - access_level: open_access checksum: 9a6e83acdf6d70bb9a6e76fa7d41a372 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:59:27Z date_updated: 2023-08-03T13:59:27Z file_id: '13832' file_name: Supplfig11_iii.tif file_size: 55257 relation: main_file success: 1 - access_level: open_access checksum: 709fdd13b7e090846a4d8edd2425f675 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T13:59:32Z date_updated: 2023-08-03T13:59:32Z file_id: '13833' file_name: Supplfig11_n2v+prediction.tif file_size: 309457551 relation: main_file success: 1 - access_level: open_access checksum: e60ea3e6bb1bf380460d0d8ccdbd1f07 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:14:32Z date_updated: 2023-08-03T14:14:32Z file_id: '13834' file_name: Supplfig12_a_01_n2v.tif file_size: 119323629 relation: main_file success: 1 - access_level: open_access checksum: 2a4e1771e2f06383894361ba2a8155b4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:14:29Z date_updated: 2023-08-03T14:14:29Z file_id: '13835' file_name: Supplfig12_a_01.tif file_size: 59680727 relation: main_file success: 1 - access_level: open_access checksum: 993c434069b9d1bcb09bfe70628f5bbe content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:14:34Z date_updated: 2023-08-03T14:14:34Z file_id: '13836' file_name: Supplfig12_a_02_n2v.tif file_size: 106696749 relation: main_file success: 1 - access_level: open_access checksum: e3b6410d68e42004ef3857967707aeb3 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:14:34Z date_updated: 2023-08-03T14:14:34Z file_id: '13837' file_name: Supplfig12_a_02.tif file_size: 53367287 relation: main_file success: 1 - access_level: open_access checksum: 0156e99806fe1539d5f48ea16c78e8c8 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:14:41Z date_updated: 2023-08-03T14:14:41Z file_id: '13838' file_name: Supplfig12_a_03_n2v.tif file_size: 149937979 relation: main_file success: 1 - access_level: open_access checksum: 6cc1533a221526a072a0b09fb44bcf50 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:14:39Z date_updated: 2023-08-03T14:14:39Z file_id: '13839' file_name: Supplfig12_a_03.tif file_size: 74987927 relation: main_file success: 1 - access_level: open_access checksum: f134834bd0d5e8c22e5a35aadf592007 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:14:53Z date_updated: 2023-08-03T14:14:53Z file_id: '13840' file_name: Supplfig12_a_04_n2v.tif file_size: 305581862 relation: main_file success: 1 - access_level: open_access checksum: 212ec76c02552fa1eef91e7bca9f07f7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:14:50Z date_updated: 2023-08-03T14:14:50Z file_id: '13841' file_name: Supplfig12_a_04.tif file_size: 152821840 relation: main_file success: 1 - access_level: open_access checksum: 7d99807d5b4313b04b4b5e0fbc08ba78 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:14:52Z date_updated: 2023-08-03T14:14:52Z file_id: '13842' file_name: Supplfig12_a_05_n2v.tif file_size: 48082029 relation: main_file success: 1 - access_level: open_access checksum: a6d4024a8c6fa073a532cc0c78323df7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:14:53Z date_updated: 2023-08-03T14:14:53Z file_id: '13843' file_name: Supplfig12_a_05.tif file_size: 24059983 relation: main_file success: 1 - access_level: open_access checksum: 1c42ad5423636478fe57495a3b506746 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:09Z date_updated: 2023-08-03T14:15:09Z file_id: '13844' file_name: Supplfig12_a_06_n2v.tif file_size: 305581860 relation: main_file success: 1 - access_level: open_access checksum: 821f1d31c6dbe68eb2513fb7520b5272 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:04Z date_updated: 2023-08-03T14:15:04Z file_id: '13845' file_name: Supplfig12_a_06.tif file_size: 152821840 relation: main_file success: 1 - access_level: open_access checksum: 86a4dc1e4948c4bc9c71e6d55b4fd104 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:08Z date_updated: 2023-08-03T14:15:08Z file_id: '13846' file_name: Supplfig12_a_07_n2v.tif file_size: 66855793 relation: main_file success: 1 - access_level: open_access checksum: fd5d45b1135800124fec635c4667dafe content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:09Z date_updated: 2023-08-03T14:15:09Z file_id: '13847' file_name: Supplfig12_a_07.tif file_size: 33446807 relation: main_file success: 1 - access_level: open_access checksum: 5683760cc119a09f0b7de8fea98cda9c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:19Z date_updated: 2023-08-03T14:15:19Z file_id: '13848' file_name: Supplfig12_a_08_n2v.tif file_size: 231476260 relation: main_file success: 1 - access_level: open_access checksum: 0c336d554bcd8524f11bd25c2188b56f content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:15Z date_updated: 2023-08-03T14:15:15Z file_id: '13849' file_name: Supplfig12_a_08.tif file_size: 115769040 relation: main_file success: 1 - access_level: open_access checksum: fcaea6c95c363bd864a524fca8ed8e9b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:31Z date_updated: 2023-08-03T14:15:31Z file_id: '13850' file_name: Supplfig12_a_09_n2v.tif file_size: 305581869 relation: main_file success: 1 - access_level: open_access checksum: f401f1875f072c345d106a1e419f9d13 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:28Z date_updated: 2023-08-03T14:15:28Z file_id: '13851' file_name: Supplfig12_a_09.tif file_size: 152821840 relation: main_file success: 1 - access_level: open_access checksum: 7ad7d5b1ac81da1ec3d5003d00ee870a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:42Z date_updated: 2023-08-03T14:15:42Z file_id: '13852' file_name: Supplfig12_a_10_n2v.tif file_size: 266386255 relation: main_file success: 1 - access_level: open_access checksum: 77b93d082debd5248348c0a1e886eab9 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:40Z date_updated: 2023-08-03T14:15:40Z file_id: '13853' file_name: Supplfig12_a_10.tif file_size: 133239040 relation: main_file success: 1 - access_level: open_access checksum: 5ece1d503f05133d07d5b867f666d7a8 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:49Z date_updated: 2023-08-03T14:15:49Z file_id: '13854' file_name: Supplfig12_a_11_n2v.tif file_size: 191866269 relation: main_file success: 1 - access_level: open_access checksum: a72ee7ab433097752ff00a63421d4b61 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:15:48Z date_updated: 2023-08-03T14:15:48Z file_id: '13855' file_name: Supplfig12_a_11.tif file_size: 95955040 relation: main_file success: 1 - access_level: open_access checksum: c9c6e4692e0e7f305a43058b201b50d3 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:16:49Z date_updated: 2023-08-03T14:16:49Z file_id: '13856' file_name: Supplfig13_i.tif file_size: 55281 relation: main_file success: 1 - access_level: open_access checksum: 345d11dbd70123d9d2723b547cbfc4fc content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:16:49Z date_updated: 2023-08-03T14:16:49Z file_id: '13857' file_name: Supplfig13_ii.tif file_size: 55193 relation: main_file success: 1 - access_level: open_access checksum: b4c74c08077cfd3e11bfd6ea9ee1c5b2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:16:49Z date_updated: 2023-08-03T14:16:49Z file_id: '13858' file_name: Supplfig13_n2v+predict.tif file_size: 539037 relation: main_file success: 1 - access_level: open_access checksum: 15f5b44257d075f9e45811304dfd5f85 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:18:10Z date_updated: 2023-08-03T14:18:10Z file_id: '13859' file_name: Supplfig14_a_n2v.tif file_size: 854898609 relation: main_file success: 1 - access_level: open_access checksum: a9ca03e3e5696988d06fc6ab1c103440 content_type: image/png creator: jdanzl date_created: 2023-08-03T14:19:58Z date_updated: 2023-08-03T14:19:58Z file_id: '13860' file_name: Supplfig15_a_1.png file_size: 7514502 relation: main_file success: 1 - access_level: open_access checksum: 4be3451e203a0fc5d9eb14279ff68a7a content_type: image/png creator: jdanzl date_created: 2023-08-03T14:19:58Z date_updated: 2023-08-03T14:19:58Z file_id: '13861' file_name: Supplfig15_a_2.png file_size: 1784041 relation: main_file success: 1 - access_level: open_access checksum: 43068c31eecddb798dbf2f51bda9b6c9 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:19:58Z date_updated: 2023-08-03T14:19:58Z file_id: '13862' file_name: Supplfig15_b_1.tif file_size: 6030878 relation: main_file success: 1 - access_level: open_access checksum: ded4c0797f1a9152dc3128f1bb8c32a5 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:19:58Z date_updated: 2023-08-03T14:19:58Z file_id: '13863' file_name: Supplfig15_b_2.tif file_size: 723293 relation: main_file success: 1 - access_level: open_access checksum: 705394732d94bd8463479aee83c2d36e content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:19:58Z date_updated: 2023-08-03T14:19:58Z file_id: '13864' file_name: Supplfig15_c_i.tif file_size: 723409 relation: main_file success: 1 - access_level: open_access checksum: e08efe220bec6a93d583cab17754dd19 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:19:58Z date_updated: 2023-08-03T14:19:58Z file_id: '13865' file_name: Supplfig15_c_ii.tif file_size: 723409 relation: main_file success: 1 - access_level: open_access checksum: 0e08e5d965815240b0a8195e0f899aab content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:19:59Z date_updated: 2023-08-03T14:19:59Z file_id: '13866' file_name: Supplfig15_c.tif file_size: 31572914 relation: main_file success: 1 - access_level: open_access checksum: 594696a77d4a9be512046be5e2d602f0 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:19:59Z date_updated: 2023-08-03T14:19:59Z file_id: '13867' file_name: Supplfig15_d_1.tif file_size: 6030752 relation: main_file success: 1 - access_level: open_access checksum: ffe6733eb77858008c4ca07b5f8c432b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:19:59Z date_updated: 2023-08-03T14:19:59Z file_id: '13868' file_name: Supplfig15_d_2.tif file_size: 8005495 relation: main_file success: 1 - access_level: open_access checksum: 663bf013cf1e5019e1e7ddd2d12fa492 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:20:56Z date_updated: 2023-08-03T14:20:56Z file_id: '13869' file_name: Supplfig16_a.tif file_size: 11117709 relation: main_file success: 1 - access_level: open_access checksum: 80aee233dc2a1f26ed8cc323270cf3a9 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:20:56Z date_updated: 2023-08-03T14:20:56Z file_id: '13870' file_name: Supplfig16_b.tif file_size: 113709 relation: main_file success: 1 - access_level: open_access checksum: 3b408e9345df2f16a942ad4ea61739b7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:20:56Z date_updated: 2023-08-03T14:20:56Z file_id: '13871' file_name: Supplfig16_c.tif file_size: 113709 relation: main_file success: 1 - access_level: open_access checksum: fbf688ef1f907149f92e9e936d02df72 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:25:47Z date_updated: 2023-08-03T14:25:47Z file_id: '13872' file_name: Supplfig17_a_1.tif file_size: 6003131 relation: main_file success: 1 - access_level: open_access checksum: 9a56470f251f14b43903036fab338f76 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:25:47Z date_updated: 2023-08-03T14:25:47Z file_id: '13873' file_name: Supplfig17_a_2.tif file_size: 8004085 relation: main_file success: 1 - access_level: open_access checksum: 4578c020ba5d0a6ffe2a8a1c22e52c75 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:25:47Z date_updated: 2023-08-03T14:25:47Z file_id: '13874' file_name: Supplfig17_a_3.tif file_size: 6003123 relation: main_file success: 1 - access_level: open_access checksum: a681d32f515da3bff8e803946f1d8b50 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:25:47Z date_updated: 2023-08-03T14:25:47Z file_id: '13875' file_name: Supplfig17_a_4.tif file_size: 6003131 relation: main_file success: 1 - access_level: open_access checksum: b89d366c39e25d17dc5d8ceee9145c8b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:25:47Z date_updated: 2023-08-03T14:25:47Z file_id: '13876' file_name: Supplfig17_a_5.tif file_size: 6003131 relation: main_file success: 1 - access_level: open_access checksum: 0b9d60f0aba79525a97c122d972f0b22 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:25:47Z date_updated: 2023-08-03T14:25:47Z file_id: '13877' file_name: Supplfig17_a_6.tif file_size: 6003079 relation: main_file success: 1 - access_level: open_access checksum: 169aad3cea521cc2a0ce4c3e41473e0c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:25:47Z date_updated: 2023-08-03T14:25:47Z file_id: '13878' file_name: Supplfig17_a_7.tif file_size: 6003115 relation: main_file success: 1 - access_level: open_access checksum: 39a44d77d9047bfa10da8d9c9bd7b391 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:25:47Z date_updated: 2023-08-03T14:25:47Z file_id: '13879' file_name: Supplfig17_a_8.tif file_size: 4002129 relation: main_file success: 1 - access_level: open_access checksum: f4ecb2bd44f2cea3d71587670344ac40 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:25:48Z date_updated: 2023-08-03T14:25:48Z file_id: '13880' file_name: Supplfig17_b.tif file_size: 8214335 relation: main_file success: 1 - access_level: open_access checksum: 44a20d2621680c90227416bf32b5a566 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:27:06Z date_updated: 2023-08-03T14:27:06Z file_id: '13881' file_name: Supplfig18_a.tif file_size: 7471479 relation: main_file success: 1 - access_level: open_access checksum: 5a5f7b616785f9213064e8c77f9d38c4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:27:06Z date_updated: 2023-08-03T14:27:06Z file_id: '13882' file_name: Supplfig18_b.tif file_size: 290625 relation: main_file success: 1 - access_level: open_access checksum: 8f621722a636e808a03d85f9597ad1a2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:27:07Z date_updated: 2023-08-03T14:27:07Z file_id: '13883' file_name: Supplfig18_c.tif file_size: 411767 relation: main_file success: 1 - access_level: open_access checksum: 3c8356f9170fe345e2ef725cd7d1b167 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:27:07Z date_updated: 2023-08-03T14:27:07Z file_id: '13884' file_name: Supplfig18_d.tif file_size: 11117685 relation: main_file success: 1 - access_level: open_access checksum: 5c8443e97724b54f359f7355483b890e content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:27:10Z date_updated: 2023-08-03T14:27:10Z file_id: '13885' file_name: Supplfig18_e_n2v.tif file_size: 259509773 relation: main_file success: 1 - access_level: open_access checksum: 413e3105c1bcd2ac2c569fa2b06253f2 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:29:25Z date_updated: 2023-08-03T14:29:25Z file_id: '13886' file_name: Supplfig19_n2v.tif file_size: 1430939360 relation: main_file success: 1 - access_level: open_access checksum: a864dc5b54f469c723e86286d538bb52 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:29:16Z date_updated: 2023-08-03T14:29:16Z file_id: '13887' file_name: Supplfig19.tif file_size: 715524468 relation: main_file success: 1 - access_level: open_access checksum: 8a78ce49446d207c0bf31196b788fa93 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:54Z date_updated: 2023-08-03T14:32:54Z file_id: '13888' file_name: Supplfig20_a_left.tif file_size: 8004743 relation: main_file success: 1 - access_level: open_access checksum: 48fa3abfd16a00c7a3757d6452a482ec content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:54Z date_updated: 2023-08-03T14:32:54Z file_id: '13889' file_name: Supplfig20_a_right.tif file_size: 5561081 relation: main_file success: 1 - access_level: open_access checksum: 85d82cd94dd3202f04b5987bc4466573 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:54Z date_updated: 2023-08-03T14:32:54Z file_id: '13890' file_name: Supplfig20_b_1.tif file_size: 8456797 relation: main_file success: 1 - access_level: open_access checksum: e16f04d5d4d40f6ec33456d0cf02e1eb content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:54Z date_updated: 2023-08-03T14:32:54Z file_id: '13891' file_name: Supplfig20_b_2.tif file_size: 8456795 relation: main_file success: 1 - access_level: open_access checksum: ff190edb269c28b25d27bffaeb7d25cf content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:54Z date_updated: 2023-08-03T14:32:54Z file_id: '13892' file_name: Supplfig20_b_3.tif file_size: 8456796 relation: main_file success: 1 - access_level: open_access checksum: deb10b81bae62d9e20e681411fb75fcc content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:54Z date_updated: 2023-08-03T14:32:54Z file_id: '13893' file_name: Supplfig20_b_4.tif file_size: 8538887 relation: main_file success: 1 - access_level: open_access checksum: 5c64bb94e76030d7a9d8624bac4b0f57 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:54Z date_updated: 2023-08-03T14:32:54Z file_id: '13894' file_name: Supplfig20_b_5.tif file_size: 8538851 relation: main_file success: 1 - access_level: open_access checksum: d6c20232c4bd36e213b4c456c5009644 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:54Z date_updated: 2023-08-03T14:32:54Z file_id: '13895' file_name: Supplfig20_c_1.tif file_size: 11077737 relation: main_file success: 1 - access_level: open_access checksum: 49c3396b8960af3f6fd8f6b078971d51 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:54Z date_updated: 2023-08-03T14:32:54Z file_id: '13896' file_name: Supplfig20_c_2.tif file_size: 11077737 relation: main_file success: 1 - access_level: open_access checksum: 73471528f691fb337839b84c31014da4 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:55Z date_updated: 2023-08-03T14:32:55Z file_id: '13897' file_name: Supplfig20_c_3.tif file_size: 11077737 relation: main_file success: 1 - access_level: open_access checksum: 47a0fd1a36d7e7907ce18007bdaaa145 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:55Z date_updated: 2023-08-03T14:32:55Z file_id: '13898' file_name: Supplfig20_c_4.tif file_size: 11077737 relation: main_file success: 1 - access_level: open_access checksum: 0c74b07f13fb08a91e61669368f38c9a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:55Z date_updated: 2023-08-03T14:32:55Z file_id: '13899' file_name: Supplfig20_c_5.tif file_size: 11077737 relation: main_file success: 1 - access_level: open_access checksum: fe3b76446ec8bd0d5cdba94a128a84b8 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:55Z date_updated: 2023-08-03T14:32:55Z file_id: '13900' file_name: Supplfig20_d_1.tif file_size: 4002133 relation: main_file success: 1 - access_level: open_access checksum: 0570bab9a471af3d0d1d8bf9a3cb17e7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:55Z date_updated: 2023-08-03T14:32:55Z file_id: '13901' file_name: Supplfig20_d_2.tif file_size: 4002133 relation: main_file success: 1 - access_level: open_access checksum: 59f330990b5c95f98a768761a009940c content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:55Z date_updated: 2023-08-03T14:32:55Z file_id: '13902' file_name: Supplfig20_d_3.tif file_size: 4002199 relation: main_file success: 1 - access_level: open_access checksum: f0da06f2a278dff4bbd1aeace11700bf content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:55Z date_updated: 2023-08-03T14:32:55Z file_id: '13903' file_name: Supplfig20_d_4.tif file_size: 4002133 relation: main_file success: 1 - access_level: open_access checksum: e61d49dcc0952af3623cc26a78cc6495 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:32:55Z date_updated: 2023-08-03T14:32:55Z file_id: '13904' file_name: Supplfig20_d_5.tif file_size: 4002133 relation: main_file success: 1 - access_level: open_access checksum: bcf8294487abaf1a75033f388fba06ec content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:42:01Z date_updated: 2023-08-03T14:42:01Z file_id: '13905' file_name: Supplfig22_b_1.tif file_size: 12627576 relation: main_file success: 1 - access_level: open_access checksum: 14097feb4a73e7bb1e1694cef0115cab content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:42:01Z date_updated: 2023-08-03T14:42:01Z file_id: '13906' file_name: Supplfig22_b_2.tif file_size: 8543366 relation: main_file success: 1 - access_level: open_access checksum: 7e74b8cff2ada56d47d135a6a9e71e76 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:42:04Z date_updated: 2023-08-03T14:42:04Z file_id: '13907' file_name: Supplfig22_b_3.tif file_size: 8394010 relation: main_file success: 1 - access_level: open_access checksum: f6e6e0f0e3854fedd201ab8ff08a7651 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T15:35:39Z date_updated: 2023-08-03T15:35:39Z file_id: '13908' file_name: Supplfig22_b_4.tif file_size: 8682992 relation: main_file success: 1 - access_level: open_access checksum: 6ddeb84249768b46b9c2072bf85bdc8b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:42:04Z date_updated: 2023-08-03T14:42:04Z file_id: '13909' file_name: Supplfig22_b_5.tif file_size: 8503466 relation: main_file success: 1 - access_level: open_access checksum: 40648b8a4ef375b8352f11a6772ea1a6 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:42:04Z date_updated: 2023-08-03T14:42:04Z file_id: '13910' file_name: Supplfig22_b_6.tif file_size: 8543342 relation: main_file success: 1 - access_level: open_access checksum: 78f601de4d88f6ccb97861eaf4a995f8 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:42:06Z date_updated: 2023-08-03T14:42:06Z file_id: '13911' file_name: Supplfig22_b_7.tif file_size: 33588990 relation: main_file success: 1 - access_level: open_access checksum: 2873c488b7c8ad4d111726025086e9ea content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:42:41Z date_updated: 2023-08-03T14:42:41Z file_id: '13912' file_name: Supplfig22_c.tif file_size: 1453171518 relation: main_file success: 1 - access_level: open_access checksum: c1d0e5e61ac0d0ddf08704769f80ac78 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:47:43Z date_updated: 2023-08-03T14:47:43Z file_id: '13913' file_name: Supplfig23_a.tif file_size: 1325919782 relation: main_file success: 1 - access_level: open_access checksum: f97632984b6a73e06cc0c8c947cdcc71 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:47:25Z date_updated: 2023-08-03T14:47:25Z file_id: '13914' file_name: Supplfig23_b.tif file_size: 31366288 relation: main_file success: 1 - access_level: open_access checksum: 16f4c17835a79d7c06e2a97b1603baf1 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:47:26Z date_updated: 2023-08-03T14:47:26Z file_id: '13915' file_name: Supplfig23_c.tif file_size: 31366288 relation: main_file success: 1 - access_level: open_access checksum: 00f35ca77165642ca9b3bc3608bd04c1 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:47:27Z date_updated: 2023-08-03T14:47:27Z file_id: '13916' file_name: Supplfig23_d.tif file_size: 31366428 relation: main_file success: 1 - access_level: open_access checksum: 1aff850f47ae8c8f05ca48ff9faa38b1 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:47:27Z date_updated: 2023-08-03T14:47:27Z file_id: '13917' file_name: Supplfig23_e.tif file_size: 31500832 relation: main_file success: 1 - access_level: open_access checksum: f644de697d142c83461ed5ad1d72a043 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:48:38Z date_updated: 2023-08-03T14:48:38Z file_id: '13918' file_name: Supplfig24_a_i.tif file_size: 44179078 relation: main_file success: 1 - access_level: open_access checksum: eccb84925a6699b396d4b07efcbc7349 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:48:38Z date_updated: 2023-08-03T14:48:38Z file_id: '13919' file_name: Supplfig24_a_ii.tif file_size: 44125924 relation: main_file success: 1 - access_level: open_access checksum: afe7253e70ec79144e59b28c3c66703a content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:48:54Z date_updated: 2023-08-03T14:48:54Z file_id: '13920' file_name: Supplfig24_a.tif file_size: 1061835435 relation: main_file success: 1 - access_level: open_access checksum: 94a03b022aa84ea6e8515450a481ad82 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:48:39Z date_updated: 2023-08-03T14:48:39Z file_id: '13921' file_name: Supplfig24_b_iii.tif file_size: 3977824 relation: main_file success: 1 - access_level: open_access checksum: 166832c173fcda88ec6e35decdf0d197 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:48:39Z date_updated: 2023-08-03T14:48:39Z file_id: '13922' file_name: Supplfig24_b_iv.tif file_size: 3977825 relation: main_file success: 1 - access_level: open_access checksum: 53175073b83ab569241ae64ef7f180b3 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:51:27Z date_updated: 2023-08-03T14:51:27Z file_id: '13923' file_name: Supplfig25_a_1.tif file_size: 37641738 relation: main_file success: 1 - access_level: open_access checksum: 70e6a1780daeae6a5bef2c27c996c442 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:51:26Z date_updated: 2023-08-03T14:51:26Z file_id: '13924' file_name: Supplfig25_a_2.tif file_size: 4932897 relation: main_file success: 1 - access_level: open_access checksum: 1748266d7b8a2ae1f6292b9c265c2068 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:51:31Z date_updated: 2023-08-03T14:51:31Z file_id: '13925' file_name: Supplfig25_b_1.tif file_size: 357433570 relation: main_file success: 1 - access_level: open_access checksum: 8490f44160a482ea06d858eb3bc25a11 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:51:27Z date_updated: 2023-08-03T14:51:27Z file_id: '13926' file_name: Supplfig25_b_2.tif file_size: 27734506 relation: main_file success: 1 - access_level: open_access checksum: e5e9c550cc934a7725dc209c79951847 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:53:43Z date_updated: 2023-08-03T14:53:43Z file_id: '13927' file_name: Suppfig26_h.tif file_size: 35082394 relation: main_file success: 1 - access_level: open_access checksum: 39ae411d1e950e78bdc12937fb36f661 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:53:42Z date_updated: 2023-08-03T14:53:42Z file_id: '13928' file_name: Supplfig26_a_1.tif file_size: 16676477 relation: main_file success: 1 - access_level: open_access checksum: 450f5d0e8091639e27eb7a7991524e88 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:53:42Z date_updated: 2023-08-03T14:53:42Z file_id: '13929' file_name: Supplfig26_a_2.tif file_size: 170493 relation: main_file success: 1 - access_level: open_access checksum: 8e5a71801fa1fcb7f679d1af23344662 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:53:43Z date_updated: 2023-08-03T14:53:43Z file_id: '13930' file_name: Supplfig26_b_1.tif file_size: 11117737 relation: main_file success: 1 - access_level: open_access checksum: 519fb0326a0f0774b3edc1dafffcdd08 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:53:43Z date_updated: 2023-08-03T14:53:43Z file_id: '13931' file_name: Supplfig26_b_2.tif file_size: 113753 relation: main_file success: 1 - access_level: open_access checksum: d051c7d717eeb6f2ca59d8727ea62200 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:53:52Z date_updated: 2023-08-03T14:53:52Z file_id: '13932' file_name: Supplfig26_c.tif file_size: 495452386 relation: main_file success: 1 - access_level: open_access checksum: 5437b53e708572e2e9ad1432c260a04f content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:53:46Z date_updated: 2023-08-03T14:53:46Z file_id: '13933' file_name: Supplfig26_d.tif file_size: 132167170 relation: main_file success: 1 - access_level: open_access checksum: 0baab38829a8587ded5e39f85068124b content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:53:46Z date_updated: 2023-08-03T14:53:46Z file_id: '13934' file_name: Supplfig26_e.tif file_size: 11431214 relation: main_file success: 1 - access_level: open_access checksum: afa57f254c9dd987d90d5e43db3fb9e6 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:53:48Z date_updated: 2023-08-03T14:53:48Z file_id: '13935' file_name: Supplfig26_f.tif file_size: 64005702 relation: main_file success: 1 - access_level: open_access checksum: c35ba67ab92c410cb4370f91f3dea819 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:53:52Z date_updated: 2023-08-03T14:53:52Z file_id: '13936' file_name: Supplfig26_g.tif file_size: 246421054 relation: main_file success: 1 - access_level: open_access checksum: 3fd6186d73cbce1be79cf14a94a7f3bd content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:56:43Z date_updated: 2023-08-03T14:56:43Z file_id: '13937' file_name: Supplfig27_a.tif file_size: 166614932 relation: main_file success: 1 - access_level: open_access checksum: d1fc4c88e8e258e4e536a26e196d09b0 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:56:42Z date_updated: 2023-08-03T14:56:42Z file_id: '13938' file_name: Supplfig27_b.tif file_size: 143583446 relation: main_file success: 1 - access_level: open_access checksum: 8d6985530e86f38548e89e6380d73771 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:56:47Z date_updated: 2023-08-03T14:56:47Z file_id: '13939' file_name: Supplfig27_c.tif file_size: 172528188 relation: main_file success: 1 - access_level: open_access checksum: d0b1309d2120892ede84e04fdf0dbfbf content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:56:46Z date_updated: 2023-08-03T14:56:46Z file_id: '13940' file_name: Supplfig27_d.tif file_size: 113699256 relation: main_file success: 1 - access_level: open_access checksum: 4789b5254d0415ce314fc9e39cc52121 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:56:47Z date_updated: 2023-08-03T14:56:47Z file_id: '13941' file_name: Supplfig27_e.tif file_size: 88664548 relation: main_file success: 1 - access_level: open_access checksum: 7ff2d06534f062b0f17dab181f6c1f4e content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:56:47Z date_updated: 2023-08-03T14:56:47Z file_id: '13942' file_name: Supplfig27_f.tif file_size: 2298356 relation: main_file success: 1 - access_level: open_access checksum: 46de66d457b0def90f753c11927536b7 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:56:47Z date_updated: 2023-08-03T14:56:47Z file_id: '13943' file_name: Supplfig27_g_1.tif file_size: 499618 relation: main_file success: 1 - access_level: open_access checksum: 9ef5fba064a73a79dbc74b5e166d08ec content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:56:50Z date_updated: 2023-08-03T14:56:50Z file_id: '13944' file_name: Supplfig27_g_2.tif file_size: 202079026 relation: main_file success: 1 - access_level: open_access checksum: bf956c2b58d3da2baa869db5206d8d49 content_type: image/tiff creator: jdanzl date_created: 2023-08-03T14:56:48Z date_updated: 2023-08-03T14:56:48Z file_id: '13945' file_name: Supplfig27_g_3.tif file_size: 14639269 relation: main_file success: 1 - access_level: open_access checksum: 327dca11f42d5375d7f47f4cbd5b36c0 content_type: application/octet-stream creator: jdanzl date_created: 2023-08-03T15:21:01Z date_updated: 2023-08-03T15:21:01Z file_id: '13946' file_name: model.p file_size: 279467712 relation: main_file success: 1 file_date_updated: 2023-08-04T13:19:47Z has_accepted_license: '1' month: '08' oa: 1 oa_version: Published Version project: - _id: 265CB4D0-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03600 name: Optical control of synaptic function via adhesion molecules - _id: 26AA4EF2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize - _id: 23889792-32DE-11EA-91FC-C7463DDC885E name: High content imaging to decode human immune cell interactions in health and allergic disease - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9 call_identifier: H2020 grant_number: '101026635' name: Synaptic computations of the hippocampal CA3 circuitry publisher: Institute of Science and Technology Austria related_material: link: - description: 'Original data for Fig. 5d, Fig. 5d (N2V) and Fig. 5f-i, provided via an external link due to the large size (>10GB) of the datasets. ' relation: research_data url: https://pub.ista.ac.at/group_danzl/data/CATS/ record: - id: '14257' relation: used_in_publication status: public status: public title: Research data for the publication "Imaging brain tissue architecture across millimeter to nanometer scales" tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13116' abstract: - lang: eng text: 'The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ -- a prokaryotic homologue of the eukaryotic protein tubulin -- polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here, we connect single filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram captures these features quantitatively, demonstrating how the flexibility, density and chirality of active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. ' acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: 'This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF). ' article_processing_charge: No author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova - first_name: Batirtze full_name: Prats Mateu, Batirtze id: 299FE892-F248-11E8-B48F-1D18A9856A87 last_name: Prats Mateu - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Keesiang full_name: Lim, Keesiang last_name: Lim - first_name: Dörte full_name: Brandis, Dörte last_name: Brandis - first_name: Philipp full_name: Velicky, Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Richard W. full_name: Wong, Richard W. last_name: Wong - first_name: Jens full_name: Elgeti, Jens last_name: Elgeti - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. 2023. doi:10.15479/AT:ISTA:13116 apa: Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:13116 chicago: Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:13116. ieee: Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments.” Institute of Science and Technology Austria, 2023. ista: Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments, Institute of Science and Technology Austria, 10.15479/AT:ISTA:13116. mla: Dunajova, Zuzana, et al. Chiral and Nematic Phases of Flexible Active Filaments. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:13116. short: Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, (2023). date_created: 2023-06-02T12:30:40Z date_published: 2023-07-26T00:00:00Z date_updated: 2024-02-21T12:19:09Z day: '26' ddc: - '539' department: - _id: MaLo - _id: EdHa - _id: JoDa doi: 10.15479/AT:ISTA:13116 ec_funded: 1 file: - access_level: open_access checksum: 4b4ec5d4df7672b3af5ba23b126b171b content_type: application/vnd.openxmlformats-officedocument.wordprocessingml.document creator: pradler date_created: 2023-08-08T11:17:28Z date_updated: 2023-08-08T11:17:28Z file_id: '13983' file_name: ReadMe File.docx file_size: 13111 relation: main_file success: 1 - access_level: open_access checksum: 6f1673d6ae4f547cd49cfe7f87d9ab7e content_type: application/octet-stream creator: pradler date_created: 2023-07-25T06:55:43Z date_updated: 2023-07-25T06:55:43Z file_id: '13298' file_name: TIRF_FtsZ WT 0.625µM.7z.001 file_size: 1499504777 relation: main_file success: 1 - access_level: open_access checksum: bc0dea871af164f7419ac838a34a4162 content_type: application/octet-stream creator: pradler date_created: 2023-07-25T08:31:07Z date_updated: 2023-07-25T08:31:07Z file_id: '13306' file_name: TIRF_FtsZ WT 0.900µM.7z.001 file_size: 3986437211 relation: main_file success: 1 - access_level: open_access checksum: dde91b799364a8456ac463dcba7bf37d content_type: application/octet-stream creator: pradler date_created: 2023-07-25T06:56:54Z date_updated: 2023-07-25T06:56:54Z file_id: '13299' file_name: TIRF_FtsZ WT 1.15µM.7z.001 file_size: 1292391225 relation: main_file success: 1 - access_level: open_access checksum: ba59f4e3f062b378f45e579ec28898ce content_type: application/octet-stream creator: pradler date_created: 2023-07-25T08:25:07Z date_updated: 2023-07-25T08:25:07Z file_id: '13305' file_name: TIRF_FtsZ WT 1.25µM.7z.001 file_size: 4494279051 relation: main_file success: 1 - access_level: open_access checksum: 906e1fe2aaacd1a746c49ffe39bcca66 content_type: application/octet-stream creator: pradler date_created: 2023-07-25T08:12:32Z date_updated: 2023-07-25T08:12:32Z file_id: '13303' file_name: TIRF_FtsZ WT 1.50µM.7z.001 file_size: 4697620480 relation: main_file success: 1 - access_level: open_access checksum: 96e416494b129cb0139c8250246bfaff content_type: application/octet-stream creator: pradler date_created: 2023-07-25T08:18:54Z date_updated: 2023-07-25T08:18:54Z file_id: '13304' file_name: TIRF_FtsZ WT 1.50µM.7z.002 file_size: 3548897162 relation: main_file success: 1 - access_level: open_access checksum: f1dfdee3d833cf8d2c6b3ecbbee566f3 content_type: application/octet-stream creator: pradler date_created: 2023-07-25T06:59:59Z date_updated: 2023-07-25T06:59:59Z file_id: '13300' file_name: TIRF_FtsZ WT 2.0µM.7z.001 file_size: 1472947913 relation: main_file success: 1 - access_level: open_access checksum: fe77296c7bfce8b95a67ecbbb07ced81 content_type: application/octet-stream creator: pradler date_created: 2023-07-25T07:05:40Z date_updated: 2023-07-25T07:05:40Z file_id: '13301' file_name: TIRF_FtsZ WT 3.0µM.7z.001 file_size: 1993549431 relation: main_file success: 1 - access_level: open_access checksum: 6bc6edb807f38b00528875b4e7070bbf content_type: application/octet-stream creator: pradler date_created: 2023-07-25T07:06:07Z date_updated: 2023-07-25T07:06:07Z file_id: '13302' file_name: TIRF_FtsZ WT 5.0µM.7z.001 file_size: 1336984015 relation: main_file success: 1 - access_level: open_access checksum: e46bbe73e90dc56e245ecda464930009 content_type: application/octet-stream creator: pradler date_created: 2023-07-24T12:10:55Z date_updated: 2023-07-24T12:10:55Z file_id: '13281' file_name: STED experiments.7z.001 file_size: 227620212 relation: main_file success: 1 - access_level: open_access checksum: 473aa9f1c097b8b03294b1f6d4f4aa04 content_type: application/octet-stream creator: pradler date_created: 2023-07-25T09:16:06Z date_updated: 2023-07-25T09:16:06Z file_id: '13307' file_name: AFM_FtsZ WT.7z.001 file_size: 3433349230 relation: main_file success: 1 - access_level: open_access checksum: bc685a414d95bcd5bba4dcad0187e928 content_type: application/octet-stream creator: pradler date_created: 2023-07-24T12:11:54Z date_updated: 2023-07-24T12:11:54Z file_id: '13282' file_name: TIRF_FtsZ WT and L169R intensity calibration.7z.001 file_size: 1416013335 relation: main_file success: 1 - access_level: open_access checksum: e6cac262a3cf5a6a45bf28edf1dac8cd content_type: application/octet-stream creator: pradler date_created: 2023-07-24T12:26:12Z date_updated: 2023-07-24T12:26:12Z file_id: '13285' file_name: TIRF_FtsZ L169R below 0.6µM.7z file_size: 2711456292 relation: main_file success: 1 - access_level: open_access checksum: 755179b242a7a4ee03133a15c5eab4ce content_type: application/octet-stream creator: pradler date_created: 2023-07-24T19:19:25Z date_updated: 2023-07-24T19:19:25Z file_id: '13296' file_name: TIRF_FtsZ L169R 0.625µM.7z file_size: 2272169467 relation: main_file success: 1 - access_level: open_access checksum: 7179ce242938a688381d7126b9a7ec45 content_type: application/octet-stream creator: pradler date_created: 2023-07-24T13:02:04Z date_updated: 2023-07-24T13:02:04Z file_id: '13287' file_name: TIRF_FtsZ L169R 0.900µM.7z file_size: 2915542985 relation: main_file success: 1 - access_level: open_access checksum: a808996cbca0f795e00de85f1922b497 content_type: application/octet-stream creator: pradler date_created: 2023-07-24T15:27:17Z date_updated: 2023-07-24T15:27:17Z file_id: '13294' file_name: TIRF_FtsZ L169R 1.15µM.7z file_size: 2769959727 relation: main_file success: 1 - access_level: open_access checksum: 9a42594d749e648a099fefd3e24108a8 content_type: application/octet-stream creator: pradler date_created: 2023-07-24T19:22:29Z date_updated: 2023-07-24T19:22:29Z file_id: '13297' file_name: TIRF_FtsZ L169R 1.25uM.7z file_size: 4440142247 relation: main_file success: 1 - access_level: open_access checksum: d8df3e458dbdb83622ab4dd6c9313a4e content_type: application/octet-stream creator: pradler date_created: 2023-07-24T15:27:09Z date_updated: 2023-07-24T15:27:09Z file_id: '13295' file_name: TIRF_FtsZ L169R 1.50µM.7z file_size: 2727119370 relation: main_file success: 1 - access_level: open_access checksum: 020db3ef1d1cbfb3cbe5bf49d6669849 content_type: application/octet-stream creator: pradler date_created: 2023-07-24T12:12:41Z date_updated: 2023-07-24T12:12:41Z file_id: '13283' file_name: TIRF_FtsZ L169R 2.0µM.7z file_size: 1479677783 relation: main_file success: 1 - access_level: open_access checksum: 22f2aa112442fb767c0a58876d974ab0 content_type: application/octet-stream creator: pradler date_created: 2023-07-24T12:13:51Z date_updated: 2023-07-24T12:13:51Z file_id: '13284' file_name: TIRF_FtsZ L169R 3.0µM.7z file_size: 1560846342 relation: main_file success: 1 - access_level: open_access checksum: 6fac58e020d7b30092945cb210100670 content_type: application/octet-stream creator: pradler date_created: 2023-07-25T09:12:45Z date_updated: 2023-07-25T09:12:45Z file_id: '13308' file_name: AFM_FtsZ L169R.7z.001 file_size: 2918160653 relation: main_file success: 1 - access_level: open_access checksum: 3cdbf4a61857cb940439473c999bdfa6 content_type: text/csv creator: mloose date_created: 2023-08-03T19:50:52Z date_updated: 2023-08-03T19:50:52Z file_id: '13947' file_name: EDFig4p_F5.csv file_size: 77476061 relation: main_file success: 1 - access_level: open_access checksum: a59d5b825b4fe830cdb8833b4851508d content_type: text/csv creator: mloose date_created: 2023-08-03T19:50:50Z date_updated: 2023-08-03T19:50:50Z file_id: '13948' file_name: EDFig4p_F40.csv file_size: 74938608 relation: main_file success: 1 - access_level: open_access checksum: fe40a48ed7708260557faa1e7e8687d4 content_type: text/csv creator: mloose date_created: 2023-08-03T19:51:14Z date_updated: 2023-08-03T19:51:14Z file_id: '13949' file_name: EDFig4p_F200.csv file_size: 81680327 relation: main_file success: 1 - access_level: open_access checksum: 30bebf102f03445445f3dd3c19209497 content_type: text/csv creator: mloose date_created: 2023-08-03T19:51:45Z date_updated: 2023-08-03T19:51:45Z file_id: '13950' file_name: Fig3a_4b_F40.csv file_size: 169151538 relation: main_file success: 1 - access_level: open_access checksum: 29db5611c9e622710fbf7b1c83c621ec content_type: text/csv creator: mloose date_created: 2023-08-03T19:51:45Z date_updated: 2023-08-03T19:51:45Z file_id: '13951' file_name: Fig3a_F5.csv file_size: 94791496 relation: main_file success: 1 - access_level: open_access checksum: 848456b4230c086e8999f57d57dba7f1 content_type: text/csv creator: mloose date_created: 2023-08-03T19:51:54Z date_updated: 2023-08-03T19:51:54Z file_id: '13952' file_name: Fig3a_F200.csv file_size: 59166206 relation: main_file success: 1 file_date_updated: 2023-08-08T11:17:28Z has_accepted_license: '1' month: '07' oa: 1 oa_version: Published Version project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d grant_number: P34607 name: "Understanding bacterial cell division by in vitro\r\nreconstitution" - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publisher: Institute of Science and Technology Austria related_material: record: - id: '13314' relation: used_in_publication status: public status: public title: Chiral and nematic phases of flexible active filaments tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14613' abstract: - lang: eng text: 'Many insects carry an ancient X chromosome - the Drosophila Muller element F - that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 MY. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of a long overlooked sister-order to Diptera: Mecoptera. We compare the scorpionfly Panorpa cognata X-chromosome gene content, expression, and structure, to that of several dipteran species as well as more distantly-related insect orders (Orthoptera and Blattodea). We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the two homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.' acknowledged_ssus: - _id: ScienComp acknowledgement: "We thank the Vicoso lab for their assistance with specimen collection, and Tim Connallon for valuable comments and suggestions on earlier versions of the manuscript. Computational resources and support were provided by the Scientific Computing unit at the ISTA. This research was supported by grants from the Austrian Science Foundation to C.L.\r\n(FWF ESP 39), and to B.V. (FWF SFB F88-10)." article_number: msad245 article_processing_charge: Yes (via OA deal) article_type: original author: - first_name: Clementine full_name: Lasne, Clementine id: 02225f57-50d2-11eb-9ed8-8c92b9a34237 last_name: Lasne orcid: 0000-0002-1197-8616 - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 - first_name: Melissa A full_name: Toups, Melissa A id: 4E099E4E-F248-11E8-B48F-1D18A9856A87 last_name: Toups orcid: 0000-0002-9752-7380 - first_name: Lorena Alexandra full_name: Layana Franco, Lorena Alexandra id: 02814589-eb8f-11eb-b029-a70074f3f18f last_name: Layana Franco orcid: 0000-0002-1253-6297 - first_name: Ariana full_name: Macon, Ariana id: 2A0848E2-F248-11E8-B48F-1D18A9856A87 last_name: Macon - first_name: Beatriz full_name: Vicoso, Beatriz id: 49E1C5C6-F248-11E8-B48F-1D18A9856A87 last_name: Vicoso orcid: 0000-0002-4579-8306 citation: ama: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 2023;40(12). doi:10.1093/molbev/msad245 apa: Lasne, C., Elkrewi, M. N., Toups, M. A., Layana Franco, L. A., Macon, A., & Vicoso, B. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. Oxford University Press. https://doi.org/10.1093/molbev/msad245 chicago: Lasne, Clementine, Marwan N Elkrewi, Melissa A Toups, Lorena Alexandra Layana Franco, Ariana Macon, and Beatriz Vicoso. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular Biology and Evolution. Oxford University Press, 2023. https://doi.org/10.1093/molbev/msad245. ieee: C. Lasne, M. N. Elkrewi, M. A. Toups, L. A. Layana Franco, A. Macon, and B. Vicoso, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome,” Molecular Biology and Evolution, vol. 40, no. 12. Oxford University Press, 2023. ista: Lasne C, Elkrewi MN, Toups MA, Layana Franco LA, Macon A, Vicoso B. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Molecular Biology and Evolution. 40(12), msad245. mla: Lasne, Clementine, et al. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Molecular Biology and Evolution, vol. 40, no. 12, msad245, Oxford University Press, 2023, doi:10.1093/molbev/msad245. short: C. Lasne, M.N. Elkrewi, M.A. Toups, L.A. Layana Franco, A. Macon, B. Vicoso, Molecular Biology and Evolution 40 (2023). date_created: 2023-11-27T16:14:37Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-02-21T12:18:35Z day: '01' ddc: - '570' department: - _id: BeVi doi: 10.1093/molbev/msad245 external_id: pmid: - '37988296' file: - access_level: open_access checksum: 47c1c72fb499f26ea52d216b242208c8 content_type: application/pdf creator: dernst date_created: 2024-01-02T11:39:38Z date_updated: 2024-01-02T11:39:38Z file_id: '14727' file_name: 2023_MolecularBioEvo_Lasne.pdf file_size: 8623505 relation: main_file success: 1 file_date_updated: 2024-01-02T11:39:38Z has_accepted_license: '1' intvolume: ' 40' issue: '12' keyword: - Genetics - Molecular Biology - Ecology - Evolution - Behavior and Systematics language: - iso: eng month: '12' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 34ae1506-11ca-11ed-8bc3-c14f4c474396 grant_number: F8810 name: The highjacking of meiosis for asexual reproduction - _id: ebb230e0-77a9-11ec-83b8-87a37e0241d3 grant_number: ESP39 49461 name: Mechanisms and Evolution of Reproductive Plasticity publication: Molecular Biology and Evolution publication_identifier: eissn: - 1537-1719 issn: - 0737-4038 publication_status: published publisher: Oxford University Press quality_controlled: '1' related_material: link: - description: News on ISTA webpage relation: press_release url: https://ista.ac.at/en/news/on-the-hunt/ record: - id: '14614' relation: research_data status: public scopus_import: '1' status: public title: The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 40 year: '2023' ... --- _id: '13314' abstract: - lang: eng text: The emergence of large-scale order in self-organized systems relies on local interactions between individual components. During bacterial cell division, FtsZ—a prokaryotic homologue of the eukaryotic protein tubulin—polymerizes into treadmilling filaments that further organize into a cytoskeletal ring. In vitro, FtsZ filaments can form dynamic chiral assemblies. However, how the active and passive properties of individual filaments relate to these large-scale self-organized structures remains poorly understood. Here we connect single-filament properties with the mesoscopic scale by combining minimal active matter simulations and biochemical reconstitution experiments. We show that the density and flexibility of active chiral filaments define their global order. At intermediate densities, curved, flexible filaments organize into chiral rings and polar bands. An effectively nematic organization dominates for high densities and for straight, mutant filaments with increased rigidity. Our predicted phase diagram quantitatively captures these features, demonstrating how the flexibility, density and chirality of the active filaments affect their collective behaviour. Our findings shed light on the fundamental properties of active chiral matter and explain how treadmilling FtsZ filaments organize during bacterial cell division. acknowledged_ssus: - _id: Bio - _id: LifeSc acknowledgement: 'This work was supported by the European Research Council through grant ERC 2015-StG-679239 and by the Austrian Science Fund (FWF) StandAlone P34607 to M.L., B. P.M. was also supported by the Kanazawa University WPI- NanoLSI Bio-SPM collaborative research program. Z.D. has received funding from Doctoral Programme of the Austrian Academy of Sciences (OeAW): Grant agreement 26360. We thank Jan Brugues (MPI CBG, Dresden, Germany), Andela Saric (ISTA, Klosterneuburg, Austria), Daniel Pearce (Uni Geneva, Switzerland) for valuable scientific input and comments on the manuscript. We are also thankful for the support by the Scientific Service Units (SSU) of IST Austria through resources provided by the Imaging and Optics Facility (IOF) and the Lab Support Facility (LSF).' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Zuzana full_name: Dunajova, Zuzana id: 4B39F286-F248-11E8-B48F-1D18A9856A87 last_name: Dunajova - first_name: Batirtze full_name: Prats Mateu, Batirtze id: 299FE892-F248-11E8-B48F-1D18A9856A87 last_name: Prats Mateu - first_name: Philipp full_name: Radler, Philipp id: 40136C2A-F248-11E8-B48F-1D18A9856A87 last_name: Radler orcid: '0000-0001-9198-2182 ' - first_name: Keesiang full_name: Lim, Keesiang last_name: Lim - first_name: Dörte full_name: Brandis, Dörte id: 21d64d35-f128-11eb-9611-b8bcca7a12fd last_name: Brandis - first_name: Philipp full_name: Velicky, Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 - first_name: Richard W. full_name: Wong, Richard W. last_name: Wong - first_name: Jens full_name: Elgeti, Jens last_name: Elgeti - first_name: Edouard B full_name: Hannezo, Edouard B id: 3A9DB764-F248-11E8-B48F-1D18A9856A87 last_name: Hannezo orcid: 0000-0001-6005-1561 - first_name: Martin full_name: Loose, Martin id: 462D4284-F248-11E8-B48F-1D18A9856A87 last_name: Loose orcid: 0000-0001-7309-9724 citation: ama: Dunajova Z, Prats Mateu B, Radler P, et al. Chiral and nematic phases of flexible active filaments. Nature Physics. 2023;19:1916-1926. doi:10.1038/s41567-023-02218-w apa: Dunajova, Z., Prats Mateu, B., Radler, P., Lim, K., Brandis, D., Velicky, P., … Loose, M. (2023). Chiral and nematic phases of flexible active filaments. Nature Physics. Springer Nature. https://doi.org/10.1038/s41567-023-02218-w chicago: Dunajova, Zuzana, Batirtze Prats Mateu, Philipp Radler, Keesiang Lim, Dörte Brandis, Philipp Velicky, Johann G Danzl, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics. Springer Nature, 2023. https://doi.org/10.1038/s41567-023-02218-w. ieee: Z. Dunajova et al., “Chiral and nematic phases of flexible active filaments,” Nature Physics, vol. 19. Springer Nature, pp. 1916–1926, 2023. ista: Dunajova Z, Prats Mateu B, Radler P, Lim K, Brandis D, Velicky P, Danzl JG, Wong RW, Elgeti J, Hannezo EB, Loose M. 2023. Chiral and nematic phases of flexible active filaments. Nature Physics. 19, 1916–1926. mla: Dunajova, Zuzana, et al. “Chiral and Nematic Phases of Flexible Active Filaments.” Nature Physics, vol. 19, Springer Nature, 2023, pp. 1916–26, doi:10.1038/s41567-023-02218-w. short: Z. Dunajova, B. Prats Mateu, P. Radler, K. Lim, D. Brandis, P. Velicky, J.G. Danzl, R.W. Wong, J. Elgeti, E.B. Hannezo, M. Loose, Nature Physics 19 (2023) 1916–1926. date_created: 2023-07-27T14:44:45Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-02-21T12:19:08Z day: '01' ddc: - '530' department: - _id: JoDa - _id: EdHa - _id: MaLo - _id: GradSch doi: 10.1038/s41567-023-02218-w ec_funded: 1 external_id: pmid: - '38075437' file: - access_level: open_access checksum: bc7673ca07d37309013a86166577b2f7 content_type: application/pdf creator: dernst date_created: 2024-01-30T14:28:30Z date_updated: 2024-01-30T14:28:30Z file_id: '14916' file_name: 2023_NaturePhysics_Dunajova.pdf file_size: 22471673 relation: main_file success: 1 file_date_updated: 2024-01-30T14:28:30Z has_accepted_license: '1' intvolume: ' 19' language: - iso: eng month: '12' oa: 1 oa_version: Published Version page: 1916-1926 pmid: 1 project: - _id: 2595697A-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '679239' name: Self-Organization of the Bacterial Cell - _id: fc38323b-9c52-11eb-aca3-ff8afb4a011d grant_number: P34607 name: "Understanding bacterial cell division by in vitro\r\nreconstitution" - _id: 34d75525-11ca-11ed-8bc3-89b6307fee9d grant_number: '26360' name: Motile active matter models of migrating cells and chiral filaments publication: Nature Physics publication_identifier: eissn: - 1745-2481 issn: - 1745-2473 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '13116' relation: research_data status: public scopus_import: '1' status: public title: Chiral and nematic phases of flexible active filaments tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 19 year: '2023' ... --- _id: '14257' abstract: - lang: eng text: Mapping the complex and dense arrangement of cells and their connectivity in brain tissue demands nanoscale spatial resolution imaging. Super-resolution optical microscopy excels at visualizing specific molecules and individual cells but fails to provide tissue context. Here we developed Comprehensive Analysis of Tissues across Scales (CATS), a technology to densely map brain tissue architecture from millimeter regional to nanometer synaptic scales in diverse chemically fixed brain preparations, including rodent and human. CATS uses fixation-compatible extracellular labeling and optical imaging, including stimulated emission depletion or expansion microscopy, to comprehensively delineate cellular structures. It enables three-dimensional reconstruction of single synapses and mapping of synaptic connectivity by identification and analysis of putative synaptic cleft regions. Applying CATS to the mouse hippocampal mossy fiber circuitry, we reconstructed and quantified the synaptic input and output structure of identified neurons. We furthermore demonstrate applicability to clinically derived human tissue samples, including formalin-fixed paraffin-embedded routine diagnostic specimens, for visualizing the cellular architecture of brain tissue in health and disease. acknowledged_ssus: - _id: ScienComp - _id: Bio - _id: PreCl - _id: LifeSc - _id: M-Shop - _id: E-Lib acknowledgement: 'We thank J. Vorlaufer, N. Agudelo-Dueñas, W. Jahr and A. Wartak for microscope maintenance and troubleshooting; C. Kreuzinger, A. Freeman and I. Erber for technical assistance; and M. Tomschik for support with obtaining human samples. We gratefully acknowledge E. Miguel for setting up webKnossos and M. Šuplata for computational support and hardware control. We are grateful to R. Shigemoto and B. Bickel for generous support and M. Sixt and S. Boyd (Stanford University) for discussions and critical reading of the paper. PSD95-HaloTag mice were kindly provided by S. Grant (University of Edinburgh). We acknowledge expert support by Institute of Science and Technology Austria’s scientific computing, imaging and optics, preclinical and lab support facilities and by the Miba machine shop and library. We gratefully acknowledge funding by the following sources: Austrian Science Fund (FWF) grant I3600-B27 (J.G.D.); Austrian Science Fund (FWF) grant DK W1232 (J.G.D. and J.M.M.); Austrian Science Fund (FWF) grant Z 312-B27, Wittgenstein award (P.J.); Austrian Science Fund (FWF) projects I4685-B, I6565-B (SYNABS) and DOC 33-B27 (R.H.); Gesellschaft für Forschungsförderung NÖ (NFB) grant LSC18-022 (J.G.D.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 715508 – REVERSEAUTISM (G.N.); European Union’s Horizon 2020 research and innovation programme, European Research Council (ERC) grant 692692 – GIANTSYN (P.J.); Marie Skłodowska-Curie Actions Fellowship GA no. 665385 under the EU Horizon 2020 program (J.M.M. and J.L.); and Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.).' article_processing_charge: Yes (in subscription journal) article_type: original author: - first_name: Julia M full_name: Michalska, Julia M id: 443DB6DE-F248-11E8-B48F-1D18A9856A87 last_name: Michalska orcid: 0000-0003-3862-1235 - first_name: Julia full_name: Lyudchik, Julia id: 46E28B80-F248-11E8-B48F-1D18A9856A87 last_name: Lyudchik - first_name: Philipp full_name: Velicky, Philipp id: 39BDC62C-F248-11E8-B48F-1D18A9856A87 last_name: Velicky orcid: 0000-0002-2340-7431 - first_name: Hana full_name: Korinkova, Hana id: ee3cb6ca-ec98-11ea-ae11-ff703e2254ed last_name: Korinkova - first_name: Jake full_name: Watson, Jake id: 63836096-4690-11EA-BD4E-32803DDC885E last_name: Watson orcid: 0000-0002-8698-3823 - first_name: Alban full_name: Cenameri, Alban id: 9ac8f577-2357-11eb-997a-e566c5550886 last_name: Cenameri - first_name: Christoph M full_name: Sommer, Christoph M id: 4DF26D8C-F248-11E8-B48F-1D18A9856A87 last_name: Sommer orcid: 0000-0003-1216-9105 - first_name: Nicole full_name: Amberg, Nicole id: 4CD6AAC6-F248-11E8-B48F-1D18A9856A87 last_name: Amberg orcid: 0000-0002-3183-8207 - first_name: Alessandro full_name: Venturino, Alessandro id: 41CB84B2-F248-11E8-B48F-1D18A9856A87 last_name: Venturino orcid: 0000-0003-2356-9403 - first_name: Karl full_name: Roessler, Karl last_name: Roessler - first_name: Thomas full_name: Czech, Thomas last_name: Czech - first_name: Romana full_name: Höftberger, Romana last_name: Höftberger - first_name: Sandra full_name: Siegert, Sandra id: 36ACD32E-F248-11E8-B48F-1D18A9856A87 last_name: Siegert orcid: 0000-0001-8635-0877 - first_name: Gaia full_name: Novarino, Gaia id: 3E57A680-F248-11E8-B48F-1D18A9856A87 last_name: Novarino orcid: 0000-0002-7673-7178 - first_name: Peter M full_name: Jonas, Peter M id: 353C1B58-F248-11E8-B48F-1D18A9856A87 last_name: Jonas orcid: 0000-0001-5001-4804 - first_name: Johann G full_name: Danzl, Johann G id: 42EFD3B6-F248-11E8-B48F-1D18A9856A87 last_name: Danzl orcid: 0000-0001-8559-3973 citation: ama: Michalska JM, Lyudchik J, Velicky P, et al. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. 2023. doi:10.1038/s41587-023-01911-8 apa: Michalska, J. M., Lyudchik, J., Velicky, P., Korinkova, H., Watson, J., Cenameri, A., … Danzl, J. G. (2023). Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. Springer Nature. https://doi.org/10.1038/s41587-023-01911-8 chicago: Michalska, Julia M, Julia Lyudchik, Philipp Velicky, Hana Korinkova, Jake Watson, Alban Cenameri, Christoph M Sommer, et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology. Springer Nature, 2023. https://doi.org/10.1038/s41587-023-01911-8. ieee: J. M. Michalska et al., “Imaging brain tissue architecture across millimeter to nanometer scales,” Nature Biotechnology. Springer Nature, 2023. ista: Michalska JM, Lyudchik J, Velicky P, Korinkova H, Watson J, Cenameri A, Sommer CM, Amberg N, Venturino A, Roessler K, Czech T, Höftberger R, Siegert S, Novarino G, Jonas PM, Danzl JG. 2023. Imaging brain tissue architecture across millimeter to nanometer scales. Nature Biotechnology. mla: Michalska, Julia M., et al. “Imaging Brain Tissue Architecture across Millimeter to Nanometer Scales.” Nature Biotechnology, Springer Nature, 2023, doi:10.1038/s41587-023-01911-8. short: J.M. Michalska, J. Lyudchik, P. Velicky, H. Korinkova, J. Watson, A. Cenameri, C.M. Sommer, N. Amberg, A. Venturino, K. Roessler, T. Czech, R. Höftberger, S. Siegert, G. Novarino, P.M. Jonas, J.G. Danzl, Nature Biotechnology (2023). date_created: 2023-09-03T22:01:15Z date_published: 2023-08-31T00:00:00Z date_updated: 2024-02-21T12:18:18Z day: '31' department: - _id: SaSi - _id: GaNo - _id: PeJo - _id: JoDa - _id: Bio - _id: RySh doi: 10.1038/s41587-023-01911-8 ec_funded: 1 external_id: isi: - '001065254200001' isi: 1 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1038/s41587-023-01911-8 month: '08' oa: 1 oa_version: Published Version project: - _id: 265CB4D0-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: I03600 name: Optical control of synaptic function via adhesion molecules - _id: 2548AE96-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: W1232-B24 name: Molecular Drug Targets - _id: 25C5A090-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z00312 name: The Wittgenstein Prize - _id: 23889792-32DE-11EA-91FC-C7463DDC885E name: High content imaging to decode human immune cell interactions in health and allergic disease - _id: 25444568-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '715508' name: Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models - _id: 25B7EB9E-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '692692' name: Biophysics and circuit function of a giant cortical glumatergic synapse - _id: 2564DBCA-B435-11E9-9278-68D0E5697425 call_identifier: H2020 grant_number: '665385' name: International IST Doctoral Program - _id: fc2be41b-9c52-11eb-aca3-faa90aa144e9 call_identifier: H2020 grant_number: '101026635' name: Synaptic computations of the hippocampal CA3 circuitry publication: Nature Biotechnology publication_identifier: eissn: - 1546-1696 issn: - 1087-0156 publication_status: epub_ahead publisher: Springer Nature quality_controlled: '1' related_material: link: - relation: software url: https://github.com/danzllab/CATS record: - id: '13126' relation: research_data status: public scopus_import: '1' status: public title: Imaging brain tissue architecture across millimeter to nanometer scales type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14614' abstract: - lang: eng text: 'Many insects carry an ancient X chromosome—the Drosophila Muller element F—that likely predates their origin. Interestingly, the X has undergone turnover in multiple fly species (Diptera) after being conserved for more than 450 My. The long evolutionary distance between Diptera and other sequenced insect clades makes it difficult to infer what could have contributed to this sudden increase in rate of turnover. Here, we produce the first genome and transcriptome of scorpionflies (genus Panorpa), an insect belonging to a long overlooked sister-order to Diptera: Mecoptera. Combining our genome assembly with genomic short-read data, we obtain genome coverage and identify X-linked super-scaffolds. We further perform a gene homology analysis between the Panorpa X and a closely related Diptera species, and we assess the conservation of the Panorpa X-linked gene content with that of more distantly related insect species. We explored the structure of the Panorpa X by determining its repeat content, GC content, and nucleotide diversity. Finally, we used RNAseq data to detect the presence of dosage compensation in somatic tissues, as well as to explore gene expression tissue-specificity, and sex-bias in gene expression. We find high conservation of gene content between the mecopteran X and the dipteran Muller F element, as well as several shared biological features, such as the presence of dosage compensation and a low amount of genetic diversity, consistent with a low recombination rate. However, the 2 homologous X chromosomes differ strikingly in their size and number of genes they carry. Our results therefore support a common ancestry of the mecopteran and ancestral dipteran X chromosomes, and suggest that Muller element F shrank in size and gene content after the split of Diptera and Mecoptera, which may have contributed to its turnover in dipteran insects.' article_processing_charge: No author: - first_name: Clementine full_name: Lasne, Clementine id: 02225f57-50d2-11eb-9ed8-8c92b9a34237 last_name: Lasne orcid: 0000-0002-1197-8616 - first_name: Marwan N full_name: Elkrewi, Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 citation: ama: Lasne C, Elkrewi MN. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. 2023. doi:10.15479/AT:ISTA:14614 apa: Lasne, C., & Elkrewi, M. N. (2023). The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome. Institute of Science and Technology Austria. https://doi.org/10.15479/AT:ISTA:14614 chicago: Lasne, Clementine, and Marwan N Elkrewi. “The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:14614. ieee: C. Lasne and M. N. Elkrewi, “The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome.” Institute of Science and Technology Austria, 2023. ista: Lasne C, Elkrewi MN. 2023. The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome, Institute of Science and Technology Austria, 10.15479/AT:ISTA:14614. mla: Lasne, Clementine, and Marwan N. Elkrewi. The Scorpionfly (Panorpa Cognata) Genome Highlights Conserved and Derived Features of the Peculiar Dipteran X Chromosome. Institute of Science and Technology Austria, 2023, doi:10.15479/AT:ISTA:14614. short: C. Lasne, M.N. Elkrewi, (2023). contributor: - contributor_type: researcher first_name: Marwan N id: 0B46FACA-A8E1-11E9-9BD3-79D1E5697425 last_name: Elkrewi orcid: 0000-0002-5328-7231 date_created: 2023-11-27T16:39:19Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-02-21T12:18:35Z day: '01' ddc: - '576' department: - _id: BeVi doi: 10.15479/AT:ISTA:14614 file: - access_level: open_access checksum: cd0f13322b5156819ecaebd2bc8e7d12 content_type: application/zip creator: clasne date_created: 2023-11-28T13:15:26Z date_updated: 2023-11-28T13:15:26Z file_id: '14625' file_name: panorpaX.zip file_size: 404968272 relation: main_file success: 1 - access_level: open_access checksum: 9ff600416577687a737cb3c96dfcb26c content_type: text/plain creator: clasne date_created: 2023-11-30T14:16:59Z date_updated: 2023-11-30T14:16:59Z file_id: '14634' file_name: panorpa_readme.txt file_size: 2625 relation: main_file success: 1 file_date_updated: 2023-11-30T14:16:59Z has_accepted_license: '1' keyword: - Panorpa - scorpionfly - genome - transcriptome month: '12' oa: 1 oa_version: Published Version publisher: Institute of Science and Technology Austria related_material: record: - id: '14613' relation: used_in_publication status: public status: public title: The scorpionfly (Panorpa cognata) genome highlights conserved and derived features of the peculiar dipteran X chromosome tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13286' abstract: - lang: eng text: Semiconductor-superconductor hybrid systems are the harbour of many intriguing mesoscopic phenomena. This material combination leads to spatial variations of the superconducting properties, which gives rise to Andreev bound states (ABSs). Some of these states might exhibit remarkable properties that render them highly desirable for topological quantum computing. The most prominent and hunted of such states are Majorana zero modes (MZMs), quasiparticles equals to their own quasiparticles that they follow non-abelian statistics. In this thesis, we first introduce the general framework of such hybrid systems and, then, we unveil a series of mesoscopic phenomena that we discovered. Firstly, we show tunneling spectroscopy experiments on full-shell nanowires (NWs) showing that unwanted quantum-dot states coupled to superconductors (Yu-Shiba-Rusinov states) can mimic MZMs signatures. Then, we introduce a novel protocol which allowed the integration of tunneling spectroscopy with Coulomb spectroscopy within the same device. Employing this approach on both full-shell NWs and partial-shell NWs, we demonstrated that longitudinally confined states reveal charge transport phenomenology similar to the one expected for MZMs. These findings shed light on the intricate interplay between superconductivity and quantum confinement, which brought us to explore another material platform, i.e. a two-dimensional Germanium hole gas. After developing a robust way to induce superconductivity in such system, we showed how to engineer the proximity effect and we revealed a superconducting hard gap. Finally, we created a superconducting radio frequency driven ideal diode and a generator of non-sinusoidal current-phase relations. Our results open the path for the exploration of protected superconducting qubits and more complex hybrid devices in planar Germanium, like Kitaev chains and hybrid qubit devices. acknowledged_ssus: - _id: NanoFab - _id: M-Shop alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Marco full_name: Valentini, Marco id: C0BB2FAC-D767-11E9-B658-BC13E6697425 last_name: Valentini citation: ama: 'Valentini M. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. 2023. doi:10.15479/at:ista:13286' apa: 'Valentini, M. (2023). Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria. https://doi.org/10.15479/at:ista:13286' chicago: 'Valentini, Marco. “Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/at:ista:13286.' ieee: 'M. Valentini, “Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium,” Institute of Science and Technology Austria, 2023.' ista: 'Valentini M. 2023. Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium. Institute of Science and Technology Austria.' mla: 'Valentini, Marco. Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium. Institute of Science and Technology Austria, 2023, doi:10.15479/at:ista:13286.' short: 'M. Valentini, Mesoscopic Phenomena in Hybrid Semiconductor-Superconductor Nanodevices : From Full-Shell Nanowires to Two-Dimensional Hole Gas in Germanium, Institute of Science and Technology Austria, 2023.' date_created: 2023-07-24T14:10:45Z date_published: 2023-07-21T00:00:00Z date_updated: 2024-02-21T12:35:34Z day: '21' ddc: - '530' degree_awarded: PhD department: - _id: GradSch - _id: GeKa doi: 10.15479/at:ista:13286 ec_funded: 1 file: - access_level: closed checksum: 666ee31c7eade89679806287c062fa14 content_type: application/x-zip-compressed creator: mvalenti date_created: 2023-08-11T09:27:39Z date_updated: 2023-08-11T10:01:34Z file_id: '14033' file_name: PhD_thesis_Valentini_final.zip file_size: 56121429 relation: source_file - access_level: open_access checksum: 0992f2ebef152dee8e70055350ebbb55 content_type: application/pdf creator: mvalenti date_created: 2023-08-11T14:39:17Z date_updated: 2023-08-11T14:39:17Z file_id: '14035' file_name: PhD_thesis_Valentini_final_validated.pdf file_size: 38199711 relation: main_file file_date_updated: 2023-08-11T14:39:17Z has_accepted_license: '1' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: '184' project: - _id: 262116AA-B435-11E9-9278-68D0E5697425 name: Hybrid Semiconductor - Superconductor Quantum Devices - _id: 237E5020-32DE-11EA-91FC-C7463DDC885E call_identifier: H2020 grant_number: '862046' name: TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS - _id: 34a66131-11ca-11ed-8bc3-a31681c6b03e grant_number: F8606 name: Conventional and unconventional topological superconductors publication_identifier: issn: - 2663 - 337X publication_status: published publisher: Institute of Science and Technology Austria related_material: record: - id: '13312' relation: part_of_dissertation status: public - id: '12118' relation: part_of_dissertation status: public - id: '8910' relation: part_of_dissertation status: public - id: '12522' relation: research_data status: public status: public supervisor: - first_name: Georgios full_name: Katsaros, Georgios id: 38DB5788-F248-11E8-B48F-1D18A9856A87 last_name: Katsaros orcid: 0000-0001-8342-202X title: 'Mesoscopic phenomena in hybrid semiconductor-superconductor nanodevices : From full-shell nanowires to two-dimensional hole gas in germanium' tmp: image: /images/cc_by_nc_sa.png legal_code_url: https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode name: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0) short: CC BY-NC-SA (4.0) type: dissertation user_id: 8b945eb4-e2f2-11eb-945a-df72226e66a9 year: '2023' ... --- _id: '15027' abstract: - lang: eng text: 'This data repository underpins the paper, published in PNAS (doi pending) and bioarxiv (doi: https://doi.org/10.1101/2023.07.05.547777).' article_processing_charge: No author: - first_name: Samo full_name: Curk, Samo id: 031eff0d-d481-11ee-8508-cd12a7a86e5b last_name: Curk orcid: 0000-0001-6160-9766 citation: ama: Curk S. aggregation_data. 2023. apa: Curk, S. (2023). aggregation_data. Figshare. chicago: Curk, Samo. “Aggregation_data.” Figshare, 2023. ieee: S. Curk, “aggregation_data.” Figshare, 2023. ista: Curk S. 2023. aggregation_data, Figshare. mla: Curk, Samo. Aggregation_data. Figshare, 2023. short: S. Curk, (2023). date_created: 2024-02-26T08:37:57Z date_published: 2023-12-13T00:00:00Z date_updated: 2024-02-26T08:45:55Z day: '13' ddc: - '570' department: - _id: AnSa has_accepted_license: '1' license: https://creativecommons.org/publicdomain/zero/1.0/ main_file_link: - open_access: '1' url: https://figshare.com/s/85798bba4ebc68d822ed month: '12' oa: 1 oa_version: Published Version publisher: Figshare related_material: record: - id: '15001' relation: used_in_publication status: public status: public title: aggregation_data tmp: image: /images/cc_0.png legal_code_url: https://creativecommons.org/publicdomain/zero/1.0/legalcode name: Creative Commons Public Domain Dedication (CC0 1.0) short: CC0 (1.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14758' abstract: - lang: eng text: 'We present a flexible and efficient toolchain to symbolically solve (standard) Rabin games, fair-adversarial Rabin games, and 2 1/2 license type-player Rabin games. To our best knowledge, our tools are the first ones to be able to solve these problems. Furthermore, using these flexible game solvers as a back-end, we implemented a tool for computing correct-by-construction controllers for stochastic dynamical systems under LTL specifications. Our implementations use the recent theoretical result that all of these games can be solved using the same symbolic fixpoint algorithm but utilizing different, domain specific calculations of the involved predecessor operators. The main feature of our toolchain is the utilization of two programming abstractions: one to separate the symbolic fixpoint computations from the predecessor calculations, and another one to allow the integration of different BDD libraries as back-ends. In particular, we employ a multi-threaded execution of the fixpoint algorithm by using the multi-threaded BDD library Sylvan, which leads to enormous computational savings.' acknowledgement: 'Authors ordered alphabetically. R. Majumdar and A.-K. Schmuck are partially supported by DFG project 389792660 TRR 248-CPEC. A.-K. Schmuck is additionally funded through DFG project (SCHM 3541/1-1). K. Mallik is supported by the ERC project ERC-2020-AdG 101020093. M. Rychlicki is supported by the EPSRC project EP/V00252X/1. S. Soudjani is supported by the following projects: EPSRC EP/V043676/1, EIC 101070802, and ERC 101089047.' alternative_title: - LNCS article_processing_charge: Yes (in subscription journal) author: - first_name: Rupak full_name: Majumdar, Rupak last_name: Majumdar - first_name: Kaushik full_name: Mallik, Kaushik id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598 last_name: Mallik orcid: 0000-0001-9864-7475 - first_name: Mateusz full_name: Rychlicki, Mateusz last_name: Rychlicki - first_name: Anne-Kathrin full_name: Schmuck, Anne-Kathrin last_name: Schmuck - first_name: Sadegh full_name: Soudjani, Sadegh last_name: Soudjani citation: ama: 'Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. In: 35th International Conference on Computer Aided Verification. Vol 13966. Springer Nature; 2023:3-15. doi:10.1007/978-3-031-37709-9_1' apa: 'Majumdar, R., Mallik, K., Rychlicki, M., Schmuck, A.-K., & Soudjani, S. (2023). A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. In 35th International Conference on Computer Aided Verification (Vol. 13966, pp. 3–15). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37709-9_1' chicago: Majumdar, Rupak, Kaushik Mallik, Mateusz Rychlicki, Anne-Kathrin Schmuck, and Sadegh Soudjani. “A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties.” In 35th International Conference on Computer Aided Verification, 13966:3–15. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37709-9_1. ieee: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, and S. Soudjani, “A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties,” in 35th International Conference on Computer Aided Verification, Paris, France, 2023, vol. 13966, pp. 3–15. ista: 'Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. 2023. A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. 35th International Conference on Computer Aided Verification. CAV: Computer Aided Verification, LNCS, vol. 13966, 3–15.' mla: Majumdar, Rupak, et al. “A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties.” 35th International Conference on Computer Aided Verification, vol. 13966, Springer Nature, 2023, pp. 3–15, doi:10.1007/978-3-031-37709-9_1. short: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, S. Soudjani, in:, 35th International Conference on Computer Aided Verification, Springer Nature, 2023, pp. 3–15. conference: end_date: 2023-07-22 location: Paris, France name: 'CAV: Computer Aided Verification' start_date: 2023-07-17 date_created: 2024-01-08T13:18:00Z date_published: 2023-07-16T00:00:00Z date_updated: 2024-02-27T07:39:51Z day: '16' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-031-37709-9_1 ec_funded: 1 file: - access_level: open_access checksum: 1a361d83db0244fd32c03b544c294b5a content_type: application/pdf creator: dernst date_created: 2024-01-09T10:01:07Z date_updated: 2024-01-09T10:01:07Z file_id: '14765' file_name: 2023_LNCSCAV_Majumdar.pdf file_size: 405147 relation: main_file success: 1 file_date_updated: 2024-01-09T10:01:07Z has_accepted_license: '1' intvolume: ' 13966' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 3-15 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 35th International Conference on Computer Aided Verification publication_identifier: eisbn: - '9783031377099' eissn: - 1611-3349 isbn: - '9783031377082' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '14994' relation: research_data status: public scopus_import: '1' status: public title: A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13966 year: '2023' ... --- _id: '14654' abstract: - lang: eng text: Two assumptions commonly applied in convection schemes—the diagnostic and quasi-equilibrium assumptions—imply that convective activity (e.g., convective precipitation) is controlled only by the large-scale (macrostate) environment at the time. In contrast, numerical experiments indicate a “memory” or dependence of convection also on its own previous activity whereby subgrid-scale (microstate) structures boost but are also boosted by convection. In this study we investigated this memory by comparing single-column model behavior in two idealized tests previously executed by a cloud-resolving model (CRM). Conventional convection schemes that employ the diagnostic assumption fail to reproduce the CRM behavior. The memory-capable org and Laboratoire de Météorologie Dynamique Zoom cold pool schemes partially capture the behavior, but fail to fully exhibit the strong reinforcing feedbacks implied by the CRM. Analysis of this failure suggests that it is because the CRM supports a linear (or superlinear) dependence of the subgrid structure growth rate on the precipitation rate, while the org scheme assumes a sublinear dependence. Among varying versions of the org scheme, the growth rate of the org variable representing subgrid structure is strongly associated with memory strength. These results demonstrate the importance of parameterizing convective memory, and the ability of idealized tests to reveal shortcomings of convection schemes and constrain model structural assumptions. acknowledgement: YLH is supported by funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 101034413. CJM gratefully acknowledges funding from the European Research Council under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, Grant Agreement No. 805041). YLH and SCS were supported by the Australian Research Council (FL150100035). The authors thank Brian Mapes, David Fuchs and Siwon Song for stimulating and helpful discussions. MC warmly thanks the LMD team in Paris for their assistance with the LMDZ model. We thank the two anonymous reviewers for their constructive comments that greatly improved this manuscript. article_number: e2023MS003726 article_processing_charge: Yes article_type: original author: - first_name: Yi-Ling full_name: Hwong, Yi-Ling id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22 last_name: Hwong orcid: 0000-0001-9281-3479 - first_name: M. full_name: Colin, M. last_name: Colin - first_name: Philipp full_name: Aglas, Philipp id: 02eace56-97fc-11ee-b81a-f0939ca85a77 last_name: Aglas - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: S. C. full_name: Sherwood, S. C. last_name: Sherwood citation: ama: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. Assessing memory in convection schemes using idealized tests. Journal of Advances in Modeling Earth Systems. 2023;15(12). doi:10.1029/2023MS003726 apa: Hwong, Y.-L., Colin, M., Aglas, P., Muller, C. J., & Sherwood, S. C. (2023). Assessing memory in convection schemes using idealized tests. Journal of Advances in Modeling Earth Systems. Wiley. https://doi.org/10.1029/2023MS003726 chicago: Hwong, Yi-Ling, M. Colin, Philipp Aglas, Caroline J Muller, and S. C. Sherwood. “Assessing Memory in Convection Schemes Using Idealized Tests.” Journal of Advances in Modeling Earth Systems. Wiley, 2023. https://doi.org/10.1029/2023MS003726. ieee: Y.-L. Hwong, M. Colin, P. Aglas, C. J. Muller, and S. C. Sherwood, “Assessing memory in convection schemes using idealized tests,” Journal of Advances in Modeling Earth Systems, vol. 15, no. 12. Wiley, 2023. ista: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. 2023. Assessing memory in convection schemes using idealized tests. Journal of Advances in Modeling Earth Systems. 15(12), e2023MS003726. mla: Hwong, Yi-Ling, et al. “Assessing Memory in Convection Schemes Using Idealized Tests.” Journal of Advances in Modeling Earth Systems, vol. 15, no. 12, e2023MS003726, Wiley, 2023, doi:10.1029/2023MS003726. short: Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S.C. Sherwood, Journal of Advances in Modeling Earth Systems 15 (2023). date_created: 2023-12-10T23:00:57Z date_published: 2023-12-01T00:00:00Z date_updated: 2024-02-27T07:26:30Z day: '01' ddc: - '550' department: - _id: CaMu doi: 10.1029/2023MS003726 ec_funded: 1 file: - access_level: open_access checksum: 4d060b293da3d203de8769e398edf711 content_type: application/pdf creator: dernst date_created: 2023-12-11T08:08:44Z date_updated: 2023-12-11T08:08:44Z file_id: '14670' file_name: 2023_JAMES_Hwong.pdf file_size: 2783677 relation: main_file success: 1 file_date_updated: 2023-12-11T08:08:44Z has_accepted_license: '1' intvolume: ' 15' issue: '12' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 629205d8-2b32-11ec-9570-e1356ff73576 call_identifier: H2020 grant_number: '805041' name: organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate publication: Journal of Advances in Modeling Earth Systems publication_identifier: eissn: - 1942-2466 publication_status: published publisher: Wiley quality_controlled: '1' related_material: record: - id: '14991' relation: research_data status: public scopus_import: '1' status: public title: Assessing memory in convection schemes using idealized tests tmp: image: /images/cc_by_nc_nd.png legal_code_url: https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode name: Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0) short: CC BY-NC-ND (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 15 year: '2023' ... --- _id: '13139' abstract: - lang: eng text: A classical problem for Markov chains is determining their stationary (or steady-state) distribution. This problem has an equally classical solution based on eigenvectors and linear equation systems. However, this approach does not scale to large instances, and iterative solutions are desirable. It turns out that a naive approach, as used by current model checkers, may yield completely wrong results. We present a new approach, which utilizes recent advances in partial exploration and mean payoff computation to obtain a correct, converging approximation. alternative_title: - LNCS article_processing_charge: No author: - first_name: Tobias full_name: Meggendorfer, Tobias id: b21b0c15-30a2-11eb-80dc-f13ca25802e1 last_name: Meggendorfer orcid: 0000-0002-1712-2165 citation: ama: 'Meggendorfer T. Correct approximation of stationary distributions. In: TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems. Vol 13993. Springer Nature; 2023:489-507. doi:10.1007/978-3-031-30823-9_25' apa: 'Meggendorfer, T. (2023). Correct approximation of stationary distributions. In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems (Vol. 13993, pp. 489–507). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-30823-9_25' chicago: 'Meggendorfer, Tobias. “Correct Approximation of Stationary Distributions.” In TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, 13993:489–507. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-30823-9_25.' ieee: 'T. Meggendorfer, “Correct approximation of stationary distributions,” in TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Paris, France, 2023, vol. 13993, pp. 489–507.' ista: 'Meggendorfer T. 2023. Correct approximation of stationary distributions. 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. 13993, 489–507.' mla: 'Meggendorfer, Tobias. “Correct Approximation of Stationary Distributions.” TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, vol. 13993, Springer Nature, 2023, pp. 489–507, doi:10.1007/978-3-031-30823-9_25.' short: 'T. Meggendorfer, in:, TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems, Springer Nature, 2023, pp. 489–507.' conference: end_date: 2023-04-27 location: Paris, France name: 'TACAS: Tools and Algorithms for the Construction and Analysis of Systems' start_date: 2023-04-22 date_created: 2023-06-18T22:00:46Z date_published: 2023-04-22T00:00:00Z date_updated: 2024-02-27T07:19:33Z day: '22' ddc: - '000' department: - _id: KrCh doi: 10.1007/978-3-031-30823-9_25 external_id: arxiv: - '2301.08137' file: - access_level: open_access checksum: 59f707a3949c03793251b0d04c62542a content_type: application/pdf creator: dernst date_created: 2023-06-19T07:18:40Z date_updated: 2023-06-19T07:18:40Z file_id: '13148' file_name: 2023_LNCS_Meggendorfer.pdf file_size: 521951 relation: main_file success: 1 file_date_updated: 2023-06-19T07:18:40Z has_accepted_license: '1' intvolume: ' 13993' language: - iso: eng month: '04' oa: 1 oa_version: Published Version page: 489-507 publication: 'TACAS 2023: Tools and Algorithms for the Construction and Analysis of Systems' publication_identifier: eissn: - 1611-3349 isbn: - '9783031308222' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '14990' relation: research_data status: public scopus_import: '1' status: public title: Correct approximation of stationary distributions tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13993 year: '2023' ... --- _id: '14991' abstract: - lang: eng text: This repository contains the data, scripts, WRF codes and files required to reproduce the results of the manuscript "Assessing Memory in Convection Schemes Using Idealized Tests" submitted to the Journal of Advances in Modeling Earth Systems (JAMES). article_processing_charge: No author: - first_name: Yi-Ling full_name: Hwong, Yi-Ling id: 1217aa61-4dd1-11ec-9ac3-f2ba3f17ee22 last_name: Hwong orcid: 0000-0001-9281-3479 - first_name: Maxime full_name: Colin, Maxime last_name: Colin - first_name: Philipp full_name: Aglas, Philipp id: 02eace56-97fc-11ee-b81a-f0939ca85a77 last_name: Aglas - first_name: Caroline J full_name: Muller, Caroline J id: f978ccb0-3f7f-11eb-b193-b0e2bd13182b last_name: Muller orcid: 0000-0001-5836-5350 - first_name: Steven C. full_name: Sherwood, Steven C. last_name: Sherwood citation: ama: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. Data-assessing memory in convection schemes using idealized tests. 2023. doi:10.5281/ZENODO.7757041 apa: Hwong, Y.-L., Colin, M., Aglas, P., Muller, C. J., & Sherwood, S. C. (2023). Data-assessing memory in convection schemes using idealized tests. Zenodo. https://doi.org/10.5281/ZENODO.7757041 chicago: Hwong, Yi-Ling, Maxime Colin, Philipp Aglas, Caroline J Muller, and Steven C. Sherwood. “Data-Assessing Memory in Convection Schemes Using Idealized Tests.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7757041. ieee: Y.-L. Hwong, M. Colin, P. Aglas, C. J. Muller, and S. C. Sherwood, “Data-assessing memory in convection schemes using idealized tests.” Zenodo, 2023. ista: Hwong Y-L, Colin M, Aglas P, Muller CJ, Sherwood SC. 2023. Data-assessing memory in convection schemes using idealized tests, Zenodo, 10.5281/ZENODO.7757041. mla: Hwong, Yi-Ling, et al. Data-Assessing Memory in Convection Schemes Using Idealized Tests. Zenodo, 2023, doi:10.5281/ZENODO.7757041. short: Y.-L. Hwong, M. Colin, P. Aglas, C.J. Muller, S.C. Sherwood, (2023). date_created: 2024-02-14T14:37:57Z date_published: 2023-06-23T00:00:00Z date_updated: 2024-02-27T07:26:31Z day: '23' ddc: - '550' department: - _id: CaMu doi: 10.5281/ZENODO.7757041 ec_funded: 1 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7757041 month: '06' oa: 1 oa_version: Published Version project: - _id: fc2ed2f7-9c52-11eb-aca3-c01059dda49c call_identifier: H2020 grant_number: '101034413' name: 'IST-BRIDGE: International postdoctoral program' publisher: Zenodo related_material: record: - id: '14654' relation: used_in_publication status: public status: public title: Data-assessing memory in convection schemes using idealized tests tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14990' abstract: - lang: eng text: The software artefact to evaluate the approximation of stationary distributions implementation. article_processing_charge: No author: - first_name: Tobias full_name: Meggendorfer, Tobias id: b21b0c15-30a2-11eb-80dc-f13ca25802e1 last_name: Meggendorfer orcid: 0000-0002-1712-2165 citation: ama: 'Meggendorfer T. Artefact for: Correct Approximation of Stationary Distributions. 2023. doi:10.5281/ZENODO.7548214' apa: 'Meggendorfer, T. (2023). Artefact for: Correct Approximation of Stationary Distributions. Zenodo. https://doi.org/10.5281/ZENODO.7548214' chicago: 'Meggendorfer, Tobias. “Artefact for: Correct Approximation of Stationary Distributions.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7548214.' ieee: 'T. Meggendorfer, “Artefact for: Correct Approximation of Stationary Distributions.” Zenodo, 2023.' ista: 'Meggendorfer T. 2023. Artefact for: Correct Approximation of Stationary Distributions, Zenodo, 10.5281/ZENODO.7548214.' mla: 'Meggendorfer, Tobias. Artefact for: Correct Approximation of Stationary Distributions. Zenodo, 2023, doi:10.5281/ZENODO.7548214.' short: T. Meggendorfer, (2023). date_created: 2024-02-14T14:27:06Z date_published: 2023-01-18T00:00:00Z date_updated: 2024-02-27T07:19:32Z day: '18' ddc: - '000' department: - _id: KrCh doi: 10.5281/ZENODO.7548214 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7548214 month: '01' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '13139' relation: used_in_publication status: public status: public title: 'Artefact for: Correct Approximation of Stationary Distributions' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14260' abstract: - lang: eng text: "This paper presents Lincheck, a new practical and user-friendly framework for testing concurrent algorithms on the Java Virtual Machine (JVM). Lincheck provides a simple and declarative way to write concurrent tests: instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. The framework automatically generates a set of concurrent scenarios, examines them using stress-testing or bounded model checking, and verifies that the results of each invocation are correct. Notably, if an error is detected via model checking, Lincheck provides an easy-to-follow trace to reproduce it, significantly simplifying the bug investigation.\r\n\r\nTo the best of our knowledge, Lincheck is the first production-ready tool on the JVM that offers such a simple way of writing concurrent tests, without requiring special skills or expertise. We successfully integrated Lincheck in the development process of several large projects, such as Kotlin Coroutines, and identified new bugs in popular concurrency libraries, such as a race in Java’s standard ConcurrentLinkedDeque and a liveliness bug in Java’s AbstractQueuedSynchronizer framework, which is used in most of the synchronization primitives. We believe that Lincheck can significantly improve the quality and productivity of concurrent algorithms research and development and become the state-of-the-art tool for checking their correctness." alternative_title: - LNCS article_processing_charge: Yes (in subscription journal) author: - first_name: Nikita full_name: Koval, Nikita id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87 last_name: Koval - first_name: Alexander full_name: Fedorov, Alexander id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6 last_name: Fedorov - first_name: Maria full_name: Sokolova, Maria last_name: Sokolova - first_name: Dmitry full_name: Tsitelov, Dmitry last_name: Tsitelov - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. In: 35th International Conference on Computer Aided Verification . Vol 13964. Springer Nature; 2023:156-169. doi:10.1007/978-3-031-37706-8_8' apa: 'Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. In 35th International Conference on Computer Aided Verification (Vol. 13964, pp. 156–169). Paris, France: Springer Nature. https://doi.org/10.1007/978-3-031-37706-8_8' chicago: 'Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” In 35th International Conference on Computer Aided Verification , 13964:156–69. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-37706-8_8.' ieee: 'N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM,” in 35th International Conference on Computer Aided Verification , Paris, France, 2023, vol. 13964, pp. 156–169.' ista: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM. 35th International Conference on Computer Aided Verification . CAV: Computer Aided Verification, LNCS, vol. 13964, 156–169.' mla: 'Koval, Nikita, et al. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” 35th International Conference on Computer Aided Verification , vol. 13964, Springer Nature, 2023, pp. 156–69, doi:10.1007/978-3-031-37706-8_8.' short: N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, in:, 35th International Conference on Computer Aided Verification , Springer Nature, 2023, pp. 156–169. conference: end_date: 2023-07-22 location: Paris, France name: 'CAV: Computer Aided Verification' start_date: 2023-07-17 date_created: 2023-09-03T22:01:16Z date_published: 2023-07-17T00:00:00Z date_updated: 2024-02-27T07:46:52Z day: '17' ddc: - '000' department: - _id: DaAl - _id: GradSch doi: 10.1007/978-3-031-37706-8_8 file: - access_level: open_access checksum: c346016393123a0a2338ad4d976f61bc content_type: application/pdf creator: dernst date_created: 2023-09-06T08:16:25Z date_updated: 2023-09-06T08:16:25Z file_id: '14275' file_name: 2023_LNCS_Koval.pdf file_size: 421408 relation: main_file success: 1 file_date_updated: 2023-09-06T08:16:25Z has_accepted_license: '1' intvolume: ' 13964' language: - iso: eng month: '07' oa: 1 oa_version: Published Version page: 156-169 publication: '35th International Conference on Computer Aided Verification ' publication_identifier: eissn: - 1611-3349 isbn: - '9783031377051' issn: - 0302-9743 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '14995' relation: research_data status: public scopus_import: '1' status: public title: 'Lincheck: A practical framework for testing concurrent data structures on JVM' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 13964 year: '2023' ... --- _id: '14995' abstract: - lang: eng text: "Lincheck is a new practical and user-friendly framework for testing concurrent data structures on the Java Virtual Machine (JVM). It provides a simple and declarative way to write concurrent tests. Instead of describing how to perform the test, users specify what to test by declaring all the operations to examine; the framework automatically handles the rest. As a result, tests written with Lincheck are concise and easy to understand. \r\nThe artifact presents a collection of Lincheck tests that discover new bugs in popular libraries and implementations from the concurrency literature -- they are listed in Table 1, Section 3. To evaluate the performance of Lincheck analysis, the collection of tests also includes those which check correct data structures and, thus, always succeed. Similarly to Table 2, Section 3, the experiments demonstrate the reasonable time to perform a test. Finally, Lincheck provides user-friendly output with an easy-to-follow trace to reproduce a detected error, significantly simplifying further investigation." article_processing_charge: No author: - first_name: Nikita full_name: Koval, Nikita id: 2F4DB10C-F248-11E8-B48F-1D18A9856A87 last_name: Koval - first_name: Alexander full_name: Fedorov, Alexander id: 2e711909-896a-11ed-bdf8-eb0f5a2984c6 last_name: Fedorov - first_name: Maria full_name: Sokolova, Maria last_name: Sokolova - first_name: Dmitry full_name: Tsitelov, Dmitry last_name: Tsitelov - first_name: Dan-Adrian full_name: Alistarh, Dan-Adrian id: 4A899BFC-F248-11E8-B48F-1D18A9856A87 last_name: Alistarh orcid: 0000-0003-3650-940X citation: ama: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. Lincheck: A practical framework for testing concurrent data structures on JVM. 2023. doi:10.5281/ZENODO.7877757' apa: 'Koval, N., Fedorov, A., Sokolova, M., Tsitelov, D., & Alistarh, D.-A. (2023). Lincheck: A practical framework for testing concurrent data structures on JVM. Zenodo. https://doi.org/10.5281/ZENODO.7877757' chicago: 'Koval, Nikita, Alexander Fedorov, Maria Sokolova, Dmitry Tsitelov, and Dan-Adrian Alistarh. “Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7877757.' ieee: 'N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, and D.-A. Alistarh, “Lincheck: A practical framework for testing concurrent data structures on JVM.” Zenodo, 2023.' ista: 'Koval N, Fedorov A, Sokolova M, Tsitelov D, Alistarh D-A. 2023. Lincheck: A practical framework for testing concurrent data structures on JVM, Zenodo, 10.5281/ZENODO.7877757.' mla: 'Koval, Nikita, et al. Lincheck: A Practical Framework for Testing Concurrent Data Structures on JVM. Zenodo, 2023, doi:10.5281/ZENODO.7877757.' short: N. Koval, A. Fedorov, M. Sokolova, D. Tsitelov, D.-A. Alistarh, (2023). date_created: 2024-02-14T15:14:13Z date_published: 2023-04-28T00:00:00Z date_updated: 2024-02-27T07:46:52Z day: '28' ddc: - '000' department: - _id: DaAl doi: 10.5281/ZENODO.7877757 main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7877757 month: '04' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14260' relation: used_in_publication status: public status: public title: 'Lincheck: A practical framework for testing concurrent data structures on JVM' type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14994' abstract: - lang: eng text: This resource contains the artifacts for reproducing the experimental results presented in the paper titled "A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties" that has been submitted in CAV 2023. article_processing_charge: No author: - first_name: Rupak full_name: Majumdar, Rupak last_name: Majumdar - first_name: Kaushik full_name: Mallik, Kaushik id: 0834ff3c-6d72-11ec-94e0-b5b0a4fb8598 last_name: Mallik orcid: 0000-0001-9864-7475 - first_name: Mateusz full_name: Rychlicki, Mateusz last_name: Rychlicki - first_name: Anne-Kathrin full_name: Schmuck, Anne-Kathrin last_name: Schmuck - first_name: Sadegh full_name: Soudjani, Sadegh last_name: Soudjani citation: ama: Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. 2023. doi:10.5281/ZENODO.7877790 apa: Majumdar, R., Mallik, K., Rychlicki, M., Schmuck, A.-K., & Soudjani, S. (2023). A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties. Zenodo. https://doi.org/10.5281/ZENODO.7877790 chicago: Majumdar, Rupak, Kaushik Mallik, Mateusz Rychlicki, Anne-Kathrin Schmuck, and Sadegh Soudjani. “A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.7877790. ieee: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, and S. Soudjani, “A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties.” Zenodo, 2023. ista: Majumdar R, Mallik K, Rychlicki M, Schmuck A-K, Soudjani S. 2023. A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties, Zenodo, 10.5281/ZENODO.7877790. mla: Majumdar, Rupak, et al. A Flexible Toolchain for Symbolic Rabin Games under Fair and Stochastic Uncertainties. Zenodo, 2023, doi:10.5281/ZENODO.7877790. short: R. Majumdar, K. Mallik, M. Rychlicki, A.-K. Schmuck, S. Soudjani, (2023). date_created: 2024-02-14T15:13:00Z date_published: 2023-04-28T00:00:00Z date_updated: 2024-02-27T07:39:51Z day: '28' ddc: - '000' department: - _id: ToHe doi: 10.5281/ZENODO.7877790 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.7877790 month: '04' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14758' relation: used_in_publication status: public status: public title: A flexible toolchain for symbolic rabin games under fair and stochastic uncertainties tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '15023' abstract: - lang: eng text: Reinforcement learning has shown promising results in learning neural network policies for complicated control tasks. However, the lack of formal guarantees about the behavior of such policies remains an impediment to their deployment. We propose a novel method for learning a composition of neural network policies in stochastic environments, along with a formal certificate which guarantees that a specification over the policy's behavior is satisfied with the desired probability. Unlike prior work on verifiable RL, our approach leverages the compositional nature of logical specifications provided in SpectRL, to learn over graphs of probabilistic reach-avoid specifications. The formal guarantees are provided by learning neural network policies together with reach-avoid supermartingales (RASM) for the graph’s sub-tasks and then composing them into a global policy. We also derive a tighter lower bound compared to previous work on the probability of reach-avoidance implied by a RASM, which is required to find a compositional policy with an acceptable probabilistic threshold for complex tasks with multiple edge policies. We implement a prototype of our approach and evaluate it on a Stochastic Nine Rooms environment. acknowledgement: "This work was supported in part by the ERC-2020-AdG 101020093 (VAMOS) and the ERC-2020-\r\nCoG 863818 (FoRM-SMArt)." article_processing_charge: No author: - first_name: Dorde full_name: Zikelic, Dorde id: 294AA7A6-F248-11E8-B48F-1D18A9856A87 last_name: Zikelic orcid: 0000-0002-4681-1699 - first_name: Mathias full_name: Lechner, Mathias id: 3DC22916-F248-11E8-B48F-1D18A9856A87 last_name: Lechner - first_name: Abhinav full_name: Verma, Abhinav id: a235593c-d7fa-11eb-a0c5-b22ca3c66ee6 last_name: Verma - first_name: Krishnendu full_name: Chatterjee, Krishnendu id: 2E5DCA20-F248-11E8-B48F-1D18A9856A87 last_name: Chatterjee orcid: 0000-0002-4561-241X - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: 'Zikelic D, Lechner M, Verma A, Chatterjee K, Henzinger TA. Compositional policy learning in stochastic control systems with formal guarantees. In: 37th Conference on Neural Information Processing Systems. ; 2023.' apa: Zikelic, D., Lechner, M., Verma, A., Chatterjee, K., & Henzinger, T. A. (2023). Compositional policy learning in stochastic control systems with formal guarantees. In 37th Conference on Neural Information Processing Systems. New Orleans, LO, United States. chicago: Zikelic, Dorde, Mathias Lechner, Abhinav Verma, Krishnendu Chatterjee, and Thomas A Henzinger. “Compositional Policy Learning in Stochastic Control Systems with Formal Guarantees.” In 37th Conference on Neural Information Processing Systems, 2023. ieee: D. Zikelic, M. Lechner, A. Verma, K. Chatterjee, and T. A. Henzinger, “Compositional policy learning in stochastic control systems with formal guarantees,” in 37th Conference on Neural Information Processing Systems, New Orleans, LO, United States, 2023. ista: 'Zikelic D, Lechner M, Verma A, Chatterjee K, Henzinger TA. 2023. Compositional policy learning in stochastic control systems with formal guarantees. 37th Conference on Neural Information Processing Systems. NeurIPS: Neural Information Processing Systems.' mla: Zikelic, Dorde, et al. “Compositional Policy Learning in Stochastic Control Systems with Formal Guarantees.” 37th Conference on Neural Information Processing Systems, 2023. short: D. Zikelic, M. Lechner, A. Verma, K. Chatterjee, T.A. Henzinger, in:, 37th Conference on Neural Information Processing Systems, 2023. conference: end_date: 2023-12-16 location: New Orleans, LO, United States name: 'NeurIPS: Neural Information Processing Systems' start_date: 2023-12-10 date_created: 2024-02-25T09:23:24Z date_published: 2023-12-15T00:00:00Z date_updated: 2024-02-28T12:20:11Z day: '15' department: - _id: ToHe - _id: KrCh ec_funded: 1 external_id: arxiv: - '2312.01456' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2312.01456 month: '12' oa: 1 oa_version: Preprint project: - _id: 0599E47C-7A3F-11EA-A408-12923DDC885E call_identifier: H2020 grant_number: '863818' name: 'Formal Methods for Stochastic Models: Algorithms and Applications' - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 37th Conference on Neural Information Processing Systems publication_status: epub_ahead quality_controlled: '1' status: public title: Compositional policy learning in stochastic control systems with formal guarantees type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14993' abstract: - lang: eng text: "Traditional top-down approaches for global health have historically failed to achieve social progress (Hoffman et al., 2015; Hoffman & Røttingen, 2015). Recently, however, a more holistic, multi-level approach termed One Health (OH) (Osterhaus et al., 2020) is being adopted. Several sets of challenges have been identified for the implementation of OH (dos S. Ribeiro et al., 2019), including policy and funding, education and training, and multi-actor, multi-domain, and multi-level collaborations. These exist despite the increasing accessibility to\r\nknowledge and digital collaborative research tools through the internet. To address some of these challenges, we propose a general framework for grassroots community-based means of participatory research. Additionally, we present a specific roadmap to create a Machine Learning for Global Health community in Africa. The proposed framework aims to enable any small group of individuals with scarce resources to build and sustain an online community within approximately two years. We provide a discussion on the potential impact of the proposed framework for global health research collaborations." acknowledgement: "Houcemeddine Turki’s contributions to this final output have been funded through the Adapting\r\nWikidata to support clinical practice using Data Science, Semantic Web and Machine Learning\r\nproject, which is part of the Wikimedia Research Fund maintained by the Wikimedia Foundation in San Francisco, California, United States of America." article_processing_charge: No author: - first_name: Christopher full_name: Currin, Christopher id: e8321fc5-3091-11eb-8a53-83f309a11ac9 last_name: Currin orcid: 0000-0002-4809-5059 - first_name: Mercy Nyamewaa full_name: Asiedu , Mercy Nyamewaa last_name: 'Asiedu ' - first_name: Chris full_name: Fourie, Chris last_name: Fourie - first_name: Benjamin full_name: Rosman, Benjamin last_name: Rosman - first_name: Houcemeddine full_name: Turki, Houcemeddine last_name: Turki - first_name: Atnafu full_name: Lambebo Tonja, Atnafu last_name: Lambebo Tonja - first_name: Jade full_name: Abbott, Jade last_name: Abbott - first_name: Marvellous full_name: Ajala, Marvellous last_name: Ajala - first_name: Sadiq Adewale full_name: Adedayo, Sadiq Adewale last_name: Adedayo - first_name: Chris Chinenye full_name: Emezue, Chris Chinenye last_name: Emezue - first_name: Daphne full_name: Machangara, Daphne last_name: Machangara citation: ama: 'Currin C, Asiedu MN, Fourie C, et al. A framework for grassroots research collaboration in machine learning and global health. In: 1st Workshop on Machine Learning & Global Health. OpenReview; 2023.' apa: 'Currin, C., Asiedu , M. N., Fourie, C., Rosman, B., Turki, H., Lambebo Tonja, A., … Machangara, D. (2023). A framework for grassroots research collaboration in machine learning and global health. In 1st Workshop on Machine Learning & Global Health. Kigali, Rwanda: OpenReview.' chicago: Currin, Christopher, Mercy Nyamewaa Asiedu , Chris Fourie, Benjamin Rosman, Houcemeddine Turki, Atnafu Lambebo Tonja, Jade Abbott, et al. “A Framework for Grassroots Research Collaboration in Machine Learning and Global Health.” In 1st Workshop on Machine Learning & Global Health. OpenReview, 2023. ieee: C. Currin et al., “A framework for grassroots research collaboration in machine learning and global health,” in 1st Workshop on Machine Learning & Global Health, Kigali, Rwanda, 2023. ista: 'Currin C, Asiedu MN, Fourie C, Rosman B, Turki H, Lambebo Tonja A, Abbott J, Ajala M, Adedayo SA, Emezue CC, Machangara D. 2023. A framework for grassroots research collaboration in machine learning and global health. 1st Workshop on Machine Learning & Global Health. ICLR: International Conference on Learning Representations.' mla: Currin, Christopher, et al. “A Framework for Grassroots Research Collaboration in Machine Learning and Global Health.” 1st Workshop on Machine Learning & Global Health, OpenReview, 2023. short: C. Currin, M.N. Asiedu , C. Fourie, B. Rosman, H. Turki, A. Lambebo Tonja, J. Abbott, M. Ajala, S.A. Adedayo, C.C. Emezue, D. Machangara, in:, 1st Workshop on Machine Learning & Global Health, OpenReview, 2023. conference: end_date: 2023-05-05 location: Kigali, Rwanda name: 'ICLR: International Conference on Learning Representations' start_date: 2023-05-05 date_created: 2024-02-14T15:11:48Z date_published: 2023-03-02T00:00:00Z date_updated: 2024-02-28T12:12:00Z day: '02' department: - _id: TiVo language: - iso: eng main_file_link: - open_access: '1' url: https://openreview.net/forum?id=jHY_G91R880 month: '03' oa: 1 oa_version: Published Version publication: 1st Workshop on Machine Learning & Global Health publication_status: published publisher: OpenReview quality_controlled: '1' status: public title: A framework for grassroots research collaboration in machine learning and global health type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '12979' abstract: - lang: eng text: 'Color and gloss are fundamental aspects of surface appearance. State-of-the-art fabrication techniques can manipulate both properties of the printed 3D objects. However, in the context of appearance reproduction, perceptual aspects of color and gloss are usually handled separately, even though previous perceptual studies suggest their interaction. Our work is motivated by previous studies demonstrating a perceived color shift due to a change in the object''s gloss, i.e., two samples with the same color but different surface gloss appear as they have different colors. In this paper, we conduct new experiments which support this observation and provide insights into the magnitude and direction of the perceived color change. We use the observations as guidance to design a new method that estimates and corrects the color shift enabling the fabrication of objects with the same perceived color but different surface gloss. We formulate the problem as an optimization procedure solved using differentiable rendering. We evaluate the effectiveness of our method in perceptual experiments with 3D objects fabricated using a multi-material 3D printer and demonstrate potential applications. ' acknowledgement: We thank Matthew S Zurawski for the 3D model of the car speed shape. This research has been supported by the Swiss National Science Foundation (SNSF, Grant 200502) and the FWF Lise Meitner (Grant M 3319). article_number: '21' article_processing_charge: No author: - first_name: Jorge full_name: Condor, Jorge last_name: Condor - first_name: Michael full_name: Piovarci, Michael id: 62E473F4-5C99-11EA-A40E-AF823DDC885E last_name: Piovarci orcid: 0000-0002-5062-4474 - first_name: Bernd full_name: Bickel, Bernd id: 49876194-F248-11E8-B48F-1D18A9856A87 last_name: Bickel orcid: 0000-0001-6511-9385 - first_name: Piotr full_name: Didyk, Piotr last_name: Didyk citation: ama: 'Condor J, Piovarci M, Bickel B, Didyk P. Gloss-aware color correction for 3D printing. In: SIGGRAPH ’23 Conference Proceedings. Association for Computing Machinery; 2023. doi:10.1145/3588432.3591546' apa: 'Condor, J., Piovarci, M., Bickel, B., & Didyk, P. (2023). Gloss-aware color correction for 3D printing. In SIGGRAPH ’23 Conference Proceedings. Los Angeles, CA, United States: Association for Computing Machinery. https://doi.org/10.1145/3588432.3591546' chicago: Condor, Jorge, Michael Piovarci, Bernd Bickel, and Piotr Didyk. “Gloss-Aware Color Correction for 3D Printing.” In SIGGRAPH ’23 Conference Proceedings. Association for Computing Machinery, 2023. https://doi.org/10.1145/3588432.3591546. ieee: J. Condor, M. Piovarci, B. Bickel, and P. Didyk, “Gloss-aware color correction for 3D printing,” in SIGGRAPH ’23 Conference Proceedings, Los Angeles, CA, United States, 2023. ista: 'Condor J, Piovarci M, Bickel B, Didyk P. 2023. Gloss-aware color correction for 3D printing. SIGGRAPH ’23 Conference Proceedings. SIGGRAPH: Computer Graphics and Interactive Techniques Conference, 21.' mla: Condor, Jorge, et al. “Gloss-Aware Color Correction for 3D Printing.” SIGGRAPH ’23 Conference Proceedings, 21, Association for Computing Machinery, 2023, doi:10.1145/3588432.3591546. short: J. Condor, M. Piovarci, B. Bickel, P. Didyk, in:, SIGGRAPH ’23 Conference Proceedings, Association for Computing Machinery, 2023. conference: end_date: 2023-08-10 location: Los Angeles, CA, United States name: 'SIGGRAPH: Computer Graphics and Interactive Techniques Conference' start_date: 2023-08-06 date_created: 2023-05-16T09:34:13Z date_published: 2023-07-23T00:00:00Z date_updated: 2024-02-28T12:52:04Z day: '23' ddc: - '004' department: - _id: BeBi doi: 10.1145/3588432.3591546 external_id: isi: - '001117690500021' file: - access_level: open_access checksum: 84a437739af5d46507928939b20c0c28 content_type: application/pdf creator: mpiovarc date_created: 2023-05-16T09:32:50Z date_updated: 2023-05-16T09:32:50Z file_id: '12983' file_name: Condor2023_supplemental.pdf file_size: 42323971 relation: main_file success: 1 - access_level: open_access checksum: 0f5c8b242e8e7c153c04888c4d0c6f37 content_type: application/pdf creator: dernst date_created: 2024-01-29T10:14:10Z date_updated: 2024-01-29T10:14:10Z file_id: '14893' file_name: 2023_Siggraph_Condor.pdf file_size: 26079404 relation: main_file success: 1 file_date_updated: 2024-01-29T10:14:10Z has_accepted_license: '1' isi: 1 keyword: - color - gloss - perception - color compensation - color management language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: eb901961-77a9-11ec-83b8-f5c883a62027 grant_number: M03319 name: Perception-Aware Appearance Fabrication publication: SIGGRAPH ’23 Conference Proceedings publication_identifier: isbn: - '9798400701597' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' status: public title: Gloss-aware color correction for 3D printing tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14076' abstract: - lang: eng text: Hyperproperties are properties that relate multiple execution traces. Previous work on monitoring hyperproperties focused on synchronous hyperproperties, usually specified in HyperLTL. When monitoring synchronous hyperproperties, all traces are assumed to proceed at the same speed. We introduce (multi-trace) prefix transducers and show how to use them for monitoring synchronous as well as, for the first time, asynchronous hyperproperties. Prefix transducers map multiple input traces into one or more output traces by incrementally matching prefixes of the input traces against expressions similar to regular expressions. The prefixes of different traces which are consumed by a single matching step of the monitor may have different lengths. The deterministic and executable nature of prefix transducers makes them more suitable as an intermediate formalism for runtime verification than logical specifications, which tend to be highly non-deterministic, especially in the case of asynchronous hyperproperties. We report on a set of experiments about monitoring asynchronous version of observational determinism. acknowledgement: This work was supported in part by the ERC-2020-AdG 101020093. The authors would like to thank Ana Oliveira da Costa for commenting on a draft of the paper. alternative_title: - LNCS article_processing_charge: Yes (in subscription journal) author: - first_name: Marek full_name: Chalupa, Marek id: 87e34708-d6c6-11ec-9f5b-9391e7be2463 last_name: Chalupa - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: 'Chalupa M, Henzinger TA. Monitoring hyperproperties with prefix transducers. In: 23nd International Conference on Runtime Verification. Vol 14245. Springer Nature; 2023:168-190. doi:10.1007/978-3-031-44267-4_9' apa: 'Chalupa, M., & Henzinger, T. A. (2023). Monitoring hyperproperties with prefix transducers. In 23nd International Conference on Runtime Verification (Vol. 14245, pp. 168–190). Thessaloniki, Greek: Springer Nature. https://doi.org/10.1007/978-3-031-44267-4_9' chicago: Chalupa, Marek, and Thomas A Henzinger. “Monitoring Hyperproperties with Prefix Transducers.” In 23nd International Conference on Runtime Verification, 14245:168–90. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-44267-4_9. ieee: M. Chalupa and T. A. Henzinger, “Monitoring hyperproperties with prefix transducers,” in 23nd International Conference on Runtime Verification, Thessaloniki, Greek, 2023, vol. 14245, pp. 168–190. ista: 'Chalupa M, Henzinger TA. 2023. Monitoring hyperproperties with prefix transducers. 23nd International Conference on Runtime Verification. RV: Conference on Runtime Verification, LNCS, vol. 14245, 168–190.' mla: Chalupa, Marek, and Thomas A. Henzinger. “Monitoring Hyperproperties with Prefix Transducers.” 23nd International Conference on Runtime Verification, vol. 14245, Springer Nature, 2023, pp. 168–90, doi:10.1007/978-3-031-44267-4_9. short: M. Chalupa, T.A. Henzinger, in:, 23nd International Conference on Runtime Verification, Springer Nature, 2023, pp. 168–190. conference: end_date: 2023-10-07 location: Thessaloniki, Greek name: 'RV: Conference on Runtime Verification' start_date: 2023-10-04 date_created: 2023-08-16T20:46:08Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-02-28T12:33:08Z day: '01' ddc: - '000' department: - _id: ToHe doi: 10.1007/978-3-031-44267-4_9 ec_funded: 1 file: - access_level: open_access checksum: ee33bd6f1a26f4dae7a8192584869fd8 content_type: application/pdf creator: dernst date_created: 2023-10-16T07:15:11Z date_updated: 2023-10-16T07:15:11Z file_id: '14430' file_name: 2023_LNCS_RV_Chalupa.pdf file_size: 867256 relation: main_file success: 1 file_date_updated: 2023-10-16T07:15:11Z has_accepted_license: '1' intvolume: ' 14245' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 168-190 project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publication: 23nd International Conference on Runtime Verification publication_identifier: eisbn: - 978-3-031-44267-4 isbn: - 978-3-031-44266-7 publication_status: published publisher: Springer Nature quality_controlled: '1' related_material: record: - id: '15035' relation: research_data status: public status: public title: Monitoring hyperproperties with prefix transducers tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 14245 year: '2023' ... --- _id: '14743' abstract: - lang: eng text: Leader-based consensus algorithms are fast and efficient under normal conditions, but lack robustness to adverse conditions due to their reliance on timeouts for liveness. We present QuePaxa, the first protocol offering state-of-the-art normal-case efficiency without depending on timeouts. QuePaxa uses a novel randomized asynchronous consensus core to tolerate adverse conditions such as denial-of-service (DoS) attacks, while a one-round-trip fast path preserves the normal-case efficiency of Multi-Paxos or Raft. By allowing simultaneous proposers without destructive interference, and using short hedging delays instead of conservative timeouts to limit redundant effort, QuePaxa permits rapid recovery after leader failure without risking costly view changes due to false timeouts. By treating leader choice and hedging delay as a multi-armed-bandit optimization, QuePaxa achieves responsiveness to prevalent conditions, and can choose the best leader even if the current one has not failed. Experiments with a prototype confirm that QuePaxa achieves normal-case LAN and WAN performance of 584k and 250k cmd/sec in throughput, respectively, comparable to Multi-Paxos. Under conditions such as DoS attacks, misconfigurations, or slow leaders that severely impact existing protocols, we find that QuePaxa remains live with median latency under 380ms in WAN experiments. acknowledgement: The authors would like to thank Marcos K. Aguilera, Pierluca Borsò, Aleksey Charapko, Rachid Guerraoui, Jovan Komatovic, Derek Leung, Louis-Henri Merino, Shailesh Mishra, Haochen Pan, Rodrigo Rodrigues, Lewis Tseng, and Haoqian Zhang for their helpful feedback on early drafts of this paper. article_processing_charge: No author: - first_name: Pasindu full_name: Tennage, Pasindu last_name: Tennage - first_name: Cristina full_name: Basescu, Cristina last_name: Basescu - first_name: Eleftherios full_name: Kokoris Kogias, Eleftherios id: f5983044-d7ef-11ea-ac6d-fd1430a26d30 last_name: Kokoris Kogias - first_name: Ewa full_name: Syta, Ewa last_name: Syta - first_name: Philipp full_name: Jovanovic, Philipp last_name: Jovanovic - first_name: Vero full_name: Estrada-Galinanes, Vero last_name: Estrada-Galinanes - first_name: Bryan full_name: Ford, Bryan last_name: Ford citation: ama: 'Tennage P, Basescu C, Kokoris Kogias E, et al. QuePaxa: Escaping the tyranny of timeouts in consensus. In: Proceedings of the 29th Symposium on Operating Systems Principles. Association for Computing Machinery; 2023:281-297. doi:10.1145/3600006.3613150' apa: 'Tennage, P., Basescu, C., Kokoris Kogias, E., Syta, E., Jovanovic, P., Estrada-Galinanes, V., & Ford, B. (2023). QuePaxa: Escaping the tyranny of timeouts in consensus. In Proceedings of the 29th Symposium on Operating Systems Principles (pp. 281–297). Koblenz, Germany: Association for Computing Machinery. https://doi.org/10.1145/3600006.3613150' chicago: 'Tennage, Pasindu, Cristina Basescu, Eleftherios Kokoris Kogias, Ewa Syta, Philipp Jovanovic, Vero Estrada-Galinanes, and Bryan Ford. “QuePaxa: Escaping the Tyranny of Timeouts in Consensus.” In Proceedings of the 29th Symposium on Operating Systems Principles, 281–97. Association for Computing Machinery, 2023. https://doi.org/10.1145/3600006.3613150.' ieee: 'P. Tennage et al., “QuePaxa: Escaping the tyranny of timeouts in consensus,” in Proceedings of the 29th Symposium on Operating Systems Principles, Koblenz, Germany, 2023, pp. 281–297.' ista: 'Tennage P, Basescu C, Kokoris Kogias E, Syta E, Jovanovic P, Estrada-Galinanes V, Ford B. 2023. QuePaxa: Escaping the tyranny of timeouts in consensus. Proceedings of the 29th Symposium on Operating Systems Principles. SOSP: Symposium on Operating Systems Principles, 281–297.' mla: 'Tennage, Pasindu, et al. “QuePaxa: Escaping the Tyranny of Timeouts in Consensus.” Proceedings of the 29th Symposium on Operating Systems Principles, Association for Computing Machinery, 2023, pp. 281–97, doi:10.1145/3600006.3613150.' short: P. Tennage, C. Basescu, E. Kokoris Kogias, E. Syta, P. Jovanovic, V. Estrada-Galinanes, B. Ford, in:, Proceedings of the 29th Symposium on Operating Systems Principles, Association for Computing Machinery, 2023, pp. 281–297. conference: end_date: 2023-10-26 location: Koblenz, Germany name: 'SOSP: Symposium on Operating Systems Principles' start_date: 2023-10-23 date_created: 2024-01-08T12:54:35Z date_published: 2023-10-01T00:00:00Z date_updated: 2024-02-28T12:51:24Z day: '01' department: - _id: ElKo doi: 10.1145/3600006.3613150 language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.1145/3600006.3613150 month: '10' oa: 1 oa_version: Published Version page: 281-297 publication: Proceedings of the 29th Symposium on Operating Systems Principles publication_identifier: isbn: - '9798400702297' publication_status: published publisher: Association for Computing Machinery quality_controlled: '1' scopus_import: '1' status: public title: 'QuePaxa: Escaping the tyranny of timeouts in consensus' type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '15035' abstract: - lang: eng text: "This artifact aims to reproduce experiments from the paper Monitoring Hyperproperties With Prefix Transducers accepted at RV'23, and give further pointers to implementation of prefix transducers.\r\nIt has two parts: a pre-compiled docker image and sources that one can use to compile (locally or in docker) the software and run the experiments." article_processing_charge: No author: - first_name: Marek full_name: Chalupa, Marek id: 87e34708-d6c6-11ec-9f5b-9391e7be2463 last_name: Chalupa - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000-0002-2985-7724 citation: ama: Chalupa M, Henzinger TA. Monitoring hyperproperties with prefix transducers. 2023. doi:10.5281/ZENODO.8191723 apa: Chalupa, M., & Henzinger, T. A. (2023). Monitoring hyperproperties with prefix transducers. Zenodo. https://doi.org/10.5281/ZENODO.8191723 chicago: Chalupa, Marek, and Thomas A Henzinger. “Monitoring Hyperproperties with Prefix Transducers.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8191723. ieee: M. Chalupa and T. A. Henzinger, “Monitoring hyperproperties with prefix transducers.” Zenodo, 2023. ista: Chalupa M, Henzinger TA. 2023. Monitoring hyperproperties with prefix transducers, Zenodo, 10.5281/ZENODO.8191723. mla: Chalupa, Marek, and Thomas A. Henzinger. Monitoring Hyperproperties with Prefix Transducers. Zenodo, 2023, doi:10.5281/ZENODO.8191723. short: M. Chalupa, T.A. Henzinger, (2023). date_created: 2024-02-28T07:34:34Z date_published: 2023-07-28T00:00:00Z date_updated: 2024-02-28T12:33:09Z day: '28' ddc: - '000' department: - _id: ToHe doi: 10.5281/ZENODO.8191723 ec_funded: 1 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8191722 month: '07' oa: 1 oa_version: Published Version project: - _id: 62781420-2b32-11ec-9570-8d9b63373d4d call_identifier: H2020 grant_number: '101020093' name: Vigilant Algorithmic Monitoring of Software publisher: Zenodo related_material: record: - id: '14076' relation: used_in_publication status: public status: public title: Monitoring hyperproperties with prefix transducers tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '15039' abstract: - lang: eng text: 'A crucial property for achieving secure, trustworthy and interpretable deep learning systems is their robustness: small changes to a system''s inputs should not result in large changes to its outputs. Mathematically, this means one strives for networks with a small Lipschitz constant. Several recent works have focused on how to construct such Lipschitz networks, typically by imposing constraints on the weight matrices. In this work, we study an orthogonal aspect, namely the role of the activation function. We show that commonly used activation functions, such as MaxMin, as well as all piece-wise linear ones with two segments unnecessarily restrict the class of representable functions, even in the simplest one-dimensional setting. We furthermore introduce the new N-activation function that is provably more expressive than currently popular activation functions. We provide code at this https URL.' article_number: '2311.06103' article_processing_charge: No author: - first_name: Bernd full_name: Prach, Bernd id: 2D561D42-C427-11E9-89B4-9C1AE6697425 last_name: Prach - first_name: Christoph full_name: Lampert, Christoph id: 40C20FD2-F248-11E8-B48F-1D18A9856A87 last_name: Lampert orcid: 0000-0001-8622-7887 citation: ama: Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. arXiv. doi:10.48550/ARXIV.2311.06103 apa: Prach, B., & Lampert, C. (n.d.). 1-Lipschitz neural networks are more expressive with N-activations. arXiv. https://doi.org/10.48550/ARXIV.2311.06103 chicago: Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2311.06103. ieee: B. Prach and C. Lampert, “1-Lipschitz neural networks are more expressive with N-activations,” arXiv. . ista: Prach B, Lampert C. 1-Lipschitz neural networks are more expressive with N-activations. arXiv, 2311.06103. mla: Prach, Bernd, and Christoph Lampert. “1-Lipschitz Neural Networks Are More Expressive with N-Activations.” ArXiv, 2311.06103, doi:10.48550/ARXIV.2311.06103. short: B. Prach, C. Lampert, ArXiv (n.d.). date_created: 2024-02-28T17:59:32Z date_published: 2023-11-10T00:00:00Z date_updated: 2024-03-04T07:02:39Z day: '10' department: - _id: GradSch - _id: ChLa doi: 10.48550/ARXIV.2311.06103 external_id: arxiv: - '2311.06103' language: - iso: eng main_file_link: - open_access: '1' url: https://doi.org/10.48550/arXiv.2311.06103 month: '11' oa: 1 oa_version: Preprint publication: arXiv publication_status: submitted status: public title: 1-Lipschitz neural networks are more expressive with N-activations type: preprint user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '14812' abstract: - lang: eng text: This repository contains the code and VCF files needed to conduct the analyses in our MS. Each folder contains a readMe document explaining the nature of each file and dataset and the results and analyses that they relate to. The same anlaysis code (but not VCF files) is also available at https://github.com/seanstankowski/Littorina_reproductive_mode article_processing_charge: No author: - first_name: Sean full_name: Stankowski, Sean id: 43161670-5719-11EA-8025-FABC3DDC885E last_name: Stankowski citation: ama: 'Stankowski S. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. 2023. doi:10.5281/ZENODO.8318995' apa: 'Stankowski, S. (2023). Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails. Zenodo. https://doi.org/10.5281/ZENODO.8318995' chicago: 'Stankowski, Sean. “Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails.” Zenodo, 2023. https://doi.org/10.5281/ZENODO.8318995.' ieee: 'S. Stankowski, “Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails.” Zenodo, 2023.' ista: 'Stankowski S. 2023. Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails, Zenodo, 10.5281/ZENODO.8318995.' mla: 'Stankowski, Sean. Data and Code for: The Genetic Architecture of a Recent Transition to Live-Bearing in Marine Snails. Zenodo, 2023, doi:10.5281/ZENODO.8318995.' short: S. Stankowski, (2023). contributor: - first_name: Zusanna last_name: Zagrodzka - first_name: Martin last_name: Garlovsky - first_name: Arka id: 6AAB2240-CA9A-11E9-9C1A-D9D1E5697425 last_name: Pal orcid: 0000-0002-4530-8469 - first_name: Daria id: 428A94B0-F248-11E8-B48F-1D18A9856A87 last_name: Shipilina orcid: 0000-0002-1145-9226 - first_name: Diego Fernando id: ae681a14-dc74-11ea-a0a7-c6ef18161701 last_name: Garcia Castillo - first_name: Hila id: d6ab5470-2fb3-11ed-8633-986a9b84edac last_name: Lifchitz - first_name: Alan last_name: Le Moan - first_name: Erica last_name: Leder - first_name: James last_name: Reeve - first_name: Kerstin last_name: Johannesson - first_name: Anja M id: 3C147470-F248-11E8-B48F-1D18A9856A87 last_name: Westram orcid: 0000-0003-1050-4969 - first_name: Roger last_name: Butlin date_created: 2024-01-16T10:23:01Z date_published: 2023-09-05T00:00:00Z date_updated: 2024-03-05T09:35:25Z day: '05' ddc: - '570' department: - _id: NiBa doi: 10.5281/ZENODO.8318995 has_accepted_license: '1' main_file_link: - open_access: '1' url: https://doi.org/10.5281/zenodo.8318995 month: '09' oa: 1 oa_version: Published Version publisher: Zenodo related_material: record: - id: '14796' relation: used_in_publication status: public status: public title: 'Data and code for: The genetic architecture of a recent transition to live-bearing in marine snails' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: research_data_reference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 year: '2023' ... --- _id: '13214' abstract: - lang: eng text: Nitrogen is an important macronutrient required for plant growth and development, thus directly impacting agricultural productivity. In recent years, numerous studies have shown that nitrogen-driven growth depends on pathways that control nitrate/nitrogen homeostasis and hormonal networks that act both locally and systemically to coordinate growth and development of plant organs. In this review, we will focus on recent advances in understanding the role of the plant hormones auxin and cytokinin and their crosstalk in nitrate-regulated growth and discuss the significance of novel findings and possible missing links. acknowledgement: 'This work was supported by the Austrian Academy of Sciences ÖAW: Doc fellowship (26130) to Stefan Riegler.' article_number: '1613' article_processing_charge: Yes article_type: review author: - first_name: R full_name: Abualia, R last_name: Abualia - first_name: Stefan full_name: Riegler, Stefan id: FF6018E0-D806-11E9-8E43-0B14E6697425 last_name: Riegler orcid: 0000-0003-3413-1343 - first_name: Eva full_name: Benková, Eva id: 38F4F166-F248-11E8-B48F-1D18A9856A87 last_name: Benková orcid: 0000-0002-8510-9739 citation: ama: Abualia R, Riegler S, Benková E. Nitrate, auxin and cytokinin - a trio to tango. Cells. 2023;12(12). doi:10.3390/cells12121613 apa: Abualia, R., Riegler, S., & Benková, E. (2023). Nitrate, auxin and cytokinin - a trio to tango. Cells. MDPI. https://doi.org/10.3390/cells12121613 chicago: Abualia, R, Stefan Riegler, and Eva Benková. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” Cells. MDPI, 2023. https://doi.org/10.3390/cells12121613. ieee: R. Abualia, S. Riegler, and E. Benková, “Nitrate, auxin and cytokinin - a trio to tango,” Cells, vol. 12, no. 12. MDPI, 2023. ista: Abualia R, Riegler S, Benková E. 2023. Nitrate, auxin and cytokinin - a trio to tango. Cells. 12(12), 1613. mla: Abualia, R., et al. “Nitrate, Auxin and Cytokinin - a Trio to Tango.” Cells, vol. 12, no. 12, 1613, MDPI, 2023, doi:10.3390/cells12121613. short: R. Abualia, S. Riegler, E. Benková, Cells 12 (2023). date_created: 2023-07-12T07:41:25Z date_published: 2023-06-13T00:00:00Z date_updated: 2024-03-06T14:00:33Z day: '13' ddc: - '570' department: - _id: EvBe doi: 10.3390/cells12121613 external_id: isi: - '001017033600001' pmid: - '37371083' file: - access_level: open_access checksum: 6dc9df5f4f59fc27c509c275060354a5 content_type: application/pdf creator: alisjak date_created: 2023-07-12T10:01:54Z date_updated: 2023-07-12T10:01:54Z file_id: '13218' file_name: 2023_cells_Abualia.pdf file_size: 1066802 relation: main_file success: 1 file_date_updated: 2023-07-12T10:01:54Z has_accepted_license: '1' intvolume: ' 12' isi: 1 issue: '12' language: - iso: eng month: '06' oa: 1 oa_version: Published Version pmid: 1 project: - _id: 62883ed7-2b32-11ec-9570-93580204e56b grant_number: '26130' name: Functional asymmetry of medial habenula outputs in mice publication: Cells publication_identifier: issn: - 2073-4409 publication_status: published publisher: MDPI quality_controlled: '1' status: public title: Nitrate, auxin and cytokinin - a trio to tango tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2023' ...