[{"oa":1,"publisher":"Oxford University Press","quality_controlled":"1","year":"2023","has_accepted_license":"1","publication":"The Plant Cell","day":"23","date_created":"2024-01-02T11:19:37Z","doi":"10.1093/plcell/koad324","date_published":"2023-12-23T00:00:00Z","article_number":"koad324","citation":{"chicago":"Zhou, Liang-Zi, Lele Wang, Xia Chen, Zengxiang Ge, Julia Mergner, Xingli Li, Bernhard Küster, Gernot Längst, Li-Jia Qu, and Thomas Dresselhaus. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” The Plant Cell. Oxford University Press, 2023. https://doi.org/10.1093/plcell/koad324.","ista":"Zhou L-Z, Wang L, Chen X, Ge Z, Mergner J, Li X, Küster B, Längst G, Qu L-J, Dresselhaus T. 2023. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell., koad324.","mla":"Zhou, Liang-Zi, et al. “The RALF Signaling Pathway Regulates Cell Wall Integrity during Pollen Tube Growth in Maize.” The Plant Cell, koad324, Oxford University Press, 2023, doi:10.1093/plcell/koad324.","apa":"Zhou, L.-Z., Wang, L., Chen, X., Ge, Z., Mergner, J., Li, X., … Dresselhaus, T. (2023). The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. Oxford University Press. https://doi.org/10.1093/plcell/koad324","ama":"Zhou L-Z, Wang L, Chen X, et al. The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize. The Plant Cell. 2023. doi:10.1093/plcell/koad324","ieee":"L.-Z. Zhou et al., “The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize,” The Plant Cell. Oxford University Press, 2023.","short":"L.-Z. Zhou, L. Wang, X. Chen, Z. Ge, J. Mergner, X. Li, B. Küster, G. Längst, L.-J. Qu, T. Dresselhaus, The Plant Cell (2023)."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","author":[{"full_name":"Zhou, Liang-Zi","last_name":"Zhou","first_name":"Liang-Zi"},{"first_name":"Lele","last_name":"Wang","full_name":"Wang, Lele"},{"first_name":"Xia","last_name":"Chen","full_name":"Chen, Xia"},{"first_name":"Zengxiang","id":"f43371a3-09ff-11eb-8013-bd0c6a2f6de8","last_name":"Ge","full_name":"Ge, Zengxiang","orcid":"0000-0001-9381-3577"},{"first_name":"Julia","last_name":"Mergner","full_name":"Mergner, Julia"},{"first_name":"Xingli","full_name":"Li, Xingli","last_name":"Li"},{"full_name":"Küster, Bernhard","last_name":"Küster","first_name":"Bernhard"},{"first_name":"Gernot","full_name":"Längst, Gernot","last_name":"Längst"},{"last_name":"Qu","full_name":"Qu, Li-Jia","first_name":"Li-Jia"},{"first_name":"Thomas","full_name":"Dresselhaus, Thomas","last_name":"Dresselhaus"}],"title":"The RALF signaling pathway regulates cell wall integrity during pollen tube growth in maize","abstract":[{"text":"Autocrine signaling pathways regulated by RAPID ALKALINIZATION FACTORs (RALFs) control cell wall integrity during pollen tube germination and growth in Arabidopsis (Arabidopsis thaliana). To investigate the role of pollen-specific RALFs in another plant species, we combined gene expression data with phylogenetic and biochemical studies to identify candidate orthologs in maize (Zea mays). We show that Clade IB ZmRALF2/3 mutations, but not Clade III ZmRALF1/5 mutations, cause cell wall instability in the sub-apical region of the growing pollen tube. ZmRALF2/3 are mainly located in the cell wall and are partially able to complement the pollen germination defect of their Arabidopsis orthologs AtRALF4/19. Mutations in ZmRALF2/3 compromise pectin distribution patterns leading to altered cell wall organization and thickness culminating in pollen tube burst. Clade IB, but not Clade III ZmRALFs, strongly interact as ligands with the pollen-specific Catharanthus roseus RLK1-like (CrRLK1L) receptor kinases Zea mays FERONIA-like (ZmFERL) 4/7/9, LORELEI-like glycosylphosphatidylinositol-anchor (LLG) proteins Zea mays LLG 1 and 2 (ZmLLG1/2) and Zea mays pollen extension-like (PEX) cell wall proteins ZmPEX2/4. Notably, ZmFERL4 outcompetes ZmLLG2 and ZmPEX2 outcompetes ZmFERL4 for ZmRALF2 binding. Based on these data, we suggest that Clade IB RALFs act in a dual role as cell wall components and extracellular sensors to regulate cell wall integrity and thickness during pollen tube growth in maize and probably other plants.","lang":"eng"}],"oa_version":"Published Version","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1093/plcell/koad324"}],"month":"12","publication_status":"epub_ahead","publication_identifier":{"eissn":["1532-298X"],"issn":["1040-4651"]},"language":[{"iso":"eng"}],"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","_id":"14726","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","keyword":["Cell Biology","Plant Science"],"status":"public","date_updated":"2024-01-03T12:43:41Z","ddc":["580"],"extern":"1"},{"article_number":"9","article_processing_charge":"No","external_id":{"arxiv":["1903.06981"]},"author":[{"first_name":"Ahmad","last_name":"Biniaz","full_name":"Biniaz, Ahmad"},{"first_name":"Kshitij","last_name":"Jain","full_name":"Jain, Kshitij"},{"first_name":"Anna","last_name":"Lubiw","full_name":"Lubiw, Anna"},{"first_name":"Zuzana","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová","orcid":"0000-0002-6660-1322","full_name":"Masárová, Zuzana"},{"first_name":"Tillmann","last_name":"Miltzow","full_name":"Miltzow, Tillmann"},{"full_name":"Mondal, Debajyoti","last_name":"Mondal","first_name":"Debajyoti"},{"full_name":"Naredla, Anurag Murty","last_name":"Naredla","first_name":"Anurag Murty"},{"id":"3F24CCC8-F248-11E8-B48F-1D18A9856A87","first_name":"Josef","orcid":"0000-0002-1097-9684","full_name":"Tkadlec, Josef","last_name":"Tkadlec"},{"first_name":"Alexi","full_name":"Turcotte, Alexi","last_name":"Turcotte"}],"title":"Token swapping on trees","citation":{"apa":"Biniaz, A., Jain, K., Lubiw, A., Masárová, Z., Miltzow, T., Mondal, D., … Turcotte, A. (2023). Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. EPI Sciences. https://doi.org/10.46298/DMTCS.8383","ama":"Biniaz A, Jain K, Lubiw A, et al. Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. 2023;24(2). doi:10.46298/DMTCS.8383","ieee":"A. Biniaz et al., “Token swapping on trees,” Discrete Mathematics and Theoretical Computer Science, vol. 24, no. 2. EPI Sciences, 2023.","short":"A. Biniaz, K. Jain, A. Lubiw, Z. Masárová, T. Miltzow, D. Mondal, A.M. Naredla, J. Tkadlec, A. Turcotte, Discrete Mathematics and Theoretical Computer Science 24 (2023).","mla":"Biniaz, Ahmad, et al. “Token Swapping on Trees.” Discrete Mathematics and Theoretical Computer Science, vol. 24, no. 2, 9, EPI Sciences, 2023, doi:10.46298/DMTCS.8383.","ista":"Biniaz A, Jain K, Lubiw A, Masárová Z, Miltzow T, Mondal D, Naredla AM, Tkadlec J, Turcotte A. 2023. Token swapping on trees. Discrete Mathematics and Theoretical Computer Science. 24(2), 9.","chicago":"Biniaz, Ahmad, Kshitij Jain, Anna Lubiw, Zuzana Masárová, Tillmann Miltzow, Debajyoti Mondal, Anurag Murty Naredla, Josef Tkadlec, and Alexi Turcotte. “Token Swapping on Trees.” Discrete Mathematics and Theoretical Computer Science. EPI Sciences, 2023. https://doi.org/10.46298/DMTCS.8383."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"EPI Sciences","acknowledgement":"This work was begun at the University of Waterloo and was partially supported by the Natural Sciences and Engineering Council of Canada (NSERC).\r\n","date_created":"2023-04-16T22:01:08Z","date_published":"2023-01-18T00:00:00Z","doi":"10.46298/DMTCS.8383","year":"2023","has_accepted_license":"1","publication":"Discrete Mathematics and Theoretical Computer Science","day":"18","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","_id":"12833","file_date_updated":"2023-04-17T08:10:28Z","department":[{"_id":"KrCh"},{"_id":"HeEd"},{"_id":"UlWa"}],"date_updated":"2024-01-04T12:42:09Z","ddc":["000"],"scopus_import":"1","intvolume":" 24","month":"01","abstract":[{"lang":"eng","text":"The input to the token swapping problem is a graph with vertices v1, v2, . . . , vn, and n tokens with labels 1,2, . . . , n, one on each vertex. The goal is to get token i to vertex vi for all i= 1, . . . , n using a minimum number of swaps, where a swap exchanges the tokens on the endpoints of an edge.Token swapping on a tree, also known as “sorting with a transposition tree,” is not known to be in P nor NP-complete. We present some partial results: 1. An optimum swap sequence may need to perform a swap on a leaf vertex that has the correct token (a “happy leaf”), disproving a conjecture of Vaughan. 2. Any algorithm that fixes happy leaves—as all known approximation algorithms for the problem do—has approximation factor at least 4/3. Furthermore, the two best-known 2-approximation algorithms have approximation factor exactly 2. 3. A generalized problem—weighted coloured token swapping—is NP-complete on trees, but solvable in polynomial time on paths and stars. In this version, tokens and vertices have colours, and colours have weights. The goal is to get every token to a vertex of the same colour, and the cost of a swap is the sum of the weights of the two tokens involved."}],"oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","issue":"2","volume":24,"related_material":{"record":[{"id":"7950","status":"public","relation":"earlier_version"}]},"publication_status":"published","publication_identifier":{"issn":["1462-7264"],"eissn":["1365-8050"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"439102ea4f6e2aeefd7107dfb9ccf532","file_id":"12844","success":1,"date_updated":"2023-04-17T08:10:28Z","file_size":2072197,"creator":"dernst","date_created":"2023-04-17T08:10:28Z","file_name":"2022_DMTCS_Biniaz.pdf"}]},{"department":[{"_id":"ElKo"},{"_id":"GradSch"}],"date_updated":"2024-01-08T09:28:14Z","conference":{"name":"FC: Financial Cryptography and Data Security","start_date":"2023-05-01","location":"Bol, Brac, Croatia","end_date":"2023-05-05"},"type":"conference","status":"public","_id":"14735","volume":13950,"publication_status":"published","publication_identifier":{"eisbn":["9783031477546"],"issn":["1611-3349"],"isbn":["9783031477539"],"eissn":["0302-9743"]},"language":[{"iso":"eng"}],"main_file_link":[{"url":"https://eprint.iacr.org/2022/1554","open_access":"1"}],"alternative_title":["LNCS"],"scopus_import":"1","intvolume":" 13950","month":"12","abstract":[{"text":"Scaling blockchain protocols to perform on par with the expected needs of Web3.0 has been proven to be a challenging task with almost a decade of research. In the forefront of the current solution is the idea of separating the execution of the updates encoded in a block from the ordering of blocks. In order to achieve this, a new class of protocols called rollups has emerged. Rollups have as input a total ordering of valid and invalid transactions and as output a new valid state-transition.\r\nIf we study rollups from a distributed computing perspective, we uncover that rollups take as input the output of a Byzantine Atomic Broadcast (BAB) protocol and convert it to a State Machine Replication (SMR) protocol. BAB and SMR, however, are considered equivalent as far as distributed computing is concerned and a solution to one can easily be retrofitted to solve the other simply by adding/removing an execution step before the validation of the input.\r\nThis “easy” step of retrofitting an atomic broadcast solution to implement an SMR has, however, been overlooked in practice. In this paper, we formalize the problem and show that after BAB is solved, traditional impossibility results for consensus no longer apply towards an SMR. Leveraging this we propose a distributed execution protocol that allows reduced execution and storage cost per executor (O(log2n/n)) without relaxing the network assumptions of the underlying BAB protocol and providing censorship-resistance. Finally, we propose efficient non-interactive light client constructions that leverage our efficient execution protocols and do not require any synchrony assumptions or expensive ZK-proofs.","lang":"eng"}],"oa_version":"Preprint","article_processing_charge":"No","author":[{"id":"a20e8902-32b0-11ee-9fa8-b23fa638b793","first_name":"Christos","last_name":"Stefo","full_name":"Stefo, Christos"},{"first_name":"Zhuolun","full_name":"Xiang, Zhuolun","last_name":"Xiang"},{"full_name":"Kokoris Kogias, Eleftherios","last_name":"Kokoris Kogias","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","first_name":"Eleftherios"}],"title":"Executing and proving over dirty ledgers","citation":{"mla":"Stefo, Christos, et al. “Executing and Proving over Dirty Ledgers.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 3–20, doi:10.1007/978-3-031-47754-6_1.","apa":"Stefo, C., Xiang, Z., & Kokoris Kogias, E. (2023). Executing and proving over dirty ledgers. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 3–20). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_1","ama":"Stefo C, Xiang Z, Kokoris Kogias E. Executing and proving over dirty ledgers. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:3-20. doi:10.1007/978-3-031-47754-6_1","ieee":"C. Stefo, Z. Xiang, and E. Kokoris Kogias, “Executing and proving over dirty ledgers,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 3–20.","short":"C. Stefo, Z. Xiang, E. Kokoris Kogias, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 3–20.","chicago":"Stefo, Christos, Zhuolun Xiang, and Eleftherios Kokoris Kogias. “Executing and Proving over Dirty Ledgers.” In 27th International Conference on Financial Cryptography and Data Security, 13950:3–20. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_1.","ista":"Stefo C, Xiang Z, Kokoris Kogias E. 2023. Executing and proving over dirty ledgers. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 3–20."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"_id":"34a4ce89-11ca-11ed-8bc3-8cc37fb6e11f","name":"Secure Network and Hardware for Efficient Blockchains","grant_number":"F8512"}],"page":"3-20","date_created":"2024-01-08T09:17:38Z","doi":"10.1007/978-3-031-47754-6_1","date_published":"2023-12-01T00:00:00Z","year":"2023","publication":"27th International Conference on Financial Cryptography and Data Security","day":"01","oa":1,"publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Eleftherios Kokoris-Kogias is partially supported by Austrian Science Fund (FWF) grant No: F8512-N."},{"keyword":["Electrical and Electronic Engineering","Materials Chemistry","Electrochemistry","Energy Engineering and Power Technology","Chemical Engineering (miscellaneous)"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"14733","department":[{"_id":"StFr"}],"ddc":["540"],"date_updated":"2024-01-08T09:03:01Z","month":"12","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1021/acsaem.3c02223"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Redox flow batteries (RFBs) rely on the development of cheap, highly soluble, and high-energy-density electrolytes. Several candidate quinones have already been investigated in the literature as two-electron anolytes or catholytes, benefiting from fast kinetics, high tunability, and low cost. Here, an investigation of nitrogen-rich fused heteroaromatic quinones was carried out to explore avenues for electrolyte development. These quinones were synthesized and screened by using electrochemical techniques. The most promising candidate, 4,8-dioxo-4,8-dihydrobenzo[1,2-d:4,5-d′]bis([1,2,3]triazole)-1,5-diide (−0.68 V(SHE)), was tested in both an asymmetric and symmetric full-cell setup resulting in capacity fade rates of 0.35% per cycle and 0.0124% per cycle, respectively. In situ ultraviolet-visible spectroscopy (UV–Vis), nuclear magnetic resonance (NMR), and electron paramagnetic resonance (EPR) spectroscopies were used to investigate the electrochemical stability of the charged species during operation. UV–Vis spectroscopy, supported by density functional theory (DFT) modeling, reaffirmed that the two-step charging mechanism observed during battery operation consisted of two, single-electron transfers. The radical concentration during battery operation and the degree of delocalization of the unpaired electron were quantified with NMR and EPR spectroscopy."}],"ec_funded":1,"language":[{"iso":"eng"}],"publication_status":"epub_ahead","publication_identifier":{"eissn":["2574-0962"]},"project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"}],"title":"Exploring the landscape of heterocyclic quinones for redox flow batteries","article_processing_charge":"Yes (in subscription journal)","author":[{"id":"4cc538d5-803f-11ed-ab7e-8139573aad8f","first_name":"Rajesh B","last_name":"Jethwa","orcid":"0000-0002-0404-4356","full_name":"Jethwa, Rajesh B"},{"first_name":"Dominic","full_name":"Hey, Dominic","last_name":"Hey"},{"first_name":"Rachel N.","full_name":"Kerber, Rachel N.","last_name":"Kerber"},{"last_name":"Bond","full_name":"Bond, Andrew D.","first_name":"Andrew D."},{"full_name":"Wright, Dominic S.","last_name":"Wright","first_name":"Dominic S."},{"first_name":"Clare P.","last_name":"Grey","full_name":"Grey, Clare P."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"R. B. Jethwa, D. Hey, R. N. Kerber, A. D. Bond, D. S. Wright, and C. P. Grey, “Exploring the landscape of heterocyclic quinones for redox flow batteries,” ACS Applied Energy Materials. American Chemical Society, 2023.","short":"R.B. Jethwa, D. Hey, R.N. Kerber, A.D. Bond, D.S. Wright, C.P. Grey, ACS Applied Energy Materials (2023).","apa":"Jethwa, R. B., Hey, D., Kerber, R. N., Bond, A. D., Wright, D. S., & Grey, C. P. (2023). Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. American Chemical Society. https://doi.org/10.1021/acsaem.3c02223","ama":"Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials. 2023. doi:10.1021/acsaem.3c02223","mla":"Jethwa, Rajesh B., et al. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” ACS Applied Energy Materials, American Chemical Society, 2023, doi:10.1021/acsaem.3c02223.","ista":"Jethwa RB, Hey D, Kerber RN, Bond AD, Wright DS, Grey CP. 2023. Exploring the landscape of heterocyclic quinones for redox flow batteries. ACS Applied Energy Materials.","chicago":"Jethwa, Rajesh B, Dominic Hey, Rachel N. Kerber, Andrew D. Bond, Dominic S. Wright, and Clare P. Grey. “Exploring the Landscape of Heterocyclic Quinones for Redox Flow Batteries.” ACS Applied Energy Materials. American Chemical Society, 2023. https://doi.org/10.1021/acsaem.3c02223."},"oa":1,"publisher":"American Chemical Society","quality_controlled":"1","date_created":"2024-01-05T09:20:48Z","doi":"10.1021/acsaem.3c02223","date_published":"2023-12-28T00:00:00Z","publication":"ACS Applied Energy Materials","day":"28","year":"2023","has_accepted_license":"1"},{"day":"28","language":[{"iso":"eng"}],"publication":"Small Methods","publication_identifier":{"eissn":["2366-9608"]},"year":"2023","publication_status":"epub_ahead","doi":"10.1002/smtd.202301377","date_published":"2023-12-28T00:00:00Z","date_created":"2024-01-07T23:00:51Z","oa_version":"None","pmid":1,"acknowledgement":"Y.L. acknowledges funding from the National Natural Science Foundation of China (NSFC) (Grants No. 22209034), the Innovation and Entrepreneurship Project of Overseas Returnees in Anhui Province (Grant No. 2022LCX002). K.H.L. acknowledges financial support from the National Natural Science Foundation of China (NSFC) (Grant No. 22208293). M.I. acknowledges financial support from ISTA and the Werner Siemens Foundation.","abstract":[{"lang":"eng","text":"Developing cost-effective and high-performance thermoelectric (TE) materials to assemble efficient TE devices presents a multitude of challenges and opportunities. Cu3SbSe4 is a promising p-type TE material based on relatively earth abundant elements. However, the challenge lies in its poor electrical conductivity. Herein, an efficient and scalable solution-based approach is developed to synthesize high-quality Cu3SbSe4 nanocrystals doped with Pb at the Sb site. After ligand displacement and annealing treatments, the dried powders are consolidated into dense pellets, and their TE properties are investigated. Pb doping effectively increases the charge carrier concentration, resulting in a significant increase in electrical conductivity, while the Seebeck coefficients remain consistently high. The calculated band structure shows that Pb doping induces band convergence, thereby increasing the effective mass. Furthermore, the large ionic radius of Pb2+ results in the generation of additional point and plane defects and interphases, dramatically enhancing phonon scattering, which significantly decreases the lattice thermal conductivity at high temperatures. Overall, a maximum figure of merit (zTmax) ≈ 0.85 at 653 K is obtained in Cu3Sb0.97Pb0.03Se4. This represents a 1.6-fold increase compared to the undoped sample and exceeds most doped Cu3SbSe4-based materials produced by solid-state, demonstrating advantages of versatility and cost-effectiveness using a solution-based technology."}],"month":"12","scopus_import":"1","publisher":"Wiley","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-08T09:17:04Z","citation":{"mla":"Wan, Shanhong, et al. “Band Engineering through Pb-Doping of Nanocrystal Building Blocks to Enhance Thermoelectric Performance in Cu3SbSe4.” Small Methods, Wiley, 2023, doi:10.1002/smtd.202301377.","short":"S. Wan, S. Xiao, M. Li, X. Wang, K.H. Lim, M. Hong, M. Ibáñez, A. Cabot, Y. Liu, Small Methods (2023).","ieee":"S. Wan et al., “Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4,” Small Methods. Wiley, 2023.","ama":"Wan S, Xiao S, Li M, et al. Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. 2023. doi:10.1002/smtd.202301377","apa":"Wan, S., Xiao, S., Li, M., Wang, X., Lim, K. H., Hong, M., … Liu, Y. (2023). Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods. Wiley. https://doi.org/10.1002/smtd.202301377","chicago":"Wan, Shanhong, Shanshan Xiao, Mingquan Li, Xin Wang, Khak Ho Lim, Min Hong, Maria Ibáñez, Andreu Cabot, and Yu Liu. “Band Engineering through Pb-Doping of Nanocrystal Building Blocks to Enhance Thermoelectric Performance in Cu3SbSe4.” Small Methods. Wiley, 2023. https://doi.org/10.1002/smtd.202301377.","ista":"Wan S, Xiao S, Li M, Wang X, Lim KH, Hong M, Ibáñez M, Cabot A, Liu Y. 2023. Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4. Small Methods."},"department":[{"_id":"MaIb"}],"title":"Band engineering through Pb-doping of nanocrystal building blocks to enhance thermoelectric performance in Cu3SbSe4","author":[{"first_name":"Shanhong","last_name":"Wan","full_name":"Wan, Shanhong"},{"first_name":"Shanshan","full_name":"Xiao, Shanshan","last_name":"Xiao"},{"full_name":"Li, Mingquan","last_name":"Li","first_name":"Mingquan"},{"first_name":"Xin","full_name":"Wang, Xin","last_name":"Wang"},{"first_name":"Khak Ho","full_name":"Lim, Khak Ho","last_name":"Lim"},{"first_name":"Min","last_name":"Hong","full_name":"Hong, Min"},{"first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87","full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez"},{"full_name":"Cabot, Andreu","last_name":"Cabot","first_name":"Andreu"},{"last_name":"Liu","full_name":"Liu, Yu","orcid":"0000-0001-7313-6740","first_name":"Yu","id":"2A70014E-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["38152986"]},"article_processing_charge":"No","_id":"14734","status":"public","project":[{"name":"HighTE: The Werner Siemens Laboratory for the High Throughput Discovery of Semiconductors for Waste Heat Recovery","_id":"9B8F7476-BA93-11EA-9121-9846C619BF3A"}],"type":"journal_article","article_type":"original"},{"citation":{"ista":"Ivanov G, Naszódi M. 2023. Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. 2023(23), 20613–20669.","chicago":"Ivanov, Grigory, and Márton Naszódi. “Functional John and Löwner Conditions for Pairs of Log-Concave Functions.” International Mathematics Research Notices. Oxford University Press, 2023. https://doi.org/10.1093/imrn/rnad210.","short":"G. Ivanov, M. Naszódi, International Mathematics Research Notices 2023 (2023) 20613–20669.","ieee":"G. Ivanov and M. Naszódi, “Functional John and Löwner conditions for pairs of log-concave functions,” International Mathematics Research Notices, vol. 2023, no. 23. Oxford University Press, pp. 20613–20669, 2023.","ama":"Ivanov G, Naszódi M. Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. 2023;2023(23):20613-20669. doi:10.1093/imrn/rnad210","apa":"Ivanov, G., & Naszódi, M. (2023). Functional John and Löwner conditions for pairs of log-concave functions. International Mathematics Research Notices. Oxford University Press. https://doi.org/10.1093/imrn/rnad210","mla":"Ivanov, Grigory, and Márton Naszódi. “Functional John and Löwner Conditions for Pairs of Log-Concave Functions.” International Mathematics Research Notices, vol. 2023, no. 23, Oxford University Press, 2023, pp. 20613–69, doi:10.1093/imrn/rnad210."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"arxiv":["2212.11781"]},"article_processing_charge":"Yes (via OA deal)","author":[{"last_name":"Ivanov","full_name":"Ivanov, Grigory","first_name":"Grigory","id":"87744F66-5C6F-11EA-AFE0-D16B3DDC885E"},{"full_name":"Naszódi, Márton","last_name":"Naszódi","first_name":"Márton"}],"title":"Functional John and Löwner conditions for pairs of log-concave functions","acknowledgement":"We thank Alexander Litvak for the many discussions on Theorem 1.1. Igor Tsiutsiurupa participated in the early stage of this project. To our deep regret, Igor chose another road for his life and stopped working with us.\r\nThis work was supported by the János Bolyai Scholarship of the Hungarian Academy of Sciences [to M.N.]; the National Research, Development, and Innovation Fund (NRDI) [K119670 and K131529 to M.N.]; and the ÚNKP-22-5 New National Excellence Program of the Ministry for Innovation and Technology from the source of the NRDI [to M.N.].","oa":1,"quality_controlled":"1","publisher":"Oxford University Press","year":"2023","has_accepted_license":"1","publication":"International Mathematics Research Notices","day":"01","page":"20613-20669","date_created":"2024-01-08T09:48:56Z","doi":"10.1093/imrn/rnad210","date_published":"2023-12-01T00:00:00Z","_id":"14737","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","keyword":["General Mathematics"],"status":"public","date_updated":"2024-01-08T09:57:25Z","ddc":["510"],"file_date_updated":"2024-01-08T09:53:09Z","department":[{"_id":"UlWa"}],"abstract":[{"lang":"eng","text":"John’s fundamental theorem characterizing the largest volume ellipsoid contained in a convex body $K$ in $\\mathbb{R}^{d}$ has seen several generalizations and extensions. One direction, initiated by V. Milman is to replace ellipsoids by positions (affine images) of another body $L$. Another, more recent direction is to consider logarithmically concave functions on $\\mathbb{R}^{d}$ instead of convex bodies: we designate some special, radially symmetric log-concave function $g$ as the analogue of the Euclidean ball, and want to find its largest integral position under the constraint that it is pointwise below some given log-concave function $f$. We follow both directions simultaneously: we consider the functional question, and allow essentially any meaningful function to play the role of $g$ above. Our general theorems jointly extend known results in both directions. The dual problem in the setting of convex bodies asks for the smallest volume ellipsoid, called Löwner’s ellipsoid, containing $K$. We consider the analogous problem for functions: we characterize the solutions of the optimization problem of finding a smallest integral position of some log-concave function $g$ under the constraint that it is pointwise above $f$. It turns out that in the functional setting, the relationship between the John and the Löwner problems is more intricate than it is in the setting of convex bodies."}],"oa_version":"Published Version","intvolume":" 2023","month":"12","publication_status":"published","publication_identifier":{"eissn":["1687-0247"],"issn":["1073-7928"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2023_IMRN_Ivanov.pdf","date_created":"2024-01-08T09:53:09Z","creator":"dernst","file_size":815777,"date_updated":"2024-01-08T09:53:09Z","success":1,"file_id":"14738","checksum":"353666cea80633beb0f1ffd342dff6d4","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"volume":2023,"issue":"23"},{"page":"309-325","date_created":"2024-01-08T09:30:22Z","date_published":"2023-12-01T00:00:00Z","doi":"10.1007/978-3-031-47754-6_18","year":"2023","publication":"27th International Conference on Financial Cryptography and Data Security","day":"01","publisher":"Springer Nature","quality_controlled":"1","acknowledgement":"Supported by the German Federal Ministry of Education and Research (BMBF), grant 16KISK020K (6G-RIC), 2021–2025, and ERC CoG 863818 (ForM-SMArt).","article_processing_charge":"No","author":[{"last_name":"Bastankhah","full_name":"Bastankhah, Mahsa","first_name":"Mahsa"},{"full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","last_name":"Chatterjee","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Maddah-Ali","full_name":"Maddah-Ali, Mohammad Ali","first_name":"Mohammad Ali"},{"last_name":"Schmid","full_name":"Schmid, Stefan","first_name":"Stefan"},{"last_name":"Svoboda","full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","first_name":"Jakub","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425"},{"first_name":"Michelle X","id":"2D82B818-F248-11E8-B48F-1D18A9856A87","last_name":"Yeo","full_name":"Yeo, Michelle X"}],"title":"R2: Boosting liquidity in payment channel networks with online admission control","citation":{"ista":"Bastankhah M, Chatterjee K, Maddah-Ali MA, Schmid S, Svoboda J, Yeo MX. 2023. R2: Boosting liquidity in payment channel networks with online admission control. 27th International Conference on Financial Cryptography and Data Security. FC: Financial Cryptography and Data Security, LNCS, vol. 13950, 309–325.","chicago":"Bastankhah, Mahsa, Krishnendu Chatterjee, Mohammad Ali Maddah-Ali, Stefan Schmid, Jakub Svoboda, and Michelle X Yeo. “R2: Boosting Liquidity in Payment Channel Networks with Online Admission Control.” In 27th International Conference on Financial Cryptography and Data Security, 13950:309–25. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-47754-6_18.","short":"M. Bastankhah, K. Chatterjee, M.A. Maddah-Ali, S. Schmid, J. Svoboda, M.X. Yeo, in:, 27th International Conference on Financial Cryptography and Data Security, Springer Nature, 2023, pp. 309–325.","ieee":"M. Bastankhah, K. Chatterjee, M. A. Maddah-Ali, S. Schmid, J. Svoboda, and M. X. Yeo, “R2: Boosting liquidity in payment channel networks with online admission control,” in 27th International Conference on Financial Cryptography and Data Security, Bol, Brac, Croatia, 2023, vol. 13950, pp. 309–325.","ama":"Bastankhah M, Chatterjee K, Maddah-Ali MA, Schmid S, Svoboda J, Yeo MX. R2: Boosting liquidity in payment channel networks with online admission control. In: 27th International Conference on Financial Cryptography and Data Security. Vol 13950. Springer Nature; 2023:309-325. doi:10.1007/978-3-031-47754-6_18","apa":"Bastankhah, M., Chatterjee, K., Maddah-Ali, M. A., Schmid, S., Svoboda, J., & Yeo, M. X. (2023). R2: Boosting liquidity in payment channel networks with online admission control. In 27th International Conference on Financial Cryptography and Data Security (Vol. 13950, pp. 309–325). Bol, Brac, Croatia: Springer Nature. https://doi.org/10.1007/978-3-031-47754-6_18","mla":"Bastankhah, Mahsa, et al. “R2: Boosting Liquidity in Payment Channel Networks with Online Admission Control.” 27th International Conference on Financial Cryptography and Data Security, vol. 13950, Springer Nature, 2023, pp. 309–25, doi:10.1007/978-3-031-47754-6_18."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"ec_funded":1,"volume":13950,"publication_status":"published","publication_identifier":{"eisbn":["9783031477546"],"isbn":["9783031477539"],"eissn":["1611-3349"],"issn":["0302-9743"]},"language":[{"iso":"eng"}],"alternative_title":["LNCS"],"intvolume":" 13950","month":"12","abstract":[{"text":"Payment channel networks (PCNs) are a promising technology to improve the scalability of cryptocurrencies. PCNs, however, face the challenge that the frequent usage of certain routes may deplete channels in one direction, and hence prevent further transactions. In order to reap the full potential of PCNs, recharging and rebalancing mechanisms are required to provision channels, as well as an admission control logic to decide which transactions to reject in case capacity is insufficient. This paper presents a formal model of this optimisation problem. In particular, we consider an online algorithms perspective, where transactions arrive over time in an unpredictable manner. Our main contributions are competitive online algorithms which come with provable guarantees over time. We empirically evaluate our algorithms on randomly generated transactions to compare the average performance of our algorithms to our theoretical bounds. We also show how this model and approach differs from related problems in classic communication networks.","lang":"eng"}],"oa_version":"None","department":[{"_id":"KrCh"},{"_id":"KrPi"}],"date_updated":"2024-01-08T09:36:36Z","conference":{"name":"FC: Financial Cryptography and Data Security","start_date":"2023-05-01","end_date":"2023-05-05","location":"Bol, Brac, Croatia"},"type":"conference","status":"public","_id":"14736"},{"page":"14069-14080","date_published":"2023-12-01T00:00:00Z","doi":"10.1109/tpami.2023.3308391","date_created":"2024-01-08T09:59:46Z","has_accepted_license":"1","year":"2023","day":"01","publication":"IEEE Transactions on Pattern Analysis and Machine Intelligence","publisher":"IEEE","quality_controlled":"1","oa":1,"acknowledgement":"The work of Maria-Jose Jimenez, Eduardo Paluzo-Hidalgo and Manuel Soriano-Trigueros was supported in part by the Spanish grant Ministerio de Ciencia e Innovacion under Grants TED2021-129438B-I00 and PID2019-107339GB-I00, and in part by REXASI-PRO H-EU project, call HORIZON-CL4-2021-HUMAN-01-01 under Grant 101070028. The work of\r\nMaria-Jose Jimenez was supported by a grant of Convocatoria de la Universidad de Sevilla para la recualificacion del sistema universitario español, 2021-23, funded by the European Union, NextGenerationEU. The work of Vidit Nanda was supported in part by EPSRC under Grant EP/R018472/1 and in part by US AFOSR under Grant FA9550-22-1-0462. \r\nWe are grateful to the team of GUDHI and TEASPOON developers, for their work and their support. We are also grateful to Streamlit for providing extra resources to deploy the web app\r\nonline on Streamlit community cloud. We thank the anonymous referees for their helpful suggestions.","author":[{"first_name":"Dashti","full_name":"Ali, Dashti","last_name":"Ali"},{"first_name":"Aras","last_name":"Asaad","full_name":"Asaad, Aras"},{"full_name":"Jimenez, Maria-Jose","last_name":"Jimenez","first_name":"Maria-Jose"},{"first_name":"Vidit","last_name":"Nanda","full_name":"Nanda, Vidit"},{"last_name":"Paluzo-Hidalgo","full_name":"Paluzo-Hidalgo, Eduardo","first_name":"Eduardo"},{"first_name":"Manuel","id":"15ebd7cf-15bf-11ee-aebd-bb4bb5121ea8","last_name":"Soriano Trigueros","full_name":"Soriano Trigueros, Manuel","orcid":"0000-0003-2449-1433"}],"article_processing_charge":"Yes (in subscription journal)","title":"A survey of vectorization methods in topological data analysis","citation":{"ista":"Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. 2023. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 45(12), 14069–14080.","chicago":"Ali, Dashti, Aras Asaad, Maria-Jose Jimenez, Vidit Nanda, Eduardo Paluzo-Hidalgo, and Manuel Soriano Trigueros. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE, 2023. https://doi.org/10.1109/tpami.2023.3308391.","ieee":"D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, and M. Soriano Trigueros, “A survey of vectorization methods in topological data analysis,” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12. IEEE, pp. 14069–14080, 2023.","short":"D. Ali, A. Asaad, M.-J. Jimenez, V. Nanda, E. Paluzo-Hidalgo, M. Soriano Trigueros, IEEE Transactions on Pattern Analysis and Machine Intelligence 45 (2023) 14069–14080.","ama":"Ali D, Asaad A, Jimenez M-J, Nanda V, Paluzo-Hidalgo E, Soriano Trigueros M. A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. 2023;45(12):14069-14080. doi:10.1109/tpami.2023.3308391","apa":"Ali, D., Asaad, A., Jimenez, M.-J., Nanda, V., Paluzo-Hidalgo, E., & Soriano Trigueros, M. (2023). A survey of vectorization methods in topological data analysis. IEEE Transactions on Pattern Analysis and Machine Intelligence. IEEE. https://doi.org/10.1109/tpami.2023.3308391","mla":"Ali, Dashti, et al. “A Survey of Vectorization Methods in Topological Data Analysis.” IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 45, no. 12, IEEE, 2023, pp. 14069–80, doi:10.1109/tpami.2023.3308391."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","issue":"12","volume":45,"publication_identifier":{"issn":["0162-8828"],"eissn":["1939-3539"]},"publication_status":"published","file":[{"success":1,"file_id":"14740","checksum":"465c28ef0b151b4b1fb47977ed5581ab","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_IEEEToP_Ali.pdf","date_created":"2024-01-08T10:09:14Z","creator":"dernst","file_size":2370988,"date_updated":"2024-01-08T10:09:14Z"}],"language":[{"iso":"eng"}],"month":"12","intvolume":" 45","abstract":[{"lang":"eng","text":"Attempts to incorporate topological information in supervised learning tasks have resulted in the creation of several techniques for vectorizing persistent homology barcodes. In this paper, we study thirteen such methods. Besides describing an organizational framework for these methods, we comprehensively benchmark them against three well-known classification tasks. Surprisingly, we discover that the best-performing method is a simple vectorization, which consists only of a few elementary summary statistics. Finally, we provide a convenient web application which has been designed to facilitate exploration and experimentation with various vectorization methods."}],"oa_version":"Published Version","department":[{"_id":"HeEd"}],"file_date_updated":"2024-01-08T10:09:14Z","date_updated":"2024-01-08T10:11:46Z","ddc":["000"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Applied Mathematics","Artificial Intelligence","Computational Theory and Mathematics","Computer Vision and Pattern Recognition","Software"],"_id":"14739"},{"article_number":"a041447","citation":{"mla":"Lucek, Kay, et al. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11, a041447, Cold Spring Harbor Laboratory, 2023, doi:10.1101/cshperspect.a041447.","short":"K. Lucek, M.D. Giménez, M. Joron, M. Rafajlović, J.B. Searle, N. Walden, A.M. Westram, R. Faria, Cold Spring Harbor Perspectives in Biology 15 (2023).","ieee":"K. Lucek et al., “The impact of chromosomal rearrangements in speciation: From micro- to macroevolution,” Cold Spring Harbor Perspectives in Biology, vol. 15, no. 11. Cold Spring Harbor Laboratory, 2023.","ama":"Lucek K, Giménez MD, Joron M, et al. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 2023;15(11). doi:10.1101/cshperspect.a041447","apa":"Lucek, K., Giménez, M. D., Joron, M., Rafajlović, M., Searle, J. B., Walden, N., … Faria, R. (2023). The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory. https://doi.org/10.1101/cshperspect.a041447","chicago":"Lucek, Kay, Mabel D. Giménez, Mathieu Joron, Marina Rafajlović, Jeremy B. Searle, Nora Walden, Anja M Westram, and Rui Faria. “The Impact of Chromosomal Rearrangements in Speciation: From Micro- to Macroevolution.” Cold Spring Harbor Perspectives in Biology. Cold Spring Harbor Laboratory, 2023. https://doi.org/10.1101/cshperspect.a041447.","ista":"Lucek K, Giménez MD, Joron M, Rafajlović M, Searle JB, Walden N, Westram AM, Faria R. 2023. The impact of chromosomal rearrangements in speciation: From micro- to macroevolution. Cold Spring Harbor Perspectives in Biology. 15(11), a041447."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"pmid":["37604585"]},"article_processing_charge":"No","author":[{"last_name":"Lucek","full_name":"Lucek, Kay","first_name":"Kay"},{"last_name":"Giménez","full_name":"Giménez, Mabel D.","first_name":"Mabel D."},{"full_name":"Joron, Mathieu","last_name":"Joron","first_name":"Mathieu"},{"full_name":"Rafajlović, Marina","last_name":"Rafajlović","first_name":"Marina"},{"last_name":"Searle","full_name":"Searle, Jeremy B.","first_name":"Jeremy B."},{"full_name":"Walden, Nora","last_name":"Walden","first_name":"Nora"},{"orcid":"0000-0003-1050-4969","full_name":"Westram, Anja M","last_name":"Westram","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Faria","full_name":"Faria, Rui","first_name":"Rui"}],"title":"The impact of chromosomal rearrangements in speciation: From micro- to macroevolution","acknowledgement":"K.L. was funded by a Swiss National Science Foundation Eccellenza project: The evolution of strong reproductive barriers towards the completion of speciation (PCEFP3_202869). R.F.\r\nwas funded by an FCT CEEC (Fundação para a Ciênca e a Tecnologia, Concurso Estímulo ao\r\nEmprego Científico) contract (2020.00275. CEECIND) and by an FCT research project\r\n(PTDC/BIA-EVL/1614/2021). M.R. was funded by the Swedish Research Council Vetenskapsrådet (grant number 2021-05243). A.M.W. was partly funded by the Norwegian Research Council RCN. We thank Luis Silva for his help preparing Figure 1. We are grateful to Maren Wellenreuther, Daniel Bolnick, and two anonymous reviewers for their constructive feedback on an earlier version of this paper.","oa":1,"publisher":"Cold Spring Harbor Laboratory","quality_controlled":"1","year":"2023","publication":"Cold Spring Harbor Perspectives in Biology","day":"01","date_created":"2024-01-08T12:43:48Z","doi":"10.1101/cshperspect.a041447","date_published":"2023-11-01T00:00:00Z","_id":"14742","type":"journal_article","article_type":"original","keyword":["General Biochemistry","Genetics and Molecular Biology"],"status":"public","date_updated":"2024-01-08T12:52:29Z","department":[{"_id":"NiBa"},{"_id":"BeVi"}],"abstract":[{"text":"Chromosomal rearrangements (CRs) have been known since almost the beginning of genetics.\r\nWhile an important role for CRs in speciation has been suggested, evidence primarily stems\r\nfrom theoretical and empirical studies focusing on the microevolutionary level (i.e., on taxon\r\npairs where speciation is often incomplete). Although the role of CRs in eukaryotic speciation at\r\na macroevolutionary level has been supported by associations between species diversity and\r\nrates of evolution of CRs across phylogenies, these findings are limited to a restricted range of\r\nCRs and taxa. Now that more broadly applicable and precise CR detection approaches have\r\nbecome available, we address the challenges in filling some of the conceptual and empirical\r\ngaps between micro- and macroevolutionary studies on the role of CRs in speciation. We\r\nsynthesize what is known about the macroevolutionary impact of CRs and suggest new research avenues to overcome the pitfalls of previous studies to gain a more comprehensive understanding of the evolutionary significance of CRs in speciation across the tree of life.","lang":"eng"}],"pmid":1,"oa_version":"Published Version","main_file_link":[{"url":"https://doi.org/10.1101/cshperspect.a041447","open_access":"1"}],"scopus_import":"1","intvolume":" 15","month":"11","publication_status":"published","publication_identifier":{"issn":["1943-0264"]},"language":[{"iso":"eng"}],"issue":"11","volume":15},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Avarikioti, Zeta, Antoine Desjardins, Eleftherios Kokoris Kogias, and Roger Wattenhofer. “Divide & Scale: Formalization and Roadmap to Robust Sharding.” In 30th International Colloquium on Structural Information and Communication Complexity, 13892:199–245. Springer Nature, 2023. https://doi.org/10.1007/978-3-031-32733-9_10.","ista":"Avarikioti Z, Desjardins A, Kokoris Kogias E, Wattenhofer R. 2023. Divide & Scale: Formalization and roadmap to robust sharding. 30th International Colloquium on Structural Information and Communication Complexity. SIROCCO: Structural Information and Communication Complexity, LNCS, vol. 13892, 199–245.","mla":"Avarikioti, Zeta, et al. “Divide & Scale: Formalization and Roadmap to Robust Sharding.” 30th International Colloquium on Structural Information and Communication Complexity, vol. 13892, Springer Nature, 2023, pp. 199–245, doi:10.1007/978-3-031-32733-9_10.","apa":"Avarikioti, Z., Desjardins, A., Kokoris Kogias, E., & Wattenhofer, R. (2023). Divide & Scale: Formalization and roadmap to robust sharding. In 30th International Colloquium on Structural Information and Communication Complexity (Vol. 13892, pp. 199–245). Alcalá de Henares, Spain: Springer Nature. https://doi.org/10.1007/978-3-031-32733-9_10","ama":"Avarikioti Z, Desjardins A, Kokoris Kogias E, Wattenhofer R. Divide & Scale: Formalization and roadmap to robust sharding. In: 30th International Colloquium on Structural Information and Communication Complexity. Vol 13892. Springer Nature; 2023:199-245. doi:10.1007/978-3-031-32733-9_10","short":"Z. Avarikioti, A. Desjardins, E. Kokoris Kogias, R. Wattenhofer, in:, 30th International Colloquium on Structural Information and Communication Complexity, Springer Nature, 2023, pp. 199–245.","ieee":"Z. Avarikioti, A. Desjardins, E. Kokoris Kogias, and R. Wattenhofer, “Divide & Scale: Formalization and roadmap to robust sharding,” in 30th International Colloquium on Structural Information and Communication Complexity, Alcalá de Henares, Spain, 2023, vol. 13892, pp. 199–245."},"title":"Divide & Scale: Formalization and roadmap to robust sharding","article_processing_charge":"No","author":[{"last_name":"Avarikioti","full_name":"Avarikioti, Zeta","first_name":"Zeta"},{"id":"06d0c166-aec1-11ee-a7c0-b96e840a602b","first_name":"Antoine","full_name":"Desjardins, Antoine","last_name":"Desjardins"},{"first_name":"Eleftherios","id":"f5983044-d7ef-11ea-ac6d-fd1430a26d30","last_name":"Kokoris Kogias","full_name":"Kokoris Kogias, Eleftherios"},{"full_name":"Wattenhofer, Roger","last_name":"Wattenhofer","first_name":"Roger"}],"acknowledgement":"The work was partially supported by the Austrian Science Fund (FWF) through the project CoRaF (grant agreement 2020388).","quality_controlled":"1","publisher":"Springer Nature","publication":"30th International Colloquium on Structural Information and Communication Complexity","day":"01","year":"2023","date_created":"2024-01-08T12:56:46Z","doi":"10.1007/978-3-031-32733-9_10","date_published":"2023-06-01T00:00:00Z","page":"199-245","_id":"14744","status":"public","conference":{"start_date":"2023-06-06","location":"Alcalá de Henares, Spain","end_date":"2023-06-09","name":"SIROCCO: Structural Information and Communication Complexity"},"type":"conference","date_updated":"2024-01-09T07:40:57Z","department":[{"_id":"ElKo"}],"oa_version":"None","abstract":[{"text":"Sharding distributed ledgers is a promising on-chain solution for scaling blockchains but lacks formal grounds, nurturing skepticism on whether such complex systems can scale blockchains securely. We fill this gap by introducing the first formal framework as well as a roadmap to robust sharding. In particular, we first define the properties sharded distributed ledgers should fulfill. We build upon and extend the Bitcoin backbone protocol by defining consistency and scalability. Consistency encompasses the need for atomic execution of cross-shard transactions to preserve safety, whereas scalability encapsulates the speedup a sharded system can gain in comparison to a non-sharded system.\r\nUsing our model, we explore the limitations of sharding. We show that a sharded ledger with n participants cannot scale under a fully adaptive adversary, but it can scale up to m shards where n=c'm log m, under an epoch-adaptive adversary; the constant c' encompasses the trade-off between security and scalability. This is possible only if the sharded ledgers create succinct proofs of the valid state updates at every epoch. We leverage our results to identify the sufficient components for robust sharding, which we incorporate in a protocol abstraction termed Divide & Scale. To demonstrate the power of our framework, we analyze the most prominent sharded blockchains (Elastico, Monoxide, OmniLedger, RapidChain) and pinpoint where they fail to meet the desired properties.","lang":"eng"}],"intvolume":" 13892","month":"06","alternative_title":["LNCS"],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eisbn":["9783031327339"],"issn":["0302-9743"],"isbn":["9783031327322"],"eissn":["1611-3349"]},"volume":13892},{"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0146-9592"],"eissn":["1539-4794"]},"issue":"15","volume":48,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"We unveil a powerful method for the stabilization of laser injection locking based on sensing variations in the output beam ellipticity of an optically seeded laser. The effect arises due to an interference between the seeding beam and the injected laser output. We demonstrate the method for a commercial semiconductor laser without the need for any internal changes to the readily operational injection locked laser system that was used. The method can also be used to increase the mode-hop free tuning range of lasers, and has the potential to fill a void in the low-noise laser industry."}],"intvolume":" 48","month":"07","scopus_import":"1","date_updated":"2024-01-09T08:09:32Z","department":[{"_id":"OnHo"}],"_id":"14749","keyword":["Atomic and Molecular Physics","and Optics"],"status":"public","type":"journal_article","article_type":"original","publication":"Optics Letters","day":"21","year":"2023","date_created":"2024-01-08T13:01:46Z","date_published":"2023-07-21T00:00:00Z","doi":"10.1364/ol.495553","page":"3973-3976","quality_controlled":"1","publisher":"Optica Publishing Group","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. 2023. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 48(15), 3973–3976.","chicago":"Mishra, Umang, Vyacheslav Li, Sebastian Wald, Sofya Agafonova, Fritz R Diorico, and Onur Hosten. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” Optics Letters. Optica Publishing Group, 2023. https://doi.org/10.1364/ol.495553.","ieee":"U. Mishra, V. Li, S. Wald, S. Agafonova, F. R. Diorico, and O. Hosten, “Monitoring and active stabilization of laser injection locking using beam ellipticity,” Optics Letters, vol. 48, no. 15. Optica Publishing Group, pp. 3973–3976, 2023.","short":"U. Mishra, V. Li, S. Wald, S. Agafonova, F.R. Diorico, O. Hosten, Optics Letters 48 (2023) 3973–3976.","ama":"Mishra U, Li V, Wald S, Agafonova S, Diorico FR, Hosten O. Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. 2023;48(15):3973-3976. doi:10.1364/ol.495553","apa":"Mishra, U., Li, V., Wald, S., Agafonova, S., Diorico, F. R., & Hosten, O. (2023). Monitoring and active stabilization of laser injection locking using beam ellipticity. Optics Letters. Optica Publishing Group. https://doi.org/10.1364/ol.495553","mla":"Mishra, Umang, et al. “Monitoring and Active Stabilization of Laser Injection Locking Using Beam Ellipticity.” Optics Letters, vol. 48, no. 15, Optica Publishing Group, 2023, pp. 3973–76, doi:10.1364/ol.495553."},"title":"Monitoring and active stabilization of laser injection locking using beam ellipticity","article_processing_charge":"No","external_id":{"arxiv":["2212.01266"]},"author":[{"first_name":"Umang","id":"4328fa4c-f128-11eb-9611-c107b0fe4d51","full_name":"Mishra, Umang","last_name":"Mishra"},{"first_name":"Vyacheslav","id":"3A4FAA92-F248-11E8-B48F-1D18A9856A87","last_name":"Li","full_name":"Li, Vyacheslav"},{"full_name":"Wald, Sebastian","last_name":"Wald","id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian"},{"orcid":"0000-0003-0582-2946","full_name":"Agafonova, Sofya","last_name":"Agafonova","id":"09501ff6-dca7-11ea-a8ae-b3e0b9166e80","first_name":"Sofya"},{"full_name":"Diorico, Fritz R","last_name":"Diorico","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87","first_name":"Fritz R"},{"first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","last_name":"Hosten","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur"}]},{"oa":1,"publisher":"American Geophysical Union","quality_controlled":"1","acknowledgement":"The authors would like to thank two anonymous reviews and gratefully acknowledge diverse funding agencies and resources used for this work. B.F. and C.M. thank funding from the European Research Council (ERC) under the European Union's Horizon 2020 research and innovation program (Project CLUSTER, grant agreement no. 805041), and the EUREC4A campaign organizers for giving the opportunity to take part to the campaign and use the data early on. R. P. was supported by the US National Science Foundation (award AGS 19–16908), by the National Oceanic and Atmospheric Administration (award NA200AR4310375), and the Vetlesen Foundation.","date_created":"2024-01-08T13:07:49Z","doi":"10.1029/2023av000880","date_published":"2023-06-01T00:00:00Z","publication":"AGU Advances","day":"01","year":"2023","has_accepted_license":"1","project":[{"grant_number":"805041","name":"organization of CLoUdS, and implications of Tropical cyclones and for the Energetics of the tropics, in current and waRming climate","call_identifier":"H2020","_id":"629205d8-2b32-11ec-9570-e1356ff73576"}],"article_number":"e2023AV000880","title":"How moisture shapes low‐level radiative cooling in subsidence regimes","article_processing_charge":"Yes","author":[{"first_name":"B.","last_name":"Fildier","full_name":"Fildier, B."},{"orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","last_name":"Muller","id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J"},{"first_name":"R.","last_name":"Pincus","full_name":"Pincus, R."},{"first_name":"S.","last_name":"Fueglistaler","full_name":"Fueglistaler, S."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Fildier, B., Muller, C. J., Pincus, R., & Fueglistaler, S. (2023). How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. American Geophysical Union. https://doi.org/10.1029/2023av000880","ama":"Fildier B, Muller CJ, Pincus R, Fueglistaler S. How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. 2023;4(3). doi:10.1029/2023av000880","short":"B. Fildier, C.J. Muller, R. Pincus, S. Fueglistaler, AGU Advances 4 (2023).","ieee":"B. Fildier, C. J. Muller, R. Pincus, and S. Fueglistaler, “How moisture shapes low‐level radiative cooling in subsidence regimes,” AGU Advances, vol. 4, no. 3. American Geophysical Union, 2023.","mla":"Fildier, B., et al. “How Moisture Shapes Low‐level Radiative Cooling in Subsidence Regimes.” AGU Advances, vol. 4, no. 3, e2023AV000880, American Geophysical Union, 2023, doi:10.1029/2023av000880.","ista":"Fildier B, Muller CJ, Pincus R, Fueglistaler S. 2023. How moisture shapes low‐level radiative cooling in subsidence regimes. AGU Advances. 4(3), e2023AV000880.","chicago":"Fildier, B., Caroline J Muller, R. Pincus, and S. Fueglistaler. “How Moisture Shapes Low‐level Radiative Cooling in Subsidence Regimes.” AGU Advances. American Geophysical Union, 2023. https://doi.org/10.1029/2023av000880."},"intvolume":" 4","month":"06","scopus_import":"1","oa_version":"Published Version","abstract":[{"text":"Radiative cooling of the lowest atmospheric levels is of strong importance for modulating atmospheric circulations and organizing convection, but detailed observations and a robust theoretical understanding are lacking. Here we use unprecedented observational constraints from subsidence regimes in the tropical Atlantic to develop a theory for the shape and magnitude of low‐level longwave radiative cooling in clear‐sky, showing peaks larger than 5–10 K/day at the top of the boundary layer. A suite of novel scaling approximations is first developed from simplified spectral theory, in close agreement with the measurements. The radiative cooling peak height is set by the maximum lapse rate in water vapor path, and its magnitude is mainly controlled by the ratio of column relative humidity above and below the peak. We emphasize how elevated intrusions of moist air can reduce low‐level cooling, by sporadically shading the spectral range which effectively cools to space. The efficiency of this spectral shading depends both on water content and altitude of moist intrusions; its height dependence cannot be explained by the temperature difference between the emitting and absorbing layers, but by the decrease of water vapor extinction with altitude. This analytical work can help to narrow the search for low‐level cloud patterns sensitive to radiative‐convective feedbacks: the most organized patterns with largest cloud fractions occur in atmospheres below 10% relative humidity and feel the strongest low‐level cooling. This motivates further assessment of favorable conditions for radiative‐convective feedbacks and a robust quantification of corresponding shallow cloud dynamics in current and warmer climates.","lang":"eng"}],"ec_funded":1,"volume":4,"issue":"3","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"af773220a9fa194c61a8dc2fae092c16","file_id":"14761","file_size":24149551,"date_updated":"2024-01-09T08:51:25Z","creator":"dernst","file_name":"2023_AGUAdvances_Fildier.pdf","date_created":"2024-01-09T08:51:25Z"}],"publication_status":"published","publication_identifier":{"eissn":["2576-604X"]},"keyword":["General Earth and Planetary Sciences"],"status":"public","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"type":"journal_article","article_type":"original","_id":"14752","department":[{"_id":"CaMu"}],"file_date_updated":"2024-01-09T08:51:25Z","ddc":["550"],"date_updated":"2024-01-09T08:54:03Z"},{"acknowledgement":"K.D.’s research was supported by Australian Research Council Discovery Early Career Researcher Award (DE170100171). B.W., R.A., F.M. and A.M. research was supported by the Spanish Ministerio de Economía y Competitividad (grant nos. FIS2016-77849-R and FIS2017-85794-P) and Ministerio de Ciencia e Innovación (grant no. PID2020-114043GB-I00) and the Generalitat de Catalunya (grant no. 2017-SGR-785). B.W.’s research was also supported by the Chinese Scholarship Council (grant CSC no. 201806440152). F.M. is a Serra-Húnter Fellow.","oa":1,"publisher":"The Royal Society","quality_controlled":"1","publication":"Philosophical Transactions of the Royal Society A","day":"01","year":"2023","has_accepted_license":"1","date_created":"2024-01-08T13:11:45Z","doi":"10.1098/rsta.2022.0112","date_published":"2023-05-01T00:00:00Z","article_number":"0112","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Wang, B., et al. “Mean Structure of the Supercritical Turbulent Spiral in Taylor–Couette Flow.” Philosophical Transactions of the Royal Society A, vol. 381, no. 2246, 0112, The Royal Society, 2023, doi:10.1098/rsta.2022.0112.","ieee":"B. Wang, F. Mellibovsky, R. Ayats López, K. Deguchi, and A. Meseguer, “Mean structure of the supercritical turbulent spiral in Taylor–Couette flow,” Philosophical Transactions of the Royal Society A, vol. 381, no. 2246. The Royal Society, 2023.","short":"B. Wang, F. Mellibovsky, R. Ayats López, K. Deguchi, A. Meseguer, Philosophical Transactions of the Royal Society A 381 (2023).","ama":"Wang B, Mellibovsky F, Ayats López R, Deguchi K, Meseguer A. Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. 2023;381(2246). doi:10.1098/rsta.2022.0112","apa":"Wang, B., Mellibovsky, F., Ayats López, R., Deguchi, K., & Meseguer, A. (2023). Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. The Royal Society. https://doi.org/10.1098/rsta.2022.0112","chicago":"Wang, B., F. Mellibovsky, Roger Ayats López, K. Deguchi, and A. Meseguer. “Mean Structure of the Supercritical Turbulent Spiral in Taylor–Couette Flow.” Philosophical Transactions of the Royal Society A. The Royal Society, 2023. https://doi.org/10.1098/rsta.2022.0112.","ista":"Wang B, Mellibovsky F, Ayats López R, Deguchi K, Meseguer A. 2023. Mean structure of the supercritical turbulent spiral in Taylor–Couette flow. Philosophical Transactions of the Royal Society A. 381(2246), 0112."},"title":"Mean structure of the supercritical turbulent spiral in Taylor–Couette flow","article_processing_charge":"No","external_id":{"pmid":["36907214"]},"author":[{"full_name":"Wang, B.","last_name":"Wang","first_name":"B."},{"first_name":"F.","full_name":"Mellibovsky, F.","last_name":"Mellibovsky"},{"last_name":"Ayats López","full_name":"Ayats López, Roger","orcid":"0000-0001-6572-0621","id":"ab77522d-073b-11ed-8aff-e71b39258362","first_name":"Roger"},{"first_name":"K.","full_name":"Deguchi, K.","last_name":"Deguchi"},{"first_name":"A.","last_name":"Meseguer","full_name":"Meseguer, A."}],"oa_version":"Submitted Version","pmid":1,"abstract":[{"lang":"eng","text":"The large-scale laminar/turbulent spiral patterns that appear in the linearly unstable regime of counter-rotating Taylor–Couette flow are investigated from a statistical perspective by means of direct numerical simulation. Unlike the vast majority of previous numerical studies, we analyse the flow in periodic parallelogram-annular domains, following a coordinate change that aligns one of the parallelogram sides with the spiral pattern. The domain size, shape and spatial resolution have been varied and the results compared with those in a sufficiently large computational orthogonal domain with natural axial and azimuthal periodicity. We find that a minimal parallelogram of the right tilt significantly reduces the computational cost without notably compromising the statistical properties of the supercritical turbulent spiral. Its mean structure, obtained from extremely long time integrations in a co-rotating reference frame using the method of slices, bears remarkable similarity with the turbulent stripes observed in plane Couette flow, the centrifugal instability playing only a secondary role."}],"intvolume":" 381","month":"05","scopus_import":"1","language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":6421086,"date_updated":"2024-01-09T09:13:53Z","file_name":"2023_PhilTransactionsA_Wang_accepted.pdf","date_created":"2024-01-09T09:13:53Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"1978d126c0ce2f47c22ac20107cc0106","file_id":"14763"}],"publication_status":"published","publication_identifier":{"issn":["1364-503X"],"eissn":["1471-2962"]},"volume":381,"issue":"2246","_id":"14754","keyword":["General Physics and Astronomy","General Engineering","General Mathematics"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["530"],"date_updated":"2024-01-09T09:15:29Z","file_date_updated":"2024-01-09T09:13:53Z","department":[{"_id":"BjHo"}]},{"title":"Low-pT quarkonium polarization measurements: Challenges and opportunities","article_processing_charge":"Yes (via OA deal)","author":[{"full_name":"Faccioli, Pietro","last_name":"Faccioli","first_name":"Pietro"},{"first_name":"Ilse","id":"30d4014e-7753-11eb-b44b-db6d61112e73","last_name":"Krätschmer","orcid":"0000-0002-5636-9259","full_name":"Krätschmer, Ilse"},{"first_name":"Carlos","last_name":"Lourenço","full_name":"Lourenço, Carlos"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Faccioli P, Krätschmer I, Lourenço C. Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. 2023;840. doi:10.1016/j.physletb.2023.137871","apa":"Faccioli, P., Krätschmer, I., & Lourenço, C. (2023). Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. Elsevier. https://doi.org/10.1016/j.physletb.2023.137871","ieee":"P. Faccioli, I. Krätschmer, and C. Lourenço, “Low-pT quarkonium polarization measurements: Challenges and opportunities,” Physics Letters B, vol. 840. Elsevier, 2023.","short":"P. Faccioli, I. Krätschmer, C. Lourenço, Physics Letters B 840 (2023).","mla":"Faccioli, Pietro, et al. “Low-PT Quarkonium Polarization Measurements: Challenges and Opportunities.” Physics Letters B, vol. 840, 137871, Elsevier, 2023, doi:10.1016/j.physletb.2023.137871.","ista":"Faccioli P, Krätschmer I, Lourenço C. 2023. Low-pT quarkonium polarization measurements: Challenges and opportunities. Physics Letters B. 840, 137871.","chicago":"Faccioli, Pietro, Ilse Krätschmer, and Carlos Lourenço. “Low-PT Quarkonium Polarization Measurements: Challenges and Opportunities.” Physics Letters B. Elsevier, 2023. https://doi.org/10.1016/j.physletb.2023.137871."},"article_number":"137871","date_created":"2024-01-08T13:09:17Z","doi":"10.1016/j.physletb.2023.137871","date_published":"2023-05-10T00:00:00Z","publication":"Physics Letters B","day":"10","year":"2023","has_accepted_license":"1","oa":1,"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"P.F. and C.L. acknowledge support from Fundação para a Ciência e a Tecnologia, Portugal, under contract CERN/FIS-PAR/0010/2019.\r\nOpen Access funded by SCOAP3.","department":[{"_id":"MaRo"}],"file_date_updated":"2024-01-09T08:59:24Z","ddc":["530"],"date_updated":"2024-01-09T09:02:22Z","keyword":["Nuclear and High Energy Physics"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"14753","volume":840,"language":[{"iso":"eng"}],"file":[{"file_size":855494,"date_updated":"2024-01-09T08:59:24Z","creator":"dernst","file_name":"2023_PhysicsLettersB_Faccioli.pdf","date_created":"2024-01-09T08:59:24Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"file_id":"14762","checksum":"02dec160dbc81d95985e755869d8afbf"}],"publication_status":"published","publication_identifier":{"issn":["0370-2693"],"eissn":["1873-2445"]},"intvolume":" 840","month":"05","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"Several fixed-target experiments reported J/ψ and ϒ polarizations, as functions of Feynman x (xF) and transverse momentum (PT), in three different frames, using different combinations of beam particles, target nuclei, and collision energies. Despite the diverse and heterogeneous picture formed by these measurements, a detailed look allows us to discern qualitative physical patterns that inspire a simple empirical model. This data-driven scenario offers a good quantitative description of the J/ψ and ϒ(1S) polarizations measured in proton- and pion-nucleus collisions, in the xF 0.5 domain: more than 80 data points (not statistically independent) are well reproduced with only one free parameter. This study sets the context for future low-PT\r\n quarkonium polarization measurements in proton- and pion-nucleus collisions, such as those to be made by the AMBER experiment, and shows that such measurements provide significant constraints on the poorly-known parton distribution functions of the pion."}]},{"acknowledgement":"The first author is partially supported by NSF Grant DMS-2113489 and grateful for the AMS-SIMONS travel grant (2020–2023). The second author is supported by the ERC Advanced Grant “RMTBeyond” No. 101020331.\r\nThe authors would like to thank the Editor, Associate Editor and an anonymous referee for their many critical suggestions which have significantly improved the paper. We also want to thank Zhigang Bao and Ji Oon Lee for many helpful discussions and comments.","oa":1,"quality_controlled":"1","publisher":"Institute of Mathematical Statistics","publication":"The Annals of Applied Probability","day":"01","year":"2023","date_created":"2024-01-08T13:03:18Z","date_published":"2023-08-01T00:00:00Z","doi":"10.1214/22-aap1882","page":"2981-3009","project":[{"name":"Random matrices beyond Wigner-Dyson-Mehta","grant_number":"101020331","_id":"62796744-2b32-11ec-9570-940b20777f1d","call_identifier":"H2020"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"chicago":"Ding, Xiucai, and Hong Chang Ji. “Local Laws for Multiplication of Random Matrices.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-aap1882.","ista":"Ding X, Ji HC. 2023. Local laws for multiplication of random matrices. The Annals of Applied Probability. 33(4), 2981–3009.","mla":"Ding, Xiucai, and Hong Chang Ji. “Local Laws for Multiplication of Random Matrices.” The Annals of Applied Probability, vol. 33, no. 4, Institute of Mathematical Statistics, 2023, pp. 2981–3009, doi:10.1214/22-aap1882.","short":"X. Ding, H.C. Ji, The Annals of Applied Probability 33 (2023) 2981–3009.","ieee":"X. Ding and H. C. Ji, “Local laws for multiplication of random matrices,” The Annals of Applied Probability, vol. 33, no. 4. Institute of Mathematical Statistics, pp. 2981–3009, 2023.","apa":"Ding, X., & Ji, H. C. (2023). Local laws for multiplication of random matrices. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-aap1882","ama":"Ding X, Ji HC. Local laws for multiplication of random matrices. The Annals of Applied Probability. 2023;33(4):2981-3009. doi:10.1214/22-aap1882"},"title":"Local laws for multiplication of random matrices","article_processing_charge":"No","external_id":{"arxiv":["2010.16083"]},"author":[{"first_name":"Xiucai","last_name":"Ding","full_name":"Ding, Xiucai"},{"id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d","first_name":"Hong Chang","last_name":"Ji","full_name":"Ji, Hong Chang"}],"oa_version":"Preprint","abstract":[{"text":"Consider the random matrix model A1/2UBU∗A1/2, where A and B are two N × N deterministic matrices and U is either an N × N Haar unitary or orthogonal random matrix. It is well known that on the macroscopic scale (Invent. Math. 104 (1991) 201–220), the limiting empirical spectral distribution (ESD) of the above model is given by the free multiplicative convolution\r\nof the limiting ESDs of A and B, denoted as μα \u0002 μβ, where μα and μβ are the limiting ESDs of A and B, respectively. In this paper, we study the asymptotic microscopic behavior of the edge eigenvalues and eigenvectors statistics. We prove that both the density of μA \u0002μB, where μA and μB are the ESDs of A and B, respectively and the associated subordination functions\r\nhave a regular behavior near the edges. Moreover, we establish the local laws near the edges on the optimal scale. In particular, we prove that the entries of the resolvent are close to some functionals depending only on the eigenvalues of A, B and the subordination functions with optimal convergence rates. Our proofs and calculations are based on the techniques developed for the additive model A+UBU∗ in (J. Funct. Anal. 271 (2016) 672–719; Comm. Math.\r\nPhys. 349 (2017) 947–990; Adv. Math. 319 (2017) 251–291; J. Funct. Anal. 279 (2020) 108639), and our results can be regarded as the counterparts of (J. Funct. Anal. 279 (2020) 108639) for the multiplicative model. ","lang":"eng"}],"intvolume":" 33","month":"08","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2010.16083","open_access":"1"}],"scopus_import":"1","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["1050-5164"]},"ec_funded":1,"volume":33,"issue":"4","_id":"14750","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"status":"public","article_type":"original","type":"journal_article","date_updated":"2024-01-09T08:16:41Z","department":[{"_id":"LaEr"}]},{"date_published":"2023-10-16T00:00:00Z","doi":"10.4171/qt/193","date_created":"2024-01-08T13:14:48Z","page":"467-532","day":"16","publication":"Quantum Topology","has_accepted_license":"1","year":"2023","quality_controlled":"1","publisher":"European Mathematical Society","oa":1,"acknowledgement":"N.C. is supported by the DFG Heisenberg Programme.\r\nWe are grateful to Tobias Dyckerhoff, Lukas Müller, Ingo Runkel, and Christopher Schommer-Pries for helpful discussions.","title":"Fully extended r-spin TQFTs","author":[{"first_name":"Nils","full_name":"Carqueville, Nils","last_name":"Carqueville"},{"orcid":"0000-0003-2834-5054","full_name":"Szegedy, Lorant","last_name":"Szegedy","first_name":"Lorant","id":"7943226E-220E-11EA-94C7-D59F3DDC885E"}],"article_processing_charge":"Yes","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Carqueville, Nils, and Lorant Szegedy. “Fully Extended R-Spin TQFTs.” Quantum Topology, vol. 14, no. 3, European Mathematical Society, 2023, pp. 467–532, doi:10.4171/qt/193.","ama":"Carqueville N, Szegedy L. Fully extended r-spin TQFTs. Quantum Topology. 2023;14(3):467-532. doi:10.4171/qt/193","apa":"Carqueville, N., & Szegedy, L. (2023). Fully extended r-spin TQFTs. Quantum Topology. European Mathematical Society. https://doi.org/10.4171/qt/193","ieee":"N. Carqueville and L. Szegedy, “Fully extended r-spin TQFTs,” Quantum Topology, vol. 14, no. 3. European Mathematical Society, pp. 467–532, 2023.","short":"N. Carqueville, L. Szegedy, Quantum Topology 14 (2023) 467–532.","chicago":"Carqueville, Nils, and Lorant Szegedy. “Fully Extended R-Spin TQFTs.” Quantum Topology. European Mathematical Society, 2023. https://doi.org/10.4171/qt/193.","ista":"Carqueville N, Szegedy L. 2023. Fully extended r-spin TQFTs. Quantum Topology. 14(3), 467–532."},"issue":"3","volume":14,"file":[{"success":1,"file_id":"14764","checksum":"b0590aff6e7ec89cc149ba94d459d3a3","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2023_QuantumTopol_Carqueville.pdf","date_created":"2024-01-09T09:25:34Z","creator":"dernst","file_size":707344,"date_updated":"2024-01-09T09:25:34Z"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["1663-487X"]},"publication_status":"published","month":"10","intvolume":" 14","scopus_import":"1","oa_version":"Published Version","abstract":[{"lang":"eng","text":"We prove the r-spin cobordism hypothesis in the setting of (weak) 2-categories for every positive integer r: the 2-groupoid of 2-dimensional fully extended r-spin TQFTs with given target is equivalent to the homotopy fixed points of an induced Spin 2r -action. In particular, such TQFTs are classified by fully dualisable objects together with a trivialisation of the rth power of their Serre automorphisms. For r=1, we recover the oriented case (on which our proof builds), while ordinary spin structures correspond to r=2.\r\nTo construct examples, we explicitly describe Spin 2r-homotopy fixed points in the equivariant completion of any symmetric monoidal 2-category. We also show that every object in a 2-category of Landau–Ginzburg models gives rise to fully extended spin TQFTs and that half of these do not factor through the oriented bordism 2-category."}],"file_date_updated":"2024-01-09T09:25:34Z","department":[{"_id":"MiLe"}],"ddc":["530"],"date_updated":"2024-01-09T09:27:46Z","status":"public","keyword":["Geometry and Topology","Mathematical Physics"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14756"},{"department":[{"_id":"MaMo"}],"date_updated":"2024-01-09T08:45:24Z","keyword":["Computer Science Applications","Information Systems"],"status":"public","type":"journal_article","article_type":"original","_id":"14751","volume":69,"issue":"7","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"eissn":["1557-9654"],"issn":["0018-9448"]},"intvolume":" 69","month":"07","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2101.12426"}],"scopus_import":"1","oa_version":"Preprint","abstract":[{"text":"We consider zero-error communication over a two-transmitter deterministic adversarial multiple access channel (MAC) governed by an adversary who has access to the transmissions of both senders (hence called omniscient ) and aims to maliciously corrupt the communication. None of the encoders, jammer and decoder is allowed to randomize using private or public randomness. This enforces a combinatorial nature of the problem. Our model covers a large family of channels studied in the literature, including all deterministic discrete memoryless noisy or noiseless MACs. In this work, given an arbitrary two-transmitter deterministic omniscient adversarial MAC, we characterize when the capacity region: 1) has nonempty interior (in particular, is two-dimensional); 2) consists of two line segments (in particular, has empty interior); 3) consists of one line segment (in particular, is one-dimensional); 4) or only contains (0,0) (in particular, is zero-dimensional). This extends a recent result by Wang et al. (201 9) from the point-to-point setting to the multiple access setting. Indeed, our converse arguments build upon their generalized Plotkin bound and involve delicate case analysis. One of the technical challenges is to take care of both “joint confusability” and “marginal confusability”. In particular, the treatment of marginal confusability does not follow from the point-to-point results by Wang et al. Our achievability results follow from random coding with expurgation.","lang":"eng"}],"title":"Zero-error communication over adversarial MACs","external_id":{"arxiv":["2101.12426"]},"article_processing_charge":"No","author":[{"first_name":"Yihan","id":"2ce5da42-b2ea-11eb-bba5-9f264e9d002c","orcid":"0000-0002-6465-6258","full_name":"Zhang, Yihan","last_name":"Zhang"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Zhang Y. 2023. Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. 69(7), 4093–4127.","chicago":"Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers, 2023. https://doi.org/10.1109/tit.2023.3257239.","ama":"Zhang Y. Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. 2023;69(7):4093-4127. doi:10.1109/tit.2023.3257239","apa":"Zhang, Y. (2023). Zero-error communication over adversarial MACs. IEEE Transactions on Information Theory. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/tit.2023.3257239","short":"Y. Zhang, IEEE Transactions on Information Theory 69 (2023) 4093–4127.","ieee":"Y. Zhang, “Zero-error communication over adversarial MACs,” IEEE Transactions on Information Theory, vol. 69, no. 7. Institute of Electrical and Electronics Engineers, pp. 4093–4127, 2023.","mla":"Zhang, Yihan. “Zero-Error Communication over Adversarial MACs.” IEEE Transactions on Information Theory, vol. 69, no. 7, Institute of Electrical and Electronics Engineers, 2023, pp. 4093–127, doi:10.1109/tit.2023.3257239."},"date_created":"2024-01-08T13:04:54Z","doi":"10.1109/tit.2023.3257239","date_published":"2023-07-01T00:00:00Z","page":"4093-4127","publication":"IEEE Transactions on Information Theory","day":"01","year":"2023","oa":1,"publisher":"Institute of Electrical and Electronics Engineers","quality_controlled":"1","acknowledgement":"The author would like to thank Amitalok J. Budkuley and Sidharth Jaggi for many helpful discussions at the early stage of this work. He would also like to thank Nir Ailon, Qi Cao, and Chandra Nair for discussions on a related problem regarding zero-error binary adder MACs.\r\nThe work of Yihan Zhang was supported by the European Union’s Horizon 2020 Research and Innovation Programme under Grant 682203-ERC-[Inf-Speed-Tradeoff]"},{"article_type":"original","type":"journal_article","status":"public","keyword":["General Mathematics"],"_id":"14755","department":[{"_id":"JuFi"}],"date_updated":"2024-01-09T09:22:16Z","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2105.07100","open_access":"1"}],"month":"02","intvolume":" 131","abstract":[{"text":"We consider the sharp interface limit for the scalar-valued and vector-valued Allen–Cahn equation with homogeneous Neumann boundary condition in a bounded smooth domain Ω of arbitrary dimension N ⩾ 2 in the situation when a two-phase diffuse interface has developed and intersects the boundary ∂ Ω. The limit problem is mean curvature flow with 90°-contact angle and we show convergence in strong norms for well-prepared initial data as long as a smooth solution to the limit problem exists. To this end we assume that the limit problem has a smooth solution on [ 0 , T ] for some time T > 0. Based on the latter we construct suitable curvilinear coordinates and set up an asymptotic expansion for the scalar-valued and the vector-valued Allen–Cahn equation. In order to estimate the difference of the exact and approximate solutions with a Gronwall-type argument, a spectral estimate for the linearized Allen–Cahn operator in both cases is required. The latter will be shown in a separate paper, cf. (Moser (2021)).","lang":"eng"}],"oa_version":"Preprint","volume":131,"issue":"3-4","publication_identifier":{"eissn":["1875-8576"],"issn":["0921-7134"]},"publication_status":"published","language":[{"iso":"eng"}],"author":[{"first_name":"Maximilian","id":"a60047a9-da77-11eb-85b4-c4dc385ebb8c","full_name":"Moser, Maximilian","last_name":"Moser"}],"external_id":{"arxiv":["2105.07100"]},"article_processing_charge":"No","title":"Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result","citation":{"ista":"Moser M. 2023. Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. 131(3–4), 297–383.","chicago":"Moser, Maximilian. “Convergence of the Scalar- and Vector-Valued Allen–Cahn Equation to Mean Curvature Flow with 90°-Contact Angle in Higher Dimensions, Part I: Convergence Result.” Asymptotic Analysis. IOS Press, 2023. https://doi.org/10.3233/asy-221775.","ieee":"M. Moser, “Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result,” Asymptotic Analysis, vol. 131, no. 3–4. IOS Press, pp. 297–383, 2023.","short":"M. Moser, Asymptotic Analysis 131 (2023) 297–383.","ama":"Moser M. Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. 2023;131(3-4):297-383. doi:10.3233/asy-221775","apa":"Moser, M. (2023). Convergence of the scalar- and vector-valued Allen–Cahn equation to mean curvature flow with 90°-contact angle in higher dimensions, part I: Convergence result. Asymptotic Analysis. IOS Press. https://doi.org/10.3233/asy-221775","mla":"Moser, Maximilian. “Convergence of the Scalar- and Vector-Valued Allen–Cahn Equation to Mean Curvature Flow with 90°-Contact Angle in Higher Dimensions, Part I: Convergence Result.” Asymptotic Analysis, vol. 131, no. 3–4, IOS Press, 2023, pp. 297–383, doi:10.3233/asy-221775."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"IOS Press","oa":1,"acknowledgement":"The author gratefully acknowledges support through DFG, GRK 1692 “Curvature,\r\nCycles and Cohomology” during parts of the work.","page":"297-383","doi":"10.3233/asy-221775","date_published":"2023-02-02T00:00:00Z","date_created":"2024-01-08T13:13:28Z","year":"2023","day":"02","publication":"Asymptotic Analysis"},{"day":"08","publication":"Neocortical Neurogenesis in Development and Evolution","language":[{"iso":"eng"}],"publication_identifier":{"eisbn":["9781119860914"]},"publication_status":"published","year":"2023","date_published":"2023-08-08T00:00:00Z","doi":"10.1002/9781119860914.ch10","date_created":"2024-01-08T13:16:36Z","page":"169-191","oa_version":"None","abstract":[{"lang":"eng","text":"The cerebral cortex is comprised of a vast cell-type diversity sequentially generated by cortical progenitor cells. Faithful progenitor lineage progression requires the tight orchestration of distinct molecular and cellular mechanisms regulating proper progenitor proliferation behavior and differentiation. Correct execution of developmental programs involves a complex interplay of cell intrinsic and tissue-wide mechanisms. Many studies over the past decades have been able to determine a plethora of genes critically involved in cortical development. However, only a few made use of genetic paradigms with sparse and global gene deletion to probe cell-autonomous vs. tissue-wide contribution. In this chapter, we will elaborate on the importance of dissecting the cell-autonomous and tissue-wide mechanisms to gain a precise understanding of gene function during radial glial progenitor lineage progression."}],"month":"08","publisher":"Wiley","scopus_import":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-01-09T09:46:57Z","citation":{"ista":"Villalba Requena A, Amberg N, Hippenmeyer S. 2023.Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In: Neocortical Neurogenesis in Development and Evolution. , 169–191.","chicago":"Villalba Requena, Ana, Nicole Amberg, and Simon Hippenmeyer. “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression.” In Neocortical Neurogenesis in Development and Evolution, edited by Wieland Huttner, 169–91. Wiley, 2023. https://doi.org/10.1002/9781119860914.ch10.","ama":"Villalba Requena A, Amberg N, Hippenmeyer S. Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In: Huttner W, ed. Neocortical Neurogenesis in Development and Evolution. Wiley; 2023:169-191. doi:10.1002/9781119860914.ch10","apa":"Villalba Requena, A., Amberg, N., & Hippenmeyer, S. (2023). Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression. In W. Huttner (Ed.), Neocortical Neurogenesis in Development and Evolution (pp. 169–191). Wiley. https://doi.org/10.1002/9781119860914.ch10","ieee":"A. Villalba Requena, N. Amberg, and S. Hippenmeyer, “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression,” in Neocortical Neurogenesis in Development and Evolution, W. Huttner, Ed. Wiley, 2023, pp. 169–191.","short":"A. Villalba Requena, N. Amberg, S. Hippenmeyer, in:, W. Huttner (Ed.), Neocortical Neurogenesis in Development and Evolution, Wiley, 2023, pp. 169–191.","mla":"Villalba Requena, Ana, et al. “Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression.” Neocortical Neurogenesis in Development and Evolution, edited by Wieland Huttner, Wiley, 2023, pp. 169–91, doi:10.1002/9781119860914.ch10."},"department":[{"_id":"SiHi"}],"editor":[{"first_name":"Wieland","last_name":"Huttner","full_name":"Huttner, Wieland"}],"title":"Interplay of Cell‐autonomous Gene Function and Tissue‐wide Mechanisms Regulating Radial Glial Progenitor Lineage Progression","author":[{"full_name":"Villalba Requena, Ana","orcid":"0000-0002-5615-5277","last_name":"Villalba Requena","first_name":"Ana","id":"68cb85a0-39f7-11eb-9559-9aaab4f6a247"},{"id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole","full_name":"Amberg, Nicole","orcid":"0000-0002-3183-8207","last_name":"Amberg"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","first_name":"Simon","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061"}],"article_processing_charge":"No","_id":"14757","status":"public","type":"book_chapter"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Wald, Sebastian, et al. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” Applied Optics, vol. 62, no. 1, Optica Publishing Group, 2023, pp. 1–7, doi:10.1364/ao.474118.","ieee":"S. Wald, F. R. Diorico, and O. Hosten, “Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone,” Applied Optics, vol. 62, no. 1. Optica Publishing Group, pp. 1–7, 2023.","short":"S. Wald, F.R. Diorico, O. Hosten, Applied Optics 62 (2023) 1–7.","ama":"Wald S, Diorico FR, Hosten O. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 2023;62(1):1-7. doi:10.1364/ao.474118","apa":"Wald, S., Diorico, F. R., & Hosten, O. (2023). Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. Optica Publishing Group. https://doi.org/10.1364/ao.474118","chicago":"Wald, Sebastian, Fritz R Diorico, and Onur Hosten. “Analog Stabilization of an Electro-Optic I/Q Modulator with an Auxiliary Modulation Tone.” Applied Optics. Optica Publishing Group, 2023. https://doi.org/10.1364/ao.474118.","ista":"Wald S, Diorico FR, Hosten O. 2023. Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone. Applied Optics. 62(1), 1–7."},"title":"Analog stabilization of an electro-optic I/Q modulator with an auxiliary modulation tone","author":[{"id":"133F200A-B015-11E9-AD41-0EDAE5697425","first_name":"Sebastian","full_name":"Wald, Sebastian","orcid":"0000-0002-5869-1604","last_name":"Wald"},{"full_name":"Diorico, Fritz R","orcid":"0000-0002-4947-8924","last_name":"Diorico","first_name":"Fritz R","id":"2E054C4C-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Onur","id":"4C02D85E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2031-204X","full_name":"Hosten, Onur","last_name":"Hosten"}],"external_id":{"arxiv":["2208.11591"]},"article_processing_charge":"No","day":"01","publication":"Applied Optics","year":"2023","date_published":"2023-01-01T00:00:00Z","doi":"10.1364/ao.474118","date_created":"2024-01-08T13:19:14Z","page":"1-7","acknowledgement":"We thank Jakob Vorlaufer for technical contributions and Vyacheslav Li and Sofia Agafonova for comments on the manuscript.","quality_controlled":"1","publisher":"Optica Publishing Group","oa":1,"date_updated":"2024-01-09T10:10:34Z","department":[{"_id":"OnHo"}],"_id":"14759","status":"public","keyword":["Atomic and Molecular Physics","and Optics","Engineering (miscellaneous)","Electrical and Electronic Engineering"],"article_type":"original","type":"journal_article","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["2155-3165"],"issn":["1559-128X"]},"publication_status":"published","issue":"1","volume":62,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Proper operation of electro-optic I/Q modulators relies on precise adjustment and control of the relative phase biases between the modulator’s internal interferometer arms. We present an all-analog phase bias locking scheme where error signals are obtained from the beat between the optical carrier and optical tones generated by an auxiliary 2 MHz 𝑅𝐹 tone to lock the phases of all three involved interferometers for operation up to 10 GHz. With the developed method, we demonstrate an I/Q modulator in carrier-suppressed single-sideband mode, where the suppressed carrier and sideband are locked at optical power levels <−27dB\r\n relative to the transmitted sideband. We describe a simple analytical model for calculating the error signals and detail the implementation of the electronic circuitry for the implementation of the method."}],"month":"01","intvolume":" 62","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2208.11591"}]},{"license":"https://creativecommons.org/licenses/by-sa/4.0/","date_created":"2023-04-07T11:37:40Z","contributor":[{"orcid":"0000-0002-2340-7431","last_name":"Velicky","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"},{"first_name":"Eder","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","last_name":"Miguel Villalba"},{"id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M","last_name":"Michalska"},{"id":"46E28B80-F248-11E8-B48F-1D18A9856A87","first_name":"Julia","last_name":"Lyudchik"},{"first_name":"Donglai","last_name":"Wei"},{"last_name":"Lin","first_name":"Zudi"},{"orcid":"0000-0002-8698-3823","last_name":"Watson","first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E"},{"last_name":"Troidl","first_name":"Jakob"},{"first_name":"Johanna","last_name":"Beyer"},{"id":"43DF3136-F248-11E8-B48F-1D18A9856A87","first_name":"Yoav","last_name":"Ben Simon"},{"last_name":"Sommer","orcid":"0000-0003-1216-9105","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke","last_name":"Jahr"},{"last_name":"Cenameri","first_name":"Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886"},{"last_name":"Broichhagen","first_name":"Johannes"},{"last_name":"Grant","first_name":"Seth G. 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However, it has been hindered by insufficient 3D-resolution, inadequate signal-to-noise-ratio, and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine learning technology, LIONESS (Live Information-Optimized Nanoscopy Enabling Saturated Segmentation). It leverages optical modifications to stimulated emission depletion (STED) microscopy in comprehensively, extracellularly labelled tissue and prior information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise-ratio, and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D-reconstruction at synapse level incorporating molecular, activity, and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue."}],"acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"E-Lib"}],"acknowledgement":"We thank J. Vorlaufer, N. Agudelo, A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, and M. Šuplata for hardware control support, and Márcia Cunha dos Santos for initial exploration of software. We thank Paul Henderson for advice on deep-learning training and Michael Sixt, Scott Boyd, and Tamara Weiss for discussions and critical reading of the manuscript. Luke Lavis (Janelia Research Campus) generously provided JF585-HaloTag ligand. 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Research data for the publication ‘Dense 4D nanoscale reconstruction of living brain tissue’, Institute of Science and Technology Austria, 10.15479/AT:ISTA:12817.","chicago":"Danzl, Johann G. “Research Data for the Publication ‘Dense 4D Nanoscale Reconstruction of Living Brain Tissue.’” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/AT:ISTA:12817."},"date_updated":"2024-01-10T08:37:48Z","ddc":["570"],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"type":"research_data","status":"public","_id":"12817"},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Velicky, Philipp, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, Springer Nature, 2023, pp. 1256–65, doi:10.1038/s41592-023-01936-6.","short":"P. Velicky, E. Miguel Villalba, J.M. Michalska, J. Lyudchik, D. Wei, Z. Lin, J. Watson, J. Troidl, J. Beyer, Y. Ben Simon, C.M. Sommer, W. Jahr, A. Cenameri, J. Broichhagen, S.G.N. Grant, P.M. Jonas, G. Novarino, H. Pfister, B. Bickel, J.G. Danzl, Nature Methods 20 (2023) 1256–1265.","ieee":"P. Velicky et al., “Dense 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20. Springer Nature, pp. 1256–1265, 2023.","ama":"Velicky P, Miguel Villalba E, Michalska JM, et al. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20:1256-1265. doi:10.1038/s41592-023-01936-6","apa":"Velicky, P., Miguel Villalba, E., Michalska, J. M., Lyudchik, J., Wei, D., Lin, Z., … Danzl, J. G. (2023). Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01936-6","chicago":"Velicky, Philipp, Eder Miguel Villalba, Julia M Michalska, Julia Lyudchik, Donglai Wei, Zudi Lin, Jake Watson, et al. “Dense 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01936-6.","ista":"Velicky P, Miguel Villalba E, Michalska JM, Lyudchik J, Wei D, Lin Z, Watson J, Troidl J, Beyer J, Ben Simon Y, Sommer CM, Jahr W, Cenameri A, Broichhagen J, Grant SGN, Jonas PM, Novarino G, Pfister H, Bickel B, Danzl JG. 2023. Dense 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20, 1256–1265."},"title":"Dense 4D nanoscale reconstruction of living brain tissue","author":[{"last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","first_name":"Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Miguel Villalba","full_name":"Miguel Villalba, Eder","orcid":"0000-0001-5665-0430","id":"3FB91342-F248-11E8-B48F-1D18A9856A87","first_name":"Eder"},{"orcid":"0000-0003-3862-1235","full_name":"Michalska, Julia M","last_name":"Michalska","id":"443DB6DE-F248-11E8-B48F-1D18A9856A87","first_name":"Julia M"},{"first_name":"Julia","id":"46E28B80-F248-11E8-B48F-1D18A9856A87","last_name":"Lyudchik","full_name":"Lyudchik, Julia"},{"full_name":"Wei, Donglai","last_name":"Wei","first_name":"Donglai"},{"last_name":"Lin","full_name":"Lin, Zudi","first_name":"Zudi"},{"first_name":"Jake","id":"63836096-4690-11EA-BD4E-32803DDC885E","last_name":"Watson","full_name":"Watson, Jake","orcid":"0000-0002-8698-3823"},{"first_name":"Jakob","last_name":"Troidl","full_name":"Troidl, Jakob"},{"last_name":"Beyer","full_name":"Beyer, Johanna","first_name":"Johanna"},{"full_name":"Ben Simon, Yoav","last_name":"Ben Simon","first_name":"Yoav","id":"43DF3136-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M","id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87"},{"id":"425C1CE8-F248-11E8-B48F-1D18A9856A87","first_name":"Wiebke","last_name":"Jahr","full_name":"Jahr, Wiebke"},{"last_name":"Cenameri","full_name":"Cenameri, Alban","id":"9ac8f577-2357-11eb-997a-e566c5550886","first_name":"Alban"},{"first_name":"Johannes","last_name":"Broichhagen","full_name":"Broichhagen, Johannes"},{"full_name":"Grant, Seth G.N.","last_name":"Grant","first_name":"Seth G.N."},{"orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","first_name":"Peter M"},{"orcid":"0000-0002-7673-7178","full_name":"Novarino, Gaia","last_name":"Novarino","id":"3E57A680-F248-11E8-B48F-1D18A9856A87","first_name":"Gaia"},{"first_name":"Hanspeter","full_name":"Pfister, Hanspeter","last_name":"Pfister"},{"first_name":"Bernd","id":"49876194-F248-11E8-B48F-1D18A9856A87","full_name":"Bickel, Bernd","orcid":"0000-0001-6511-9385","last_name":"Bickel"},{"last_name":"Danzl","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87"}],"external_id":{"pmid":["37429995"],"isi":["001025621500001"]},"article_processing_charge":"Yes","project":[{"call_identifier":"FWF","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","name":"Optical control of synaptic function via adhesion molecules"},{"call_identifier":"FWF","_id":"2548AE96-B435-11E9-9278-68D0E5697425","name":"Molecular Drug Targets","grant_number":"W1232-B24"},{"_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"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"},{"call_identifier":"H2020","_id":"24F9549A-B435-11E9-9278-68D0E5697425","grant_number":"715767","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling"},{"grant_number":"715508","name":"Probing the Reversibility of Autism Spectrum Disorders by Employing in vivo and in vitro Models","_id":"25444568-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Biophysics and circuit function of a giant cortical glumatergic synapse","grant_number":"692692","call_identifier":"H2020","_id":"25B7EB9E-B435-11E9-9278-68D0E5697425"},{"grant_number":"101026635","name":"Synaptic computations of the hippocampal CA3 circuitry","call_identifier":"H2020","_id":"fc2be41b-9c52-11eb-aca3-faa90aa144e9"},{"_id":"2668BFA0-B435-11E9-9278-68D0E5697425","name":"High-speed 3D-nanoscopy to study the role of adhesion during 3D cell migration","grant_number":"LT00057"}],"day":"01","publication":"Nature Methods","isi":1,"year":"2023","doi":"10.1038/s41592-023-01936-6","date_published":"2023-08-01T00:00:00Z","date_created":"2023-07-23T22:01:13Z","page":"1256-1265","acknowledgement":"We thank J. Vorlaufer, N. Agudelo and A. Wartak for microscope maintenance and troubleshooting, C. Kreuzinger and A. Freeman for technical assistance, M. Šuplata for hardware control support and M. Cunha dos Santos for initial exploration of software. We\r\nthank P. Henderson for advice on deep-learning training and M. Sixt, S. Boyd and T. Weiss for discussions and critical reading of the manuscript. L. Lavis (Janelia Research Campus) generously provided the JF585-HaloTag ligand. We acknowledge expert support by IST\r\nAustria’s scientific computing, imaging and optics, preclinical, library and laboratory support facilities and by the Miba machine shop. We gratefully acknowledge funding by the following sources: Austrian Science Fund (F.W.F.) grant no. I3600-B27 (J.G.D.), grant no. DK W1232\r\n(J.G.D. and J.M.M.) and grant no. Z 312-B27, Wittgenstein award (P.J.); the Gesellschaft für Forschungsförderung NÖ grant no. LSC18-022 (J.G.D.); an ISTA Interdisciplinary project grant (J.G.D. and B.B.); the European Union’s Horizon 2020 research and innovation programme,\r\nMarie-Skłodowska Curie grant 665385 (J.M.M. and J.L.); the European Union’s Horizon 2020 research and innovation programme, European Research Council grant no. 715767, MATERIALIZABLE (B.B.); grant no. 715508, REVERSEAUTISM (G.N.); grant no. 695568, SYNNOVATE (S.G.N.G.); and grant no. 692692, GIANTSYN (P.J.); the Simons\r\nFoundation Autism Research Initiative grant no. 529085 (S.G.N.G.); the Wellcome Trust Technology Development grant no. 202932 (S.G.N.G.); the Marie Skłodowska-Curie Actions Individual Fellowship no. 101026635 under the EU Horizon 2020 program (J.F.W.);\r\nthe Human Frontier Science Program postdoctoral fellowship LT000557/2018 (W.J.); and the National Science Foundation grant no. IIS-1835231 (H.P.) and NCS-FO-2124179 (H.P.).","quality_controlled":"1","publisher":"Springer Nature","oa":1,"date_updated":"2024-01-10T08:37:48Z","department":[{"_id":"PeJo"},{"_id":"GaNo"},{"_id":"BeBi"},{"_id":"JoDa"},{"_id":"Bio"}],"_id":"13267","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1548-7105"],"issn":["1548-7091"]},"publication_status":"published","related_material":{"link":[{"url":"https://github.com/danzllab/LIONESS","relation":"software"}],"record":[{"id":"12817","status":"public","relation":"research_data"},{"relation":"shorter_version","status":"public","id":"14770"}]},"volume":20,"ec_funded":1,"pmid":1,"oa_version":"Published Version","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"Bio"},{"_id":"PreCl"},{"_id":"E-Lib"},{"_id":"LifeSc"},{"_id":"M-Shop"}],"abstract":[{"lang":"eng","text":"Three-dimensional (3D) reconstruction of living brain tissue down to an individual synapse level would create opportunities for decoding the dynamics and structure–function relationships of the brain’s complex and dense information processing network; however, this has been hindered by insufficient 3D resolution, inadequate signal-to-noise ratio and prohibitive light burden in optical imaging, whereas electron microscopy is inherently static. Here we solved these challenges by developing an integrated optical/machine-learning technology, LIONESS (live information-optimized nanoscopy enabling saturated segmentation). This leverages optical modifications to stimulated emission depletion microscopy in comprehensively, extracellularly labeled tissue and previous information on sample structure via machine learning to simultaneously achieve isotropic super-resolution, high signal-to-noise ratio and compatibility with living tissue. This allows dense deep-learning-based instance segmentation and 3D reconstruction at a synapse level, incorporating molecular, activity and morphodynamic information. LIONESS opens up avenues for studying the dynamic functional (nano-)architecture of living brain tissue."}],"month":"08","intvolume":" 20","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1038/s41592-023-01936-6","open_access":"1"}]},{"publication_status":"published","publication_identifier":{"eissn":["2575-7075"],"eisbn":["9798350301298"]},"language":[{"iso":"eng"}],"ec_funded":1,"related_material":{"link":[{"relation":"software","url":"https://github.com/IST-DASLab/pruned-vision-model-bias"}]},"abstract":[{"text":"Pruning—that is, setting a significant subset of the parameters of a neural network to zero—is one of the most popular methods of model compression. Yet, several recent works have raised the issue that pruning may induce or exacerbate bias in the output of the compressed model. Despite existing evidence for this phenomenon, the relationship between neural network pruning and induced bias is not well-understood. In this work, we systematically investigate and characterize this phenomenon in Convolutional Neural Networks for computer vision. First, we show that it is in fact possible to obtain highly-sparse models, e.g. with less than 10% remaining weights, which do not decrease in accuracy nor substantially increase in bias when compared to dense models. At the same time, we also find that, at higher sparsities, pruned models exhibit higher uncertainty in their outputs, as well as increased correlations, which we directly link to increased bias. We propose easy-to-use criteria which, based only on the uncompressed model, establish whether bias will increase with pruning, and identify the samples most susceptible to biased predictions post-compression. Our code can be found at https://github.com/IST-DASLab/pruned-vision-model-bias.","lang":"eng"}],"oa_version":"Preprint","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2304.12622"}],"month":"08","date_updated":"2024-01-10T08:59:26Z","department":[{"_id":"DaAl"},{"_id":"ChLa"}],"_id":"14771","conference":{"end_date":"2023-06-24","location":"Vancouver, BC, Canada","start_date":"2023-06-17","name":"CVPR: Conference on Computer Vision and Pattern Recognition"},"type":"conference","status":"public","year":"2023","isi":1,"publication":"2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition","day":"22","page":"24364-24373","date_created":"2024-01-10T08:42:40Z","date_published":"2023-08-22T00:00:00Z","doi":"10.1109/cvpr52729.2023.02334","acknowledgement":"The authors would like to sincerely thank Sara Hooker for her feedback during the development of this work. EI was supported in part by the FWF DK VGSCO, grant agreement number W1260-N35. AP and DA acknowledge generous ERC support, via Starting Grant 805223 ScaleML.","oa":1,"quality_controlled":"1","publisher":"IEEE","citation":{"ama":"Iofinova EB, Peste E-A, Alistarh D-A. Bias in pruned vision models: In-depth analysis and countermeasures. In: 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition. IEEE; 2023:24364-24373. doi:10.1109/cvpr52729.2023.02334","apa":"Iofinova, E. B., Peste, E.-A., & Alistarh, D.-A. (2023). Bias in pruned vision models: In-depth analysis and countermeasures. In 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition (pp. 24364–24373). Vancouver, BC, Canada: IEEE. https://doi.org/10.1109/cvpr52729.2023.02334","short":"E.B. Iofinova, E.-A. Peste, D.-A. Alistarh, in:, 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–24373.","ieee":"E. B. Iofinova, E.-A. Peste, and D.-A. Alistarh, “Bias in pruned vision models: In-depth analysis and countermeasures,” in 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, Vancouver, BC, Canada, 2023, pp. 24364–24373.","mla":"Iofinova, Eugenia B., et al. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, IEEE, 2023, pp. 24364–73, doi:10.1109/cvpr52729.2023.02334.","ista":"Iofinova EB, Peste E-A, Alistarh D-A. 2023. Bias in pruned vision models: In-depth analysis and countermeasures. 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition. CVPR: Conference on Computer Vision and Pattern Recognition, 24364–24373.","chicago":"Iofinova, Eugenia B, Elena-Alexandra Peste, and Dan-Adrian Alistarh. “Bias in Pruned Vision Models: In-Depth Analysis and Countermeasures.” In 2023 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 24364–73. IEEE, 2023. https://doi.org/10.1109/cvpr52729.2023.02334."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["001062531308068"],"arxiv":["2304.12622"]},"article_processing_charge":"No","author":[{"last_name":"Iofinova","full_name":"Iofinova, Eugenia B","orcid":"0000-0002-7778-3221","first_name":"Eugenia B","id":"f9a17499-f6e0-11ea-865d-fdf9a3f77117"},{"first_name":"Elena-Alexandra","id":"32D78294-F248-11E8-B48F-1D18A9856A87","full_name":"Peste, Elena-Alexandra","last_name":"Peste"},{"full_name":"Alistarh, Dan-Adrian","orcid":"0000-0003-3650-940X","last_name":"Alistarh","first_name":"Dan-Adrian","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87"}],"title":"Bias in pruned vision models: In-depth analysis and countermeasures","project":[{"grant_number":" W1260-N35","name":"Vienna Graduate School on Computational Optimization","_id":"9B9290DE-BA93-11EA-9121-9846C619BF3A"},{"_id":"268A44D6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Elastic Coordination for Scalable Machine Learning","grant_number":"805223"}]},{"_id":"14770","status":"public","keyword":["Cell Biology","Molecular Biology","Biochemistry","Biotechnology"],"article_type":"letter_note","type":"journal_article","date_updated":"2024-01-10T08:37:48Z","department":[{"_id":"JoDa"}],"oa_version":"None","abstract":[{"lang":"eng","text":"We developed LIONESS, a technology that leverages improvements to optical super-resolution microscopy and prior information on sample structure via machine learning to overcome the limitations (in 3D-resolution, signal-to-noise ratio and light exposure) of optical microscopy of living biological specimens. LIONESS enables dense reconstruction of living brain tissue and morphodynamics visualization at the nanoscale."}],"month":"08","intvolume":" 20","scopus_import":"1","language":[{"iso":"eng"}],"publication_identifier":{"issn":["1548-7091"],"eissn":["1548-7105"]},"publication_status":"published","issue":"8","related_material":{"record":[{"status":"public","id":"13267","relation":"extended_version"}]},"volume":20,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Danzl JG, Velicky P. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 2023;20(8):1141-1142. doi:10.1038/s41592-023-01937-5","apa":"Danzl, J. G., & Velicky, P. (2023). LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. Springer Nature. https://doi.org/10.1038/s41592-023-01937-5","short":"J.G. Danzl, P. Velicky, Nature Methods 20 (2023) 1141–1142.","ieee":"J. G. Danzl and P. Velicky, “LIONESS enables 4D nanoscale reconstruction of living brain tissue,” Nature Methods, vol. 20, no. 8. Springer Nature, pp. 1141–1142, 2023.","mla":"Danzl, Johann G., and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods, vol. 20, no. 8, Springer Nature, 2023, pp. 1141–42, doi:10.1038/s41592-023-01937-5.","ista":"Danzl JG, Velicky P. 2023. LIONESS enables 4D nanoscale reconstruction of living brain tissue. Nature Methods. 20(8), 1141–1142.","chicago":"Danzl, Johann G, and Philipp Velicky. “LIONESS Enables 4D Nanoscale Reconstruction of Living Brain Tissue.” Nature Methods. Springer Nature, 2023. https://doi.org/10.1038/s41592-023-01937-5."},"title":"LIONESS enables 4D nanoscale reconstruction of living brain tissue","author":[{"first_name":"Johann G","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8559-3973","full_name":"Danzl, Johann G","last_name":"Danzl"},{"last_name":"Velicky","orcid":"0000-0002-2340-7431","full_name":"Velicky, Philipp","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","first_name":"Philipp"}],"article_processing_charge":"No","external_id":{"isi":["001025621500002"]},"publisher":"Springer Nature","quality_controlled":"1","day":"01","publication":"Nature Methods","isi":1,"year":"2023","date_published":"2023-08-01T00:00:00Z","doi":"10.1038/s41592-023-01937-5","date_created":"2024-01-10T08:07:15Z","page":"1141-1142"},{"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","keyword":["Developmental Biology","Molecular Biology"],"status":"public","_id":"14774","department":[{"_id":"AnKi"}],"file_date_updated":"2024-01-10T12:41:13Z","date_updated":"2024-01-10T12:45:25Z","ddc":["570"],"intvolume":" 150","month":"10","abstract":[{"lang":"eng","text":"Morphogen gradients impart positional information to cells in a homogenous tissue field. Fgf8a, a highly conserved growth factor, has been proposed to act as a morphogen during zebrafish gastrulation. However, technical limitations have so far prevented direct visualization of the endogenous Fgf8a gradient and confirmation of its morphogenic activity. Here, we monitor Fgf8a propagation in the developing neural plate using a CRISPR/Cas9-mediated EGFP knock-in at the endogenous fgf8a locus. By combining sensitive imaging with single-molecule fluorescence correlation spectroscopy, we demonstrate that Fgf8a, which is produced at the embryonic margin, propagates by diffusion through the extracellular space and forms a graded distribution towards the animal pole. Overlaying the Fgf8a gradient curve with expression profiles of its downstream targets determines the precise input-output relationship of Fgf8a-mediated patterning. Manipulation of the extracellular Fgf8a levels alters the signaling outcome, thus establishing Fgf8a as a bona fide morphogen during zebrafish gastrulation. Furthermore, by hindering Fgf8a diffusion, we demonstrate that extracellular diffusion of the protein from the source is crucial for it to achieve its morphogenic potential."}],"pmid":1,"oa_version":"Published Version","issue":"19","volume":150,"publication_status":"published","publication_identifier":{"eissn":["1477-9129"],"issn":["0950-1991"]},"language":[{"iso":"eng"}],"file":[{"file_id":"14790","checksum":"2d6f52dc33260a9b2352b8f28374ba5f","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-01-10T12:41:13Z","file_name":"2023_Development_Harish.pdf","creator":"dernst","date_updated":"2024-01-10T12:41:13Z","file_size":12836306}],"article_number":"dev201559","article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001097449100002"],"pmid":["37665167"]},"author":[{"last_name":"Harish","full_name":"Harish, Rohit K","id":"1bae78aa-ee0e-11ec-9b76-bc42990f409d","first_name":"Rohit K"},{"first_name":"Mansi","last_name":"Gupta","full_name":"Gupta, Mansi"},{"first_name":"Daniela","full_name":"Zöller, Daniela","last_name":"Zöller"},{"full_name":"Hartmann, Hella","last_name":"Hartmann","first_name":"Hella"},{"first_name":"Ali","full_name":"Gheisari, Ali","last_name":"Gheisari"},{"full_name":"Machate, Anja","last_name":"Machate","first_name":"Anja"},{"full_name":"Hans, Stefan","last_name":"Hans","first_name":"Stefan"},{"first_name":"Michael","full_name":"Brand, Michael","last_name":"Brand"}],"title":"Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation","citation":{"mla":"Harish, Rohit K., et al. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” Development, vol. 150, no. 19, dev201559, The Company of Biologists, 2023, doi:10.1242/dev.201559.","short":"R.K. Harish, M. Gupta, D. Zöller, H. Hartmann, A. Gheisari, A. Machate, S. Hans, M. Brand, Development 150 (2023).","ieee":"R. K. Harish et al., “Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation,” Development, vol. 150, no. 19. The Company of Biologists, 2023.","ama":"Harish RK, Gupta M, Zöller D, et al. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 2023;150(19). doi:10.1242/dev.201559","apa":"Harish, R. K., Gupta, M., Zöller, D., Hartmann, H., Gheisari, A., Machate, A., … Brand, M. (2023). Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. The Company of Biologists. https://doi.org/10.1242/dev.201559","chicago":"Harish, Rohit K, Mansi Gupta, Daniela Zöller, Hella Hartmann, Ali Gheisari, Anja Machate, Stefan Hans, and Michael Brand. “Real-Time Monitoring of an Endogenous Fgf8a Gradient Attests to Its Role as a Morphogen during Zebrafish Gastrulation.” Development. The Company of Biologists, 2023. https://doi.org/10.1242/dev.201559.","ista":"Harish RK, Gupta M, Zöller D, Hartmann H, Gheisari A, Machate A, Hans S, Brand M. 2023. Real-time monitoring of an endogenous Fgf8a gradient attests to its role as a morphogen during zebrafish gastrulation. Development. 150(19), dev201559."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"The Company of Biologists","acknowledgement":"We thank members of the Brand lab, as well as Justina Stark (Ivo Sbalzarini group, Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany) for project-related discussions; Darren Gilmour (University of Zurich), Karuna Sampath (University of Warwick) and Gokul Kesavan (Vowels Lifesciences Private Limited, Bangalore) for comments on the manuscript; personnel of the CMCB technology platform, TU Dresden for imaging and image analysis-related support; and Maurizio Abbate (Technical support, Arivis) for help with image analysis. We are also grateful to Stapornwongkul and Briscoe for commenting on a preprint version of our work (Stapornwongkul and Briscoe, 2022).\r\nThis work was supported by the Deutsche Forschungsgemeinschaft (BR 1746/6-2, BR 1746/11-1 and BR 1746/3 to M.B.), by a Cluster of Excellence ‘Physics of Life’ seed grant and by institutional funds from Technische Universitat Dresden (to M.B.). Open Access funding provided by Technische Universitat Dresden. Deposited in PMC for immediate release.","date_created":"2024-01-10T09:18:54Z","date_published":"2023-10-01T00:00:00Z","doi":"10.1242/dev.201559","year":"2023","isi":1,"has_accepted_license":"1","publication":"Development","day":"01"},{"acknowledgement":"We thank C.U.T. Hellen for critically reading the manuscript. The MALDI MS facility and CLSM became available to us in the framework of Moscow State University Development Programs PNG 5.13 and PNR 5.13.\r\nThis work was funded by the Russian Science Foundation, grant numbers 19-14-00010 and 22-14-00071.","oa":1,"publisher":"MDPI","quality_controlled":"1","publication":"International Journal of Molecular Sciences","day":"01","year":"2023","isi":1,"has_accepted_license":"1","date_created":"2024-01-10T09:24:35Z","date_published":"2023-11-01T00:00:00Z","doi":"10.3390/ijms242216527","article_number":"16527","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Teplova, Anastasiia, et al. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal of Molecular Sciences, vol. 24, no. 22, 16527, MDPI, 2023, doi:10.3390/ijms242216527.","ieee":"A. Teplova et al., “Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3,” International Journal of Molecular Sciences, vol. 24, no. 22. MDPI, 2023.","short":"A. Teplova, A.A. Pigidanov, M.V. Serebryakova, S.A. Golyshev, R.A. Galiullina, N.V. Chichkova, A.B. Vartapetian, International Journal of Molecular Sciences 24 (2023).","ama":"Teplova A, Pigidanov AA, Serebryakova MV, et al. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 2023;24(22). doi:10.3390/ijms242216527","apa":"Teplova, A., Pigidanov, A. A., Serebryakova, M. V., Golyshev, S. A., Galiullina, R. A., Chichkova, N. V., & Vartapetian, A. B. (2023). Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. MDPI. https://doi.org/10.3390/ijms242216527","chicago":"Teplova, Anastasiia, Artemii A. Pigidanov, Marina V. Serebryakova, Sergei A. Golyshev, Raisa A. Galiullina, Nina V. Chichkova, and Andrey B. Vartapetian. “Phytaspase Is Capable of Detaching the Endoplasmic Reticulum Retrieval Signal from Tobacco Calreticulin-3.” International Journal of Molecular Sciences. MDPI, 2023. https://doi.org/10.3390/ijms242216527.","ista":"Teplova A, Pigidanov AA, Serebryakova MV, Golyshev SA, Galiullina RA, Chichkova NV, Vartapetian AB. 2023. Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3. International Journal of Molecular Sciences. 24(22), 16527."},"title":"Phytaspase Is capable of detaching the endoplasmic reticulum retrieval signal from tobacco calreticulin-3","article_processing_charge":"Yes","external_id":{"isi":["001113792600001"],"pmid":["38003717"]},"author":[{"last_name":"Teplova","full_name":"Teplova, Anastasiia","first_name":"Anastasiia","id":"e3736151-106c-11ec-b916-c2558e2762c6"},{"first_name":"Artemii A.","full_name":"Pigidanov, Artemii A.","last_name":"Pigidanov"},{"first_name":"Marina V.","last_name":"Serebryakova","full_name":"Serebryakova, Marina V."},{"first_name":"Sergei A.","last_name":"Golyshev","full_name":"Golyshev, Sergei A."},{"full_name":"Galiullina, Raisa A.","last_name":"Galiullina","first_name":"Raisa A."},{"first_name":"Nina V.","full_name":"Chichkova, Nina V.","last_name":"Chichkova"},{"first_name":"Andrey B.","full_name":"Vartapetian, Andrey B.","last_name":"Vartapetian"}],"oa_version":"Published Version","pmid":1,"abstract":[{"lang":"eng","text":"Soluble chaperones residing in the endoplasmic reticulum (ER) play vitally important roles in folding and quality control of newly synthesized proteins that transiently pass through the ER en route to their final destinations. These soluble residents of the ER are themselves endowed with an ER retrieval signal that enables the cell to bring the escaped residents back from the Golgi. Here, by using purified proteins, we showed that Nicotiana tabacum phytaspase, a plant aspartate-specific protease, introduces two breaks at the C-terminus of the N. tabacum ER resident calreticulin-3. These cleavages resulted in removal of either a dipeptide or a hexapeptide from the C-terminus of calreticulin-3 encompassing part or all of the ER retrieval signal. Consistently, expression of the calreticulin-3 derivative mimicking the phytaspase cleavage product in Nicotiana benthamiana cells demonstrated loss of the ER accumulation of the protein. Notably, upon its escape from the ER, calreticulin-3 was further processed by an unknown protease(s) to generate the free N-terminal (N) domain of calreticulin-3, which was ultimately secreted into the apoplast. Our study thus identified a specific proteolytic enzyme capable of precise detachment of the ER retrieval signal from a plant ER resident protein, with implications for the further fate of the escaped resident."}],"intvolume":" 24","month":"11","language":[{"iso":"eng"}],"file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"4df7d206ba022b7f54eff1f0aec1659a","file_id":"14791","success":1,"creator":"dernst","date_updated":"2024-01-10T13:39:42Z","file_size":2637784,"date_created":"2024-01-10T13:39:42Z","file_name":"2023_IJMS_Teplova.pdf"}],"publication_status":"published","publication_identifier":{"issn":["1422-0067"]},"volume":24,"issue":"22","_id":"14776","keyword":["Inorganic Chemistry","Organic Chemistry","Physical and Theoretical Chemistry","Computer Science Applications","Spectroscopy","Molecular Biology","General Medicine","Catalysis"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","ddc":["580"],"date_updated":"2024-01-10T13:41:10Z","department":[{"_id":"JiFr"}],"file_date_updated":"2024-01-10T13:39:42Z"},{"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2108.02728","open_access":"1"}],"month":"02","intvolume":" 33","abstract":[{"lang":"eng","text":"We establish a quantitative version of the Tracy–Widom law for the largest eigenvalue of high-dimensional sample covariance matrices. To be precise, we show that the fluctuations of the largest eigenvalue of a sample covariance matrix X∗X converge to its Tracy–Widom limit at a rate nearly N−1/3, where X is an M×N random matrix whose entries are independent real or complex random variables, assuming that both M and N tend to infinity at a constant rate. This result improves the previous estimate N−2/9 obtained by Wang (2019). Our proof relies on a Green function comparison method (Adv. Math. 229 (2012) 1435–1515) using iterative cumulant expansions, the local laws for the Green function and asymptotic properties of the correlation kernel of the white Wishart ensemble."}],"oa_version":"Preprint","issue":"1","volume":33,"ec_funded":1,"publication_identifier":{"issn":["1050-5164"]},"publication_status":"published","language":[{"iso":"eng"}],"type":"journal_article","article_type":"original","status":"public","keyword":["Statistics","Probability and Uncertainty","Statistics and Probability"],"_id":"14775","department":[{"_id":"LaEr"}],"date_updated":"2024-01-10T13:31:46Z","publisher":"Institute of Mathematical Statistics","quality_controlled":"1","oa":1,"acknowledgement":"K. Schnelli was supported by the Swedish Research Council Grants VR-2017-05195, and the Knut and Alice Wallenberg Foundation. Y. Xu was supported by the Swedish Research Council Grant VR-2017-05195 and the ERC Advanced Grant “RMTBeyond” No. 101020331.","page":"677-725","date_published":"2023-02-01T00:00:00Z","doi":"10.1214/22-aap1826","date_created":"2024-01-10T09:23:31Z","isi":1,"year":"2023","day":"01","publication":"The Annals of Applied Probability","project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}],"author":[{"orcid":"0000-0003-0954-3231","full_name":"Schnelli, Kevin","last_name":"Schnelli","id":"434AD0AE-F248-11E8-B48F-1D18A9856A87","first_name":"Kevin"},{"last_name":"Xu","orcid":"0000-0003-1559-1205","full_name":"Xu, Yuanyuan","first_name":"Yuanyuan","id":"7902bdb1-a2a4-11eb-a164-c9216f71aea3"}],"external_id":{"arxiv":["2108.02728"],"isi":["000946432400021"]},"article_processing_charge":"No","title":"Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices","citation":{"chicago":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Sample Covariance Matrices.” The Annals of Applied Probability. Institute of Mathematical Statistics, 2023. https://doi.org/10.1214/22-aap1826.","ista":"Schnelli K, Xu Y. 2023. Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. The Annals of Applied Probability. 33(1), 677–725.","mla":"Schnelli, Kevin, and Yuanyuan Xu. “Convergence Rate to the Tracy–Widom Laws for the Largest Eigenvalue of Sample Covariance Matrices.” The Annals of Applied Probability, vol. 33, no. 1, Institute of Mathematical Statistics, 2023, pp. 677–725, doi:10.1214/22-aap1826.","apa":"Schnelli, K., & Xu, Y. (2023). Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. The Annals of Applied Probability. Institute of Mathematical Statistics. https://doi.org/10.1214/22-aap1826","ama":"Schnelli K, Xu Y. Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices. The Annals of Applied Probability. 2023;33(1):677-725. doi:10.1214/22-aap1826","short":"K. Schnelli, Y. Xu, The Annals of Applied Probability 33 (2023) 677–725.","ieee":"K. Schnelli and Y. Xu, “Convergence rate to the Tracy–Widom laws for the largest eigenvalue of sample covariance matrices,” The Annals of Applied Probability, vol. 33, no. 1. Institute of Mathematical Statistics, pp. 677–725, 2023."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"intvolume":" 76","month":"05","main_file_link":[{"url":"https://www.lmd.ens.fr/muller/Pubs/2023-MullerAbramianPhysToday.pdf","open_access":"1"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Through a combination of idealized simulations and real-world data, researchers are uncovering how internal feedbacks and large-scale motions influence cloud dynamics."}],"issue":"5","volume":76,"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0031-9228"],"eissn":["1945-0699"]},"keyword":["General Physics and Astronomy"],"status":"public","type":"journal_article","article_type":"original","_id":"14773","department":[{"_id":"CaMu"}],"date_updated":"2024-01-10T12:38:02Z","oa":1,"publisher":"AIP Publishing","quality_controlled":"1","date_created":"2024-01-10T09:18:04Z","doi":"10.1063/pt.3.5234","date_published":"2023-05-01T00:00:00Z","publication":"Physics Today","day":"01","year":"2023","isi":1,"article_number":"28","title":"The cloud dynamics of convective storm systems","article_processing_charge":"No","external_id":{"isi":["000984516100007"]},"author":[{"id":"f978ccb0-3f7f-11eb-b193-b0e2bd13182b","first_name":"Caroline J","orcid":"0000-0001-5836-5350","full_name":"Muller, Caroline J","last_name":"Muller"},{"full_name":"Abramian, Sophie","last_name":"Abramian","first_name":"Sophie"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Muller, Caroline J., and Sophie Abramian. “The Cloud Dynamics of Convective Storm Systems.” Physics Today, vol. 76, no. 5, 28, AIP Publishing, 2023, doi:10.1063/pt.3.5234.","apa":"Muller, C. J., & Abramian, S. (2023). The cloud dynamics of convective storm systems. Physics Today. AIP Publishing. https://doi.org/10.1063/pt.3.5234","ama":"Muller CJ, Abramian S. The cloud dynamics of convective storm systems. Physics Today. 2023;76(5). doi:10.1063/pt.3.5234","short":"C.J. Muller, S. Abramian, Physics Today 76 (2023).","ieee":"C. J. Muller and S. Abramian, “The cloud dynamics of convective storm systems,” Physics Today, vol. 76, no. 5. AIP Publishing, 2023.","chicago":"Muller, Caroline J, and Sophie Abramian. “The Cloud Dynamics of Convective Storm Systems.” Physics Today. AIP Publishing, 2023. https://doi.org/10.1063/pt.3.5234.","ista":"Muller CJ, Abramian S. 2023. The cloud dynamics of convective storm systems. Physics Today. 76(5), 28."}},{"publication_identifier":{"eissn":["2158-3226"]},"publication_status":"published","file":[{"success":1,"file_id":"14792","checksum":"a7098388b8ff822b47f5ddd37ed3bdbc","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_AIPAdvances_Sato.pdf","date_created":"2024-01-10T13:47:31Z","file_size":9676071,"date_updated":"2024-01-10T13:47:31Z","creator":"dernst"}],"language":[{"iso":"eng"}],"issue":"12","volume":13,"abstract":[{"lang":"eng","text":"The effects of the partial V-substitution for Ag on the thermoelectric (TE) properties are investigated for a flexible semiconducting compound Ag2S0.55Se0.45. Density functional theory calculations predict that such a partial V-substitution constructively modifies the electronic structure near the bottom of the conduction band to improve the TE performance. The synthesized Ag1.97V0.03S0.55Se0.45 is found to possess a TE dimensionless figure-of-merit (ZT) of 0.71 at 350 K with maintaining its flexible nature. This ZT value is relatively high in comparison with those reported for flexible TE materials below 360 K. The increase in the ZT value is caused by the enhanced absolute value of the Seebeck coefficient with less significant variation in electrical resistivity. The high ZT value with the flexible nature naturally allows us to employ the Ag1.97V0.03S0.55Se0.45 as a component of flexible TE generators."}],"oa_version":"Published Version","month":"12","intvolume":" 13","date_updated":"2024-01-10T13:49:09Z","ddc":["540"],"department":[{"_id":"MaIb"}],"file_date_updated":"2024-01-10T13:47:31Z","_id":"14777","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["General Physics and Astronomy"],"has_accepted_license":"1","isi":1,"year":"2023","day":"01","publication":"AIP Advances","doi":"10.1063/5.0171888","date_published":"2023-12-01T00:00:00Z","date_created":"2024-01-10T09:26:08Z","acknowledgement":"This work received financial support partially from Japan Science and Technology Agency (JST) CREST Grant No. JPMJCR18I2, Japan. The powder-XRD experiments were conducted at BL5S2 of Aichi Synchrotron Radiation Center, Aichi Science & Technology Foundation, Aichi, Japan (Proposal No. 202301057).","quality_controlled":"1","publisher":"AIP Publishing","oa":1,"citation":{"apa":"Sato, K., Singh, S., Yamazaki, I., Hirata, K., Ang, A. K. R., Matsunami, M., & Takeuchi, T. (2023). Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances. AIP Publishing. https://doi.org/10.1063/5.0171888","ama":"Sato K, Singh S, Yamazaki I, et al. Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances. 2023;13(12). doi:10.1063/5.0171888","short":"K. Sato, S. Singh, I. Yamazaki, K. Hirata, A.K.R. Ang, M. Matsunami, T. Takeuchi, AIP Advances 13 (2023).","ieee":"K. Sato et al., “Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag,” AIP Advances, vol. 13, no. 12. AIP Publishing, 2023.","mla":"Sato, Kosuke, et al. “Improvement of Thermoelectric Performance of Flexible Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution for Ag.” AIP Advances, vol. 13, no. 12, 125206, AIP Publishing, 2023, doi:10.1063/5.0171888.","ista":"Sato K, Singh S, Yamazaki I, Hirata K, Ang AKR, Matsunami M, Takeuchi T. 2023. Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag. AIP Advances. 13(12), 125206.","chicago":"Sato, Kosuke, Saurabh Singh, Itsuki Yamazaki, Keisuke Hirata, Artoni Kevin R. Ang, Masaharu Matsunami, and Tsunehiro Takeuchi. “Improvement of Thermoelectric Performance of Flexible Compound Ag2S0.55Se0.45 by Means of Partial V-Substitution for Ag.” AIP Advances. AIP Publishing, 2023. https://doi.org/10.1063/5.0171888."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"first_name":"Kosuke","full_name":"Sato, Kosuke","last_name":"Sato"},{"full_name":"Singh, Saurabh","orcid":"0000-0003-2209-5269","last_name":"Singh","first_name":"Saurabh","id":"12d625da-9cb3-11ed-9667-af09d37d3f0a"},{"full_name":"Yamazaki, Itsuki","last_name":"Yamazaki","first_name":"Itsuki"},{"first_name":"Keisuke","last_name":"Hirata","full_name":"Hirata, Keisuke"},{"last_name":"Ang","full_name":"Ang, Artoni Kevin R.","first_name":"Artoni Kevin R."},{"full_name":"Matsunami, Masaharu","last_name":"Matsunami","first_name":"Masaharu"},{"full_name":"Takeuchi, Tsunehiro","last_name":"Takeuchi","first_name":"Tsunehiro"}],"external_id":{"isi":["001114917200005"]},"article_processing_charge":"Yes","title":"Improvement of thermoelectric performance of flexible compound Ag2S0.55Se0.45 by means of partial V-substitution for Ag","article_number":"125206"},{"abstract":[{"text":"We introduce a hierachy of equivalence relations on the set of separated nets of a given Euclidean space, indexed by concave increasing functions ϕ:(0,∞)→(0,∞). Two separated nets are called ϕ-displacement equivalent if, roughly speaking, there is a bijection between them which, for large radii R, displaces points of norm at most R by something of order at most ϕ(R). We show that the spectrum of ϕ-displacement equivalence spans from the established notion of bounded displacement equivalence, which corresponds to bounded ϕ, to the indiscrete equivalence relation, coresponding to ϕ(R)∈Ω(R), in which all separated nets are equivalent. In between the two ends of this spectrum, the notions of ϕ-displacement equivalence are shown to be pairwise distinct with respect to the asymptotic classes of ϕ(R) for R→∞. We further undertake a comparison of our notion of ϕ-displacement equivalence with previously studied relations on separated nets. Particular attention is given to the interaction of the notions of ϕ-displacement equivalence with that of bilipschitz equivalence.","lang":"eng"}],"oa_version":"Published Version","scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.1007/s10711-023-00862-3","open_access":"1"}],"month":"11","publication_identifier":{"issn":["0046-5755"],"eissn":["1572-9168"]},"publication_status":"epub_ahead","language":[{"iso":"eng"}],"_id":"9651","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-01-11T13:06:32Z","department":[{"_id":"UlWa"}],"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). This work was started while both authors were employed at the University of Innsbruck and enjoyed the full support of Austrian Science Fund (FWF): P 30902-N35. It was continued when the first named author was employed at University of Leipzig and the second named author was employed at Institute of Science and Technology of Austria, where he was supported by an IST Fellowship.","quality_controlled":"1","publisher":"Springer Nature","oa":1,"isi":1,"year":"2023","day":"17","publication":"Geometriae Dedicata","doi":"10.1007/s10711-023-00862-3","date_published":"2023-11-17T00:00:00Z","date_created":"2021-07-14T07:01:27Z","article_number":"15","citation":{"mla":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata, 15, Springer Nature, 2023, doi:10.1007/s10711-023-00862-3.","short":"M. Dymond, V. Kaluza, Geometriae Dedicata (2023).","ieee":"M. Dymond and V. Kaluza, “Divergence of separated nets with respect to displacement equivalence,” Geometriae Dedicata. Springer Nature, 2023.","ama":"Dymond M, Kaluza V. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. 2023. doi:10.1007/s10711-023-00862-3","apa":"Dymond, M., & Kaluza, V. (2023). Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata. Springer Nature. https://doi.org/10.1007/s10711-023-00862-3","chicago":"Dymond, Michael, and Vojtech Kaluza. “Divergence of Separated Nets with Respect to Displacement Equivalence.” Geometriae Dedicata. Springer Nature, 2023. https://doi.org/10.1007/s10711-023-00862-3.","ista":"Dymond M, Kaluza V. 2023. Divergence of separated nets with respect to displacement equivalence. Geometriae Dedicata., 15."},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","author":[{"last_name":"Dymond","full_name":"Dymond, Michael","first_name":"Michael"},{"orcid":"0000-0002-2512-8698","full_name":"Kaluza, Vojtech","last_name":"Kaluza","first_name":"Vojtech","id":"21AE5134-9EAC-11EA-BEA2-D7BD3DDC885E"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001105681500001"],"arxiv":["2102.13046"]},"title":"Divergence of separated nets with respect to displacement equivalence"},{"date_updated":"2024-01-16T07:28:06Z","department":[{"_id":"MoHe"}],"_id":"14768","type":"conference","conference":{"end_date":"2023-11-09","location":"Santa Cruz, CA, United States","start_date":"2023-11-06","name":"FOCS: Symposium on Foundations of Computer Science"},"status":"public","publication_identifier":{"eisbn":["9798350318944"]},"publication_status":"published","language":[{"iso":"eng"}],"ec_funded":1,"abstract":[{"text":"In all state-of-the-art sketching and coreset techniques for clustering, as well as in the best known fixed-parameter tractable approximation algorithms, randomness plays a key role. For the classic k-median and k-means problems, there are no known deterministic dimensionality reduction procedure or coreset construction that avoid an exponential dependency on the input dimension d, the precision parameter $\\varepsilon^{-1}$ or k. Furthermore, there is no coreset construction that succeeds with probability $1-1/n$ and whose size does not depend on the number of input points, n. This has led researchers in the area to ask what is the power of randomness for clustering sketches [Feldman WIREs Data Mining Knowl. Discov’20].Similarly, the best approximation ratio achievable deterministically without a complexity exponential in the dimension are $1+\\sqrt{2}$ for k-median [Cohen-Addad, Esfandiari, Mirrokni, Narayanan, STOC’22] and 6.12903 for k-means [Grandoni, Ostrovsky, Rabani, Schulman, Venkat, Inf. Process. Lett.’22]. Those are the best results, even when allowing a complexity FPT in the number of clusters k: this stands in sharp contrast with the $(1+\\varepsilon)$-approximation achievable in that case, when allowing randomization.In this paper, we provide deterministic sketches constructions for clustering, whose size bounds are close to the best-known randomized ones. We show how to compute a dimension reduction onto $\\varepsilon^{-O(1)} \\log k$ dimensions in time $k^{O\\left(\\varepsilon^{-O(1)}+\\log \\log k\\right)}$ poly $(n d)$, and how to build a coreset of size $O\\left(k^{2} \\log ^{3} k \\varepsilon^{-O(1)}\\right)$ in time $2^{\\varepsilon^{O(1)} k \\log ^{3} k}+k^{O\\left(\\varepsilon^{-O(1)}+\\log \\log k\\right)}$ poly $(n d)$. In the case where k is small, this answers an open question of [Feldman WIDM’20] and [Munteanu and Schwiegelshohn, Künstliche Intell. ’18] on whether it is possible to efficiently compute coresets deterministically.We also construct a deterministic algorithm for computing $(1+$ $\\varepsilon)$-approximation to k-median and k-means in high dimensional Euclidean spaces in time $2^{k^{2} \\log ^{3} k / \\varepsilon^{O(1)}}$ poly $(n d)$, close to the best randomized complexity of $2^{(k / \\varepsilon)^{O(1)}}$ nd (see [Kumar, Sabharwal, Sen, JACM 10] and [Bhattacharya, Jaiswal, Kumar, TCS’18]).Furthermore, our new insights on sketches also yield a randomized coreset construction that uses uniform sampling, that immediately improves over the recent results of [Braverman et al. FOCS ’22] by a factor k.","lang":"eng"}],"oa_version":"Preprint","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.2310.04076"}],"month":"12","citation":{"short":"V. Cohen-Addad, D. Saulpic, C. Schwiegelshohn, in:, 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, IEEE, 2023, pp. 1105–1130.","ieee":"V. Cohen-Addad, D. Saulpic, and C. Schwiegelshohn, “Deterministic clustering in high dimensional spaces: Sketches and approximation,” in 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, Santa Cruz, CA, United States, 2023, pp. 1105–1130.","apa":"Cohen-Addad, V., Saulpic, D., & Schwiegelshohn, C. (2023). Deterministic clustering in high dimensional spaces: Sketches and approximation. In 2023 IEEE 64th Annual Symposium on Foundations of Computer Science (pp. 1105–1130). Santa Cruz, CA, United States: IEEE. https://doi.org/10.1109/focs57990.2023.00066","ama":"Cohen-Addad V, Saulpic D, Schwiegelshohn C. Deterministic clustering in high dimensional spaces: Sketches and approximation. In: 2023 IEEE 64th Annual Symposium on Foundations of Computer Science. IEEE; 2023:1105-1130. doi:10.1109/focs57990.2023.00066","mla":"Cohen-Addad, Vincent, et al. “Deterministic Clustering in High Dimensional Spaces: Sketches and Approximation.” 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, IEEE, 2023, pp. 1105–30, doi:10.1109/focs57990.2023.00066.","ista":"Cohen-Addad V, Saulpic D, Schwiegelshohn C. 2023. Deterministic clustering in high dimensional spaces: Sketches and approximation. 2023 IEEE 64th Annual Symposium on Foundations of Computer Science. FOCS: Symposium on Foundations of Computer Science, 1105–1130.","chicago":"Cohen-Addad, Vincent, David Saulpic, and Chris Schwiegelshohn. “Deterministic Clustering in High Dimensional Spaces: Sketches and Approximation.” In 2023 IEEE 64th Annual Symposium on Foundations of Computer Science, 1105–30. IEEE, 2023. https://doi.org/10.1109/focs57990.2023.00066."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Cohen-Addad, Vincent","last_name":"Cohen-Addad","first_name":"Vincent"},{"first_name":"David","id":"f8e48cf0-b0ff-11ed-b0e9-b4c35598f964","last_name":"Saulpic","full_name":"Saulpic, David"},{"full_name":"Schwiegelshohn, Chris","last_name":"Schwiegelshohn","first_name":"Chris"}],"article_processing_charge":"No","external_id":{"arxiv":["2310.04076"]},"title":"Deterministic clustering in high dimensional spaces: Sketches and approximation","project":[{"_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020","name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413"},{"grant_number":"101019564","name":"The design and evaluation of modern fully dynamic data structures","call_identifier":"H2020","_id":"bd9ca328-d553-11ed-ba76-dc4f890cfe62"}],"year":"2023","day":"22","publication":"2023 IEEE 64th Annual Symposium on Foundations of Computer Science","page":"1105-1130","date_published":"2023-12-22T00:00:00Z","doi":"10.1109/focs57990.2023.00066","date_created":"2024-01-09T16:20:09Z","acknowledgement":"D. Sauplic has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 101034413, and Grant agreement No. 101019564 “The Design of Modern Fully Dynamic Data Structures (MoDynStruct)”.\r\nC. Schwiegelshohn acknowledges the support of the Independent Research Fund Denmark (DFF) under a Sapere Aude Research Leader grant No 1051-00106B.","publisher":"IEEE","quality_controlled":"1","oa":1},{"abstract":[{"lang":"eng","text":"The next steps of deep space exploration are manned missions to Moon and Mars. For safe space missions for crew members, it is important to understand the impact of space flight on the immune system. We studied the effects of 21 days dry immersion (DI) exposure on the transcriptomes of T cells isolated from blood samples of eight healthy volunteers. Samples were collected 7 days before DI, at day 7, 14, and 21 during DI, and 7 days after DI. RNA sequencing of CD3+T cells revealed transcriptional alterations across all time points, with most changes occurring 14 days after DI exposure. At day 21, T cells showed evidence of adaptation with a transcriptional profile resembling that of 7 days before DI. At 7 days after DI, T cells again changed their transcriptional profile. These data suggest that T cells adapt by rewiring their transcriptomes in response to simulated weightlessness and that remodeling cues persist when reexposed to normal gravity."}],"oa_version":"Published Version","pmid":1,"month":"08","intvolume":" 9","publication_identifier":{"issn":["2375-2548"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14809","checksum":"b9072e20e2d5d9d34d2c53319bafee41","success":1,"creator":"dernst","date_updated":"2024-01-16T09:35:28Z","file_size":1596639,"date_created":"2024-01-16T09:35:28Z","file_name":"2023_ScienceAdvances_GallardoDodd.pdf"}],"language":[{"iso":"eng"}],"issue":"34","volume":9,"_id":"14784","type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Multidisciplinary"],"date_updated":"2024-01-16T09:38:58Z","ddc":["570"],"department":[{"_id":"FlSc"}],"file_date_updated":"2024-01-16T09:35:28Z","acknowledgement":"This work was supported by a postdoctoral fellowship from the Swedish Society for Medical Research to J.R., a CAPES-STINT joint grant to R.G.G. and L.S.W., a PhD fellowship from Karolinska Institutet (KID) to E.D., a PhD fellowship from Fundação para a Ciência e a Tecnologia and European Social Fund to M.M.S.O., the program of fundamental research (theme 65.1) of the Institute for Biomedical Problems of the Russian Academy of Sciences (IBMP RAS) to A.A.S., S.M.S., V.A.S., O.V.K., D.D.V., K.D.O., M.P.R., and S.A.P., the Tamkeen under the NYU Abu Dhabi Research Institute Award to the NYUAD Center for Genomics and Systems Biology (ADHPG-CGSB) to P.P., the Knut and Alice Wallenberg foundation to C.K., the Swedish National Space Agency to N.V.K. and L.S.W., Swedish Research Council, Gösta Fraenckel Foundation, and Karolinska Institutet to L.S.W.","publisher":"American Association for the Advancement of Science","quality_controlled":"1","oa":1,"isi":1,"has_accepted_license":"1","year":"2023","day":"25","publication":"Science Advances","date_published":"2023-08-25T00:00:00Z","doi":"10.1126/sciadv.adg1610","date_created":"2024-01-10T09:48:01Z","article_number":"adg1610","citation":{"mla":"Gallardo-Dodd, Carlos J., et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” Science Advances, vol. 9, no. 34, adg1610, American Association for the Advancement of Science, 2023, doi:10.1126/sciadv.adg1610.","ieee":"C. J. Gallardo-Dodd et al., “Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells,” Science Advances, vol. 9, no. 34. American Association for the Advancement of Science, 2023.","short":"C.J. Gallardo-Dodd, C. Oertlin, J. Record, R.G. Galvani, C. Sommerauer, N.V. Kuznetsov, E. Doukoumopoulos, L. Ali, M.M.S. Oliveira, C. Seitz, M. Percipalle, T. Nikić, A.A. Sadova, S.M. Shulgina, V.A. Shmarov, O.V. Kutko, D.D. Vlasova, K.D. Orlova, M.P. Rykova, J. Andersson, P. Percipalle, C. Kutter, S.A. Ponomarev, L.S. Westerberg, Science Advances 9 (2023).","ama":"Gallardo-Dodd CJ, Oertlin C, Record J, et al. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 2023;9(34). doi:10.1126/sciadv.adg1610","apa":"Gallardo-Dodd, C. J., Oertlin, C., Record, J., Galvani, R. G., Sommerauer, C., Kuznetsov, N. V., … Westerberg, L. S. (2023). Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. American Association for the Advancement of Science. https://doi.org/10.1126/sciadv.adg1610","chicago":"Gallardo-Dodd, Carlos J., Christian Oertlin, Julien Record, Rômulo G. Galvani, Christian Sommerauer, Nikolai V. Kuznetsov, Evangelos Doukoumopoulos, et al. “Exposure of Volunteers to Microgravity by Dry Immersion Bed over 21 Days Results in Gene Expression Changes and Adaptation of T Cells.” Science Advances. American Association for the Advancement of Science, 2023. https://doi.org/10.1126/sciadv.adg1610.","ista":"Gallardo-Dodd CJ, Oertlin C, Record J, Galvani RG, Sommerauer C, Kuznetsov NV, Doukoumopoulos E, Ali L, Oliveira MMS, Seitz C, Percipalle M, Nikić T, Sadova AA, Shulgina SM, Shmarov VA, Kutko OV, Vlasova DD, Orlova KD, Rykova MP, Andersson J, Percipalle P, Kutter C, Ponomarev SA, Westerberg LS. 2023. Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells. Science Advances. 9(34), adg1610."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Gallardo-Dodd, Carlos J.","last_name":"Gallardo-Dodd","first_name":"Carlos J."},{"first_name":"Christian","full_name":"Oertlin, Christian","last_name":"Oertlin"},{"last_name":"Record","full_name":"Record, Julien","first_name":"Julien"},{"first_name":"Rômulo G.","last_name":"Galvani","full_name":"Galvani, Rômulo G."},{"first_name":"Christian","full_name":"Sommerauer, Christian","last_name":"Sommerauer"},{"first_name":"Nikolai V.","full_name":"Kuznetsov, Nikolai V.","last_name":"Kuznetsov"},{"last_name":"Doukoumopoulos","full_name":"Doukoumopoulos, Evangelos","first_name":"Evangelos"},{"first_name":"Liaqat","full_name":"Ali, Liaqat","last_name":"Ali"},{"last_name":"Oliveira","full_name":"Oliveira, Mariana M. S.","first_name":"Mariana M. S."},{"first_name":"Christina","last_name":"Seitz","full_name":"Seitz, Christina"},{"last_name":"Percipalle","full_name":"Percipalle, Mathias","id":"45adb726-eb97-11eb-a6c2-c7c3d3caabe9","first_name":"Mathias"},{"last_name":"Nikić","full_name":"Nikić, Tijana","first_name":"Tijana"},{"first_name":"Anastasia A.","full_name":"Sadova, Anastasia A.","last_name":"Sadova"},{"last_name":"Shulgina","full_name":"Shulgina, Sofia M.","first_name":"Sofia M."},{"full_name":"Shmarov, Vjacheslav A.","last_name":"Shmarov","first_name":"Vjacheslav A."},{"first_name":"Olga V.","last_name":"Kutko","full_name":"Kutko, Olga V."},{"last_name":"Vlasova","full_name":"Vlasova, Daria D.","first_name":"Daria D."},{"first_name":"Kseniya D.","full_name":"Orlova, Kseniya D.","last_name":"Orlova"},{"full_name":"Rykova, Marina P.","last_name":"Rykova","first_name":"Marina P."},{"first_name":"John","last_name":"Andersson","full_name":"Andersson, John"},{"first_name":"Piergiorgio","last_name":"Percipalle","full_name":"Percipalle, Piergiorgio"},{"last_name":"Kutter","full_name":"Kutter, Claudia","first_name":"Claudia"},{"first_name":"Sergey A.","last_name":"Ponomarev","full_name":"Ponomarev, Sergey A."},{"last_name":"Westerberg","full_name":"Westerberg, Lisa S.","first_name":"Lisa S."}],"article_processing_charge":"Yes","external_id":{"pmid":["37624890"],"isi":["001054596800007"]},"title":"Exposure of volunteers to microgravity by dry immersion bed over 21 days results in gene expression changes and adaptation of T cells"},{"_id":"14782","article_type":"original","type":"journal_article","tmp":{"short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png"},"status":"public","keyword":["Biophysics"],"date_updated":"2024-01-16T09:20:03Z","ddc":["570"],"file_date_updated":"2024-01-16T09:09:29Z","department":[{"_id":"AnSa"}],"abstract":[{"text":"The actin cortex is a complex cytoskeletal machinery that drives and responds to changes in cell shape. It must generate or adapt to plasma membrane curvature to facilitate diverse functions such as cell division, migration, and phagocytosis. Due to the complex molecular makeup of the actin cortex, it remains unclear whether actin networks are inherently able to sense and generate membrane curvature, or whether they rely on their diverse binding partners to accomplish this. Here, we show that curvature sensing is an inherent capability of branched actin networks nucleated by Arp2/3 and VCA. We develop a robust method to encapsulate actin inside giant unilamellar vesicles (GUVs) and assemble an actin cortex at the inner surface of the GUV membrane. We show that actin forms a uniform and thin cortical layer when present at high concentration and distinct patches associated with negative membrane curvature at low concentration. Serendipitously, we find that the GUV production method also produces dumbbell-shaped GUVs, which we explain using mathematical modeling in terms of membrane hemifusion of nested GUVs. We find that branched actin networks preferentially assemble at the neck of the dumbbells, which possess a micrometer-range convex curvature comparable with the curvature of the actin patches found in spherical GUVs. Minimal branched actin networks can thus sense membrane curvature, which may help mammalian cells to robustly recruit actin to curved membranes to facilitate diverse cellular functions such as cytokinesis and migration.","lang":"eng"}],"oa_version":"Published Version","pmid":1,"month":"06","intvolume":" 122","publication_identifier":{"issn":["0006-3495"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_id":"14807","checksum":"70566e54cd95ea6df340909ad44c5cd5","success":1,"creator":"dernst","date_updated":"2024-01-16T09:09:29Z","file_size":3285810,"date_created":"2024-01-16T09:09:29Z","file_name":"2023_BiophysicalJournal_Baldauf.pdf"}],"language":[{"iso":"eng"}],"related_material":{"link":[{"url":"https://github.com/BioSoftMatterGroup/actin-curvature-sensing","relation":"software"}]},"volume":122,"issue":"11","citation":{"short":"L. Baldauf, F.F. Frey, M. Arribas Perez, T. Idema, G.H. Koenderink, Biophysical Journal 122 (2023) 2311–2324.","ieee":"L. Baldauf, F. F. Frey, M. Arribas Perez, T. Idema, and G. H. Koenderink, “Branched actin cortices reconstituted in vesicles sense membrane curvature,” Biophysical Journal, vol. 122, no. 11. Elsevier, pp. 2311–2324, 2023.","ama":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 2023;122(11):2311-2324. doi:10.1016/j.bpj.2023.02.018","apa":"Baldauf, L., Frey, F. F., Arribas Perez, M., Idema, T., & Koenderink, G. H. (2023). Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. Elsevier. https://doi.org/10.1016/j.bpj.2023.02.018","mla":"Baldauf, Lucia, et al. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” Biophysical Journal, vol. 122, no. 11, Elsevier, 2023, pp. 2311–24, doi:10.1016/j.bpj.2023.02.018.","ista":"Baldauf L, Frey FF, Arribas Perez M, Idema T, Koenderink GH. 2023. Branched actin cortices reconstituted in vesicles sense membrane curvature. Biophysical Journal. 122(11), 2311–2324.","chicago":"Baldauf, Lucia, Felix F Frey, Marcos Arribas Perez, Timon Idema, and Gijsje H. Koenderink. “Branched Actin Cortices Reconstituted in Vesicles Sense Membrane Curvature.” Biophysical Journal. Elsevier, 2023. https://doi.org/10.1016/j.bpj.2023.02.018."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","author":[{"full_name":"Baldauf, Lucia","last_name":"Baldauf","first_name":"Lucia"},{"id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","first_name":"Felix F","last_name":"Frey","full_name":"Frey, Felix F"},{"last_name":"Arribas Perez","full_name":"Arribas Perez, Marcos","first_name":"Marcos"},{"first_name":"Timon","last_name":"Idema","full_name":"Idema, Timon"},{"first_name":"Gijsje H.","full_name":"Koenderink, Gijsje H.","last_name":"Koenderink"}],"external_id":{"pmid":["36806830"],"isi":["001016792600001"]},"article_processing_charge":"Yes (in subscription journal)","title":"Branched actin cortices reconstituted in vesicles sense membrane curvature","acknowledgement":"We thank Jeffrey den Haan for protein purification, Kristina Ganzinger (AMOLF) for providing the 10xHis VCA construct, David Kovar (University of Chicago) for the CP constructs, and Michael Way (Crick Institute) for providing purified human Arp2/3 proteins. We are grateful to Iris Lambert for early actin encapsulation experiments that formed the basis for establishing the eDICE method, to Federico Fanalista for acquiring images of dumbbell-shaped GUVs in samples produced by cDICE, and to Tom Aarts for images of dumbbell-shaped GUVs produced by gel-assisted swelling. Lennard van Buren is thanked for his help with image analysis to quantify actin concentrations in GUVs. We thank Kristina Ganzinger (AMOLF) for hosting us to perform pyrene assays in her lab, and Balász Antalicz (AMOLF) for technical assistance with the spectrophotometer. The authors also thank Matthieu Piel and Daniel Fletcher for insightful and inspiring discussions. We acknowledge financial support from The Netherlands Organization of Scientific Research (NWO/OCW) Gravitation program Building a Synthetic Cell (BaSyC) (024.003.019). F.F. gratefully acknowledges funding from the Kavli Synergy program of the Kavli Institute of Nanoscience Delft.","quality_controlled":"1","publisher":"Elsevier","oa":1,"has_accepted_license":"1","isi":1,"year":"2023","day":"06","publication":"Biophysical Journal","page":"2311-2324","date_published":"2023-06-06T00:00:00Z","doi":"10.1016/j.bpj.2023.02.018","date_created":"2024-01-10T09:45:48Z"},{"citation":{"ama":"Cheung GT, Chever O, Rollenhagen A, et al. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. 2023;12(8). doi:10.3390/cells12081133","apa":"Cheung, G. T., Chever, O., Rollenhagen, A., Quenech’du, N., Ezan, P., Lübke, J. H. R., & Rouach, N. (2023). Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. MDPI. https://doi.org/10.3390/cells12081133","ieee":"G. T. Cheung et al., “Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses,” Cells, vol. 12, no. 8. MDPI, 2023.","short":"G.T. Cheung, O. Chever, A. Rollenhagen, N. Quenech’du, P. Ezan, J.H.R. Lübke, N. Rouach, Cells 12 (2023).","mla":"Cheung, Giselle T., et al. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” Cells, vol. 12, no. 8, 1133, MDPI, 2023, doi:10.3390/cells12081133.","ista":"Cheung GT, Chever O, Rollenhagen A, Quenech’du N, Ezan P, Lübke JHR, Rouach N. 2023. Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses. Cells. 12(8), 1133.","chicago":"Cheung, Giselle T, Oana Chever, Astrid Rollenhagen, Nicole Quenech’du, Pascal Ezan, Joachim H. R. Lübke, and Nathalie Rouach. “Astroglial Connexin 43 Regulates Synaptic Vesicle Release at Hippocampal Synapses.” Cells. MDPI, 2023. https://doi.org/10.3390/cells12081133."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"Yes","external_id":{"pmid":["37190042"],"isi":["000977445700001"]},"author":[{"full_name":"Cheung, Giselle T","orcid":"0000-0001-8457-2572","last_name":"Cheung","id":"471195F6-F248-11E8-B48F-1D18A9856A87","first_name":"Giselle T"},{"full_name":"Chever, Oana","last_name":"Chever","first_name":"Oana"},{"first_name":"Astrid","last_name":"Rollenhagen","full_name":"Rollenhagen, Astrid"},{"first_name":"Nicole","last_name":"Quenech’du","full_name":"Quenech’du, Nicole"},{"first_name":"Pascal","full_name":"Ezan, Pascal","last_name":"Ezan"},{"first_name":"Joachim H. R.","full_name":"Lübke, Joachim H. R.","last_name":"Lübke"},{"full_name":"Rouach, Nathalie","last_name":"Rouach","first_name":"Nathalie"}],"title":"Astroglial connexin 43 regulates synaptic vesicle release at hippocampal synapses","article_number":"1133","year":"2023","isi":1,"has_accepted_license":"1","publication":"Cells","day":"11","date_created":"2024-01-10T09:46:35Z","doi":"10.3390/cells12081133","date_published":"2023-04-11T00:00:00Z","acknowledgement":"This research was funded by grants from the European Research Council (Consolidator grant #683154) and European Union’s Horizon 2020 research and innovation program (Marie Sklodowska-Curie Innovative Training Networks, grant #722053, EU-GliaPhD) to N.R., as well as from FP7-PEOPLE Marie Curie Intra-European Fellowship for career development (grant #622289) to G.C. We thank Elena Dossi, Grégory Ghézali, and Jérémie Teillon for support with setting up the MEA system for the two-photon microscope. We would also like to thank Tayfun Palaz for their technical assistance with the EM preparations.","oa":1,"publisher":"MDPI","quality_controlled":"1","date_updated":"2024-01-16T09:29:35Z","ddc":["570"],"department":[{"_id":"SiHi"}],"file_date_updated":"2024-01-16T09:26:52Z","_id":"14783","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","keyword":["General Medicine"],"status":"public","publication_status":"published","publication_identifier":{"issn":["2073-4409"]},"language":[{"iso":"eng"}],"file":[{"creator":"dernst","file_size":7931643,"date_updated":"2024-01-16T09:26:52Z","file_name":"2023_Cells_Cheung.pdf","date_created":"2024-01-16T09:26:52Z","relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"6798cd75d8857976fbc58a43fd173d68","file_id":"14808"}],"volume":12,"issue":"8","abstract":[{"lang":"eng","text":"Connexin 43, an astroglial gap junction protein, is enriched in perisynaptic astroglial processes and plays major roles in synaptic transmission. We have previously found that astroglial Cx43 controls synaptic glutamate levels and allows for activity-dependent glutamine release to sustain physiological synaptic transmissions and cognitiogns. However, whether Cx43 is important for the release of synaptic vesicles, which is a critical component of synaptic efficacy, remains unanswered. Here, using transgenic mice with a glial conditional knockout of Cx43 (Cx43−/−), we investigate whether and how astrocytes regulate the release of synaptic vesicles from hippocampal synapses. We report that CA1 pyramidal neurons and their synapses develop normally in the absence of astroglial Cx43. However, a significant impairment in synaptic vesicle distribution and release dynamics were observed. In particular, the FM1-43 assays performed using two-photon live imaging and combined with multi-electrode array stimulation in acute hippocampal slices, revealed a slower rate of synaptic vesicle release in Cx43−/− mice. Furthermore, paired-pulse recordings showed that synaptic vesicle release probability was also reduced and is dependent on glutamine supply via Cx43 hemichannel (HC). Taken together, we have uncovered a role for Cx43 in regulating presynaptic functions by controlling the rate and probability of synaptic vesicle release. Our findings further highlight the significance of astroglial Cx43 in synaptic transmission and efficacy."}],"oa_version":"Published Version","pmid":1,"intvolume":" 12","month":"04"},{"intvolume":" 15","month":"12","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Small cryptic plasmids have no clear effect on the host fitness and their functional repertoire remains obscure. The naturally competent cyanobacterium Synechocystis sp. PCC 6803 harbours several small cryptic plasmids; whether their evolution with this species is supported by horizontal transfer remains understudied. Here, we show that the small cryptic plasmid DNA is transferred in the population exclusively by natural transformation, where the transfer frequency of plasmid‐encoded genes is similar to that of chromosome‐encoded genes. Establishing a system to follow gene transfer, we compared the transfer frequency of genes encoded in cryptic plasmids pCA2.4 (2378 bp) and pCB2.4 (2345 bp) within and between populations of two Synechocystis sp. PCC 6803 labtypes (termed Kiel and Sevilla). Our results reveal that plasmid gene transfer frequency depends on the recipient labtype. Furthermore, gene transfer via whole plasmid uptake in the Sevilla labtype ranged among the lowest detected transfer rates in our experiments. Our study indicates that horizontal DNA transfer via natural transformation is frequent in the evolution of small cryptic plasmids that reside in naturally competent organisms. Furthermore, we suggest that the contribution of natural transformation to cryptic plasmid persistence in Synechocystis is limited.","lang":"eng"}],"issue":"6","volume":15,"language":[{"iso":"eng"}],"file":[{"checksum":"d09ebb68fee61f4e2e09ec286c9cf1d3","file_id":"14810","success":1,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","date_created":"2024-01-16T09:42:10Z","file_name":"2023_EnvirMicroBiolReports_Nies.pdf","date_updated":"2024-01-16T09:42:10Z","file_size":1518350,"creator":"dernst"}],"publication_status":"published","publication_identifier":{"eissn":["1758-2229"]},"keyword":["Agricultural and Biological Sciences (miscellaneous)","Ecology","Evolution","Behavior and Systematics"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","_id":"14785","department":[{"_id":"MaLo"}],"file_date_updated":"2024-01-16T09:42:10Z","ddc":["570"],"date_updated":"2024-01-16T09:46:12Z","oa":1,"quality_controlled":"1","publisher":"Wiley","acknowledgement":"We thank the lab of Francisco Javier Florencio Bel-lido, Sevilla, Spain for supplying theSynechocystislabtype Sevilla used in this work and the lab of MartinHagemann, Rostock, Germany for supplying the pIGAplasmidusedinthiswork.WethankNilsHülterforfruitful discussions. We thank Fenna Stücker forgraphical illustrations and Katrin Schumann, FennaStücker, and Lidusha Manivannan for technicalsupport.\r\nChilean National Agency for Research andDevelopment (ANID), Grant/Award Number:21191763; DeutscheForschungsgemeinschaft, Grant/AwardNumbers: 456882089, RTG2501; EuropeanResearch Council (ERC), Grant/AwardNumber: 101043835","date_created":"2024-01-10T10:41:07Z","date_published":"2023-12-01T00:00:00Z","doi":"10.1111/1758-2229.13203","page":"656-668","publication":"Environmental Microbiology Reports","day":"01","year":"2023","has_accepted_license":"1","isi":1,"title":"Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803","article_processing_charge":"Yes (in subscription journal)","external_id":{"pmid":["37794696"],"isi":["001080203100001"]},"author":[{"first_name":"Fabian","last_name":"Nies","full_name":"Nies, Fabian"},{"last_name":"Wein","full_name":"Wein, Tanita","first_name":"Tanita"},{"full_name":"Hanke, Dustin M.","last_name":"Hanke","first_name":"Dustin M."},{"last_name":"Springstein","full_name":"Springstein, Benjamin L","orcid":"0000-0002-3461-5391","id":"b4eb62ef-ac72-11ed-9503-ed3b4d66c083","first_name":"Benjamin L"},{"first_name":"Jaime","full_name":"Alcorta, Jaime","last_name":"Alcorta"},{"full_name":"Taubenheim, Claudia","last_name":"Taubenheim","first_name":"Claudia"},{"last_name":"Dagan","full_name":"Dagan, Tal","first_name":"Tal"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"apa":"Nies, F., Wein, T., Hanke, D. M., Springstein, B. L., Alcorta, J., Taubenheim, C., & Dagan, T. (2023). Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. Wiley. https://doi.org/10.1111/1758-2229.13203","ama":"Nies F, Wein T, Hanke DM, et al. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 2023;15(6):656-668. doi:10.1111/1758-2229.13203","short":"F. Nies, T. Wein, D.M. Hanke, B.L. Springstein, J. Alcorta, C. Taubenheim, T. Dagan, Environmental Microbiology Reports 15 (2023) 656–668.","ieee":"F. Nies et al., “Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803,” Environmental Microbiology Reports, vol. 15, no. 6. Wiley, pp. 656–668, 2023.","mla":"Nies, Fabian, et al. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental Microbiology Reports, vol. 15, no. 6, Wiley, 2023, pp. 656–68, doi:10.1111/1758-2229.13203.","ista":"Nies F, Wein T, Hanke DM, Springstein BL, Alcorta J, Taubenheim C, Dagan T. 2023. Role of natural transformation in the evolution of small cryptic plasmids in Synechocystis sp. PCC 6803. Environmental Microbiology Reports. 15(6), 656–668.","chicago":"Nies, Fabian, Tanita Wein, Dustin M. Hanke, Benjamin L Springstein, Jaime Alcorta, Claudia Taubenheim, and Tal Dagan. “Role of Natural Transformation in the Evolution of Small Cryptic Plasmids in Synechocystis Sp. PCC 6803.” Environmental Microbiology Reports. Wiley, 2023. https://doi.org/10.1111/1758-2229.13203."}},{"volume":163,"ec_funded":1,"file":[{"file_size":1870349,"date_updated":"2024-01-16T08:47:31Z","creator":"dernst","file_name":"2023_StochasticProcAppl_Ding.pdf","date_created":"2024-01-16T08:47:31Z","content_type":"application/pdf","relation":"main_file","access_level":"open_access","success":1,"checksum":"46a708b0cd5569a73d0f3d6c3e0a44dc","file_id":"14806"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0304-4149"],"eissn":["1879-209X"]},"publication_status":"published","month":"09","intvolume":" 163","oa_version":"Published Version","abstract":[{"lang":"eng","text":"In this paper, we study the eigenvalues and eigenvectors of the spiked invariant multiplicative models when the randomness is from Haar matrices. We establish the limits of the outlier eigenvalues λˆi and the generalized components (⟨v,uˆi⟩ for any deterministic vector v) of the outlier eigenvectors uˆi with optimal convergence rates. Moreover, we prove that the non-outlier eigenvalues stick with those of the unspiked matrices and the non-outlier eigenvectors are delocalized. The results also hold near the so-called BBP transition and for degenerate spikes. On one hand, our results can be regarded as a refinement of the counterparts of [12] under additional regularity conditions. On the other hand, they can be viewed as an analog of [34] by replacing the random matrix with i.i.d. entries with Haar random matrix."}],"file_date_updated":"2024-01-16T08:47:31Z","department":[{"_id":"LaEr"}],"ddc":["510"],"date_updated":"2024-01-16T08:49:51Z","status":"public","keyword":["Applied Mathematics","Modeling and Simulation","Statistics and Probability"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"_id":"14780","doi":"10.1016/j.spa.2023.05.009","date_published":"2023-09-01T00:00:00Z","date_created":"2024-01-10T09:29:25Z","page":"25-60","day":"01","publication":"Stochastic Processes and their Applications","has_accepted_license":"1","isi":1,"year":"2023","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"The authors would like to thank the editor, the associated editor and two anonymous referees for their many critical suggestions which have significantly improved the paper. The authors are also grateful to Zhigang Bao and Ji Oon Lee for many helpful discussions. The first author also wants to thank Hari Bercovici for many useful comments. The first author is partially supported by National Science Foundation DMS-2113489 and the second author is supported by ERC Advanced Grant “RMTBeyond” No. 101020331.","title":"Spiked multiplicative random matrices and principal components","author":[{"full_name":"Ding, Xiucai","last_name":"Ding","first_name":"Xiucai"},{"full_name":"Ji, Hong Chang","last_name":"Ji","first_name":"Hong Chang","id":"dd216c0a-c1f9-11eb-beaf-e9ea9d2de76d"}],"article_processing_charge":"Yes (in subscription journal)","external_id":{"arxiv":["2302.13502"],"isi":["001113615900001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"X. Ding, H.C. Ji, Stochastic Processes and Their Applications 163 (2023) 25–60.","ieee":"X. Ding and H. C. Ji, “Spiked multiplicative random matrices and principal components,” Stochastic Processes and their Applications, vol. 163. Elsevier, pp. 25–60, 2023.","apa":"Ding, X., & Ji, H. C. (2023). Spiked multiplicative random matrices and principal components. Stochastic Processes and Their Applications. Elsevier. https://doi.org/10.1016/j.spa.2023.05.009","ama":"Ding X, Ji HC. Spiked multiplicative random matrices and principal components. Stochastic Processes and their Applications. 2023;163:25-60. doi:10.1016/j.spa.2023.05.009","mla":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” Stochastic Processes and Their Applications, vol. 163, Elsevier, 2023, pp. 25–60, doi:10.1016/j.spa.2023.05.009.","ista":"Ding X, Ji HC. 2023. Spiked multiplicative random matrices and principal components. Stochastic Processes and their Applications. 163, 25–60.","chicago":"Ding, Xiucai, and Hong Chang Ji. “Spiked Multiplicative Random Matrices and Principal Components.” Stochastic Processes and Their Applications. Elsevier, 2023. https://doi.org/10.1016/j.spa.2023.05.009."},"project":[{"grant_number":"101020331","name":"Random matrices beyond Wigner-Dyson-Mehta","call_identifier":"H2020","_id":"62796744-2b32-11ec-9570-940b20777f1d"}]},{"intvolume":" 50","month":"06","oa_version":"Published Version","abstract":[{"lang":"eng","text":"The presence of a developed boundary layer decouples a glacier's response from ambient conditions, suggesting that sensitivity to climate change is increased by glacier retreat. To test this hypothesis, we explore six years of distributed meteorological data on a small Swiss glacier in the period 2001–2022. Large glacier fragmentation has occurred since 2001 (−35% area change up to 2022) coinciding with notable frontal retreat, an observed switch from down‐glacier katabatic to up‐glacier valley winds and an increased sensitivity (ratio) of on‐glacier to off‐glacier temperature. As the glacier ceases to develop density‐driven katabatic winds, sensible heat fluxes on the glacier are increasingly determined by the conditions occurring outside the boundary layer of the glacier, sealing the glacier's demise as the climate continues to warm and experience an increased frequency of extreme summers."}],"issue":"11","volume":50,"language":[{"iso":"eng"}],"file":[{"file_name":"2023_GeophysicalResearchLetter_Shaw.pdf","date_created":"2024-01-16T08:35:02Z","creator":"dernst","file_size":2529327,"date_updated":"2024-01-16T08:35:02Z","success":1,"file_id":"14805","checksum":"391a3005c95340a0ae129ce4fbdf2bae","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"publication_status":"published","publication_identifier":{"eissn":["1944-8007"],"issn":["0094-8276"]},"keyword":["General Earth and Planetary Sciences","Geophysics"],"status":"public","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"article_type":"original","type":"journal_article","_id":"14779","department":[{"_id":"FrPe"}],"file_date_updated":"2024-01-16T08:35:02Z","ddc":["550"],"date_updated":"2024-01-16T08:42:36Z","oa":1,"quality_controlled":"1","publisher":"American Geophysical Union","acknowledgement":"This work was funded by the EU Horizon 2020 Marie Skłodowska-Curie Actions Grant 101026058. The authors acknowl-edge the dedicated collection of field data by many parties since 2001, including those acknowledged for the cited works on Arolla Glacier. The authors would like to thank Fabienne Meier, Alice Zaugg, Raphael Willi, Maria Grundmann, and Marta Corrà for assistance in the field for the summers of 2021 and 2022. Off-glacier data provided by Grand Dixence SA (Arolla) and MeteoSwiss are kindly acknowledged. Simone Fatichi is thanked for the provision and support in the use of the Tethys-Chloris model. We thank Editor Mathieu Morlighem and two anonymous reviewers whose comments have helped to improve the quality of the manuscript.","date_created":"2024-01-10T09:28:34Z","date_published":"2023-06-16T00:00:00Z","doi":"10.1029/2023gl103043","publication":"Geophysical Research Letters","day":"16","year":"2023","isi":1,"has_accepted_license":"1","article_number":"e2023GL103043","title":"The decaying near‐surface boundary layer of a retreating alpine glacier","article_processing_charge":"No","external_id":{"isi":["000999436400001"]},"author":[{"full_name":"Shaw, Thomas E.","last_name":"Shaw","first_name":"Thomas E."},{"first_name":"Pascal","full_name":"Buri, Pascal","last_name":"Buri"},{"last_name":"McCarthy","full_name":"McCarthy, Michael","first_name":"Michael"},{"first_name":"Evan S.","last_name":"Miles","full_name":"Miles, Evan S."},{"last_name":"Ayala","full_name":"Ayala, Álvaro","first_name":"Álvaro"},{"id":"b28f055a-81ea-11ed-b70c-a9fe7f7b0e70","first_name":"Francesca","last_name":"Pellicciotti","full_name":"Pellicciotti, Francesca","orcid":"0000-0002-5554-8087"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ama":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. 2023;50(11). doi:10.1029/2023gl103043","apa":"Shaw, T. E., Buri, P., McCarthy, M., Miles, E. S., Ayala, Á., & Pellicciotti, F. (2023). The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. American Geophysical Union. https://doi.org/10.1029/2023gl103043","short":"T.E. Shaw, P. Buri, M. McCarthy, E.S. Miles, Á. Ayala, F. Pellicciotti, Geophysical Research Letters 50 (2023).","ieee":"T. E. Shaw, P. Buri, M. McCarthy, E. S. Miles, Á. Ayala, and F. Pellicciotti, “The decaying near‐surface boundary layer of a retreating alpine glacier,” Geophysical Research Letters, vol. 50, no. 11. American Geophysical Union, 2023.","mla":"Shaw, Thomas E., et al. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” Geophysical Research Letters, vol. 50, no. 11, e2023GL103043, American Geophysical Union, 2023, doi:10.1029/2023gl103043.","ista":"Shaw TE, Buri P, McCarthy M, Miles ES, Ayala Á, Pellicciotti F. 2023. The decaying near‐surface boundary layer of a retreating alpine glacier. Geophysical Research Letters. 50(11), e2023GL103043.","chicago":"Shaw, Thomas E., Pascal Buri, Michael McCarthy, Evan S. Miles, Álvaro Ayala, and Francesca Pellicciotti. “The Decaying Near‐surface Boundary Layer of a Retreating Alpine Glacier.” Geophysical Research Letters. American Geophysical Union, 2023. https://doi.org/10.1029/2023gl103043."}},{"department":[{"_id":"Bio"}],"date_updated":"2024-01-16T08:56:36Z","type":"journal_article","article_type":"original","status":"public","keyword":["Developmental Biology","Cell Biology","General Biochemistry","Genetics and Molecular Biology","Molecular Biology"],"_id":"14781","issue":"17","volume":58,"publication_identifier":{"issn":["1534-5807"]},"publication_status":"published","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://www.biorxiv.org/content/10.1101/2023.07.09.548244","open_access":"1"}],"month":"09","intvolume":" 58","abstract":[{"lang":"eng","text":"Germ granules, condensates of phase-separated RNA and protein, are organelles that are essential for germline development in different organisms. The patterning of the granules and their relevance for germ cell fate are not fully understood. Combining three-dimensional in vivo structural and functional analyses, we study the dynamic spatial organization of molecules within zebrafish germ granules. We find that the localization of RNA molecules to the periphery of the granules, where ribosomes are localized, depends on translational activity at this location. In addition, we find that the vertebrate-specific Dead end (Dnd1) protein is essential for nanos3 RNA localization at the condensates’ periphery. Accordingly, in the absence of Dnd1, or when translation is inhibited, nanos3 RNA translocates into the granule interior, away from the ribosomes, a process that is correlated with the loss of germ cell fate. These findings highlight the relevance of sub-granule compartmentalization for post-transcriptional control and its importance for preserving germ cell totipotency."}],"pmid":1,"oa_version":"Preprint","author":[{"first_name":"Kim Joana","full_name":"Westerich, Kim Joana","last_name":"Westerich"},{"first_name":"Katsiaryna","full_name":"Tarbashevich, Katsiaryna","last_name":"Tarbashevich"},{"full_name":"Schick, Jan","last_name":"Schick","first_name":"Jan"},{"first_name":"Antra","last_name":"Gupta","full_name":"Gupta, Antra"},{"first_name":"Mingzhao","last_name":"Zhu","full_name":"Zhu, Mingzhao"},{"last_name":"Hull","full_name":"Hull, Kenneth","first_name":"Kenneth"},{"last_name":"Romo","full_name":"Romo, Daniel","first_name":"Daniel"},{"last_name":"Zeuschner","full_name":"Zeuschner, Dagmar","first_name":"Dagmar"},{"id":"3384113A-F248-11E8-B48F-1D18A9856A87","first_name":"Mohammad","last_name":"Goudarzi","full_name":"Goudarzi, Mohammad"},{"last_name":"Gross-Thebing","full_name":"Gross-Thebing, Theresa","first_name":"Theresa"},{"last_name":"Raz","full_name":"Raz, Erez","first_name":"Erez"}],"article_processing_charge":"No","external_id":{"pmid":["37463577"]},"title":"Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1","citation":{"mla":"Westerich, Kim Joana, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental Cell, vol. 58, no. 17, Elsevier, 2023, p. 1578–1592.e5, doi:10.1016/j.devcel.2023.06.009.","apa":"Westerich, K. J., Tarbashevich, K., Schick, J., Gupta, A., Zhu, M., Hull, K., … Raz, E. (2023). Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. Elsevier. https://doi.org/10.1016/j.devcel.2023.06.009","ama":"Westerich KJ, Tarbashevich K, Schick J, et al. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 2023;58(17):1578-1592.e5. doi:10.1016/j.devcel.2023.06.009","short":"K.J. Westerich, K. Tarbashevich, J. Schick, A. Gupta, M. Zhu, K. Hull, D. Romo, D. Zeuschner, M. Goudarzi, T. Gross-Thebing, E. Raz, Developmental Cell 58 (2023) 1578–1592.e5.","ieee":"K. J. Westerich et al., “Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1,” Developmental Cell, vol. 58, no. 17. Elsevier, p. 1578–1592.e5, 2023.","chicago":"Westerich, Kim Joana, Katsiaryna Tarbashevich, Jan Schick, Antra Gupta, Mingzhao Zhu, Kenneth Hull, Daniel Romo, et al. “Spatial Organization and Function of RNA Molecules within Phase-Separated Condensates in Zebrafish Are Controlled by Dnd1.” Developmental Cell. Elsevier, 2023. https://doi.org/10.1016/j.devcel.2023.06.009.","ista":"Westerich KJ, Tarbashevich K, Schick J, Gupta A, Zhu M, Hull K, Romo D, Zeuschner D, Goudarzi M, Gross-Thebing T, Raz E. 2023. Spatial organization and function of RNA molecules within phase-separated condensates in zebrafish are controlled by Dnd1. Developmental Cell. 58(17), 1578–1592.e5."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"1578-1592.e5","date_published":"2023-09-11T00:00:00Z","doi":"10.1016/j.devcel.2023.06.009","date_created":"2024-01-10T09:41:21Z","year":"2023","day":"11","publication":"Developmental Cell","quality_controlled":"1","publisher":"Elsevier","oa":1,"acknowledgement":"We thank Celeste Brennecka for editing and Michal Reichman-Fried for critical comments on the manuscript. We thank Ursula Jordan, Esther Messerschmidt, and Ines Sandbote for technical assistance. This work was supported by funding from the University of Münster (K.J.W., K.T., E.R., A.G., T.G.-T., J.S., and M.G.), the Max Planck Institute for Molecular Biomedicine (D.Z.), the German Research Foundation grant CRU 326 (P2) RA863/12-2 (E.R.), Baylor University (K.H. and D.R.), and the National Institutes of Health grant R35 GM 134910 (D.R.). We thank the referees for insightful comments that helped improve the manuscript."},{"project":[{"_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818"},{"call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","grant_number":"665385"}],"author":[{"last_name":"Zikelic","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"}],"article_processing_charge":"No","title":"Automated verification and control of infinite state stochastic systems","citation":{"ista":"Zikelic D. 2023. Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria.","chicago":"Zikelic, Dorde. “Automated Verification and Control of Infinite State Stochastic Systems.” Institute of Science and Technology Austria, 2023. https://doi.org/10.15479/14539.","ama":"Zikelic D. Automated verification and control of infinite state stochastic systems. 2023. doi:10.15479/14539","apa":"Zikelic, D. (2023). Automated verification and control of infinite state stochastic systems. Institute of Science and Technology Austria. https://doi.org/10.15479/14539","ieee":"D. Zikelic, “Automated verification and control of infinite state stochastic systems,” Institute of Science and Technology Austria, 2023.","short":"D. Zikelic, Automated Verification and Control of Infinite State Stochastic Systems, Institute of Science and Technology Austria, 2023.","mla":"Zikelic, Dorde. Automated Verification and Control of Infinite State Stochastic Systems. Institute of Science and Technology Austria, 2023, doi:10.15479/14539."},"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","publisher":"Institute of Science and Technology Austria","oa":1,"page":"256","doi":"10.15479/14539","date_published":"2023-11-15T00:00:00Z","date_created":"2023-11-15T13:39:10Z","year":"2023","day":"15","type":"dissertation","tmp":{"name":"Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International (CC BY-NC-SA 4.0)","image":"/images/cc_by_nc_sa.png","legal_code_url":"https://creativecommons.org/licenses/by-nc-sa/4.0/legalcode","short":"CC BY-NC-SA (4.0)"},"status":"public","_id":"14539","file_date_updated":"2023-11-15T13:44:24Z","department":[{"_id":"KrCh"},{"_id":"GradSch"}],"supervisor":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"}],"date_updated":"2024-01-16T11:58:15Z","ddc":["000"],"alternative_title":["ISTA Thesis"],"month":"11","abstract":[{"text":"Stochastic systems provide a formal framework for modelling and quantifying uncertainty in systems and have been widely adopted in many application domains. Formal\r\nverification and control of finite state stochastic systems, a subfield of formal methods\r\nalso known as probabilistic model checking, is well studied. In contrast, formal verification and control of infinite state stochastic systems have received comparatively\r\nless attention. However, infinite state stochastic systems commonly arise in practice.\r\nFor instance, probabilistic models that contain continuous probability distributions such\r\nas normal or uniform, or stochastic dynamical systems which are a classical model for\r\ncontrol under uncertainty, both give rise to infinite state systems.\r\nThe goal of this thesis is to contribute to laying theoretical and algorithmic foundations\r\nof fully automated formal verification and control of infinite state stochastic systems,\r\nwith a particular focus on systems that may be executed over a long or infinite time.\r\nWe consider formal verification of infinite state stochastic systems in the setting of\r\nstatic analysis of probabilistic programs and formal control in the setting of controller\r\nsynthesis in stochastic dynamical systems. For both problems, we present some of the\r\nfirst fully automated methods for probabilistic (a.k.a. quantitative) reachability and\r\nsafety analysis applicable to infinite time horizon systems. We also advance the state\r\nof the art of probability 1 (a.k.a. qualitative) reachability analysis for both problems.\r\nFinally, for formal controller synthesis in stochastic dynamical systems, we present a\r\nnovel framework for learning neural network control policies in stochastic dynamical\r\nsystems with formal guarantees on correctness with respect to quantitative reachability,\r\nsafety or reach-avoid specifications.\r\n","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"1194","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"12000"},{"status":"public","id":"9644","relation":"part_of_dissertation"},{"status":"public","id":"12511","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","status":"public","id":"14600"},{"status":"public","id":"14601","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"10414","status":"public"}]},"license":"https://creativecommons.org/licenses/by-nc-sa/4.0/","ec_funded":1,"publication_identifier":{"isbn":["978-3-99078-036-7"],"issn":["2663 - 337X"]},"publication_status":"published","degree_awarded":"PhD","file":[{"creator":"cchlebak","date_updated":"2023-11-15T13:43:28Z","file_size":2116426,"date_created":"2023-11-15T13:43:28Z","file_name":"main.pdf","access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"f23e002b0059ca78e1fbb864da52dd7e","file_id":"14540","success":1},{"date_updated":"2023-11-15T13:44:24Z","file_size":35884057,"creator":"cchlebak","date_created":"2023-11-15T13:44:24Z","file_name":"thesis_source.zip","content_type":"application/x-zip-compressed","access_level":"closed","relation":"source_file","checksum":"80ca37618a3c7b59866875f8be9b15ed","file_id":"14541"}],"language":[{"iso":"eng"}]},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Mund, Markus, et al. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” Journal of Cell Biology, vol. 222, no. 3, e202206038, Rockefeller University Press, 2023, doi:10.1083/jcb.202206038.","ieee":"M. Mund et al., “Clathrin coats partially preassemble and subsequently bend during endocytosis,” Journal of Cell Biology, vol. 222, no. 3. Rockefeller University Press, 2023.","short":"M. Mund, A. Tschanz, Y.-L. Wu, F.F. Frey, J.L. Mehl, M. Kaksonen, O. Avinoam, U.S. Schwarz, J. Ries, Journal of Cell Biology 222 (2023).","ama":"Mund M, Tschanz A, Wu Y-L, et al. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 2023;222(3). doi:10.1083/jcb.202206038","apa":"Mund, M., Tschanz, A., Wu, Y.-L., Frey, F. F., Mehl, J. L., Kaksonen, M., … Ries, J. (2023). Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. Rockefeller University Press. https://doi.org/10.1083/jcb.202206038","chicago":"Mund, Markus, Aline Tschanz, Yu-Le Wu, Felix F Frey, Johanna L. Mehl, Marko Kaksonen, Ori Avinoam, Ulrich S. Schwarz, and Jonas Ries. “Clathrin Coats Partially Preassemble and Subsequently Bend during Endocytosis.” Journal of Cell Biology. Rockefeller University Press, 2023. https://doi.org/10.1083/jcb.202206038.","ista":"Mund M, Tschanz A, Wu Y-L, Frey FF, Mehl JL, Kaksonen M, Avinoam O, Schwarz US, Ries J. 2023. Clathrin coats partially preassemble and subsequently bend during endocytosis. Journal of Cell Biology. 222(3), e202206038."},"title":"Clathrin coats partially preassemble and subsequently bend during endocytosis","author":[{"first_name":"Markus","last_name":"Mund","full_name":"Mund, Markus"},{"full_name":"Tschanz, Aline","last_name":"Tschanz","first_name":"Aline"},{"first_name":"Yu-Le","full_name":"Wu, Yu-Le","last_name":"Wu"},{"first_name":"Felix F","id":"a0270b37-8f1a-11ec-95c7-8e710c59a4f3","last_name":"Frey","orcid":"0000-0001-8501-6017","full_name":"Frey, Felix F"},{"first_name":"Johanna L.","last_name":"Mehl","full_name":"Mehl, Johanna L."},{"full_name":"Kaksonen, Marko","last_name":"Kaksonen","first_name":"Marko"},{"full_name":"Avinoam, Ori","last_name":"Avinoam","first_name":"Ori"},{"first_name":"Ulrich S.","full_name":"Schwarz, Ulrich S.","last_name":"Schwarz"},{"full_name":"Ries, Jonas","last_name":"Ries","first_name":"Jonas"}],"article_processing_charge":"No","external_id":{"pmid":["36734980"],"isi":["000978065000001"]},"article_number":"e202206038","day":"03","publication":"Journal of Cell Biology","isi":1,"has_accepted_license":"1","year":"2023","doi":"10.1083/jcb.202206038","date_published":"2023-02-03T00:00:00Z","date_created":"2024-01-10T10:45:55Z","acknowledgement":"We thank the entire Ries and Kaksonen labs for fruitful discussions and support. This work was supported by the European Research Council (ERC CoG-724489 to J. Ries), the National Institutes of Health Common Fund 4D Nucleome Program (Grant U01 to J. Ries), the Human Frontier Science Program (RGY0065/2017 to J. Ries), the EMBL Interdisciplinary Postdoc Programme (EIPOD) under Marie Curie Actions COFUND (Grant 229597 to O. Avinoam), the European Molecular Biology Laboratory (M. Mund, A. Tschanz, Y.-L. Wu and J. Ries), and the Swiss National Science Foundation (grant 310030B_182825 and NCCR Chemical Biology to M. Kaksonen). O. Avinoam is an incumbent of the Miriam Berman Presidential Development Chair.","publisher":"Rockefeller University Press","quality_controlled":"1","oa":1,"ddc":["570"],"date_updated":"2024-01-16T10:17:05Z","file_date_updated":"2024-01-16T10:15:09Z","department":[{"_id":"AnSa"}],"_id":"14788","status":"public","keyword":["Cell Biology"],"type":"journal_article","article_type":"original","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"file":[{"success":1,"checksum":"505d5cac36c14b073b68c7fed1a92bd3","file_id":"14811","content_type":"application/pdf","relation":"main_file","access_level":"open_access","file_name":"2023_JCB_Mund.pdf","date_created":"2024-01-16T10:15:09Z","file_size":5678069,"date_updated":"2024-01-16T10:15:09Z","creator":"dernst"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-9525"],"eissn":["1540-8140"]},"publication_status":"published","volume":222,"issue":"3","pmid":1,"oa_version":"Published Version","abstract":[{"text":"Eukaryotic cells use clathrin-mediated endocytosis to take up a large range of extracellular cargo. During endocytosis, a clathrin coat forms on the plasma membrane, but it remains controversial when and how it is remodeled into a spherical vesicle.\r\nHere, we use 3D superresolution microscopy to determine the precise geometry of the clathrin coat at large numbers of endocytic sites. Through pseudo-temporal sorting, we determine the average trajectory of clathrin remodeling during endocytosis. We find that clathrin coats assemble first on flat membranes to 50% of the coat area before they become rapidly and continuously bent, and this mechanism is confirmed in three cell lines. We introduce the cooperative curvature model, which is based on positive feedback for curvature generation. It accurately describes the measured shapes and dynamics of the clathrin coat and could represent a general mechanism for clathrin coat remodeling on the plasma membrane.","lang":"eng"}],"month":"02","intvolume":" 222"},{"publisher":"Elsevier","quality_controlled":"1","acknowledgement":"The authors thank the Czech Science Foundation (project No. 19-28399X) and the Czech Academy of Sciences (RVO: 60077344) and are sincerely grateful to the Bordeaux Imaging Centre (member of the France BioImaging national infrastructure, ANR-10-INBS-04) for help with TEM and to members of the Laboratory of Biological Effects of Metals and Laboratory of Aquaculture and Pathology of Aquatic Organisms (Ruđer Bošković Institute, Croatia) for the assistance with fieldwork.","date_created":"2024-01-10T10:43:08Z","doi":"10.1016/j.scitotenv.2023.164010","date_published":"2023-08-20T00:00:00Z","year":"2023","isi":1,"publication":"Science of The Total Environment","day":"20","article_number":"164010","article_processing_charge":"No","external_id":{"pmid":["37169189"],"isi":["001002645100001"]},"author":[{"first_name":"Vlatka","last_name":"Filipović Marijić","full_name":"Filipović Marijić, Vlatka"},{"full_name":"Subirana, Maria Angels","last_name":"Subirana","first_name":"Maria Angels"},{"first_name":"Dirk","last_name":"Schaumlöffel","full_name":"Schaumlöffel, Dirk"},{"first_name":"Josip","last_name":"Barišić","full_name":"Barišić, Josip"},{"first_name":"Etienne","last_name":"Gontier","full_name":"Gontier, Etienne"},{"last_name":"Krasnici","full_name":"Krasnici, Nesrete","first_name":"Nesrete","id":"cb5852d4-287f-11ed-baf0-bc1dd2d5c745"},{"full_name":"Mijošek, Tatjana","last_name":"Mijošek","first_name":"Tatjana"},{"last_name":"Hernández-Orts","full_name":"Hernández-Orts, Jesús S.","first_name":"Jesús S."},{"full_name":"Scholz, Tomáš","last_name":"Scholz","first_name":"Tomáš"},{"first_name":"Marijana","last_name":"Erk","full_name":"Erk, Marijana"}],"title":"First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS","citation":{"ieee":"V. Filipović Marijić et al., “First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS,” Science of The Total Environment, vol. 887. Elsevier, 2023.","short":"V. Filipović Marijić, M.A. Subirana, D. Schaumlöffel, J. Barišić, E. Gontier, N. Krasnici, T. Mijošek, J.S. Hernández-Orts, T. Scholz, M. Erk, Science of The Total Environment 887 (2023).","apa":"Filipović Marijić, V., Subirana, M. A., Schaumlöffel, D., Barišić, J., Gontier, E., Krasnici, N., … Erk, M. (2023). First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. Elsevier. https://doi.org/10.1016/j.scitotenv.2023.164010","ama":"Filipović Marijić V, Subirana MA, Schaumlöffel D, et al. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. 2023;887. doi:10.1016/j.scitotenv.2023.164010","mla":"Filipović Marijić, Vlatka, et al. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” Science of The Total Environment, vol. 887, 164010, Elsevier, 2023, doi:10.1016/j.scitotenv.2023.164010.","ista":"Filipović Marijić V, Subirana MA, Schaumlöffel D, Barišić J, Gontier E, Krasnici N, Mijošek T, Hernández-Orts JS, Scholz T, Erk M. 2023. First insight in element localisation in different body parts of the acanthocephalan Dentitruncus truttae using TEM and NanoSIMS. Science of The Total Environment. 887, 164010.","chicago":"Filipović Marijić, Vlatka, Maria Angels Subirana, Dirk Schaumlöffel, Josip Barišić, Etienne Gontier, Nesrete Krasnici, Tatjana Mijošek, Jesús S. Hernández-Orts, Tomáš Scholz, and Marijana Erk. “First Insight in Element Localisation in Different Body Parts of the Acanthocephalan Dentitruncus Truttae Using TEM and NanoSIMS.” Science of The Total Environment. Elsevier, 2023. https://doi.org/10.1016/j.scitotenv.2023.164010."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":" 887","month":"08","abstract":[{"lang":"eng","text":"Acanthocephalans, intestinal parasites of vertebrates, are characterised by orders of magnitude higher metal accumulation than free-living organisms, but the mechanism of such effective metal accumulation is still unknown. The aim of our study was to gain new insights into the high-resolution localization of elements in the bodies of acanthocephalans, thus taking an initial step towards elucidating metal uptake and accumulation in organisms under real environmental conditions. For the first time, nanoscale secondary ion mass spectrometry (NanoSIMS) was used for high-resolution mapping of 12 elements (C, Ca, Cu, Fe, N, Na, O, P, Pb, S, Se, and Tl) in three selected body parts (trunk spines, inner part of the proboscis receptacle and inner surface of the tegument) of Dentitruncus truttae, a parasite of brown trout (Salmo trutta) from the Krka River in Croatia. In addition, the same body parts were examined using transmission electron microscopy (TEM) and correlated with NanoSIMS images. Metal concentrations determined using HR ICP-MS confirmed higher accumulation in D. truttae than in the fish intestine. The chemical composition of the acanthocephalan body showed the highest density of C, Ca, N, Na, O, S, as important and constitutive elements in living cells in all studied structures, while Fe was predominant among trace elements. In general, higher element density was found in trunk spines and tegument, as body structures responsible for substance absorption in parasites. The results obtained with NanoSIMS and TEM-NanoSIMS correlative imaging represent pilot data for mapping of elements at nanoscale resolution in the ultrastructure of various body parts of acanthocephalans and generally provide a contribution for further application of this technique in all parasite species."}],"oa_version":"None","pmid":1,"volume":887,"publication_status":"published","publication_identifier":{"issn":["0048-9697"]},"language":[{"iso":"eng"}],"article_type":"original","type":"journal_article","keyword":["Pollution","Waste Management and Disposal","Environmental Chemistry","Environmental Engineering"],"status":"public","_id":"14786","department":[{"_id":"LifeSc"}],"date_updated":"2024-01-16T10:04:57Z"},{"_id":"14787","status":"public","keyword":["Genetics","Ecology","Evolution","Behavior and Systematics"],"type":"journal_article","article_type":"original","date_updated":"2024-01-16T10:10:00Z","department":[{"_id":"NiBa"}],"pmid":1,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"Understanding the phenotypic and genetic architecture of reproductive isolation is a long‐standing goal of speciation research. In several systems, large‐effect loci contributing to barrier phenotypes have been characterized, but such causal connections are rarely known for more complex genetic architectures. In this study, we combine “top‐down” and “bottom‐up” approaches with demographic modelling toward an integrated understanding of speciation across a monkeyflower hybrid zone. Previous work suggests that pollinator visitation acts as a primary barrier to gene flow between two divergent red‐ and yellow‐flowered ecotypes ofMimulus aurantiacus. Several candidate isolating traits and anonymous single nucleotide polymorphism loci under divergent selection have been identified, but their genomic positions remain unknown. Here, we report findings from demographic analyses that indicate this hybrid zone formed by secondary contact, but that subsequent gene flow was restricted by widespread barrier loci across the genome. Using a novel, geographic cline‐based genome scan, we demonstrate that candidate barrier loci are broadly distributed across the genome, rather than mapping to one or a few “islands of speciation.” Quantitative trait locus (QTL) mapping reveals that most floral traits are highly polygenic, with little evidence that QTL colocalize, indicating that most traits are genetically independent. Finally, we find little evidence that QTL and candidate barrier loci overlap, suggesting that some loci contribute to other forms of reproductive isolation. Our findings highlight the challenges of understanding the genetic architecture of reproductive isolation and reveal that barriers to gene flow other than pollinator isolation may play an important role in this system."}],"month":"04","intvolume":" 32","main_file_link":[{"url":"https://doi.org/10.1101/2022.01.28.478139","open_access":"1"}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0962-1083"],"eissn":["1365-294X"]},"publication_status":"published","issue":"8","volume":32,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"mla":"Stankowski, Sean, et al. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology, vol. 32, no. 8, Wiley, 2023, pp. 2041–54, doi:10.1111/mec.16849.","apa":"Stankowski, S., Chase, M. A., McIntosh, H., & Streisfeld, M. A. (2023). Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. Wiley. https://doi.org/10.1111/mec.16849","ama":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 2023;32(8):2041-2054. doi:10.1111/mec.16849","short":"S. Stankowski, M.A. Chase, H. McIntosh, M.A. Streisfeld, Molecular Ecology 32 (2023) 2041–2054.","ieee":"S. Stankowski, M. A. Chase, H. McIntosh, and M. A. Streisfeld, “Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone,” Molecular Ecology, vol. 32, no. 8. Wiley, pp. 2041–2054, 2023.","chicago":"Stankowski, Sean, Madeline A. Chase, Hanna McIntosh, and Matthew A. Streisfeld. “Integrating Top‐down and Bottom‐up Approaches to Understand the Genetic Architecture of Speciation across a Monkeyflower Hybrid Zone.” Molecular Ecology. Wiley, 2023. https://doi.org/10.1111/mec.16849.","ista":"Stankowski S, Chase MA, McIntosh H, Streisfeld MA. 2023. Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone. Molecular Ecology. 32(8), 2041–2054."},"title":"Integrating top‐down and bottom‐up approaches to understand the genetic architecture of speciation across a monkeyflower hybrid zone","author":[{"first_name":"Sean","id":"43161670-5719-11EA-8025-FABC3DDC885E","full_name":"Stankowski, Sean","last_name":"Stankowski"},{"full_name":"Chase, Madeline A.","last_name":"Chase","first_name":"Madeline A."},{"first_name":"Hanna","last_name":"McIntosh","full_name":"McIntosh, Hanna"},{"first_name":"Matthew A.","full_name":"Streisfeld, Matthew A.","last_name":"Streisfeld"}],"article_processing_charge":"No","external_id":{"isi":["000919244600001"],"pmid":["36651268"]},"acknowledgement":"We thank Julian Catchen for making modifications to Stacks to aid this project. Peter L. Ralph, Thomas Nelson, Roger K. Butlin, Anja M. Westram and Nicholas H. Barton provided advice, stimulating discussion and critical feedback. The project was supported by National Science Foundation grant DEB-1258199.","quality_controlled":"1","publisher":"Wiley","oa":1,"day":"01","publication":"Molecular Ecology","isi":1,"year":"2023","doi":"10.1111/mec.16849","date_published":"2023-04-01T00:00:00Z","date_created":"2024-01-10T10:44:45Z","page":"2041-2054"},{"project":[{"_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020","name":"Design Principles of Branching Morphogenesis","grant_number":"851288"}],"author":[{"first_name":"Bernat","id":"43BE2298-F248-11E8-B48F-1D18A9856A87","last_name":"Corominas-Murtra","orcid":"0000-0001-9806-5643","full_name":"Corominas-Murtra, Bernat"},{"orcid":"0000-0001-6005-1561","full_name":"Hannezo, Edouard B","last_name":"Hannezo","id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","first_name":"Edouard B"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"isi":["001053522200001"],"pmid":["36470715"]},"title":"Modelling the dynamics of mammalian gut homeostasis","citation":{"mla":"Corominas-Murtra, Bernat, and Edouard B. Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology, vol. 150–151, Elsevier, 2023, pp. 58–65, doi:10.1016/j.semcdb.2022.11.005.","ama":"Corominas-Murtra B, Hannezo EB. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 2023;150-151:58-65. doi:10.1016/j.semcdb.2022.11.005","apa":"Corominas-Murtra, B., & Hannezo, E. B. (2023). Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. Elsevier. https://doi.org/10.1016/j.semcdb.2022.11.005","short":"B. Corominas-Murtra, E.B. Hannezo, Seminars in Cell & Developmental Biology 150–151 (2023) 58–65.","ieee":"B. Corominas-Murtra and E. B. Hannezo, “Modelling the dynamics of mammalian gut homeostasis,” Seminars in Cell & Developmental Biology, vol. 150–151. Elsevier, pp. 58–65, 2023.","chicago":"Corominas-Murtra, Bernat, and Edouard B Hannezo. “Modelling the Dynamics of Mammalian Gut Homeostasis.” Seminars in Cell & Developmental Biology. Elsevier, 2023. https://doi.org/10.1016/j.semcdb.2022.11.005.","ista":"Corominas-Murtra B, Hannezo EB. 2023. Modelling the dynamics of mammalian gut homeostasis. Seminars in Cell & Developmental Biology. 150–151, 58–65."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Elsevier","quality_controlled":"1","oa":1,"acknowledgement":"This work received funding from the ERC under the European Union’s Horizon 2020 research and innovation programme (grant agreement No. 851288 to E.H.).\r\nB. C-M wants to acknowledge the support of the field of excellence Complexity of Life, in Basic Research and Innovation of the University of Graz.","page":"58-65","doi":"10.1016/j.semcdb.2022.11.005","date_published":"2023-12-02T00:00:00Z","date_created":"2023-01-12T12:09:47Z","isi":1,"has_accepted_license":"1","year":"2023","day":"02","publication":"Seminars in Cell & Developmental Biology","type":"journal_article","article_type":"review","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Cell Biology","Developmental Biology"],"_id":"12162","file_date_updated":"2024-01-08T10:16:04Z","department":[{"_id":"EdHa"}],"date_updated":"2024-01-16T13:22:32Z","ddc":["570"],"scopus_import":"1","month":"12","abstract":[{"lang":"eng","text":"Homeostatic balance in the intestinal epithelium relies on a fast cellular turnover, which is coordinated by an intricate interplay between biochemical signalling, mechanical forces and organ geometry. We review recent modelling approaches that have been developed to understand different facets of this remarkable homeostatic equilibrium. Existing models offer different, albeit complementary, perspectives on the problem. First, biomechanical models aim to explain the local and global mechanical stresses driving cell renewal as well as tissue shape maintenance. Second, compartmental models provide insights into the conditions necessary to keep a constant flow of cells with well-defined ratios of cell types, and how perturbations can lead to an unbalance of relative compartment sizes. A third family of models address, at the cellular level, the nature and regulation of stem fate choices that are necessary to fuel cellular turnover. We also review how these different approaches are starting to be integrated together across scales, to provide quantitative predictions and new conceptual frameworks to think about the dynamics of cell renewal in complex tissues."}],"pmid":1,"oa_version":"Published Version","volume":"150-151","ec_funded":1,"publication_identifier":{"issn":["1084-9521"]},"publication_status":"published","file":[{"relation":"main_file","access_level":"open_access","content_type":"application/pdf","success":1,"checksum":"c619887cf130f4649bf3035417186004","file_id":"14741","creator":"dernst","file_size":1343750,"date_updated":"2024-01-08T10:16:04Z","file_name":"2023_SeminarsCellDevBiology_CorominasMurtra.pdf","date_created":"2024-01-08T10:16:04Z"}],"language":[{"iso":"eng"}]},{"_id":"13268","article_type":"original","type":"journal_article","status":"public","date_updated":"2024-01-16T12:00:47Z","department":[{"_id":"TaHa"}],"abstract":[{"lang":"eng","text":"We give a simple argument to prove Nagai’s conjecture for type II degenerations of compact hyperkähler manifolds and cohomology classes of middle degree. Under an additional assumption, the techniques yield the conjecture in arbitrary degree. This would complete the proof of Nagai’s conjecture in general, as it was proved already for type I degenerations by Kollár, Laza, Saccà, and Voisin [10] and independently by Soldatenkov [18], while it is immediate for type III degenerations. Our arguments are close in spirit to a recent paper by Harder [8] proving similar results for the restrictive class of good degenerations."}],"oa_version":"Preprint","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2108.01587","open_access":"1"}],"scopus_import":"1","intvolume":" 30","month":"06","publication_status":"published","publication_identifier":{"issn":["1073-2780"],"eissn":["1945-001X"]},"language":[{"iso":"eng"}],"ec_funded":1,"issue":"1","volume":30,"project":[{"name":"IST-BRIDGE: International postdoctoral program","grant_number":"101034413","_id":"fc2ed2f7-9c52-11eb-aca3-c01059dda49c","call_identifier":"H2020"}],"citation":{"ieee":"D. Huybrechts and M. Mauri, “On type II degenerations of hyperkähler manifolds,” Mathematical Research Letters, vol. 30, no. 1. International Press, pp. 125–141, 2023.","short":"D. Huybrechts, M. Mauri, Mathematical Research Letters 30 (2023) 125–141.","apa":"Huybrechts, D., & Mauri, M. (2023). On type II degenerations of hyperkähler manifolds. Mathematical Research Letters. International Press. https://doi.org/10.4310/mrl.2023.v30.n1.a6","ama":"Huybrechts D, Mauri M. On type II degenerations of hyperkähler manifolds. Mathematical Research Letters. 2023;30(1):125-141. doi:10.4310/mrl.2023.v30.n1.a6","mla":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” Mathematical Research Letters, vol. 30, no. 1, International Press, 2023, pp. 125–41, doi:10.4310/mrl.2023.v30.n1.a6.","ista":"Huybrechts D, Mauri M. 2023. On type II degenerations of hyperkähler manifolds. Mathematical Research Letters. 30(1), 125–141.","chicago":"Huybrechts, D., and Mirko Mauri. “On Type II Degenerations of Hyperkähler Manifolds.” Mathematical Research Letters. International Press, 2023. https://doi.org/10.4310/mrl.2023.v30.n1.a6."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","external_id":{"arxiv":["2108.01587"],"isi":["001027656000006"]},"author":[{"first_name":"D.","full_name":"Huybrechts, D.","last_name":"Huybrechts"},{"last_name":"Mauri","full_name":"Mauri, Mirko","id":"2cf70c34-09c1-11ed-bd8d-c34fac206130","first_name":"Mirko"}],"title":"On type II degenerations of hyperkähler manifolds","acknowledgement":"The first author is supported by the ERC Synergy Grant HyperK. The second author is supported by the Max Planck Institute for Mathematics and the Institute of Science and Technology Austria. 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.","oa":1,"quality_controlled":"1","publisher":"International Press","year":"2023","isi":1,"publication":"Mathematical Research Letters","day":"21","page":"125-141","date_created":"2023-07-23T22:01:14Z","date_published":"2023-06-21T00:00:00Z","doi":"10.4310/mrl.2023.v30.n1.a6"},{"date_updated":"2024-01-16T12:03:05Z","department":[{"_id":"JuFi"}],"_id":"14661","status":"public","type":"journal_article","article_type":"original","language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"issn":["0944-6532"],"eissn":["2363-6394"]},"issue":"1","volume":30,"oa_version":"Preprint","abstract":[{"lang":"eng","text":"This paper is concerned with equilibrium configurations of one-dimensional particle systems with non-convex nearest-neighbour and next-to-nearest-neighbour interactions and its passage to the continuum. The goal is to derive compactness results for a Γ-development of the energy with the novelty that external forces are allowed. In particular, the forces may depend on Lagrangian or Eulerian coordinates and thus may model dead as well as live loads. Our result is based on a new technique for deriving compactness results which are required for calculating the first-order Γ-limit in the presence of external forces: instead of comparing a configuration of n atoms to a global minimizer of the Γ-limit, we compare the configuration to a minimizer in some subclass of functions which in some sense are \"close to\" the configuration. The paper is complemented with the study of the minimizers of the Γ-limit."}],"intvolume":" 30","month":"01","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1811.09857"}],"scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ieee":"M. Carioni, J. L. Fischer, and A. Schlömerkemper, “External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development,” Journal of Convex Analysis, vol. 30, no. 1. Heldermann Verlag, pp. 217–247, 2023.","short":"M. Carioni, J.L. Fischer, A. Schlömerkemper, Journal of Convex Analysis 30 (2023) 217–247.","ama":"Carioni M, Fischer JL, Schlömerkemper A. External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. Journal of Convex Analysis. 2023;30(1):217-247.","apa":"Carioni, M., Fischer, J. L., & Schlömerkemper, A. (2023). External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. Journal of Convex Analysis. Heldermann Verlag.","mla":"Carioni, Marcello, et al. “External Forces in the Continuum Limit of Discrete Systems with Non-Convex Interaction Potentials: Compactness for a Γ-Development.” Journal of Convex Analysis, vol. 30, no. 1, Heldermann Verlag, 2023, pp. 217–47.","ista":"Carioni M, Fischer JL, Schlömerkemper A. 2023. External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development. Journal of Convex Analysis. 30(1), 217–247.","chicago":"Carioni, Marcello, Julian L Fischer, and Anja Schlömerkemper. “External Forces in the Continuum Limit of Discrete Systems with Non-Convex Interaction Potentials: Compactness for a Γ-Development.” Journal of Convex Analysis. Heldermann Verlag, 2023."},"title":"External forces in the continuum limit of discrete systems with non-convex interaction potentials: Compactness for a Γ-development","article_processing_charge":"No","external_id":{"arxiv":["1811.09857"],"isi":["001115503400013"]},"author":[{"first_name":"Marcello","last_name":"Carioni","full_name":"Carioni, Marcello"},{"first_name":"Julian L","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-0479-558X","full_name":"Fischer, Julian L","last_name":"Fischer"},{"full_name":"Schlömerkemper, Anja","last_name":"Schlömerkemper","first_name":"Anja"}],"publication":"Journal of Convex Analysis","day":"01","year":"2023","isi":1,"date_created":"2023-12-10T23:00:59Z","date_published":"2023-01-01T00:00:00Z","page":"217-247","oa":1,"quality_controlled":"1","publisher":"Heldermann Verlag"},{"_id":"14799","status":"public","article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"ddc":["540"],"date_updated":"2024-01-17T07:49:52Z","department":[{"_id":"LifeSc"}],"file_date_updated":"2024-01-17T07:47:35Z","oa_version":"Published Version","abstract":[{"text":"A round-robin study has been carried out to estimate the impact of the human element in small-angle scattering data analysis. Four corrected datasets were provided to participants ready for analysis. All datasets were measured on samples containing spherical scatterers, with two datasets in dilute dispersions and two from powders. Most of the 46 participants correctly identified the number of populations in the dilute dispersions, with half of the population\r\nmean entries within 1.5% and half of the population width entries within 40%. Due to the added complexity of the structure factor, far fewer people submitted answers on the powder datasets. For those that did, half of the entries for the means and widths were within 44 and 86%, respectively. This round-robin experiment highlights several causes for the discrepancies, for which solutions are proposed.","lang":"eng"}],"month":"12","intvolume":" 56","scopus_import":"1","file":[{"checksum":"dab30d4556360f2cecf99f4b7efb0ee9","file_id":"14822","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","date_created":"2024-01-17T07:47:35Z","file_name":"2023_JourApplCrystallography_Pauw.pdf","creator":"dernst","date_updated":"2024-01-17T07:47:35Z","file_size":2165864}],"language":[{"iso":"eng"}],"publication_identifier":{"issn":["0021-8898"],"eissn":["1600-5767"]},"publication_status":"published","issue":"6","volume":56,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"ista":"Pauw BR, Smales GJ, Anker AS, Annadurai V, Balazs D, Bienert R, Bouwman WG, Breßler I, Breternitz J, Brok ES, Bryant G, Clulow AJ, Crater ER, De Geuser F, Giudice AD, Deumer J, Disch S, Dutt S, Frank K, Fratini E, Garcia PRAF, Gilbert EP, Hahn MB, Hallett J, Hohenschutz M, Hollamby M, Huband S, Ilavsky J, Jochum JK, Juelsholt M, Mansel BW, Penttilä P, Pittkowski RK, Portale G, Pozzo LD, Rochels L, Rosalie JM, Saloga PEJ, Seibt S, Smith AJ, Smith GN, Spiering GA, Stawski TM, Taché O, Thünemann AF, Toth K, Whitten AE, Wuttke J. 2023. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 56(6), 1618–1629.","chicago":"Pauw, Brian R., Glen J. Smales, Andy S. Anker, Venkatasamy Annadurai, Daniel Balazs, Ralf Bienert, Wim G. Bouwman, et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” Journal of Applied Crystallography, 2023. https://doi.org/10.1107/S1600576723008324.","ama":"Pauw BR, Smales GJ, Anker AS, et al. The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. 2023;56(6):1618-1629. doi:10.1107/S1600576723008324","apa":"Pauw, B. R., Smales, G. J., Anker, A. S., Annadurai, V., Balazs, D., Bienert, R., … Wuttke, J. (2023). The human factor: Results of a small-angle scattering data analysis round robin. Journal of Applied Crystallography. https://doi.org/10.1107/S1600576723008324","short":"B.R. Pauw, G.J. Smales, A.S. Anker, V. Annadurai, D. Balazs, R. Bienert, W.G. Bouwman, I. Breßler, J. Breternitz, E.S. Brok, G. Bryant, A.J. Clulow, E.R. Crater, F. De Geuser, A.D. Giudice, J. Deumer, S. Disch, S. Dutt, K. Frank, E. Fratini, P.R.A.F. Garcia, E.P. Gilbert, M.B. Hahn, J. Hallett, M. Hohenschutz, M. Hollamby, S. Huband, J. Ilavsky, J.K. Jochum, M. Juelsholt, B.W. Mansel, P. Penttilä, R.K. Pittkowski, G. Portale, L.D. Pozzo, L. Rochels, J.M. Rosalie, P.E.J. Saloga, S. Seibt, A.J. Smith, G.N. Smith, G.A. Spiering, T.M. Stawski, O. Taché, A.F. Thünemann, K. Toth, A.E. Whitten, J. Wuttke, Journal of Applied Crystallography 56 (2023) 1618–1629.","ieee":"B. R. Pauw et al., “The human factor: Results of a small-angle scattering data analysis round robin,” Journal of Applied Crystallography, vol. 56, no. 6. pp. 1618–1629, 2023.","mla":"Pauw, Brian R., et al. “The Human Factor: Results of a Small-Angle Scattering Data Analysis Round Robin.” Journal of Applied Crystallography, vol. 56, no. 6, 2023, pp. 1618–29, doi:10.1107/S1600576723008324."},"title":"The human factor: Results of a small-angle scattering data analysis round robin","author":[{"last_name":"Pauw","full_name":"Pauw, Brian R.","first_name":"Brian R."},{"last_name":"Smales","full_name":"Smales, Glen J.","first_name":"Glen J."},{"first_name":"Andy S.","last_name":"Anker","full_name":"Anker, Andy S."},{"first_name":"Venkatasamy","full_name":"Annadurai, Venkatasamy","last_name":"Annadurai"},{"first_name":"Daniel","id":"302BADF6-85FC-11EA-9E3B-B9493DDC885E","last_name":"Balazs","orcid":"0000-0001-7597-043X","full_name":"Balazs, Daniel"},{"last_name":"Bienert","full_name":"Bienert, Ralf","first_name":"Ralf"},{"full_name":"Bouwman, Wim G.","last_name":"Bouwman","first_name":"Wim G."},{"last_name":"Breßler","full_name":"Breßler, Ingo","first_name":"Ingo"},{"full_name":"Breternitz, Joachim","last_name":"Breternitz","first_name":"Joachim"},{"first_name":"Erik S.","last_name":"Brok","full_name":"Brok, Erik S."},{"first_name":"Gary","last_name":"Bryant","full_name":"Bryant, Gary"},{"first_name":"Andrew J.","full_name":"Clulow, Andrew J.","last_name":"Clulow"},{"full_name":"Crater, Erin R.","last_name":"Crater","first_name":"Erin R."},{"last_name":"De Geuser","full_name":"De Geuser, Frédéric","first_name":"Frédéric"},{"full_name":"Giudice, Alessandra Del","last_name":"Giudice","first_name":"Alessandra Del"},{"first_name":"Jérôme","last_name":"Deumer","full_name":"Deumer, Jérôme"},{"full_name":"Disch, Sabrina","last_name":"Disch","first_name":"Sabrina"},{"first_name":"Shankar","full_name":"Dutt, Shankar","last_name":"Dutt"},{"first_name":"Kilian","last_name":"Frank","full_name":"Frank, Kilian"},{"last_name":"Fratini","full_name":"Fratini, Emiliano","first_name":"Emiliano"},{"first_name":"Paulo R.A.F.","last_name":"Garcia","full_name":"Garcia, Paulo R.A.F."},{"first_name":"Elliot P.","full_name":"Gilbert, Elliot P.","last_name":"Gilbert"},{"first_name":"Marc B.","full_name":"Hahn, Marc B.","last_name":"Hahn"},{"first_name":"James","full_name":"Hallett, James","last_name":"Hallett"},{"last_name":"Hohenschutz","full_name":"Hohenschutz, Max","first_name":"Max"},{"full_name":"Hollamby, Martin","last_name":"Hollamby","first_name":"Martin"},{"last_name":"Huband","full_name":"Huband, Steven","first_name":"Steven"},{"first_name":"Jan","last_name":"Ilavsky","full_name":"Ilavsky, Jan"},{"last_name":"Jochum","full_name":"Jochum, Johanna K.","first_name":"Johanna K."},{"first_name":"Mikkel","full_name":"Juelsholt, Mikkel","last_name":"Juelsholt"},{"full_name":"Mansel, Bradley W.","last_name":"Mansel","first_name":"Bradley W."},{"first_name":"Paavo","full_name":"Penttilä, Paavo","last_name":"Penttilä"},{"last_name":"Pittkowski","full_name":"Pittkowski, Rebecca K.","first_name":"Rebecca K."},{"last_name":"Portale","full_name":"Portale, Giuseppe","first_name":"Giuseppe"},{"last_name":"Pozzo","full_name":"Pozzo, Lilo D.","first_name":"Lilo D."},{"first_name":"Leonhard","last_name":"Rochels","full_name":"Rochels, Leonhard"},{"first_name":"Julian M.","full_name":"Rosalie, Julian M.","last_name":"Rosalie"},{"last_name":"Saloga","full_name":"Saloga, Patrick E.J.","first_name":"Patrick E.J."},{"last_name":"Seibt","full_name":"Seibt, Susanne","first_name":"Susanne"},{"first_name":"Andrew J.","full_name":"Smith, Andrew J.","last_name":"Smith"},{"full_name":"Smith, Gregory N.","last_name":"Smith","first_name":"Gregory N."},{"first_name":"Glenn A.","last_name":"Spiering","full_name":"Spiering, Glenn A."},{"first_name":"Tomasz M.","last_name":"Stawski","full_name":"Stawski, Tomasz M."},{"last_name":"Taché","full_name":"Taché, Olivier","first_name":"Olivier"},{"last_name":"Thünemann","full_name":"Thünemann, Andreas F.","first_name":"Andreas F."},{"first_name":"Kristof","last_name":"Toth","full_name":"Toth, Kristof"},{"first_name":"Andrew E.","last_name":"Whitten","full_name":"Whitten, Andrew E."},{"last_name":"Wuttke","full_name":"Wuttke, Joachim","first_name":"Joachim"}],"external_id":{"arxiv":["2303.03772"]},"article_processing_charge":"Yes (via OA deal)","acknowledgement":"KT acknowledges the NIST–NRC postdoctoral fellowship program for support. This work was partially funded through the European Metrology Programme for Innovation and Research (EMPIR) project No. 17NRM04.\r\nCertain commercial equipment, instruments, materials or software are identified in this article in order to specify the experimental procedure adequately. Such identification is not intended to imply recommendation or endorsement by NIST, nor is it intended to imply that the materials or equipment identified are necessarily the best available for the purpose. Open access funding enabled and organized by Projekt DEAL.","quality_controlled":"1","oa":1,"day":"01","publication":"Journal of Applied Crystallography","has_accepted_license":"1","year":"2023","date_published":"2023-12-01T00:00:00Z","doi":"10.1107/S1600576723008324","date_created":"2024-01-14T23:00:57Z","page":"1618-1629"},{"author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"first_name":"Ehsan","full_name":"Kafshdar Goharshady, Ehsan","last_name":"Kafshdar Goharshady"},{"last_name":"Novotný","full_name":"Novotný, Petr","first_name":"Petr","id":"3CC3B868-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Jiří","last_name":"Zárevúcky","full_name":"Zárevúcky, Jiří"},{"last_name":"Zikelic","full_name":"Zikelic, Dorde","orcid":"0000-0002-4681-1699","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde"}],"article_processing_charge":"Yes (via OA deal)","external_id":{"arxiv":["2108.02188"]},"title":"On lexicographic proof rules for probabilistic termination","citation":{"chicago":"Chatterjee, Krishnendu, Ehsan Kafshdar Goharshady, Petr Novotný, Jiří Zárevúcky, and Dorde Zikelic. “On Lexicographic Proof Rules for Probabilistic Termination.” Formal Aspects of Computing. Association for Computing Machinery, 2023. https://doi.org/10.1145/3585391.","ista":"Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. 2023. On lexicographic proof rules for probabilistic termination. Formal Aspects of Computing. 35(2), 11.","mla":"Chatterjee, Krishnendu, et al. “On Lexicographic Proof Rules for Probabilistic Termination.” Formal Aspects of Computing, vol. 35, no. 2, 11, Association for Computing Machinery, 2023, doi:10.1145/3585391.","ieee":"K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, and D. Zikelic, “On lexicographic proof rules for probabilistic termination,” Formal Aspects of Computing, vol. 35, no. 2. Association for Computing Machinery, 2023.","short":"K. Chatterjee, E. Kafshdar Goharshady, P. Novotný, J. Zárevúcky, D. Zikelic, Formal Aspects of Computing 35 (2023).","ama":"Chatterjee K, Kafshdar Goharshady E, Novotný P, Zárevúcky J, Zikelic D. On lexicographic proof rules for probabilistic termination. Formal Aspects of Computing. 2023;35(2). doi:10.1145/3585391","apa":"Chatterjee, K., Kafshdar Goharshady, E., Novotný, P., Zárevúcky, J., & Zikelic, D. (2023). On lexicographic proof rules for probabilistic termination. Formal Aspects of Computing. Association for Computing Machinery. https://doi.org/10.1145/3585391"},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","grant_number":"863818","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"article_number":"11","doi":"10.1145/3585391","date_published":"2023-06-23T00:00:00Z","date_created":"2024-01-10T09:27:43Z","has_accepted_license":"1","year":"2023","day":"23","publication":"Formal Aspects of Computing","quality_controlled":"1","publisher":"Association for Computing Machinery","oa":1,"acknowledgement":"This research was partially supported by the ERC CoG (grant no. 863818; ForM-SMArt), the Czech Science Foundation (grant no. GA21-24711S), and the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 665385.","department":[{"_id":"KrCh"}],"file_date_updated":"2024-01-16T08:11:24Z","date_updated":"2024-01-17T08:19:41Z","ddc":["000"],"article_type":"original","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"status":"public","keyword":["Theoretical Computer Science","Software"],"_id":"14778","related_material":{"record":[{"id":"10414","status":"public","relation":"earlier_version"}]},"issue":"2","volume":35,"ec_funded":1,"publication_identifier":{"issn":["0934-5043"],"eissn":["1433-299X"]},"publication_status":"published","file":[{"access_level":"open_access","relation":"main_file","content_type":"application/pdf","checksum":"3bb133eeb27ec01649a9a36445d952d9","file_id":"14804","success":1,"creator":"dernst","date_updated":"2024-01-16T08:11:24Z","file_size":502522,"date_created":"2024-01-16T08:11:24Z","file_name":"2023_FormalAspectsComputing_Chatterjee.pdf"}],"language":[{"iso":"eng"}],"month":"06","intvolume":" 35","abstract":[{"text":"We consider the almost-sure (a.s.) termination problem for probabilistic programs, which are a stochastic extension of classical imperative programs. Lexicographic ranking functions provide a sound and practical approach for termination of non-probabilistic programs, and their extension to probabilistic programs is achieved via lexicographic ranking supermartingales (LexRSMs). However, LexRSMs introduced in the previous work have a limitation that impedes their automation: all of their components have to be non-negative in all reachable states. This might result in a LexRSM not existing even for simple terminating programs. Our contributions are twofold. First, we introduce a generalization of LexRSMs that allows for some components to be negative. This standard feature of non-probabilistic termination proofs was hitherto not known to be sound in the probabilistic setting, as the soundness proof requires a careful analysis of the underlying stochastic process. Second, we present polynomial-time algorithms using our generalized LexRSMs for proving a.s. termination in broad classes of linear-arithmetic programs.","lang":"eng"}],"oa_version":"Published Version"},{"project":[{"_id":"eb901961-77a9-11ec-83b8-f5c883a62027","grant_number":"M03319","name":"Perception-Aware Appearance Fabrication"}],"article_number":"90","article_processing_charge":"Yes (in subscription journal)","author":[{"first_name":"Bin","last_name":"Chen","full_name":"Chen, Bin"},{"first_name":"Akshay","full_name":"Jindal, Akshay","last_name":"Jindal"},{"full_name":"Piovarci, Michael","orcid":"0000-0002-5062-4474","last_name":"Piovarci","first_name":"Michael","id":"62E473F4-5C99-11EA-A40E-AF823DDC885E"},{"first_name":"Chao","full_name":"Wang, Chao","last_name":"Wang"},{"full_name":"Seidel, Hans Peter","last_name":"Seidel","first_name":"Hans Peter"},{"full_name":"Didyk, Piotr","last_name":"Didyk","first_name":"Piotr"},{"last_name":"Myszkowski","full_name":"Myszkowski, Karol","first_name":"Karol"},{"full_name":"Serrano, Ana","last_name":"Serrano","first_name":"Ana"},{"full_name":"Mantiuk, Rafał K.","last_name":"Mantiuk","first_name":"Rafał K."}],"title":"The effect of display capabilities on the gloss consistency between real and virtual objects","citation":{"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.","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.","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.","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.","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","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","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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"quality_controlled":"1","publisher":"Association for Computing Machinery","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.","date_created":"2024-01-14T23:00:57Z","date_published":"2023-12-10T00:00:00Z","doi":"10.1145/3610548.3618226","year":"2023","has_accepted_license":"1","publication":"Proceedings of the SIGGRAPH Asia 2023 Conference","day":"10","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"conference":{"name":"SIGGRAPH: Computer Graphics and Interactive Techniques Conference","location":"Sydney, Australia","end_date":"2023-12-15","start_date":"2023-12-12"},"type":"conference","status":"public","_id":"14798","file_date_updated":"2024-01-17T08:33:06Z","department":[{"_id":"BeBi"}],"date_updated":"2024-01-17T08:38:35Z","ddc":["000"],"scopus_import":"1","month":"12","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."}],"oa_version":"Published Version","publication_status":"published","publication_identifier":{"isbn":["9798400703157"]},"language":[{"iso":"eng"}],"file":[{"file_name":"2023_SA_Chen.pdf","date_created":"2024-01-17T08:33:06Z","creator":"dernst","file_size":95967451,"date_updated":"2024-01-17T08:33:06Z","success":1,"checksum":"8abe27432ed222b50d1af9b3388db1b0","file_id":"14823","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}]},{"citation":{"ista":"Beznosikov A, Horvath S, Richtarik P, Safaryan M. 2023. On biased compression for distributed learning. Journal of Machine Learning Research. 24, 1–50.","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.","short":"A. Beznosikov, S. Horvath, P. Richtarik, M. Safaryan, Journal of Machine Learning Research 24 (2023) 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.","ama":"Beznosikov A, Horvath S, Richtarik P, Safaryan M. On biased compression for distributed learning. Journal of Machine Learning Research. 2023;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."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","external_id":{"isi":["001111578500001"],"arxiv":["2002.12410"]},"article_processing_charge":"Yes (in subscription journal)","author":[{"last_name":"Beznosikov","full_name":"Beznosikov, Aleksandr","first_name":"Aleksandr"},{"first_name":"Samuel","last_name":"Horvath","full_name":"Horvath, Samuel"},{"first_name":"Peter","last_name":"Richtarik","full_name":"Richtarik, Peter"},{"full_name":"Safaryan, Mher","last_name":"Safaryan","id":"dd546b39-0804-11ed-9c55-ef075c39778d","first_name":"Mher"}],"title":"On biased compression for distributed learning","year":"2023","isi":1,"has_accepted_license":"1","publication":"Journal of Machine Learning Research","day":"01","page":"1-50","date_created":"2024-01-16T12:13:36Z","date_published":"2023-10-01T00:00:00Z","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. ","oa":1,"quality_controlled":"1","publisher":"Journal of Machine Learning Research","date_updated":"2024-01-17T09:14:13Z","ddc":["000"],"department":[{"_id":"DaAl"}],"file_date_updated":"2024-01-16T12:13:27Z","_id":"14815","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)"},"type":"journal_article","article_type":"original","status":"public","publication_status":"published","publication_identifier":{"eissn":["1533-7928"]},"language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"c50f2b9db53938b755e30a085f464059","file_id":"14816","success":1,"date_updated":"2024-01-16T12:13:27Z","file_size":1510993,"creator":"dernst","date_created":"2024-01-16T12:13:27Z","file_name":"2023_JMLR_Beznosikov.pdf"}],"volume":24,"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."}],"oa_version":"Published Version","intvolume":" 24","month":"10"},{"department":[{"_id":"KrCh"}],"date_updated":"2024-01-22T08:10:49Z","status":"public","type":"conference","conference":{"location":"Trier, Germany","end_date":"2023-09-21","start_date":"2023-09-18","name":"FCT: Fundamentals of Computation Theory"},"_id":"14456","related_material":{"link":[{"url":"https://doi.org/10.1007/978-3-031-43587-4_31","relation":"erratum"}]},"volume":14292,"language":[{"iso":"eng"}],"publication_identifier":{"isbn":["9783031435867"],"eissn":["1611-3349"],"issn":["0302-9743"]},"publication_status":"published","month":"09","intvolume":" 14292","alternative_title":["LNCS"],"scopus_import":"1","main_file_link":[{"url":"https://doi.org/10.48550/arXiv.2307.10847","open_access":"1"}],"oa_version":"Preprint","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."}],"title":"Shortest dominating set reconfiguration under token sliding","author":[{"last_name":"Křišťan","full_name":"Křišťan, Jan Matyáš","first_name":"Jan Matyáš"},{"full_name":"Svoboda, Jakub","orcid":"0000-0002-1419-3267","last_name":"Svoboda","id":"130759D2-D7DD-11E9-87D2-DE0DE6697425","first_name":"Jakub"}],"external_id":{"arxiv":["2307.10847"]},"article_processing_charge":"No","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"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.","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.","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","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.","short":"J.M. Křišťan, J. Svoboda, in:, 24th International Symposium on Fundamentals of Computation Theory, Springer Nature, 2023, pp. 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."},"doi":"10.1007/978-3-031-43587-4_24","date_published":"2023-09-21T00:00:00Z","date_created":"2023-10-29T23:01:16Z","page":"333-347","day":"21","publication":"24th International Symposium on Fundamentals of Computation Theory","year":"2023","publisher":"Springer Nature","quality_controlled":"1","oa":1}]