[{"author":[{"orcid":"0000-0001-6619-7502","last_name":"Podlaski","full_name":"Podlaski, William F.","first_name":"William F."},{"first_name":"Everton J.","full_name":"Agnes, Everton J.","last_name":"Agnes","orcid":"0000-0001-7184-7311"},{"first_name":"Tim P","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","last_name":"Vogels","full_name":"Vogels, Tim P","orcid":"0000-0003-3295-6181"}],"oa":1,"title":"High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating","_id":"8125","year":"2022","abstract":[{"lang":"eng","text":"Context, such as behavioral state, is known to modulate memory formation and retrieval, but is usually ignored in associative memory models. Here, we propose several types of contextual modulation for associative memory networks that greatly increase their performance. In these networks, context inactivates specific neurons and connections, which modulates the effective connectivity of the network. Memories are stored only by the active components, thereby reducing interference from memories acquired in other contexts. Such networks exhibit several beneficial characteristics, including enhanced memory capacity, high robustness to noise, increased robustness to memory overloading, and better memory retention during continual learning. Furthermore, memories can be biased to have different relative strengths, or even gated on or off, according to contextual cues, providing a candidate model for cognitive control of memory and efficient memory search. An external context-encoding network can dynamically switch the memory network to a desired state, which we liken to experimentally observed contextual signals in prefrontal cortex and hippocampus. Overall, our work illustrates the benefits of organizing memory around context, and provides an important link between behavioral studies of memory and mechanistic details of neural circuits.SIGNIFICANCEMemory is context dependent — both encoding and recall vary in effectiveness and speed depending on factors like location and brain state during a task. We apply this idea to a simple computational model of associative memory through contextual gating of neurons and synaptic connections. Intriguingly, this results in several advantages, including vastly enhanced memory capacity, better robustness, and flexible memory gating. Our model helps to explain (i) how gating and inhibition contribute to memory processes, (ii) how memory access dynamically changes over time, and (iii) how context representations, such as those observed in hippocampus and prefrontal cortex, may interact with and control memory processes."}],"doi":"10.1101/2020.01.08.898528","publication":"bioRxiv","date_updated":"2024-03-06T12:03:59Z","publication_status":"published","status":"public","day":"21","department":[{"_id":"TiVo"}],"citation":{"mla":"Podlaski, William F., et al. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” BioRxiv, Cold Spring Harbor Laboratory, 2022, doi:10.1101/2020.01.08.898528.","chicago":"Podlaski, William F., Everton J. Agnes, and Tim P Vogels. “High Capacity and Dynamic Accessibility in Associative Memory Networks with Context-Dependent Neuronal and Synaptic Gating.” BioRxiv. Cold Spring Harbor Laboratory, 2022. https://doi.org/10.1101/2020.01.08.898528.","ista":"Podlaski WF, Agnes EJ, Vogels TP. 2022. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. bioRxiv, 10.1101/2020.01.08.898528.","short":"W.F. Podlaski, E.J. Agnes, T.P. Vogels, BioRxiv (2022).","ama":"Podlaski WF, Agnes EJ, Vogels TP. High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. bioRxiv. 2022. doi:10.1101/2020.01.08.898528","apa":"Podlaski, W. F., Agnes, E. J., & Vogels, T. P. (2022). High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating. bioRxiv. Cold Spring Harbor Laboratory. https://doi.org/10.1101/2020.01.08.898528","ieee":"W. F. Podlaski, E. J. Agnes, and T. P. Vogels, “High capacity and dynamic accessibility in associative memory networks with context-dependent neuronal and synaptic gating,” bioRxiv. Cold Spring Harbor Laboratory, 2022."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","date_published":"2022-12-21T00:00:00Z","oa_version":"Preprint","date_created":"2020-07-16T12:24:28Z","main_file_link":[{"url":"https://doi.org/10.1101/2020.01.08.898528 ","open_access":"1"}],"publisher":"Cold Spring Harbor Laboratory","locked":"1","type":"preprint","language":[{"iso":"eng"}],"article_processing_charge":"No"},{"scopus_import":"1","date_created":"2020-03-09T07:06:52Z","date_published":"2022-01-01T00:00:00Z","external_id":{"arxiv":["2101.08057"],"isi":["000518364100001"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"VlKo"}],"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"isi":1,"intvolume":" 101","publisher":"Taylor & Francis","year":"2022","oa":1,"article_type":"original","page":"192-216","date_updated":"2024-03-05T14:01:52Z","publication":"Applicable Analysis","oa_version":"Submitted Version","ddc":["510","515","518"],"file_date_updated":"2021-03-16T23:30:06Z","month":"01","day":"01","citation":{"short":"Y. Shehu, O.S. Iyiola, Applicable Analysis 101 (2022) 192–216.","ista":"Shehu Y, Iyiola OS. 2022. Weak convergence for variational inequalities with inertial-type method. Applicable Analysis. 101(1), 192–216.","ama":"Shehu Y, Iyiola OS. Weak convergence for variational inequalities with inertial-type method. Applicable Analysis. 2022;101(1):192-216. doi:10.1080/00036811.2020.1736287","ieee":"Y. Shehu and O. S. Iyiola, “Weak convergence for variational inequalities with inertial-type method,” Applicable Analysis, vol. 101, no. 1. Taylor & Francis, pp. 192–216, 2022.","apa":"Shehu, Y., & Iyiola, O. S. (2022). Weak convergence for variational inequalities with inertial-type method. Applicable Analysis. Taylor & Francis. https://doi.org/10.1080/00036811.2020.1736287","chicago":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” Applicable Analysis. Taylor & Francis, 2022. https://doi.org/10.1080/00036811.2020.1736287.","mla":"Shehu, Yekini, and Olaniyi S. Iyiola. “Weak Convergence for Variational Inequalities with Inertial-Type Method.” Applicable Analysis, vol. 101, no. 1, Taylor & Francis, 2022, pp. 192–216, doi:10.1080/00036811.2020.1736287."},"volume":101,"article_processing_charge":"No","has_accepted_license":"1","file":[{"date_created":"2020-10-12T10:42:54Z","file_id":"8648","file_size":4282586,"creator":"dernst","relation":"main_file","file_name":"2020_ApplicAnalysis_Shehu.pdf","embargo":"2021-03-15","checksum":"869efe8cb09505dfa6012f67d20db63d","content_type":"application/pdf","access_level":"open_access","date_updated":"2021-03-16T23:30:06Z"}],"arxiv":1,"doi":"10.1080/00036811.2020.1736287","issue":"1","abstract":[{"text":"Weak convergence of inertial iterative method for solving variational inequalities is the focus of this paper. The cost function is assumed to be non-Lipschitz and monotone. We propose a projection-type method with inertial terms and give weak convergence analysis under appropriate conditions. Some test results are performed and compared with relevant methods in the literature to show the efficiency and advantages given by our proposed methods.","lang":"eng"}],"_id":"7577","author":[{"orcid":"0000-0001-9224-7139","last_name":"Shehu","full_name":"Shehu, Yekini","first_name":"Yekini","id":"3FC7CB58-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Olaniyi S.","full_name":"Iyiola, Olaniyi S.","last_name":"Iyiola"}],"title":"Weak convergence for variational inequalities with inertial-type method","ec_funded":1,"status":"public","publication_status":"published","acknowledgement":"The project of the first author has received funding from the European Research Council (ERC) under the European Union's Seventh Framework Program (FP7 - 2007-2013) (Grant agreement No. 616160).","project":[{"grant_number":"616160","_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice"}],"publication_identifier":{"issn":["0003-6811"],"eissn":["1563-504X"]}},{"_id":"14355","title":"A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease","author":[{"first_name":"Elisa","last_name":"Cali","full_name":"Cali, Elisa"},{"last_name":"Lin","full_name":"Lin, Sheng-Jia","first_name":"Sheng-Jia"},{"last_name":"Rocca","full_name":"Rocca, Clarissa","first_name":"Clarissa"},{"first_name":"Yavuz","full_name":"Sahin, Yavuz","last_name":"Sahin"},{"first_name":"Aisha","last_name":"Al Shamsi","full_name":"Al Shamsi, Aisha"},{"first_name":"Salima","last_name":"El Chehadeh","full_name":"El Chehadeh, Salima"},{"first_name":"Myriam","full_name":"Chaabouni, Myriam","last_name":"Chaabouni"},{"first_name":"Kshitij","last_name":"Mankad","full_name":"Mankad, Kshitij"},{"last_name":"Galanaki","full_name":"Galanaki, Evangelia","first_name":"Evangelia"},{"first_name":"Stephanie","full_name":"Efthymiou, Stephanie","last_name":"Efthymiou"},{"last_name":"Sudhakar","full_name":"Sudhakar, Sniya","first_name":"Sniya"},{"full_name":"Athanasiou-Fragkouli, Alkyoni","last_name":"Athanasiou-Fragkouli","first_name":"Alkyoni"},{"last_name":"Celik","full_name":"Celik, Tamer","first_name":"Tamer"},{"first_name":"Nejat","full_name":"Narli, Nejat","last_name":"Narli"},{"first_name":"Sebastiano","last_name":"Bianca","full_name":"Bianca, Sebastiano"},{"first_name":"David","last_name":"Murphy","full_name":"Murphy, David"},{"first_name":"Francisco Martins De Carvalho","full_name":"Moreira, Francisco Martins De Carvalho","last_name":"Moreira"},{"full_name":"Accogli, Andrea","last_name":"Accogli","first_name":"Andrea"},{"full_name":"Petree, Cassidy","last_name":"Petree","first_name":"Cassidy"},{"first_name":"Kevin","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","last_name":"Huang","full_name":"Huang, Kevin","orcid":"0000-0002-2512-7812"},{"full_name":"Monastiri, Kamel","last_name":"Monastiri","first_name":"Kamel"},{"full_name":"Edizadeh, Masoud","last_name":"Edizadeh","first_name":"Masoud"},{"first_name":"Rosaria","full_name":"Nardello, Rosaria","last_name":"Nardello"},{"first_name":"Marzia","last_name":"Ognibene","full_name":"Ognibene, Marzia"},{"first_name":"Patrizia","full_name":"De Marco, Patrizia","last_name":"De Marco"},{"first_name":"Martino","last_name":"Ruggieri","full_name":"Ruggieri, Martino"},{"last_name":"Zara","full_name":"Zara, Federico","first_name":"Federico"},{"first_name":"Pasquale","full_name":"Striano, Pasquale","last_name":"Striano"},{"full_name":"Sahin, Yavuz","last_name":"Sahin","first_name":"Yavuz"},{"first_name":"Lihadh","full_name":"Al-Gazali, Lihadh","last_name":"Al-Gazali"},{"first_name":"Marie Therese Abi","last_name":"Warde","full_name":"Warde, Marie Therese Abi"},{"full_name":"Gerard, Benedicte","last_name":"Gerard","first_name":"Benedicte"},{"first_name":"Giovanni","last_name":"Zifarelli","full_name":"Zifarelli, Giovanni"},{"first_name":"Christian","last_name":"Beetz","full_name":"Beetz, Christian"},{"first_name":"Sara","last_name":"Fortuna","full_name":"Fortuna, Sara"},{"full_name":"Soler, Miguel","last_name":"Soler","first_name":"Miguel"},{"first_name":"Enza Maria","full_name":"Valente, Enza Maria","last_name":"Valente"},{"first_name":"Gaurav","last_name":"Varshney","full_name":"Varshney, Gaurav"},{"first_name":"Reza","last_name":"Maroofian","full_name":"Maroofian, Reza"},{"full_name":"Salpietro, Vincenzo","last_name":"Salpietro","first_name":"Vincenzo"},{"full_name":"Houlden, Henry","last_name":"Houlden","first_name":"Henry"},{"full_name":"Grp, SYNaPS Study","last_name":"Grp","first_name":"SYNaPS Study"}],"doi":"10.1016/j.gim.2022.07.013","abstract":[{"lang":"eng","text":"Purpose: The mediator (MED) multisubunit-complex modulates the activity of the transcriptional machinery, and genetic defects in different MED subunits (17, 20, 27) have been implicated in neurologic diseases. In this study, we identified a recurrent homozygous variant in MED11 (c.325C>T; p.Arg109Ter) in 7 affected individuals from 5 unrelated families. Methods: To investigate the genetic cause of the disease, exome or genome sequencing were performed in 5 unrelated families identified via different research networks and Matchmaker Exchange. Deep clinical and brain imaging evaluations were performed by clinical pediatric neurologists and neuroradiologists. The functional effect of the candidate variant on both MED11 RNA and protein was assessed using reverse transcriptase polymerase chain reaction and western blotting using fibroblast cell lines derived from 1 affected individual and controls and through computational approaches. Knockouts in zebrafish were generated using clustered regularly interspaced short palindromic repeats/Cas9. Results: The disease was characterized by microcephaly, profound neurodevelopmental impairment, exaggerated startle response, myoclonic seizures, progressive widespread neurodegeneration, and premature death. Functional studies on patient-derived fibroblasts did not show a loss of protein function but rather disruption of the C-terminal of MED11, likely impairing binding to other MED subunits. A zebrafish knockout model recapitulates key clinical phenotypes. Conclusion: Loss of the C-terminal of MED subunit 11 may affect its binding efficiency to other MED subunits, thus implicating the MED-complex stability in brain development and neurodegeneration. (C) 2022 The Authors. Published by Elsevier Inc. on behalf of American College of Medical Genetics and Genomics."}],"issue":"10","publication_identifier":{"issn":["1098-3600"]},"status":"public","publication_status":"published","month":"10","file_date_updated":"2023-09-25T08:56:06Z","ddc":["570"],"citation":{"mla":"Cali, Elisa, et al. “A Homozygous MED11 C-Terminal Variant Causes a Lethal Neurodegenerative Disease.” Genetics in Medicine, vol. 24, no. 10, Elsevier, 2022, pp. 2194–203, doi:10.1016/j.gim.2022.07.013.","chicago":"Cali, Elisa, Sheng-Jia Lin, Clarissa Rocca, Yavuz Sahin, Aisha Al Shamsi, Salima El Chehadeh, Myriam Chaabouni, et al. “A Homozygous MED11 C-Terminal Variant Causes a Lethal Neurodegenerative Disease.” Genetics in Medicine. Elsevier, 2022. https://doi.org/10.1016/j.gim.2022.07.013.","ieee":"E. Cali et al., “A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease,” Genetics in Medicine, vol. 24, no. 10. Elsevier, pp. 2194–2203, 2022.","apa":"Cali, E., Lin, S.-J., Rocca, C., Sahin, Y., Al Shamsi, A., El Chehadeh, S., … Grp, Syn. S. (2022). A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. Elsevier. https://doi.org/10.1016/j.gim.2022.07.013","ama":"Cali E, Lin S-J, Rocca C, et al. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. 2022;24(10):2194-2203. doi:10.1016/j.gim.2022.07.013","short":"E. Cali, S.-J. Lin, C. Rocca, Y. Sahin, A. Al Shamsi, S. El Chehadeh, M. Chaabouni, K. Mankad, E. Galanaki, S. Efthymiou, S. Sudhakar, A. Athanasiou-Fragkouli, T. Celik, N. Narli, S. Bianca, D. Murphy, F.M.D.C. Moreira, A. Accogli, C. Petree, K. Huang, K. Monastiri, M. Edizadeh, R. Nardello, M. Ognibene, P. De Marco, M. Ruggieri, F. Zara, P. Striano, Y. Sahin, L. Al-Gazali, M.T.A. Warde, B. Gerard, G. Zifarelli, C. Beetz, S. Fortuna, M. Soler, E.M. Valente, G. Varshney, R. Maroofian, V. Salpietro, H. Houlden, Syn.S. Grp, Genetics in Medicine 24 (2022) 2194–2203.","ista":"Cali E, Lin S-J, Rocca C, Sahin Y, Al Shamsi A, El Chehadeh S, Chaabouni M, Mankad K, Galanaki E, Efthymiou S, Sudhakar S, Athanasiou-Fragkouli A, Celik T, Narli N, Bianca S, Murphy D, Moreira FMDC, Accogli A, Petree C, Huang K, Monastiri K, Edizadeh M, Nardello R, Ognibene M, De Marco P, Ruggieri M, Zara F, Striano P, Sahin Y, Al-Gazali L, Warde MTA, Gerard B, Zifarelli G, Beetz C, Fortuna S, Soler M, Valente EM, Varshney G, Maroofian R, Salpietro V, Houlden H, Grp SynS. 2022. A homozygous MED11 C-terminal variant causes a lethal neurodegenerative disease. Genetics in Medicine. 24(10), 2194–2203."},"day":"01","oa_version":"Published Version","license":"https://creativecommons.org/licenses/by/4.0/","file":[{"file_id":"14371","date_created":"2023-09-25T08:56:06Z","success":1,"date_updated":"2023-09-25T08:56:06Z","access_level":"open_access","checksum":"8117175a89129eb5022d81ffe7625f9f","content_type":"application/pdf","file_name":"2022_GeneticsMedicine_Calin.pdf","file_size":1434037,"relation":"main_file","creator":"dernst"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":24,"article_processing_charge":"No","has_accepted_license":"1","oa":1,"keyword":["Human mediator complex","MED11","MEDopathies"],"year":"2022","date_updated":"2023-09-25T08:57:07Z","publication":"Genetics in Medicine","page":"2194-2203","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"GradSch"}],"date_created":"2023-09-20T20:57:18Z","scopus_import":"1","extern":"1","date_published":"2022-10-01T00:00:00Z","publisher":"Elsevier","intvolume":" 24","language":[{"iso":"eng"}],"type":"journal_article","quality_controlled":"1"},{"_id":"14356","title":"Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function","author":[{"full_name":"Lin, Sheng-Jia","last_name":"Lin","first_name":"Sheng-Jia"},{"last_name":"Vona","full_name":"Vona, Barbara","first_name":"Barbara"},{"first_name":"Hillary M.","full_name":"Porter, Hillary M.","last_name":"Porter"},{"last_name":"Izadi","full_name":"Izadi, Mahmoud","first_name":"Mahmoud"},{"full_name":"Huang, Kevin","last_name":"Huang","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3","first_name":"Kevin","orcid":"0000-0002-2512-7812"},{"full_name":"Lacassie, Yves","last_name":"Lacassie","first_name":"Yves"},{"first_name":"Jill A.","last_name":"Rosenfeld","full_name":"Rosenfeld, Jill A."},{"first_name":"Saadullah","last_name":"Khan","full_name":"Khan, Saadullah"},{"full_name":"Petree, Cassidy","last_name":"Petree","first_name":"Cassidy"},{"first_name":"Tayyiba A.","last_name":"Ali","full_name":"Ali, Tayyiba A."},{"last_name":"Muhammad","full_name":"Muhammad, Nazif","first_name":"Nazif"},{"full_name":"Khan, Sher A.","last_name":"Khan","first_name":"Sher A."},{"first_name":"Noor","full_name":"Muhammad, Noor","last_name":"Muhammad"},{"first_name":"Pengfei","full_name":"Liu, Pengfei","last_name":"Liu"},{"first_name":"Marie-Louise","last_name":"Haymon","full_name":"Haymon, Marie-Louise"},{"first_name":"Franz","last_name":"Rueschendorf","full_name":"Rueschendorf, Franz"},{"first_name":"Il-Keun","last_name":"Kong","full_name":"Kong, Il-Keun"},{"first_name":"Linda","full_name":"Schnapp, Linda","last_name":"Schnapp"},{"full_name":"Shur, Natasha","last_name":"Shur","first_name":"Natasha"},{"first_name":"Lynn","last_name":"Chorich","full_name":"Chorich, Lynn"},{"last_name":"Layman","full_name":"Layman, Lawrence","first_name":"Lawrence"},{"full_name":"Haaf, Thomas","last_name":"Haaf","first_name":"Thomas"},{"first_name":"Ehsan","last_name":"Pourkarimi","full_name":"Pourkarimi, Ehsan"},{"first_name":"Hyung-Goo","full_name":"Kim, Hyung-Goo","last_name":"Kim"},{"full_name":"Varshney, Gaurav K.","last_name":"Varshney","first_name":"Gaurav K."}],"doi":"10.1002/humu.24435","abstract":[{"text":"Aminoacyl-tRNA synthetases (ARSs) are essential enzymes for faithful assignment of amino acids to their cognate tRNA. Variants in ARS genes are frequently associated with clinically heterogeneous phenotypes in humans and follow both autosomal dominant or recessive inheritance patterns in many instances. Variants in tryptophanyl-tRNA synthetase 1 (WARS1) cause autosomal dominantly inherited distal hereditary motor neuropathy and Charcot-Marie-Tooth disease. Presently, only one family with biallelic WARS1 variants has been described. We present three affected individuals from two families with biallelic variants (p.Met1? and p.(Asp419Asn)) in WARS1, showing varying severities of developmental delay and intellectual disability. Hearing impairment and microcephaly, as well as abnormalities of the brain, skeletal system, movement/gait, and behavior were variable features. Phenotyping of knocked down wars-1 in a Caenorhabditis elegans model showed depletion is associated with defects in germ cell development. A wars1 knockout vertebrate model recapitulates the human clinical phenotypes, confirms variant pathogenicity, and uncovers evidence implicating the p.Met1? variant as potentially impacting an exon critical for normal hearing. Together, our findings provide consolidating evidence for biallelic disruption of WARS1 as causal for an autosomal recessive neurodevelopmental syndrome and present a vertebrate model that recapitulates key phenotypes observed in patients.","lang":"eng"}],"issue":"10","publication_identifier":{"issn":["1059-7794"]},"publication_status":"published","status":"public","ddc":["570"],"month":"10","file_date_updated":"2023-09-25T08:52:54Z","citation":{"mla":"Lin, Sheng-Jia, et al. “Biallelic Variants in WARS1 Cause a Highly Variable Neurodevelopmental Syndrome and Implicate a Critical Exon for Normal Auditory Function.” Human Mutation, vol. 43, no. 10, Wiley, 2022, pp. 1472–89, doi:10.1002/humu.24435.","chicago":"Lin, Sheng-Jia, Barbara Vona, Hillary M. Porter, Mahmoud Izadi, Kevin Huang, Yves Lacassie, Jill A. Rosenfeld, et al. “Biallelic Variants in WARS1 Cause a Highly Variable Neurodevelopmental Syndrome and Implicate a Critical Exon for Normal Auditory Function.” Human Mutation. Wiley, 2022. https://doi.org/10.1002/humu.24435.","ista":"Lin S-J, Vona B, Porter HM, Izadi M, Huang K, Lacassie Y, Rosenfeld JA, Khan S, Petree C, Ali TA, Muhammad N, Khan SA, Muhammad N, Liu P, Haymon M-L, Rueschendorf F, Kong I-K, Schnapp L, Shur N, Chorich L, Layman L, Haaf T, Pourkarimi E, Kim H-G, Varshney GK. 2022. Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. Human Mutation. 43(10), 1472–1489.","short":"S.-J. Lin, B. Vona, H.M. Porter, M. Izadi, K. Huang, Y. Lacassie, J.A. Rosenfeld, S. Khan, C. Petree, T.A. Ali, N. Muhammad, S.A. Khan, N. Muhammad, P. Liu, M.-L. Haymon, F. Rueschendorf, I.-K. Kong, L. Schnapp, N. Shur, L. Chorich, L. Layman, T. Haaf, E. Pourkarimi, H.-G. Kim, G.K. Varshney, Human Mutation 43 (2022) 1472–1489.","ama":"Lin S-J, Vona B, Porter HM, et al. Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. Human Mutation. 2022;43(10):1472-1489. doi:10.1002/humu.24435","apa":"Lin, S.-J., Vona, B., Porter, H. M., Izadi, M., Huang, K., Lacassie, Y., … Varshney, G. K. (2022). Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function. Human Mutation. Wiley. https://doi.org/10.1002/humu.24435","ieee":"S.-J. Lin et al., “Biallelic variants in WARS1 cause a highly variable neurodevelopmental syndrome and implicate a critical exon for normal auditory function,” Human Mutation, vol. 43, no. 10. Wiley, pp. 1472–1489, 2022."},"day":"01","oa_version":"Published Version","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file":[{"success":1,"date_updated":"2023-09-25T08:52:54Z","access_level":"open_access","checksum":"74b01d4e4084b2f64c30ed32b18ee928","content_type":"application/pdf","file_name":"2022_HumanMutation_Lin.pdf","relation":"main_file","file_size":12131312,"creator":"dernst","file_id":"14370","date_created":"2023-09-25T08:52:54Z"}],"article_processing_charge":"No","volume":43,"has_accepted_license":"1","oa":1,"keyword":["autosomal recessive","biallelic variants","C","elegans","translation initiation sites","tryptophanyl-tRNA synthetase 1 (WARS1)","WHEP domain","zebrafish"],"year":"2022","date_updated":"2023-09-25T08:54:14Z","publication":"Human Mutation","page":"1472-1489","article_type":"original","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-09-20T20:58:24Z","scopus_import":"1","date_published":"2022-10-01T00:00:00Z","extern":"1","publisher":"Wiley","intvolume":" 43","language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article"},{"status":"public","publication_status":"published","publication_identifier":{"issn":["1059-7794"]},"issue":"10","abstract":[{"text":"Aminoacylation of transfer RNA (tRNA) is a key step in protein biosynthesis, carried out by highly specific aminoacyl-tRNA synthetases (ARSs). ARSs have been implicated in autosomal dominant and autosomal recessive human disorders. Autosomal dominant variants in tryptophanyl-tRNA synthetase 1 (WARS1) are known to cause distal hereditary motor neuropathy and Charcot-Marie-Tooth disease, but a recessively inherited phenotype is yet to be clearly defined. Seryl-tRNA synthetase 1 (SARS1) has rarely been implicated in an autosomal recessive developmental disorder. Here, we report five individuals with biallelic missense variants in WARS1 or SARS1, who presented with an overlapping phenotype of microcephaly, developmental delay, intellectual disability, and brain anomalies. Structural mapping showed that the SARS1 variant is located directly within the enzyme’s active site, most likely diminishing activity, while the WARS1 variant is located in the N-terminal domain. We further characterize the identified WARS1 variant by showing that it negatively impacts protein abundance and is unable to rescue the phenotype of a CRISPR/Cas9 wars1 knockout zebrafish model. In summary, we describe two overlapping autosomal recessive syndromes caused by variants in WARS1 and SARS1, present functional insights into the pathogenesis of the WARS1-related syndrome and define an emerging disease spectrum: ARS-related developmental disorders with or without microcephaly.","lang":"eng"}],"doi":"10.1002/humu.24430","author":[{"last_name":"Boegershausen","full_name":"Boegershausen, Nina","first_name":"Nina"},{"last_name":"Krawczyk","full_name":"Krawczyk, Hannah E.","first_name":"Hannah E."},{"first_name":"Rami A.","full_name":"Jamra, Rami A.","last_name":"Jamra"},{"first_name":"Sheng-Jia","last_name":"Lin","full_name":"Lin, Sheng-Jia"},{"full_name":"Yigit, Goekhan","last_name":"Yigit","first_name":"Goekhan"},{"last_name":"Huening","full_name":"Huening, Irina","first_name":"Irina"},{"first_name":"Anna M.","last_name":"Polo","full_name":"Polo, Anna M."},{"first_name":"Barbara","full_name":"Vona, Barbara","last_name":"Vona"},{"orcid":"0000-0002-2512-7812","last_name":"Huang","full_name":"Huang, Kevin","first_name":"Kevin","id":"3b3d2888-1ff6-11ee-9fa6-8f209ca91fe3"},{"full_name":"Schmidt, Julia","last_name":"Schmidt","first_name":"Julia"},{"full_name":"Altmueller, Janine","last_name":"Altmueller","first_name":"Janine"},{"first_name":"Johannes","last_name":"Luppe","full_name":"Luppe, Johannes"},{"last_name":"Platzer","full_name":"Platzer, Konrad","first_name":"Konrad"},{"first_name":"Beate B.","full_name":"Doergeloh, Beate B.","last_name":"Doergeloh"},{"last_name":"Busche","full_name":"Busche, Andreas","first_name":"Andreas"},{"first_name":"Saskia","last_name":"Biskup","full_name":"Biskup, Saskia"},{"full_name":"Mendes, I, Marisa","last_name":"Mendes, I","first_name":"Marisa"},{"last_name":"Smith","full_name":"Smith, Desiree E. C.","first_name":"Desiree E. C."},{"full_name":"Salomons, Gajja S.","last_name":"Salomons","first_name":"Gajja S."},{"full_name":"Zibat, Arne","last_name":"Zibat","first_name":"Arne"},{"last_name":"Bueltmann","full_name":"Bueltmann, Eva","first_name":"Eva"},{"last_name":"Nuernberg","full_name":"Nuernberg, Peter","first_name":"Peter"},{"full_name":"Spielmann, Malte","last_name":"Spielmann","first_name":"Malte"},{"full_name":"Lemke, Johannes R.","last_name":"Lemke","first_name":"Johannes R."},{"full_name":"Li, Yun","last_name":"Li","first_name":"Yun"},{"first_name":"Martin","last_name":"Zenker","full_name":"Zenker, Martin"},{"last_name":"Varshney","full_name":"Varshney, Gaurav K.","first_name":"Gaurav K."},{"first_name":"Hauke S.","full_name":"Hillen, Hauke S.","last_name":"Hillen"},{"first_name":"Christian P.","last_name":"Kratz","full_name":"Kratz, Christian P."},{"last_name":"Wollnik","full_name":"Wollnik, Bernd","first_name":"Bernd"}],"title":"WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly","_id":"14357","has_accepted_license":"1","article_processing_charge":"No","volume":43,"file":[{"date_created":"2023-09-25T08:41:23Z","file_id":"14367","file_size":4863605,"creator":"dernst","relation":"main_file","file_name":"2022_HumanMutation_Boegershausen.pdf","content_type":"application/pdf","checksum":"c31fc91e0445c35b9da83eb911a9b552","access_level":"open_access","date_updated":"2023-09-25T08:41:23Z","success":1}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","oa_version":"Published Version","day":"01","citation":{"chicago":"Boegershausen, Nina, Hannah E. Krawczyk, Rami A. Jamra, Sheng-Jia Lin, Goekhan Yigit, Irina Huening, Anna M. Polo, et al. “WARS1 and SARS1: Two TRNA Synthetases Implicated in Autosomal Recessive Microcephaly.” Human Mutation. Wiley, 2022. https://doi.org/10.1002/humu.24430.","mla":"Boegershausen, Nina, et al. “WARS1 and SARS1: Two TRNA Synthetases Implicated in Autosomal Recessive Microcephaly.” Human Mutation, vol. 43, no. 10, Wiley, 2022, pp. 1454–71, doi:10.1002/humu.24430.","apa":"Boegershausen, N., Krawczyk, H. E., Jamra, R. A., Lin, S.-J., Yigit, G., Huening, I., … Wollnik, B. (2022). WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. Human Mutation. Wiley. https://doi.org/10.1002/humu.24430","ieee":"N. Boegershausen et al., “WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly,” Human Mutation, vol. 43, no. 10. Wiley, pp. 1454–1471, 2022.","ista":"Boegershausen N, Krawczyk HE, Jamra RA, Lin S-J, Yigit G, Huening I, Polo AM, Vona B, Huang K, Schmidt J, Altmueller J, Luppe J, Platzer K, Doergeloh BB, Busche A, Biskup S, Mendes, I M, Smith DEC, Salomons GS, Zibat A, Bueltmann E, Nuernberg P, Spielmann M, Lemke JR, Li Y, Zenker M, Varshney GK, Hillen HS, Kratz CP, Wollnik B. 2022. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. Human Mutation. 43(10), 1454–1471.","ama":"Boegershausen N, Krawczyk HE, Jamra RA, et al. WARS1 and SARS1: Two tRNA synthetases implicated in autosomal recessive microcephaly. Human Mutation. 2022;43(10):1454-1471. doi:10.1002/humu.24430","short":"N. Boegershausen, H.E. Krawczyk, R.A. Jamra, S.-J. Lin, G. Yigit, I. Huening, A.M. Polo, B. Vona, K. Huang, J. Schmidt, J. Altmueller, J. Luppe, K. Platzer, B.B. Doergeloh, A. Busche, S. Biskup, M. Mendes, I, D.E.C. Smith, G.S. Salomons, A. Zibat, E. Bueltmann, P. Nuernberg, M. Spielmann, J.R. Lemke, Y. Li, M. Zenker, G.K. Varshney, H.S. Hillen, C.P. Kratz, B. Wollnik, Human Mutation 43 (2022) 1454–1471."},"pmid":1,"month":"10","ddc":["570"],"file_date_updated":"2023-09-25T08:41:23Z","article_type":"original","page":"1454-1471","publication":"Human Mutation","date_updated":"2023-09-25T08:43:06Z","year":"2022","keyword":["aminoacylation","aminoacyl-tRNA synthetase","ARS","CRISPR","Cas9","intellectual disability","microcephaly","SARS1","tRNA","WARS1","zebrafish"],"oa":1,"type":"journal_article","quality_controlled":"1","language":[{"iso":"eng"}],"intvolume":" 43","publisher":"Wiley","extern":"1","external_id":{"pmid":["35790048"]},"date_published":"2022-10-01T00:00:00Z","scopus_import":"1","date_created":"2023-09-20T20:59:33Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2024-09-10T12:23:57Z","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"14517"}]},"status":"public","_id":"14520","title":"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses","oa":1,"author":[{"full_name":"Zemlicka, Martin","last_name":"Zemlicka","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","first_name":"Martin"},{"last_name":"Redchenko","full_name":"Redchenko, Elena","first_name":"Elena","id":"2C21D6E8-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-3415-4628","first_name":"Matilda","id":"3F920B30-F248-11E8-B48F-1D18A9856A87","last_name":"Peruzzo","full_name":"Peruzzo, Matilda"},{"first_name":"Farid","id":"2AED110C-F248-11E8-B48F-1D18A9856A87","last_name":"Hassani","full_name":"Hassani, Farid","orcid":"0000-0001-6937-5773"},{"last_name":"Trioni","full_name":"Trioni, Andrea","first_name":"Andrea","id":"42F71B44-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shabir","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","last_name":"Barzanjeh","full_name":"Barzanjeh, Shabir","orcid":"0000-0003-0415-1423"},{"orcid":"0000-0001-8112-028X","last_name":"Fink","full_name":"Fink, Johannes M","first_name":"Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87"}],"doi":"10.5281/ZENODO.8408897","abstract":[{"text":"This dataset comprises all data shown in the figures of the submitted article \"Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses\" at arxiv.org/abs/2206.14104. Additional raw data are available from the corresponding author on reasonable request.","lang":"eng"}],"year":"2022","publisher":"Zenodo","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5281/ZENODO.8408897"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"article_processing_charge":"No","type":"research_data_reference","has_accepted_license":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["530"],"month":"06","citation":{"ama":"Zemlicka M, Redchenko E, Peruzzo M, et al. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. 2022. doi:10.5281/ZENODO.8408897","short":"M. Zemlicka, E. Redchenko, M. Peruzzo, F. Hassani, A. Trioni, S. Barzanjeh, J.M. Fink, (2022).","ista":"Zemlicka M, Redchenko E, Peruzzo M, Hassani F, Trioni A, Barzanjeh S, Fink JM. 2022. Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses, Zenodo, 10.5281/ZENODO.8408897.","apa":"Zemlicka, M., Redchenko, E., Peruzzo, M., Hassani, F., Trioni, A., Barzanjeh, S., & Fink, J. M. (2022). Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses. Zenodo. https://doi.org/10.5281/ZENODO.8408897","ieee":"M. Zemlicka et al., “Compact vacuum gap transmon qubits: Selective and sensitive probes for superconductor surface losses.” Zenodo, 2022.","mla":"Zemlicka, Martin, et al. Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses. Zenodo, 2022, doi:10.5281/ZENODO.8408897.","chicago":"Zemlicka, Martin, Elena Redchenko, Matilda Peruzzo, Farid Hassani, Andrea Trioni, Shabir Barzanjeh, and Johannes M Fink. “Compact Vacuum Gap Transmon Qubits: Selective and Sensitive Probes for Superconductor Surface Losses.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.8408897."},"day":"28","department":[{"_id":"JoFi"}],"oa_version":"Published Version","date_created":"2023-11-13T08:09:10Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","date_published":"2022-06-28T00:00:00Z"},{"article_processing_charge":"No","type":"preprint","language":[{"iso":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/2203.17143","open_access":"1"}],"arxiv":1,"external_id":{"arxiv":["2203.17143"]},"date_published":"2022-03-31T00:00:00Z","oa_version":"Preprint","date_created":"2023-11-23T09:30:02Z","citation":{"mla":"Fischer, Julian L., and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” ArXiv, doi:10.48550/ARXIV.2203.17143.","chicago":"Fischer, Julian L, and Alice Marveggio. “Quantitative Convergence of the Vectorial Allen-Cahn Equation towards Multiphase Mean Curvature Flow.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2203.17143.","ama":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. arXiv. doi:10.48550/ARXIV.2203.17143","ista":"Fischer JL, Marveggio A. Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. arXiv, 10.48550/ARXIV.2203.17143.","short":"J.L. Fischer, A. Marveggio, ArXiv (n.d.).","ieee":"J. L. Fischer and A. Marveggio, “Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow,” arXiv. .","apa":"Fischer, J. L., & Marveggio, A. (n.d.). Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow. arXiv. https://doi.org/10.48550/ARXIV.2203.17143"},"department":[{"_id":"JuFi"}],"day":"31","month":"03","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14587"}]},"publication_status":"submitted","status":"public","ec_funded":1,"publication":"arXiv","date_updated":"2023-11-30T13:25:02Z","project":[{"grant_number":"948819","_id":"0aa76401-070f-11eb-9043-b5bb049fa26d","call_identifier":"H2020","name":"Bridging Scales in Random Materials"}],"abstract":[{"lang":"eng","text":"Phase-field models such as the Allen-Cahn equation may give rise to the formation and evolution of geometric shapes, a phenomenon that may be analyzed rigorously in suitable scaling regimes. In its sharp-interface limit, the vectorial Allen-Cahn equation with a potential with N≥3 distinct minima has been conjectured to describe the evolution of branched interfaces by multiphase mean curvature flow.\r\nIn the present work, we give a rigorous proof for this statement in two and three ambient dimensions and for a suitable class of potentials: As long as a strong solution to multiphase mean curvature flow exists, solutions to the vectorial Allen-Cahn equation with well-prepared initial data converge towards multiphase mean curvature flow in the limit of vanishing interface width parameter ε↘0. We even establish the rate of convergence O(ε1/2).\r\nOur approach is based on the gradient flow structure of the Allen-Cahn equation and its limiting motion: Building on the recent concept of \"gradient flow calibrations\" for multiphase mean curvature flow, we introduce a notion of relative entropy for the vectorial Allen-Cahn equation with multi-well potential. This enables us to overcome the limitations of other approaches, e.g. avoiding the need for a stability analysis of the Allen-Cahn operator or additional convergence hypotheses for the energy at positive times."}],"year":"2022","doi":"10.48550/ARXIV.2203.17143","oa":1,"title":"Quantitative convergence of the vectorial Allen-Cahn equation towards multiphase mean curvature flow","author":[{"orcid":"0000-0002-0479-558X","id":"2C12A0B0-F248-11E8-B48F-1D18A9856A87","first_name":"Julian L","full_name":"Fischer, Julian L","last_name":"Fischer"},{"id":"25647992-AA84-11E9-9D75-8427E6697425","first_name":"Alice","full_name":"Marveggio, Alice","last_name":"Marveggio"}],"_id":"14597"},{"title":"Learning control policies for stochastic systems with reach-avoid guarantees","oa":1,"author":[{"full_name":"Zikelic, Dorde","last_name":"Zikelic","id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","orcid":"0000-0002-4681-1699"},{"last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2985-7724","id":"40876CD8-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas A","full_name":"Henzinger, Thomas A","last_name":"Henzinger"},{"orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","first_name":"Krishnendu"}],"_id":"14600","abstract":[{"text":"We study the problem of learning controllers for discrete-time non-linear stochastic dynamical systems with formal reach-avoid guarantees. This work presents the first method for providing formal reach-avoid guarantees, which combine and generalize stability and safety guarantees, with a tolerable probability threshold $p\\in[0,1]$ over the infinite time horizon. Our method leverages advances in machine learning literature and it represents formal certificates as neural networks. In particular, we learn a certificate in the form of a reach-avoid supermartingale (RASM), a novel notion that we introduce in this work. Our RASMs provide reachability and avoidance guarantees by imposing constraints on what can be viewed as a stochastic extension of level sets of Lyapunov functions for deterministic systems. Our approach solves several important problems -- it can be used to learn a control policy from scratch, to verify a reach-avoid specification for a fixed control policy, or to fine-tune a pre-trained policy if it does not satisfy the reach-avoid specification. We validate our approach on $3$ stochastic non-linear reinforcement learning tasks.","lang":"eng"}],"year":"2022","doi":"10.48550/ARXIV.2210.05308","publication":"arXiv","date_updated":"2025-07-14T09:10:02Z","project":[{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E","grant_number":"863818"},{"call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","grant_number":"101020093"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"14539"},{"relation":"later_version","status":"public","id":"14830"}]},"publication_status":"submitted","status":"public","ec_funded":1,"citation":{"mla":"Zikelic, Dorde, et al. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” ArXiv, doi:10.48550/ARXIV.2210.05308.","chicago":"Zikelic, Dorde, Mathias Lechner, Thomas A Henzinger, and Krishnendu Chatterjee. “Learning Control Policies for Stochastic Systems with Reach-Avoid Guarantees.” ArXiv, n.d. https://doi.org/10.48550/ARXIV.2210.05308.","apa":"Zikelic, D., Lechner, M., Henzinger, T. A., & Chatterjee, K. (n.d.). Learning control policies for stochastic systems with reach-avoid guarantees. arXiv. https://doi.org/10.48550/ARXIV.2210.05308","ieee":"D. Zikelic, M. Lechner, T. A. Henzinger, and K. Chatterjee, “Learning control policies for stochastic systems with reach-avoid guarantees,” arXiv. .","ista":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. arXiv, 10.48550/ARXIV.2210.05308.","short":"D. Zikelic, M. Lechner, T.A. Henzinger, K. Chatterjee, ArXiv (n.d.).","ama":"Zikelic D, Lechner M, Henzinger TA, Chatterjee K. Learning control policies for stochastic systems with reach-avoid guarantees. arXiv. doi:10.48550/ARXIV.2210.05308"},"day":"29","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"month":"11","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","license":"https://creativecommons.org/licenses/by-sa/4.0/","date_published":"2022-11-29T00:00:00Z","external_id":{"arxiv":["2210.05308"]},"oa_version":"Preprint","date_created":"2023-11-24T13:10:09Z","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","short":"CC BY-SA (4.0)","image":"/images/cc_by_sa.png","name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)"},"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2210.05308"}],"arxiv":1,"article_processing_charge":"No","language":[{"iso":"eng"}],"type":"preprint"},{"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"14539"}]},"publication_status":"submitted","status":"public","ec_funded":1,"publication":"arXiv","project":[{"grant_number":"101020093","_id":"62781420-2b32-11ec-9570-8d9b63373d4d","call_identifier":"H2020","name":"Vigilant Algorithmic Monitoring of Software"},{"name":"Formal Methods for Stochastic Models: Algorithms and Applications","call_identifier":"H2020","grant_number":"863818","_id":"0599E47C-7A3F-11EA-A408-12923DDC885E"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"date_updated":"2025-07-14T09:10:00Z","abstract":[{"text":"In this work, we address the problem of learning provably stable neural\r\nnetwork policies for stochastic control systems. While recent work has\r\ndemonstrated the feasibility of certifying given policies using martingale\r\ntheory, the problem of how to learn such policies is little explored. Here, we\r\nstudy the effectiveness of jointly learning a policy together with a martingale\r\ncertificate that proves its stability using a single learning algorithm. We\r\nobserve that the joint optimization problem becomes easily stuck in local\r\nminima when starting from a randomly initialized policy. Our results suggest\r\nthat some form of pre-training of the policy is required for the joint\r\noptimization to repair and verify the policy successfully.","lang":"eng"}],"year":"2022","doi":"10.48550/arXiv.2205.11991","oa":1,"title":"Learning stabilizing policies in stochastic control systems","author":[{"id":"294AA7A6-F248-11E8-B48F-1D18A9856A87","first_name":"Dorde","full_name":"Zikelic, Dorde","last_name":"Zikelic","orcid":"0000-0002-4681-1699"},{"last_name":"Lechner","full_name":"Lechner, Mathias","first_name":"Mathias","id":"3DC22916-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X"},{"orcid":"0000-0002-2985-7724","last_name":"Henzinger","full_name":"Henzinger, Thomas A","first_name":"Thomas A","id":"40876CD8-F248-11E8-B48F-1D18A9856A87"}],"_id":"14601","article_processing_charge":"No","language":[{"iso":"eng"}],"type":"preprint","main_file_link":[{"url":"https://arxiv.org/abs/2205.11991","open_access":"1"}],"arxiv":1,"external_id":{"arxiv":["2205.11991"]},"date_published":"2022-05-24T00:00:00Z","date_created":"2023-11-24T13:22:30Z","oa_version":"Preprint","citation":{"chicago":"Zikelic, Dorde, Mathias Lechner, Krishnendu Chatterjee, and Thomas A Henzinger. “Learning Stabilizing Policies in Stochastic Control Systems.” ArXiv, n.d. https://doi.org/10.48550/arXiv.2205.11991.","mla":"Zikelic, Dorde, et al. “Learning Stabilizing Policies in Stochastic Control Systems.” ArXiv, doi:10.48550/arXiv.2205.11991.","ama":"Zikelic D, Lechner M, Chatterjee K, Henzinger TA. Learning stabilizing policies in stochastic control systems. arXiv. doi:10.48550/arXiv.2205.11991","ista":"Zikelic D, Lechner M, Chatterjee K, Henzinger TA. Learning stabilizing policies in stochastic control systems. arXiv, 10.48550/arXiv.2205.11991.","short":"D. Zikelic, M. Lechner, K. Chatterjee, T.A. Henzinger, ArXiv (n.d.).","ieee":"D. Zikelic, M. Lechner, K. Chatterjee, and T. A. Henzinger, “Learning stabilizing policies in stochastic control systems,” arXiv. .","apa":"Zikelic, D., Lechner, M., Chatterjee, K., & Henzinger, T. A. (n.d.). Learning stabilizing policies in stochastic control systems. arXiv. https://doi.org/10.48550/arXiv.2205.11991"},"day":"24","department":[{"_id":"KrCh"},{"_id":"ToHe"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","month":"05"},{"date_published":"2022-09-02T00:00:00Z","oa_version":"Published Version","date_created":"2023-05-23T16:28:13Z","citation":{"mla":"Orliac, Etienne, et al. Improving Genome-Wide Association Discovery and Genomic Prediction Accuracy in Biobank Data. Dryad, 2022, doi:10.5061/DRYAD.GTHT76HMZ.","chicago":"Orliac, Etienne, Daniel Trejo Banos, Sven Ojavee, Kristi Läll, Reedik Mägi, Peter Visscher, and Matthew Richard Robinson. “Improving Genome-Wide Association Discovery and Genomic Prediction Accuracy in Biobank Data.” Dryad, 2022. https://doi.org/10.5061/DRYAD.GTHT76HMZ.","short":"E. Orliac, D. Trejo Banos, S. Ojavee, K. Läll, R. Mägi, P. Visscher, M.R. Robinson, (2022).","ama":"Orliac E, Trejo Banos D, Ojavee S, et al. Improving genome-wide association discovery and genomic prediction accuracy in biobank data. 2022. doi:10.5061/DRYAD.GTHT76HMZ","ista":"Orliac E, Trejo Banos D, Ojavee S, Läll K, Mägi R, Visscher P, Robinson MR. 2022. Improving genome-wide association discovery and genomic prediction accuracy in biobank data, Dryad, 10.5061/DRYAD.GTHT76HMZ.","apa":"Orliac, E., Trejo Banos, D., Ojavee, S., Läll, K., Mägi, R., Visscher, P., & Robinson, M. R. (2022). Improving genome-wide association discovery and genomic prediction accuracy in biobank data. Dryad. https://doi.org/10.5061/DRYAD.GTHT76HMZ","ieee":"E. Orliac et al., “Improving genome-wide association discovery and genomic prediction accuracy in biobank data.” Dryad, 2022."},"day":"02","department":[{"_id":"MaRo"}],"ddc":["570"],"month":"09","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","type":"research_data_reference","publisher":"Dryad","main_file_link":[{"open_access":"1","url":"https://doi.org/10.5061/dryad.gtht76hmz"}],"tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"abstract":[{"lang":"eng","text":"Genetically informed, deep-phenotyped biobanks are an important research resource and it is imperative that the most powerful, versatile, and efficient analysis approaches are used. Here, we apply our recently developed Bayesian grouped mixture of regressions model (GMRM) in the UK and Estonian Biobanks and obtain the highest genomic prediction accuracy reported to date across 21 heritable traits. When compared to other approaches, GMRM accuracy was greater than annotation prediction models run in the LDAK or LDPred-funct software by 15% (SE 7%) and 14% (SE 2%), respectively, and was 18% (SE 3%) greater than a baseline BayesR model without single-nucleotide polymorphism (SNP) markers grouped into minor allele frequency–linkage disequilibrium (MAF-LD) annotation categories. For height, the prediction accuracy R 2 was 47% in a UK Biobank holdout sample, which was 76% of the estimated h SNP 2 . We then extend our GMRM prediction model to provide mixed-linear model association (MLMA) SNP marker estimates for genome-wide association (GWAS) discovery, which increased the independent loci detected to 16,162 in unrelated UK Biobank individuals, compared to 10,550 from BoltLMM and 10,095 from Regenie, a 62 and 65% increase, respectively. The average χ2 value of the leading markers increased by 15.24 (SE 0.41) for every 1% increase in prediction accuracy gained over a baseline BayesR model across the traits. Thus, we show that modeling genetic associations accounting for MAF and LD differences among SNP markers, and incorporating prior knowledge of genomic function, is important for both genomic prediction and discovery in large-scale individual-level studies."}],"year":"2022","doi":"10.5061/DRYAD.GTHT76HMZ","title":"Improving genome-wide association discovery and genomic prediction accuracy in biobank data","oa":1,"author":[{"first_name":"Etienne","full_name":"Orliac, Etienne","last_name":"Orliac"},{"last_name":"Trejo Banos","full_name":"Trejo Banos, Daniel","first_name":"Daniel"},{"first_name":"Sven","last_name":"Ojavee","full_name":"Ojavee, Sven"},{"first_name":"Kristi","last_name":"Läll","full_name":"Läll, Kristi"},{"last_name":"Mägi","full_name":"Mägi, Reedik","first_name":"Reedik"},{"full_name":"Visscher, Peter","last_name":"Visscher","first_name":"Peter"},{"first_name":"Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","last_name":"Robinson","full_name":"Robinson, Matthew Richard","orcid":"0000-0001-8982-8813"}],"_id":"13064","related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"11733"}]},"status":"public","date_updated":"2023-08-03T12:40:37Z"},{"author":[{"first_name":"Eva","full_name":"Koch, Eva","last_name":"Koch"},{"full_name":"Ravinet, Mark","last_name":"Ravinet","first_name":"Mark"},{"last_name":"Westram","full_name":"Westram, Anja M","first_name":"Anja M","id":"3C147470-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1050-4969"},{"first_name":"Kerstin","last_name":"Jonannesson","full_name":"Jonannesson, Kerstin"},{"last_name":"Butlin","full_name":"Butlin, Roger","first_name":"Roger"}],"title":"Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution","oa":1,"_id":"13066","year":"2022","abstract":[{"text":"Chromosomal inversions have been shown to play a major role in local adaptation by suppressing recombination between alternative arrangements and maintaining beneficial allele combinations. However, so far, their importance relative to the remaining genome remains largely unknown. Understanding the genetic architecture of adaptation requires better estimates of how loci of different effect sizes contribute to phenotypic variation. Here, we used three Swedish islands where the marine snail Littorina saxatilis has repeatedly evolved into two distinct ecotypes along a habitat transition. We estimated the contribution of inversion polymorphisms to phenotypic divergence while controlling for polygenic effects in the remaining genome using a quantitative genetics framework. We confirmed the importance of inversions but showed that contributions of loci outside inversions are of similar magnitude, with variable proportions dependent on the trait and the population. Some inversions showed consistent effects across all sites, whereas others exhibited site-specific effects, indicating that the genomic basis for replicated phenotypic divergence is only partly shared. The contributions of sexual dimorphism as well as environmental factors to phenotypic variation were significant but minor compared to inversions and polygenic background. Overall, this integrated approach provides insight into the multiple mechanisms contributing to parallel phenotypic divergence.","lang":"eng"}],"doi":"10.5061/DRYAD.M905QFV4B","date_updated":"2023-08-04T09:42:10Z","status":"public","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"12247"}]},"department":[{"_id":"NiBa"}],"day":"28","citation":{"ista":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. 2022. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution, Dryad, 10.5061/DRYAD.M905QFV4B.","ama":"Koch E, Ravinet M, Westram AM, Jonannesson K, Butlin R. Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. 2022. doi:10.5061/DRYAD.M905QFV4B","short":"E. Koch, M. Ravinet, A.M. Westram, K. Jonannesson, R. Butlin, (2022).","ieee":"E. Koch, M. Ravinet, A. M. Westram, K. Jonannesson, and R. Butlin, “Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution.” Dryad, 2022.","apa":"Koch, E., Ravinet, M., Westram, A. M., Jonannesson, K., & Butlin, R. (2022). Data from: Genetic architecture of repeated phenotypic divergence in Littorina saxatilis ecotype evolution. Dryad. https://doi.org/10.5061/DRYAD.M905QFV4B","mla":"Koch, Eva, et al. Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution. Dryad, 2022, doi:10.5061/DRYAD.M905QFV4B.","chicago":"Koch, Eva, Mark Ravinet, Anja M Westram, Kerstin Jonannesson, and Roger Butlin. “Data from: Genetic Architecture of Repeated Phenotypic Divergence in Littorina Saxatilis Ecotype Evolution.” Dryad, 2022. https://doi.org/10.5061/DRYAD.M905QFV4B."},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["570"],"month":"07","date_published":"2022-07-28T00:00:00Z","date_created":"2023-05-23T16:33:12Z","oa_version":"Published Version","tmp":{"short":"CC0 (1.0)","legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"main_file_link":[{"url":"https://doi.org/10.5061/dryad.m905qfv4b","open_access":"1"}],"publisher":"Dryad","type":"research_data_reference","article_processing_charge":"No"},{"_id":"13076","author":[{"last_name":"Postnikova","full_name":"Postnikova, Anastasiia","first_name":"Anastasiia"},{"first_name":"Nikita","id":"2F4DB10C-F248-11E8-B48F-1D18A9856A87","last_name":"Koval","full_name":"Koval, Nikita"},{"first_name":"Giorgi","id":"3279A00C-F248-11E8-B48F-1D18A9856A87","last_name":"Nadiradze","full_name":"Nadiradze, Giorgi"},{"orcid":"0000-0003-3650-940X","full_name":"Alistarh, Dan-Adrian","last_name":"Alistarh","id":"4A899BFC-F248-11E8-B48F-1D18A9856A87","first_name":"Dan-Adrian"}],"oa":1,"title":"Multi-queues can be state-of-the-art priority schedulers","doi":"10.5281/ZENODO.5733408","year":"2022","abstract":[{"text":"The source code for replicating experiments presented in the paper.\r\n\r\nThe implementation of the designed priority schedulers can be found in Galois-2.2.1/include/Galois/WorkList/:\r\nStealingMultiQueue.h is the StealingMultiQueue.\r\nMQOptimized/ contains MQ Optimized variants.\r\n\r\nWe provide images that contain all the dependencies and datasets. Images can be pulled from npostnikova/mq-based-schedulers repository, or downloaded from Zenodo. See readme for more detail.","lang":"eng"}],"date_updated":"2023-08-03T06:48:34Z","status":"public","related_material":{"record":[{"id":"11180","status":"public","relation":"used_in_publication"}],"link":[{"relation":"software","url":"https://github.com/npostnikova/mq-based-schedulers/tree/v1.1"}]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ddc":["510"],"month":"01","department":[{"_id":"DaAl"}],"day":"03","citation":{"mla":"Postnikova, Anastasiia, et al. Multi-Queues Can Be State-of-the-Art Priority Schedulers. Zenodo, 2022, doi:10.5281/ZENODO.5733408.","chicago":"Postnikova, Anastasiia, Nikita Koval, Giorgi Nadiradze, and Dan-Adrian Alistarh. “Multi-Queues Can Be State-of-the-Art Priority Schedulers.” Zenodo, 2022. https://doi.org/10.5281/ZENODO.5733408.","ieee":"A. Postnikova, N. Koval, G. Nadiradze, and D.-A. Alistarh, “Multi-queues can be state-of-the-art priority schedulers.” Zenodo, 2022.","apa":"Postnikova, A., Koval, N., Nadiradze, G., & Alistarh, D.-A. (2022). Multi-queues can be state-of-the-art priority schedulers. Zenodo. https://doi.org/10.5281/ZENODO.5733408","ista":"Postnikova A, Koval N, Nadiradze G, Alistarh D-A. 2022. Multi-queues can be state-of-the-art priority schedulers, Zenodo, 10.5281/ZENODO.5733408.","ama":"Postnikova A, Koval N, Nadiradze G, Alistarh D-A. Multi-queues can be state-of-the-art priority schedulers. 2022. doi:10.5281/ZENODO.5733408","short":"A. Postnikova, N. Koval, G. Nadiradze, D.-A. Alistarh, (2022)."},"oa_version":"Published Version","date_created":"2023-05-23T17:05:40Z","date_published":"2022-01-03T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5813846","open_access":"1"}],"publisher":"Zenodo","type":"research_data_reference","article_processing_charge":"No"},{"oa":1,"year":"2022","date_updated":"2023-07-18T06:36:28Z","publication":"Proceedings of Machine Learning Research","page":"518-531","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"TiVo"}],"scopus_import":"1","date_created":"2023-07-16T22:01:12Z","date_published":"2022-12-01T00:00:00Z","intvolume":" 199","publisher":"ML Research Press","type":"conference","quality_controlled":"1","language":[{"iso":"eng"}],"_id":"13239","author":[{"last_name":"Van Der Plas","full_name":"Van Der Plas, Thijs L.","first_name":"Thijs L."},{"full_name":"Vogels, Tim P","last_name":"Vogels","id":"CB6FF8D2-008F-11EA-8E08-2637E6697425","first_name":"Tim P","orcid":"0000-0003-3295-6181"},{"last_name":"Manohar","full_name":"Manohar, Sanjay G.","first_name":"Sanjay G."}],"title":"Predictive learning enables neural networks to learn complex working memory tasks","abstract":[{"text":"Brains are thought to engage in predictive learning - learning to predict upcoming stimuli - to construct an internal model of their environment. This is especially notable for spatial navigation, as first described by Tolman’s latent learning tasks. However, predictive learning has also been observed in sensory cortex, in settings unrelated to spatial navigation. Apart from normative frameworks such as active inference or efficient coding, what could be the utility of learning to predict the patterns of occurrence of correlated stimuli? Here we show that prediction, and thereby the construction of an internal model of sequential stimuli, can bootstrap the learning process of a working memory task in a recurrent neural network. We implemented predictive learning alongside working memory match-tasks, and networks emerged to solve the prediction task first by encoding information across time to predict upcoming stimuli, and then eavesdropped on this solution to solve the matching task. Eavesdropping was most beneficial when neural resources were limited. Hence, predictive learning acts as a general neural mechanism to learn to store sensory information that can later be essential for working memory tasks.","lang":"eng"}],"project":[{"_id":"0aacfa84-070f-11eb-9043-d7eb2c709234","grant_number":"819603","name":"Learning the shape of synaptic plasticity rules for neuronal architectures and function through machine learning.","call_identifier":"H2020"}],"publication_identifier":{"eissn":["2640-3498"]},"ec_funded":1,"publication_status":"published","acknowledgement":"The authors would like to thank members of the Vogels lab and Manohar lab, as well as Adam Packer, Andrew Saxe, Stefano Sarao Mannelli and Jacob Bakermans for fruitful discussions and comments on earlier versions of the manuscript.\r\nTLvdP was supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC) [grant number BB/M011224/1]. TPV was supported by an ERC Consolidator Grant (SYNAPSEEK). SGM was funded by a MRC Clinician Scientist Fellowship MR/P00878X and Leverhulme Grant RPG-2018-310.","status":"public","month":"12","ddc":["000"],"file_date_updated":"2023-07-18T06:32:38Z","day":"01","citation":{"ieee":"T. L. Van Der Plas, T. P. Vogels, and S. G. Manohar, “Predictive learning enables neural networks to learn complex working memory tasks,” in Proceedings of Machine Learning Research, 2022, vol. 199, pp. 518–531.","apa":"Van Der Plas, T. L., Vogels, T. P., & Manohar, S. G. (2022). Predictive learning enables neural networks to learn complex working memory tasks. In Proceedings of Machine Learning Research (Vol. 199, pp. 518–531). ML Research Press.","short":"T.L. Van Der Plas, T.P. Vogels, S.G. Manohar, in:, Proceedings of Machine Learning Research, ML Research Press, 2022, pp. 518–531.","ista":"Van Der Plas TL, Vogels TP, Manohar SG. 2022. Predictive learning enables neural networks to learn complex working memory tasks. Proceedings of Machine Learning Research. vol. 199, 518–531.","ama":"Van Der Plas TL, Vogels TP, Manohar SG. Predictive learning enables neural networks to learn complex working memory tasks. In: Proceedings of Machine Learning Research. Vol 199. ML Research Press; 2022:518-531.","mla":"Van Der Plas, Thijs L., et al. “Predictive Learning Enables Neural Networks to Learn Complex Working Memory Tasks.” Proceedings of Machine Learning Research, vol. 199, ML Research Press, 2022, pp. 518–31.","chicago":"Van Der Plas, Thijs L., Tim P Vogels, and Sanjay G. Manohar. “Predictive Learning Enables Neural Networks to Learn Complex Working Memory Tasks.” In Proceedings of Machine Learning Research, 199:518–31. ML Research Press, 2022."},"oa_version":"Published Version","file":[{"success":1,"date_updated":"2023-07-18T06:32:38Z","access_level":"open_access","content_type":"application/pdf","checksum":"7530a93ef42e10b4db1e5e4b69796e93","file_name":"2022_PMLR_vanderPlas.pdf","creator":"dernst","relation":"main_file","file_size":585135,"file_id":"13243","date_created":"2023-07-18T06:32:38Z"}],"article_processing_charge":"No","volume":199,"has_accepted_license":"1"},{"oa":1,"year":"2022","publication":"Frontiers in Fungal Biology","date_updated":"2024-03-06T14:01:57Z","article_type":"original","article_number":"1029114","department":[{"_id":"JiFr"}],"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","date_published":"2022-10-19T00:00:00Z","scopus_import":"1","date_created":"2023-07-16T22:01:12Z","intvolume":" 3","publisher":"Frontiers Media","quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"author":[{"last_name":"Ingole","full_name":"Ingole, Kishor D.","first_name":"Kishor D."},{"first_name":"Nithya","last_name":"Nagarajan","full_name":"Nagarajan, Nithya"},{"last_name":"Uhse","full_name":"Uhse, Simon","first_name":"Simon"},{"id":"e3fdddd5-f6e0-11ea-865d-ca99ee6367f4","first_name":"Caterina","full_name":"Giannini, Caterina","last_name":"Giannini"},{"last_name":"Djamei","full_name":"Djamei, Armin","first_name":"Armin"}],"title":"Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis","_id":"13240","abstract":[{"lang":"eng","text":"Ustilago maydis is a biotrophic phytopathogenic fungus that causes corn smut disease. As a well-established model system, U. maydis is genetically fully accessible with large omics datasets available and subject to various biological questions ranging from DNA-repair, RNA-transport, and protein secretion to disease biology. For many genetic approaches, tight control of transgene regulation is important. Here we established an optimised version of the Tetracycline-ON (TetON) system for U. maydis. We demonstrate the Tetracycline concentration-dependent expression of fluorescent protein transgenes and the system’s suitability for the induced expression of the toxic protein BCL2 Associated X-1 (Bax1). The Golden Gate compatible vector system contains a native minimal promoter from the mating factor a-1 encoding gene, mfa with ten copies of the tet-regulated operator (tetO) and a codon optimised Tet-repressor (tetR*) which is translationally fused to the native transcriptional corepressor Mql1 (UMAG_05501). The metabolism-independent transcriptional regulator system is functional both, in liquid culture as well as on solid media in the presence of the inducer and can become a useful tool for toxin-antitoxin studies, identification of antifungal proteins, and to study functions of toxic gene products in Ustilago maydis."}],"doi":"10.3389/ffunb.2022.1029114","publication_identifier":{"eissn":["2673-6128"]},"acknowledgement":"The research leading to these results received funding from the European Research Council under the European Union’s Seventh Framework Programme ERC-2013-STG (grant agreement: 335691), the Austrian Science Fund (I 3033-B22), the Austrian Academy of Sciences, and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's Excellence Strategy EXC-2070-390732324 (PhenoRob) and DFG grant (DJ 64/5-1).\r\nWe would like to thank the GMI/IMBA/IMP core facilities for their excellent technical support. We would like to acknowledge Dr. Sinéad A. O’Sullivan from DZNE, University of Bonn for providing anti-GFP antibodies. The authors are thankful to the Excellence University of Bonn for providing infrastructure and instrumentation facilities at the INRES-Plant Pathology department.","publication_status":"published","status":"public","day":"19","citation":{"chicago":"Ingole, Kishor D., Nithya Nagarajan, Simon Uhse, Caterina Giannini, and Armin Djamei. “Tetracycline-Controlled (TetON) Gene Expression System for the Smut Fungus Ustilago Maydis.” Frontiers in Fungal Biology. Frontiers Media, 2022. https://doi.org/10.3389/ffunb.2022.1029114.","mla":"Ingole, Kishor D., et al. “Tetracycline-Controlled (TetON) Gene Expression System for the Smut Fungus Ustilago Maydis.” Frontiers in Fungal Biology, vol. 3, 1029114, Frontiers Media, 2022, doi:10.3389/ffunb.2022.1029114.","ista":"Ingole KD, Nagarajan N, Uhse S, Giannini C, Djamei A. 2022. Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. Frontiers in Fungal Biology. 3, 1029114.","short":"K.D. Ingole, N. Nagarajan, S. Uhse, C. Giannini, A. Djamei, Frontiers in Fungal Biology 3 (2022).","ama":"Ingole KD, Nagarajan N, Uhse S, Giannini C, Djamei A. Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. Frontiers in Fungal Biology. 2022;3. doi:10.3389/ffunb.2022.1029114","apa":"Ingole, K. D., Nagarajan, N., Uhse, S., Giannini, C., & Djamei, A. (2022). Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis. Frontiers in Fungal Biology. Frontiers Media. https://doi.org/10.3389/ffunb.2022.1029114","ieee":"K. D. Ingole, N. Nagarajan, S. Uhse, C. Giannini, and A. Djamei, “Tetracycline-controlled (TetON) gene expression system for the smut fungus Ustilago maydis,” Frontiers in Fungal Biology, vol. 3. Frontiers Media, 2022."},"ddc":["579"],"month":"10","file_date_updated":"2023-07-17T11:46:34Z","oa_version":"Published Version","file":[{"success":1,"date_updated":"2023-07-17T11:46:34Z","access_level":"open_access","content_type":"application/pdf","checksum":"2254e0119c0749d6f7237084fefcece6","file_name":"2023_FrontiersFungalBio_Ingole.pdf","file_size":27966699,"relation":"main_file","creator":"dernst","file_id":"13242","date_created":"2023-07-17T11:46:34Z"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","volume":3,"article_processing_charge":"Yes"},{"publisher":"ML Research Press","main_file_link":[{"url":"https://arxiv.org/abs/2102.06004","open_access":"1"}],"intvolume":" 171","quality_controlled":"1","language":[{"iso":"eng"}],"type":"conference","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"}],"date_created":"2023-07-16T22:01:13Z","scopus_import":"1","external_id":{"arxiv":["2102.06004"]},"date_published":"2022-12-01T00:00:00Z","date_updated":"2023-09-26T10:44:37Z","publication":"Proceedings of Machine Learning Research","page":"59-83","related_material":{"record":[{"relation":"extended_version","status":"public","id":"10802"}]},"oa":1,"year":"2022","arxiv":1,"article_processing_charge":"No","volume":171,"month":"12","citation":{"chicago":"Konstantinov, Nikola H, and Christoph Lampert. “On the Impossibility of Fairness-Aware Learning from Corrupted Data.” In Proceedings of Machine Learning Research, 171:59–83. ML Research Press, 2022.","mla":"Konstantinov, Nikola H., and Christoph Lampert. “On the Impossibility of Fairness-Aware Learning from Corrupted Data.” Proceedings of Machine Learning Research, vol. 171, ML Research Press, 2022, pp. 59–83.","ama":"Konstantinov NH, Lampert C. On the impossibility of fairness-aware learning from corrupted data. In: Proceedings of Machine Learning Research. Vol 171. ML Research Press; 2022:59-83.","short":"N.H. Konstantinov, C. Lampert, in:, Proceedings of Machine Learning Research, ML Research Press, 2022, pp. 59–83.","ista":"Konstantinov NH, Lampert C. 2022. On the impossibility of fairness-aware learning from corrupted data. Proceedings of Machine Learning Research. vol. 171, 59–83.","ieee":"N. H. Konstantinov and C. Lampert, “On the impossibility of fairness-aware learning from corrupted data,” in Proceedings of Machine Learning Research, 2022, vol. 171, pp. 59–83.","apa":"Konstantinov, N. H., & Lampert, C. (2022). On the impossibility of fairness-aware learning from corrupted data. In Proceedings of Machine Learning Research (Vol. 171, pp. 59–83). ML Research Press."},"day":"01","oa_version":"Preprint","publication_identifier":{"eissn":["2640-3498"]},"publication_status":"published","acknowledgement":"This paper is a shortened, workshop version of Konstantinov and Lampert (2021),\r\nhttps://arxiv.org/abs/2102.06004. For further results, including an analysis of algorithms achieving the lower bounds from this paper, we refer to the full version.","status":"public","_id":"13241","title":"On the impossibility of fairness-aware learning from corrupted data","author":[{"first_name":"Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87","last_name":"Konstantinov","full_name":"Konstantinov, Nikola H"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","first_name":"Christoph","full_name":"Lampert, Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887"}],"abstract":[{"text":"Addressing fairness concerns about machine learning models is a crucial step towards their long-term adoption in real-world automated systems. Many approaches for training fair models from data have been developed and an implicit assumption about such algorithms is that they are able to recover a fair model, despite potential historical biases in the data. In this work we show a number of impossibility results that indicate that there is no learning algorithm that can recover a fair model when a proportion of the dataset is subject to arbitrary manipulations. Specifically, we prove that there are situations in which an adversary can force any learner to return a biased classifier, with or without degrading accuracy, and that the strength of this bias increases for learning problems with underrepresented protected groups in the data. Our results emphasize on the importance of studying further data corruption models of various strength and of establishing stricter data collection practices for fairness-aware learning.","lang":"eng"}]},{"extern":"1","date_published":"2022-04-08T00:00:00Z","date_created":"2023-08-01T09:30:08Z","oa_version":"Preprint","day":"08","citation":{"mla":"Bian, Tong, et al. “Catalan Solids from Superionic Nanoparticles.” ChemRxiv, doi:10.26434/chemrxiv-2022-klncg.","chicago":"Bian, Tong, Ivan Lobato, Ji Wang, Tara A. Nitka, Tzuf Shay Peled, Byeongdu Lee, Sandra Van Aert, et al. “Catalan Solids from Superionic Nanoparticles.” ChemRxiv, n.d. https://doi.org/10.26434/chemrxiv-2022-klncg.","ista":"Bian T, Lobato I, Wang J, Nitka TA, Peled TS, Lee B, Van Aert S, Bals S, Vuković L, Altantzis T, Král P, Klajn R. Catalan solids from superionic nanoparticles. ChemRxiv, 10.26434/chemrxiv-2022-klncg.","ama":"Bian T, Lobato I, Wang J, et al. Catalan solids from superionic nanoparticles. ChemRxiv. doi:10.26434/chemrxiv-2022-klncg","short":"T. Bian, I. Lobato, J. Wang, T.A. Nitka, T.S. Peled, B. Lee, S. Van Aert, S. Bals, L. Vuković, T. Altantzis, P. Král, R. Klajn, ChemRxiv (n.d.).","ieee":"T. Bian et al., “Catalan solids from superionic nanoparticles,” ChemRxiv. .","apa":"Bian, T., Lobato, I., Wang, J., Nitka, T. A., Peled, T. S., Lee, B., … Klajn, R. (n.d.). Catalan solids from superionic nanoparticles. ChemRxiv. https://doi.org/10.26434/chemrxiv-2022-klncg"},"month":"04","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","type":"preprint","language":[{"iso":"eng"}],"article_processing_charge":"No","main_file_link":[{"open_access":"1","url":"https://doi.org/10.26434/chemrxiv-2022-klncg"}],"year":"2022","abstract":[{"lang":"eng","text":"The self-assembly of inorganic nanoparticles (NPs) into ordered structures (superlattices) has led to a wide range of nanomaterials with unique optical, magnetic, electronic, and catalytic properties. Various interactions have been employed to direct the crystallization of NPs, including van der Waals forces, hydrogen bonding, as well as electric and magnetic dipolar interactions. Among them, Coulombic interactions—ubiquitous in nature and the main driving force behind the formation of many minerals, such as fluorite or rock salt—have remained largely underexplored, owing to the rapid charge exchange between NPs bearing high densities of opposite charges (superionic NPs). Here, we worked with superionic NPs under conditions (room temperature, concentrated salt solutions) that preserved their native surface charge density. We demonstrate that under these conditions, the Coulombic interactions between superionic NPs are reminiscent of short-range intermolecular interactions. Our methodology was used to assemble oppositely charged NPs into high-quality superlattices exhibiting Catalan shapes. Depending on their size ratio, the NPs assembled into either rhombic dodecahedra or triakis tetrahedra with structures mimicking those of the ionic solids CsCl and Th3P4, respectively. We envision that the methodology described here can be applied to a wide range of charged NPs of various sizes, shapes, and compositions, thus facilitating the discovery of new nanomaterials."}],"doi":"10.26434/chemrxiv-2022-klncg","author":[{"full_name":"Bian, Tong","last_name":"Bian","first_name":"Tong"},{"first_name":"Ivan","full_name":"Lobato, Ivan","last_name":"Lobato"},{"last_name":"Wang","full_name":"Wang, Ji","first_name":"Ji"},{"first_name":"Tara A.","last_name":"Nitka","full_name":"Nitka, Tara A."},{"first_name":"Tzuf Shay","last_name":"Peled","full_name":"Peled, Tzuf Shay"},{"last_name":"Lee","full_name":"Lee, Byeongdu","first_name":"Byeongdu"},{"last_name":"Van Aert","full_name":"Van Aert, Sandra","first_name":"Sandra"},{"first_name":"Sara","full_name":"Bals, Sara","last_name":"Bals"},{"first_name":"Lela","last_name":"Vuković","full_name":"Vuković, Lela"},{"first_name":"Thomas","full_name":"Altantzis, Thomas","last_name":"Altantzis"},{"last_name":"Král","full_name":"Král, Petr","first_name":"Petr"},{"full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"title":"Catalan solids from superionic nanoparticles","oa":1,"_id":"13345","status":"public","publication_status":"submitted","publication":"ChemRxiv","date_updated":"2023-08-02T06:48:27Z"},{"volume":5,"article_processing_charge":"No","citation":{"apa":"Yanshyna, O., Białek, M. J., Chashchikhin, O. V., & Klajn, R. (2022). Encapsulation within a coordination cage modulates the reactivity of redox-active dyes. Communications Chemistry. Springer Nature. https://doi.org/10.1038/s42004-022-00658-8","ieee":"O. Yanshyna, M. J. Białek, O. V. Chashchikhin, and R. Klajn, “Encapsulation within a coordination cage modulates the reactivity of redox-active dyes,” Communications Chemistry, vol. 5. Springer Nature, 2022.","short":"O. Yanshyna, M.J. Białek, O.V. Chashchikhin, R. Klajn, Communications Chemistry 5 (2022).","ista":"Yanshyna O, Białek MJ, Chashchikhin OV, Klajn R. 2022. Encapsulation within a coordination cage modulates the reactivity of redox-active dyes. Communications Chemistry. 5, 44.","ama":"Yanshyna O, Białek MJ, Chashchikhin OV, Klajn R. Encapsulation within a coordination cage modulates the reactivity of redox-active dyes. Communications Chemistry. 2022;5. doi:10.1038/s42004-022-00658-8","mla":"Yanshyna, Oksana, et al. “Encapsulation within a Coordination Cage Modulates the Reactivity of Redox-Active Dyes.” Communications Chemistry, vol. 5, 44, Springer Nature, 2022, doi:10.1038/s42004-022-00658-8.","chicago":"Yanshyna, Oksana, Michał J. Białek, Oleg V. Chashchikhin, and Rafal Klajn. “Encapsulation within a Coordination Cage Modulates the Reactivity of Redox-Active Dyes.” Communications Chemistry. Springer Nature, 2022. https://doi.org/10.1038/s42004-022-00658-8."},"day":"30","month":"03","oa_version":"Published Version","publication_identifier":{"eissn":["2399-3669"]},"status":"public","publication_status":"published","title":"Encapsulation within a coordination cage modulates the reactivity of redox-active dyes","author":[{"first_name":"Oksana","full_name":"Yanshyna, Oksana","last_name":"Yanshyna"},{"first_name":"Michał J.","last_name":"Białek","full_name":"Białek, Michał J."},{"first_name":"Oleg V.","last_name":"Chashchikhin","full_name":"Chashchikhin, Oleg V."},{"full_name":"Klajn, Rafal","last_name":"Klajn","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal"}],"_id":"13347","abstract":[{"text":"Confining molecules within well-defined nanosized spaces can profoundly alter their physicochemical characteristics. For example, the controlled aggregation of chromophores into discrete oligomers has been shown to tune their optical properties whereas encapsulation of reactive species within molecular hosts can increase their stability. The resazurin/resorufin pair has been widely used for detecting redox processes in biological settings; yet, how tight confinement affects the properties of these two dyes remains to be explored. Here, we show that a flexible PdII6L4 coordination cage can efficiently encapsulate both resorufin and resazurin in the form of dimers, dramatically modulating their optical properties. Furthermore, binding within the cage significantly decreases the reduction rate of resazurin to resorufin, and the rate of the subsequent reduction of resorufin to dihydroresorufin. During our studies, we also found that upon dilution, the PdII6L4 cage disassembles to afford PdII2L2 species, which lacks the ability to form inclusion complexes – a process that can be reversed upon the addition of the strongly binding resorufin/resazurin guests. We expect that the herein disclosed ability of a water-soluble cage to reversibly modulate the optical and chemical properties of a molecular redox probe will expand the versatility of synthetic fluorescent probes in biologically relevant environments.","lang":"eng"}],"doi":"10.1038/s42004-022-00658-8","publisher":"Springer Nature","intvolume":" 5","main_file_link":[{"url":"https://doi.org/10.1038/s42004-022-00658-8","open_access":"1"}],"language":[{"iso":"eng"}],"quality_controlled":"1","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_published":"2022-03-30T00:00:00Z","extern":"1","date_created":"2023-08-01T09:30:47Z","scopus_import":"1","publication":"Communications Chemistry","date_updated":"2023-08-02T06:41:54Z","article_number":"44","article_type":"original","oa":1,"year":"2022","keyword":["Materials Chemistry","Biochemistry","Environmental Chemistry","General Chemistry"]},{"page":"21244-21254","article_type":"original","publication":"Journal of the American Chemical Society","date_updated":"2023-08-02T06:39:50Z","year":"2022","keyword":["Colloid and Surface Chemistry","Biochemistry","General Chemistry","Catalysis"],"oa":1,"quality_controlled":"1","type":"journal_article","language":[{"iso":"eng"}],"publisher":"American Chemical Society","intvolume":" 144","main_file_link":[{"url":"https://doi.org/10.1021/jacs.2c08901","open_access":"1"}],"date_published":"2022-11-15T00:00:00Z","extern":"1","date_created":"2023-08-01T09:31:01Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","status":"public","publication_identifier":{"issn":["0002-7863"],"eissn":["1520-5126"]},"abstract":[{"text":"Molecular confinement effects can profoundly alter the physicochemical properties of the confined species. A plethora of organic molecules were encapsulated within the cavities of supramolecular hosts, and the impact of the cavity size and polarity was widely investigated. However, the extent to which the properties of the confined guests can be affected by the symmetry of the cage─which dictates the shape of the cavity─remains to be understood. Here we show that cage symmetry has a dramatic effect on the equilibrium between two isomers of the encapsulated spiropyran guests. Working with two Pd-based coordination cages featuring similarly sized but differently shaped hydrophobic cavities, we found a highly selective stabilization of the isomer whose shape matches that of the cavity of the cage. A Td-symmetric cage stabilized the spiropyrans’ colorless form and rendered them photochemically inert. In contrast, a D2h-symmetric cage favored the colored isomer, while maintaining reversible photoswitching between the two states of the encapsulated spiropyrans. We also show that the switching kinetics strongly depend on the substitution pattern on the spiropyran scaffold. This finding was used to fabricate a time-sensitive information storage medium with tunable lifetimes of the encoded messages.","lang":"eng"}],"issue":"46","doi":"10.1021/jacs.2c08901","title":"Altering the properties of spiropyran switches using coordination cages with different symmetries","author":[{"full_name":"Wang, Jinhua","last_name":"Wang","first_name":"Jinhua"},{"first_name":"Liat","last_name":"Avram","full_name":"Avram, Liat"},{"full_name":"Diskin-Posner, Yael","last_name":"Diskin-Posner","first_name":"Yael"},{"first_name":"Michał J.","full_name":"Białek, Michał J.","last_name":"Białek"},{"first_name":"Wojciech","full_name":"Stawski, Wojciech","last_name":"Stawski"},{"first_name":"Moran","full_name":"Feller, Moran","last_name":"Feller"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn"}],"_id":"13348","volume":144,"article_processing_charge":"No","oa_version":"Published Version","citation":{"chicago":"Wang, Jinhua, Liat Avram, Yael Diskin-Posner, Michał J. Białek, Wojciech Stawski, Moran Feller, and Rafal Klajn. “Altering the Properties of Spiropyran Switches Using Coordination Cages with Different Symmetries.” Journal of the American Chemical Society. American Chemical Society, 2022. https://doi.org/10.1021/jacs.2c08901.","mla":"Wang, Jinhua, et al. “Altering the Properties of Spiropyran Switches Using Coordination Cages with Different Symmetries.” Journal of the American Chemical Society, vol. 144, no. 46, American Chemical Society, 2022, pp. 21244–54, doi:10.1021/jacs.2c08901.","short":"J. Wang, L. Avram, Y. Diskin-Posner, M.J. Białek, W. Stawski, M. Feller, R. Klajn, Journal of the American Chemical Society 144 (2022) 21244–21254.","ista":"Wang J, Avram L, Diskin-Posner Y, Białek MJ, Stawski W, Feller M, Klajn R. 2022. Altering the properties of spiropyran switches using coordination cages with different symmetries. Journal of the American Chemical Society. 144(46), 21244–21254.","ama":"Wang J, Avram L, Diskin-Posner Y, et al. Altering the properties of spiropyran switches using coordination cages with different symmetries. Journal of the American Chemical Society. 2022;144(46):21244-21254. doi:10.1021/jacs.2c08901","ieee":"J. Wang et al., “Altering the properties of spiropyran switches using coordination cages with different symmetries,” Journal of the American Chemical Society, vol. 144, no. 46. American Chemical Society, pp. 21244–21254, 2022.","apa":"Wang, J., Avram, L., Diskin-Posner, Y., Białek, M. J., Stawski, W., Feller, M., & Klajn, R. (2022). Altering the properties of spiropyran switches using coordination cages with different symmetries. Journal of the American Chemical Society. American Chemical Society. https://doi.org/10.1021/jacs.2c08901"},"day":"15","month":"11"},{"volume":8,"article_processing_charge":"No","oa_version":"Published Version","citation":{"chicago":"Gemen, Julius, Michał J. Białek, Miri Kazes, Linda J.W. Shimon, Moran Feller, Sergey N. Semenov, Yael Diskin-Posner, Dan Oron, and Rafal Klajn. “Ternary Host-Guest Complexes with Rapid Exchange Kinetics and Photoswitchable Fluorescence.” Chem. Elsevier, 2022. https://doi.org/10.1016/j.chempr.2022.05.008.","mla":"Gemen, Julius, et al. “Ternary Host-Guest Complexes with Rapid Exchange Kinetics and Photoswitchable Fluorescence.” Chem, vol. 8, no. 9, Elsevier, 2022, pp. 2362–79, doi:10.1016/j.chempr.2022.05.008.","ama":"Gemen J, Białek MJ, Kazes M, et al. Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence. Chem. 2022;8(9):2362-2379. doi:10.1016/j.chempr.2022.05.008","ista":"Gemen J, Białek MJ, Kazes M, Shimon LJW, Feller M, Semenov SN, Diskin-Posner Y, Oron D, Klajn R. 2022. Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence. Chem. 8(9), 2362–2379.","short":"J. Gemen, M.J. Białek, M. Kazes, L.J.W. Shimon, M. Feller, S.N. Semenov, Y. Diskin-Posner, D. Oron, R. Klajn, Chem 8 (2022) 2362–2379.","apa":"Gemen, J., Białek, M. J., Kazes, M., Shimon, L. J. W., Feller, M., Semenov, S. N., … Klajn, R. (2022). Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence. Chem. Elsevier. https://doi.org/10.1016/j.chempr.2022.05.008","ieee":"J. Gemen et al., “Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence,” Chem, vol. 8, no. 9. Elsevier, pp. 2362–2379, 2022."},"day":"08","month":"09","pmid":1,"status":"public","publication_status":"published","publication_identifier":{"eissn":["2451-9294"],"issn":["2451-9308"]},"abstract":[{"text":"Confinement within molecular cages can dramatically modify the physicochemical properties of the encapsulated guest molecules, but such host-guest complexes have mainly been studied in a static context. Combining confinement effects with fast guest exchange kinetics could pave the way toward stimuli-responsive supramolecular systems—and ultimately materials—whose desired properties could be tailored “on demand” rapidly and reversibly. Here, we demonstrate rapid guest exchange between inclusion complexes of an open-window coordination cage that can simultaneously accommodate two guest molecules. Working with two types of guests, anthracene derivatives and BODIPY dyes, we show that the former can substantially modify the optical properties of the latter upon noncovalent heterodimer formation. We also studied the light-induced covalent dimerization of encapsulated anthracenes and found large effects of confinement on reaction rates. By coupling the photodimerization with the rapid guest exchange, we developed a new way to modulate fluorescence using external irradiation.","lang":"eng"}],"issue":"9","doi":"10.1016/j.chempr.2022.05.008","title":"Ternary host-guest complexes with rapid exchange kinetics and photoswitchable fluorescence","author":[{"first_name":"Julius","full_name":"Gemen, Julius","last_name":"Gemen"},{"first_name":"Michał J.","last_name":"Białek","full_name":"Białek, Michał J."},{"first_name":"Miri","full_name":"Kazes, Miri","last_name":"Kazes"},{"full_name":"Shimon, Linda J.W.","last_name":"Shimon","first_name":"Linda J.W."},{"full_name":"Feller, Moran","last_name":"Feller","first_name":"Moran"},{"last_name":"Semenov","full_name":"Semenov, Sergey N.","first_name":"Sergey N."},{"first_name":"Yael","last_name":"Diskin-Posner","full_name":"Diskin-Posner, Yael"},{"full_name":"Oron, Dan","last_name":"Oron","first_name":"Dan"},{"last_name":"Klajn","full_name":"Klajn, Rafal","first_name":"Rafal","id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b"}],"_id":"13350","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","publisher":"Elsevier","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.chempr.2022.05.008"}],"intvolume":" 8","date_published":"2022-09-08T00:00:00Z","extern":"1","external_id":{"pmid":["36133801"]},"date_created":"2023-08-01T09:32:14Z","scopus_import":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"2362-2379","article_type":"original","publication":"Chem","date_updated":"2023-08-02T09:39:35Z","year":"2022","keyword":["Materials Chemistry","Biochemistry (medical)","General Chemical Engineering","Environmental Chemistry","Biochemistry","General Chemistry"],"oa":1},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2023-08-01T09:32:27Z","scopus_import":"1","extern":"1","date_published":"2022-05-12T00:00:00Z","publisher":"Elsevier","main_file_link":[{"url":"https://doi.org/10.1016/j.chempr.2022.04.022","open_access":"1"}],"intvolume":" 8","type":"journal_article","language":[{"iso":"eng"}],"quality_controlled":"1","oa":1,"keyword":["Materials Chemistry","Biochemistry (medical)","General Chemical Engineering","Environmental Chemistry","Biochemistry","General Chemistry"],"year":"2022","date_updated":"2023-08-02T07:24:57Z","publication":"Chem","page":"1183-1186","article_type":"original","month":"05","citation":{"mla":"Gemen, Julius, and Rafal Klajn. “Electron Catalysis Expands the Supramolecular Chemist’s Toolbox.” Chem, vol. 8, no. 5, Elsevier, 2022, pp. 1183–86, doi:10.1016/j.chempr.2022.04.022.","chicago":"Gemen, Julius, and Rafal Klajn. “Electron Catalysis Expands the Supramolecular Chemist’s Toolbox.” Chem. Elsevier, 2022. https://doi.org/10.1016/j.chempr.2022.04.022.","ieee":"J. Gemen and R. Klajn, “Electron catalysis expands the supramolecular chemist’s toolbox,” Chem, vol. 8, no. 5. Elsevier, pp. 1183–1186, 2022.","apa":"Gemen, J., & Klajn, R. (2022). Electron catalysis expands the supramolecular chemist’s toolbox. Chem. Elsevier. https://doi.org/10.1016/j.chempr.2022.04.022","short":"J. Gemen, R. Klajn, Chem 8 (2022) 1183–1186.","ama":"Gemen J, Klajn R. Electron catalysis expands the supramolecular chemist’s toolbox. Chem. 2022;8(5):1183-1186. doi:10.1016/j.chempr.2022.04.022","ista":"Gemen J, Klajn R. 2022. Electron catalysis expands the supramolecular chemist’s toolbox. Chem. 8(5), 1183–1186."},"day":"12","oa_version":"Published Version","article_processing_charge":"No","volume":8,"_id":"13351","title":"Electron catalysis expands the supramolecular chemist’s toolbox","author":[{"full_name":"Gemen, Julius","last_name":"Gemen","first_name":"Julius"},{"id":"8e84690e-1e48-11ed-a02b-a1e6fb8bb53b","first_name":"Rafal","full_name":"Klajn, Rafal","last_name":"Klajn"}],"doi":"10.1016/j.chempr.2022.04.022","abstract":[{"lang":"eng","text":"Molecular recognition is at the heart of the noncovalent synthesis of supramolecular assemblies and, at higher length scales, supramolecular materials. In a recent publication in Nature, Stoddart and co-workers demonstrate that the formation of host-guest complexes can be catalyzed by one of the simplest possible catalysts: the electron."}],"issue":"5","publication_identifier":{"issn":["2451-9308"],"eissn":["2451-9294"]},"publication_status":"published","status":"public"}]