[{"acknowledgement":"A.H.H. was a recipient of a DOC Fellowship (24812) of the Austrian Academy of Sciences. This work also received support from IST Austria institutional funds; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007–2013) under REA grant agreement No 618444 to S.H.\r\nAPC funding was obtained by IST Austria institutional funds.\r\nWe thank A. Sommer and C. Czepe (VBCF GmbH, NGS Unit), L. Andersen, J. Sonntag and J. Renno for technical support and/or initial experiments; M. Sixt, J. Nimpf and all members of the Hippenmeyer lab for discussion. This research was supported by the Scientific Service Units of IST Austria through resources provided by the Imaging and Optics Facility, Lab Support Facility and Preclinical Facility.","volume":1,"ddc":["570"],"doi":"10.1093/oons/kvac009","day":"07","abstract":[{"lang":"eng","text":"The mammalian neocortex is composed of diverse neuronal and glial cell classes that broadly arrange in six distinct laminae. Cortical layers emerge during development and defects in the developmental programs that orchestrate cortical lamination are associated with neurodevelopmental diseases. The developmental principle of cortical layer formation depends on concerted radial projection neuron migration, from their birthplace to their final target position. Radial migration occurs in defined sequential steps, regulated by a large array of signaling pathways. However, based on genetic loss-of-function experiments, most studies have thus far focused on the role of cell-autonomous gene function. Yet, cortical neuron migration in situ is a complex process and migrating neurons traverse along diverse cellular compartments and environments. The role of tissue-wide properties and genetic state in radial neuron migration is however not clear. Here we utilized mosaic analysis with double markers (MADM) technology to either sparsely or globally delete gene function, followed by quantitative single-cell phenotyping. The MADM-based gene ablation paradigms in combination with computational modeling demonstrated that global tissue-wide effects predominate cell-autonomous gene function albeit in a gene-specific manner. Our results thus suggest that the genetic landscape in a tissue critically affects the overall migration phenotype of individual cortical projection neurons. In a broader context, our findings imply that global tissue-wide effects represent an essential component of the underlying etiology associated with focal malformations of cortical development in particular, and neurological diseases in general."}],"date_updated":"2023-11-30T10:55:12Z","citation":{"ama":"Hansen AH, Pauler F, Riedl M, et al. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. 2022;1(1). doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>","apa":"Hansen, A. H., Pauler, F., Riedl, M., Streicher, C., Heger, A.-M., Laukoter, S., … Hippenmeyer, S. (2022). Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. <i>Oxford Open Neuroscience</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>","ieee":"A. H. Hansen <i>et al.</i>, “Tissue-wide effects override cell-intrinsic gene function in radial neuron migration,” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1. Oxford Academic, 2022.","chicago":"Hansen, Andi H, Florian Pauler, Michael Riedl, Carmen Streicher, Anna-Magdalena Heger, Susanne Laukoter, Christoph M Sommer, et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/oons/kvac009\">https://doi.org/10.1093/oons/kvac009</a>.","short":"A.H. Hansen, F. Pauler, M. Riedl, C. Streicher, A.-M. Heger, S. Laukoter, C.M. Sommer, A. Nicolas, B. Hof, L.H. Tsai, T. Rülicke, S. Hippenmeyer, Oxford Open Neuroscience 1 (2022).","mla":"Hansen, Andi H., et al. “Tissue-Wide Effects Override Cell-Intrinsic Gene Function in Radial Neuron Migration.” <i>Oxford Open Neuroscience</i>, vol. 1, no. 1, kvac009, Oxford Academic, 2022, doi:<a href=\"https://doi.org/10.1093/oons/kvac009\">10.1093/oons/kvac009</a>.","ista":"Hansen AH, Pauler F, Riedl M, Streicher C, Heger A-M, Laukoter S, Sommer CM, Nicolas A, Hof B, Tsai LH, Rülicke T, Hippenmeyer S. 2022. Tissue-wide effects override cell-intrinsic gene function in radial neuron migration. Oxford Open Neuroscience. 1(1), kvac009."},"year":"2022","publisher":"Oxford Academic","article_type":"original","quality_controlled":"1","ec_funded":1,"file_date_updated":"2023-08-16T08:00:30Z","publication_status":"published","department":[{"_id":"SiHi"},{"_id":"BjHo"},{"_id":"LifeSc"},{"_id":"EM-Fac"}],"date_created":"2022-02-25T07:52:11Z","article_processing_charge":"No","title":"Tissue-wide effects override cell-intrinsic gene function in radial neuron migration","intvolume":"         1","_id":"10791","author":[{"id":"38853E16-F248-11E8-B48F-1D18A9856A87","last_name":"Hansen","first_name":"Andi H","full_name":"Hansen, Andi H"},{"id":"48EA0138-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7462-0048","full_name":"Pauler, Florian","first_name":"Florian","last_name":"Pauler"},{"id":"3BE60946-F248-11E8-B48F-1D18A9856A87","last_name":"Riedl","first_name":"Michael","full_name":"Riedl, Michael","orcid":"0000-0003-4844-6311"},{"last_name":"Streicher","first_name":"Carmen","full_name":"Streicher, Carmen","id":"36BCB99C-F248-11E8-B48F-1D18A9856A87"},{"id":"4B76FFD2-F248-11E8-B48F-1D18A9856A87","first_name":"Anna-Magdalena","last_name":"Heger","full_name":"Heger, Anna-Magdalena"},{"id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","first_name":"Susanne","last_name":"Laukoter","orcid":"0000-0002-7903-3010","full_name":"Laukoter, Susanne"},{"id":"4DF26D8C-F248-11E8-B48F-1D18A9856A87","full_name":"Sommer, Christoph M","orcid":"0000-0003-1216-9105","last_name":"Sommer","first_name":"Christoph M"},{"full_name":"Nicolas, Armel","first_name":"Armel","last_name":"Nicolas","id":"2A103192-F248-11E8-B48F-1D18A9856A87"},{"id":"3A374330-F248-11E8-B48F-1D18A9856A87","last_name":"Hof","first_name":"Björn","full_name":"Hof, Björn","orcid":"0000-0003-2057-2754"},{"full_name":"Tsai, Li Huei","last_name":"Tsai","first_name":"Li Huei"},{"first_name":"Thomas","last_name":"Rülicke","full_name":"Rülicke, Thomas"},{"first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061","full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87"}],"issue":"1","file":[{"access_level":"open_access","relation":"main_file","success":1,"file_id":"14061","creator":"dernst","date_created":"2023-08-16T08:00:30Z","file_size":4846551,"checksum":"822e76e056c07099d1fb27d1ece5941b","date_updated":"2023-08-16T08:00:30Z","file_name":"2023_OxfordOpenNeuroscience_Hansen.pdf","content_type":"application/pdf"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"status":"public","id":"12726","relation":"dissertation_contains"},{"status":"public","id":"14530","relation":"dissertation_contains"}]},"status":"public","publication_identifier":{"eissn":["2753-149X"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_published":"2022-07-07T00:00:00Z","type":"journal_article","language":[{"iso":"eng"}],"oa_version":"Published Version","acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"PreCl"},{"_id":"Bio"}],"project":[{"_id":"25D61E48-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"618444","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"name":"Molecular Mechanisms of Radial Neuronal Migration","grant_number":"24812","_id":"2625A13E-B435-11E9-9278-68D0E5697425"}],"month":"07","article_number":"kvac009","publication":"Oxford Open Neuroscience","has_accepted_license":"1"},{"abstract":[{"lang":"eng","text":"Background\r\nProper cerebral cortical development depends on the tightly orchestrated migration of newly born neurons from the inner ventricular and subventricular zones to the outer cortical plate. Any disturbance in this process during prenatal stages may lead to neuronal migration disorders (NMDs), which can vary in extent from focal to global. Furthermore, NMDs show a substantial comorbidity with other neurodevelopmental disorders, notably autism spectrum disorders (ASDs). Our previous work demonstrated focal neuronal migration defects in mice carrying loss-of-function alleles of the recognized autism risk gene WDFY3. However, the cellular origins of these defects in Wdfy3 mutant mice remain elusive and uncovering it will provide critical insight into WDFY3-dependent disease pathology .\r\nMethods\r\nHere, in an effort to untangle the origins of NMDs in Wdfy3lacZ mice, we employed mosaic analysis with double markers (MADM). MADM technology enabled us to genetically distinctly track and phenotypically analyze mutant and wild type cells concomitantly in vivo using immunofluorescent techniques.\r\nResults\r\nWe revealed a cell autonomous requirement of WDFY3 for accurate laminar positioning of cortical projection neurons and elimination of mispositioned cells during early postnatal life. In addition, we identified significant deviations in dendritic arborization, as well as synaptic density and morphology between wild type, heterozygous, and homozygous Wdfy3 mutant neurons in Wdfy3-MADM reporter mice at postnatal stages. Limitations While Wdfy3 mutant mice have provided valuable insight into prenatal aspects of ASD pathology that remain inaccessible to investigation in humans, like most animal models, they do not a perfectly replicate all aspects of human ASD biology. The lack of human data makes it indeterminate whether morphological deviations described here apply to ASD patients.\r\nConclusions\r\nOur genetic approach revealed several cell autonomous requirements of Wdfy3 in neuronal development that could underly the pathogenic mechanisms of WDFY3-related ASD conditions. The results are also consistent with findings in other ASD animal models and patients and suggest an important role for Wdfy3 in regulating neuronal function and interconnectivity in postnatal life."}],"oa":1,"doi":"10.21203/rs.3.rs-1316167/v1","publication_identifier":{"eissn":["2693-5015"]},"day":"16","date_published":"2022-02-16T00:00:00Z","external_id":{"pmid":["PPR454733"]},"type":"preprint","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2023-10-17T13:06:52Z","citation":{"chicago":"Schaaf, Zachary, Lyvin Tat, Noemi Cannizzaro, Ralph Green, Thomas Rülicke, Simon Hippenmeyer, and K Zarbalis. “WDFY3 Cell Autonomously Controls Neuronal Migration.” Research Square, n.d. <a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">https://doi.org/10.21203/rs.3.rs-1316167/v1</a>.","ieee":"Z. Schaaf <i>et al.</i>, “WDFY3 cell autonomously controls neuronal migration.” Research Square.","ama":"Schaaf Z, Tat L, Cannizzaro N, et al. WDFY3 cell autonomously controls neuronal migration. doi:<a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">10.21203/rs.3.rs-1316167/v1</a>","apa":"Schaaf, Z., Tat, L., Cannizzaro, N., Green, R., Rülicke, T., Hippenmeyer, S., &#38; Zarbalis, K. (n.d.). WDFY3 cell autonomously controls neuronal migration. Research Square. <a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">https://doi.org/10.21203/rs.3.rs-1316167/v1</a>","ista":"Schaaf Z, Tat L, Cannizzaro N, Green R, Rülicke T, Hippenmeyer S, Zarbalis K. WDFY3 cell autonomously controls neuronal migration. <a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">10.21203/rs.3.rs-1316167/v1</a>.","mla":"Schaaf, Zachary, et al. <i>WDFY3 Cell Autonomously Controls Neuronal Migration</i>. Research Square, doi:<a href=\"https://doi.org/10.21203/rs.3.rs-1316167/v1\">10.21203/rs.3.rs-1316167/v1</a>.","short":"Z. Schaaf, L. Tat, N. Cannizzaro, R. Green, T. Rülicke, S. Hippenmeyer, K. Zarbalis, (n.d.)."},"year":"2022","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"url":"https://doi.org/10.21203/rs.3.rs-1316167/v1","open_access":"1"}],"title":"WDFY3 cell autonomously controls neuronal migration","month":"02","oa_version":"Preprint","publication_status":"submitted","article_processing_charge":"No","department":[{"_id":"SiHi"}],"date_created":"2022-02-25T07:53:26Z","author":[{"last_name":"Schaaf","first_name":"Zachary","full_name":"Schaaf, Zachary"},{"last_name":"Tat","first_name":"Lyvin","full_name":"Tat, Lyvin"},{"first_name":"Noemi","last_name":"Cannizzaro","full_name":"Cannizzaro, Noemi"},{"last_name":"Green","first_name":"Ralph","full_name":"Green, Ralph"},{"full_name":"Rülicke, Thomas","first_name":"Thomas","last_name":"Rülicke"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon"},{"first_name":"K","last_name":"Zarbalis","full_name":"Zarbalis, K"}],"pmid":1,"_id":"10792","publisher":"Research Square","language":[{"iso":"eng"}],"page":"30"},{"language":[{"iso":"eng"}],"project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"oa_version":"Preprint","month":"02","publication":"Annales de l'institut Henri Poincare (B) Probability and Statistics","main_file_link":[{"url":"https://arxiv.org/abs/2007.08272","open_access":"1"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_identifier":{"issn":["0246-0203"]},"oa":1,"type":"journal_article","date_published":"2022-02-01T00:00:00Z","publisher":"Institute of Mathematical Statistics","article_type":"original","ec_funded":1,"quality_controlled":"1","page":"220-247","date_created":"2022-02-27T23:01:50Z","department":[{"_id":"JaMa"}],"article_processing_charge":"No","publication_status":"published","intvolume":"        58","title":"Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations","scopus_import":"1","_id":"10797","issue":"1","author":[{"full_name":"Floreani, Simone","first_name":"Simone","last_name":"Floreani"},{"first_name":"Frank","last_name":"Redig","full_name":"Redig, Frank"},{"id":"E1836206-9F16-11E9-8814-AEFDE5697425","full_name":"Sau, Federico","first_name":"Federico","last_name":"Sau"}],"acknowledgement":"The authors would like to thank Gioia Carinci and Cristian Giardinà for useful discussions. F.R. and S.F. thank Jean-René Chazottes for a stay at CPHT (Institut Polytechnique de Paris), in the realm of Chaire d’Alembert (Paris-Saclay University), where part of this work was performed. S.F. acknowledges Simona Villa for her support in creating the picture. S.F. acknowledges financial support from NWO via the grant TOP1.17.019. F.S. acknowledges financial support from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411.","volume":58,"day":"01","doi":"10.1214/21-AIHP1163","arxiv":1,"abstract":[{"text":"We consider symmetric partial exclusion and inclusion processes in a general graph in contact with reservoirs, where we allow both for edge disorder and well-chosen site disorder. We extend the classical dualities to this context and then we derive new orthogonal polynomial dualities. From the classical dualities, we derive the uniqueness of the non-equilibrium steady state and obtain correlation inequalities. Starting from the orthogonal polynomial dualities, we show universal properties of n-point correlation functions in the non-equilibrium steady state for systems with at most two different reservoir parameters, such as a chain with reservoirs at left and right ends.","lang":"eng"},{"text":"Nous considérons des processus d’exclusion partielle, et des processus d’inclusion sur un graphe général en contact avec des réservoirs. Nous autorisons la présence de inhomogenéités sur les arrêts ainsi que sur les sommets du graph. Nous généralisons les “dualités classiques” dans ce contexte et nous démontrons des nouvelles dualités orthogonales. À partir des dualités classiques, nous démontrons l’unicité de l’état stationnaire non-équilibre, ainsi que des inégalités de corrélation. À partir des dualités orthogonales nous démontrons des propriétés universelles des fonctions de corrélation à n points dans l’état stationnaire non-équilibre pour des systèmes avec deux paramètres de réservoirs inégaux, comme par exemple une chaîne avec des réservoirs à droite et à gauche.","lang":"fre"}],"citation":{"short":"S. Floreani, F. Redig, F. Sau, Annales de l’institut Henri Poincare (B) Probability and Statistics 58 (2022) 220–247.","mla":"Floreani, Simone, et al. “Orthogonal Polynomial Duality of Boundary Driven Particle Systems and Non-Equilibrium Correlations.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 58, no. 1, Institute of Mathematical Statistics, 2022, pp. 220–47, doi:<a href=\"https://doi.org/10.1214/21-AIHP1163\">10.1214/21-AIHP1163</a>.","ista":"Floreani S, Redig F, Sau F. 2022. Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations. Annales de l’institut Henri Poincare (B) Probability and Statistics. 58(1), 220–247.","ama":"Floreani S, Redig F, Sau F. Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. 2022;58(1):220-247. doi:<a href=\"https://doi.org/10.1214/21-AIHP1163\">10.1214/21-AIHP1163</a>","apa":"Floreani, S., Redig, F., &#38; Sau, F. (2022). Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations. <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/21-AIHP1163\">https://doi.org/10.1214/21-AIHP1163</a>","chicago":"Floreani, Simone, Frank Redig, and Federico Sau. “Orthogonal Polynomial Duality of Boundary Driven Particle Systems and Non-Equilibrium Correlations.” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>. Institute of Mathematical Statistics, 2022. <a href=\"https://doi.org/10.1214/21-AIHP1163\">https://doi.org/10.1214/21-AIHP1163</a>.","ieee":"S. Floreani, F. Redig, and F. Sau, “Orthogonal polynomial duality of boundary driven particle systems and non-equilibrium correlations,” <i>Annales de l’institut Henri Poincare (B) Probability and Statistics</i>, vol. 58, no. 1. Institute of Mathematical Statistics, pp. 220–247, 2022."},"year":"2022","date_updated":"2023-10-17T12:49:43Z","external_id":{"isi":["000752489300010"],"arxiv":["2007.08272"]},"isi":1},{"date_published":"2022-03-08T00:00:00Z","type":"dissertation","publication_identifier":{"isbn":["978-3-99078-015-2"],"issn":["2663-337X"]},"supervisor":[{"first_name":"Christoph","last_name":"Lampert","orcid":"0000-0001-8622-7887","full_name":"Lampert, Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"oa":1,"file":[{"creator":"nkonstan","file_id":"10823","access_level":"open_access","success":1,"relation":"main_file","content_type":"application/pdf","file_name":"thesis.pdf","date_updated":"2022-03-06T11:42:54Z","checksum":"626bc523ae8822d20e635d0e2d95182e","file_size":4204905,"date_created":"2022-03-06T11:42:54Z"},{"relation":"source_file","access_level":"closed","file_id":"10824","creator":"nkonstan","date_created":"2022-03-06T11:42:57Z","file_size":22841103,"checksum":"e2ca2b88350ac8ea1515b948885cbcb1","date_updated":"2022-03-10T12:11:48Z","content_type":"application/x-zip-compressed","file_name":"thesis.zip"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8724"},{"relation":"part_of_dissertation","id":"10803","status":"public"},{"relation":"part_of_dissertation","id":"10802","status":"public"},{"status":"public","id":"6590","relation":"part_of_dissertation"}]},"status":"public","has_accepted_license":"1","oa_version":"Published Version","project":[{"name":"International IST Doctoral Program","grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"month":"03","language":[{"iso":"eng"}],"keyword":["robustness","fairness","machine learning","PAC learning","adversarial learning"],"date_updated":"2023-10-17T12:31:54Z","citation":{"ieee":"N. H. Konstantinov, “Robustness and fairness in machine learning,” Institute of Science and Technology Austria, 2022.","chicago":"Konstantinov, Nikola H. “Robustness and Fairness in Machine Learning.” Institute of Science and Technology Austria, 2022. <a href=\"https://doi.org/10.15479/at:ista:10799\">https://doi.org/10.15479/at:ista:10799</a>.","apa":"Konstantinov, N. H. (2022). <i>Robustness and fairness in machine learning</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:10799\">https://doi.org/10.15479/at:ista:10799</a>","ama":"Konstantinov NH. Robustness and fairness in machine learning. 2022. doi:<a href=\"https://doi.org/10.15479/at:ista:10799\">10.15479/at:ista:10799</a>","ista":"Konstantinov NH. 2022. Robustness and fairness in machine learning. Institute of Science and Technology Austria.","mla":"Konstantinov, Nikola H. <i>Robustness and Fairness in Machine Learning</i>. Institute of Science and Technology Austria, 2022, doi:<a href=\"https://doi.org/10.15479/at:ista:10799\">10.15479/at:ista:10799</a>.","short":"N.H. Konstantinov, Robustness and Fairness in Machine Learning, Institute of Science and Technology Austria, 2022."},"year":"2022","doi":"10.15479/at:ista:10799","degree_awarded":"PhD","day":"08","abstract":[{"text":"Because of the increasing popularity of machine learning methods, it is becoming important to understand the impact of learned components on automated decision-making systems and to guarantee that their consequences are beneficial to society. In other words, it is necessary to ensure that machine learning is sufficiently trustworthy to be used in real-world applications. This thesis studies two properties of machine learning models that are highly desirable for the\r\nsake of reliability: robustness and fairness. In the first part of the thesis we study the robustness of learning algorithms to training data corruption. Previous work has shown that machine learning models are vulnerable to a range\r\nof training set issues, varying from label noise through systematic biases to worst-case data manipulations. This is an especially relevant problem from a present perspective, since modern machine learning methods are particularly data hungry and therefore practitioners often have to rely on data collected from various external sources, e.g. from the Internet, from app users or via crowdsourcing. Naturally, such sources vary greatly in the quality and reliability of the\r\ndata they provide. With these considerations in mind, we study the problem of designing machine learning algorithms that are robust to corruptions in data coming from multiple sources. We show that, in contrast to the case of a single dataset with outliers, successful learning within this model is possible both theoretically and practically, even under worst-case data corruptions. The second part of this thesis deals with fairness-aware machine learning. There are multiple areas where machine learning models have shown promising results, but where careful considerations are required, in order to avoid discrimanative decisions taken by such learned components. Ensuring fairness can be particularly challenging, because real-world training datasets are expected to contain various forms of historical bias that may affect the learning process. In this thesis we show that data corruption can indeed render the problem of achieving fairness impossible, by tightly characterizing the theoretical limits of fair learning under worst-case data manipulations. However, assuming access to clean data, we also show how fairness-aware learning can be made practical in contexts beyond binary classification, in particular in the challenging learning to rank setting.","lang":"eng"}],"ddc":["000"],"_id":"10799","author":[{"first_name":"Nikola H","last_name":"Konstantinov","full_name":"Konstantinov, Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","department":[{"_id":"GradSch"},{"_id":"ChLa"}],"date_created":"2022-02-28T13:03:49Z","article_processing_charge":"No","title":"Robustness and fairness in machine learning","alternative_title":["ISTA Thesis"],"page":"176","ec_funded":1,"file_date_updated":"2022-03-10T12:11:48Z","publisher":"Institute of Science and Technology Austria"},{"keyword":["Fairness","robustness","data poisoning","trustworthy machine learning","PAC learning"],"language":[{"iso":"eng"}],"oa_version":"Published Version","month":"05","has_accepted_license":"1","publication":"Journal of Machine Learning Research","file":[{"creator":"kschuh","file_id":"11570","success":1,"access_level":"open_access","relation":"main_file","content_type":"application/pdf","file_name":"2022_JournalMachineLearningResearch_Konstantinov.pdf","date_updated":"2022-07-12T15:08:28Z","file_size":551862,"checksum":"9cac897b54a0ddf3a553a2c33e88cfda","date_created":"2022-07-12T15:08:28Z"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"relation":"dissertation_contains","id":"10799","status":"public"},{"id":"13241","relation":"shorter_version","status":"public"}]},"publication_identifier":{"issn":["1532-4435"],"eissn":["1533-7928"]},"oa":1,"tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","date_published":"2022-05-01T00:00:00Z","publisher":"ML Research Press","article_type":"original","quality_controlled":"1","page":"1-60","file_date_updated":"2022-07-12T15:08:28Z","department":[{"_id":"ChLa"}],"date_created":"2022-02-28T14:05:42Z","article_processing_charge":"No","publication_status":"published","intvolume":"        23","title":"Fairness-aware PAC learning from corrupted data","scopus_import":"1","_id":"10802","author":[{"first_name":"Nikola H","last_name":"Konstantinov","full_name":"Konstantinov, Nikola H","id":"4B9D76E4-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Lampert","first_name":"Christoph","full_name":"Lampert, Christoph","orcid":"0000-0002-4561-241X","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87"}],"acknowledgement":"The authors thank Eugenia Iofinova and Bernd Prach for providing feedback on early versions of this paper. This publication was made possible by an ETH AI Center postdoctoral fellowship to Nikola Konstantinov.","volume":23,"ddc":["004"],"day":"01","arxiv":1,"abstract":[{"text":"Addressing fairness concerns about machine learning models is a crucial step towards their long-term adoption in real-world automated systems. While many approaches have been developed for training fair models from data, little is known about the robustness of these methods to data corruption. In this work we consider fairness-aware learning under worst-case data manipulations. We show that an adversary can in some situations force any learner to return an overly biased classifier, regardless of the sample size and with or without degrading\r\naccuracy, and that the strength of the excess bias increases for learning problems with underrepresented protected groups in the data. We also prove that our hardness results are tight up to constant factors. To this end, we study two natural learning algorithms that optimize for both accuracy and fairness and show that these algorithms enjoy guarantees that are order-optimal in terms of the corruption ratio and the protected groups frequencies in the large data\r\nlimit.","lang":"eng"}],"citation":{"apa":"Konstantinov, N. H., &#38; Lampert, C. (2022). Fairness-aware PAC learning from corrupted data. <i>Journal of Machine Learning Research</i>. ML Research Press.","ama":"Konstantinov NH, Lampert C. Fairness-aware PAC learning from corrupted data. <i>Journal of Machine Learning Research</i>. 2022;23:1-60.","ieee":"N. H. Konstantinov and C. Lampert, “Fairness-aware PAC learning from corrupted data,” <i>Journal of Machine Learning Research</i>, vol. 23. ML Research Press, pp. 1–60, 2022.","chicago":"Konstantinov, Nikola H, and Christoph Lampert. “Fairness-Aware PAC Learning from Corrupted Data.” <i>Journal of Machine Learning Research</i>. ML Research Press, 2022.","short":"N.H. Konstantinov, C. Lampert, Journal of Machine Learning Research 23 (2022) 1–60.","mla":"Konstantinov, Nikola H., and Christoph Lampert. “Fairness-Aware PAC Learning from Corrupted Data.” <i>Journal of Machine Learning Research</i>, vol. 23, ML Research Press, 2022, pp. 1–60.","ista":"Konstantinov NH, Lampert C. 2022. Fairness-aware PAC learning from corrupted data. Journal of Machine Learning Research. 23, 1–60."},"year":"2022","date_updated":"2023-09-26T10:44:37Z","external_id":{"arxiv":["2102.06004"]}},{"language":[{"iso":"eng"}],"keyword":["General Immunology and Microbiology","Microbiology","Infectious Diseases"],"month":"08","oa_version":"None","publication":"Nature Reviews Microbiology","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","publication_identifier":{"issn":["1740-1526"],"eissn":["1740-1534"]},"date_published":"2022-08-01T00:00:00Z","type":"journal_article","article_type":"review","publisher":"Springer Nature","page":"478-490","quality_controlled":"1","title":"The physiology and genetics of bacterial responses to antibiotic combinations","intvolume":"        20","publication_status":"published","article_processing_charge":"No","department":[{"_id":"CaGu"}],"date_created":"2022-03-04T04:33:49Z","author":[{"id":"68E56E44-62B0-11EA-B963-444F3DDC885E","first_name":"Roderich","last_name":"Römhild","orcid":"0000-0001-9480-5261","full_name":"Römhild, Roderich"},{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","last_name":"Bollenbach","first_name":"Mark Tobias","full_name":"Bollenbach, Mark Tobias","orcid":"0000-0003-4398-476X"},{"last_name":"Andersson","first_name":"Dan I.","full_name":"Andersson, Dan I."}],"pmid":1,"_id":"10812","scopus_import":"1","volume":20,"acknowledgement":"The authors thank B. Kavčič and H. Schulenburg for constructive feedback on the manuscript.","abstract":[{"lang":"eng","text":"Several promising strategies based on combining or cycling different antibiotics have been proposed to increase efficacy and counteract resistance evolution, but we still lack a deep understanding of the physiological responses and genetic mechanisms that underlie antibiotic interactions and the clinical applicability of these strategies. In antibiotic-exposed bacteria, the combined effects of physiological stress responses and emerging resistance mutations (occurring at different time scales) generate complex and often unpredictable dynamics. In this Review, we present our current understanding of bacterial cell physiology and genetics of responses to antibiotics. We emphasize recently discovered mechanisms of synergistic and antagonistic drug interactions, hysteresis in temporal interactions between antibiotics that arise from microbial physiology and interactions between antibiotics and resistance mutations that can cause collateral sensitivity or cross-resistance. We discuss possible connections between the different phenomena and indicate relevant research directions. A better and more unified understanding of drug and genetic interactions is likely to advance antibiotic therapy."}],"doi":"10.1038/s41579-022-00700-5","day":"01","isi":1,"external_id":{"pmid":["35241807"],"isi":["000763891900001"]},"date_updated":"2023-08-02T14:41:44Z","year":"2022","citation":{"ieee":"R. Römhild, M. T. Bollenbach, and D. I. Andersson, “The physiology and genetics of bacterial responses to antibiotic combinations,” <i>Nature Reviews Microbiology</i>, vol. 20. Springer Nature, pp. 478–490, 2022.","chicago":"Römhild, Roderich, Mark Tobias Bollenbach, and Dan I. Andersson. “The Physiology and Genetics of Bacterial Responses to Antibiotic Combinations.” <i>Nature Reviews Microbiology</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41579-022-00700-5\">https://doi.org/10.1038/s41579-022-00700-5</a>.","ama":"Römhild R, Bollenbach MT, Andersson DI. The physiology and genetics of bacterial responses to antibiotic combinations. <i>Nature Reviews Microbiology</i>. 2022;20:478-490. doi:<a href=\"https://doi.org/10.1038/s41579-022-00700-5\">10.1038/s41579-022-00700-5</a>","apa":"Römhild, R., Bollenbach, M. T., &#38; Andersson, D. I. (2022). The physiology and genetics of bacterial responses to antibiotic combinations. <i>Nature Reviews Microbiology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41579-022-00700-5\">https://doi.org/10.1038/s41579-022-00700-5</a>","ista":"Römhild R, Bollenbach MT, Andersson DI. 2022. The physiology and genetics of bacterial responses to antibiotic combinations. Nature Reviews Microbiology. 20, 478–490.","short":"R. Römhild, M.T. Bollenbach, D.I. Andersson, Nature Reviews Microbiology 20 (2022) 478–490.","mla":"Römhild, Roderich, et al. “The Physiology and Genetics of Bacterial Responses to Antibiotic Combinations.” <i>Nature Reviews Microbiology</i>, vol. 20, Springer Nature, 2022, pp. 478–90, doi:<a href=\"https://doi.org/10.1038/s41579-022-00700-5\">10.1038/s41579-022-00700-5</a>."}},{"keyword":["Process Chemistry and Technology","Biochemistry","Bioengineering","Catalysis"],"language":[{"iso":"eng"}],"publication":"Nature Catalysis","month":"03","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","related_material":{"record":[{"status":"public","id":"9978","relation":"earlier_version"}]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.21203/rs.3.rs-750965/v1"}],"type":"journal_article","date_published":"2022-03-03T00:00:00Z","oa":1,"publication_identifier":{"issn":["2520-1158"]},"quality_controlled":"1","page":"193-201","article_type":"original","publisher":"Springer Nature","author":[{"full_name":"Cao, Deqing","last_name":"Cao","first_name":"Deqing"},{"first_name":"Xiaoxiao","last_name":"Shen","full_name":"Shen, Xiaoxiao"},{"first_name":"Aiping","last_name":"Wang","full_name":"Wang, Aiping"},{"last_name":"Yu","first_name":"Fengjiao","full_name":"Yu, Fengjiao"},{"first_name":"Yuping","last_name":"Wu","full_name":"Wu, Yuping"},{"first_name":"Siqi","last_name":"Shi","full_name":"Shi, Siqi"},{"first_name":"Stefan Alexander","last_name":"Freunberger","orcid":"0000-0003-2902-5319","full_name":"Freunberger, Stefan Alexander","id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425"},{"first_name":"Yuhui","last_name":"Chen","full_name":"Chen, Yuhui"}],"scopus_import":"1","_id":"10813","intvolume":"         5","title":"Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries","article_processing_charge":"No","department":[{"_id":"StFr"}],"date_created":"2022-03-04T07:50:10Z","publication_status":"published","volume":5,"acknowledgement":"This work was financially supported by the National Natural Science Foundation of China (grant nos. 51773092, 21975124, 11874254, 51802187 and U2030206). It was further supported by Fujian science & technology innovation laboratory for energy devices of China (21C-LAB), Key Research Project of Zhejiang Laboratory (grant no. 2021PE0AC02) and the Cultivation Program for the Excellent Doctoral Dissertation of Nanjing Tech University. S.A.F. is indebted to IST Austria for support.","external_id":{"isi":["000763879400001"]},"isi":1,"year":"2022","citation":{"chicago":"Cao, Deqing, Xiaoxiao Shen, Aiping Wang, Fengjiao Yu, Yuping Wu, Siqi Shi, Stefan Alexander Freunberger, and Yuhui Chen. “Threshold Potentials for Fast Kinetics during Mediated Redox Catalysis of Insulators in Li–O2 and Li–S Batteries.” <i>Nature Catalysis</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1038/s41929-022-00752-z\">https://doi.org/10.1038/s41929-022-00752-z</a>.","ieee":"D. Cao <i>et al.</i>, “Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries,” <i>Nature Catalysis</i>, vol. 5. Springer Nature, pp. 193–201, 2022.","ama":"Cao D, Shen X, Wang A, et al. Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries. <i>Nature Catalysis</i>. 2022;5:193-201. doi:<a href=\"https://doi.org/10.1038/s41929-022-00752-z\">10.1038/s41929-022-00752-z</a>","apa":"Cao, D., Shen, X., Wang, A., Yu, F., Wu, Y., Shi, S., … Chen, Y. (2022). Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries. <i>Nature Catalysis</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41929-022-00752-z\">https://doi.org/10.1038/s41929-022-00752-z</a>","ista":"Cao D, Shen X, Wang A, Yu F, Wu Y, Shi S, Freunberger SA, Chen Y. 2022. Threshold potentials for fast kinetics during mediated redox catalysis of insulators in Li–O2 and Li–S batteries. Nature Catalysis. 5, 193–201.","short":"D. Cao, X. Shen, A. Wang, F. Yu, Y. Wu, S. Shi, S.A. Freunberger, Y. Chen, Nature Catalysis 5 (2022) 193–201.","mla":"Cao, Deqing, et al. “Threshold Potentials for Fast Kinetics during Mediated Redox Catalysis of Insulators in Li–O2 and Li–S Batteries.” <i>Nature Catalysis</i>, vol. 5, Springer Nature, 2022, pp. 193–201, doi:<a href=\"https://doi.org/10.1038/s41929-022-00752-z\">10.1038/s41929-022-00752-z</a>."},"date_updated":"2023-10-17T13:06:28Z","abstract":[{"text":"Redox mediators could catalyse otherwise slow and energy-inefficient cycling of Li–S and Li–O2 batteries by shuttling electrons or holes between the electrode and the solid insulating storage materials. For mediators to work efficiently they need to oxidize the solid with fast kinetics but with the lowest possible overpotential. However, the dependence of kinetics and overpotential is unclear, which hinders informed improvement. Here, we find that when the redox potentials of mediators are tuned via, for example, Li+ concentration in the electrolyte, they exhibit distinct threshold potentials, where the kinetics accelerate several-fold within a range as small as 10 mV. This phenomenon is independent of types of mediator and electrolyte. The acceleration originates from the overpotentials required to activate fast Li+/e− extraction and the following chemical step at specific abundant surface facets. Efficient redox catalysis at insulating solids therefore requires careful consideration of the surface conditions of the storage materials and electrolyte-dependent redox potentials, which may be tuned by salt concentrations or solvents.","lang":"eng"}],"day":"03","doi":"10.1038/s41929-022-00752-z"},{"scopus_import":"1","license":"https://creativecommons.org/licenses/by-nc/4.0/","_id":"10818","pmid":1,"issue":"1","author":[{"id":"36035796-5ACA-11E9-A75E-7AF2E5697425","orcid":"0000-0003-1843-3173","full_name":"Basilico, Bernadette","first_name":"Bernadette","last_name":"Basilico"},{"full_name":"Ferrucci, Laura","last_name":"Ferrucci","first_name":"Laura"},{"full_name":"Ratano, Patrizia","first_name":"Patrizia","last_name":"Ratano"},{"last_name":"Golia","first_name":"Maria T.","full_name":"Golia, Maria T."},{"first_name":"Alfonso","last_name":"Grimaldi","full_name":"Grimaldi, Alfonso"},{"first_name":"Maria","last_name":"Rosito","full_name":"Rosito, Maria"},{"first_name":"Valentina","last_name":"Ferretti","full_name":"Ferretti, Valentina"},{"full_name":"Reverte, Ingrid","last_name":"Reverte","first_name":"Ingrid"},{"full_name":"Sanchini, Caterina","first_name":"Caterina","last_name":"Sanchini"},{"full_name":"Marrone, Maria C.","first_name":"Maria C.","last_name":"Marrone"},{"first_name":"Maria","last_name":"Giubettini","full_name":"Giubettini, Maria"},{"full_name":"De Turris, Valeria","first_name":"Valeria","last_name":"De Turris"},{"last_name":"Salerno","first_name":"Debora","full_name":"Salerno, Debora"},{"first_name":"Stefano","last_name":"Garofalo","full_name":"Garofalo, Stefano"},{"first_name":"Marie‐Kim","last_name":"St‐Pierre","full_name":"St‐Pierre, Marie‐Kim"},{"full_name":"Carrier, Micael","first_name":"Micael","last_name":"Carrier"},{"last_name":"Renzi","first_name":"Massimiliano","full_name":"Renzi, Massimiliano"},{"first_name":"Francesca","last_name":"Pagani","full_name":"Pagani, Francesca"},{"full_name":"Modi, Brijesh","first_name":"Brijesh","last_name":"Modi"},{"first_name":"Marcello","last_name":"Raspa","full_name":"Raspa, Marcello"},{"full_name":"Scavizzi, Ferdinando","first_name":"Ferdinando","last_name":"Scavizzi"},{"full_name":"Gross, Cornelius T.","first_name":"Cornelius T.","last_name":"Gross"},{"full_name":"Marinelli, Silvia","first_name":"Silvia","last_name":"Marinelli"},{"last_name":"Tremblay","first_name":"Marie‐Ève","full_name":"Tremblay, Marie‐Ève"},{"first_name":"Daniele","last_name":"Caprioli","full_name":"Caprioli, Daniele"},{"full_name":"Maggi, Laura","first_name":"Laura","last_name":"Maggi"},{"full_name":"Limatola, Cristina","first_name":"Cristina","last_name":"Limatola"},{"full_name":"Di Angelantonio, Silvia","last_name":"Di Angelantonio","first_name":"Silvia"},{"full_name":"Ragozzino, Davide","last_name":"Ragozzino","first_name":"Davide"}],"article_processing_charge":"No","date_created":"2022-03-04T08:53:37Z","department":[{"_id":"GaNo"}],"publication_status":"published","intvolume":"        70","title":"Microglia control glutamatergic synapses in the adult mouse hippocampus","quality_controlled":"1","page":"173-195","file_date_updated":"2022-03-04T08:55:27Z","publisher":"Wiley","article_type":"original","citation":{"ama":"Basilico B, Ferrucci L, Ratano P, et al. Microglia control glutamatergic synapses in the adult mouse hippocampus. <i>Glia</i>. 2022;70(1):173-195. doi:<a href=\"https://doi.org/10.1002/glia.24101\">10.1002/glia.24101</a>","apa":"Basilico, B., Ferrucci, L., Ratano, P., Golia, M. T., Grimaldi, A., Rosito, M., … Ragozzino, D. (2022). Microglia control glutamatergic synapses in the adult mouse hippocampus. <i>Glia</i>. Wiley. <a href=\"https://doi.org/10.1002/glia.24101\">https://doi.org/10.1002/glia.24101</a>","chicago":"Basilico, Bernadette, Laura Ferrucci, Patrizia Ratano, Maria T. Golia, Alfonso Grimaldi, Maria Rosito, Valentina Ferretti, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” <i>Glia</i>. Wiley, 2022. <a href=\"https://doi.org/10.1002/glia.24101\">https://doi.org/10.1002/glia.24101</a>.","ieee":"B. Basilico <i>et al.</i>, “Microglia control glutamatergic synapses in the adult mouse hippocampus,” <i>Glia</i>, vol. 70, no. 1. Wiley, pp. 173–195, 2022.","short":"B. Basilico, L. Ferrucci, P. Ratano, M.T. Golia, A. Grimaldi, M. Rosito, V. Ferretti, I. Reverte, C. Sanchini, M.C. Marrone, M. Giubettini, V. De Turris, D. Salerno, S. Garofalo, M. St‐Pierre, M. Carrier, M. Renzi, F. Pagani, B. Modi, M. Raspa, F. Scavizzi, C.T. Gross, S. Marinelli, M. Tremblay, D. Caprioli, L. Maggi, C. Limatola, S. Di Angelantonio, D. Ragozzino, Glia 70 (2022) 173–195.","mla":"Basilico, Bernadette, et al. “Microglia Control Glutamatergic Synapses in the Adult Mouse Hippocampus.” <i>Glia</i>, vol. 70, no. 1, Wiley, 2022, pp. 173–95, doi:<a href=\"https://doi.org/10.1002/glia.24101\">10.1002/glia.24101</a>.","ista":"Basilico B, Ferrucci L, Ratano P, Golia MT, Grimaldi A, Rosito M, Ferretti V, Reverte I, Sanchini C, Marrone MC, Giubettini M, De Turris V, Salerno D, Garofalo S, St‐Pierre M, Carrier M, Renzi M, Pagani F, Modi B, Raspa M, Scavizzi F, Gross CT, Marinelli S, Tremblay M, Caprioli D, Maggi L, Limatola C, Di Angelantonio S, Ragozzino D. 2022. Microglia control glutamatergic synapses in the adult mouse hippocampus. Glia. 70(1), 173–195."},"year":"2022","date_updated":"2023-09-05T16:01:23Z","external_id":{"pmid":["34661306"],"isi":["000708025800001"]},"isi":1,"day":"01","doi":"10.1002/glia.24101","abstract":[{"text":"Microglia cells are active players in regulating synaptic development and plasticity in the brain. However, how they influence the normal functioning of synapses is largely unknown. In this study, we characterized the effects of pharmacological microglia depletion, achieved by administration of PLX5622, on hippocampal CA3-CA1 synapses of adult wild type mice. Following microglial depletion, we observed a reduction of spontaneous and evoked glutamatergic activity associated with a decrease of dendritic spine density. We also observed the appearance of immature synaptic features and higher levels of plasticity. Microglia depleted mice showed a deficit in the acquisition of the Novel Object Recognition task. These events were accompanied by hippocampal astrogliosis, although in the absence ofneuroinflammatory condition. PLX-induced synaptic changes were absent in Cx3cr1−/− mice, highlighting the role of CX3CL1/CX3CR1 axis in microglia control of synaptic functioning. Remarkably, microglia repopulation after PLX5622 withdrawal was associated with the recovery of hippocampal synapses and learning functions. Altogether, these data demonstrate that microglia contribute to normal synaptic functioning in the adult brain and that their removal induces reversible changes in organization and activity of glutamatergic synapses.","lang":"eng"}],"volume":70,"acknowledgement":"The work was supported by a grant from MIUR (PRIN 2017HPTFFC_003) to Davide Ragozzino and in part by funds to Silvia Di Angelantonio (CrestOptics-IIT JointLab for Advanced Microscopy) and Daniele Caprioli (Istituto Pasteur-Fondazione Cenci Bolognetti). Bernadette Basilico, and Laura Ferrucci were supported by the PhD program in Clinical-Experimental Neuroscience and Psychiatry, Sapienza University, Rome; Caterina Sanchini was supported by the PhD program in Life Science, Sapienza University, Rome and by the Italian Institute of Technology, Rome. The authors thank Alessandro Felici, Claudia Valeri, Arsenio Armagno, and Senthilkumar Deivasigamani for help with animal husbandry and transgenic colonies management. They also wish to thank Piotr Bregestovski and Michal Schwartz for helpful discussions and criticism. PLX5622 was provided under Materials Transfer Agreement by Plexxikon Inc. (Berkeley, CA). Open Access Funding provided by Universita degli Studi di Roma La Sapienza within the CRUI-CARE Agreement.","ddc":["570"],"has_accepted_license":"1","publication":"Glia","oa_version":"Published Version","month":"01","keyword":["Cellular and Molecular Neuroscience","Neurology"],"language":[{"iso":"eng"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode"},"type":"journal_article","date_published":"2022-01-01T00:00:00Z","publication_identifier":{"issn":["0894-1491"],"eissn":["1098-1136"]},"oa":1,"file":[{"file_name":"2021_Glia_Basilico.pdf","content_type":"application/pdf","date_updated":"2022-03-04T08:55:27Z","checksum":"f10a897290e66c0a062e04ba91db6c17","file_size":5340294,"date_created":"2022-03-04T08:55:27Z","creator":"dernst","file_id":"10819","access_level":"open_access","success":1,"relation":"main_file"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","status":"public"},{"publication_identifier":{"eisbn":["9783030679026"],"eissn":["1875-3493"],"issn":["1875-3507"],"isbn":["9783030679019"]},"type":"book_chapter","date_published":"2022-01-01T00:00:00Z","place":"Cham","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"None","month":"01","publication":"IUTAM Laminar-Turbulent Transition","conference":{"location":"London, United Kingdom","end_date":"2019-09-06","name":"IUTAM Symposium","start_date":"2019-09-02"},"language":[{"iso":"eng"}],"day":"01","edition":"1","doi":"10.1007/978-3-030-67902-6_51","abstract":[{"lang":"eng","text":"Streaky structures in the boundary layers are often generated by surface roughness elements and/or free-stream turbulence, and are known to have significant effects on boundary-layer instability. In this paper, we investigate the impact of two forms of streaks on the instability of supersonic boundary layers. The first concerns the streaks generated by an array of spanwise periodic and streamwise elongated surface roughness elements, and our interest is how these streaks influence the lower-branch viscous first modes, whose characteristic wavelength and frequency are on the classical triple-deck scales. By adapting the triple-deck theory in the incompressible regime to the supersonic one, we first derived a simplified system which allows for efficient calculation of the streaks. The asymptotic analysis simplifies a bi-global eigenvalue problem to a one-dimensional problem in the spanwise direction, showing that the instability is controlled at leading order solely by the spanwise-dependent wall shear. In the fundamental configuration, the streaks stabilize first modes at low frequencies but destabilize the high-frequency ones. In the subharmonic configuration, the streaks generally destabilize the first mode across the entire frequency band. Importantly, the spanwise even modes are of radiating nature, i.e. they emit acoustic waves spontaneously to the far field. Streaks of the second form are generated by low-frequency vortical disturbances representing free-stream turbulence. They alter the flow in the entire layer and their effects on instability are investigated by solving the inviscid bi-global eigenvalue problem. Different from the incompressible case, a multitude of compressible instability modes exists, of which the dominant mode is an inviscid instability associated with the spanwise shear. In addition, there exists a separate branch of instability modes that have smaller growth rates but are spontaneously radiating."}],"year":"2022","citation":{"ista":"Liu J, Marensi E, Wu X. 2022.Effects of streaky structures on the instability of supersonic boundary layers. In: IUTAM Laminar-Turbulent Transition. vol. 38, 587–598.","mla":"Liu, Jianxin, et al. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” <i>IUTAM Laminar-Turbulent Transition</i>, edited by Spencer Sherwin et al., 1st ed., vol. 38, Springer Nature, 2022, pp. 587–98, doi:<a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">10.1007/978-3-030-67902-6_51</a>.","short":"J. Liu, E. Marensi, X. Wu, in:, S. Sherwin, P. Schmid, X. Wu (Eds.), IUTAM Laminar-Turbulent Transition, 1st ed., Springer Nature, Cham, 2022, pp. 587–598.","ieee":"J. Liu, E. Marensi, and X. Wu, “Effects of streaky structures on the instability of supersonic boundary layers,” in <i>IUTAM Laminar-Turbulent Transition</i>, 1st ed., vol. 38, S. Sherwin, P. Schmid, and X. Wu, Eds. Cham: Springer Nature, 2022, pp. 587–598.","chicago":"Liu, Jianxin, Elena Marensi, and Xuesong Wu. “Effects of Streaky Structures on the Instability of Supersonic Boundary Layers.” In <i>IUTAM Laminar-Turbulent Transition</i>, edited by Spencer Sherwin, Peter Schmid, and Xuesong Wu, 1st ed., 38:587–98. IUTAM Bookseries. Cham: Springer Nature, 2022. <a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">https://doi.org/10.1007/978-3-030-67902-6_51</a>.","ama":"Liu J, Marensi E, Wu X. Effects of streaky structures on the instability of supersonic boundary layers. In: Sherwin S, Schmid P, Wu X, eds. <i>IUTAM Laminar-Turbulent Transition</i>. Vol 38. 1st ed. IUTAM Bookseries. Cham: Springer Nature; 2022:587-598. doi:<a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">10.1007/978-3-030-67902-6_51</a>","apa":"Liu, J., Marensi, E., &#38; Wu, X. (2022). Effects of streaky structures on the instability of supersonic boundary layers. In S. Sherwin, P. Schmid, &#38; X. Wu (Eds.), <i>IUTAM Laminar-Turbulent Transition</i> (1st ed., Vol. 38, pp. 587–598). Cham: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-67902-6_51\">https://doi.org/10.1007/978-3-030-67902-6_51</a>"},"date_updated":"2023-08-03T12:54:59Z","external_id":{"isi":["000709087600051"]},"isi":1,"volume":38,"acknowledgement":"The work is supported by the National Key Research and Development Program of China (No. 2016YFA0401200), the National Natural Science Foundation of China (Grant Nos. 91952202 and 11402167).","article_processing_charge":"No","department":[{"_id":"BjHo"}],"date_created":"2022-03-04T09:14:34Z","publication_status":"published","intvolume":"        38","title":"Effects of streaky structures on the instability of supersonic boundary layers","scopus_import":"1","_id":"10820","author":[{"last_name":"Liu","first_name":"Jianxin","full_name":"Liu, Jianxin"},{"first_name":"Elena","last_name":"Marensi","full_name":"Marensi, Elena","id":"0BE7553A-1004-11EA-B805-18983DDC885E"},{"full_name":"Wu, Xuesong","last_name":"Wu","first_name":"Xuesong"}],"editor":[{"full_name":"Sherwin, Spencer","last_name":"Sherwin","first_name":"Spencer"},{"first_name":"Peter","last_name":"Schmid","full_name":"Schmid, Peter"},{"full_name":"Wu, Xuesong","last_name":"Wu","first_name":"Xuesong"}],"publisher":"Springer Nature","series_title":"IUTAM Bookseries","quality_controlled":"1","page":"587-598"},{"project":[{"grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"date_created":"2022-03-04T22:20:59Z","article_processing_charge":"No","department":[{"_id":"GaTk"}],"publication_status":"published","oa_version":"Preprint","month":"03","title":"Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades","publication":"bioRxiv","_id":"10821","author":[{"id":"A057D288-3E88-11E9-986D-0CF4E5697425","first_name":"Fabrizio","last_name":"Lombardi","orcid":"0000-0003-2623-5249","full_name":"Lombardi, Fabrizio"},{"first_name":"Hans J.","last_name":"Herrmann","full_name":"Herrmann, Hans J."},{"full_name":"Parrino, Liborio","last_name":"Parrino","first_name":"Liborio"},{"first_name":"Dietmar","last_name":"Plenz","full_name":"Plenz, Dietmar"},{"last_name":"Scarpetta","first_name":"Silvia","full_name":"Scarpetta, Silvia"},{"full_name":"Vaudano, Anna Elisabetta","first_name":"Anna Elisabetta","last_name":"Vaudano"},{"first_name":"Lucilla","last_name":"de Arcangelis","full_name":"de Arcangelis, Lucilla"},{"first_name":"Oren","last_name":"Shriki","full_name":"Shriki, Oren"}],"publisher":"Cold Spring Harbor Laboratory","ec_funded":1,"page":"25","language":[{"iso":"eng"}],"day":"04","doi":"10.1101/2022.03.03.482657","oa":1,"abstract":[{"text":"Rhythmical cortical activity has long been recognized as a pillar in the architecture of brain functions. Yet, the dynamic organization of its underlying neuronal population activity remains elusive. Here we uncover a unique organizational principle regulating collective neural dynamics associated with the alpha rhythm in the awake resting-state. We demonstrate that cascades of neural activity obey attenuation-amplification dynamics (AAD), with a transition from the attenuation regime—within alpha cycles—to the amplification regime—across a few alpha cycles—that correlates with the characteristic frequency of the alpha rhythm. We find that this short-term AAD is part of a large-scale, size-dependent temporal structure of neural cascades that obeys the Omori law: Following large cascades, smaller cascades occur at a rate that decays as a power-law of the time elapsed from such events—a long-term AAD regulating brain activity over the timescale of seconds. We show that such an organization corresponds to the \"waxing and waning\" of the alpha rhythm. Importantly, we observe that short- and long-term AAD are unique to the awake resting-state, being absent during NREM sleep. These results provide a quantitative, dynamical description of the so-far-qualitative notion of the \"waxing and waning\" phenomenon, and suggest the AAD as a key principle governing resting-state dynamics across timescales.","lang":"eng"}],"year":"2022","citation":{"ista":"Lombardi F, Herrmann HJ, Parrino L, Plenz D, Scarpetta S, Vaudano AE, de Arcangelis L, Shriki O. 2022. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. bioRxiv, <a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>.","mla":"Lombardi, Fabrizio, et al. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2022, doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>.","short":"F. Lombardi, H.J. Herrmann, L. Parrino, D. Plenz, S. Scarpetta, A.E. Vaudano, L. de Arcangelis, O. Shriki, BioRxiv (2022).","ieee":"F. Lombardi <i>et al.</i>, “Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2022.","chicago":"Lombardi, Fabrizio, Hans J. Herrmann, Liborio Parrino, Dietmar Plenz, Silvia Scarpetta, Anna Elisabetta Vaudano, Lucilla de Arcangelis, and Oren Shriki. “Alpha Rhythm Induces Attenuation-Amplification Dynamics in Neural Activity Cascades.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2022. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>.","ama":"Lombardi F, Herrmann HJ, Parrino L, et al. Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. 2022. doi:<a href=\"https://doi.org/10.1101/2022.03.03.482657\">10.1101/2022.03.03.482657</a>","apa":"Lombardi, F., Herrmann, H. J., Parrino, L., Plenz, D., Scarpetta, S., Vaudano, A. E., … Shriki, O. (2022). Alpha rhythm induces attenuation-amplification dynamics in neural activity cascades. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2022.03.03.482657\">https://doi.org/10.1101/2022.03.03.482657</a>"},"date_updated":"2022-03-07T07:28:34Z","type":"preprint","date_published":"2022-03-04T00:00:00Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2022.03.03.482657"}],"acknowledgement":"FL acknowledges support from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411. LdA acknowledges the Italian MIUR project PRIN2017WZFTZP for financial support and the project E-PASSION of the program VALERE 2019 funded by the University of Campania, Italy “L. Vanvitelli”. OS acknowledges support from the Israel Science Foundation, Grant No. 504/17. Supported in part by DIRP ZIAMH02797 to DP.","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public"},{"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"access_level":"open_access","success":1,"relation":"main_file","creator":"dernst","file_id":"10831","checksum":"ae305060e8031297771b89dae9e36a29","file_size":8478995,"date_created":"2022-03-07T07:55:23Z","file_name":"2022_Cell_Yanagida.pdf","content_type":"application/pdf","date_updated":"2022-03-07T07:55:23Z"}],"date_published":"2022-02-22T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"language":[{"iso":"eng"}],"publication":"Cell","has_accepted_license":"1","month":"02","oa_version":"Published Version","project":[{"name":"Design Principles of Branching Morphogenesis","grant_number":"851288","_id":"05943252-7A3F-11EA-A408-12923DDC885E","call_identifier":"H2020"}],"ddc":["570"],"acknowledgement":"We are grateful to H. Niwa for Dox regulatable PB vector; G. Charras for EzrinT567D cDNA; K. Jones for tdTomato ESCs, R26-Confetti ESCs, and laboratory assistance; M. Kinoshita for pPB-CAG-H2B-BFP plasmid; P. Humphreys and D. Clements for imaging support; G. Chu, P. Attlesey, and staff for animal husbandry; S. Pallett for laboratory assistance; C. Mulas for critical feedback on the project; T. Boroviak for single-cell RNA-seq; the EMBL Genomics Core Facility for sequencing; and M. Merkel for developing and sharing the original version of the 3D Voronoi code. This work was financially supported by BBSRC ( BB/Moo4023/1 and BB/T007044/1 to K.J.C. and J.N., Alert16 grant BB/R000042 to E.K.P.), Leverhulme Trust ( RPG-2014-080 to K.J.C. and J.N.), European Research Council ( 772798 -CellFateTech to K.J.C., 311637 -MorphoCorDiv and 820188 -NanoMechShape to E.K.P., Starting Grant 851288 to E.H., and 772426 -MeChemGui to K.F.), the Isaac Newton Trust (to E.K.P.), Medical Research Council UK (MRC program award MC_UU_00012/5 to E.K.P.), the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 641639 ( ITN Biopol , H.D.B. and E.K.P.), the Alexander von Humboldt Foundation (Alexander von Humboldt Professorship to K.F.), EMBO ALTF 522-2021 (to P.S.), Centre for Trophoblast Research (Next Generation fellowship to S.A.), and JSPS Overseas Research Fellowships (to A.Y.). The Wellcome-MRC Cambridge Stem Cell Institute receives core funding from Wellcome Trust ( 203151/Z/16/Z ) and MRC ( MC_PC_17230 ). For the purpose of open access, the author has applied a CC BY public copyright licence to any Author Accepted Manuscript version arising from this submission.","volume":185,"isi":1,"external_id":{"pmid":["35196500"],"isi":["000796293700007"]},"date_updated":"2023-08-02T14:43:50Z","citation":{"chicago":"Yanagida, Ayaka, Elena Corujo-Simon, Christopher K. Revell, Preeti Sahu, Giuliano G. Stirparo, Irene M. Aspalter, Alex K. Winkel, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” <i>Cell</i>. Cell Press, 2022. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>.","ieee":"A. Yanagida <i>et al.</i>, “Cell surface fluctuations regulate early embryonic lineage sorting,” <i>Cell</i>, vol. 185, no. 5. Cell Press, p. 777–793.e20, 2022.","apa":"Yanagida, A., Corujo-Simon, E., Revell, C. K., Sahu, P., Stirparo, G. G., Aspalter, I. M., … Chalut, K. J. (2022). Cell surface fluctuations regulate early embryonic lineage sorting. <i>Cell</i>. Cell Press. <a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">https://doi.org/10.1016/j.cell.2022.01.022</a>","ama":"Yanagida A, Corujo-Simon E, Revell CK, et al. Cell surface fluctuations regulate early embryonic lineage sorting. <i>Cell</i>. 2022;185(5):777-793.e20. doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>","ista":"Yanagida A, Corujo-Simon E, Revell CK, Sahu P, Stirparo GG, Aspalter IM, Winkel AK, Peters R, De Belly H, Cassani DAD, Achouri S, Blumenfeld R, Franze K, Hannezo EB, Paluch EK, Nichols J, Chalut KJ. 2022. Cell surface fluctuations regulate early embryonic lineage sorting. Cell. 185(5), 777–793.e20.","mla":"Yanagida, Ayaka, et al. “Cell Surface Fluctuations Regulate Early Embryonic Lineage Sorting.” <i>Cell</i>, vol. 185, no. 5, Cell Press, 2022, p. 777–793.e20, doi:<a href=\"https://doi.org/10.1016/j.cell.2022.01.022\">10.1016/j.cell.2022.01.022</a>.","short":"A. Yanagida, E. Corujo-Simon, C.K. Revell, P. Sahu, G.G. Stirparo, I.M. Aspalter, A.K. Winkel, R. Peters, H. De Belly, D.A.D. Cassani, S. Achouri, R. Blumenfeld, K. Franze, E.B. Hannezo, E.K. Paluch, J. Nichols, K.J. Chalut, Cell 185 (2022) 777–793.e20."},"year":"2022","abstract":[{"lang":"eng","text":"In development, lineage segregation is coordinated in time and space. An important example is the mammalian inner cell mass, in which the primitive endoderm (PrE, founder of the yolk sac) physically segregates from the epiblast (EPI, founder of the fetus). While the molecular requirements have been well studied, the physical mechanisms determining spatial segregation between EPI and PrE remain elusive. Here, we investigate the mechanical basis of EPI and PrE sorting. We find that rather than the differences in static cell surface mechanical parameters as in classical sorting models, it is the differences in surface fluctuations that robustly ensure physical lineage sorting. These differential surface fluctuations systematically correlate with differential cellular fluidity, which we propose together constitute a non-equilibrium sorting mechanism for EPI and PrE lineages. By combining experiments and modeling, we identify cell surface dynamics as a key factor orchestrating the correct spatial segregation of the founder embryonic lineages."}],"doi":"10.1016/j.cell.2022.01.022","day":"22","file_date_updated":"2022-03-07T07:55:23Z","page":"777-793.e20","ec_funded":1,"quality_controlled":"1","article_type":"original","publisher":"Cell Press","author":[{"first_name":"Ayaka","last_name":"Yanagida","full_name":"Yanagida, Ayaka"},{"full_name":"Corujo-Simon, Elena","first_name":"Elena","last_name":"Corujo-Simon"},{"first_name":"Christopher K.","last_name":"Revell","full_name":"Revell, Christopher K."},{"id":"55BA52EE-A185-11EA-88FD-18AD3DDC885E","full_name":"Sahu, Preeti","last_name":"Sahu","first_name":"Preeti"},{"last_name":"Stirparo","first_name":"Giuliano G.","full_name":"Stirparo, Giuliano G."},{"last_name":"Aspalter","first_name":"Irene M.","full_name":"Aspalter, Irene M."},{"full_name":"Winkel, Alex K.","last_name":"Winkel","first_name":"Alex K."},{"last_name":"Peters","first_name":"Ruby","full_name":"Peters, Ruby"},{"full_name":"De Belly, Henry","last_name":"De Belly","first_name":"Henry"},{"full_name":"Cassani, Davide A.D.","first_name":"Davide A.D.","last_name":"Cassani"},{"full_name":"Achouri, Sarra","first_name":"Sarra","last_name":"Achouri"},{"full_name":"Blumenfeld, Raphael","last_name":"Blumenfeld","first_name":"Raphael"},{"last_name":"Franze","first_name":"Kristian","full_name":"Franze, Kristian"},{"id":"3A9DB764-F248-11E8-B48F-1D18A9856A87","full_name":"Hannezo, Edouard B","orcid":"0000-0001-6005-1561","last_name":"Hannezo","first_name":"Edouard B"},{"full_name":"Paluch, Ewa K.","first_name":"Ewa K.","last_name":"Paluch"},{"full_name":"Nichols, Jennifer","first_name":"Jennifer","last_name":"Nichols"},{"full_name":"Chalut, Kevin J.","first_name":"Kevin J.","last_name":"Chalut"}],"issue":"5","_id":"10825","pmid":1,"scopus_import":"1","title":"Cell surface fluctuations regulate early embryonic lineage sorting","intvolume":"       185","publication_status":"published","date_created":"2022-03-06T23:01:52Z","department":[{"_id":"EdHa"}],"article_processing_charge":"No"},{"language":[{"iso":"eng"}],"month":"02","article_number":"e68040","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"ScienComp"}],"oa_version":"Published Version","project":[{"grant_number":"209504/A/17/Z","name":"Molecular mechanisms of neural circuit function","_id":"23870BE8-32DE-11EA-91FC-C7463DDC885E"}],"publication":"eLife","has_accepted_license":"1","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","file":[{"file_id":"10830","creator":"dernst","relation":"main_file","access_level":"open_access","success":1,"date_updated":"2022-03-07T07:39:25Z","content_type":"application/pdf","file_name":"2022_eLife_Valperga.pdf","date_created":"2022-03-07T07:39:25Z","file_size":4095591,"checksum":"cc1b9bf866d0f61f965556e0dd03d3ac"}],"oa":1,"publication_identifier":{"eissn":["2050084X"]},"date_published":"2022-02-24T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","publisher":"eLife Sciences Publications","file_date_updated":"2022-03-07T07:39:25Z","quality_controlled":"1","title":"Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans","intvolume":"        11","publication_status":"published","date_created":"2022-03-06T23:01:52Z","department":[{"_id":"MaDe"}],"article_processing_charge":"No","author":[{"first_name":"Giulio","last_name":"Valperga","full_name":"Valperga, Giulio","id":"67F289DE-0D8F-11EA-9BDD-54AE3DDC885E"},{"id":"4E3FF80E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8347-0443","full_name":"De Bono, Mario","first_name":"Mario","last_name":"De Bono"}],"pmid":1,"_id":"10826","scopus_import":"1","ddc":["570"],"acknowledgement":"We would like to thank Gemma Chandratillake and Merav Cohen for identifying mutants and José David Moñino Sánchez for his help on neurosecretion assays. We are grateful to Kaveh Ashrafi (UCSF), Piali Sengupta (Brandeis), and the Caenorhabditis Genetic Center (funded by National Institutes of Health Infrastructure Program P40 OD010440) for strains and reagents ... and Rebecca Butcher (Univ. Florida) for C9 pheromone. We thank Tim Stevens, Paula Freire-Pritchett, Alastair Crisp, GurpreetGhattaoraya, and Fabian Amman for help with bioinformatic analysis, Ekaterina Lashmanova for help with injections, Iris Hardege for strains, and Isabel Beets (KU Leuven) and members of the de Bono Lab for comments on the manuscript. We thank the CRUK Cambridge Research Institute Genomics Core for next generation sequencing and the Flow Cytometry Facility at LMB for FACS. This research was supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Bioimaging Facility (BIF), the Life Science Facility (LSF) and Scientific Computing (SciCo-p– Bioinformatics).\r\nThis work was supported by the Medical Research Council UK (Studentship to GV), an\r\nAdvanced ERC grant (269,058 ACMO to MdB), and a Wellcome Investigator Award (209504/Z/17/Z to MdB).","volume":11,"abstract":[{"text":"Animals that lose one sensory modality often show augmented responses to other sensory inputs. The mechanisms underpinning this cross-modal plasticity are poorly understood. We probe such mechanisms by performing a forward genetic screen for mutants with enhanced O2 perception in Caenorhabditis elegans. Multiple mutants exhibiting increased O2 responsiveness concomitantly show defects in other sensory responses. One mutant, qui-1, defective in a conserved NACHT/WD40 protein, abolishes pheromone-evoked Ca2+ responses in the ADL pheromone-sensing neurons. At the same time, ADL responsiveness to pre-synaptic input from O2-sensing neurons is heightened in qui-1, and other sensory defective mutants, resulting in enhanced neurosecretion although not increased Ca2+ responses. Expressing qui-1 selectively in ADL rescues both the qui-1 ADL neurosecretory phenotype and enhanced escape from 21% O2. Profiling ADL neurons in qui-1 mutants highlights extensive changes in gene expression, notably of many neuropeptide receptors. We show that elevated ADL expression of the conserved neuropeptide receptor NPR-22 is necessary for enhanced ADL neurosecretion in qui-1 mutants, and is sufficient to confer increased ADL neurosecretion in control animals. Sensory loss can thus confer cross-modal plasticity by changing the peptidergic connectome.","lang":"eng"}],"doi":"10.7554/eLife.68040","day":"24","isi":1,"external_id":{"isi":["000763432300001"],"pmid":["35201977"]},"date_updated":"2023-08-02T14:42:55Z","citation":{"ista":"Valperga G, de Bono M. 2022. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. eLife. 11, e68040.","short":"G. Valperga, M. de Bono, ELife 11 (2022).","mla":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>, vol. 11, e68040, eLife Sciences Publications, 2022, doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>.","ieee":"G. Valperga and M. de Bono, “Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans,” <i>eLife</i>, vol. 11. eLife Sciences Publications, 2022.","chicago":"Valperga, Giulio, and Mario de Bono. “Impairing One Sensory Modality Enhances Another by Reconfiguring Peptidergic Signalling in Caenorhabditis Elegans.” <i>ELife</i>. eLife Sciences Publications, 2022. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>.","ama":"Valperga G, de Bono M. Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>eLife</i>. 2022;11. doi:<a href=\"https://doi.org/10.7554/eLife.68040\">10.7554/eLife.68040</a>","apa":"Valperga, G., &#38; de Bono, M. (2022). Impairing one sensory modality enhances another by reconfiguring peptidergic signalling in Caenorhabditis elegans. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.68040\">https://doi.org/10.7554/eLife.68040</a>"},"year":"2022"},{"volume":156,"acknowledgement":"J.G.L. and B.C. acknowledge the resources provided by the Cambridge Tier-2 system operated by the University of Cambridge Research Computing Service funded by the EPSRC Tier-2 capital (Grant No. EP/P020259/1).","external_id":{"isi":["000796704500014"],"arxiv":["2111.12968"]},"isi":1,"year":"2022","citation":{"ieee":"J. G. Lee, C. J. Pickard, and B. Cheng, “High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential,” <i>The Journal of chemical physics</i>, vol. 156, no. 7. AIP Publishing, 2022.","chicago":"Lee, Jacob G., Chris J. Pickard, and Bingqing Cheng. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>. AIP Publishing, 2022. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>.","apa":"Lee, J. G., Pickard, C. J., &#38; Cheng, B. (2022). High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of Chemical Physics</i>. AIP Publishing. <a href=\"https://doi.org/10.1063/5.0079844\">https://doi.org/10.1063/5.0079844</a>","ama":"Lee JG, Pickard CJ, Cheng B. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. <i>The Journal of chemical physics</i>. 2022;156(7). doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>","ista":"Lee JG, Pickard CJ, Cheng B. 2022. High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential. The Journal of chemical physics. 156(7), 074106.","short":"J.G. Lee, C.J. Pickard, B. Cheng, The Journal of Chemical Physics 156 (2022).","mla":"Lee, Jacob G., et al. “High-Pressure Phase Behaviors of Titanium Dioxide Revealed by a Δ-Learning Potential.” <i>The Journal of Chemical Physics</i>, vol. 156, no. 7, 074106, AIP Publishing, 2022, doi:<a href=\"https://doi.org/10.1063/5.0079844\">10.1063/5.0079844</a>."},"date_updated":"2023-08-02T14:45:46Z","abstract":[{"lang":"eng","text":"Titanium dioxide has been extensively studied in the rutile or anatase phase, while its high-pressure phases are less well-understood, despite that many are thought to have interesting optical, mechanical, and electrochemical properties. First-principles methods, such as density functional theory (DFT), are often used to compute the enthalpies of TiO2 phases at 0 K, but they are expensive and, thus, impractical for long time scale and large system-size simulations at finite temperatures. On the other hand, cheap empirical potentials fail to capture the relative stabilities of various polymorphs. To model the thermodynamic behaviors of ambient and high-pressure phases of TiO2, we design an empirical model as a baseline and then train a machine learning potential based on the difference between the DFT data and the empirical model. This so-called Δ-learning potential contains long-range electrostatic interactions and predicts the 0 K enthalpies of stable TiO2 phases that are in good agreement with DFT. We construct a pressure–temperature phase diagram of TiO2 in the range 0 < P < 70 GPa and 100 < T < 1500 K. We then simulate dynamic phase transition processes by compressing anatase at different temperatures. At 300 K, we predominantly observe an anatase-to-baddeleyite transformation at about 20 GPa via a martensitic two-step mechanism with a highly ordered and collective atomic motion. At 2000 K, anatase can transform into cotunnite around 45–55 GPa in a thermally activated and probabilistic manner, accompanied by diffusive movement of oxygen atoms. The pressures computed for these transitions show good agreement with experiments. Our results shed light on how to synthesize and stabilize high-pressure TiO2 phases, and our method is generally applicable to other functional materials with multiple polymorphs."}],"day":"16","arxiv":1,"doi":"10.1063/5.0079844","quality_controlled":"1","article_type":"original","publisher":"AIP Publishing","issue":"7","author":[{"first_name":"Jacob G.","last_name":"Lee","full_name":"Lee, Jacob G."},{"first_name":"Chris J.","last_name":"Pickard","full_name":"Pickard, Chris J."},{"id":"cbe3cda4-d82c-11eb-8dc7-8ff94289fcc9","first_name":"Bingqing","last_name":"Cheng","orcid":"0000-0002-3584-9632","full_name":"Cheng, Bingqing"}],"scopus_import":"1","_id":"10827","intvolume":"       156","title":"High-pressure phase behaviors of titanium dioxide revealed by a Δ-learning potential","article_processing_charge":"No","date_created":"2022-03-06T23:01:53Z","department":[{"_id":"BiCh"}],"publication_status":"published","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://arxiv.org/abs/2111.12968","open_access":"1"}],"type":"journal_article","date_published":"2022-02-16T00:00:00Z","oa":1,"publication_identifier":{"eissn":["10897690"]},"language":[{"iso":"eng"}],"publication":"The Journal of chemical physics","article_number":"074106","month":"02","oa_version":"Preprint"},{"type":"conference","date_published":"2022-01-13T00:00:00Z","oa":1,"publication_identifier":{"isbn":["9781665439022"]},"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","main_file_link":[{"url":"https://arxiv.org/abs/2111.05663","open_access":"1"}],"publication":"2021 IEEE International Conference on Big Data","month":"01","oa_version":"Preprint","language":[{"iso":"eng"}],"conference":{"end_date":"2021-12-18","location":"Orlando, FL, United States; Virtuell","name":"Big Data: International Conference on Big Data","start_date":"2021-12-15"},"external_id":{"isi":["000800559503126"],"arxiv":["2111.05663"]},"isi":1,"citation":{"chicago":"Heiss, Teresa, Sarah Tymochko, Brittany Story, Adélie Garin, Hoa Bui, Bea Bleile, and Vanessa Robins. “The Impact of Changes in Resolution on the Persistent Homology of Images.” In <i>2021 IEEE International Conference on Big Data</i>, 3824–34. IEEE, 2022. <a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">https://doi.org/10.1109/BigData52589.2021.9671483</a>.","ieee":"T. Heiss <i>et al.</i>, “The impact of changes in resolution on the persistent homology of images,” in <i>2021 IEEE International Conference on Big Data</i>, Orlando, FL, United States; Virtuell, 2022, pp. 3824–3834.","apa":"Heiss, T., Tymochko, S., Story, B., Garin, A., Bui, H., Bleile, B., &#38; Robins, V. (2022). The impact of changes in resolution on the persistent homology of images. In <i>2021 IEEE International Conference on Big Data</i> (pp. 3824–3834). Orlando, FL, United States; Virtuell: IEEE. <a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">https://doi.org/10.1109/BigData52589.2021.9671483</a>","ama":"Heiss T, Tymochko S, Story B, et al. The impact of changes in resolution on the persistent homology of images. In: <i>2021 IEEE International Conference on Big Data</i>. IEEE; 2022:3824-3834. doi:<a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">10.1109/BigData52589.2021.9671483</a>","ista":"Heiss T, Tymochko S, Story B, Garin A, Bui H, Bleile B, Robins V. 2022. The impact of changes in resolution on the persistent homology of images. 2021 IEEE International Conference on Big Data. Big Data: International Conference on Big Data, 3824–3834.","short":"T. Heiss, S. Tymochko, B. Story, A. Garin, H. Bui, B. Bleile, V. Robins, in:, 2021 IEEE International Conference on Big Data, IEEE, 2022, pp. 3824–3834.","mla":"Heiss, Teresa, et al. “The Impact of Changes in Resolution on the Persistent Homology of Images.” <i>2021 IEEE International Conference on Big Data</i>, IEEE, 2022, pp. 3824–34, doi:<a href=\"https://doi.org/10.1109/BigData52589.2021.9671483\">10.1109/BigData52589.2021.9671483</a>."},"year":"2022","date_updated":"2023-08-02T14:44:21Z","abstract":[{"lang":"eng","text":"Digital images enable quantitative analysis of material properties at micro and macro length scales, but choosing an appropriate resolution when acquiring the image is challenging. A high resolution means longer image acquisition and larger data requirements for a given sample, but if the resolution is too low, significant information may be lost. This paper studies the impact of changes in resolution on persistent homology, a tool from topological data analysis that provides a signature of structure in an image across all length scales. Given prior information about a function, the geometry of an object, or its density distribution at a given resolution, we provide methods to select the coarsest resolution yielding results within an acceptable tolerance. We present numerical case studies for an illustrative synthetic example and samples from porous materials where the theoretical bounds are unknown."}],"day":"13","arxiv":1,"doi":"10.1109/BigData52589.2021.9671483","author":[{"id":"4879BB4E-F248-11E8-B48F-1D18A9856A87","first_name":"Teresa","last_name":"Heiss","orcid":"0000-0002-1780-2689","full_name":"Heiss, Teresa"},{"last_name":"Tymochko","first_name":"Sarah","full_name":"Tymochko, Sarah"},{"first_name":"Brittany","last_name":"Story","full_name":"Story, Brittany"},{"last_name":"Garin","first_name":"Adélie","full_name":"Garin, Adélie"},{"full_name":"Bui, Hoa","last_name":"Bui","first_name":"Hoa"},{"first_name":"Bea","last_name":"Bleile","full_name":"Bleile, Bea"},{"full_name":"Robins, Vanessa","first_name":"Vanessa","last_name":"Robins"}],"scopus_import":"1","_id":"10828","title":"The impact of changes in resolution on the persistent homology of images","date_created":"2022-03-06T23:01:53Z","article_processing_charge":"No","department":[{"_id":"HeEd"}],"publication_status":"published","quality_controlled":"1","page":"3824-3834","publisher":"IEEE"},{"article_type":"original","publisher":"American Chemical Society","file_date_updated":"2022-03-07T08:15:01Z","page":"504-512","quality_controlled":"1","title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","intvolume":"         7","publication_status":"published","article_processing_charge":"No","department":[{"_id":"MaIb"}],"date_created":"2022-03-06T23:01:54Z","author":[{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"full_name":"Reiner-Rozman, Ciril","first_name":"Ciril","last_name":"Reiner-Rozman"},{"full_name":"Fossati, Stefan","last_name":"Fossati","first_name":"Stefan"},{"full_name":"Aspermair, Patrik","last_name":"Aspermair","first_name":"Patrik"},{"full_name":"Dostalek, Jakub","first_name":"Jakub","last_name":"Dostalek"},{"id":"BB243B88-D767-11E9-B658-BC13E6697425","full_name":"Lee, Seungho","orcid":"0000-0002-6962-8598","last_name":"Lee","first_name":"Seungho"},{"full_name":"Ibáñez, Maria","orcid":"0000-0001-5013-2843","last_name":"Ibáñez","first_name":"Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bintinger","first_name":"Johannes","full_name":"Bintinger, Johannes"},{"full_name":"Knoll, Wolfgang","first_name":"Wolfgang","last_name":"Knoll"}],"issue":"2","_id":"10829","scopus_import":"1","ddc":["540"],"volume":7,"acknowledgement":"This project has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under the Marie Skłodowska-Curie grant agreement No. 813863-\r\nBORGES. Additionally, we gratefully acknowledge the financial support from the Austrian Research Promotion Agency (FFG; 870025 and 873541) for this research. The data that support the findings of this study are openly available in Zenodo (DOI: 10.5281/zenodo.5500360)","abstract":[{"lang":"eng","text":"A novel multivariable system, combining a transistor with fiber optic-based surface plasmon resonance spectroscopy with the gate electrode simultaneously acting as the fiber optic sensor surface, is reported. The dual-mode sensor allows for discrimination of mass and charge contributions for binding assays on the same sensor surface. Furthermore, we optimize the sensor geometry by investigating the influence of the fiber area to transistor channel area ratio and distance. We show that larger fiber optic tip diameters are favorable for electronic and optical signals and demonstrate the reversibility of plasmon resonance wavelength shifts after electric field application. As a proof of principle, a layer-by-layer assembly of polyelectrolytes is performed to benchmark the system against multivariable sensing platforms with planar surface plasmon resonance configurations. Furthermore, the biosensing performance is assessed using a thrombin binding assay with surface-immobilized aptamers as receptors, allowing for the detection of medically relevant thrombin concentrations."}],"doi":"10.1021/acssensors.1c02313","day":"08","isi":1,"external_id":{"isi":["000765113000016"]},"date_updated":"2023-08-02T14:46:17Z","year":"2022","citation":{"short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, ACS Sensors 7 (2022) 504–512.","mla":"Hasler, Roger, et al. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” <i>ACS Sensors</i>, vol. 7, no. 2, American Chemical Society, 2022, pp. 504–12, doi:<a href=\"https://doi.org/10.1021/acssensors.1c02313\">10.1021/acssensors.1c02313</a>.","ista":"Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. ACS Sensors. 7(2), 504–512.","apa":"Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. <i>ACS Sensors</i>. American Chemical Society. <a href=\"https://doi.org/10.1021/acssensors.1c02313\">https://doi.org/10.1021/acssensors.1c02313</a>","ama":"Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. <i>ACS Sensors</i>. 2022;7(2):504-512. doi:<a href=\"https://doi.org/10.1021/acssensors.1c02313\">10.1021/acssensors.1c02313</a>","ieee":"R. Hasler <i>et al.</i>, “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device,” <i>ACS Sensors</i>, vol. 7, no. 2. American Chemical Society, pp. 504–512, 2022.","chicago":"Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” <i>ACS Sensors</i>. American Chemical Society, 2022. <a href=\"https://doi.org/10.1021/acssensors.1c02313\">https://doi.org/10.1021/acssensors.1c02313</a>."},"language":[{"iso":"eng"}],"month":"02","oa_version":"Published Version","publication":"ACS Sensors","has_accepted_license":"1","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"record":[{"status":"public","id":"10833","relation":"research_data"}]},"file":[{"date_created":"2022-03-07T08:15:01Z","checksum":"d704af7262cd484da9bb84b7d84e2b09","file_size":2969415,"date_updated":"2022-03-07T08:15:01Z","file_name":"2022_ACSSensors_Hasler.pdf","content_type":"application/pdf","access_level":"open_access","success":1,"relation":"main_file","file_id":"10832","creator":"dernst"}],"oa":1,"publication_identifier":{"eissn":["23793694"]},"date_published":"2022-02-08T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png"}},{"main_file_link":[{"url":"https://doi.org/10.5281/zenodo.5500360","open_access":"1"}],"ddc":["540"],"related_material":{"record":[{"status":"public","id":"10829","relation":"used_in_publication"}]},"status":"public","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","day":"08","doi":"10.5281/ZENODO.5500360","oa":1,"abstract":[{"lang":"eng","text":"Detailed information about the data set see \"dataset description.txt\" file."}],"citation":{"apa":"Hasler, R., Reiner-Rozman, C., Fossati, S., Aspermair, P., Dostalek, J., Lee, S., … Knoll, W. (2022). Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. Zenodo. <a href=\"https://doi.org/10.5281/ZENODO.5500360\">https://doi.org/10.5281/ZENODO.5500360</a>","ama":"Hasler R, Reiner-Rozman C, Fossati S, et al. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device. 2022. doi:<a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>","chicago":"Hasler, Roger, Ciril Reiner-Rozman, Stefan Fossati, Patrik Aspermair, Jakub Dostalek, Seungho Lee, Maria Ibáñez, Johannes Bintinger, and Wolfgang Knoll. “Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device.” Zenodo, 2022. <a href=\"https://doi.org/10.5281/ZENODO.5500360\">https://doi.org/10.5281/ZENODO.5500360</a>.","ieee":"R. Hasler <i>et al.</i>, “Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device.” Zenodo, 2022.","short":"R. Hasler, C. Reiner-Rozman, S. Fossati, P. Aspermair, J. Dostalek, S. Lee, M. Ibáñez, J. Bintinger, W. Knoll, (2022).","mla":"Hasler, Roger, et al. <i>Field-Effect Transistor with a Plasmonic Fiber Optic Gate Electrode as a Multivariable Biosensor Device</i>. Zenodo, 2022, doi:<a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>.","ista":"Hasler R, Reiner-Rozman C, Fossati S, Aspermair P, Dostalek J, Lee S, Ibáñez M, Bintinger J, Knoll W. 2022. Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device, Zenodo, <a href=\"https://doi.org/10.5281/ZENODO.5500360\">10.5281/ZENODO.5500360</a>."},"year":"2022","date_updated":"2023-08-02T14:46:16Z","type":"research_data_reference","date_published":"2022-02-08T00:00:00Z","publisher":"Zenodo","department":[{"_id":"MaIb"}],"date_created":"2022-03-07T08:19:11Z","article_processing_charge":"No","oa_version":"Published Version","title":"Field-effect transistor with a plasmonic fiber optic gate electrode as a multivariable biosensor device","month":"02","_id":"10833","author":[{"full_name":"Hasler, Roger","last_name":"Hasler","first_name":"Roger"},{"first_name":"Ciril","last_name":"Reiner-Rozman","full_name":"Reiner-Rozman, Ciril"},{"full_name":"Fossati, Stefan","last_name":"Fossati","first_name":"Stefan"},{"last_name":"Aspermair","first_name":"Patrik","full_name":"Aspermair, Patrik"},{"full_name":"Dostalek, Jakub","last_name":"Dostalek","first_name":"Jakub"},{"first_name":"Seungho","last_name":"Lee","orcid":"0000-0002-6962-8598","full_name":"Lee, Seungho","id":"BB243B88-D767-11E9-B658-BC13E6697425"},{"first_name":"Maria","last_name":"Ibáñez","orcid":"0000-0001-5013-2843","full_name":"Ibáñez, Maria","id":"43C61214-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Bintinger","first_name":"Johannes","full_name":"Bintinger, Johannes"},{"last_name":"Knoll","first_name":"Wolfgang","full_name":"Knoll, Wolfgang"}]},{"department":[{"_id":"JiFr"},{"_id":"EM-Fac"}],"date_created":"2022-03-08T13:47:51Z","article_processing_charge":"No","publication_status":"published","intvolume":"        34","title":"Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components","scopus_import":"1","_id":"10841","pmid":1,"issue":"6","author":[{"full_name":"Dahhan, DA","last_name":"Dahhan","first_name":"DA"},{"full_name":"Reynolds, GD","first_name":"GD","last_name":"Reynolds"},{"last_name":"Cárdenas","first_name":"JJ","full_name":"Cárdenas, JJ"},{"last_name":"Eeckhout","first_name":"D","full_name":"Eeckhout, D"},{"orcid":"0000-0002-2739-8843","full_name":"Johnson, Alexander J","first_name":"Alexander J","last_name":"Johnson","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87"},{"first_name":"K","last_name":"Yperman","full_name":"Yperman, K"},{"last_name":"Kaufmann","first_name":"Walter","full_name":"Kaufmann, Walter","orcid":"0000-0001-9735-5315","id":"3F99E422-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Vang, N","first_name":"N","last_name":"Vang"},{"first_name":"X","last_name":"Yan","full_name":"Yan, X"},{"full_name":"Hwang, I","first_name":"I","last_name":"Hwang"},{"first_name":"A","last_name":"Heese","full_name":"Heese, A"},{"full_name":"De Jaeger, G","first_name":"G","last_name":"De Jaeger"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","last_name":"Friml","first_name":"Jiří"},{"full_name":"Van Damme, D","last_name":"Van Damme","first_name":"D"},{"full_name":"Pan, J","last_name":"Pan","first_name":"J"},{"full_name":"Bednarek, SY","last_name":"Bednarek","first_name":"SY"}],"publisher":"Oxford Academic","article_type":"original","quality_controlled":"1","page":"2150-2173","day":"01","doi":"10.1093/plcell/koac071","abstract":[{"lang":"eng","text":"In eukaryotes, clathrin-coated vesicles (CCVs) facilitate the internalization of material from the cell surface as well as the movement of cargo in post-Golgi trafficking pathways. This diversity of functions is partially provided by multiple monomeric and multimeric clathrin adaptor complexes that provide compartment and cargo selectivity. The adaptor-protein assembly polypeptide-1 (AP-1) complex operates as part of the secretory pathway at the trans-Golgi network (TGN), while the AP-2 complex and the TPLATE complex jointly operate at the plasma membrane to execute clathrin-mediated endocytosis. Key to our further understanding of clathrin-mediated trafficking in plants will be the comprehensive identification and characterization of the network of evolutionarily conserved and plant-specific core and accessory machinery involved in the formation and targeting of CCVs. To facilitate these studies, we have analyzed the proteome of enriched TGN/early endosome-derived and endocytic CCVs isolated from dividing and expanding suspension-cultured Arabidopsis (Arabidopsis thaliana) cells. Tandem mass spectrometry analysis results were validated by differential chemical labeling experiments to identify proteins co-enriching with CCVs. Proteins enriched in CCVs included previously characterized CCV components and cargos such as the vacuolar sorting receptors in addition to conserved and plant-specific components whose function in clathrin-mediated trafficking has not been previously defined. Notably, in addition to AP-1 and AP-2, all subunits of the AP-4 complex, but not AP-3 or AP-5, were found to be in high abundance in the CCV proteome. The association of AP-4 with suspension-cultured Arabidopsis CCVs is further supported via additional biochemical data."}],"citation":{"short":"D. Dahhan, G. Reynolds, J. Cárdenas, D. Eeckhout, A.J. Johnson, K. Yperman, W. Kaufmann, N. Vang, X. Yan, I. Hwang, A. Heese, G. De Jaeger, J. Friml, D. Van Damme, J. Pan, S. Bednarek, Plant Cell 34 (2022) 2150–2173.","mla":"Dahhan, DA, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>, vol. 34, no. 6, Oxford Academic, 2022, pp. 2150–73, doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>.","ista":"Dahhan D, Reynolds G, Cárdenas J, Eeckhout D, Johnson AJ, Yperman K, Kaufmann W, Vang N, Yan X, Hwang I, Heese A, De Jaeger G, Friml J, Van Damme D, Pan J, Bednarek S. 2022. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. Plant Cell. 34(6), 2150–2173.","apa":"Dahhan, D., Reynolds, G., Cárdenas, J., Eeckhout, D., Johnson, A. J., Yperman, K., … Bednarek, S. (2022). Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. Oxford Academic. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>","ama":"Dahhan D, Reynolds G, Cárdenas J, et al. Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components. <i>Plant Cell</i>. 2022;34(6):2150-2173. doi:<a href=\"https://doi.org/10.1093/plcell/koac071\">10.1093/plcell/koac071</a>","chicago":"Dahhan, DA, GD Reynolds, JJ Cárdenas, D Eeckhout, Alexander J Johnson, K Yperman, Walter Kaufmann, et al. “Proteomic Characterization of Isolated Arabidopsis Clathrin-Coated Vesicles Reveals Evolutionarily Conserved and Plant-Specific Components.” <i>Plant Cell</i>. Oxford Academic, 2022. <a href=\"https://doi.org/10.1093/plcell/koac071\">https://doi.org/10.1093/plcell/koac071</a>.","ieee":"D. Dahhan <i>et al.</i>, “Proteomic characterization of isolated Arabidopsis clathrin-coated vesicles reveals evolutionarily conserved and plant-specific components,” <i>Plant Cell</i>, vol. 34, no. 6. Oxford Academic, pp. 2150–2173, 2022."},"year":"2022","date_updated":"2023-08-02T14:46:48Z","external_id":{"isi":["000767438800001"],"pmid":["35218346"]},"isi":1,"acknowledgement":"The authors would like to acknowledge the VIB Proteomics Core Facility (VIB-UGent Center for Medical Biotechnology in Ghent, Belgium) and the Research Technology Support Facility Proteomics Core (Michigan State University in East Lansing, Michigan) for sample analysis, as well as the University of Wisconsin Biotechnology Center Mass Spectrometry Core Facility (Madison, WI) for help with data processing. Additionally, we are grateful to Sue Weintraub (UT Health San Antonio) and Sydney Thomas (UW- Madison) for assistance with data analysis. This research was supported by grants to S.Y.B. from the National Science Foundation (Nos. 1121998 and 1614915) and a Vilas Associate Award (University of Wisconsin, Madison, Graduate School); to J.P. from the National Natural Science Foundation of China (Nos. 91754104, 31820103008, and 31670283); to I.H. from the National Research Foundation of Korea (No. 2019R1A2B5B03099982). This research was also supported by the Scientific Service Units (SSU) of IST Austria through resources provided by the Electron microscopy Facility (EMF). A.J. is supported by funding from the Austrian Science Fund (FWF): I3630B25 to J.F. A.H. is supported by funding from the National Science Foundation (NSF IOS Nos. 1025837 and 1147032).","volume":34,"project":[{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"acknowledged_ssus":[{"_id":"EM-Fac"}],"oa_version":"Preprint","month":"06","publication":"Plant Cell","language":[{"iso":"eng"}],"publication_identifier":{"eissn":["1532-298x"],"issn":["1040-4651"]},"oa":1,"type":"journal_article","date_published":"2022-06-01T00:00:00Z","main_file_link":[{"url":"https://doi.org/10.1101/2021.09.16.460678","open_access":"1"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"keyword":["Applied Mathematics","Computational Theory and Mathematics","Computer Networks and Communications"],"language":[{"iso":"eng"}],"publication":"Cryptography and Communications","month":"07","oa_version":"None","status":"public","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","type":"journal_article","date_published":"2022-07-01T00:00:00Z","publication_identifier":{"eissn":["1936-2455"],"issn":["1936-2447"]},"quality_controlled":"1","page":"933-948","article_type":"original","publisher":"Springer Nature","issue":"4","author":[{"last_name":"Köse","first_name":"Seyda","full_name":"Köse, Seyda","id":"8ba3170d-dc85-11ea-9058-c4251c96a6eb"},{"full_name":"Özbudak, Ferruh","first_name":"Ferruh","last_name":"Özbudak"}],"scopus_import":"1","_id":"10842","intvolume":"        14","title":"Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes","department":[{"_id":"GradSch"}],"date_created":"2022-03-10T12:16:19Z","article_processing_charge":"No","publication_status":"published","acknowledgement":"The authors would like to thank Prof. Dr. Minjia Shi for bringing [13, Conjecture 3.5] to our attention. We would also like to thank the associate editor and anonymous reviewers for their valuable comments and suggestions which improved and clarified the manuscript.","volume":14,"external_id":{"isi":["000766422000002"]},"isi":1,"citation":{"ieee":"S. Köse and F. Özbudak, “Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes,” <i>Cryptography and Communications</i>, vol. 14, no. 4. Springer Nature, pp. 933–948, 2022.","chicago":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” <i>Cryptography and Communications</i>. Springer Nature, 2022. <a href=\"https://doi.org/10.1007/s12095-022-00557-8\">https://doi.org/10.1007/s12095-022-00557-8</a>.","ama":"Köse S, Özbudak F. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. <i>Cryptography and Communications</i>. 2022;14(4):933-948. doi:<a href=\"https://doi.org/10.1007/s12095-022-00557-8\">10.1007/s12095-022-00557-8</a>","apa":"Köse, S., &#38; Özbudak, F. (2022). Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. <i>Cryptography and Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s12095-022-00557-8\">https://doi.org/10.1007/s12095-022-00557-8</a>","ista":"Köse S, Özbudak F. 2022. Factorization of some polynomials over finite local commutative rings and applications to certain self-dual and LCD codes. Cryptography and Communications. 14(4), 933–948.","short":"S. Köse, F. Özbudak, Cryptography and Communications 14 (2022) 933–948.","mla":"Köse, Seyda, and Ferruh Özbudak. “Factorization of Some Polynomials over Finite Local Commutative Rings and Applications to Certain Self-Dual and LCD Codes.” <i>Cryptography and Communications</i>, vol. 14, no. 4, Springer Nature, 2022, pp. 933–48, doi:<a href=\"https://doi.org/10.1007/s12095-022-00557-8\">10.1007/s12095-022-00557-8</a>."},"year":"2022","date_updated":"2023-09-05T15:35:55Z","abstract":[{"lang":"eng","text":"We determine the unique factorization of some polynomials over a finite local commutative ring with identity explicitly. This solves and generalizes the main conjecture of Qian, Shi and Solé in [13]. We also give some applications to enumeration of certain generalized double circulant self-dual and linear complementary dual (LCD) codes over some finite rings together with an application in asymptotic coding theory."}],"day":"01","doi":"10.1007/s12095-022-00557-8"},{"language":[{"iso":"eng"}],"publication":"Physical Review Research","has_accepted_license":"1","month":"03","article_number":"013160","oa_version":"Published Version","project":[{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902","name":"Quantum rotations in the presence of a many-body environment"},{"_id":"2688CF98-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","grant_number":"801770"},{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"status":"public","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"10848","creator":"dernst","relation":"main_file","access_level":"open_access","success":1,"date_updated":"2022-03-14T08:38:49Z","file_name":"2022_PhysicalReviewResearch_Maslov.pdf","content_type":"application/pdf","date_created":"2022-03-14T08:38:49Z","file_size":1258324,"checksum":"62f64b3421a969656ebf52467fa7b6e8"}],"date_published":"2022-03-01T00:00:00Z","type":"journal_article","tmp":{"legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"oa":1,"publication_identifier":{"issn":["2643-1564"]},"file_date_updated":"2022-03-14T08:38:49Z","quality_controlled":"1","ec_funded":1,"article_type":"original","publisher":"American Physical Society","author":[{"id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","full_name":"Maslov, Mikhail","orcid":"0000-0003-4074-2570","last_name":"Maslov","first_name":"Mikhail"},{"full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","last_name":"Lemeshko","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","first_name":"Artem","last_name":"Volosniev","id":"37D278BC-F248-11E8-B48F-1D18A9856A87"}],"_id":"10845","scopus_import":"1","title":"Impurity with a resonance in the vicinity of the Fermi energy","intvolume":"         4","publication_status":"published","date_created":"2022-03-13T23:01:46Z","department":[{"_id":"MiLe"}],"article_processing_charge":"No","ddc":["530"],"volume":4,"acknowledgement":"M.L. acknowledges support by the Austrian Science Fund (FWF), under Project No. P29902-N27, and by the European Research Council (ERC) starting Grant No. 801770 (ANGULON). A.G.V. acknowledges support by European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement No. 754411.","external_id":{"arxiv":["2111.13570"]},"date_updated":"2022-03-14T08:42:24Z","citation":{"ama":"Maslov M, Lemeshko M, Volosniev A. Impurity with a resonance in the vicinity of the Fermi energy. <i>Physical Review Research</i>. 2022;4. doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">10.1103/PhysRevResearch.4.013160</a>","apa":"Maslov, M., Lemeshko, M., &#38; Volosniev, A. (2022). Impurity with a resonance in the vicinity of the Fermi energy. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">https://doi.org/10.1103/PhysRevResearch.4.013160</a>","ieee":"M. Maslov, M. Lemeshko, and A. Volosniev, “Impurity with a resonance in the vicinity of the Fermi energy,” <i>Physical Review Research</i>, vol. 4. American Physical Society, 2022.","chicago":"Maslov, Mikhail, Mikhail Lemeshko, and Artem Volosniev. “Impurity with a Resonance in the Vicinity of the Fermi Energy.” <i>Physical Review Research</i>. American Physical Society, 2022. <a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">https://doi.org/10.1103/PhysRevResearch.4.013160</a>.","mla":"Maslov, Mikhail, et al. “Impurity with a Resonance in the Vicinity of the Fermi Energy.” <i>Physical Review Research</i>, vol. 4, 013160, American Physical Society, 2022, doi:<a href=\"https://doi.org/10.1103/PhysRevResearch.4.013160\">10.1103/PhysRevResearch.4.013160</a>.","short":"M. Maslov, M. Lemeshko, A. Volosniev, Physical Review Research 4 (2022).","ista":"Maslov M, Lemeshko M, Volosniev A. 2022. Impurity with a resonance in the vicinity of the Fermi energy. Physical Review Research. 4, 013160."},"year":"2022","abstract":[{"lang":"eng","text":"We study an impurity with a resonance level whose position coincides with the Fermi energy of the surrounding Fermi gas. An impurity causes a rapid variation of the scattering phase shift for fermions at the Fermi surface, introducing a new characteristic length scale into the problem. We investigate manifestations of this length scale in the self-energy of the impurity and in the density of the bath. Our calculations reveal a model-independent deformation of the density of the Fermi gas, which is determined by the width of the resonance. To provide a broader picture, we investigate time evolution of the density in quench dynamics, and study the behavior of the system at finite temperatures. Finally, we briefly discuss implications of our findings for the Fermi-polaron problem."}],"doi":"10.1103/PhysRevResearch.4.013160","arxiv":1,"day":"01"},{"isi":1,"external_id":{"isi":["000758859600001"],"pmid":["35188063"]},"date_updated":"2023-10-03T10:54:54Z","year":"2022","citation":{"mla":"Artan, Murat, et al. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>, vol. 18, no. 5, Taylor &#38; Francis, 2022, pp. 1208–10, doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>.","short":"M. Artan, J. Sohn, C. Lee, S.Y. Park, S.J.V. Lee, Autophagy 18 (2022) 1208–1210.","ista":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. 2022. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. Autophagy. 18(5), 1208–1210.","ama":"Artan M, Sohn J, Lee C, Park SY, Lee SJV. MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. 2022;18(5):1208-1210. doi:<a href=\"https://doi.org/10.1080/15548627.2022.2039523\">10.1080/15548627.2022.2039523</a>","apa":"Artan, M., Sohn, J., Lee, C., Park, S. Y., &#38; Lee, S. J. V. (2022). MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications. <i>Autophagy</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>","chicago":"Artan, Murat, Jooyeon Sohn, Cheolju Lee, Seung Yeol Park, and Seung Jae V. Lee. “MON-2, a Golgi Protein, Promotes Longevity by Upregulating Autophagy through Mediating Inter-Organelle Communications.” <i>Autophagy</i>. Taylor &#38; Francis, 2022. <a href=\"https://doi.org/10.1080/15548627.2022.2039523\">https://doi.org/10.1080/15548627.2022.2039523</a>.","ieee":"M. Artan, J. Sohn, C. Lee, S. Y. Park, and S. J. V. Lee, “MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications,” <i>Autophagy</i>, vol. 18, no. 5. Taylor &#38; Francis, pp. 1208–1210, 2022."},"abstract":[{"text":"The Golgi apparatus regulates the process of modification and subcellular localization of macromolecules, including proteins and lipids. Aberrant protein sorting caused by defects in the Golgi leads to various diseases in mammals. However, the role of the Golgi apparatus in organismal longevity remained largely unknown. By employing a quantitative proteomic approach, we demonstrated that MON-2, an evolutionarily conserved Arf-GEF protein implicated in Golgi-to-endosome trafficking, promotes longevity via upregulating macroautophagy/autophagy in C. elegans. Our data using cultured mammalian cells indicate that MON2 translocates from the Golgi to the endosome under starvation conditions, subsequently increasing autophagic flux by binding LGG-1/GABARAPL2. Thus, Golgi-to-endosome trafficking appears to be an evolutionarily conserved process for the upregulation of autophagy, which contributes to organismal longevity.","lang":"eng"}],"doi":"10.1080/15548627.2022.2039523","day":"19","volume":18,"acknowledgement":"This work is funded by National Research Foundation of Korea (NRF) grants NRF-2019R1A3B2067745 from the Korean Government (Ministry of Science and Information and Communications Technology (S-J.V.L.). NRF-2017R1A5A1015366 (S.Y.P, S-J.V.L). Korea Institute of Science and Technology (KIST) intramural grant (C.L).","author":[{"full_name":"Artan, Murat","orcid":"0000-0001-8945-6992","last_name":"Artan","first_name":"Murat","id":"C407B586-6052-11E9-B3AE-7006E6697425"},{"last_name":"Sohn","first_name":"Jooyeon","full_name":"Sohn, Jooyeon"},{"full_name":"Lee, Cheolju","last_name":"Lee","first_name":"Cheolju"},{"full_name":"Park, Seung Yeol","first_name":"Seung Yeol","last_name":"Park"},{"full_name":"Lee, Seung Jae V.","last_name":"Lee","first_name":"Seung Jae V."}],"issue":"5","pmid":1,"_id":"10846","scopus_import":"1","title":"MON-2, a Golgi protein, promotes longevity by upregulating autophagy through mediating inter-organelle communications","intvolume":"        18","publication_status":"published","date_created":"2022-03-13T23:01:47Z","article_processing_charge":"No","department":[{"_id":"MaDe"}],"page":"1208-1210","quality_controlled":"1","article_type":"original","publisher":"Taylor & Francis","date_published":"2022-02-19T00:00:00Z","type":"journal_article","oa":1,"publication_identifier":{"issn":["1554-8627"],"eissn":["1554-8635"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","status":"public","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1080/15548627.2022.2039523"}],"publication":"Autophagy","month":"02","oa_version":"Published Version","language":[{"iso":"eng"}]}]