[{"date_published":"2020-03-19T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","file_name":"2020_FrontiersCellularNeurosc_Eguchi.pdf","access_level":"open_access","checksum":"1c145123c6f8dc3e2e4bd5a66a1ad60e","relation":"main_file","date_created":"2020-04-20T10:59:49Z","creator":"dernst","file_id":"7668","file_size":9227283,"date_updated":"2020-07-14T12:48:01Z"}],"article_type":"original","date_updated":"2023-08-21T06:12:48Z","external_id":{"isi":["000525582200001"]},"publication_identifier":{"issn":["16625102"]},"month":"03","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","_id":"7665","oa_version":"Published Version","has_accepted_license":"1","doi":"10.3389/fncel.2020.00063","ddc":["570"],"publisher":"Frontiers Media","status":"public","title":"Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions","year":"2020","author":[{"orcid":"0000-0002-6170-2546","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","last_name":"Eguchi","first_name":"Kohgaku","full_name":"Eguchi, Kohgaku"},{"orcid":"0000-0002-2340-7431","id":"39BDC62C-F248-11E8-B48F-1D18A9856A87","full_name":"Velicky, Philipp","last_name":"Velicky","first_name":"Philipp"},{"id":"3C054040-F248-11E8-B48F-1D18A9856A87","full_name":"Hollergschwandtner, Elena","last_name":"Hollergschwandtner","first_name":"Elena"},{"full_name":"Itakura, Makoto","first_name":"Makoto","last_name":"Itakura"},{"last_name":"Fukazawa","first_name":"Yugo","full_name":"Fukazawa, Yugo"},{"orcid":"0000-0001-8559-3973","id":"42EFD3B6-F248-11E8-B48F-1D18A9856A87","full_name":"Danzl, Johann G","last_name":"Danzl","first_name":"Johann G"},{"orcid":"0000-0001-8761-9444","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","full_name":"Shigemoto, Ryuichi","first_name":"Ryuichi","last_name":"Shigemoto"}],"file_date_updated":"2020-07-14T12:48:01Z","type":"journal_article","date_created":"2020-04-19T22:00:55Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        14","volume":14,"article_number":"63","project":[{"call_identifier":"H2020","_id":"2659CC84-B435-11E9-9278-68D0E5697425","name":"Ultrastructural analysis of phosphoinositides in nerve terminals: distribution, dynamics and physiological roles in synaptic transmission","grant_number":"793482"},{"grant_number":"694539","_id":"25CA28EA-B435-11E9-9278-68D0E5697425","name":"In situ analysis of single channel subunit composition in neurons: physiological implication in synaptic plasticity and behaviour","call_identifier":"H2020"},{"name":"Optical control of synaptic function via adhesion molecules","_id":"265CB4D0-B435-11E9-9278-68D0E5697425","grant_number":"I03600","call_identifier":"FWF"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"abstract":[{"lang":"eng","text":"Acute brain slice preparation is a powerful experimental model for investigating the characteristics of synaptic function in the brain. Although brain tissue is usually cut at ice-cold temperature (CT) to facilitate slicing and avoid neuronal damage, exposure to CT causes molecular and architectural changes of synapses. To address these issues, we investigated ultrastructural and electrophysiological features of synapses in mouse acute cerebellar slices prepared at ice-cold and physiological temperature (PT). In the slices prepared at CT, we found significant spine loss and reconstruction, synaptic vesicle rearrangement and decrease in synaptic proteins, all of which were not detected in slices prepared at PT. Consistent with these structural findings, slices prepared at PT showed higher release probability. Furthermore, preparation at PT allows electrophysiological recording immediately after slicing resulting in higher detectability of long-term depression (LTD) after motor learning compared with that at CT. These results indicate substantial advantages of the slice preparation at PT for investigating synaptic functions in different physiological conditions."}],"publication_status":"published","ec_funded":1,"oa":1,"department":[{"_id":"JoDa"},{"_id":"RySh"}],"citation":{"apa":"Eguchi, K., Velicky, P., Saeckl, E., Itakura, M., Fukazawa, Y., Danzl, J. G., &#38; Shigemoto, R. (2020). Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. <i>Frontiers in Cellular Neuroscience</i>. Frontiers Media. <a href=\"https://doi.org/10.3389/fncel.2020.00063\">https://doi.org/10.3389/fncel.2020.00063</a>","ieee":"K. Eguchi <i>et al.</i>, “Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions,” <i>Frontiers in Cellular Neuroscience</i>, vol. 14. Frontiers Media, 2020.","mla":"Eguchi, Kohgaku, et al. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” <i>Frontiers in Cellular Neuroscience</i>, vol. 14, 63, Frontiers Media, 2020, doi:<a href=\"https://doi.org/10.3389/fncel.2020.00063\">10.3389/fncel.2020.00063</a>.","chicago":"Eguchi, Kohgaku, Philipp Velicky, Elena Saeckl, Makoto Itakura, Yugo Fukazawa, Johann G Danzl, and Ryuichi Shigemoto. “Advantages of Acute Brain Slices Prepared at Physiological Temperature in the Characterization of Synaptic Functions.” <i>Frontiers in Cellular Neuroscience</i>. Frontiers Media, 2020. <a href=\"https://doi.org/10.3389/fncel.2020.00063\">https://doi.org/10.3389/fncel.2020.00063</a>.","short":"K. Eguchi, P. Velicky, E. Saeckl, M. Itakura, Y. Fukazawa, J.G. Danzl, R. Shigemoto, Frontiers in Cellular Neuroscience 14 (2020).","ista":"Eguchi K, Velicky P, Saeckl E, Itakura M, Fukazawa Y, Danzl JG, Shigemoto R. 2020. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. Frontiers in Cellular Neuroscience. 14, 63.","ama":"Eguchi K, Velicky P, Saeckl E, et al. Advantages of acute brain slices prepared at physiological temperature in the characterization of synaptic functions. <i>Frontiers in Cellular Neuroscience</i>. 2020;14. doi:<a href=\"https://doi.org/10.3389/fncel.2020.00063\">10.3389/fncel.2020.00063</a>"},"publication":"Frontiers in Cellular Neuroscience","isi":1,"license":"https://creativecommons.org/licenses/by/4.0/","day":"19","scopus_import":"1"},{"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"name":"Alpha Shape Theory Extended","grant_number":"788183","_id":"266A2E9E-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"call_identifier":"FWF","grant_number":"I02979-N35","_id":"2561EBF4-B435-11E9-9278-68D0E5697425","name":"Persistence and stability of geometric complexes"}],"publication_status":"published","abstract":[{"lang":"eng","text":"Generalizing the decomposition of a connected planar graph into a tree and a dual tree, we prove a combinatorial analog of the classic Helmholtz–Hodge decomposition of a smooth vector field. Specifically, we show that for every polyhedral complex, K, and every dimension, p, there is a partition of the set of p-cells into a maximal p-tree, a maximal p-cotree, and a collection of p-cells whose cardinality is the p-th reduced Betti number of K. Given an ordering of the p-cells, this tri-partition is unique, and it can be computed by a matrix reduction algorithm that also constructs canonical bases of cycle and boundary groups."}],"volume":64,"intvolume":"        64","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-04-19T22:00:56Z","scopus_import":"1","day":"20","isi":1,"oa":1,"ec_funded":1,"publication":"Discrete and Computational Geometry","department":[{"_id":"HeEd"}],"citation":{"chicago":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” <i>Discrete and Computational Geometry</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00454-020-00188-x\">https://doi.org/10.1007/s00454-020-00188-x</a>.","mla":"Edelsbrunner, Herbert, and Katharina Ölsböck. “Tri-Partitions and Bases of an Ordered Complex.” <i>Discrete and Computational Geometry</i>, vol. 64, Springer Nature, 2020, pp. 759–75, doi:<a href=\"https://doi.org/10.1007/s00454-020-00188-x\">10.1007/s00454-020-00188-x</a>.","apa":"Edelsbrunner, H., &#38; Ölsböck, K. (2020). Tri-partitions and bases of an ordered complex. <i>Discrete and Computational Geometry</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00454-020-00188-x\">https://doi.org/10.1007/s00454-020-00188-x</a>","ieee":"H. Edelsbrunner and K. Ölsböck, “Tri-partitions and bases of an ordered complex,” <i>Discrete and Computational Geometry</i>, vol. 64. Springer Nature, pp. 759–775, 2020.","ista":"Edelsbrunner H, Ölsböck K. 2020. Tri-partitions and bases of an ordered complex. Discrete and Computational Geometry. 64, 759–775.","ama":"Edelsbrunner H, Ölsböck K. Tri-partitions and bases of an ordered complex. <i>Discrete and Computational Geometry</i>. 2020;64:759-775. doi:<a href=\"https://doi.org/10.1007/s00454-020-00188-x\">10.1007/s00454-020-00188-x</a>","short":"H. Edelsbrunner, K. Ölsböck, Discrete and Computational Geometry 64 (2020) 759–775."},"publication_identifier":{"eissn":["14320444"],"issn":["01795376"]},"_id":"7666","article_processing_charge":"Yes (via OA deal)","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"month":"03","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-03-20T00:00:00Z","date_updated":"2023-08-21T06:13:48Z","external_id":{"isi":["000520918800001"]},"article_type":"original","file":[{"content_type":"application/pdf","relation":"main_file","checksum":"f8cc96e497f00c38340b5dafe0cb91d7","access_level":"open_access","file_name":"2020_DiscreteCompGeo_Edelsbrunner.pdf","creator":"dernst","file_id":"8786","success":1,"date_created":"2020-11-20T13:22:21Z","date_updated":"2020-11-20T13:22:21Z","file_size":701673}],"page":"759-775","file_date_updated":"2020-11-20T13:22:21Z","author":[{"orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","first_name":"Herbert","last_name":"Edelsbrunner","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87"},{"id":"4D4AA390-F248-11E8-B48F-1D18A9856A87","full_name":"Ölsböck, Katharina","last_name":"Ölsböck","first_name":"Katharina","orcid":"0000-0002-4672-8297"}],"type":"journal_article","oa_version":"Published Version","has_accepted_license":"1","year":"2020","status":"public","title":"Tri-partitions and bases of an ordered complex","acknowledgement":"This project has received funding from the European Research Council under the European Union’s Horizon 2020 research and innovation programme (Grant Agreement No. 78818 Alpha). It is also partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through Grant No. I02979-N35 of the Austrian Science Fund (FWF).","ddc":["510"],"publisher":"Springer Nature","doi":"10.1007/s00454-020-00188-x"},{"type":"journal_article","file_date_updated":"2020-10-01T13:20:45Z","author":[{"first_name":"Aleksej","last_name":"Samojlov","full_name":"Samojlov, Aleksej"},{"full_name":"Schuster, David","last_name":"Schuster","first_name":"David"},{"last_name":"Kahr","first_name":"Jürgen","full_name":"Kahr, Jürgen"},{"id":"A8CA28E6-CE23-11E9-AD2D-EC27E6697425","last_name":"Freunberger","first_name":"Stefan Alexander","full_name":"Freunberger, Stefan Alexander","orcid":"0000-0003-2902-5319"}],"acknowledgement":"S.A.F. thanks the International Society of Electrochemistry for awarding the Tajima Prize 2019 “in recognition of outstanding re- searches on Li-Air batteries by the use of a range of in-situ elec- trochemical methods to achieve comprehensive understanding of the reactions taking place at the oxygen electrode”. This article is dedicated to the special issue of Electrochmica Acta associated with the awarding conference. S.A.F. is indebted to and the Austrian Federal Ministry of Science, Research and Economy and the Austrian Research Promotion Agency (grant No. 845364 ) and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 636069). The authors thank J. Schlegl for manufacturing instrumentation, M. Winkler of Acib GmbH and G. Strohmeier for help with HPLC measurements, S. Eder for cyclic voltammetry measurements, and C. Slugovc for discussions and continuous support. We thank S. Borisov for access and advice with fluorescence measurements. We thank EL-Cell GmbH, Hamburg, Germany for providing the PAT-Cell-Press electrochemical cell.","year":"2020","title":"Surface and catalyst driven singlet oxygen formation in Li-O2 cells","status":"public","doi":"10.1016/j.electacta.2020.137175","ddc":["540"],"publisher":"Elsevier","has_accepted_license":"1","oa_version":"Published Version","_id":"7672","month":"12","article_processing_charge":"Yes (via OA deal)","tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode"},"article_type":"original","date_updated":"2023-08-21T06:14:21Z","external_id":{"isi":["000582869700060"]},"issue":"12","file":[{"success":1,"file_id":"8593","creator":"dernst","date_created":"2020-10-01T13:20:45Z","date_updated":"2020-10-01T13:20:45Z","file_size":1404030,"content_type":"application/pdf","access_level":"open_access","relation":"main_file","checksum":"1ab1aa2024d431e2a089ea336bc08298","file_name":"2020_ElectrochimicaActa_Samojlov.pdf"}],"language":[{"iso":"eng"}],"date_published":"2020-12-01T00:00:00Z","quality_controlled":"1","scopus_import":"1","day":"01","isi":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","publication":"Electrochimica Acta","department":[{"_id":"StFr"}],"citation":{"apa":"Samojlov, A., Schuster, D., Kahr, J., &#38; Freunberger, S. A. (2020). Surface and catalyst driven singlet oxygen formation in Li-O2 cells. <i>Electrochimica Acta</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.electacta.2020.137175\">https://doi.org/10.1016/j.electacta.2020.137175</a>","ieee":"A. Samojlov, D. Schuster, J. Kahr, and S. A. Freunberger, “Surface and catalyst driven singlet oxygen formation in Li-O2 cells,” <i>Electrochimica Acta</i>, vol. 362, no. 12. Elsevier, 2020.","chicago":"Samojlov, Aleksej, David Schuster, Jürgen Kahr, and Stefan Alexander Freunberger. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” <i>Electrochimica Acta</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.electacta.2020.137175\">https://doi.org/10.1016/j.electacta.2020.137175</a>.","mla":"Samojlov, Aleksej, et al. “Surface and Catalyst Driven Singlet Oxygen Formation in Li-O2 Cells.” <i>Electrochimica Acta</i>, vol. 362, no. 12, 137175, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.electacta.2020.137175\">10.1016/j.electacta.2020.137175</a>.","ista":"Samojlov A, Schuster D, Kahr J, Freunberger SA. 2020. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. Electrochimica Acta. 362(12), 137175.","ama":"Samojlov A, Schuster D, Kahr J, Freunberger SA. Surface and catalyst driven singlet oxygen formation in Li-O2 cells. <i>Electrochimica Acta</i>. 2020;362(12). doi:<a href=\"https://doi.org/10.1016/j.electacta.2020.137175\">10.1016/j.electacta.2020.137175</a>","short":"A. Samojlov, D. Schuster, J. Kahr, S.A. Freunberger, Electrochimica Acta 362 (2020)."},"oa":1,"publication_status":"published","abstract":[{"lang":"eng","text":"Large overpotentials upon discharge and charge of Li-O2 cells have motivated extensive research into heterogeneous solid electrocatalysts or non-carbon electrodes with the aim to improve rate capability, round-trip efficiency and cycle life. These features are equally governed by parasitic reactions, which are now recognized to be caused by the highly reactive singlet oxygen (1O2). However, the link between the presence of electrocatalysts and 1O2 formation in metal-O2 cells is unknown. Here, we show that, compared to pristine carbon black electrodes, a representative selection of electrocatalysts or non-carbon electrodes (noble metal, transition metal compounds) may both slightly reduce or severely increase the 1O2 formation. The individual reaction steps, where the surfaces impact the 1O2 yield are deciphered, showing that 1O2 yield from superoxide disproportionation as well as the decomposition of trace H2O2 are sensitive to catalysts. Transition metal compounds in general are prone to increase 1O2."}],"article_number":"137175","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"       362","volume":362,"date_created":"2020-04-20T19:29:31Z"},{"publisher":"Cold Spring Harbor Laboratory","citation":{"mla":"Kavcic, Bor, et al. “A Minimal Biophysical Model of Combined Antibiotic Action.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2020, doi:<a href=\"https://doi.org/10.1101/2020.04.18.047886\">10.1101/2020.04.18.047886</a>.","chicago":"Kavcic, Bor, Gašper Tkačik, and Mark Tobias Bollenbach. “A Minimal Biophysical Model of Combined Antibiotic Action.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2020. <a href=\"https://doi.org/10.1101/2020.04.18.047886\">https://doi.org/10.1101/2020.04.18.047886</a>.","ieee":"B. Kavcic, G. Tkačik, and M. T. Bollenbach, “A minimal biophysical model of combined antibiotic action,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2020.","apa":"Kavcic, B., Tkačik, G., &#38; Bollenbach, M. T. (2020). A minimal biophysical model of combined antibiotic action. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.04.18.047886\">https://doi.org/10.1101/2020.04.18.047886</a>","short":"B. Kavcic, G. Tkačik, M.T. Bollenbach, BioRxiv (2020).","ama":"Kavcic B, Tkačik G, Bollenbach MT. A minimal biophysical model of combined antibiotic action. <i>bioRxiv</i>. 2020. doi:<a href=\"https://doi.org/10.1101/2020.04.18.047886\">10.1101/2020.04.18.047886</a>","ista":"Kavcic B, Tkačik G, Bollenbach MT. 2020. A minimal biophysical model of combined antibiotic action. bioRxiv, <a href=\"https://doi.org/10.1101/2020.04.18.047886\">10.1101/2020.04.18.047886</a>."},"doi":"10.1101/2020.04.18.047886","department":[{"_id":"GaTk"}],"status":"public","publication":"bioRxiv","year":"2020","title":"A minimal biophysical model of combined antibiotic action","oa_version":"Preprint","oa":1,"type":"preprint","day":"18","related_material":{"record":[{"id":"8997","status":"public","relation":"later_version"},{"status":"public","relation":"dissertation_contains","id":"8657"}]},"author":[{"orcid":"0000-0001-6041-254X","id":"350F91D2-F248-11E8-B48F-1D18A9856A87","last_name":"Kavcic","first_name":"Bor","full_name":"Kavcic, Bor"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455"},{"last_name":"Bollenbach","first_name":"Tobias","full_name":"Bollenbach, Tobias","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-4398-476X"}],"main_file_link":[{"url":"https://doi.org/10.1101/2020.04.18.047886 ","open_access":"1"}],"date_updated":"2024-03-25T23:30:05Z","date_published":"2020-04-18T00:00:00Z","date_created":"2020-04-22T08:27:56Z","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","article_processing_charge":"No","abstract":[{"lang":"eng","text":"Combining drugs can improve the efficacy of treatments. However, predicting the effect of drug combinations is still challenging. The combined potency of drugs determines the drug interaction, which is classified as synergistic, additive, antagonistic, or suppressive. While probabilistic, non-mechanistic models exist, there is currently no biophysical model that can predict antibiotic interactions. Here, we present a physiologically relevant model of the combined action of antibiotics that inhibit protein synthesis by targeting the ribosome. This model captures the kinetics of antibiotic binding and transport, and uses bacterial growth laws to predict growth in the presence of antibiotic combinations. We find that this biophysical model can produce all drug interaction types except suppression. We show analytically that antibiotics which cannot bind to the ribosome simultaneously generally act as substitutes for one another, leading to additive drug interactions. Previously proposed null expectations for higher-order drug interactions follow as a limiting case of our model. We further extend the model to include the effects of direct physical or allosteric interactions between individual drugs on the ribosome. Notably, such direct interactions profoundly change the combined drug effect, depending on the kinetic parameters of the drugs used. The model makes additional predictions for the effects of resistance genes on drug interactions and for interactions between ribosome-targeting antibiotics and antibiotics with other targets. These findings enhance our understanding of the interplay between drug action and cell physiology and are a key step toward a general framework for predicting drug interactions."}],"publication_status":"published","month":"04","_id":"7673","project":[{"name":"Revealing the mechanisms underlying drug interactions","grant_number":"P27201-B22","_id":"25E9AF9E-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"call_identifier":"FWF","name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425"}]},{"project":[{"grant_number":"RGP0034/2018","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?"},{"_id":"267C84F4-B435-11E9-9278-68D0E5697425","name":"Biophysically realistic genotype-phenotype maps for regulatory networks"}],"_id":"7675","article_processing_charge":"No","publication_status":"published","abstract":[{"lang":"eng","text":"In prokaryotes, thermodynamic models of gene regulation provide a highly quantitative mapping from promoter sequences to gene expression levels that is compatible with in vivo and in vitro bio-physical measurements. Such concordance has not been achieved for models of enhancer function in eukaryotes. In equilibrium models, it is difficult to reconcile the reported short transcription factor (TF) residence times on the DNA with the high specificity of regulation. In non-equilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal non-equilibrium enhancer models that yield desired regulatory phenotypes: low TF residence time, high specificity and tunable cooperativity. We find that a single extra parameter, interpretable as the “linking rate” by which bound TFs interact with Mediator components, enables our models to escape equilibrium bounds and access optimal regulatory phenotypes, while remaining consistent with the reported phenomenology and simple enough to be inferred from upcoming experiments. We further find that high specificity in non-equilibrium models is in a tradeoff with gene expression noise, predicting bursty dynamics — an experimentally-observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space to a much smaller subspace that optimally realizes biological function prior to inference from data, our normative approach holds promise for mathematical models in systems biology."}],"month":"04","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_created":"2020-04-23T10:12:51Z","date_published":"2020-04-09T00:00:00Z","date_updated":"2023-09-07T13:13:26Z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.04.08.029405 "}],"related_material":{"record":[{"id":"8155","status":"public","relation":"dissertation_contains"}]},"author":[{"orcid":"0000-0003-2539-3560","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","full_name":"Grah, Rok","last_name":"Grah","first_name":"Rok"},{"full_name":"Zoller, Benjamin","first_name":"Benjamin","last_name":"Zoller"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"day":"09","type":"preprint","oa_version":"Preprint","oa":1,"publication":"bioRxiv","year":"2020","status":"public","title":"Normative models of enhancer function","publisher":"Cold Spring Harbor Laboratory","doi":"10.1101/2020.04.08.029405","citation":{"ista":"Grah R, Zoller B, Tkačik G. 2020. Normative models of enhancer function. bioRxiv, <a href=\"https://doi.org/10.1101/2020.04.08.029405\">10.1101/2020.04.08.029405</a>.","ama":"Grah R, Zoller B, Tkačik G. Normative models of enhancer function. <i>bioRxiv</i>. 2020. doi:<a href=\"https://doi.org/10.1101/2020.04.08.029405\">10.1101/2020.04.08.029405</a>","short":"R. Grah, B. Zoller, G. Tkačik, BioRxiv (2020).","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Normative Models of Enhancer Function.” <i>BioRxiv</i>. Cold Spring Harbor Laboratory, 2020. <a href=\"https://doi.org/10.1101/2020.04.08.029405\">https://doi.org/10.1101/2020.04.08.029405</a>.","mla":"Grah, Rok, et al. “Normative Models of Enhancer Function.” <i>BioRxiv</i>, Cold Spring Harbor Laboratory, 2020, doi:<a href=\"https://doi.org/10.1101/2020.04.08.029405\">10.1101/2020.04.08.029405</a>.","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Normative models of enhancer function,” <i>bioRxiv</i>. Cold Spring Harbor Laboratory, 2020.","apa":"Grah, R., Zoller, B., &#38; Tkačik, G. (2020). Normative models of enhancer function. <i>bioRxiv</i>. Cold Spring Harbor Laboratory. <a href=\"https://doi.org/10.1101/2020.04.08.029405\">https://doi.org/10.1101/2020.04.08.029405</a>"},"department":[{"_id":"CaGu"},{"_id":"GaTk"}]},{"date_published":"2020-04-24T00:00:00Z","language":[{"iso":"eng"}],"file":[{"content_type":"application/pdf","relation":"main_file","checksum":"fb9a4468eb27be92690728e35c823796","access_level":"open_access","file_name":"Thesis_without-signatures_PDFA.pdf","file_id":"7692","creator":"stgingl","date_created":"2020-04-28T11:19:21Z","date_updated":"2021-10-31T23:30:05Z","embargo":"2021-10-30","file_size":3268017},{"file_size":5167703,"date_updated":"2021-10-31T23:30:05Z","date_created":"2020-04-28T11:19:24Z","file_id":"7693","creator":"stgingl","file_name":"Thesis_without signatures.docx","checksum":"f6c80ca97104a631a328cb79a2c53493","access_level":"closed","relation":"source_file","embargo_to":"open_access","content_type":"application/octet-stream"}],"page":"98","date_updated":"2023-09-22T09:20:10Z","publication_identifier":{"eissn":["2663-337X"]},"article_processing_charge":"No","month":"04","_id":"7680","oa_version":"None","has_accepted_license":"1","publisher":"Institute of Science and Technology Austria","ddc":["570"],"doi":"10.15479/AT:ISTA:7680","title":"Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals","status":"public","year":"2020","author":[{"full_name":"Kainrath, Stephanie","first_name":"Stephanie","last_name":"Kainrath","id":"32CFBA64-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2021-10-31T23:30:05Z","type":"dissertation","date_created":"2020-04-24T16:00:51Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","degree_awarded":"PhD","supervisor":[{"orcid":"0000-0002-8023-9315","id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","full_name":"Janovjak, Harald L","last_name":"Janovjak","first_name":"Harald L"}],"abstract":[{"lang":"eng","text":"Proteins and their complex dynamic interactions regulate cellular mechanisms from sensing and transducing extracellular signals, to mediating genetic responses, and sustaining or changing cell morphology. To manipulate these protein-protein interactions (PPIs) that govern the behavior and fate of cells, synthetically constructed, genetically encoded tools provide the means to precisely target proteins of interest (POIs), and control their subcellular localization and activity in vitro and in vivo. Ideal synthetic tools react to an orthogonal cue, i.e. a trigger that does not activate any other endogenous process, thereby allowing manipulation of the POI alone.\r\nIn optogenetics, naturally occurring photosensory domain from plants, algae and bacteria are re-purposed and genetically fused to POIs. Illumination with light of a specific wavelength triggers a conformational change that can mediate PPIs, such as dimerization or oligomerization. By using light as a trigger, these tools can be activated with high spatial and temporal precision, on subcellular and millisecond scales. Chemogenetic tools consist of protein domains that recognize and bind small molecules. By genetic fusion to POIs, these domains can mediate PPIs upon addition of their specific ligands, which are often synthetically designed to provide highly specific interactions and exhibit good bioavailability.\r\nMost optogenetic tools to mediate PPIs are based on well-studied photoreceptors responding to red, blue or near-UV light, leaving a striking gap in the green band of the visible light spectrum. Among both optogenetic and chemogenetic tools, there is an abundance of methods to induce PPIs, but tools to disrupt them require UV illumination, rely on covalent linkage and subsequent enzymatic cleavage or initially result in protein clustering of unknown stoichiometry.\r\nThis work describes how the recently structurally and photochemically characterized green-light responsive cobalamin-binding domains (CBDs) from bacterial transcription factors were re-purposed to function as a green-light responsive optogenetic tool. In contrast to previously engineered optogenetic tools, CBDs do not induce PPI, but rather confer a PPI already upon expression, which can be rapidly disrupted by illumination. This was employed to mimic inhibition of constitutive activity of a growth factor receptor, and successfully implement for cell signalling in mammalian cells and in vivo to rescue development in zebrafish. This work further describes the development and application of a chemically induced de-dimerizer (CDD) based on a recently identified and structurally described bacterial oxyreductase. CDD forms a dimer upon expression in absence of its cofactor, the flavin derivative F420. Safety and of domain expression and ligand exposure are demonstrated in vitro and in vivo in zebrafish. The system is further applied to inhibit cell signalling output from a chimeric receptor upon F420 treatment.\r\nCBDs and CDD expand the repertoire of synthetic tools by providing novel mechanisms of mediating PPIs, and by recognizing previously not utilized cues. In the future, they can readily be combined with existing synthetic tools to functionally manipulate PPIs in vitro and in vivo."}],"publication_status":"published","oa":1,"department":[{"_id":"CaGu"}],"citation":{"short":"S. Kainrath, Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals, Institute of Science and Technology Austria, 2020.","ista":"Kainrath S. 2020. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. Institute of Science and Technology Austria.","ama":"Kainrath S. Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7680\">10.15479/AT:ISTA:7680</a>","ieee":"S. Kainrath, “Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals,” Institute of Science and Technology Austria, 2020.","apa":"Kainrath, S. (2020). <i>Synthetic tools for optogenetic and chemogenetic inhibition of cellular signals</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7680\">https://doi.org/10.15479/AT:ISTA:7680</a>","mla":"Kainrath, Stephanie. <i>Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7680\">10.15479/AT:ISTA:7680</a>.","chicago":"Kainrath, Stephanie. “Synthetic Tools for Optogenetic and Chemogenetic Inhibition of Cellular Signals.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7680\">https://doi.org/10.15479/AT:ISTA:7680</a>."},"related_material":{"record":[{"id":"1028","relation":"dissertation_contains","status":"public"}]},"day":"24","alternative_title":["ISTA Thesis"]},{"type":"journal_article","file_date_updated":"2020-07-14T12:48:02Z","author":[{"orcid":"0000-0003-3883-1806","id":"3E7C5304-F248-11E8-B48F-1D18A9856A87","last_name":"Minets","first_name":"Sasha","full_name":"Minets, Sasha"}],"year":"2020","status":"public","title":"Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces","publisher":"Springer Nature","ddc":["510"],"doi":"10.1007/s00029-020-00553-x","oa_version":"Published Version","has_accepted_license":"1","_id":"7683","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","month":"04","publication_identifier":{"issn":["10221824"],"eissn":["14209020"]},"external_id":{"isi":["000526036400001"],"arxiv":["1801.01429"]},"date_updated":"2023-08-21T06:14:58Z","article_type":"original","file":[{"creator":"dernst","file_id":"7690","date_created":"2020-04-28T10:57:58Z","date_updated":"2020-07-14T12:48:02Z","file_size":792469,"content_type":"application/pdf","relation":"main_file","checksum":"2368c4662629b4759295eb365323b2ad","access_level":"open_access","file_name":"2020_SelectaMathematica_Minets.pdf"}],"issue":"2","language":[{"iso":"eng"}],"date_published":"2020-04-15T00:00:00Z","quality_controlled":"1","scopus_import":"1","day":"15","isi":1,"publication":"Selecta Mathematica, New Series","department":[{"_id":"TaHa"}],"citation":{"apa":"Minets, S. (2020). Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. <i>Selecta Mathematica, New Series</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00029-020-00553-x\">https://doi.org/10.1007/s00029-020-00553-x</a>","ieee":"S. Minets, “Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces,” <i>Selecta Mathematica, New Series</i>, vol. 26, no. 2. Springer Nature, 2020.","chicago":"Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” <i>Selecta Mathematica, New Series</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00029-020-00553-x\">https://doi.org/10.1007/s00029-020-00553-x</a>.","mla":"Minets, Sasha. “Cohomological Hall Algebras for Higgs Torsion Sheaves, Moduli of Triples and Sheaves on Surfaces.” <i>Selecta Mathematica, New Series</i>, vol. 26, no. 2, 30, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1007/s00029-020-00553-x\">10.1007/s00029-020-00553-x</a>.","ama":"Minets S. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. <i>Selecta Mathematica, New Series</i>. 2020;26(2). doi:<a href=\"https://doi.org/10.1007/s00029-020-00553-x\">10.1007/s00029-020-00553-x</a>","ista":"Minets S. 2020. Cohomological Hall algebras for Higgs torsion sheaves, moduli of triples and sheaves on surfaces. Selecta Mathematica, New Series. 26(2), 30.","short":"S. Minets, Selecta Mathematica, New Series 26 (2020)."},"oa":1,"publication_status":"published","abstract":[{"text":"For any free oriented Borel–Moore homology theory A, we construct an associative product on the A-theory of the stack of Higgs torsion sheaves over a projective curve C. We show that the resulting algebra AHa0C admits a natural shuffle presentation, and prove it is faithful when A is replaced with usual Borel–Moore homology groups. We also introduce moduli spaces of stable triples, heavily inspired by Nakajima quiver varieties, whose A-theory admits an AHa0C-action. These triples can be interpreted as certain sheaves on PC(ωC⊕OC). In particular, we obtain an action of AHa0C on the cohomology of Hilbert schemes of points on T∗C.","lang":"eng"}],"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"}],"arxiv":1,"article_number":"30","volume":26,"intvolume":"        26","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_created":"2020-04-26T22:00:44Z"},{"publication_status":"published","project":[{"call_identifier":"FP7","name":"Memory-related information processing in neuronal circuits of the hippocampus and entorhinal cortex","grant_number":"281511","_id":"257A4776-B435-11E9-9278-68D0E5697425"}],"pmid":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":106,"intvolume":"       106","date_created":"2020-04-26T22:00:45Z","day":"22","scopus_import":"1","isi":1,"related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/librarian-of-memory/","relation":"press_release"}]},"publication":"Neuron","department":[{"_id":"JoCs"}],"citation":{"chicago":"Gridchyn, Igor, Philipp Schönenberger, Joseph O’Neill, and Jozsef L Csicsvari. “Assembly-Specific Disruption of Hippocampal Replay Leads to Selective Memory Deficit.” <i>Neuron</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuron.2020.01.021\">https://doi.org/10.1016/j.neuron.2020.01.021</a>.","mla":"Gridchyn, Igor, et al. “Assembly-Specific Disruption of Hippocampal Replay Leads to Selective Memory Deficit.” <i>Neuron</i>, vol. 106, no. 2, Elsevier, 2020, p. 291–300.e6, doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.01.021\">10.1016/j.neuron.2020.01.021</a>.","apa":"Gridchyn, I., Schönenberger, P., O’Neill, J., &#38; Csicsvari, J. L. (2020). Assembly-specific disruption of hippocampal replay leads to selective memory deficit. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2020.01.021\">https://doi.org/10.1016/j.neuron.2020.01.021</a>","ieee":"I. Gridchyn, P. Schönenberger, J. O’Neill, and J. L. Csicsvari, “Assembly-specific disruption of hippocampal replay leads to selective memory deficit,” <i>Neuron</i>, vol. 106, no. 2. Elsevier, p. 291–300.e6, 2020.","ama":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. Assembly-specific disruption of hippocampal replay leads to selective memory deficit. <i>Neuron</i>. 2020;106(2):291-300.e6. doi:<a href=\"https://doi.org/10.1016/j.neuron.2020.01.021\">10.1016/j.neuron.2020.01.021</a>","ista":"Gridchyn I, Schönenberger P, O’Neill J, Csicsvari JL. 2020. Assembly-specific disruption of hippocampal replay leads to selective memory deficit. Neuron. 106(2), 291–300.e6.","short":"I. Gridchyn, P. Schönenberger, J. O’Neill, J.L. Csicsvari, Neuron 106 (2020) 291–300.e6."},"ec_funded":1,"oa":1,"_id":"7684","month":"04","article_processing_charge":"No","publication_identifier":{"eissn":["10974199"],"issn":["08966273"]},"article_type":"original","external_id":{"isi":["000528268200013"],"pmid":["32070475"]},"date_updated":"2023-08-21T06:15:31Z","page":"291-300.e6","issue":"2","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-04-22T00:00:00Z","type":"journal_article","main_file_link":[{"url":"https://doi.org/10.1016/j.neuron.2020.01.021","open_access":"1"}],"author":[{"full_name":"Gridchyn, Igor","last_name":"Gridchyn","first_name":"Igor","id":"4B60654C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-1807-1929"},{"id":"3B9D816C-F248-11E8-B48F-1D18A9856A87","full_name":"Schönenberger, Philipp","first_name":"Philipp","last_name":"Schönenberger"},{"last_name":"O'Neill","first_name":"Joseph","full_name":"O'Neill, Joseph","id":"426376DC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","last_name":"Csicsvari"}],"status":"public","title":"Assembly-specific disruption of hippocampal replay leads to selective memory deficit","year":"2020","doi":"10.1016/j.neuron.2020.01.021","publisher":"Elsevier","oa_version":"Published Version"},{"oa_version":"None","doi":"10.1016/j.tplants.2020.04.001","publisher":"Elsevier","status":"public","year":"2020","title":"Neo-gibberellin signaling: Guiding the next generation of the green revolution","author":[{"full_name":"Xue, Huidan","last_name":"Xue","first_name":"Huidan"},{"orcid":"0000-0003-2627-6956","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","full_name":"Zhang, Yuzhou","last_name":"Zhang","first_name":"Yuzhou"},{"first_name":"Guanghui","last_name":"Xiao","full_name":"Xiao, Guanghui"}],"type":"journal_article","date_published":"2020-06-01T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"issue":"6","page":"520-522","article_type":"original","date_updated":"2023-08-21T06:16:01Z","external_id":{"pmid":["32407691"],"isi":["000533518400003"]},"publication_identifier":{"issn":["1360-1385"]},"month":"06","article_processing_charge":"No","_id":"7686","department":[{"_id":"JiFr"}],"citation":{"ista":"Xue H, Zhang Y, Xiao G. 2020. Neo-gibberellin signaling: Guiding the next generation of the green revolution. Trends in Plant Science. 25(6), 520–522.","ama":"Xue H, Zhang Y, Xiao G. Neo-gibberellin signaling: Guiding the next generation of the green revolution. <i>Trends in Plant Science</i>. 2020;25(6):520-522. doi:<a href=\"https://doi.org/10.1016/j.tplants.2020.04.001\">10.1016/j.tplants.2020.04.001</a>","short":"H. Xue, Y. Zhang, G. Xiao, Trends in Plant Science 25 (2020) 520–522.","chicago":"Xue, Huidan, Yuzhou Zhang, and Guanghui Xiao. “Neo-Gibberellin Signaling: Guiding the next Generation of the Green Revolution.” <i>Trends in Plant Science</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.tplants.2020.04.001\">https://doi.org/10.1016/j.tplants.2020.04.001</a>.","mla":"Xue, Huidan, et al. “Neo-Gibberellin Signaling: Guiding the next Generation of the Green Revolution.” <i>Trends in Plant Science</i>, vol. 25, no. 6, Elsevier, 2020, pp. 520–22, doi:<a href=\"https://doi.org/10.1016/j.tplants.2020.04.001\">10.1016/j.tplants.2020.04.001</a>.","apa":"Xue, H., Zhang, Y., &#38; Xiao, G. (2020). Neo-gibberellin signaling: Guiding the next generation of the green revolution. <i>Trends in Plant Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.tplants.2020.04.001\">https://doi.org/10.1016/j.tplants.2020.04.001</a>","ieee":"H. Xue, Y. Zhang, and G. Xiao, “Neo-gibberellin signaling: Guiding the next generation of the green revolution,” <i>Trends in Plant Science</i>, vol. 25, no. 6. Elsevier, pp. 520–522, 2020."},"publication":"Trends in Plant Science","isi":1,"day":"01","scopus_import":"1","date_created":"2020-04-26T22:00:46Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"        25","volume":25,"pmid":1,"publication_status":"published","abstract":[{"text":"The agricultural green revolution spectacularly enhanced crop yield and lodging resistance with modified DELLA-mediated gibberellin signaling. However, this was achieved at the expense of reduced nitrogen-use efficiency (NUE). Recently, Wu et al. revealed novel gibberellin signaling that provides a blueprint for improving tillering and NUE in Green Revolution varieties (GRVs). ","lang":"eng"}]},{"department":[{"_id":"E-Lib"}],"citation":{"apa":"Ernst, D., Novotny, G., &#38; Schönher, E. M. (2020). (Core Trust) Seal your repository! <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare. <a href=\"https://doi.org/10.31263/voebm.v73i1.3491\">https://doi.org/10.31263/voebm.v73i1.3491</a>","ieee":"D. Ernst, G. Novotny, and E. M. Schönher, “(Core Trust) Seal your repository!,” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 73, no. 1. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, pp. 46–59, 2020.","chicago":"Ernst, Doris, Gertraud Novotny, and Eva Maria Schönher. “(Core Trust) Seal your repository!” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020. <a href=\"https://doi.org/10.31263/voebm.v73i1.3491\">https://doi.org/10.31263/voebm.v73i1.3491</a>.","mla":"Ernst, Doris, et al. “(Core Trust) Seal your repository!” <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>, vol. 73, no. 1, Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare, 2020, pp. 46–59, doi:<a href=\"https://doi.org/10.31263/voebm.v73i1.3491\">10.31263/voebm.v73i1.3491</a>.","ista":"Ernst D, Novotny G, Schönher EM. 2020. (Core Trust) Seal your repository! Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare. 73(1), 46–59.","ama":"Ernst D, Novotny G, Schönher EM. (Core Trust) Seal your repository! <i>Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare</i>. 2020;73(1):46-59. doi:<a href=\"https://doi.org/10.31263/voebm.v73i1.3491\">10.31263/voebm.v73i1.3491</a>","short":"D. Ernst, G. Novotny, E.M. Schönher, Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare 73 (2020) 46–59."},"publication":"Mitteilungen der Vereinigung Österreichischer Bibliothekarinnen und Bibliothekare","oa":1,"day":"28","scopus_import":"1","date_created":"2020-04-28T08:37:38Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":73,"intvolume":"        73","abstract":[{"text":"A working group, which was established within the Network of Repository Managers  (RepManNet),  has  dealt  with  common  certifications  for  repositories.  In addition,  current  requirements  of  the  research  funding  agencies  FWF  and  EU  were also taken into account. The Core Trust Seal was examined in more detail. For this purpose,  a  questionnaire  was  sent  to  those  organizations  that  are  already  certified with CTS in Austria. The answers were summarized and evaluated anonymously. It is recommended to go for a repository certification. Moreover, the development of a DINI certificate in Austria is strongly suggested.","lang":"eng"},{"lang":"ger","text":" Eine Arbeitsgruppe, die im Rahmen des Netzwerks für RepositorienmanagerInnen (RepManNet) entstanden ist, hat sich mit gängigen Zertifizierungen für Repositorien beschäftigt. Weiters wurden aktuelle Vorgaben der Forschungsförderer FWF und EU herangezogen. Das Core Trust Seal wurde genauer betrachtet. Hierfür  wurden jenen  Organisationen,  die  in  Österreich  bereits  mit  CTS  zertifiziert sind, ein Fragebogen übermittelt. Die Antworten wurden anonymisiert zusammengefasst und ausgewertet. Plädiert wird für eine Zertifizierung von Repositorien und die Entwicklung einer DINI-Zertifizierung in Österreich."}],"publication_status":"published","doi":"10.31263/voebm.v73i1.3491","publisher":"Vereinigung Osterreichischer Bibliothekarinnen und Bibliothekare","ddc":["020"],"title":"(Core Trust) Seal your repository!","status":"public","year":"2020","has_accepted_license":"1","oa_version":"Published Version","type":"journal_article","author":[{"last_name":"Ernst","first_name":"Doris","full_name":"Ernst, Doris","id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2354-0195"},{"full_name":"Novotny, Gertraud","first_name":"Gertraud","last_name":"Novotny"},{"last_name":"Schönher","first_name":"Eva Maria","full_name":"Schönher, Eva Maria"}],"file_date_updated":"2023-04-03T09:17:25Z","page":"46-59","issue":"1","file":[{"creator":"dernst","file_id":"7970","date_created":"2020-06-17T10:50:13Z","date_updated":"2023-04-03T09:17:25Z","file_size":579291,"content_type":"application/pdf","checksum":"fee784f15a489deb7def6ccf8c5bf8c3","relation":"main_file","access_level":"open_access","file_name":"2020_VOEB_Ernst.pdf"}],"popular_science":"1","article_type":"original","date_updated":"2024-02-27T13:41:03Z","date_published":"2020-04-28T00:00:00Z","language":[{"iso":"ger"}],"month":"04","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","_id":"7687","publication_identifier":{"issn":["1022-2588"]}},{"related_material":{"record":[{"status":"public","relation":"used_in_publication","id":"8203"}]},"author":[{"id":"38DB5788-F248-11E8-B48F-1D18A9856A87","full_name":"Katsaros, Georgios","first_name":"Georgios","last_name":"Katsaros","orcid":"0000-0001-8342-202X"}],"file_date_updated":"2020-07-14T12:48:02Z","license":"https://creativecommons.org/publicdomain/zero/1.0/","type":"research_data","day":"01","has_accepted_license":"1","ec_funded":1,"oa":1,"oa_version":"Published Version","publisher":"Institute of Science and Technology Austria","ddc":["530"],"department":[{"_id":"GeKa"}],"doi":"10.15479/AT:ISTA:7689","citation":{"chicago":"Katsaros, Georgios. “Supplementary Data for ‘Zero Field Splitting of Heavy-Hole States in Quantum Dots.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7689\">https://doi.org/10.15479/AT:ISTA:7689</a>.","mla":"Katsaros, Georgios. <i>Supplementary Data for “Zero Field Splitting of Heavy-Hole States in Quantum Dots.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7689\">10.15479/AT:ISTA:7689</a>.","ieee":"G. Katsaros, “Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots.’” Institute of Science and Technology Austria, 2020.","apa":"Katsaros, G. (2020). Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7689\">https://doi.org/10.15479/AT:ISTA:7689</a>","ista":"Katsaros G. 2020. Supplementary data for ‘Zero field splitting of heavy-hole states in quantum dots’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:7689\">10.15479/AT:ISTA:7689</a>.","ama":"Katsaros G. Supplementary data for “Zero field splitting of heavy-hole states in quantum dots.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7689\">10.15479/AT:ISTA:7689</a>","short":"G. Katsaros, (2020)."},"title":"Supplementary data for \"Zero field splitting of heavy-hole states in quantum dots\"","status":"public","year":"2020","project":[{"call_identifier":"H2020","grant_number":"862046","name":"TOPOLOGICALLY PROTECTED AND SCALABLE QUANTUM BITS","_id":"237E5020-32DE-11EA-91FC-C7463DDC885E"},{"name":"Towards scalable hut wire quantum devices","_id":"237B3DA4-32DE-11EA-91FC-C7463DDC885E","grant_number":"P32235","call_identifier":"FWF"}],"tmp":{"legal_code_url":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","short":"CC0 (1.0)","image":"/images/cc_0.png","name":"Creative Commons Public Domain Dedication (CC0 1.0)"},"article_processing_charge":"No","month":"05","abstract":[{"text":"These are the supplementary research data to the publication \"Zero field splitting of heavy-hole states in quantum dots\". All matrix files have the same format. Within each column the bias voltage is changed. Each column corresponds to either a different gate voltage or magnetic field. The voltage values are given in mV, the current values in pA. Find a specific description in the included Readme file.\r\n","lang":"eng"}],"_id":"7689","contributor":[{"last_name":"Katsaros","first_name":"Georgios","contributor_type":"contact_person","id":"38DB5788-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2020-05-01T00:00:00Z","date_created":"2020-05-01T15:14:46Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"7786","creator":"gkatsaro","date_created":"2020-05-01T15:13:28Z","date_updated":"2020-07-14T12:48:02Z","file_size":5514403,"content_type":"application/x-zip-compressed","access_level":"open_access","relation":"main_file","checksum":"d23c0cb9e2d19e14e2f902b88b97c05d","file_name":"DOI_ZeroFieldSplitting.zip"}],"date_updated":"2024-02-21T12:44:02Z"},{"scopus_import":"1","day":"01","isi":1,"oa":1,"publication":"Plant Physiology","department":[{"_id":"JiFr"}],"citation":{"mla":"Wang, J., et al. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” <i>Plant Physiology</i>, vol. 183, no. 3, American Society of Plant Biologists, 2020, pp. 986–97, doi:<a href=\"https://doi.org/10.1104/pp.20.00178\">10.1104/pp.20.00178</a>.","chicago":"Wang, J, E Mylle, Alexander J Johnson, N Besbrugge, G De Jaeger, Jiří Friml, R Pleskot, and D van Damme. “High Temporal Resolution Reveals Simultaneous Plasma Membrane Recruitment of TPLATE Complex Subunits.” <i>Plant Physiology</i>. American Society of Plant Biologists, 2020. <a href=\"https://doi.org/10.1104/pp.20.00178\">https://doi.org/10.1104/pp.20.00178</a>.","apa":"Wang, J., Mylle, E., Johnson, A. J., Besbrugge, N., De Jaeger, G., Friml, J., … van Damme, D. (2020). High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. <i>Plant Physiology</i>. American Society of Plant Biologists. <a href=\"https://doi.org/10.1104/pp.20.00178\">https://doi.org/10.1104/pp.20.00178</a>","ieee":"J. Wang <i>et al.</i>, “High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits,” <i>Plant Physiology</i>, vol. 183, no. 3. American Society of Plant Biologists, pp. 986–997, 2020.","short":"J. Wang, E. Mylle, A.J. Johnson, N. Besbrugge, G. De Jaeger, J. Friml, R. Pleskot, D. van Damme, Plant Physiology 183 (2020) 986–997.","ama":"Wang J, Mylle E, Johnson AJ, et al. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. <i>Plant Physiology</i>. 2020;183(3):986-997. doi:<a href=\"https://doi.org/10.1104/pp.20.00178\">10.1104/pp.20.00178</a>","ista":"Wang J, Mylle E, Johnson AJ, Besbrugge N, De Jaeger G, Friml J, Pleskot R, van Damme D. 2020. High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits. Plant Physiology. 183(3), 986–997."},"project":[{"call_identifier":"FWF","_id":"26538374-B435-11E9-9278-68D0E5697425","name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630"}],"publication_status":"published","abstract":[{"text":"The TPLATE complex (TPC) is a key endocytic adaptor protein complex in plants. TPC in Arabidopsis (Arabidopsis thaliana) contains six evolutionarily conserved subunits and two plant-specific subunits, AtEH1/Pan1 and AtEH2/Pan1, although cytoplasmic proteins are not associated with the hexameric subcomplex in the cytoplasm. To investigate the dynamic assembly of the octameric TPC at the plasma membrane (PM), we performed state-of-the-art dual-color live cell imaging at physiological and lowered temperatures. Lowering the temperature slowed down endocytosis, thereby enhancing the temporal resolution of the differential recruitment of endocytic components. Under both normal and lowered temperature conditions, the core TPC subunit TPLATE and the AtEH/Pan1 proteins exhibited simultaneous recruitment at the PM. These results, together with co-localization analysis of different TPC subunits, allow us to conclude that TPC in plant cells is not recruited to the PM sequentially but as an octameric complex.","lang":"eng"}],"intvolume":"       183","volume":183,"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2020-04-29T15:23:00Z","pmid":1,"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/2020.02.13.948109"}],"author":[{"last_name":"Wang","first_name":"J","full_name":"Wang, J"},{"full_name":"Mylle, E","first_name":"E","last_name":"Mylle"},{"full_name":"Johnson, Alexander J","last_name":"Johnson","first_name":"Alexander J","id":"46A62C3A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2739-8843"},{"last_name":"Besbrugge","first_name":"N","full_name":"Besbrugge, N"},{"first_name":"G","last_name":"De Jaeger","full_name":"De Jaeger, G"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří","orcid":"0000-0002-8302-7596"},{"full_name":"Pleskot, R","first_name":"R","last_name":"Pleskot"},{"full_name":"van Damme, D","last_name":"van Damme","first_name":"D"}],"type":"journal_article","oa_version":"Preprint","title":"High temporal resolution reveals simultaneous plasma membrane recruitment of TPLATE complex subunits","year":"2020","status":"public","publisher":"American Society of Plant Biologists","doi":"10.1104/pp.20.00178","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"_id":"7695","article_processing_charge":"No","month":"07","language":[{"iso":"eng"}],"date_published":"2020-07-01T00:00:00Z","quality_controlled":"1","external_id":{"isi":["000550682000018"],"pmid":["32321842"]},"date_updated":"2023-09-05T12:20:02Z","article_type":"original","page":"986-997","issue":"3"},{"oa":1,"ec_funded":1,"citation":{"ista":"Zhang Y, Hartinger C, Wang X, Friml J. 2020. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. New Phytologist. 227(5), 1406–1416.","ama":"Zhang Y, Hartinger C, Wang X, Friml J. Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. <i>New Phytologist</i>. 2020;227(5):1406-1416. doi:<a href=\"https://doi.org/10.1111/nph.16629\">10.1111/nph.16629</a>","short":"Y. Zhang, C. Hartinger, X. Wang, J. Friml, New Phytologist 227 (2020) 1406–1416.","chicago":"Zhang, Yuzhou, Corinna Hartinger, Xiaojuan Wang, and Jiří Friml. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” <i>New Phytologist</i>. Wiley, 2020. <a href=\"https://doi.org/10.1111/nph.16629\">https://doi.org/10.1111/nph.16629</a>.","mla":"Zhang, Yuzhou, et al. “Directional Auxin Fluxes in Plants by Intramolecular Domain‐domain Co‐evolution of PIN Auxin Transporters.” <i>New Phytologist</i>, vol. 227, no. 5, Wiley, 2020, pp. 1406–16, doi:<a href=\"https://doi.org/10.1111/nph.16629\">10.1111/nph.16629</a>.","apa":"Zhang, Y., Hartinger, C., Wang, X., &#38; Friml, J. (2020). Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters. <i>New Phytologist</i>. Wiley. <a href=\"https://doi.org/10.1111/nph.16629\">https://doi.org/10.1111/nph.16629</a>","ieee":"Y. Zhang, C. Hartinger, X. Wang, and J. Friml, “Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters,” <i>New Phytologist</i>, vol. 227, no. 5. Wiley, pp. 1406–1416, 2020."},"department":[{"_id":"JiFr"}],"publication":"New Phytologist","isi":1,"scopus_import":"1","day":"01","date_created":"2020-04-30T08:43:29Z","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","intvolume":"       227","volume":227,"pmid":1,"project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","grant_number":"I03630","_id":"26538374-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"abstract":[{"text":"* Morphogenesis and adaptive tropic growth in plants depend on gradients of the phytohormone auxin, mediated by the membrane‐based PIN‐FORMED (PIN) auxin transporters. PINs localize to a particular side of the plasma membrane (PM) or to the endoplasmic reticulum (ER) to directionally transport auxin and maintain intercellular and intracellular auxin homeostasis, respectively. However, the molecular cues that confer their diverse cellular localizations remain largely unknown.\r\n* In this study, we systematically swapped the domains between ER‐ and PM‐localized PIN proteins, as well as between apical and basal PM‐localized PINs from Arabidopsis thaliana , to shed light on why PIN family members with similar topological structures reside at different membrane compartments within cells.\r\n* Our results show that not only do the N‐ and C‐terminal transmembrane domains (TMDs) and central hydrophilic loop contribute to their differential subcellular localizations and cellular polarity, but that the pairwise‐matched N‐ and C‐terminal TMDs resulting from intramolecular domain–domain coevolution are also crucial for their divergent patterns of localization.\r\n* These findings illustrate the complexity of the evolutionary path of PIN proteins in acquiring their plethora of developmental functions and adaptive growth in plants.","lang":"eng"}],"publication_status":"published","has_accepted_license":"1","oa_version":"Published Version","doi":"10.1111/nph.16629","publisher":"Wiley","ddc":["580"],"status":"public","title":"Directional auxin fluxes in plants by intramolecular domain‐domain co‐evolution of PIN auxin transporters","year":"2020","author":[{"orcid":"0000-0003-2627-6956","full_name":"Zhang, Yuzhou","first_name":"Yuzhou","last_name":"Zhang","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87"},{"id":"AEFB2266-8ABF-11EA-AA39-812C3623CBE4","full_name":"Hartinger, Corinna","last_name":"Hartinger","first_name":"Corinna","orcid":"0000-0003-1618-2737"},{"first_name":"Xiaojuan","last_name":"Wang","full_name":"Wang, Xiaojuan"},{"orcid":"0000-0002-8302-7596","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","last_name":"Friml","first_name":"Jiří"}],"file_date_updated":"2020-11-24T12:19:38Z","type":"journal_article","date_published":"2020-09-01T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"issue":"5","page":"1406-1416","file":[{"date_updated":"2020-11-24T12:19:38Z","file_size":3643395,"file_id":"8799","success":1,"creator":"dernst","date_created":"2020-11-24T12:19:38Z","checksum":"8e8150dbbba8cb65b72f81d1f0864b8b","relation":"main_file","access_level":"open_access","file_name":"2020_09_NewPhytologist_Zhang.pdf","content_type":"application/pdf"}],"article_type":"original","date_updated":"2023-09-05T15:46:04Z","external_id":{"pmid":["32350870"],"isi":["000534092400001"]},"publication_identifier":{"issn":["0028-646X"],"eissn":["1469-8137"]},"month":"09","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"Yes (via OA deal)","_id":"7697"},{"month":"03","publication_status":"published","abstract":[{"text":"The growing sample size of genome-wide association studies has facilitated the discovery of gene-environment interactions (GxE). Here we propose a maximum likelihood method to estimate the contribution of GxE to continuous traits taking into account all interacting environmental variables, without the need to measure any. Extensive simulations demonstrate that our method provides unbiased interaction estimates and excellent coverage. We also offer strategies to distinguish specific GxE from general scale effects. Applying our method to 32 traits in the UK Biobank reveals that while the genetic risk score (GRS) of 376 variants explains 5.2% of body mass index (BMI) variance, GRSxE explains an additional 1.9%. Nevertheless, this interaction holds for any variable with identical correlation to BMI as the GRS, hence may not be GRS-specific. Still, we observe that the global contribution of specific GRSxE to complex traits is substantial for nine obesity-related measures (including leg impedance and trunk fat-free mass).","lang":"eng"}],"article_processing_charge":"No","_id":"7707","article_number":"1385","publication_identifier":{"issn":["2041-1723"]},"extern":"1","article_type":"original","date_updated":"2021-01-12T08:14:59Z","date_created":"2020-04-30T10:39:33Z","date_published":"2020-03-20T00:00:00Z","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":11,"intvolume":"        11","language":[{"iso":"eng"}],"type":"journal_article","day":"20","author":[{"last_name":"Sulc","first_name":"Jonathan","full_name":"Sulc, Jonathan"},{"first_name":"Ninon","last_name":"Mounier","full_name":"Mounier, Ninon"},{"first_name":"Felix","last_name":"Günther","full_name":"Günther, Felix"},{"full_name":"Winkler, Thomas","first_name":"Thomas","last_name":"Winkler"},{"first_name":"Andrew R.","last_name":"Wood","full_name":"Wood, Andrew R."},{"full_name":"Frayling, Timothy M.","first_name":"Timothy M.","last_name":"Frayling"},{"first_name":"Iris M.","last_name":"Heid","full_name":"Heid, Iris M."},{"orcid":"0000-0001-8982-8813","last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425"},{"last_name":"Kutalik","first_name":"Zoltán","full_name":"Kutalik, Zoltán"}],"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41467-020-15107-0"}],"doi":"10.1038/s41467-020-15107-0","citation":{"ieee":"J. Sulc <i>et al.</i>, “Quantification of the overall contribution of gene-environment interaction for obesity-related traits,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020.","apa":"Sulc, J., Mounier, N., Günther, F., Winkler, T., Wood, A. R., Frayling, T. M., … Kutalik, Z. (2020). Quantification of the overall contribution of gene-environment interaction for obesity-related traits. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-15107-0\">https://doi.org/10.1038/s41467-020-15107-0</a>","mla":"Sulc, Jonathan, et al. “Quantification of the Overall Contribution of Gene-Environment Interaction for Obesity-Related Traits.” <i>Nature Communications</i>, vol. 11, 1385, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-15107-0\">10.1038/s41467-020-15107-0</a>.","chicago":"Sulc, Jonathan, Ninon Mounier, Felix Günther, Thomas Winkler, Andrew R. Wood, Timothy M. Frayling, Iris M. Heid, Matthew Richard Robinson, and Zoltán Kutalik. “Quantification of the Overall Contribution of Gene-Environment Interaction for Obesity-Related Traits.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-15107-0\">https://doi.org/10.1038/s41467-020-15107-0</a>.","short":"J. Sulc, N. Mounier, F. Günther, T. Winkler, A.R. Wood, T.M. Frayling, I.M. Heid, M.R. Robinson, Z. Kutalik, Nature Communications 11 (2020).","ista":"Sulc J, Mounier N, Günther F, Winkler T, Wood AR, Frayling TM, Heid IM, Robinson MR, Kutalik Z. 2020. Quantification of the overall contribution of gene-environment interaction for obesity-related traits. Nature Communications. 11, 1385.","ama":"Sulc J, Mounier N, Günther F, et al. Quantification of the overall contribution of gene-environment interaction for obesity-related traits. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-15107-0\">10.1038/s41467-020-15107-0</a>"},"publisher":"Springer Nature","publication":"Nature Communications","title":"Quantification of the overall contribution of gene-environment interaction for obesity-related traits","status":"public","year":"2020","oa_version":"Published Version","oa":1},{"oa":1,"oa_version":"Published Version","title":"Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis","publication":"npj Genomic Medicine","year":"2020","status":"public","doi":"10.1038/s41525-020-0118-3","citation":{"ista":"Nabais MF, Lin T, Benyamin B, Williams KL, Garton FC, Vinkhuyzen AAE, Zhang F, Vallerga CL, Restuadi R, Freydenzon A, Zwamborn RAJ, Hop PJ, Robinson MR, Gratten J, Visscher PM, Hannon E, Mill J, Brown MA, Laing NG, Mather KA, Sachdev PS, Ngo ST, Steyn FJ, Wallace L, Henders AK, Needham M, Veldink JH, Mathers S, Nicholson G, Rowe DB, Henderson RD, McCombe PA, Pamphlett R, Yang J, Blair IP, McRae AF, Wray NR. 2020. Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. npj Genomic Medicine. 5, 10.","ama":"Nabais MF, Lin T, Benyamin B, et al. Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. <i>npj Genomic Medicine</i>. 2020;5. doi:<a href=\"https://doi.org/10.1038/s41525-020-0118-3\">10.1038/s41525-020-0118-3</a>","short":"M.F. Nabais, T. Lin, B. Benyamin, K.L. Williams, F.C. Garton, A.A.E. Vinkhuyzen, F. Zhang, C.L. Vallerga, R. Restuadi, A. Freydenzon, R.A.J. Zwamborn, P.J. Hop, M.R. Robinson, J. Gratten, P.M. Visscher, E. Hannon, J. Mill, M.A. Brown, N.G. Laing, K.A. Mather, P.S. Sachdev, S.T. Ngo, F.J. Steyn, L. Wallace, A.K. Henders, M. Needham, J.H. Veldink, S. Mathers, G. Nicholson, D.B. Rowe, R.D. Henderson, P.A. McCombe, R. Pamphlett, J. Yang, I.P. Blair, A.F. McRae, N.R. Wray, Npj Genomic Medicine 5 (2020).","apa":"Nabais, M. F., Lin, T., Benyamin, B., Williams, K. L., Garton, F. C., Vinkhuyzen, A. A. E., … Wray, N. R. (2020). Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis. <i>Npj Genomic Medicine</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41525-020-0118-3\">https://doi.org/10.1038/s41525-020-0118-3</a>","ieee":"M. F. Nabais <i>et al.</i>, “Significant out-of-sample classification from methylation profile scoring for amyotrophic lateral sclerosis,” <i>npj Genomic Medicine</i>, vol. 5. Springer Nature, 2020.","chicago":"Nabais, Marta F., Tian Lin, Beben Benyamin, Kelly L. Williams, Fleur C. Garton, Anna A. E. Vinkhuyzen, Futao Zhang, et al. “Significant Out-of-Sample Classification from Methylation Profile Scoring for Amyotrophic Lateral Sclerosis.” <i>Npj Genomic Medicine</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41525-020-0118-3\">https://doi.org/10.1038/s41525-020-0118-3</a>.","mla":"Nabais, Marta F., et al. “Significant Out-of-Sample Classification from Methylation Profile Scoring for Amyotrophic Lateral Sclerosis.” <i>Npj Genomic Medicine</i>, vol. 5, 10, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41525-020-0118-3\">10.1038/s41525-020-0118-3</a>."},"publisher":"Springer Nature","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41525-020-0118-3"}],"author":[{"first_name":"Marta F.","last_name":"Nabais","full_name":"Nabais, Marta F."},{"full_name":"Lin, Tian","first_name":"Tian","last_name":"Lin"},{"first_name":"Beben","last_name":"Benyamin","full_name":"Benyamin, Beben"},{"first_name":"Kelly L.","last_name":"Williams","full_name":"Williams, Kelly L."},{"last_name":"Garton","first_name":"Fleur C.","full_name":"Garton, Fleur C."},{"last_name":"Vinkhuyzen","first_name":"Anna A. E.","full_name":"Vinkhuyzen, Anna A. E."},{"first_name":"Futao","last_name":"Zhang","full_name":"Zhang, Futao"},{"full_name":"Vallerga, Costanza L.","last_name":"Vallerga","first_name":"Costanza L."},{"first_name":"Restuadi","last_name":"Restuadi","full_name":"Restuadi, Restuadi"},{"first_name":"Anna","last_name":"Freydenzon","full_name":"Freydenzon, Anna"},{"full_name":"Zwamborn, Ramona A. J.","first_name":"Ramona A. J.","last_name":"Zwamborn"},{"first_name":"Paul J.","last_name":"Hop","full_name":"Hop, Paul J."},{"last_name":"Robinson","first_name":"Matthew Richard","full_name":"Robinson, Matthew Richard","id":"E5D42276-F5DA-11E9-8E24-6303E6697425","orcid":"0000-0001-8982-8813"},{"first_name":"Jacob","last_name":"Gratten","full_name":"Gratten, Jacob"},{"last_name":"Visscher","first_name":"Peter M.","full_name":"Visscher, Peter M."},{"last_name":"Hannon","first_name":"Eilis","full_name":"Hannon, Eilis"},{"full_name":"Mill, Jonathan","first_name":"Jonathan","last_name":"Mill"},{"full_name":"Brown, Matthew A.","last_name":"Brown","first_name":"Matthew A."},{"full_name":"Laing, Nigel G.","last_name":"Laing","first_name":"Nigel G."},{"full_name":"Mather, Karen A.","first_name":"Karen A.","last_name":"Mather"},{"full_name":"Sachdev, Perminder S.","first_name":"Perminder S.","last_name":"Sachdev"},{"full_name":"Ngo, Shyuan T.","first_name":"Shyuan T.","last_name":"Ngo"},{"full_name":"Steyn, Frederik J.","first_name":"Frederik J.","last_name":"Steyn"},{"last_name":"Wallace","first_name":"Leanne","full_name":"Wallace, Leanne"},{"full_name":"Henders, Anjali K.","last_name":"Henders","first_name":"Anjali K."},{"full_name":"Needham, Merrilee","last_name":"Needham","first_name":"Merrilee"},{"first_name":"Jan H.","last_name":"Veldink","full_name":"Veldink, Jan H."},{"full_name":"Mathers, Susan","last_name":"Mathers","first_name":"Susan"},{"last_name":"Nicholson","first_name":"Garth","full_name":"Nicholson, Garth"},{"last_name":"Rowe","first_name":"Dominic B.","full_name":"Rowe, Dominic B."},{"full_name":"Henderson, Robert D.","first_name":"Robert D.","last_name":"Henderson"},{"full_name":"McCombe, Pamela A.","first_name":"Pamela A.","last_name":"McCombe"},{"full_name":"Pamphlett, Roger","first_name":"Roger","last_name":"Pamphlett"},{"last_name":"Yang","first_name":"Jian","full_name":"Yang, Jian"},{"full_name":"Blair, Ian P.","first_name":"Ian P.","last_name":"Blair"},{"first_name":"Allan F.","last_name":"McRae","full_name":"McRae, Allan F."},{"last_name":"Wray","first_name":"Naomi R.","full_name":"Wray, Naomi R."}],"day":"27","type":"journal_article","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","volume":5,"intvolume":"         5","language":[{"iso":"eng"}],"date_published":"2020-02-27T00:00:00Z","quality_controlled":"1","date_created":"2020-04-30T10:39:54Z","article_type":"original","date_updated":"2021-01-12T08:14:59Z","extern":"1","publication_identifier":{"issn":["2056-7944"]},"article_number":"10","_id":"7708","month":"02","abstract":[{"text":"We conducted DNA methylation association analyses using Illumina 450K data from whole blood for an Australian amyotrophic lateral sclerosis (ALS) case–control cohort (782 cases and 613 controls). Analyses used mixed linear models as implemented in the OSCA software. We found a significantly higher proportion of neutrophils in cases compared to controls which replicated in an independent cohort from the Netherlands (1159 cases and 637 controls). The OSCA MOMENT linear mixed model has been shown in simulations to best account for confounders. When combined in a methylation profile score, the 25 most-associated probes identified by MOMENT significantly classified case–control status in the Netherlands sample (area under the curve, AUC = 0.65, CI95% = [0.62–0.68], p = 8.3 × 10−22). The maximum AUC achieved was 0.69 (CI95% = [0.66–0.71], p = 4.3 × 10−34) when cell-type proportion was included in the predictor.","lang":"eng"}],"publication_status":"published","article_processing_charge":"No"},{"file_date_updated":"2020-10-08T08:34:53Z","author":[{"full_name":"Hikaru, Ibayashi","last_name":"Hikaru","first_name":"Ibayashi"},{"orcid":"0000-0001-6646-5546","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","last_name":"Wojtan","first_name":"Christopher J","full_name":"Wojtan, Christopher J"},{"full_name":"Thuerey, Nils","last_name":"Thuerey","first_name":"Nils"},{"full_name":"Igarashi, Takeo","first_name":"Takeo","last_name":"Igarashi"},{"last_name":"Ando","first_name":"Ryoichi","full_name":"Ando, Ryoichi"}],"type":"journal_article","oa_version":"Submitted Version","has_accepted_license":"1","status":"public","year":"2020","title":"Simulating liquids on dynamically warping grids","acknowledgement":"This work was partially supported by JSPS Grant-in-Aid forYoung Scientists (Start-up) 16H07410, the ERC StartingGrantsrealFlow(StG-2015-637014) andBigSplash(StG-2014-638176). This research was supported by the Scientific Ser-vice Units (SSU) of IST Austria through resources providedby Scientific Computing. We would like to express my grati-tude to Nobuyuki Umetani and Tomas Skrivan for insight-ful discussion.","ddc":["006"],"publisher":"IEEE","doi":"10.1109/TVCG.2018.2883628","publication_identifier":{"issn":["10772626"],"eissn":["19410506"]},"_id":"5681","article_processing_charge":"No","month":"06","language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-06-01T00:00:00Z","date_updated":"2023-09-18T09:30:01Z","external_id":{"pmid":["30507534"],"isi":["000532295600014"]},"article_type":"original","file":[{"date_updated":"2020-10-08T08:34:53Z","file_size":21910098,"creator":"wojtan","file_id":"8626","success":1,"date_created":"2020-10-08T08:34:53Z","relation":"main_file","access_level":"open_access","checksum":"8d4c55443a0ee335bb5bb652de503042","file_name":"preprint.pdf","content_type":"application/pdf"}],"page":"2288-2302","issue":"6","acknowledged_ssus":[{"_id":"ScienComp"}],"day":"01","scopus_import":"1","isi":1,"oa":1,"publication":"IEEE Transactions on Visualization and Computer Graphics","department":[{"_id":"ChWo"}],"citation":{"ieee":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, and R. Ando, “Simulating liquids on dynamically warping grids,” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 26, no. 6. IEEE, pp. 2288–2302, 2020.","apa":"Hikaru, I., Wojtan, C., Thuerey, N., Igarashi, T., &#38; Ando, R. (2020). Simulating liquids on dynamically warping grids. <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE. <a href=\"https://doi.org/10.1109/TVCG.2018.2883628\">https://doi.org/10.1109/TVCG.2018.2883628</a>","mla":"Hikaru, Ibayashi, et al. “Simulating Liquids on Dynamically Warping Grids.” <i>IEEE Transactions on Visualization and Computer Graphics</i>, vol. 26, no. 6, IEEE, 2020, pp. 2288–302, doi:<a href=\"https://doi.org/10.1109/TVCG.2018.2883628\">10.1109/TVCG.2018.2883628</a>.","chicago":"Hikaru, Ibayashi, Chris Wojtan, Nils Thuerey, Takeo Igarashi, and Ryoichi Ando. “Simulating Liquids on Dynamically Warping Grids.” <i>IEEE Transactions on Visualization and Computer Graphics</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/TVCG.2018.2883628\">https://doi.org/10.1109/TVCG.2018.2883628</a>.","short":"I. Hikaru, C. Wojtan, N. Thuerey, T. Igarashi, R. Ando, IEEE Transactions on Visualization and Computer Graphics 26 (2020) 2288–2302.","ista":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. 2020. Simulating liquids on dynamically warping grids. IEEE Transactions on Visualization and Computer Graphics. 26(6), 2288–2302.","ama":"Hikaru I, Wojtan C, Thuerey N, Igarashi T, Ando R. Simulating liquids on dynamically warping grids. <i>IEEE Transactions on Visualization and Computer Graphics</i>. 2020;26(6):2288-2302. doi:<a href=\"https://doi.org/10.1109/TVCG.2018.2883628\">10.1109/TVCG.2018.2883628</a>"},"abstract":[{"lang":"eng","text":"We introduce dynamically warping grids for adaptive liquid simulation. Our primary contributions are a strategy for dynamically deforming regular grids over the course of a simulation and a method for efficiently utilizing these deforming grids for liquid simulation. Prior work has shown that unstructured grids are very effective for adaptive fluid simulations. However, unstructured grids often lead to complicated implementations and a poor cache hit rate due to inconsistent memory access. Regular grids, on the other hand, provide a fast, fixed memory access pattern and straightforward implementation. Our method combines the advantages of both: we leverage the simplicity of regular grids while still achieving practical and controllable spatial adaptivity. We demonstrate that our method enables adaptive simulations that are fast, flexible, and robust to null-space issues. At the same time, our method is simple to implement and takes advantage of existing highly-tuned algorithms."}],"publication_status":"published","volume":26,"intvolume":"        26","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_created":"2018-12-16T22:59:21Z","pmid":1},{"page":"963-1001","issue":"2","article_type":"original","date_updated":"2024-02-22T14:34:33Z","external_id":{"arxiv":["1804.07744"],"isi":["000528269100013"]},"date_published":"2020-03-01T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"month":"03","article_processing_charge":"No","_id":"6184","publication_identifier":{"issn":["0091-1798"]},"doi":"10.1214/19-AOP1379","publisher":"Institute of Mathematical Statistics","title":"Correlated random matrices: Band rigidity and edge universality","year":"2020","status":"public","oa_version":"Preprint","type":"journal_article","author":[{"id":"36D3D8B6-F248-11E8-B48F-1D18A9856A87","first_name":"Johannes","last_name":"Alt","full_name":"Alt, Johannes"},{"full_name":"Erdös, László","first_name":"László","last_name":"Erdös","id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5366-9603"},{"orcid":"0000-0002-4821-3297","first_name":"Torben H","last_name":"Krüger","full_name":"Krüger, Torben H","id":"3020C786-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-2904-1856","full_name":"Schröder, Dominik J","first_name":"Dominik J","last_name":"Schröder","id":"408ED176-F248-11E8-B48F-1D18A9856A87"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1804.07744"}],"date_created":"2019-03-28T09:20:08Z","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","volume":48,"intvolume":"        48","publication_status":"published","abstract":[{"text":"We prove edge universality for a general class of correlated real symmetric or complex Hermitian Wigner matrices with arbitrary expectation. Our theorem also applies to internal edges of the self-consistent density of states. In particular, we establish a strong form of band rigidity which excludes mismatches between location and label of eigenvalues close to internal edges in these general models.","lang":"eng"}],"arxiv":1,"project":[{"call_identifier":"FP7","name":"Random matrices, universality and disordered quantum systems","grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425"}],"citation":{"short":"J. Alt, L. Erdös, T.H. Krüger, D.J. Schröder, Annals of Probability 48 (2020) 963–1001.","ista":"Alt J, Erdös L, Krüger TH, Schröder DJ. 2020. Correlated random matrices: Band rigidity and edge universality. Annals of Probability. 48(2), 963–1001.","ama":"Alt J, Erdös L, Krüger TH, Schröder DJ. Correlated random matrices: Band rigidity and edge universality. <i>Annals of Probability</i>. 2020;48(2):963-1001. doi:<a href=\"https://doi.org/10.1214/19-AOP1379\">10.1214/19-AOP1379</a>","mla":"Alt, Johannes, et al. “Correlated Random Matrices: Band Rigidity and Edge Universality.” <i>Annals of Probability</i>, vol. 48, no. 2, Institute of Mathematical Statistics, 2020, pp. 963–1001, doi:<a href=\"https://doi.org/10.1214/19-AOP1379\">10.1214/19-AOP1379</a>.","chicago":"Alt, Johannes, László Erdös, Torben H Krüger, and Dominik J Schröder. “Correlated Random Matrices: Band Rigidity and Edge Universality.” <i>Annals of Probability</i>. Institute of Mathematical Statistics, 2020. <a href=\"https://doi.org/10.1214/19-AOP1379\">https://doi.org/10.1214/19-AOP1379</a>.","apa":"Alt, J., Erdös, L., Krüger, T. H., &#38; Schröder, D. J. (2020). Correlated random matrices: Band rigidity and edge universality. <i>Annals of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/19-AOP1379\">https://doi.org/10.1214/19-AOP1379</a>","ieee":"J. Alt, L. Erdös, T. H. Krüger, and D. J. Schröder, “Correlated random matrices: Band rigidity and edge universality,” <i>Annals of Probability</i>, vol. 48, no. 2. Institute of Mathematical Statistics, pp. 963–1001, 2020."},"department":[{"_id":"LaEr"}],"publication":"Annals of Probability","oa":1,"ec_funded":1,"isi":1,"scopus_import":"1","day":"01","related_material":{"record":[{"id":"149","relation":"dissertation_contains","status":"public"},{"id":"6179","status":"public","relation":"dissertation_contains"}]}},{"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","volume":378,"intvolume":"       378","date_created":"2019-03-28T10:21:15Z","abstract":[{"text":"For complex Wigner-type matrices, i.e. Hermitian random matrices with independent, not necessarily identically distributed entries above the diagonal, we show that at any cusp singularity of the limiting eigenvalue distribution the local eigenvalue statistics are universal and form a Pearcey process. Since the density of states typically exhibits only square root or cubic root cusp singularities, our work complements previous results on the bulk and edge universality and it thus completes the resolution of the Wigner–Dyson–Mehta universality conjecture for the last remaining universality type in the complex Hermitian class. Our analysis holds not only for exact cusps, but approximate cusps as well, where an extended Pearcey process emerges. As a main technical ingredient we prove an optimal local law at the cusp for both symmetry classes. This result is also the key input in the companion paper (Cipolloni et al. in Pure Appl Anal, 2018. arXiv:1811.04055) where the cusp universality for real symmetric Wigner-type matrices is proven. The novel cusp fluctuation mechanism is also essential for the recent results on the spectral radius of non-Hermitian random matrices (Alt et al. in Spectral radius of random matrices with independent entries, 2019. arXiv:1907.13631), and the non-Hermitian edge universality (Cipolloni et al. in Edge universality for non-Hermitian random matrices, 2019. arXiv:1908.00969).","lang":"eng"}],"publication_status":"published","project":[{"grant_number":"338804","_id":"258DCDE6-B435-11E9-9278-68D0E5697425","name":"Random matrices, universality and disordered quantum systems","call_identifier":"FP7"},{"_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854","name":"IST Austria Open Access Fund"}],"arxiv":1,"publication":"Communications in Mathematical Physics","citation":{"chicago":"Erdös, László, Torben H Krüger, and Dominik J Schröder. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00220-019-03657-4\">https://doi.org/10.1007/s00220-019-03657-4</a>.","mla":"Erdös, László, et al. “Cusp Universality for Random Matrices I: Local Law and the Complex Hermitian Case.” <i>Communications in Mathematical Physics</i>, vol. 378, Springer Nature, 2020, pp. 1203–78, doi:<a href=\"https://doi.org/10.1007/s00220-019-03657-4\">10.1007/s00220-019-03657-4</a>.","ieee":"L. Erdös, T. H. Krüger, and D. J. Schröder, “Cusp universality for random matrices I: Local law and the complex Hermitian case,” <i>Communications in Mathematical Physics</i>, vol. 378. Springer Nature, pp. 1203–1278, 2020.","apa":"Erdös, L., Krüger, T. H., &#38; Schröder, D. J. (2020). Cusp universality for random matrices I: Local law and the complex Hermitian case. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-019-03657-4\">https://doi.org/10.1007/s00220-019-03657-4</a>","ista":"Erdös L, Krüger TH, Schröder DJ. 2020. Cusp universality for random matrices I: Local law and the complex Hermitian case. Communications in Mathematical Physics. 378, 1203–1278.","ama":"Erdös L, Krüger TH, Schröder DJ. Cusp universality for random matrices I: Local law and the complex Hermitian case. <i>Communications in Mathematical Physics</i>. 2020;378:1203-1278. doi:<a href=\"https://doi.org/10.1007/s00220-019-03657-4\">10.1007/s00220-019-03657-4</a>","short":"L. Erdös, T.H. Krüger, D.J. Schröder, Communications in Mathematical Physics 378 (2020) 1203–1278."},"department":[{"_id":"LaEr"}],"ec_funded":1,"oa":1,"scopus_import":"1","day":"01","isi":1,"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"6179"}]},"article_type":"original","date_updated":"2023-09-07T12:54:12Z","external_id":{"arxiv":["1809.03971"],"isi":["000529483000001"]},"page":"1203-1278","file":[{"file_size":2904574,"date_updated":"2020-11-18T11:14:37Z","date_created":"2020-11-18T11:14:37Z","creator":"dernst","file_id":"8771","success":1,"file_name":"2020_CommMathPhysics_Erdoes.pdf","relation":"main_file","checksum":"c3a683e2afdcea27afa6880b01e53dc2","access_level":"open_access","content_type":"application/pdf"}],"language":[{"iso":"eng"}],"quality_controlled":"1","date_published":"2020-09-01T00:00:00Z","_id":"6185","month":"09","article_processing_charge":"Yes (via OA deal)","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"acknowledgement":"Open access funding provided by Institute of Science and Technology (IST Austria). The authors are very grateful to Johannes Alt for numerous discussions on the Dyson equation and for his invaluable help in adjusting [10] to the needs of the present work.","status":"public","year":"2020","title":"Cusp universality for random matrices I: Local law and the complex Hermitian case","doi":"10.1007/s00220-019-03657-4","publisher":"Springer Nature","ddc":["530","510"],"oa_version":"Published Version","has_accepted_license":"1","type":"journal_article","file_date_updated":"2020-11-18T11:14:37Z","author":[{"id":"4DBD5372-F248-11E8-B48F-1D18A9856A87","full_name":"Erdös, László","last_name":"Erdös","first_name":"László","orcid":"0000-0001-5366-9603"},{"id":"3020C786-F248-11E8-B48F-1D18A9856A87","last_name":"Krüger","first_name":"Torben H","full_name":"Krüger, Torben H","orcid":"0000-0002-4821-3297"},{"orcid":"0000-0002-2904-1856","id":"408ED176-F248-11E8-B48F-1D18A9856A87","full_name":"Schröder, Dominik J","first_name":"Dominik J","last_name":"Schröder"}]},{"related_material":{"link":[{"url":"https://doi.org/10.1007/s10955-020-02671-4","relation":"erratum"}]},"isi":1,"scopus_import":"1","day":"01","oa":1,"ec_funded":1,"department":[{"_id":"JaMa"}],"citation":{"short":"E.A. Carlen, J. Maas, Journal of Statistical Physics 178 (2020) 319–378.","ama":"Carlen EA, Maas J. Non-commutative calculus, optimal transport and functional inequalities  in dissipative quantum systems. <i>Journal of Statistical Physics</i>. 2020;178(2):319-378. doi:<a href=\"https://doi.org/10.1007/s10955-019-02434-w\">10.1007/s10955-019-02434-w</a>","ista":"Carlen EA, Maas J. 2020. Non-commutative calculus, optimal transport and functional inequalities  in dissipative quantum systems. Journal of Statistical Physics. 178(2), 319–378.","mla":"Carlen, Eric A., and Jan Maas. “Non-Commutative Calculus, Optimal Transport and Functional Inequalities  in Dissipative Quantum Systems.” <i>Journal of Statistical Physics</i>, vol. 178, no. 2, Springer Nature, 2020, pp. 319–78, doi:<a href=\"https://doi.org/10.1007/s10955-019-02434-w\">10.1007/s10955-019-02434-w</a>.","chicago":"Carlen, Eric A., and Jan Maas. “Non-Commutative Calculus, Optimal Transport and Functional Inequalities  in Dissipative Quantum Systems.” <i>Journal of Statistical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s10955-019-02434-w\">https://doi.org/10.1007/s10955-019-02434-w</a>.","apa":"Carlen, E. A., &#38; Maas, J. (2020). Non-commutative calculus, optimal transport and functional inequalities  in dissipative quantum systems. <i>Journal of Statistical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s10955-019-02434-w\">https://doi.org/10.1007/s10955-019-02434-w</a>","ieee":"E. A. Carlen and J. Maas, “Non-commutative calculus, optimal transport and functional inequalities  in dissipative quantum systems,” <i>Journal of Statistical Physics</i>, vol. 178, no. 2. Springer Nature, pp. 319–378, 2020."},"publication":"Journal of Statistical Physics","arxiv":1,"project":[{"name":"IST Austria Open Access Fund","_id":"B67AFEDC-15C9-11EA-A837-991A96BB2854"},{"name":"Optimal Transport and Stochastic Dynamics","grant_number":"716117","_id":"256E75B8-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"},{"name":"Taming Complexity in Partial Di erential Systems","_id":"260482E2-B435-11E9-9278-68D0E5697425","grant_number":" F06504","call_identifier":"FWF"}],"publication_status":"published","abstract":[{"lang":"eng","text":"We study dynamical optimal transport metrics between density matricesassociated to symmetric Dirichlet forms on finite-dimensional C∗-algebras.  Our settingcovers  arbitrary  skew-derivations  and  it  provides  a  unified  framework  that  simultaneously  generalizes  recently  constructed  transport  metrics  for  Markov  chains,  Lindblad  equations,  and  the  Fermi  Ornstein–Uhlenbeck  semigroup.   We  develop  a  non-nommutative differential calculus that allows us to obtain non-commutative Ricci curvature  bounds,  logarithmic  Sobolev  inequalities,  transport-entropy  inequalities,  andspectral gap estimates."}],"date_created":"2019-04-30T07:34:18Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","intvolume":"       178","volume":178,"author":[{"last_name":"Carlen","first_name":"Eric A.","full_name":"Carlen, Eric A."},{"orcid":"0000-0002-0845-1338","first_name":"Jan","last_name":"Maas","full_name":"Maas, Jan","id":"4C5696CE-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:47:28Z","type":"journal_article","has_accepted_license":"1","oa_version":"Published Version","doi":"10.1007/s10955-019-02434-w","ddc":["500"],"publisher":"Springer Nature","status":"public","title":"Non-commutative calculus, optimal transport and functional inequalities  in dissipative quantum systems","year":"2020","publication_identifier":{"issn":["00224715"],"eissn":["15729613"]},"month":"01","article_processing_charge":"Yes (via OA deal)","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"_id":"6358","date_published":"2020-01-01T00:00:00Z","quality_controlled":"1","language":[{"iso":"eng"}],"issue":"2","page":"319-378","file":[{"file_size":905538,"date_updated":"2020-07-14T12:47:28Z","date_created":"2019-12-23T12:03:09Z","file_id":"7209","creator":"dernst","file_name":"2019_JourStatistPhysics_Carlen.pdf","access_level":"open_access","checksum":"7b04befbdc0d4982c0ee945d25d19872","relation":"main_file","content_type":"application/pdf"}],"article_type":"original","external_id":{"arxiv":["1811.04572"],"isi":["000498933300001"]},"date_updated":"2023-08-17T13:49:40Z"},{"publication_status":"published","abstract":[{"text":"The strong rate of convergence of the Euler-Maruyama scheme for nondegenerate SDEs with irregular drift coefficients is considered. In the case of α-Hölder drift in the recent literature the rate α/2 was proved in many related situations. By exploiting the regularising effect of the noise more efficiently, we show that the rate is in fact arbitrarily close to 1/2 for all α>0. The result extends to Dini continuous coefficients, while in d=1 also to all bounded measurable coefficients.","lang":"eng"}],"arxiv":1,"article_number":"82","date_created":"2019-04-30T07:40:17Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"        25","volume":25,"isi":1,"scopus_import":"1","day":"16","citation":{"ieee":"K. Dareiotis and M. Gerencser, “On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift,” <i>Electronic Journal of Probability</i>, vol. 25. Institute of Mathematical Statistics, 2020.","apa":"Dareiotis, K., &#38; Gerencser, M. (2020). On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/20-EJP479\">https://doi.org/10.1214/20-EJP479</a>","chicago":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” <i>Electronic Journal of Probability</i>. Institute of Mathematical Statistics, 2020. <a href=\"https://doi.org/10.1214/20-EJP479\">https://doi.org/10.1214/20-EJP479</a>.","mla":"Dareiotis, Konstantinos, and Mate Gerencser. “On the Regularisation of the Noise for the Euler-Maruyama Scheme with Irregular Drift.” <i>Electronic Journal of Probability</i>, vol. 25, 82, Institute of Mathematical Statistics, 2020, doi:<a href=\"https://doi.org/10.1214/20-EJP479\">10.1214/20-EJP479</a>.","ama":"Dareiotis K, Gerencser M. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. <i>Electronic Journal of Probability</i>. 2020;25. doi:<a href=\"https://doi.org/10.1214/20-EJP479\">10.1214/20-EJP479</a>","ista":"Dareiotis K, Gerencser M. 2020. On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift. Electronic Journal of Probability. 25, 82.","short":"K. Dareiotis, M. Gerencser, Electronic Journal of Probability 25 (2020)."},"department":[{"_id":"JaMa"}],"publication":"Electronic Journal of Probability","oa":1,"month":"07","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","_id":"6359","publication_identifier":{"eissn":["1083-6489"]},"file":[{"file_name":"2020_EJournProbab_Dareiotis.pdf","relation":"main_file","access_level":"open_access","checksum":"8e7c42e72596f6889d786e8e8b89994f","content_type":"application/pdf","file_size":273042,"date_updated":"2020-09-21T13:15:02Z","date_created":"2020-09-21T13:15:02Z","success":1,"file_id":"8549","creator":"dernst"}],"article_type":"original","date_updated":"2023-10-16T09:22:50Z","external_id":{"isi":["000550150700001"],"arxiv":["1812.04583"]},"quality_controlled":"1","date_published":"2020-07-16T00:00:00Z","language":[{"iso":"eng"}],"type":"journal_article","author":[{"full_name":"Dareiotis, Konstantinos","first_name":"Konstantinos","last_name":"Dareiotis"},{"id":"44ECEDF2-F248-11E8-B48F-1D18A9856A87","full_name":"Gerencser, Mate","first_name":"Mate","last_name":"Gerencser"}],"file_date_updated":"2020-09-21T13:15:02Z","doi":"10.1214/20-EJP479","publisher":"Institute of Mathematical Statistics","ddc":["510"],"status":"public","year":"2020","title":"On the regularisation of the noise for the Euler-Maruyama scheme with irregular drift","oa_version":"Published Version","has_accepted_license":"1"}]