[{"publication":"Neuroscience","day":"01","year":"2020","language":[{"iso":"eng"}],"file_date_updated":"2020-12-03T11:45:26Z","author":[{"full_name":"Salamatina, Alina","last_name":"Salamatina","first_name":"Alina"},{"full_name":"Yang, Jerry H","first_name":"Jerry H","last_name":"Yang"},{"full_name":"Brenner-Morton, Susan","last_name":"Brenner-Morton","first_name":"Susan"},{"first_name":"Jay B ","last_name":"Bikoff","full_name":"Bikoff, Jay B "},{"first_name":"Linjing","last_name":"Fang","full_name":"Fang, Linjing"},{"full_name":"Kintner, Christopher R","last_name":"Kintner","first_name":"Christopher R"},{"full_name":"Jessell, Thomas M","last_name":"Jessell","first_name":"Thomas M"},{"first_name":"Lora Beatrice Jaeger","last_name":"Sweeney","orcid":"0000-0001-9242-5601","full_name":"Sweeney, Lora Beatrice Jaeger","id":"56BE8254-C4F0-11E9-8E45-0B23E6697425"}],"abstract":[{"text":"Amyotrophic lateral sclerosis (ALS) leads to a loss of specific motor neuron populations in the spinal cord and cortex. Emerging evidence suggests that interneurons may also be affected, but a detailed characterization of interneuron loss and its potential impacts on motor neuron loss and disease progression is lacking. To examine this issue, the fate of V1 inhibitory neurons during ALS was assessed in the ventral spinal cord using the SODG93A mouse model. The V1 population makes up ∼30% of all ventral inhibitory neurons, ∼50% of direct inhibitory synaptic contacts onto motor neuron cell bodies, and is thought to play a key role in modulating motor output, in part through recurrent and reciprocal inhibitory circuits. We find that approximately half of V1 inhibitory neurons are lost in SODG93A mice at late disease stages, but that this loss is delayed relative to the loss of motor neurons and V2a excitatory neurons. We further identify V1 subpopulations based on transcription factor expression that are differentially susceptible to degeneration in SODG93A mice. At an early disease stage, we show that V1 synaptic contacts with motor neuron cell bodies increase, suggesting an upregulation of inhibition before V1 neurons are lost in substantial numbers. These data support a model in which progressive changes in V1 synaptic contacts early in disease, and in select V1 subpopulations at later stages, represent a compensatory upregulation and then deleterious breakdown of specific interneuron circuits within the spinal cord.","lang":"eng"}],"volume":450,"date_published":"2020-12-01T00:00:00Z","article_type":"original","date_created":"2020-12-03T11:47:31Z","publisher":"Elsevier","file":[{"content_type":"application/pdf","date_updated":"2020-12-03T11:45:26Z","file_size":4071247,"access_level":"open_access","file_name":"2020_Neuroscience_Salamatina.pdf","file_id":"8915","checksum":"da7413c819e079720669c82451b49294","relation":"main_file","date_created":"2020-12-03T11:45:26Z","creator":"dernst","success":1}],"pmid":1,"scopus_import":"1","oa_version":"Published Version","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"publication_status":"published","ddc":["570"],"date_updated":"2024-01-31T10:15:34Z","publication_identifier":{"issn":["0306-4522"]},"has_accepted_license":"1","doi":"10.1016/j.neuroscience.2020.08.011","external_id":{"isi":["000595588700008"],"pmid":["32858144"]},"page":"81-95","_id":"8914","intvolume":"       450","acknowledgement":"This work was made possible by the generous support of Project ALS. Imaging and related analyses were facilitated by The Waitt Advanced Biophotonics Center Core at the Salk Institute, supported by grants from NIH-NCI CCSG (P30 014195) and NINDS Neuroscience Center (NS072031). The authors would like to additionally thank Drs. Jane Dodd, Robert Brownstone, and Laskaro Zagoraiou for helpful comments on the manuscript. This manuscript is dedicated to Tom Jessell, an inspirational scientist, friend and mentor.","quality_controlled":"1","department":[{"_id":"LoSw"}],"article_processing_charge":"Yes (via OA deal)","citation":{"ieee":"A. Salamatina <i>et al.</i>, “Differential loss of spinal interneurons in a mouse model of ALS,” <i>Neuroscience</i>, vol. 450. Elsevier, pp. 81–95, 2020.","ista":"Salamatina A, Yang JH, Brenner-Morton S, Bikoff JB, Fang L, Kintner CR, Jessell TM, Sweeney LB. 2020. Differential loss of spinal interneurons in a mouse model of ALS. Neuroscience. 450, 81–95.","mla":"Salamatina, Alina, et al. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” <i>Neuroscience</i>, vol. 450, Elsevier, 2020, pp. 81–95, doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">10.1016/j.neuroscience.2020.08.011</a>.","apa":"Salamatina, A., Yang, J. H., Brenner-Morton, S., Bikoff, J. B., Fang, L., Kintner, C. R., … Sweeney, L. B. (2020). Differential loss of spinal interneurons in a mouse model of ALS. <i>Neuroscience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">https://doi.org/10.1016/j.neuroscience.2020.08.011</a>","ama":"Salamatina A, Yang JH, Brenner-Morton S, et al. Differential loss of spinal interneurons in a mouse model of ALS. <i>Neuroscience</i>. 2020;450:81-95. doi:<a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">10.1016/j.neuroscience.2020.08.011</a>","chicago":"Salamatina, Alina, Jerry H Yang, Susan Brenner-Morton, Jay B  Bikoff, Linjing Fang, Christopher R Kintner, Thomas M Jessell, and Lora B. Sweeney. “Differential Loss of Spinal Interneurons in a Mouse Model of ALS.” <i>Neuroscience</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.neuroscience.2020.08.011\">https://doi.org/10.1016/j.neuroscience.2020.08.011</a>.","short":"A. Salamatina, J.H. Yang, S. Brenner-Morton, J.B. Bikoff, L. Fang, C.R. Kintner, T.M. Jessell, L.B. Sweeney, Neuroscience 450 (2020) 81–95."},"isi":1,"tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Differential loss of spinal interneurons in a mouse model of ALS","type":"journal_article","status":"public"},{"article_number":"586870","has_accepted_license":"1","publication_identifier":{"eissn":["1664-462X"]},"ddc":["580"],"date_updated":"2023-08-24T10:50:00Z","oa":1,"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Published Version","month":"11","status":"public","type":"journal_article","title":"A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"isi":1,"article_processing_charge":"No","citation":{"chicago":"Nibau, Candida, Despoina Dadarou, Nestoras Kargios, Areti Mallioura, Narcis Fernandez-Fuentes, Nicola Cavallari, and John H. Doonan. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” <i>Frontiers in Plant Science</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fpls.2020.586870\">https://doi.org/10.3389/fpls.2020.586870</a>.","ama":"Nibau C, Dadarou D, Kargios N, et al. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. <i>Frontiers in Plant Science</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fpls.2020.586870\">10.3389/fpls.2020.586870</a>","short":"C. Nibau, D. Dadarou, N. Kargios, A. Mallioura, N. Fernandez-Fuentes, N. Cavallari, J.H. Doonan, Frontiers in Plant Science 11 (2020).","apa":"Nibau, C., Dadarou, D., Kargios, N., Mallioura, A., Fernandez-Fuentes, N., Cavallari, N., &#38; Doonan, J. H. (2020). A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. <i>Frontiers in Plant Science</i>. Frontiers. <a href=\"https://doi.org/10.3389/fpls.2020.586870\">https://doi.org/10.3389/fpls.2020.586870</a>","mla":"Nibau, Candida, et al. “A Functional Kinase Is Necessary for Cyclin-Dependent Kinase G1 (CDKG1) to Maintain Fertility at High Ambient Temperature in Arabidopsis.” <i>Frontiers in Plant Science</i>, vol. 11, 586870, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fpls.2020.586870\">10.3389/fpls.2020.586870</a>.","ista":"Nibau C, Dadarou D, Kargios N, Mallioura A, Fernandez-Fuentes N, Cavallari N, Doonan JH. 2020. A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis. Frontiers in Plant Science. 11, 586870.","ieee":"C. Nibau <i>et al.</i>, “A functional kinase is necessary for cyclin-dependent kinase G1 (CDKG1) to maintain fertility at high ambient temperature in Arabidopsis,” <i>Frontiers in Plant Science</i>, vol. 11. Frontiers, 2020."},"department":[{"_id":"EvBe"}],"quality_controlled":"1","acknowledgement":"CN, DD, NF-F, and JD were funded by the BBSRC (grant number BB/M009459/1). NK and AM were funded through the ERASMUS+Program. NC was funded by the VIPS Program of the Austrian Federal Ministry of Science and Research and the City of Vienna.","intvolume":"        11","_id":"8924","external_id":{"isi":["000591637000001"]},"doi":"10.3389/fpls.2020.586870","date_published":"2020-11-10T00:00:00Z","volume":11,"abstract":[{"lang":"eng","text":"Maintaining fertility in a fluctuating environment is key to the reproductive success of flowering plants. Meiosis and pollen formation are particularly sensitive to changes in growing conditions, especially temperature. We have previously identified cyclin-dependent kinase G1 (CDKG1) as a master regulator of temperature-dependent meiosis and this may involve the regulation of alternative splicing (AS), including of its own transcript. CDKG1 mRNA can undergo several AS events, potentially producing two protein variants: CDKG1L and CDKG1S, differing in their N-terminal domain which may be involved in co-factor interaction. In leaves, both isoforms have distinct temperature-dependent functions on target mRNA processing, but their role in pollen development is unknown. In the present study, we characterize the role of CDKG1L and CDKG1S in maintaining Arabidopsis fertility. We show that the long (L) form is necessary and sufficient to rescue the fertility defects of the cdkg1-1 mutant, while the short (S) form is unable to rescue fertility. On the other hand, an extra copy of CDKG1L reduces fertility. In addition, mutation of the ATP binding pocket of the kinase indicates that kinase activity is necessary for the function of CDKG1. Kinase mutants of CDKG1L and CDKG1S correctly localize to the cell nucleus and nucleus and cytoplasm, respectively, but are unable to rescue either the fertility or the splicing defects of the cdkg1-1 mutant. Furthermore, we show that there is partial functional overlap between CDKG1 and its paralog CDKG2 that could in part be explained by overlapping gene expression."}],"author":[{"full_name":"Nibau, Candida","first_name":"Candida","last_name":"Nibau"},{"first_name":"Despoina","last_name":"Dadarou","full_name":"Dadarou, Despoina"},{"full_name":"Kargios, Nestoras","first_name":"Nestoras","last_name":"Kargios"},{"full_name":"Mallioura, Areti","first_name":"Areti","last_name":"Mallioura"},{"first_name":"Narcis","last_name":"Fernandez-Fuentes","full_name":"Fernandez-Fuentes, Narcis"},{"full_name":"Cavallari, Nicola","id":"457160E6-F248-11E8-B48F-1D18A9856A87","last_name":"Cavallari","first_name":"Nicola"},{"first_name":"John H.","last_name":"Doonan","full_name":"Doonan, John H."}],"file_date_updated":"2020-12-09T09:14:19Z","language":[{"iso":"eng"}],"year":"2020","day":"10","publication":"Frontiers in Plant Science","scopus_import":"1","file":[{"file_id":"8929","checksum":"1c0ee6ce9950aa665d6a5cc64aa6b752","relation":"main_file","creator":"dernst","date_created":"2020-12-09T09:14:19Z","content_type":"application/pdf","date_updated":"2020-12-09T09:14:19Z","file_size":1833244,"access_level":"open_access","file_name":"2020_Frontiers_Nibau.pdf","success":1}],"publisher":"Frontiers","article_type":"original","date_created":"2020-12-06T23:01:14Z"},{"type":"research_data","status":"public","title":"Analysis scripts and research data for the paper \"Minimal biophysical model of combined antibiotic action\"","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"publisher":"Institute of Science and Technology Austria","file":[{"file_id":"8932","relation":"main_file","checksum":"60a818edeffaa7da1ebf5f8fbea9ba18","date_created":"2020-12-09T15:00:19Z","creator":"bkavcic","content_type":"application/zip","date_updated":"2020-12-09T15:00:19Z","file_size":315494370,"access_level":"open_access","file_name":"PLoSCompBiol2020_datarep.zip","success":1}],"citation":{"ieee":"B. Kavcic, “Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action.’” Institute of Science and Technology Austria, 2020.","ista":"Kavcic B. 2020. Analysis scripts and research data for the paper ‘Minimal biophysical model of combined antibiotic action’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>.","short":"B. Kavcic, (2020).","chicago":"Kavcic, Bor. “Analysis Scripts and Research Data for the Paper ‘Minimal Biophysical Model of Combined Antibiotic Action.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>.","ama":"Kavcic B. Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>","apa":"Kavcic, B. (2020). Analysis scripts and research data for the paper “Minimal biophysical model of combined antibiotic action.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8930\">https://doi.org/10.15479/AT:ISTA:8930</a>","mla":"Kavcic, Bor. <i>Analysis Scripts and Research Data for the Paper “Minimal Biophysical Model of Combined Antibiotic Action.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8930\">10.15479/AT:ISTA:8930</a>."},"article_processing_charge":"No","contributor":[{"first_name":"Gašper","last_name":"Tkačik","orcid":"0000-0002-6699-1455","contributor_type":"supervisor","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Tobias","last_name":"Bollenbach","contributor_type":"supervisor","id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87"}],"department":[{"_id":"GaTk"}],"_id":"8930","date_created":"2020-12-09T15:04:02Z","doi":"10.15479/AT:ISTA:8930","abstract":[{"text":"Phenomenological relations such as Ohm’s or Fourier’s law have a venerable history in physics but are still scarce in biology. This situation restrains predictive theory. Here, we build on bacterial “growth laws,” which capture physiological feedback between translation and cell growth, to construct a minimal biophysical model for the combined action of ribosome-targeting antibiotics. Our model predicts drug interactions like antagonism or synergy solely from responses to individual drugs. We provide analytical results for limiting cases, which agree well with numerical results. We systematically refine the model by including direct physical interactions of different antibiotics on the ribosome. In a limiting case, our model provides a mechanistic underpinning for recent predictions of higher-order interactions that were derived using entropy maximization. We further refine the model to include the effects of antibiotics that mimic starvation and the presence of resistance genes. We describe the impact of a starvation-mimicking antibiotic on drug interactions analytically and verify it experimentally. Our extended model suggests a change in the type of drug interaction that depends on the strength of resistance, which challenges established rescaling paradigms. We experimentally show that the presence of unregulated resistance genes can lead to altered drug interaction, which agrees with the prediction of the model. While minimal, the model is readily adaptable and opens the door to predicting interactions of second and higher-order in a broad range of biological systems.","lang":"eng"}],"date_published":"2020-12-10T00:00:00Z","author":[{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","full_name":"Kavcic, Bor","first_name":"Bor","last_name":"Kavcic","orcid":"0000-0001-6041-254X"}],"file_date_updated":"2020-12-09T15:00:19Z","has_accepted_license":"1","keyword":["Escherichia coli","antibiotic combinations","translation","growth laws","drug interactions","bacterial physiology","translation inhibitors"],"ddc":["570"],"date_updated":"2024-02-21T12:41:42Z","oa":1,"day":"10","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","related_material":{"record":[{"id":"8997","relation":"used_in_publication","status":"public"}]},"year":"2020","month":"12","oa_version":"Published Version"},{"author":[{"id":"2DE75584-F248-11E8-B48F-1D18A9856A87","full_name":"Tan, Shutang","orcid":"0000-0002-0471-8285","first_name":"Shutang","last_name":"Tan"},{"full_name":"Di Donato, Martin","first_name":"Martin","last_name":"Di Donato"},{"first_name":"Matous","last_name":"Glanc","orcid":"0000-0003-0619-7783","id":"1AE1EA24-02D0-11E9-9BAA-DAF4881429F2","full_name":"Glanc, Matous"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang"},{"last_name":"Klíma","first_name":"Petr","full_name":"Klíma, Petr"},{"full_name":"Liu, Jie","first_name":"Jie","last_name":"Liu"},{"full_name":"Bailly, Aurélien","first_name":"Aurélien","last_name":"Bailly"},{"first_name":"Noel","last_name":"Ferro","full_name":"Ferro, Noel"},{"full_name":"Petrášek, Jan","last_name":"Petrášek","first_name":"Jan"},{"first_name":"Markus","last_name":"Geisler","full_name":"Geisler, Markus"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml"}],"volume":33,"abstract":[{"text":"The widely used non-steroidal anti-inflammatory drugs (NSAIDs) are derivatives of the phytohormone salicylic acid (SA). SA is well known to regulate plant immunity and development, whereas there have been few reports focusing on the effects of NSAIDs in plants. Our studies here reveal that NSAIDs exhibit largely overlapping physiological activities to SA in the model plant Arabidopsis. NSAID treatments lead to shorter and agravitropic primary roots and inhibited lateral root organogenesis. Notably, in addition to the SA-like action, which in roots involves binding to the protein phosphatase 2A (PP2A), NSAIDs also exhibit PP2A-independent effects. Cell biological and biochemical analyses reveal that many NSAIDs bind directly to and inhibit the chaperone activity of TWISTED DWARF1, thereby regulating actin cytoskeleton dynamics and subsequent endosomal trafficking. Our findings uncover an unexpected bioactivity of human pharmaceuticals in plants and provide insights into the molecular mechanism underlying the cellular action of this class of anti-inflammatory compounds.","lang":"eng"}],"date_published":"2020-12-01T00:00:00Z","file_date_updated":"2020-12-14T07:33:39Z","issue":"9","ec_funded":1,"publication":"Cell Reports","day":"01","language":[{"iso":"eng"}],"year":"2020","scopus_import":"1","publisher":"Elsevier","file":[{"success":1,"checksum":"ed18cba0fb48ed2e789381a54cc21904","relation":"main_file","date_created":"2020-12-14T07:33:39Z","creator":"dernst","file_id":"8948","access_level":"open_access","file_size":8056434,"file_name":"2020_CellReports_Tan.pdf","content_type":"application/pdf","date_updated":"2020-12-14T07:33:39Z"}],"pmid":1,"article_type":"original","date_created":"2020-12-13T23:01:21Z","project":[{"_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","grant_number":"742985","call_identifier":"H2020"},{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734"},{"grant_number":"723-2015","_id":"256FEF10-B435-11E9-9278-68D0E5697425","name":"Long Term Fellowship"}],"article_number":"108463","has_accepted_license":"1","oa":1,"publication_status":"published","date_updated":"2023-11-16T13:03:31Z","ddc":["580"],"publication_identifier":{"eissn":["22111247"]},"oa_version":"Published Version","month":"12","related_material":{"link":[{"relation":"press_release","description":"News on IST Homepage","url":"https://ist.ac.at/en/news/plants-on-aspirin/"}]},"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","title":"Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"type":"journal_article","status":"public","article_processing_charge":"Yes","citation":{"ista":"Tan S, Di Donato M, Glanc M, Zhang X, Klíma P, Liu J, Bailly A, Ferro N, Petrášek J, Geisler M, Friml J. 2020. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. Cell Reports. 33(9), 108463.","ieee":"S. Tan <i>et al.</i>, “Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development,” <i>Cell Reports</i>, vol. 33, no. 9. Elsevier, 2020.","short":"S. Tan, M. Di Donato, M. Glanc, X. Zhang, P. Klíma, J. Liu, A. Bailly, N. Ferro, J. Petrášek, M. Geisler, J. Friml, Cell Reports 33 (2020).","ama":"Tan S, Di Donato M, Glanc M, et al. Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. <i>Cell Reports</i>. 2020;33(9). doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">10.1016/j.celrep.2020.108463</a>","chicago":"Tan, Shutang, Martin Di Donato, Matous Glanc, Xixi Zhang, Petr Klíma, Jie Liu, Aurélien Bailly, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” <i>Cell Reports</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">https://doi.org/10.1016/j.celrep.2020.108463</a>.","apa":"Tan, S., Di Donato, M., Glanc, M., Zhang, X., Klíma, P., Liu, J., … Friml, J. (2020). Non-steroidal anti-inflammatory drugs target TWISTED DWARF1-regulated actin dynamics and auxin transport-mediated plant development. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">https://doi.org/10.1016/j.celrep.2020.108463</a>","mla":"Tan, Shutang, et al. “Non-Steroidal Anti-Inflammatory Drugs Target TWISTED DWARF1-Regulated Actin Dynamics and Auxin Transport-Mediated Plant Development.” <i>Cell Reports</i>, vol. 33, no. 9, 108463, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.108463\">10.1016/j.celrep.2020.108463</a>."},"isi":1,"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"}],"acknowledgement":"We thank Drs. Sebastian Bednarek (University of Wisconsin-Madison), Niko Geldner (University of Lausanne), and Karin Schumacher (Heidelberg University) for kindly sharing published Arabidopsis lines; Dr. Satoshi Naramoto for the pPIN2::PIN2-GFP; pVHA-a1::VHA-a1-mRFP reporter; the staff at the Life Science Facility and Bioimaging Facility, Monika Hrtyan, and Dorota Jaworska at IST Austria for technical support; and Drs. Su Tang (Texas A&M University),\r\nMelinda Abas (BOKU), Eva Benkova´ (IST Austria), Christian Luschnig (BOKU), Bartel Vanholme (Gent University), and the Friml group for valuable discussions. The research leading to these findings was funded by the European Union’s Horizon 2020 program (ERC grant agreement no. 742985, to J.F.), the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no.\r\n291734, the Swiss National Funds (31003A_165877, to M.G.), the Ministry of Education, Youth, and Sports of the Czech Republic (project no. CZ.02.1.01/0.0/0.0/16_019/0000738, EU Operational Programme ‘‘Research, development and education and Centre for Plant Experimental Biology’’), and the EU Operational Programme Prague - Competitiveness (project no. CZ.2.16/3.1.00/21519). S.T. was funded by a European Molecular Biology Organization (EMBO) long-term postdoctoral fellowship (ALTF 723-2015). X.Z. was partly supported by a PhD scholarship from the China Scholarship Council.","quality_controlled":"1","department":[{"_id":"JiFr"}],"doi":"10.1016/j.celrep.2020.108463","external_id":{"pmid":["33264621"],"isi":["000595658100018"]},"_id":"8943","intvolume":"        33"},{"date_published":"2020-11-01T00:00:00Z","volume":102,"abstract":[{"lang":"eng","text":"Superconductor insulator transition in transverse magnetic field is studied in the highly disordered MoC film with the product of the Fermi momentum and the mean free path kF*l close to unity. Surprisingly, the Zeeman paramagnetic effects dominate over orbital coupling on both sides of the transition. In superconducting state it is evidenced by a high upper critical magnetic field 𝐵𝑐2, by its square root dependence on temperature, as well as by the Zeeman splitting of the quasiparticle density of states (DOS) measured by scanning tunneling microscopy. At 𝐵𝑐2 a logarithmic anomaly in DOS is observed. This anomaly is further enhanced in increasing magnetic field, which is explained by the Zeeman splitting of the Altshuler-Aronov DOS driving\r\nthe system into a more insulating or resistive state. Spin dependent Altshuler-Aronov correction is also needed to explain the transport behavior above 𝐵𝑐2."}],"author":[{"full_name":"Zemlicka, Martin","id":"2DCF8DE6-F248-11E8-B48F-1D18A9856A87","last_name":"Zemlicka","first_name":"Martin"},{"full_name":"Kopčík, M.","last_name":"Kopčík","first_name":"M."},{"first_name":"P.","last_name":"Szabó","full_name":"Szabó, P."},{"full_name":"Samuely, T.","last_name":"Samuely","first_name":"T."},{"last_name":"Kačmarčík","first_name":"J.","full_name":"Kačmarčík, J."},{"full_name":"Neilinger, P.","last_name":"Neilinger","first_name":"P."},{"last_name":"Grajcar","first_name":"M.","full_name":"Grajcar, M."},{"last_name":"Samuely","first_name":"P.","full_name":"Samuely, P."}],"issue":"18","year":"2020","language":[{"iso":"eng"}],"day":"01","publication":"Physical Review B","scopus_import":"1","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2011.04329"}],"publisher":"American Physical Society","date_created":"2020-12-13T23:01:21Z","article_type":"original","article_number":"180508","arxiv":1,"publication_identifier":{"eissn":["24699969"],"issn":["24699950"]},"date_updated":"2023-08-24T10:53:36Z","publication_status":"published","oa":1,"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","month":"11","type":"journal_article","status":"public","title":"Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field","isi":1,"article_processing_charge":"No","citation":{"apa":"Zemlicka, M., Kopčík, M., Szabó, P., Samuely, T., Kačmarčík, J., Neilinger, P., … Samuely, P. (2020). Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>","mla":"Zemlicka, Martin, et al. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>, vol. 102, no. 18, 180508, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>.","short":"M. Zemlicka, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, P. Samuely, Physical Review B 102 (2020).","ama":"Zemlicka M, Kopčík M, Szabó P, et al. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. <i>Physical Review B</i>. 2020;102(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">10.1103/PhysRevB.102.180508</a>","chicago":"Zemlicka, Martin, M. Kopčík, P. Szabó, T. Samuely, J. Kačmarčík, P. Neilinger, M. Grajcar, and P. Samuely. “Zeeman-Driven Superconductor-Insulator Transition in Strongly Disordered MoC Films: Scanning Tunneling Microscopy and Transport Studies in a Transverse Magnetic Field.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.102.180508\">https://doi.org/10.1103/PhysRevB.102.180508</a>.","ista":"Zemlicka M, Kopčík M, Szabó P, Samuely T, Kačmarčík J, Neilinger P, Grajcar M, Samuely P. 2020. Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field. Physical Review B. 102(18), 180508.","ieee":"M. Zemlicka <i>et al.</i>, “Zeeman-driven superconductor-insulator transition in strongly disordered MoC films: Scanning tunneling microscopy and transport studies in a transverse magnetic field,” <i>Physical Review B</i>, vol. 102, no. 18. American Physical Society, 2020."},"department":[{"_id":"JoFi"}],"quality_controlled":"1","acknowledgement":"We gratefully acknowledge helpful conversations with B.L. Altshuler and R. Hlubina. The work was supported by the projects APVV-18-0358, VEGA 2/0058/20, VEGA 1/0743/19 the European Microkelvin Platform, the COST action CA16218 (Nanocohybri) and by U.S. Steel Košice. ","intvolume":"       102","_id":"8944","external_id":{"arxiv":["2011.04329"],"isi":["000591509900003"]},"doi":"10.1103/PhysRevB.102.180508"},{"date_created":"2020-12-14T08:04:03Z","project":[{"_id":"264E56E2-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms Regulating Gliogenesis in the Cerebral Cortex","grant_number":"M02416","call_identifier":"FWF"},{"_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development","call_identifier":"H2020","grant_number":"725780"}],"article_type":"original","publisher":"MDPI","file":[{"success":1,"file_id":"8950","checksum":"5095cbdc728c9a510c5761cf60a8861c","relation":"main_file","date_created":"2020-12-14T08:09:43Z","creator":"dernst","content_type":"application/pdf","date_updated":"2020-12-14T08:09:43Z","access_level":"open_access","file_size":3504525,"file_name":"2020_Cells_Zhang.pdf"}],"day":"11","language":[{"iso":"eng"}],"year":"2020","publication":"Cells","ec_funded":1,"issue":"12","file_date_updated":"2020-12-14T08:09:43Z","abstract":[{"lang":"eng","text":"<jats:p>Development of the nervous system undergoes important transitions, including one from neurogenesis to gliogenesis which occurs late during embryonic gestation. Here we report on clonal analysis of gliogenesis in mice using Mosaic Analysis with Double Markers (MADM) with quantitative and computational methods. Results reveal that developmental gliogenesis in the cerebral cortex occurs in a fraction of earlier neurogenic clones, accelerating around E16.5, and giving rise to both astrocytes and oligodendrocytes. Moreover, MADM-based genetic deletion of the epidermal growth factor receptor (Egfr) in gliogenic clones revealed that Egfr is cell autonomously required for gliogenesis in the mouse dorsolateral cortices. A broad range in the proliferation capacity, symmetry of clones, and competitive advantage of MADM cells was evident in clones that contained one cellular lineage with double dosage of Egfr relative to their environment, while their sibling Egfr-null cells failed to generate glia. Remarkably, the total numbers of glia in MADM clones balance out regardless of significant alterations in clonal symmetries. The variability in glial clones shows stochastic patterns that we define mathematically, which are different from the deterministic patterns in neuronal clones. This study sets a foundation for studying the biological significance of stochastic and deterministic clonal principles underlying tissue development, and identifying mechanisms that differentiate between neurogenesis and gliogenesis.</jats:p>"}],"volume":9,"date_published":"2020-12-11T00:00:00Z","author":[{"first_name":"Xuying","last_name":"Zhang","full_name":"Zhang, Xuying"},{"first_name":"Christine V.","last_name":"Mennicke","full_name":"Mennicke, Christine V."},{"full_name":"Xiao, Guanxi","first_name":"Guanxi","last_name":"Xiao"},{"last_name":"Beattie","first_name":"Robert J","orcid":"0000-0002-8483-8753","id":"2E26DF60-F248-11E8-B48F-1D18A9856A87","full_name":"Beattie, Robert J"},{"full_name":"Haider, Mansoor","last_name":"Haider","first_name":"Mansoor"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","full_name":"Hippenmeyer, Simon","first_name":"Simon","last_name":"Hippenmeyer","orcid":"0000-0003-2279-1061"},{"first_name":"H. Troy","last_name":"Ghashghaei","full_name":"Ghashghaei, H. Troy"}],"_id":"8949","intvolume":"         9","doi":"10.3390/cells9122662","external_id":{"isi":["000601787300001"]},"department":[{"_id":"SiHi"}],"acknowledgement":"This research was funded by grants from the National Institutes of Health to H.T.G. (R01NS098370 and R01NS089795). C.V.M. was supported by a National Science Foundation Graduate Research Fellowship (DGE-1746939). R.B. was supported by the FWF Lise-Meitner program (M 2416), and S.H. was supported by the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement No 725780 LinPro).The authors thank members of the Ghashghaei lab for discussions, technical support, and help with preparation of the manuscript.","quality_controlled":"1","isi":1,"citation":{"mla":"Zhang, Xuying, et al. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>, vol. 9, no. 12, 2662, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>.","apa":"Zhang, X., Mennicke, C. V., Xiao, G., Beattie, R. J., Haider, M., Hippenmeyer, S., &#38; Ghashghaei, H. T. (2020). Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. MDPI. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>","ama":"Zhang X, Mennicke CV, Xiao G, et al. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. <i>Cells</i>. 2020;9(12). doi:<a href=\"https://doi.org/10.3390/cells9122662\">10.3390/cells9122662</a>","short":"X. Zhang, C.V. Mennicke, G. Xiao, R.J. Beattie, M. Haider, S. Hippenmeyer, H.T. Ghashghaei, Cells 9 (2020).","chicago":"Zhang, Xuying, Christine V. Mennicke, Guanxi Xiao, Robert J Beattie, Mansoor Haider, Simon Hippenmeyer, and H. Troy Ghashghaei. “Clonal Analysis of Gliogenesis in the Cerebral Cortex Reveals Stochastic Expansion of Glia and Cell Autonomous Responses to Egfr Dosage.” <i>Cells</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/cells9122662\">https://doi.org/10.3390/cells9122662</a>.","ista":"Zhang X, Mennicke CV, Xiao G, Beattie RJ, Haider M, Hippenmeyer S, Ghashghaei HT. 2020. Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage. Cells. 9(12), 2662.","ieee":"X. Zhang <i>et al.</i>, “Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage,” <i>Cells</i>, vol. 9, no. 12. MDPI, 2020."},"article_processing_charge":"No","status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Clonal analysis of gliogenesis in the cerebral cortex reveals stochastic expansion of glia and cell autonomous responses to Egfr dosage","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"12","oa_version":"Published Version","date_updated":"2023-08-24T10:57:48Z","ddc":["570"],"publication_identifier":{"issn":["2073-4409"]},"oa":1,"publication_status":"published","has_accepted_license":"1","article_number":"2662"},{"article_processing_charge":"No","citation":{"ista":"Nagy-Staron AA. 2020. Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network’, Institute of Science and Technology Austria, <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>.","ieee":"A. A. Nagy-Staron, “Sequences of gene regulatory network permutations for the article ‘Local genetic context shapes the function of a gene regulatory network.’” Institute of Science and Technology Austria, 2020.","short":"A.A. Nagy-Staron, (2020).","chicago":"Nagy-Staron, Anna A. “Sequences of Gene Regulatory Network Permutations for the Article ‘Local Genetic Context Shapes the Function of a Gene Regulatory Network.’” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>.","ama":"Nagy-Staron AA. Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>","apa":"Nagy-Staron, A. A. (2020). Sequences of gene regulatory network permutations for the article “Local genetic context shapes the function of a gene regulatory network.” Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8951\">https://doi.org/10.15479/AT:ISTA:8951</a>","mla":"Nagy-Staron, Anna A. <i>Sequences of Gene Regulatory Network Permutations for the Article “Local Genetic Context Shapes the Function of a Gene Regulatory Network.”</i> Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8951\">10.15479/AT:ISTA:8951</a>."},"file":[{"file_name":"readme.txt","access_level":"open_access","file_size":523,"date_updated":"2020-12-20T09:52:52Z","content_type":"text/plain","date_created":"2020-12-20T09:52:52Z","creator":"bkavcic","checksum":"f57862aeee1690c7effd2b1117d40ed1","relation":"main_file","file_id":"8952","success":1},{"content_type":"application/octet-stream","date_updated":"2020-12-20T22:01:44Z","access_level":"open_access","file_size":379228,"file_name":"GRNs Research depository.gb","file_id":"8954","relation":"main_file","checksum":"f2c6d5232ec6d551b6993991e8689e9f","creator":"bkavcic","date_created":"2020-12-20T22:01:44Z","success":1}],"publisher":"Institute of Science and Technology Austria","title":"Sequences of gene regulatory network permutations for the article \"Local genetic context shapes the function of a gene regulatory network\"","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"status":"public","type":"research_data","date_created":"2020-12-20T10:00:26Z","doi":"10.15479/AT:ISTA:8951","_id":"8951","contributor":[{"contributor_type":"project_member","last_name":"Nagy-Staron","first_name":"Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Kathrin","last_name":"Tomasek","contributor_type":"project_member","id":"3AEC8556-F248-11E8-B48F-1D18A9856A87"},{"contributor_type":"project_member","first_name":"Caroline","last_name":"Caruso Carter"},{"contributor_type":"project_member","first_name":"Elisabeth","last_name":"Sonnleitner"},{"id":"350F91D2-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_member","orcid":"0000-0001-6041-254X","last_name":"Kavcic","first_name":"Bor"},{"contributor_type":"project_member","first_name":"Tiago","last_name":"Paixão"},{"id":"47F8433E-F248-11E8-B48F-1D18A9856A87","contributor_type":"project_manager","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet"}],"department":[{"_id":"CaGu"}],"file_date_updated":"2020-12-20T22:01:44Z","has_accepted_license":"1","author":[{"orcid":"0000-0002-1391-8377","first_name":"Anna A","last_name":"Nagy-Staron","full_name":"Nagy-Staron, Anna A","id":"3ABC5BA6-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2020-12-21T00:00:00Z","abstract":[{"text":"Gene expression levels are influenced by multiple coexisting molecular mechanisms. Some of these interactions, such as those of transcription factors and promoters have been studied extensively. However, predicting phenotypes of gene regulatory networks remains a major challenge. Here, we use a well-defined synthetic gene regulatory network to study how network phenotypes depend on local genetic context, i.e. the genetic neighborhood of a transcription factor and its relative position. We show that one gene regulatory network with fixed topology can display not only quantitatively but also qualitatively different phenotypes, depending solely on the local genetic context of its components. Our results demonstrate that changes in local genetic context can place a single transcriptional unit within two separate regulons without the need for complex regulatory sequences. We propose that relative order of individual transcriptional units, with its potential for combinatorial complexity, plays an important role in shaping phenotypes of gene regulatory networks.","lang":"eng"}],"month":"12","oa_version":"Published Version","year":"2020","related_material":{"record":[{"status":"public","id":"9283","relation":"used_in_publication"}]},"day":"21","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa":1,"keyword":["Gene regulatory networks","Gene expression","Escherichia coli","Synthetic Biology"],"date_updated":"2024-02-21T12:41:57Z","ddc":["570"]},{"ec_funded":1,"publication":"Frontiers in Physiology","language":[{"iso":"eng"}],"year":"2020","day":"26","author":[{"full_name":"Rizzo, Rossella","first_name":"Rossella","last_name":"Rizzo"},{"full_name":"Zhang, Xiyun","last_name":"Zhang","first_name":"Xiyun"},{"full_name":"Wang, Jilin W.J.L.","last_name":"Wang","first_name":"Jilin W.J.L."},{"orcid":"0000-0003-2623-5249","last_name":"Lombardi","first_name":"Fabrizio","full_name":"Lombardi, Fabrizio","id":"A057D288-3E88-11E9-986D-0CF4E5697425"},{"last_name":"Ivanov","first_name":"Plamen Ch","full_name":"Ivanov, Plamen Ch"}],"date_published":"2020-11-26T00:00:00Z","volume":11,"abstract":[{"text":"Skeletal muscle activity is continuously modulated across physiologic states to provide coordination, flexibility and responsiveness to body tasks and external inputs. Despite the central role the muscular system plays in facilitating vital body functions, the network of brain-muscle interactions required to control hundreds of muscles and synchronize their activation in relation to distinct physiologic states has not been investigated. Recent approaches have focused on general associations between individual brain rhythms and muscle activation during movement tasks. However, the specific forms of coupling, the functional network of cortico-muscular coordination, and how network structure and dynamics are modulated by autonomic regulation across physiologic states remains unknown. To identify and quantify the cortico-muscular interaction network and uncover basic features of neuro-autonomic control of muscle function, we investigate the coupling between synchronous bursts in cortical rhythms and peripheral muscle activation during sleep and wake. Utilizing the concept of time delay stability and a novel network physiology approach, we find that the brain-muscle network exhibits complex dynamic patterns of communication involving multiple brain rhythms across cortical locations and different electromyographic frequency bands. Moreover, our results show that during each physiologic state the cortico-muscular network is characterized by a specific profile of network links strength, where particular brain rhythms play role of main mediators of interaction and control. Further, we discover a hierarchical reorganization in network structure across physiologic states, with high connectivity and network link strength during wake, intermediate during REM and light sleep, and low during deep sleep, a sleep-stage stratification that demonstrates a unique association between physiologic states and cortico-muscular network structure. The reported empirical observations are consistent across individual subjects, indicating universal behavior in network structure and dynamics, and high sensitivity of cortico-muscular control to changes in autonomic regulation, even at low levels of physical activity and muscle tone during sleep. Our findings demonstrate previously unrecognized basic principles of brain-muscle network communication and control, and provide new perspectives on the regulatory mechanisms of brain dynamics and locomotor activation, with potential clinical implications for neurodegenerative, movement and sleep disorders, and for developing efficient treatment strategies.","lang":"eng"}],"file_date_updated":"2020-12-21T10:37:50Z","date_created":"2020-12-20T23:01:18Z","article_type":"original","project":[{"call_identifier":"H2020","grant_number":"754411","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships"}],"scopus_import":"1","pmid":1,"file":[{"file_id":"8961","relation":"main_file","checksum":"ef9515b28c5619b7126c0f347958bcb3","creator":"dernst","date_created":"2020-12-21T10:37:50Z","content_type":"application/pdf","date_updated":"2020-12-21T10:37:50Z","file_size":13380030,"access_level":"open_access","file_name":"2020_Frontiers_Rizzo.pdf","success":1}],"publisher":"Frontiers","oa":1,"publication_status":"published","publication_identifier":{"eissn":["1664042X"]},"ddc":["570"],"date_updated":"2023-08-24T11:00:45Z","oa_version":"Published Version","month":"11","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"558070","has_accepted_license":"1","quality_controlled":"1","acknowledgement":"We acknowledge support from the W. M. Keck Foundation, National Institutes of Health (NIH Grant 1R01-HL098437), the US-Israel Binational Science Foundation (BSF Grant 2012219), and the Office of Naval Research (ONR Grant 000141010078). FL acknowledges support also from the European Union's Horizon 2020 research and innovation program under the Marie Sklodowska-Curie Grant Agreement No. 754411.","department":[{"_id":"GaTk"}],"external_id":{"pmid":["33324233"],"isi":["000596849400001"]},"doi":"10.3389/fphys.2020.558070","intvolume":"        11","_id":"8955","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Network physiology of cortico–muscular interactions","status":"public","type":"journal_article","citation":{"ista":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. 2020. Network physiology of cortico–muscular interactions. Frontiers in Physiology. 11, 558070.","ieee":"R. Rizzo, X. Zhang, J. W. J. L. Wang, F. Lombardi, and P. C. Ivanov, “Network physiology of cortico–muscular interactions,” <i>Frontiers in Physiology</i>, vol. 11. Frontiers, 2020.","chicago":"Rizzo, Rossella, Xiyun Zhang, Jilin W.J.L. Wang, Fabrizio Lombardi, and Plamen Ch Ivanov. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>. Frontiers, 2020. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>.","ama":"Rizzo R, Zhang X, Wang JWJL, Lombardi F, Ivanov PC. Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. 2020;11. doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>","short":"R. Rizzo, X. Zhang, J.W.J.L. Wang, F. Lombardi, P.C. Ivanov, Frontiers in Physiology 11 (2020).","apa":"Rizzo, R., Zhang, X., Wang, J. W. J. L., Lombardi, F., &#38; Ivanov, P. C. (2020). Network physiology of cortico–muscular interactions. <i>Frontiers in Physiology</i>. Frontiers. <a href=\"https://doi.org/10.3389/fphys.2020.558070\">https://doi.org/10.3389/fphys.2020.558070</a>","mla":"Rizzo, Rossella, et al. “Network Physiology of Cortico–Muscular Interactions.” <i>Frontiers in Physiology</i>, vol. 11, 558070, Frontiers, 2020, doi:<a href=\"https://doi.org/10.3389/fphys.2020.558070\">10.3389/fphys.2020.558070</a>."},"article_processing_charge":"No","isi":1},{"has_accepted_license":"1","alternative_title":["ISTA Thesis"],"publication_status":"published","oa":1,"publication_identifier":{"issn":["2663-337X"]},"date_updated":"2024-08-07T07:16:53Z","ddc":["539"],"oa_version":"Published Version","month":"12","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"relation":"part_of_dissertation","id":"5886","status":"public"},{"relation":"part_of_dissertation","id":"1120","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"8587"}]},"title":"Rotation of coupled cold molecules in the presence of a many-body environment","status":"public","type":"dissertation","article_processing_charge":"No","citation":{"ieee":"X. Li, “Rotation of coupled cold molecules in the presence of a many-body environment,” Institute of Science and Technology Austria, 2020.","ista":"Li X. 2020. Rotation of coupled cold molecules in the presence of a many-body environment. Institute of Science and Technology Austria.","short":"X. Li, Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment, Institute of Science and Technology Austria, 2020.","chicago":"Li, Xiang. “Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8958\">https://doi.org/10.15479/AT:ISTA:8958</a>.","ama":"Li X. Rotation of coupled cold molecules in the presence of a many-body environment. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8958\">10.15479/AT:ISTA:8958</a>","apa":"Li, X. (2020). <i>Rotation of coupled cold molecules in the presence of a many-body environment</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8958\">https://doi.org/10.15479/AT:ISTA:8958</a>","mla":"Li, Xiang. <i>Rotation of Coupled Cold Molecules in the Presence of a Many-Body Environment</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8958\">10.15479/AT:ISTA:8958</a>."},"degree_awarded":"PhD","department":[{"_id":"MiLe"}],"doi":"10.15479/AT:ISTA:8958","page":"125","_id":"8958","author":[{"first_name":"Xiang","last_name":"Li","full_name":"Li, Xiang","id":"4B7E523C-F248-11E8-B48F-1D18A9856A87"}],"date_published":"2020-12-21T00:00:00Z","abstract":[{"lang":"eng","text":"The oft-quoted dictum by Arthur Schawlow: ``A diatomic molecule has one atom too many'' has been disavowed. Inspired by the possibility to experimentally manipulate and enhance chemical reactivity in helium nanodroplets, we investigate the rotation of coupled cold molecules in the presence of a many-body environment.\r\nIn this thesis, we introduce new variational approaches to quantum impurities and apply them to the Fröhlich polaron - a quasiparticle formed out of an electron (or other point-like impurity) in a polar medium, and to the angulon - a quasiparticle formed out of a rotating molecule in a bosonic bath.\r\nWith this theoretical toolbox, we reveal the self-localization transition for the angulon quasiparticle. We show that, unlike for polarons, self-localization of angulons occurs at finite impurity-bath coupling already at the mean-field level. The transition is accompanied by the spherical-symmetry breaking of the angulon ground state and a discontinuity in the first derivative of the ground-state energy. Moreover, the type of symmetry breaking is dictated by the symmetry of the microscopic impurity-bath interaction, which leads to a number of distinct self-localized states. \r\nFor the system containing multiple impurities, by analogy with the bipolaron, we introduce the biangulon quasiparticle describing two rotating molecules that align with respect to each other due to the effective attractive interaction mediated by the excitations of the bath. We study this system from the strong-coupling regime to the weak molecule-bath interaction regime. We show that the molecules tend to have a strong alignment in the ground state, the biangulon shows shifted angulon instabilities and an additional spectral instability, where resonant angular momentum transfer between the molecules and the bath takes place. Finally, we introduce a diagonalization scheme that allows us to describe the transition from two separated angulons to a biangulon as a function of the distance between the two molecules."}],"file_date_updated":"2020-12-30T07:18:03Z","ec_funded":1,"year":"2020","language":[{"iso":"eng"}],"day":"21","supervisor":[{"id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802","first_name":"Mikhail","last_name":"Lemeshko"}],"file":[{"file_id":"8967","creator":"xli","date_created":"2020-12-22T10:55:56Z","checksum":"3994c54a1241451d561db1d4f43bad30","relation":"main_file","date_updated":"2020-12-22T10:55:56Z","content_type":"application/pdf","file_name":"THESIS_Xiang_Li.pdf","access_level":"open_access","file_size":3622305,"success":1},{"file_id":"8968","date_created":"2020-12-22T10:56:03Z","creator":"xli","checksum":"0954ecfc5554c05615c14de803341f00","relation":"source_file","date_updated":"2020-12-30T07:18:03Z","content_type":"application/x-zip-compressed","file_name":"THESIS_Xiang_Li.zip","file_size":4018859,"access_level":"closed"}],"publisher":"Institute of Science and Technology Austria","project":[{"grant_number":"P29902","call_identifier":"FWF","_id":"26031614-B435-11E9-9278-68D0E5697425","name":"Quantum rotations in the presence of a many-body environment"},{"grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"date_created":"2020-12-21T09:44:30Z"},{"date_created":"2020-12-23T08:25:45Z","article_type":"original","project":[{"grant_number":"P33367","_id":"9B954C5C-BA93-11EA-9121-9846C619BF3A","name":"Structure and isoform diversity of the Arp2/3 complex"},{"_id":"2674F658-B435-11E9-9278-68D0E5697425","name":"Protein structure and function in filopodia across scales","call_identifier":"FWF","grant_number":"M02495"}],"file":[{"content_type":"application/pdf","date_updated":"2020-12-28T08:16:10Z","file_size":3958727,"access_level":"open_access","file_name":"2020_NatureComm_Faessler.pdf","file_id":"8975","checksum":"55d43ea0061cc4027ba45e966e1db8cc","relation":"main_file","date_created":"2020-12-28T08:16:10Z","creator":"dernst","success":1}],"publisher":"Springer Nature","scopus_import":"1","publication":"Nature Communications","year":"2020","language":[{"iso":"eng"}],"day":"22","keyword":["General Biochemistry","Genetics and Molecular Biology","General Physics and Astronomy","General Chemistry"],"file_date_updated":"2020-12-28T08:16:10Z","author":[{"id":"404F5528-F248-11E8-B48F-1D18A9856A87","full_name":"Fäßler, Florian","first_name":"Florian","last_name":"Fäßler","orcid":"0000-0001-7149-769X"},{"full_name":"Dimchev, Georgi A","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8370-6161","first_name":"Georgi A","last_name":"Dimchev"},{"last_name":"Hodirnau","first_name":"Victor-Valentin","id":"3661B498-F248-11E8-B48F-1D18A9856A87","full_name":"Hodirnau, Victor-Valentin"},{"last_name":"Wan","first_name":"William","full_name":"Wan, William"},{"id":"48AD8942-F248-11E8-B48F-1D18A9856A87","full_name":"Schur, Florian KM","first_name":"Florian KM","last_name":"Schur","orcid":"0000-0003-4790-8078"}],"date_published":"2020-12-22T00:00:00Z","abstract":[{"lang":"eng","text":"The actin-related protein (Arp)2/3 complex nucleates branched actin filament networks pivotal for cell migration, endocytosis and pathogen infection. Its activation is tightly regulated and involves complex structural rearrangements and actin filament binding, which are yet to be understood. Here, we report a 9.0 Å resolution structure of the actin filament Arp2/3 complex branch junction in cells using cryo-electron tomography and subtomogram averaging. This allows us to generate an accurate model of the active Arp2/3 complex in the branch junction and its interaction with actin filaments. Notably, our model reveals a previously undescribed set of interactions of the Arp2/3 complex with the mother filament, significantly different to the previous branch junction model. Our structure also indicates a central role for the ArpC3 subunit in stabilizing the active conformation."}],"volume":11,"external_id":{"isi":["000603078000003"]},"doi":"10.1038/s41467-020-20286-x","intvolume":"        11","_id":"8971","quality_controlled":"1","acknowledgement":"This research was supported by the Scientific Service Units (SSUs) of IST Austria through resources provided by Scientific Computing (SciComp), the Life Science Facility (LSF), the BioImaging Facility (BIF), and the Electron Microscopy Facility (EMF). We also thank Dimitry Tegunov (MPI for Biophysical Chemistry) for helpful discussions\r\nabout the M software, and Michael Sixt (IST Austria) and Klemens Rottner (Technical University Braunschweig, HZI Braunschweig) for critical reading of the manuscript. We also thank Gregory Voth (University of Chicago) for providing us the MD-derived branch junction model for comparison. The authors acknowledge support from IST Austria and from the Austrian Science Fund (FWF): M02495 to G.D. and Austrian Science Fund (FWF): P33367 to F.K.M.S. ","department":[{"_id":"FlSc"},{"_id":"EM-Fac"}],"citation":{"mla":"Fäßler, Florian, et al. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>, vol. 11, 6437, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>.","apa":"Fäßler, F., Dimchev, G. A., Hodirnau, V.-V., Wan, W., &#38; Schur, F. K. (2020). Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>","chicago":"Fäßler, Florian, Georgi A Dimchev, Victor-Valentin Hodirnau, William Wan, and Florian KM Schur. “Cryo-Electron Tomography Structure of Arp2/3 Complex in Cells Reveals New Insights into the Branch Junction.” <i>Nature Communications</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41467-020-20286-x\">https://doi.org/10.1038/s41467-020-20286-x</a>.","ama":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. <i>Nature Communications</i>. 2020;11. doi:<a href=\"https://doi.org/10.1038/s41467-020-20286-x\">10.1038/s41467-020-20286-x</a>","short":"F. Fäßler, G.A. Dimchev, V.-V. Hodirnau, W. Wan, F.K. Schur, Nature Communications 11 (2020).","ista":"Fäßler F, Dimchev GA, Hodirnau V-V, Wan W, Schur FK. 2020. Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction. Nature Communications. 11, 6437.","ieee":"F. Fäßler, G. A. Dimchev, V.-V. Hodirnau, W. Wan, and F. K. Schur, “Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction,” <i>Nature Communications</i>, vol. 11. Springer Nature, 2020."},"article_processing_charge":"No","acknowledged_ssus":[{"_id":"ScienComp"},{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"EM-Fac"}],"isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Cryo-electron tomography structure of Arp2/3 complex in cells reveals new insights into the branch junction","status":"public","type":"journal_article","month":"12","oa_version":"Published Version","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","related_material":{"link":[{"url":"https://ist.ac.at/en/news/cutting-edge-technology-reveals-structures-within-cells/","description":"News on IST Homepage","relation":"press_release"}]},"oa":1,"publication_status":"published","publication_identifier":{"issn":["2041-1723"]},"date_updated":"2023-08-24T11:01:50Z","ddc":["570"],"has_accepted_license":"1","article_number":"6437"},{"publisher":" Institute of Mathematical Statistics","file":[{"success":1,"date_updated":"2020-12-28T08:24:08Z","content_type":"application/pdf","file_name":"2020_ElectronJProbab_Redig.pdf","file_size":696653,"access_level":"open_access","file_id":"8976","creator":"dernst","date_created":"2020-12-28T08:24:08Z","relation":"main_file","checksum":"d75359b9814e78d57c0a481b7cde3751"}],"scopus_import":"1","date_created":"2020-12-27T23:01:17Z","project":[{"name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"754411"}],"article_type":"original","file_date_updated":"2020-12-28T08:24:08Z","author":[{"last_name":"Redig","first_name":"Frank","full_name":"Redig, Frank"},{"full_name":"Saada, Ellen","last_name":"Saada","first_name":"Ellen"},{"full_name":"Sau, Federico","id":"E1836206-9F16-11E9-8814-AEFDE5697425","last_name":"Sau","first_name":"Federico"}],"volume":25,"abstract":[{"lang":"eng","text":"We consider the symmetric simple exclusion process in Zd with quenched bounded dynamic random conductances and prove its hydrodynamic limit in path space. The main tool is the connection, due to the self-duality of the process, between the invariance principle for single particles starting from all points and the macroscopic behavior of the density field. While the hydrodynamic limit at fixed macroscopic times is obtained via a generalization to the time-inhomogeneous context of the strategy introduced in [41], in order to prove tightness for the sequence of empirical density fields we develop a new criterion based on the notion of uniform conditional stochastic continuity, following [50]. In conclusion, we show that uniform elliptic dynamic conductances provide an example of environments in which the so-called arbitrary starting point invariance principle may be derived from the invariance principle of a single particle starting from the origin. Therefore, our hydrodynamics result applies to the examples of quenched environments considered in, e.g., [1], [3], [6] in combination with the hypothesis of uniform ellipticity."}],"date_published":"2020-10-21T00:00:00Z","publication":"Electronic Journal of Probability","day":"21","language":[{"iso":"eng"}],"year":"2020","ec_funded":1,"article_processing_charge":"No","citation":{"short":"F. Redig, E. Saada, F. Sau, Electronic Journal of Probability 25 (2020).","chicago":"Redig, Frank, Ellen Saada, and Federico Sau. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” <i>Electronic Journal of Probability</i>.  Institute of Mathematical Statistics, 2020. <a href=\"https://doi.org/10.1214/20-EJP536\">https://doi.org/10.1214/20-EJP536</a>.","ama":"Redig F, Saada E, Sau F. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. <i>Electronic Journal of Probability</i>. 2020;25. doi:<a href=\"https://doi.org/10.1214/20-EJP536\">10.1214/20-EJP536</a>","mla":"Redig, Frank, et al. “Symmetric Simple Exclusion Process in Dynamic Environment: Hydrodynamics.” <i>Electronic Journal of Probability</i>, vol. 25, 138,  Institute of Mathematical Statistics, 2020, doi:<a href=\"https://doi.org/10.1214/20-EJP536\">10.1214/20-EJP536</a>.","apa":"Redig, F., Saada, E., &#38; Sau, F. (2020). Symmetric simple exclusion process in dynamic environment: Hydrodynamics. <i>Electronic Journal of Probability</i>.  Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/20-EJP536\">https://doi.org/10.1214/20-EJP536</a>","ista":"Redig F, Saada E, Sau F. 2020. Symmetric simple exclusion process in dynamic environment: Hydrodynamics. Electronic Journal of Probability. 25, 138.","ieee":"F. Redig, E. Saada, and F. Sau, “Symmetric simple exclusion process in dynamic environment: Hydrodynamics,” <i>Electronic Journal of Probability</i>, vol. 25.  Institute of Mathematical Statistics, 2020."},"isi":1,"title":"Symmetric simple exclusion process in dynamic environment: Hydrodynamics","status":"public","type":"journal_article","doi":"10.1214/20-EJP536","external_id":{"arxiv":["1811.01366"],"isi":["000591737500001"]},"_id":"8973","intvolume":"        25","acknowledgement":"We warmly thank S.R.S. Varadhan for many enlightening discussions at an early stage of this work. We are indebted to Francesca Collet for fruitful discussions and constant support all throughout this work. We thank Simone Floreani\r\nand Alberto Chiarini for helpful conversations on the final part of this paper as well as both referees for their careful reading and for raising relevant issues on some weak points contained in a previous version of this manuscript; we believe this helped us to improve it.\r\nPart of this work was done during the authors’ stay at the Institut Henri Poincaré (UMS 5208 CNRS-Sorbonne Université) – Centre Emile Borel during the trimester Stochastic Dynamics Out of Equilibrium. The authors thank this institution for hospitality and support (through LabEx CARMIN, ANR-10-LABX-59-01). F.S. thanks laboratoire\r\nMAP5 of Université de Paris, and E.S. thanks Delft University, for financial support and hospitality. F.S. acknowledges NWO for financial support via the TOP1 grant 613.001.552 as well as funding from the European Union’s Horizon 2020 research and innovation programme under the Marie-Skłodowska-Curie grant agreement No. 754411. This research has been conducted within the FP2M federation (CNRS FR 2036).","quality_controlled":"1","department":[{"_id":"JaMa"}],"has_accepted_license":"1","arxiv":1,"article_number":"138","month":"10","oa_version":"Published Version","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publication_status":"published","oa":1,"date_updated":"2023-10-17T12:51:56Z","ddc":["510"],"publication_identifier":{"eissn":["1083-6489"]}},{"author":[{"full_name":"Laukoter, Susanne","id":"2D6B7A9A-F248-11E8-B48F-1D18A9856A87","last_name":"Laukoter","first_name":"Susanne"},{"full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-3183-8207","first_name":"Nicole","last_name":"Amberg"},{"last_name":"Pauler","first_name":"Florian","id":"48EA0138-F248-11E8-B48F-1D18A9856A87","full_name":"Pauler, Florian"},{"full_name":"Hippenmeyer, Simon","id":"37B36620-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2279-1061","last_name":"Hippenmeyer","first_name":"Simon"}],"date_published":"2020-12-18T00:00:00Z","volume":1,"abstract":[{"lang":"eng","text":"Mosaic analysis with double markers (MADM) technology enables concomitant fluorescent cell labeling and induction of uniparental chromosome disomy (UPD) with single-cell resolution. In UPD, imprinted genes are either overexpressed 2-fold or are not expressed. Here, the MADM platform is utilized to probe imprinting phenotypes at the transcriptional level. This protocol highlights major steps for the generation and isolation of projection neurons and astrocytes with MADM-induced UPD from mouse cerebral cortex for downstream single-cell and low-input sample RNA-sequencing experiments.\r\n\r\nFor complete details on the use and execution of this protocol, please refer to Laukoter et al. (2020b)."}],"file_date_updated":"2021-01-07T15:57:27Z","issue":"3","ec_funded":1,"publication":"STAR Protocols","language":[{"iso":"eng"}],"year":"2020","day":"18","pmid":1,"file":[{"success":1,"date_created":"2021-01-07T15:57:27Z","creator":"dernst","checksum":"f1e9a433e9cb0f41f7b6df6b76db1f6e","relation":"main_file","file_id":"8996","file_name":"2020_STARProtocols_Laukoter.pdf","access_level":"open_access","file_size":4031449,"date_updated":"2021-01-07T15:57:27Z","content_type":"application/pdf"}],"publisher":"Elsevier","project":[{"name":"Role of Eed in neural stem cell lineage progression","_id":"268F8446-B435-11E9-9278-68D0E5697425","grant_number":"T0101031","call_identifier":"FWF"},{"grant_number":"F07805","_id":"059F6AB4-7A3F-11EA-A408-12923DDC885E","name":"Molecular Mechanisms of Neural Stem Cell Lineage Progression"},{"_id":"25D92700-B435-11E9-9278-68D0E5697425","name":"Mapping Cell-Type Specificity of the Genomic Imprintome in the Brain","grant_number":"LS13-002"},{"call_identifier":"FP7","grant_number":"618444","_id":"25D61E48-B435-11E9-9278-68D0E5697425","name":"Molecular Mechanisms of Cerebral Cortex Development"},{"grant_number":"725780","call_identifier":"H2020","_id":"260018B0-B435-11E9-9278-68D0E5697425","name":"Principles of Neural Stem Cell Lineage Progression in Cerebral Cortex Development"}],"article_type":"original","date_created":"2020-12-30T10:17:07Z","article_number":"100215","has_accepted_license":"1","oa":1,"publication_status":"published","publication_identifier":{"issn":["2666-1667"]},"date_updated":"2021-01-12T08:21:36Z","ddc":["570"],"oa_version":"Published Version","month":"12","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"title":"Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy","status":"public","type":"journal_article","citation":{"ieee":"S. Laukoter, N. Amberg, F. Pauler, and S. Hippenmeyer, “Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy,” <i>STAR Protocols</i>, vol. 1, no. 3. Elsevier, 2020.","ista":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. 2020. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. STAR Protocols. 1(3), 100215.","ama":"Laukoter S, Amberg N, Pauler F, Hippenmeyer S. Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. <i>STAR Protocols</i>. 2020;1(3). doi:<a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">10.1016/j.xpro.2020.100215</a>","short":"S. Laukoter, N. Amberg, F. Pauler, S. Hippenmeyer, STAR Protocols 1 (2020).","chicago":"Laukoter, Susanne, Nicole Amberg, Florian Pauler, and Simon Hippenmeyer. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” <i>STAR Protocols</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">https://doi.org/10.1016/j.xpro.2020.100215</a>.","mla":"Laukoter, Susanne, et al. “Generation and Isolation of Single Cells from Mouse Brain with Mosaic Analysis with Double Markers-Induced Uniparental Chromosome Disomy.” <i>STAR Protocols</i>, vol. 1, no. 3, 100215, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">10.1016/j.xpro.2020.100215</a>.","apa":"Laukoter, S., Amberg, N., Pauler, F., &#38; Hippenmeyer, S. (2020). Generation and isolation of single cells from mouse brain with mosaic analysis with double markers-induced uniparental chromosome disomy. <i>STAR Protocols</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.xpro.2020.100215\">https://doi.org/10.1016/j.xpro.2020.100215</a>"},"article_processing_charge":"No","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"}],"quality_controlled":"1","acknowledgement":"This research was supported by the Scientific Service Units (SSU) at IST Austria through resources provided by the Bioimaging (BIF) and Preclinical Facilities (PCF). N.A received support from the FWF Firnberg-Programm (T 1031). This work was also supported by IST Austria institutional funds; FWF SFB F78 to S.H.; NÖ Forschung und Bildung n[f+b] life science call grant (C13-002) to S.H.; the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 618444 to S.H.; and the European Research Council (ERC) under the European Union’s Horizon 2020 research and innovation programme (grant agreement no. 725780 LinPro) to S.H.","department":[{"_id":"SiHi"}],"external_id":{"pmid":["33377108"]},"doi":"10.1016/j.xpro.2020.100215","intvolume":"         1","_id":"8978"},{"page":"141","_id":"8983","doi":"10.15479/AT:ISTA:8983","department":[{"_id":"DaSi"}],"degree_awarded":"PhD","acknowledgement":"Also, I would like to express my appreciation and thanks to the Bioimaging facility, LSF, GSO, library, and IT people at IST Austria.","acknowledged_ssus":[{"_id":"Bio"},{"_id":"LifeSc"},{"_id":"E-Lib"},{"_id":"CampIT"}],"article_processing_charge":"No","citation":{"ieee":"S. Emtenani, “Metabolic regulation of Drosophila macrophage tissue invasion,” Institute of Science and Technology Austria, 2020.","ista":"Emtenani S. 2020. Metabolic regulation of Drosophila macrophage tissue invasion. Institute of Science and Technology Austria.","chicago":"Emtenani, Shamsi. “Metabolic Regulation of Drosophila Macrophage Tissue Invasion.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>.","short":"S. Emtenani, Metabolic Regulation of Drosophila Macrophage Tissue Invasion, Institute of Science and Technology Austria, 2020.","ama":"Emtenani S. Metabolic regulation of Drosophila macrophage tissue invasion. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>","apa":"Emtenani, S. (2020). <i>Metabolic regulation of Drosophila macrophage tissue invasion</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:8983\">https://doi.org/10.15479/AT:ISTA:8983</a>","mla":"Emtenani, Shamsi. <i>Metabolic Regulation of Drosophila Macrophage Tissue Invasion</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:8983\">10.15479/AT:ISTA:8983</a>."},"type":"dissertation","status":"public","title":"Metabolic regulation of Drosophila macrophage tissue invasion","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"8557"},{"status":"public","relation":"part_of_dissertation","id":"6187"}]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"12","oa_version":"Published Version","publication_identifier":{"issn":["2663-337X"]},"ddc":["570"],"date_updated":"2023-09-07T13:24:17Z","oa":1,"publication_status":"published","alternative_title":["ISTA Thesis"],"has_accepted_license":"1","date_created":"2020-12-30T15:41:26Z","publisher":"Institute of Science and Technology Austria","file":[{"embargo":"2021-12-30","file_name":"Thesis_Shamsi_Emtenani_pdfA.pdf","file_size":10848175,"access_level":"open_access","date_updated":"2021-12-31T23:30:04Z","content_type":"application/pdf","date_created":"2020-12-30T15:34:01Z","creator":"semtenan","relation":"main_file","checksum":"ec2797ab7a6f253b35df0572b36d1b43","file_id":"8984"},{"file_id":"8985","creator":"semtenan","date_created":"2020-12-30T15:37:36Z","checksum":"cc30e6608a9815414024cf548dff3b3a","relation":"source_file","date_updated":"2021-12-31T23:30:04Z","content_type":"application/pdf","embargo_to":"open_access","file_name":"Thesis_Shamsi_Emtenani_source file.pdf","access_level":"closed","file_size":10073648}],"supervisor":[{"orcid":"0000-0001-8323-8353","first_name":"Daria E","last_name":"Siekhaus","full_name":"Siekhaus, Daria E","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"year":"2020","day":"30","file_date_updated":"2021-12-31T23:30:04Z","date_published":"2020-12-30T00:00:00Z","abstract":[{"lang":"eng","text":"Metabolic adaptation is a critical feature of migrating cells. It tunes the metabolic programs of migrating cells to allow them to efficiently exert their crucial roles in development, inflammatory responses and tumor metastasis. Cell migration through physically challenging contexts requires energy. However, how the metabolic reprogramming that underlies in vivo cell invasion is controlled is still unanswered. In my PhD project, I identify a novel conserved metabolic shift in Drosophila melanogaster immune cells that by modulating their bioenergetic potential controls developmentally programmed tissue invasion. We show that this regulation requires a novel conserved nuclear protein, named Atossa. Atossa enhances the transcription of a set of proteins, including an RNA helicase Porthos and two metabolic enzymes, each of which increases the tissue invasion of leading Drosophila macrophages and can rescue the atossa mutant phenotype. Porthos selectively regulates the translational efficiency of a subset of mRNAs containing a 5’-UTR cis-regulatory TOP-like sequence. These 5’TOPL mRNA targets encode mitochondrial-related proteins, including subunits of mitochondrial oxidative phosphorylation (OXPHOS) components III and V and other metabolic-related proteins. Porthos powers up mitochondrial OXPHOS to engender a sufficient ATP supply, which is required for tissue invasion of leading macrophages. Atossa’s two vertebrate orthologs rescue the invasion defect. In my PhD project, I elucidate that Atossa displays a conserved developmental metabolic control to modulate metabolic capacities and the cellular energy state, through altered transcription and translation, to aid the tissue infiltration of leading cells into energy demanding barriers."}],"author":[{"full_name":"Emtenani, Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","last_name":"Emtenani","first_name":"Shamsi","orcid":"0000-0001-6981-6938"}]},{"date_created":"2021-01-03T23:01:23Z","project":[{"call_identifier":"H2020","grant_number":"742985","_id":"261099A6-B435-11E9-9278-68D0E5697425","name":"Tracing Evolution of Auxin Transport and Polarity in Plants"},{"name":"Molecular mechanisms of endocytic cargo recognition in plants","_id":"26538374-B435-11E9-9278-68D0E5697425","grant_number":"I03630","call_identifier":"FWF"},{"name":"A Case Study of Plant Growth Regulation: Molecular Mechanism of Auxin-mediated Rapid Growth Inhibition in Arabidopsis Root","_id":"26B4D67E-B435-11E9-9278-68D0E5697425","grant_number":"25351"}],"article_type":"original","scopus_import":"1","file":[{"creator":"dernst","date_created":"2021-01-07T12:44:33Z","checksum":"5ac2500b191c08ef6dab5327f40ff663","relation":"main_file","file_id":"8994","file_name":"2020_ScienceAdvances_Zhang.pdf","file_size":10578145,"access_level":"open_access","date_updated":"2021-01-07T12:44:33Z","content_type":"application/pdf","success":1}],"publisher":"AAAS","pmid":1,"ec_funded":1,"publication":"Science Advances","day":"11","year":"2020","language":[{"iso":"eng"}],"author":[{"full_name":"Zhang, Yuzhou","id":"3B6137F2-F248-11E8-B48F-1D18A9856A87","first_name":"Yuzhou","last_name":"Zhang","orcid":"0000-0003-2627-6956"},{"full_name":"Rodriguez Solovey, Lesia","id":"3922B506-F248-11E8-B48F-1D18A9856A87","last_name":"Rodriguez Solovey","first_name":"Lesia","orcid":"0000-0002-7244-7237"},{"first_name":"Lanxin","last_name":"Li","orcid":"0000-0002-5607-272X","full_name":"Li, Lanxin","id":"367EF8FA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zhang, Xixi","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","orcid":"0000-0001-7048-4627","first_name":"Xixi","last_name":"Zhang"},{"orcid":"0000-0002-8302-7596","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"volume":6,"abstract":[{"text":"Flowering plants display the highest diversity among plant species and have notably shaped terrestrial landscapes. Nonetheless, the evolutionary origin of their unprecedented morphological complexity remains largely an enigma. Here, we show that the coevolution of cis-regulatory and coding regions of PIN-FORMED (PIN) auxin transporters confined their expression to certain cell types and directed their subcellular localization to particular cell sides, which together enabled dynamic auxin gradients across tissues critical to the complex architecture of flowering plants. Extensive intraspecies and interspecies genetic complementation experiments with PINs from green alga up to flowering plant lineages showed that PIN genes underwent three subsequent, critical evolutionary innovations and thus acquired a triple function to regulate the development of three essential components of the flowering plant Arabidopsis: shoot/root, inflorescence, and floral organ. Our work highlights the critical role of functional innovations within the PIN gene family as essential prerequisites for the origin of flowering plants.","lang":"eng"}],"date_published":"2020-12-11T00:00:00Z","file_date_updated":"2021-01-07T12:44:33Z","issue":"50","acknowledgement":"We thank C.Löhne (Botanic Gardens, University of Bonn) for providing us with A. trichopoda. We would like to thank T.Han, A.Mally (IST, Austria), and C.Hartinger (University of Oxford) for constructive comment and careful reading. Funding: The research leading to these results has received funding from the European Union’s Horizon 2020 Research and Innovation Programme (ERC grant agreement number 742985), Austrian Science Fund (FWF, grant number I 3630-B25), DOC Fellowship of the Austrian Academy of Sciences, and IST Fellow program. ","quality_controlled":"1","department":[{"_id":"JiFr"}],"doi":"10.1126/sciadv.abc8895","external_id":{"isi":["000599903600014"],"pmid":["33310852"]},"_id":"8986","license":"https://creativecommons.org/licenses/by-nc/4.0/","intvolume":"         6","tmp":{"image":"/images/cc_by_nc.png","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)"},"title":"Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants","type":"journal_article","status":"public","citation":{"apa":"Zhang, Y., Rodriguez Solovey, L., Li, L., Zhang, X., &#38; Friml, J. (2020). Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.abc8895\">https://doi.org/10.1126/sciadv.abc8895</a>","mla":"Zhang, Yuzhou, et al. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” <i>Science Advances</i>, vol. 6, no. 50, eabc8895, AAAS, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.abc8895\">10.1126/sciadv.abc8895</a>.","chicago":"Zhang, Yuzhou, Lesia Rodriguez Solovey, Lanxin Li, Xixi Zhang, and Jiří Friml. “Functional Innovations of PIN Auxin Transporters Mark Crucial Evolutionary Transitions during Rise of Flowering Plants.” <i>Science Advances</i>. AAAS, 2020. <a href=\"https://doi.org/10.1126/sciadv.abc8895\">https://doi.org/10.1126/sciadv.abc8895</a>.","short":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, J. Friml, Science Advances 6 (2020).","ama":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. <i>Science Advances</i>. 2020;6(50). doi:<a href=\"https://doi.org/10.1126/sciadv.abc8895\">10.1126/sciadv.abc8895</a>","ista":"Zhang Y, Rodriguez Solovey L, Li L, Zhang X, Friml J. 2020. Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants. Science Advances. 6(50), eabc8895.","ieee":"Y. Zhang, L. Rodriguez Solovey, L. Li, X. Zhang, and J. Friml, “Functional innovations of PIN auxin transporters mark crucial evolutionary transitions during rise of flowering plants,” <i>Science Advances</i>, vol. 6, no. 50. AAAS, 2020."},"article_processing_charge":"No","isi":1,"oa":1,"publication_status":"published","date_updated":"2024-10-29T10:22:43Z","ddc":["580"],"publication_identifier":{"eissn":["2375-2548"]},"oa_version":"Published Version","month":"12","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10083"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_number":"eabc8895","has_accepted_license":"1"},{"department":[{"_id":"KrPi"}],"quality_controlled":"1","intvolume":"     12578","page":"3-15","_id":"8987","external_id":{"isi":["000927592800001"]},"doi":"10.1007/978-3-030-65277-7_1","status":"public","type":"conference","title":"Delayed authentication: Preventing replay and relay attacks in private contact tracing","isi":1,"citation":{"mla":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” <i>Progress in Cryptology</i>, vol. 12578, Springer Nature, 2020, pp. 3–15, doi:<a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">10.1007/978-3-030-65277-7_1</a>.","apa":"Pietrzak, K. Z. (2020). Delayed authentication: Preventing replay and relay attacks in private contact tracing. In <i>Progress in Cryptology</i> (Vol. 12578, pp. 3–15). Bangalore, India: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">https://doi.org/10.1007/978-3-030-65277-7_1</a>","chicago":"Pietrzak, Krzysztof Z. “Delayed Authentication: Preventing Replay and Relay Attacks in Private Contact Tracing.” In <i>Progress in Cryptology</i>, 12578:3–15. LNCS. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">https://doi.org/10.1007/978-3-030-65277-7_1</a>.","short":"K.Z. Pietrzak, in:, Progress in Cryptology, Springer Nature, 2020, pp. 3–15.","ama":"Pietrzak KZ. Delayed authentication: Preventing replay and relay attacks in private contact tracing. In: <i>Progress in Cryptology</i>. Vol 12578. LNCS. Springer Nature; 2020:3-15. doi:<a href=\"https://doi.org/10.1007/978-3-030-65277-7_1\">10.1007/978-3-030-65277-7_1</a>","ista":"Pietrzak KZ. 2020. Delayed authentication: Preventing replay and relay attacks in private contact tracing. Progress in Cryptology. INDOCRYPT: International Conference on Cryptology in IndiaLNCS vol. 12578, 3–15.","ieee":"K. Z. Pietrzak, “Delayed authentication: Preventing replay and relay attacks in private contact tracing,” in <i>Progress in Cryptology</i>, Bangalore, India, 2020, vol. 12578, pp. 3–15."},"article_processing_charge":"No","publication_identifier":{"eissn":["16113349"],"isbn":["9783030652760"],"issn":["03029743"]},"date_updated":"2023-08-24T11:08:58Z","conference":{"location":"Bangalore, India","end_date":"2020-12-16","start_date":"2020-12-13","name":"INDOCRYPT: International Conference on Cryptology in India"},"oa":1,"publication_status":"published","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","oa_version":"Preprint","month":"12","date_created":"2021-01-03T23:01:23Z","project":[{"name":"Teaching Old Crypto New Tricks","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"682815"}],"scopus_import":"1","series_title":"LNCS","main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2020/418"}],"publisher":"Springer Nature","ec_funded":1,"year":"2020","language":[{"iso":"eng"}],"day":"08","publication":"Progress in Cryptology","date_published":"2020-12-08T00:00:00Z","volume":12578,"abstract":[{"lang":"eng","text":"Currently several projects aim at designing and implementing protocols for privacy preserving automated contact tracing to help fight the current pandemic. Those proposal are quite similar, and in their most basic form basically propose an app for mobile phones which broadcasts frequently changing pseudorandom identifiers via (low energy) Bluetooth, and at the same time, the app stores IDs broadcast by phones in its proximity. Only if a user is tested positive, they upload either the beacons they did broadcast (which is the case in decentralized proposals as DP-3T, east and west coast PACT or Covid watch) or received (as in Popp-PT or ROBERT) during the last two weeks or so.\r\n\r\nVaudenay [eprint 2020/399] observes that this basic scheme (he considers the DP-3T proposal) succumbs to relay and even replay attacks, and proposes more complex interactive schemes which prevent those attacks without giving up too many privacy aspects. Unfortunately interaction is problematic for this application for efficiency and security reasons. The countermeasures that have been suggested so far are either not practical or give up on key privacy aspects. We propose a simple non-interactive variant of the basic protocol that\r\n(security) Provably prevents replay and (if location data is available) relay attacks.\r\n(privacy) The data of all parties (even jointly) reveals no information on the location or time where encounters happened.\r\n(efficiency) The broadcasted message can fit into 128 bits and uses only basic crypto (commitments and secret key authentication).\r\n\r\nTowards this end we introduce the concept of “delayed authentication”, which basically is a message authentication code where verification can be done in two steps, where the first doesn’t require the key, and the second doesn’t require the message."}],"author":[{"full_name":"Pietrzak, Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","last_name":"Pietrzak","first_name":"Krzysztof Z","orcid":"0000-0002-9139-1654"}]},{"article_type":"original","project":[{"name":"Can evolution minimize spurious signaling crosstalk to reach optimal performance?","_id":"2665AAFE-B435-11E9-9278-68D0E5697425","grant_number":"RGP0034/2018"},{"name":"Biophysically realistic genotype-phenotype maps for regulatory networks","_id":"267C84F4-B435-11E9-9278-68D0E5697425"}],"date_created":"2021-01-10T23:01:17Z","scopus_import":"1","file":[{"checksum":"69039cd402a571983aa6cb4815ffa863","relation":"main_file","date_created":"2021-01-11T08:37:31Z","creator":"dernst","file_id":"9004","access_level":"open_access","file_size":1199247,"file_name":"2020_PNAS_Grah.pdf","content_type":"application/pdf","date_updated":"2021-01-11T08:37:31Z","success":1}],"publisher":"National Academy of Sciences","pmid":1,"day":"15","year":"2020","language":[{"iso":"eng"}],"publication":"PNAS","abstract":[{"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 biophysical 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 nonequilibrium models, progress is difficult due to an explosion in the number of parameters. Here, we navigate this complexity by looking for minimal nonequilibrium 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 nonequilibrium models is in a trade-off with gene-expression noise, predicting bursty dynamics—an experimentally observed hallmark of eukaryotic transcription. By drastically reducing the vast parameter space of nonequilibrium enhancer models to a much smaller subspace that optimally realizes biological function, we deliver a rich class of models that could be tractably inferred from data in the near future.","lang":"eng"}],"volume":117,"date_published":"2020-12-15T00:00:00Z","author":[{"last_name":"Grah","first_name":"Rok","orcid":"0000-0003-2539-3560","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Zoller, Benjamin","last_name":"Zoller","first_name":"Benjamin"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455"}],"issue":"50","file_date_updated":"2021-01-11T08:37:31Z","department":[{"_id":"GaTk"}],"acknowledgement":"G.T. was supported by Human Frontiers Science Program Grant RGP0034/2018. R.G. was supported by the Austrian Academy of Sciences DOC Fellowship. R.G. thanks S. Avvakumov for helpful discussions.","quality_controlled":"1","_id":"9000","page":"31614-31622","intvolume":"       117","doi":"10.1073/pnas.2006731117","external_id":{"pmid":["33268497"],"isi":["000600608300015"]},"status":"public","type":"journal_article","title":"Nonequilibrium models of optimal enhancer function","tmp":{"short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"isi":1,"article_processing_charge":"No","citation":{"apa":"Grah, R., Zoller, B., &#38; Tkačik, G. (2020). Nonequilibrium models of optimal enhancer function. <i>PNAS</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>","mla":"Grah, Rok, et al. “Nonequilibrium Models of Optimal Enhancer Function.” <i>PNAS</i>, vol. 117, no. 50, National Academy of Sciences, 2020, pp. 31614–22, doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>.","chicago":"Grah, Rok, Benjamin Zoller, and Gašper Tkačik. “Nonequilibrium Models of Optimal Enhancer Function.” <i>PNAS</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.2006731117\">https://doi.org/10.1073/pnas.2006731117</a>.","ama":"Grah R, Zoller B, Tkačik G. Nonequilibrium models of optimal enhancer function. <i>PNAS</i>. 2020;117(50):31614-31622. doi:<a href=\"https://doi.org/10.1073/pnas.2006731117\">10.1073/pnas.2006731117</a>","short":"R. Grah, B. Zoller, G. Tkačik, PNAS 117 (2020) 31614–31622.","ista":"Grah R, Zoller B, Tkačik G. 2020. Nonequilibrium models of optimal enhancer function. PNAS. 117(50), 31614–31622.","ieee":"R. Grah, B. Zoller, and G. Tkačik, “Nonequilibrium models of optimal enhancer function,” <i>PNAS</i>, vol. 117, no. 50. National Academy of Sciences, pp. 31614–31622, 2020."},"date_updated":"2023-08-24T11:10:22Z","ddc":["570"],"publication_identifier":{"issn":["00278424"],"eissn":["10916490"]},"oa":1,"publication_status":"published","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-compact-model-for-gene-regulation-in-higher-organisms/","description":"News on IST Homepage","relation":"press_release"}]},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"12","oa_version":"Published Version","has_accepted_license":"1"},{"publication":"Annals of Mathematics","language":[{"iso":"eng"}],"year":"2020","day":"01","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","orcid":"0000-0002-8314-0177","last_name":"Browning","first_name":"Timothy D"},{"last_name":"Sawin","first_name":"Will","full_name":"Sawin, Will"}],"date_published":"2020-05-01T00:00:00Z","volume":191,"abstract":[{"text":"We develop a geometric version of the circle method and use it to compute the compactly supported cohomology of the space of rational curves through a point on a smooth affine hypersurface of sufficiently low degree.","lang":"eng"}],"issue":"3","article_type":"original","date_created":"2018-12-11T11:45:02Z","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1711.10451"}],"publisher":"Princeton University","oa":1,"publication_status":"published","date_updated":"2023-08-17T07:12:37Z","month":"05","oa_version":"Preprint","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publist_id":"7744","arxiv":1,"quality_controlled":"1","department":[{"_id":"TiBr"}],"external_id":{"arxiv":["1711.10451"],"isi":["000526986300004"]},"doi":"10.4007/annals.2020.191.3.4","intvolume":"       191","_id":"177","page":"893-948","title":"A geometric version of the circle method","status":"public","type":"journal_article","article_processing_charge":"No","citation":{"short":"T.D. Browning, W. Sawin, Annals of Mathematics 191 (2020) 893–948.","chicago":"Browning, Timothy D, and Will Sawin. “A Geometric Version of the Circle Method.” <i>Annals of Mathematics</i>. Princeton University, 2020. <a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">https://doi.org/10.4007/annals.2020.191.3.4</a>.","ama":"Browning TD, Sawin W. A geometric version of the circle method. <i>Annals of Mathematics</i>. 2020;191(3):893-948. doi:<a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">10.4007/annals.2020.191.3.4</a>","mla":"Browning, Timothy D., and Will Sawin. “A Geometric Version of the Circle Method.” <i>Annals of Mathematics</i>, vol. 191, no. 3, Princeton University, 2020, pp. 893–948, doi:<a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">10.4007/annals.2020.191.3.4</a>.","apa":"Browning, T. D., &#38; Sawin, W. (2020). A geometric version of the circle method. <i>Annals of Mathematics</i>. Princeton University. <a href=\"https://doi.org/10.4007/annals.2020.191.3.4\">https://doi.org/10.4007/annals.2020.191.3.4</a>","ista":"Browning TD, Sawin W. 2020. A geometric version of the circle method. Annals of Mathematics. 191(3), 893–948.","ieee":"T. D. Browning and W. Sawin, “A geometric version of the circle method,” <i>Annals of Mathematics</i>, vol. 191, no. 3. Princeton University, pp. 893–948, 2020."},"isi":1},{"publisher":"Duke University Press","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1805.10715"}],"article_type":"original","date_created":"2018-12-11T11:45:02Z","volume":169,"abstract":[{"lang":"eng","text":"An asymptotic formula is established for the number of rational points of bounded anticanonical height which lie on a certain Zariski dense subset of the biprojective hypersurface x1y21+⋯+x4y24=0 in ℙ3×ℙ3. This confirms the modified Manin conjecture for this variety, in which the removal of a thin set of rational points is allowed."}],"date_published":"2020-09-10T00:00:00Z","author":[{"id":"35827D50-F248-11E8-B48F-1D18A9856A87","full_name":"Browning, Timothy D","first_name":"Timothy D","last_name":"Browning","orcid":"0000-0002-8314-0177"},{"full_name":"Heath Brown, Roger","first_name":"Roger","last_name":"Heath Brown"}],"issue":"16","day":"10","language":[{"iso":"eng"}],"year":"2020","publication":"Duke Mathematical Journal","status":"public","type":"journal_article","title":"Density of rational points on a quadric bundle in ℙ3×ℙ3","isi":1,"citation":{"ista":"Browning TD, Heath Brown R. 2020. Density of rational points on a quadric bundle in ℙ3×ℙ3. Duke Mathematical Journal. 169(16), 3099–3165.","ieee":"T. D. Browning and R. Heath Brown, “Density of rational points on a quadric bundle in ℙ3×ℙ3,” <i>Duke Mathematical Journal</i>, vol. 169, no. 16. Duke University Press, pp. 3099–3165, 2020.","apa":"Browning, T. D., &#38; Heath Brown, R. (2020). Density of rational points on a quadric bundle in ℙ3×ℙ3. <i>Duke Mathematical Journal</i>. Duke University Press. <a href=\"https://doi.org/10.1215/00127094-2020-0031\">https://doi.org/10.1215/00127094-2020-0031</a>","mla":"Browning, Timothy D., and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” <i>Duke Mathematical Journal</i>, vol. 169, no. 16, Duke University Press, 2020, pp. 3099–165, doi:<a href=\"https://doi.org/10.1215/00127094-2020-0031\">10.1215/00127094-2020-0031</a>.","ama":"Browning TD, Heath Brown R. Density of rational points on a quadric bundle in ℙ3×ℙ3. <i>Duke Mathematical Journal</i>. 2020;169(16):3099-3165. doi:<a href=\"https://doi.org/10.1215/00127094-2020-0031\">10.1215/00127094-2020-0031</a>","short":"T.D. Browning, R. Heath Brown, Duke Mathematical Journal 169 (2020) 3099–3165.","chicago":"Browning, Timothy D, and Roger Heath Brown. “Density of Rational Points on a Quadric Bundle in ℙ3×ℙ3.” <i>Duke Mathematical Journal</i>. Duke University Press, 2020. <a href=\"https://doi.org/10.1215/00127094-2020-0031\">https://doi.org/10.1215/00127094-2020-0031</a>."},"article_processing_charge":"No","department":[{"_id":"TiBr"}],"quality_controlled":"1","page":"3099-3165","_id":"179","intvolume":"       169","doi":"10.1215/00127094-2020-0031","external_id":{"arxiv":["1805.10715"],"isi":["000582676300002"]},"arxiv":1,"date_updated":"2023-10-17T12:51:10Z","publication_identifier":{"issn":["0012-7094"]},"oa":1,"publication_status":"published","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","oa_version":"Preprint","month":"09"},{"isi":1,"citation":{"ista":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. 2020. Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime. Communications in Mathematical Physics. 374, 2097–2150.","ieee":"N. P. Benedikter, P. T. Nam, M. Porta, B. Schlein, and R. Seiringer, “Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime,” <i>Communications in Mathematical Physics</i>, vol. 374. Springer Nature, pp. 2097–2150, 2020.","short":"N.P. Benedikter, P.T. Nam, M. Porta, B. Schlein, R. Seiringer, Communications in Mathematical Physics 374 (2020) 2097–2150.","chicago":"Benedikter, Niels P, Phan Thành Nam, Marcello Porta, Benjamin Schlein, and Robert Seiringer. “Optimal Upper Bound for the Correlation Energy of a Fermi Gas in the Mean-Field Regime.” <i>Communications in Mathematical Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00220-019-03505-5\">https://doi.org/10.1007/s00220-019-03505-5</a>.","ama":"Benedikter NP, Nam PT, Porta M, Schlein B, Seiringer R. Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime. <i>Communications in Mathematical Physics</i>. 2020;374:2097–2150. doi:<a href=\"https://doi.org/10.1007/s00220-019-03505-5\">10.1007/s00220-019-03505-5</a>","mla":"Benedikter, Niels P., et al. “Optimal Upper Bound for the Correlation Energy of a Fermi Gas in the Mean-Field Regime.” <i>Communications in Mathematical Physics</i>, vol. 374, Springer Nature, 2020, pp. 2097–2150, doi:<a href=\"https://doi.org/10.1007/s00220-019-03505-5\">10.1007/s00220-019-03505-5</a>.","apa":"Benedikter, N. P., Nam, P. T., Porta, M., Schlein, B., &#38; Seiringer, R. (2020). Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime. <i>Communications in Mathematical Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00220-019-03505-5\">https://doi.org/10.1007/s00220-019-03505-5</a>"},"article_processing_charge":"No","status":"public","type":"journal_article","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","image":"/images/cc_by.png","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"title":"Optimal upper bound for the correlation energy of a Fermi gas in the mean-field regime","intvolume":"       374","_id":"6649","page":"2097–2150","external_id":{"isi":["000527910700019"],"arxiv":["1809.01902"]},"doi":"10.1007/s00220-019-03505-5","department":[{"_id":"RoSe"}],"quality_controlled":"1","arxiv":1,"has_accepted_license":"1","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","month":"03","oa_version":"Published Version","publication_identifier":{"issn":["0010-3616"],"eissn":["1432-0916"]},"ddc":["530"],"date_updated":"2023-08-17T13:51:50Z","oa":1,"publication_status":"published","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:47:35Z","access_level":"open_access","file_size":853289,"file_name":"2019_CommMathPhysics_Benedikter.pdf","file_id":"6668","checksum":"f9dd6dd615a698f1d3636c4a092fed23","relation":"main_file","creator":"dernst","date_created":"2019-07-24T07:19:10Z"}],"publisher":"Springer Nature","scopus_import":"1","date_created":"2019-07-18T13:30:04Z","article_type":"original","project":[{"_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1","name":"FWF Open Access Fund","call_identifier":"FWF"},{"name":"Structure of the Excitation Spectrum for Many-Body Quantum Systems","_id":"25C878CE-B435-11E9-9278-68D0E5697425","grant_number":"P27533_N27","call_identifier":"FWF"},{"grant_number":"694227","call_identifier":"H2020","name":"Analysis of quantum many-body systems","_id":"25C6DC12-B435-11E9-9278-68D0E5697425"}],"file_date_updated":"2020-07-14T12:47:35Z","date_published":"2020-03-01T00:00:00Z","abstract":[{"text":"While Hartree–Fock theory is well established as a fundamental approximation for interacting fermions, it has been unclear how to describe corrections to it due to many-body correlations. In this paper we start from the Hartree–Fock state given by plane waves and introduce collective particle–hole pair excitations. These pairs can be approximately described by a bosonic quadratic Hamiltonian. We use Bogoliubov theory to construct a trial state yielding a rigorous Gell-Mann–Brueckner–type upper bound to the ground state energy. Our result justifies the random-phase approximation in the mean-field scaling regime, for repulsive, regular interaction potentials.\r\n","lang":"eng"}],"volume":374,"author":[{"id":"3DE6C32A-F248-11E8-B48F-1D18A9856A87","full_name":"Benedikter, Niels P","orcid":"0000-0002-1071-6091","last_name":"Benedikter","first_name":"Niels P"},{"full_name":"Nam, Phan Thành","first_name":"Phan Thành","last_name":"Nam"},{"full_name":"Porta, Marcello","first_name":"Marcello","last_name":"Porta"},{"full_name":"Schlein, Benjamin","first_name":"Benjamin","last_name":"Schlein"},{"orcid":"0000-0002-6781-0521","first_name":"Robert","last_name":"Seiringer","full_name":"Seiringer, Robert","id":"4AFD0470-F248-11E8-B48F-1D18A9856A87"}],"year":"2020","language":[{"iso":"eng"}],"day":"01","publication":"Communications in Mathematical Physics","ec_funded":1},{"main_file_link":[{"url":"https://arxiv.org/abs/1901.01375","open_access":"1"}],"publisher":"Institute of Mathematical Statistics","date_created":"2019-07-31T09:39:42Z","article_type":"original","date_published":"2020-12-11T00:00:00Z","abstract":[{"text":"Fitting a function by using linear combinations of a large number N of `simple' components is one of the most fruitful ideas in statistical learning. This idea lies at the core of a variety of methods, from two-layer neural networks to kernel regression, to boosting. In general, the resulting risk minimization problem is non-convex and is solved by gradient descent or its variants. Unfortunately, little is known about global convergence properties of these approaches.\r\nHere we consider the problem of learning a concave function f on a compact convex domain Ω⊆ℝd, using linear combinations of `bump-like' components (neurons). The parameters to be fitted are the centers of N bumps, and the resulting empirical risk minimization problem is highly non-convex. We prove that, in the limit in which the number of neurons diverges, the evolution of gradient descent converges to a Wasserstein gradient flow in the space of probability distributions over Ω. Further, when the bump width δ tends to 0, this gradient flow has a limit which is a viscous porous medium equation. Remarkably, the cost function optimized by this gradient flow exhibits a special property known as displacement convexity, which implies exponential convergence rates for N→∞, δ→0. Surprisingly, this asymptotic theory appears to capture well the behavior for moderate values of δ,N. Explaining this phenomenon, and understanding the dependence on δ,N in a quantitative manner remains an outstanding challenge.","lang":"eng"}],"volume":48,"author":[{"first_name":"Adel","last_name":"Javanmard","full_name":"Javanmard, Adel"},{"orcid":"0000-0002-3242-7020","first_name":"Marco","last_name":"Mondelli","id":"27EB676C-8706-11E9-9510-7717E6697425","full_name":"Mondelli, Marco"},{"full_name":"Montanari, Andrea","last_name":"Montanari","first_name":"Andrea"}],"issue":"6","language":[{"iso":"eng"}],"year":"2020","day":"11","publication":"Annals of Statistics","type":"journal_article","status":"public","title":"Analysis of a two-layer neural network via displacement convexity","isi":1,"citation":{"mla":"Javanmard, Adel, et al. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” <i>Annals of Statistics</i>, vol. 48, no. 6, Institute of Mathematical Statistics, 2020, pp. 3619–42, doi:<a href=\"https://doi.org/10.1214/20-AOS1945\">10.1214/20-AOS1945</a>.","apa":"Javanmard, A., Mondelli, M., &#38; Montanari, A. (2020). Analysis of a two-layer neural network via displacement convexity. <i>Annals of Statistics</i>. Institute of Mathematical Statistics. <a href=\"https://doi.org/10.1214/20-AOS1945\">https://doi.org/10.1214/20-AOS1945</a>","short":"A. Javanmard, M. Mondelli, A. Montanari, Annals of Statistics 48 (2020) 3619–3642.","chicago":"Javanmard, Adel, Marco Mondelli, and Andrea Montanari. “Analysis of a Two-Layer Neural Network via Displacement Convexity.” <i>Annals of Statistics</i>. Institute of Mathematical Statistics, 2020. <a href=\"https://doi.org/10.1214/20-AOS1945\">https://doi.org/10.1214/20-AOS1945</a>.","ama":"Javanmard A, Mondelli M, Montanari A. Analysis of a two-layer neural network via displacement convexity. <i>Annals of Statistics</i>. 2020;48(6):3619-3642. doi:<a href=\"https://doi.org/10.1214/20-AOS1945\">10.1214/20-AOS1945</a>","ista":"Javanmard A, Mondelli M, Montanari A. 2020. Analysis of a two-layer neural network via displacement convexity. Annals of Statistics. 48(6), 3619–3642.","ieee":"A. Javanmard, M. Mondelli, and A. Montanari, “Analysis of a two-layer neural network via displacement convexity,” <i>Annals of Statistics</i>, vol. 48, no. 6. Institute of Mathematical Statistics, pp. 3619–3642, 2020."},"article_processing_charge":"No","department":[{"_id":"MaMo"}],"quality_controlled":"1","intvolume":"        48","page":"3619-3642","_id":"6748","external_id":{"isi":["000598369200021"],"arxiv":["1901.01375"]},"doi":"10.1214/20-AOS1945","arxiv":1,"publication_identifier":{"issn":["1932-6157"],"eissn":["1941-7330"]},"date_updated":"2024-03-06T08:28:50Z","publication_status":"published","oa":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"12","oa_version":"Preprint"}]