[{"page":"282-289","publication_status":"published","volume":20,"language":[{"iso":"eng"}],"department":[{"_id":"Bio"}],"month":"06","article_processing_charge":"No","date_created":"2020-05-17T22:00:44Z","quality_controlled":"1","scopus_import":"1","publication":"Current opinion in allergy and clinical immunology","author":[{"first_name":"Judit","orcid":"0000-0002-8777-3502","full_name":"Singer, Judit","id":"36432834-F248-11E8-B48F-1D18A9856A87","last_name":"Singer"},{"first_name":"Josef","last_name":"Singer","full_name":"Singer, Josef"},{"last_name":"Jensen-Jarolim","full_name":"Jensen-Jarolim, Erika","first_name":"Erika"}],"title":"Precision medicine in clinical oncology: the journey from IgG antibody to IgE","publication_identifier":{"eissn":["14736322"]},"type":"journal_article","doi":"10.1097/ACI.0000000000000637","_id":"7864","status":"public","oa_version":"None","isi":1,"day":"01","publisher":"Wolters Kluwer","citation":{"chicago":"Singer, Judit, Josef Singer, and Erika Jensen-Jarolim. “Precision Medicine in Clinical Oncology: The Journey from IgG Antibody to IgE.” <i>Current Opinion in Allergy and Clinical Immunology</i>. Wolters Kluwer, 2020. <a href=\"https://doi.org/10.1097/ACI.0000000000000637\">https://doi.org/10.1097/ACI.0000000000000637</a>.","mla":"Singer, Judit, et al. “Precision Medicine in Clinical Oncology: The Journey from IgG Antibody to IgE.” <i>Current Opinion in Allergy and Clinical Immunology</i>, vol. 20, no. 3, Wolters Kluwer, 2020, pp. 282–89, doi:<a href=\"https://doi.org/10.1097/ACI.0000000000000637\">10.1097/ACI.0000000000000637</a>.","short":"J. Singer, J. Singer, E. Jensen-Jarolim, Current Opinion in Allergy and Clinical Immunology 20 (2020) 282–289.","ama":"Singer J, Singer J, Jensen-Jarolim E. Precision medicine in clinical oncology: the journey from IgG antibody to IgE. <i>Current opinion in allergy and clinical immunology</i>. 2020;20(3):282-289. doi:<a href=\"https://doi.org/10.1097/ACI.0000000000000637\">10.1097/ACI.0000000000000637</a>","ista":"Singer J, Singer J, Jensen-Jarolim E. 2020. Precision medicine in clinical oncology: the journey from IgG antibody to IgE. Current opinion in allergy and clinical immunology. 20(3), 282–289.","apa":"Singer, J., Singer, J., &#38; Jensen-Jarolim, E. (2020). Precision medicine in clinical oncology: the journey from IgG antibody to IgE. <i>Current Opinion in Allergy and Clinical Immunology</i>. Wolters Kluwer. <a href=\"https://doi.org/10.1097/ACI.0000000000000637\">https://doi.org/10.1097/ACI.0000000000000637</a>","ieee":"J. Singer, J. Singer, and E. Jensen-Jarolim, “Precision medicine in clinical oncology: the journey from IgG antibody to IgE,” <i>Current opinion in allergy and clinical immunology</i>, vol. 20, no. 3. Wolters Kluwer, pp. 282–289, 2020."},"year":"2020","issue":"3","external_id":{"isi":["000561358300010"]},"intvolume":"        20","date_updated":"2023-08-21T06:28:52Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","text":"Purpose of review: Cancer is one of the leading causes of death and the incidence rates are constantly rising. The heterogeneity of tumors poses a big challenge for the treatment of the disease and natural antibodies additionally affect disease progression. The introduction of engineered mAbs for anticancer immunotherapies has substantially improved progression-free and overall survival of cancer patients, but little efforts have been made to exploit other antibody isotypes than IgG.\r\nRecent findings: In order to improve these therapies, ‘next-generation antibodies’ were engineered to enhance a specific feature of classical antibodies and form a group of highly effective and precise therapy compounds. Advanced antibody approaches include among others antibody-drug conjugates, glyco-engineered and Fc-engineered antibodies, antibody fragments, radioimmunotherapy compounds, bispecific antibodies and alternative (non-IgG) immunoglobulin classes, especially IgE.\r\nSummary: The current review describes solutions for the needs of next-generation antibody therapies through different approaches. Careful selection of the best-suited engineering methodology is a key factor in developing personalized, more specific and more efficient mAbs against cancer to improve the outcomes of cancer patients. We highlight here the large evidence of IgE exploiting a highly cytotoxic effector arm as potential next-generation anticancer immunotherapy."}],"date_published":"2020-06-01T00:00:00Z","article_type":"original","fulldoi":"https://doi.org/10.1097/ACI.0000000000000637"},{"fulldoi":"https://doi.org/10.1007/s41808-020-00068-8","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["510"],"has_accepted_license":"1","date_published":"2020-12-01T00:00:00Z","date_updated":"2025-07-17T08:12:24Z","file_date_updated":"2020-11-25T08:59:59Z","abstract":[{"text":"In this paper, we establish convergence to equilibrium for a drift–diffusion–recombination system modelling the charge transport within certain semiconductor devices. More precisely, we consider a two-level system for electrons and holes which is augmented by an intermediate energy level for electrons in so-called trapped states. The recombination dynamics use the mass action principle by taking into account this additional trap level. The main part of the paper is concerned with the derivation of an entropy–entropy production inequality, which entails exponential convergence to the equilibrium via the so-called entropy method. The novelty of our approach lies in the fact that the entropy method is applied uniformly in a fast-reaction parameter which governs the lifetime of electrons on the trap level. Thus, the resulting decay estimate for the densities of electrons and holes extends to the corresponding quasi-steady-state approximation.","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"8802","success":1,"date_created":"2020-11-25T08:59:59Z","file_size":8408694,"file_name":"2020_JourEllipticParabEquat_Fellner.pdf","relation":"main_file","access_level":"open_access","checksum":"6bc6832caacddceee1471291e93dcf1d","creator":"dernst","content_type":"application/pdf","date_updated":"2020-11-25T08:59:59Z"}],"intvolume":"         6","external_id":{"pmid":["33195442"]},"oa_version":"Published Version","_id":"7866","status":"public","acknowledgement":"Open access funding provided by Austrian Science Fund (FWF). The second author has been supported by the International Research Training Group IGDK 1754 “Optimization and Numerical Analysis for Partial Differential Equations with Nonsmooth Structures”, funded by the German Research Council (DFG) and the Austrian Science Fund (FWF) under grant number [W 1244-N18].","year":"2020","citation":{"ista":"Fellner K, Kniely M. 2020. Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. Journal of Elliptic and Parabolic Equations. 6, 529–598.","ama":"Fellner K, Kniely M. Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. <i>Journal of Elliptic and Parabolic Equations</i>. 2020;6:529-598. doi:<a href=\"https://doi.org/10.1007/s41808-020-00068-8\">10.1007/s41808-020-00068-8</a>","apa":"Fellner, K., &#38; Kniely, M. (2020). Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model. <i>Journal of Elliptic and Parabolic Equations</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s41808-020-00068-8\">https://doi.org/10.1007/s41808-020-00068-8</a>","ieee":"K. Fellner and M. Kniely, “Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model,” <i>Journal of Elliptic and Parabolic Equations</i>, vol. 6. Springer Nature, pp. 529–598, 2020.","chicago":"Fellner, Klemens, and Michael Kniely. “Uniform Convergence to Equilibrium for a Family of Drift–Diffusion Models with Trap-Assisted Recombination and the Limiting Shockley–Read–Hall Model.” <i>Journal of Elliptic and Parabolic Equations</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s41808-020-00068-8\">https://doi.org/10.1007/s41808-020-00068-8</a>.","mla":"Fellner, Klemens, and Michael Kniely. “Uniform Convergence to Equilibrium for a Family of Drift–Diffusion Models with Trap-Assisted Recombination and the Limiting Shockley–Read–Hall Model.” <i>Journal of Elliptic and Parabolic Equations</i>, vol. 6, Springer Nature, 2020, pp. 529–98, doi:<a href=\"https://doi.org/10.1007/s41808-020-00068-8\">10.1007/s41808-020-00068-8</a>.","short":"K. Fellner, M. Kniely, Journal of Elliptic and Parabolic Equations 6 (2020) 529–598."},"publisher":"Springer Nature","day":"01","doi":"10.1007/s41808-020-00068-8","type":"journal_article","pmid":1,"publication_identifier":{"eissn":["2296-9039"],"issn":["2296-9020"]},"title":"Uniform convergence to equilibrium for a family of drift–diffusion models with trap-assisted recombination and the limiting Shockley–Read–Hall model","oa":1,"scopus_import":"1","corr_author":"1","author":[{"full_name":"Fellner, Klemens","last_name":"Fellner","first_name":"Klemens"},{"orcid":"0000-0001-5645-4333","first_name":"Michael","last_name":"Kniely","id":"2CA2C08C-F248-11E8-B48F-1D18A9856A87","full_name":"Kniely, Michael"}],"publication":"Journal of Elliptic and Parabolic Equations","date_created":"2020-05-17T22:00:45Z","article_processing_charge":"No","quality_controlled":"1","project":[{"call_identifier":"FWF","name":"FWF Open Access Fund","_id":"3AC91DDA-15DF-11EA-824D-93A3E7B544D1"}],"volume":6,"department":[{"_id":"JuFi"}],"language":[{"iso":"eng"}],"publication_status":"published","page":"529-598","month":"12"},{"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"Bio"},{"_id":"PreCl"}],"intvolume":"       219","file":[{"access_level":"open_access","checksum":"cb0b9c77842ae1214caade7b77e4d82d","relation":"main_file","date_updated":"2020-11-24T13:25:13Z","content_type":"application/pdf","creator":"dernst","success":1,"file_id":"8801","file_name":"2020_JCellBiol_Kopf.pdf","date_created":"2020-11-24T13:25:13Z","file_size":7536712}],"issue":"6","external_id":{"pmid":["32379884"],"isi":["000538141100020"]},"oa_version":"Published Version","_id":"7875","status":"public","publisher":"Rockefeller University Press","citation":{"ista":"Kopf A, Renkawitz J, Hauschild R, Girkontaite I, Tedford K, Merrin J, Thorn-Seshold O, Trauner D, Häcker H, Fischer KD, Kiermaier E, Sixt MK. 2020. Microtubules control cellular shape and coherence in amoeboid migrating cells. The Journal of Cell Biology. 219(6), e201907154.","ama":"Kopf A, Renkawitz J, Hauschild R, et al. Microtubules control cellular shape and coherence in amoeboid migrating cells. <i>The Journal of Cell Biology</i>. 2020;219(6). doi:<a href=\"https://doi.org/10.1083/jcb.201907154\">10.1083/jcb.201907154</a>","apa":"Kopf, A., Renkawitz, J., Hauschild, R., Girkontaite, I., Tedford, K., Merrin, J., … Sixt, M. K. (2020). Microtubules control cellular shape and coherence in amoeboid migrating cells. <i>The Journal of Cell Biology</i>. Rockefeller University Press. <a href=\"https://doi.org/10.1083/jcb.201907154\">https://doi.org/10.1083/jcb.201907154</a>","ieee":"A. Kopf <i>et al.</i>, “Microtubules control cellular shape and coherence in amoeboid migrating cells,” <i>The Journal of Cell Biology</i>, vol. 219, no. 6. Rockefeller University Press, 2020.","chicago":"Kopf, Aglaja, Jörg Renkawitz, Robert Hauschild, Irute Girkontaite, Kerry Tedford, Jack Merrin, Oliver Thorn-Seshold, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” <i>The Journal of Cell Biology</i>. Rockefeller University Press, 2020. <a href=\"https://doi.org/10.1083/jcb.201907154\">https://doi.org/10.1083/jcb.201907154</a>.","short":"A. Kopf, J. Renkawitz, R. Hauschild, I. Girkontaite, K. Tedford, J. Merrin, O. Thorn-Seshold, D. Trauner, H. Häcker, K.D. Fischer, E. Kiermaier, M.K. Sixt, The Journal of Cell Biology 219 (2020).","mla":"Kopf, Aglaja, et al. “Microtubules Control Cellular Shape and Coherence in Amoeboid Migrating Cells.” <i>The Journal of Cell Biology</i>, vol. 219, no. 6, e201907154, Rockefeller University Press, 2020, doi:<a href=\"https://doi.org/10.1083/jcb.201907154\">10.1083/jcb.201907154</a>."},"year":"2020","acknowledgement":"The authors thank the Scientific Service Units (Life Sciences, Bioimaging, Preclinical) of the Institute of Science and Technology Austria for excellent support. This work was funded by the European Research Council (ERC StG 281556 and CoG 724373), two grants from the Austrian\r\nScience Fund (FWF; P29911 and DK Nanocell W1250-B20 to M. Sixt) and by the German Research Foundation (DFG SFB1032 project B09) to O. Thorn-Seshold and D. Trauner. J. Renkawitz was supported by ISTFELLOW funding from the People Program (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under the Research Executive Agency grant agreement (291734) and a European Molecular Biology Organization long-term fellowship (ALTF 1396-2014) co-funded by the European Commission (LTFCOFUND2013, GA-2013-609409), E. Kiermaier by the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) under Germany’s Excellence Strategy—EXC 2151—390873048, and H. Hacker by the American Lebanese Syrian Associated ¨Charities. K.-D. Fischer was supported by the Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes graduate school funded by the Ministry of Economics, Science, and Digitisation of the State Saxony-Anhalt and by the European Funds for Social and Regional Development.","isi":1,"day":"01","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","fulldoi":"https://doi.org/10.1083/jcb.201907154","date_published":"2020-06-01T00:00:00Z","has_accepted_license":"1","ddc":["570"],"date_updated":"2025-04-14T13:10:03Z","file_date_updated":"2020-11-24T13:25:13Z","ec_funded":1,"abstract":[{"text":"Cells navigating through complex tissues face a fundamental challenge: while multiple protrusions explore different paths, the cell needs to avoid entanglement. How a cell surveys and then corrects its own shape is poorly understood. Here, we demonstrate that spatially distinct microtubule dynamics regulate amoeboid cell migration by locally promoting the retraction of protrusions. In migrating dendritic cells, local microtubule depolymerization within protrusions remote from the microtubule organizing center triggers actomyosin contractility controlled by RhoA and its exchange factor Lfc. Depletion of Lfc leads to aberrant myosin localization, thereby causing two effects that rate-limit locomotion: (1) impaired cell edge coordination during path finding and (2) defective adhesion resolution. Compromised shape control is particularly hindering in geometrically complex microenvironments, where it leads to entanglement and ultimately fragmentation of the cell body. We thus demonstrate that microtubules can act as a proprioceptive device: they sense cell shape and control actomyosin retraction to sustain cellular coherence.","lang":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","article_processing_charge":"No","date_created":"2020-05-24T22:00:56Z","quality_controlled":"1","project":[{"call_identifier":"FP7","name":"Cytoskeletal force generation and force transduction of migrating leukocytes","_id":"25A603A2-B435-11E9-9278-68D0E5697425","grant_number":"281556"},{"call_identifier":"H2020","name":"Cellular Navigation Along Spatial Gradients","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"},{"call_identifier":"FWF","_id":"26018E70-B435-11E9-9278-68D0E5697425","name":"Mechanical adaptation of lamellipodial actin","grant_number":"P29911"},{"grant_number":"W1250-B20","_id":"252C3B08-B435-11E9-9278-68D0E5697425","name":"Nano-Analytics of Cellular Systems","call_identifier":"FWF"},{"call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734"},{"name":"Molecular and system level view of immune cell migration","_id":"25A48D24-B435-11E9-9278-68D0E5697425","grant_number":"ALTF 1396-2014"}],"publication_status":"published","language":[{"iso":"eng"}],"volume":219,"department":[{"_id":"MiSi"},{"_id":"Bio"},{"_id":"NanoFab"}],"month":"06","type":"journal_article","doi":"10.1083/jcb.201907154","oa":1,"title":"Microtubules control cellular shape and coherence in amoeboid migrating cells","pmid":1,"publication_identifier":{"eissn":["1540-8140"]},"article_number":"e201907154","scopus_import":"1","corr_author":"1","author":[{"full_name":"Kopf, Aglaja","id":"31DAC7B6-F248-11E8-B48F-1D18A9856A87","last_name":"Kopf","first_name":"Aglaja","orcid":"0000-0002-2187-6656"},{"orcid":"0000-0003-2856-3369","first_name":"Jörg","full_name":"Renkawitz, Jörg","id":"3F0587C8-F248-11E8-B48F-1D18A9856A87","last_name":"Renkawitz"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87","first_name":"Robert","orcid":"0000-0001-9843-3522"},{"last_name":"Girkontaite","full_name":"Girkontaite, Irute","first_name":"Irute"},{"first_name":"Kerry","last_name":"Tedford","full_name":"Tedford, Kerry"},{"last_name":"Merrin","id":"4515C308-F248-11E8-B48F-1D18A9856A87","full_name":"Merrin, Jack","orcid":"0000-0001-5145-4609","first_name":"Jack"},{"first_name":"Oliver","full_name":"Thorn-Seshold, Oliver","last_name":"Thorn-Seshold"},{"first_name":"Dirk","full_name":"Trauner, Dirk","last_name":"Trauner","id":"E8F27F48-3EBA-11E9-92A1-B709E6697425"},{"last_name":"Häcker","full_name":"Häcker, Hans","first_name":"Hans"},{"full_name":"Fischer, Klaus Dieter","last_name":"Fischer","first_name":"Klaus Dieter"},{"id":"3EB04B78-F248-11E8-B48F-1D18A9856A87","last_name":"Kiermaier","full_name":"Kiermaier, Eva","orcid":"0000-0001-6165-5738","first_name":"Eva"},{"last_name":"Sixt","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K"}],"publication":"The Journal of Cell Biology"},{"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.immuni.2020.04.020"}],"doi":"10.1016/j.immuni.2020.04.020","oa":1,"title":"T cells: Bridge-and-channel commute to the white pulp","publication_identifier":{"eissn":["1097-4180"],"issn":["1074-7613"]},"pmid":1,"author":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","orcid":"0000-0002-6620-9179","first_name":"Michael K"},{"last_name":"Lämmermann","full_name":"Lämmermann, Tim","first_name":"Tim"}],"publication":"Immunity","scopus_import":"1","quality_controlled":"1","article_processing_charge":"No","date_created":"2020-05-24T22:00:57Z","month":"05","publication_status":"published","volume":52,"language":[{"iso":"eng"}],"department":[{"_id":"MiSi"}],"page":"721-723","OA_place":"publisher","article_type":"original","fulldoi":"https://doi.org/10.1016/j.immuni.2020.04.020","OA_type":"free access","date_published":"2020-05-19T00:00:00Z","ddc":["570"],"abstract":[{"text":"In contrast to lymph nodes, the lymphoid regions of the spleen—the white pulp—are located deep within the organ, yielding the trafficking paths of T cells in the white pulp largely invisible. In an intravital microscopy tour de force reported in this issue of Immunity, Chauveau et al. show that T cells perform unidirectional, perivascular migration through the enigmatic marginal zone bridging channels. ","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-06-18T19:27:52Z","intvolume":"        52","issue":"5","external_id":{"pmid":["32433942"],"isi":["000535371100002"]},"publisher":"Elsevier","year":"2020","citation":{"short":"M.K. Sixt, T. Lämmermann, Immunity 52 (2020) 721–723.","mla":"Sixt, Michael K., and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” <i>Immunity</i>, vol. 52, no. 5, Elsevier, 2020, pp. 721–23, doi:<a href=\"https://doi.org/10.1016/j.immuni.2020.04.020\">10.1016/j.immuni.2020.04.020</a>.","chicago":"Sixt, Michael K, and Tim Lämmermann. “T Cells: Bridge-and-Channel Commute to the White Pulp.” <i>Immunity</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.immuni.2020.04.020\">https://doi.org/10.1016/j.immuni.2020.04.020</a>.","apa":"Sixt, M. K., &#38; Lämmermann, T. (2020). T cells: Bridge-and-channel commute to the white pulp. <i>Immunity</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.immuni.2020.04.020\">https://doi.org/10.1016/j.immuni.2020.04.020</a>","ieee":"M. K. Sixt and T. Lämmermann, “T cells: Bridge-and-channel commute to the white pulp,” <i>Immunity</i>, vol. 52, no. 5. Elsevier, pp. 721–723, 2020.","ama":"Sixt MK, Lämmermann T. T cells: Bridge-and-channel commute to the white pulp. <i>Immunity</i>. 2020;52(5):721-723. doi:<a href=\"https://doi.org/10.1016/j.immuni.2020.04.020\">10.1016/j.immuni.2020.04.020</a>","ista":"Sixt MK, Lämmermann T. 2020. T cells: Bridge-and-channel commute to the white pulp. Immunity. 52(5), 721–723."},"isi":1,"day":"19","oa_version":"Published Version","status":"public","_id":"7876"},{"tmp":{"image":"/images/cc_by_nc_nd.png","short":"CC BY-NC-ND (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)"},"fulldoi":"https://doi.org/10.1016/j.celrep.2020.107647","article_type":"original","date_published":"2020-05-19T00:00:00Z","has_accepted_license":"1","ddc":["570"],"date_updated":"2026-04-02T14:28:04Z","abstract":[{"text":"The NIPBL/MAU2 heterodimer loads cohesin onto chromatin. Mutations inNIPBLaccount for most cases ofthe rare developmental disorder Cornelia de Lange syndrome (CdLS). Here we report aMAU2 variant causing CdLS, a deletion of seven amino acids that impairs the interaction between MAU2 and the NIPBL N terminus.Investigating this interaction, we discovered that MAU2 and the NIPBL N terminus are largely dispensable fornormal cohesin and NIPBL function in cells with a NIPBL early truncating mutation. Despite a predicted fataloutcome of an out-of-frame single nucleotide duplication inNIPBL, engineered in two different cell lines,alternative translation initiation yields a form of NIPBL missing N-terminal residues. This form cannot interactwith MAU2, but binds DNA and mediates cohesin loading. Altogether, our work reveals that cohesin loading can occur independently of functional NIPBL/MAU2 complexes and highlights a novel mechanism protectiveagainst out-of-frame mutations that is potentially relevant for other genetic conditions.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:04Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","intvolume":"        31","file":[{"checksum":"64d8f7467731ee5c166b10b939b8310b","access_level":"open_access","relation":"main_file","creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:48:04Z","file_id":"7892","date_created":"2020-05-26T11:05:01Z","file_size":4695682,"file_name":"2020_CellReports_Parenti.pdf"}],"issue":"7","external_id":{"isi":["000535655200005"]},"oa_version":"Published Version","_id":"7877","status":"public","publisher":"Elsevier","year":"2020","citation":{"ista":"Parenti I, Diab F, Gil SR, Mulugeta E, Casa V, Berutti R, Brouwer RWW, Dupé V, Eckhold J, Graf E, Puisac B, Ramos F, Schwarzmayr T, Gines MM, Van Staveren T, Van Ijcken WFJ, Strom TM, Pié J, Watrin E, Kaiser FJ, Wendt KS. 2020. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. Cell Reports. 31(7), 107647.","ama":"Parenti I, Diab F, Gil SR, et al. MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. <i>Cell Reports</i>. 2020;31(7). doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.107647\">10.1016/j.celrep.2020.107647</a>","apa":"Parenti, I., Diab, F., Gil, S. R., Mulugeta, E., Casa, V., Berutti, R., … Wendt, K. S. (2020). MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome. <i>Cell Reports</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.celrep.2020.107647\">https://doi.org/10.1016/j.celrep.2020.107647</a>","ieee":"I. Parenti <i>et al.</i>, “MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome,” <i>Cell Reports</i>, vol. 31, no. 7. Elsevier, 2020.","chicago":"Parenti, Ilaria, Farah Diab, Sara Ruiz Gil, Eskeatnaf Mulugeta, Valentina Casa, Riccardo Berutti, Rutger W.W. Brouwer, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” <i>Cell Reports</i>. Elsevier, 2020. <a href=\"https://doi.org/10.1016/j.celrep.2020.107647\">https://doi.org/10.1016/j.celrep.2020.107647</a>.","mla":"Parenti, Ilaria, et al. “MAU2 and NIPBL Variants Impair the Heterodimerization of the Cohesin Loader Subunits and Cause Cornelia de Lange Syndrome.” <i>Cell Reports</i>, vol. 31, no. 7, 107647, Elsevier, 2020, doi:<a href=\"https://doi.org/10.1016/j.celrep.2020.107647\">10.1016/j.celrep.2020.107647</a>.","short":"I. Parenti, F. Diab, S.R. Gil, E. Mulugeta, V. Casa, R. Berutti, R.W.W. Brouwer, V. Dupé, J. Eckhold, E. Graf, B. Puisac, F. Ramos, T. Schwarzmayr, M.M. Gines, T. Van Staveren, W.F.J. Van Ijcken, T.M. Strom, J. Pié, E. Watrin, F.J. Kaiser, K.S. Wendt, Cell Reports 31 (2020)."},"isi":1,"day":"19","type":"journal_article","doi":"10.1016/j.celrep.2020.107647","oa":1,"title":"MAU2 and NIPBL variants impair the heterodimerization of the cohesin loader subunits and cause Cornelia de Lange syndrome","publication_identifier":{"eissn":["2211-1247"]},"article_number":"107647","scopus_import":"1","author":[{"full_name":"Parenti, Ilaria","id":"D93538B0-5B71-11E9-AC62-02EBE5697425","last_name":"Parenti","first_name":"Ilaria"},{"last_name":"Diab","full_name":"Diab, Farah","first_name":"Farah"},{"first_name":"Sara Ruiz","last_name":"Gil","full_name":"Gil, Sara Ruiz"},{"first_name":"Eskeatnaf","full_name":"Mulugeta, Eskeatnaf","last_name":"Mulugeta"},{"full_name":"Casa, Valentina","last_name":"Casa","first_name":"Valentina"},{"first_name":"Riccardo","last_name":"Berutti","full_name":"Berutti, Riccardo"},{"last_name":"Brouwer","full_name":"Brouwer, Rutger W.W.","first_name":"Rutger W.W."},{"full_name":"Dupé, Valerie","last_name":"Dupé","first_name":"Valerie"},{"first_name":"Juliane","last_name":"Eckhold","full_name":"Eckhold, Juliane"},{"first_name":"Elisabeth","last_name":"Graf","full_name":"Graf, Elisabeth"},{"last_name":"Puisac","full_name":"Puisac, Beatriz","first_name":"Beatriz"},{"full_name":"Ramos, Feliciano","last_name":"Ramos","first_name":"Feliciano"},{"first_name":"Thomas","last_name":"Schwarzmayr","full_name":"Schwarzmayr, Thomas"},{"full_name":"Gines, Macarena Moronta","last_name":"Gines","first_name":"Macarena Moronta"},{"first_name":"Thomas","last_name":"Van Staveren","full_name":"Van Staveren, Thomas"},{"first_name":"Wilfred F.J.","full_name":"Van Ijcken, Wilfred F.J.","last_name":"Van Ijcken"},{"first_name":"Tim M.","last_name":"Strom","full_name":"Strom, Tim M."},{"first_name":"Juan","full_name":"Pié, Juan","last_name":"Pié"},{"last_name":"Watrin","full_name":"Watrin, Erwan","first_name":"Erwan"},{"first_name":"Frank J.","last_name":"Kaiser","full_name":"Kaiser, Frank J."},{"first_name":"Kerstin S.","last_name":"Wendt","full_name":"Wendt, Kerstin S."}],"publication":"Cell Reports","article_processing_charge":"No","date_created":"2020-05-24T22:00:57Z","quality_controlled":"1","publication_status":"published","language":[{"iso":"eng"}],"volume":31,"department":[{"_id":"GaNo"}],"month":"05"},{"ddc":["570"],"date_published":"2020-05-13T00:00:00Z","has_accepted_license":"1","article_type":"original","fulldoi":"https://doi.org/10.7554/eLife.56839","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"date_updated":"2026-04-02T14:28:17Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","file_date_updated":"2020-07-14T12:48:04Z","abstract":[{"text":"Type 1 metabotropic glutamate receptors (mGluR1s) are key elements in neuronal signaling. While their function is well documented in slices, requirements for their activation in vivo are poorly understood. We examine this question in adult mice in vivo using 2-photon imaging of cerebellar molecular layer interneurons (MLIs) expressing GCaMP. In anesthetized mice, parallel fiber activation evokes beam-like Cai rises in postsynaptic MLIs which depend on co-activation of mGluR1s and ionotropic glutamate receptors (iGluRs). In awake mice, blocking mGluR1 decreases Cai rises associated with locomotion. In vitro studies and freeze-fracture electron microscopy show that the iGluR-mGluR1 interaction is synergistic and favored by close association of the two classes of receptors. Altogether our results suggest that mGluR1s, acting in synergy with iGluRs, potently contribute to processing cerebellar neuronal signaling under physiological conditions.","lang":"eng"}],"external_id":{"isi":["000535191600001"],"pmid":["32401196"]},"file":[{"access_level":"open_access","checksum":"8ea99bb6660cc407dbdb00c173b01683","relation":"main_file","date_updated":"2020-07-14T12:48:04Z","content_type":"application/pdf","creator":"dernst","file_id":"7891","file_name":"2020_eLife_Bao.pdf","file_size":4832050,"date_created":"2020-05-26T09:34:54Z"}],"intvolume":"         9","_id":"7878","status":"public","oa_version":"Published Version","day":"13","isi":1,"citation":{"short":"J. Bao, M. Graupner, G. Astorga, T. Collin, A. Jalil, D.W. Indriati, J. Bradley, R. Shigemoto, I. Llano, ELife 9 (2020).","mla":"Bao, Jin, et al. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” <i>ELife</i>, vol. 9, e56839, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.56839\">10.7554/eLife.56839</a>.","chicago":"Bao, Jin, Michael Graupner, Guadalupe Astorga, Thibault Collin, Abdelali Jalil, Dwi Wahyu Indriati, Jonathan Bradley, Ryuichi Shigemoto, and Isabel Llano. “Synergism of Type 1 Metabotropic and Ionotropic Glutamate Receptors in Cerebellar Molecular Layer Interneurons in Vivo.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.56839\">https://doi.org/10.7554/eLife.56839</a>.","ieee":"J. Bao <i>et al.</i>, “Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","apa":"Bao, J., Graupner, M., Astorga, G., Collin, T., Jalil, A., Indriati, D. W., … Llano, I. (2020). Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.56839\">https://doi.org/10.7554/eLife.56839</a>","ista":"Bao J, Graupner M, Astorga G, Collin T, Jalil A, Indriati DW, Bradley J, Shigemoto R, Llano I. 2020. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. eLife. 9, e56839.","ama":"Bao J, Graupner M, Astorga G, et al. Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.56839\">10.7554/eLife.56839</a>"},"year":"2020","publisher":"eLife Sciences Publications","publication_identifier":{"eissn":["2050-084X"]},"pmid":1,"oa":1,"title":"Synergism of type 1 metabotropic and ionotropic glutamate receptors in cerebellar molecular layer interneurons in vivo","doi":"10.7554/eLife.56839","type":"journal_article","article_number":"e56839","scopus_import":"1","publication":"eLife","author":[{"last_name":"Bao","full_name":"Bao, Jin","first_name":"Jin"},{"full_name":"Graupner, Michael","last_name":"Graupner","first_name":"Michael"},{"full_name":"Astorga, Guadalupe","last_name":"Astorga","first_name":"Guadalupe"},{"first_name":"Thibault","full_name":"Collin, Thibault","last_name":"Collin"},{"first_name":"Abdelali","full_name":"Jalil, Abdelali","last_name":"Jalil"},{"first_name":"Dwi Wahyu","full_name":"Indriati, Dwi Wahyu","last_name":"Indriati"},{"full_name":"Bradley, Jonathan","last_name":"Bradley","first_name":"Jonathan"},{"full_name":"Shigemoto, Ryuichi","id":"499F3ABC-F248-11E8-B48F-1D18A9856A87","last_name":"Shigemoto","first_name":"Ryuichi","orcid":"0000-0001-8761-9444"},{"first_name":"Isabel","last_name":"Llano","full_name":"Llano, Isabel"}],"date_created":"2020-05-24T22:00:58Z","article_processing_charge":"No","quality_controlled":"1","department":[{"_id":"RySh"}],"volume":9,"language":[{"iso":"eng"}],"publication_status":"published","month":"05"},{"month":"04","publication_status":"published","department":[{"_id":"SaSi"}],"volume":295,"language":[{"iso":"eng"}],"page":"5229-5244","quality_controlled":"1","article_processing_charge":"No","date_created":"2020-05-24T22:00:59Z","author":[{"last_name":"Fagan","full_name":"Fagan, Rita R.","first_name":"Rita R."},{"first_name":"Patrick J.","full_name":"Kearney, Patrick J.","last_name":"Kearney"},{"full_name":"Sweeney, Carolyn G.","last_name":"Sweeney","first_name":"Carolyn G."},{"full_name":"Luethi, Dino","last_name":"Luethi","first_name":"Dino"},{"last_name":"Schoot Uiterkamp","id":"3526230C-F248-11E8-B48F-1D18A9856A87","full_name":"Schoot Uiterkamp, Florianne E","first_name":"Florianne E"},{"first_name":"Klaus","full_name":"Schicker, Klaus","last_name":"Schicker"},{"first_name":"Brian S.","full_name":"Alejandro, Brian S.","last_name":"Alejandro"},{"full_name":"O'Connor, Lauren C.","last_name":"O'Connor","first_name":"Lauren C."},{"full_name":"Sitte, Harald H.","last_name":"Sitte","first_name":"Harald H."},{"first_name":"Haley E.","full_name":"Melikian, Haley E.","last_name":"Melikian"}],"publication":"Journal of Biological Chemistry","scopus_import":"1","type":"journal_article","doi":"10.1074/jbc.RA120.012628","main_file_link":[{"open_access":"1","url":"https://escholarship.umassmed.edu/oapubs/4187"}],"oa":1,"title":"Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact","publication_identifier":{"eissn":["1083-351X"],"issn":["0021-9258"]},"pmid":1,"publisher":"ASBMB Publications","citation":{"chicago":"Fagan, Rita R., Patrick J. Kearney, Carolyn G. Sweeney, Dino Luethi, Florianne E Schoot Uiterkamp, Klaus Schicker, Brian S. Alejandro, Lauren C. O’Connor, Harald H. Sitte, and Haley E. Melikian. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” <i>Journal of Biological Chemistry</i>. ASBMB Publications, 2020. <a href=\"https://doi.org/10.1074/jbc.RA120.012628\">https://doi.org/10.1074/jbc.RA120.012628</a>.","short":"R.R. Fagan, P.J. Kearney, C.G. Sweeney, D. Luethi, F.E. Schoot Uiterkamp, K. Schicker, B.S. Alejandro, L.C. O’Connor, H.H. Sitte, H.E. Melikian, Journal of Biological Chemistry 295 (2020) 5229–5244.","mla":"Fagan, Rita R., et al. “Dopamine Transporter Trafficking and Rit2 GTPase: Mechanism of Action and in Vivo Impact.” <i>Journal of Biological Chemistry</i>, vol. 295, no. 16, ASBMB Publications, 2020, pp. 5229–44, doi:<a href=\"https://doi.org/10.1074/jbc.RA120.012628\">10.1074/jbc.RA120.012628</a>.","ama":"Fagan RR, Kearney PJ, Sweeney CG, et al. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. <i>Journal of Biological Chemistry</i>. 2020;295(16):5229-5244. doi:<a href=\"https://doi.org/10.1074/jbc.RA120.012628\">10.1074/jbc.RA120.012628</a>","ista":"Fagan RR, Kearney PJ, Sweeney CG, Luethi D, Schoot Uiterkamp FE, Schicker K, Alejandro BS, O’Connor LC, Sitte HH, Melikian HE. 2020. Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. Journal of Biological Chemistry. 295(16), 5229–5244.","ieee":"R. R. Fagan <i>et al.</i>, “Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact,” <i>Journal of Biological Chemistry</i>, vol. 295, no. 16. ASBMB Publications, pp. 5229–5244, 2020.","apa":"Fagan, R. R., Kearney, P. J., Sweeney, C. G., Luethi, D., Schoot Uiterkamp, F. E., Schicker, K., … Melikian, H. E. (2020). Dopamine transporter trafficking and Rit2 GTPase: Mechanism of action and in vivo impact. <i>Journal of Biological Chemistry</i>. ASBMB Publications. <a href=\"https://doi.org/10.1074/jbc.RA120.012628\">https://doi.org/10.1074/jbc.RA120.012628</a>"},"year":"2020","isi":1,"day":"17","oa_version":"Submitted Version","_id":"7880","status":"public","intvolume":"       295","issue":"16","external_id":{"isi":["000530288000006"],"pmid":["32132171"]},"abstract":[{"text":"Following its evoked release, dopamine (DA) signaling is rapidly terminated by presynaptic reuptake, mediated by the cocaine-sensitive DA transporter (DAT). DAT surface availability is dynamically regulated by endocytic trafficking, and direct protein kinase C (PKC) activation acutely diminishes DAT surface expression by accelerating DAT internalization. Previous cell line studies demonstrated that PKC-stimulated DAT endocytosis requires both Ack1 inactivation, which releases a DAT-specific endocytic brake, and the neuronal GTPase, Rit2, which binds DAT. However, it is unknown whether Rit2 is required for PKC-stimulated DAT endocytosis in DAergic terminals or whether there are region- and/or sex-dependent differences in PKC-stimulated DAT trafficking. Moreover, the mechanisms by which Rit2 controls PKC-stimulated DAT endocytosis are unknown. Here, we directly examined these important questions. Ex vivo studies revealed that PKC activation acutely decreased DAT surface expression selectively in ventral, but not dorsal, striatum. AAV-mediated, conditional Rit2 knockdown in DAergic neurons impacted baseline DAT surface:intracellular distribution in DAergic terminals from female ventral, but not dorsal, striatum. Further, Rit2 was required for PKC-stimulated DAT internalization in both male and female ventral striatum. FRET and surface pulldown studies in cell lines revealed that PKC activation drives DAT-Rit2 surface dissociation and that the DAT N terminus is required for both PKC-mediated DAT-Rit2 dissociation and DAT internalization. Finally, we found that Rit2 and Ack1 independently converge on DAT to facilitate PKC-stimulated DAT endocytosis. Together, our data provide greater insight into mechanisms that mediate PKC-regulated DAT internalization and reveal unexpected region-specific differences in PKC-stimulated DAT trafficking in bona fide DAergic terminals. ","lang":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-07-10T11:54:48Z","fulldoi":"https://doi.org/10.1074/jbc.RA120.012628","article_type":"original","date_published":"2020-04-17T00:00:00Z"},{"type":"journal_article","doi":"10.3390/math8040484","title":"Clusters in separated tubes of tilted dipoles","oa":1,"publication_identifier":{"eissn":["2227-7390"]},"article_number":"484","scopus_import":"1","author":[{"last_name":"Armstrong","full_name":"Armstrong, Jeremy R.","first_name":"Jeremy R."},{"last_name":"Jensen","full_name":"Jensen, Aksel S.","first_name":"Aksel S."},{"first_name":"Artem","orcid":"0000-0003-0393-5525","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev","full_name":"Volosniev, Artem"},{"last_name":"Zinner","full_name":"Zinner, Nikolaj T.","first_name":"Nikolaj T."}],"publication":"Mathematics","article_processing_charge":"No","date_created":"2020-05-24T22:01:00Z","quality_controlled":"1","project":[{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"publication_status":"published","department":[{"_id":"MiLe"}],"volume":8,"language":[{"iso":"eng"}],"month":"04","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","fulldoi":"https://doi.org/10.3390/math8040484","has_accepted_license":"1","date_published":"2020-04-01T00:00:00Z","ddc":["510"],"date_updated":"2026-04-02T14:33:47Z","abstract":[{"text":"A few-body cluster is a building block of a many-body system in a gas phase provided the temperature at most is of the order of the binding energy of this cluster. Here we illustrate this statement by considering a system of tubes filled with dipolar distinguishable particles. We calculate the partition function, which determines the probability to find a few-body cluster at a given temperature. The input for our calculations—the energies of few-body clusters—is estimated using the harmonic approximation. We first describe and demonstrate the validity of our numerical procedure. Then we discuss the results featuring melting of the zero-temperature many-body state into a gas of free particles and few-body clusters. For temperature higher than its binding energy threshold, the dimers overwhelmingly dominate the ensemble, where the remaining probability is in free particles. At very high temperatures free (harmonic oscillator trap-bound) particle dominance is eventually reached. This structure evolution appears both for one and two particles in each layer providing crucial information about the behavior of ultracold dipolar gases. The investigation addresses the transition region between few- and many-body physics as a function of temperature using a system of ten dipoles in five tubes.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:04Z","ec_funded":1,"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","intvolume":"         8","file":[{"file_id":"7887","file_size":990540,"date_created":"2020-05-25T14:42:22Z","file_name":"2020_Mathematics_Armstrong.pdf","relation":"main_file","access_level":"open_access","checksum":"a05a7df724522203d079673a0d4de4bc","creator":"dernst","date_updated":"2020-07-14T12:48:04Z","content_type":"application/pdf"}],"issue":"4","external_id":{"isi":["000531824100024"]},"oa_version":"Published Version","status":"public","_id":"7882","publisher":"MDPI","year":"2020","citation":{"apa":"Armstrong, J. R., Jensen, A. S., Volosniev, A., &#38; Zinner, N. T. (2020). Clusters in separated tubes of tilted dipoles. <i>Mathematics</i>. MDPI. <a href=\"https://doi.org/10.3390/math8040484\">https://doi.org/10.3390/math8040484</a>","ieee":"J. R. Armstrong, A. S. Jensen, A. Volosniev, and N. T. Zinner, “Clusters in separated tubes of tilted dipoles,” <i>Mathematics</i>, vol. 8, no. 4. MDPI, 2020.","ista":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. 2020. Clusters in separated tubes of tilted dipoles. Mathematics. 8(4), 484.","ama":"Armstrong JR, Jensen AS, Volosniev A, Zinner NT. Clusters in separated tubes of tilted dipoles. <i>Mathematics</i>. 2020;8(4). doi:<a href=\"https://doi.org/10.3390/math8040484\">10.3390/math8040484</a>","mla":"Armstrong, Jeremy R., et al. “Clusters in Separated Tubes of Tilted Dipoles.” <i>Mathematics</i>, vol. 8, no. 4, 484, MDPI, 2020, doi:<a href=\"https://doi.org/10.3390/math8040484\">10.3390/math8040484</a>.","short":"J.R. Armstrong, A.S. Jensen, A. Volosniev, N.T. Zinner, Mathematics 8 (2020).","chicago":"Armstrong, Jeremy R., Aksel S. Jensen, Artem Volosniev, and Nikolaj T. Zinner. “Clusters in Separated Tubes of Tilted Dipoles.” <i>Mathematics</i>. MDPI, 2020. <a href=\"https://doi.org/10.3390/math8040484\">https://doi.org/10.3390/math8040484</a>."},"isi":1,"day":"01"},{"abstract":[{"lang":"eng","text":"Volatile anesthetics are widely used for surgery, but neuronal mechanisms of anesthesia remain unidentified. At the calyx of Held in brainstem slices from rats of either sex, isoflurane at clinical doses attenuated EPSCs by decreasing the release probability and the number of readily releasable vesicles. In presynaptic recordings of Ca2+ currents and exocytic capacitance changes, isoflurane attenuated exocytosis by inhibiting Ca2+ currents evoked by a short presynaptic depolarization, whereas it inhibited exocytosis evoked by a prolonged depolarization via directly blocking exocytic machinery downstream of Ca2+ influx. Since the length of presynaptic depolarization can simulate the frequency of synaptic inputs, isoflurane anesthesia is likely mediated by distinct dual mechanisms, depending on input frequencies. In simultaneous presynaptic and postsynaptic action potential recordings, isoflurane impaired the fidelity of repetitive spike transmission, more strongly at higher frequencies. Furthermore, in the cerebrum of adult mice, isoflurane inhibited monosynaptic corticocortical spike transmission, preferentially at a higher frequency. We conclude that dual presynaptic mechanisms operate for the anesthetic action of isoflurane, of which direct inhibition of exocytic machinery plays a low-pass filtering role in spike transmission at central excitatory synapses."}],"file_date_updated":"2020-07-14T12:48:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2025-03-07T08:29:32Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1523/JNEUROSCI.2946-19.2020","article_type":"original","has_accepted_license":"1","date_published":"2020-05-20T00:00:00Z","ddc":["570"],"publisher":"Society for Neuroscience","year":"2020","citation":{"chicago":"Wang, Han Ying, Kohgaku Eguchi, Takayuki Yamashita, and Tomoyuki Takahashi. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” <i>Journal of Neuroscience</i>. Society for Neuroscience, 2020. <a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">https://doi.org/10.1523/JNEUROSCI.2946-19.2020</a>.","short":"H.Y. Wang, K. Eguchi, T. Yamashita, T. Takahashi, Journal of Neuroscience 40 (2020) 4103–4115.","mla":"Wang, Han Ying, et al. “Frequency-Dependent Block of Excitatory Neurotransmission by Isoflurane via Dual Presynaptic Mechanisms.” <i>Journal of Neuroscience</i>, vol. 40, no. 21, Society for Neuroscience, 2020, pp. 4103–15, doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">10.1523/JNEUROSCI.2946-19.2020</a>.","ama":"Wang HY, Eguchi K, Yamashita T, Takahashi T. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. <i>Journal of Neuroscience</i>. 2020;40(21):4103-4115. doi:<a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">10.1523/JNEUROSCI.2946-19.2020</a>","ista":"Wang HY, Eguchi K, Yamashita T, Takahashi T. 2020. Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. Journal of Neuroscience. 40(21), 4103–4115.","apa":"Wang, H. Y., Eguchi, K., Yamashita, T., &#38; Takahashi, T. (2020). Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms. <i>Journal of Neuroscience</i>. Society for Neuroscience. <a href=\"https://doi.org/10.1523/JNEUROSCI.2946-19.2020\">https://doi.org/10.1523/JNEUROSCI.2946-19.2020</a>","ieee":"H. Y. Wang, K. Eguchi, T. Yamashita, and T. Takahashi, “Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms,” <i>Journal of Neuroscience</i>, vol. 40, no. 21. Society for Neuroscience, pp. 4103–4115, 2020."},"isi":1,"day":"20","oa_version":"Published Version","_id":"7908","status":"public","intvolume":"        40","file":[{"file_name":"2020_JourNeuroscience_Wang.pdf","file_size":3817360,"date_created":"2020-06-02T09:12:16Z","file_id":"7912","date_updated":"2020-07-14T12:48:05Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","checksum":"6571607ea9036154b67cc78e848a7f7d","relation":"main_file"}],"issue":"21","external_id":{"pmid":["32327530"],"isi":["000535694700004"]},"author":[{"first_name":"Han Ying","last_name":"Wang","full_name":"Wang, Han Ying"},{"first_name":"Kohgaku","orcid":"0000-0002-6170-2546","last_name":"Eguchi","id":"2B7846DC-F248-11E8-B48F-1D18A9856A87","full_name":"Eguchi, Kohgaku"},{"full_name":"Yamashita, Takayuki","last_name":"Yamashita","first_name":"Takayuki"},{"first_name":"Tomoyuki","full_name":"Takahashi, Tomoyuki","last_name":"Takahashi"}],"publication":"Journal of Neuroscience","scopus_import":"1","type":"journal_article","doi":"10.1523/JNEUROSCI.2946-19.2020","title":"Frequency-dependent block of excitatory neurotransmission by isoflurane via dual presynaptic mechanisms","oa":1,"pmid":1,"publication_identifier":{"eissn":["1529-2401"]},"month":"05","publication_status":"published","department":[{"_id":"RySh"}],"volume":40,"language":[{"iso":"eng"}],"page":"4103-4115","quality_controlled":"1","article_processing_charge":"No","date_created":"2020-05-31T22:00:48Z"},{"abstract":[{"text":"Cell migration entails networks and bundles of actin filaments termed lamellipodia and microspikes or filopodia, respectively, as well as focal adhesions, all of which recruit Ena/VASP family members hitherto thought to antagonize efficient cell motility. However, we find these proteins to act as positive regulators of migration in different murine cell lines. CRISPR/Cas9-mediated loss of Ena/VASP proteins reduced lamellipodial actin assembly and perturbed lamellipodial architecture, as evidenced by changed network geometry as well as reduction of filament length and number that was accompanied by abnormal Arp2/3 complex and heterodimeric capping protein accumulation. Loss of Ena/VASP function also abolished the formation of microspikes normally embedded in lamellipodia, but not of filopodia capable of emanating without lamellipodia. Ena/VASP-deficiency also impaired integrin-mediated adhesion accompanied by reduced traction forces exerted through these structures. Our data thus uncover novel Ena/VASP functions of these actin polymerases that are fully consistent with their promotion of cell migration.","lang":"eng"}],"ec_funded":1,"file_date_updated":"2020-07-14T12:48:05Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-02T14:32:12Z","article_type":"original","fulldoi":"https://doi.org/10.7554/eLife.55351","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["570"],"has_accepted_license":"1","date_published":"2020-05-11T00:00:00Z","citation":{"ama":"Damiano-Guercio J, Kurzawa L, Müller J, et al. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. <i>eLife</i>. 2020;9. doi:<a href=\"https://doi.org/10.7554/eLife.55351\">10.7554/eLife.55351</a>","ista":"Damiano-Guercio J, Kurzawa L, Müller J, Dimchev GA, Schaks M, Nemethova M, Pokrant T, Brühmann S, Linkner J, Blanchoin L, Sixt MK, Rottner K, Faix J. 2020. Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. eLife. 9, e55351.","apa":"Damiano-Guercio, J., Kurzawa, L., Müller, J., Dimchev, G. A., Schaks, M., Nemethova, M., … Faix, J. (2020). Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.55351\">https://doi.org/10.7554/eLife.55351</a>","ieee":"J. Damiano-Guercio <i>et al.</i>, “Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion,” <i>eLife</i>, vol. 9. eLife Sciences Publications, 2020.","chicago":"Damiano-Guercio, Julia, Laëtitia Kurzawa, Jan Müller, Georgi A Dimchev, Matthias Schaks, Maria Nemethova, Thomas Pokrant, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” <i>ELife</i>. eLife Sciences Publications, 2020. <a href=\"https://doi.org/10.7554/eLife.55351\">https://doi.org/10.7554/eLife.55351</a>.","short":"J. Damiano-Guercio, L. Kurzawa, J. Müller, G.A. Dimchev, M. Schaks, M. Nemethova, T. Pokrant, S. Brühmann, J. Linkner, L. Blanchoin, M.K. Sixt, K. Rottner, J. Faix, ELife 9 (2020).","mla":"Damiano-Guercio, Julia, et al. “Loss of Ena/VASP Interferes with Lamellipodium Architecture, Motility and Integrin-Dependent Adhesion.” <i>ELife</i>, vol. 9, e55351, eLife Sciences Publications, 2020, doi:<a href=\"https://doi.org/10.7554/eLife.55351\">10.7554/eLife.55351</a>."},"year":"2020","publisher":"eLife Sciences Publications","day":"11","isi":1,"oa_version":"Published Version","_id":"7909","status":"public","file":[{"content_type":"application/pdf","date_updated":"2020-07-14T12:48:05Z","creator":"dernst","checksum":"d33bd4441b9a0195718ce1ba5d2c48a6","access_level":"open_access","relation":"main_file","file_name":"2020_eLife_Damiano_Guercio.pdf","file_size":10535713,"date_created":"2020-06-02T10:35:37Z","file_id":"7914"}],"intvolume":"         9","external_id":{"isi":["000537208000001"],"pmid":["32391788"]},"author":[{"full_name":"Damiano-Guercio, Julia","last_name":"Damiano-Guercio","first_name":"Julia"},{"full_name":"Kurzawa, Laëtitia","last_name":"Kurzawa","first_name":"Laëtitia"},{"full_name":"Müller, Jan","last_name":"Müller","id":"AD07FDB4-0F61-11EA-8158-C4CC64CEAA8D","first_name":"Jan"},{"first_name":"Georgi A","orcid":"0000-0001-8370-6161","id":"38C393BE-F248-11E8-B48F-1D18A9856A87","last_name":"Dimchev","full_name":"Dimchev, Georgi A"},{"last_name":"Schaks","full_name":"Schaks, Matthias","first_name":"Matthias"},{"first_name":"Maria","last_name":"Nemethova","id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","full_name":"Nemethova, Maria"},{"last_name":"Pokrant","full_name":"Pokrant, Thomas","first_name":"Thomas"},{"full_name":"Brühmann, Stefan","last_name":"Brühmann","first_name":"Stefan"},{"last_name":"Linkner","full_name":"Linkner, Joern","first_name":"Joern"},{"first_name":"Laurent","last_name":"Blanchoin","full_name":"Blanchoin, Laurent"},{"first_name":"Michael K","orcid":"0000-0002-6620-9179","full_name":"Sixt, Michael K","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt"},{"last_name":"Rottner","full_name":"Rottner, Klemens","first_name":"Klemens"},{"first_name":"Jan","last_name":"Faix","full_name":"Faix, Jan"}],"publication":"eLife","scopus_import":"1","article_number":"e55351","doi":"10.7554/eLife.55351","type":"journal_article","publication_identifier":{"eissn":["2050-084X"]},"pmid":1,"oa":1,"title":"Loss of Ena/VASP interferes with lamellipodium architecture, motility and integrin-dependent adhesion","month":"05","department":[{"_id":"MiSi"}],"volume":9,"language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","project":[{"_id":"25FE9508-B435-11E9-9278-68D0E5697425","name":"Cellular Navigation Along Spatial Gradients","call_identifier":"H2020","grant_number":"724373"}],"date_created":"2020-05-31T22:00:49Z","article_processing_charge":"No"},{"fulldoi":"https://doi.org/10.1126/sciadv.abb0451","article_type":"original","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"ddc":["530"],"has_accepted_license":"1","date_published":"2020-05-06T00:00:00Z","date_updated":"2026-04-15T06:42:37Z","abstract":[{"text":"Quantum illumination uses entangled signal-idler photon pairs to boost the detection efficiency of low-reflectivity objects in environments with bright thermal noise. Its advantage is particularly evident at low signal powers, a promising feature for applications such as noninvasive biomedical scanning or low-power short-range radar. Here, we experimentally investigate the concept of quantum illumination at microwave frequencies. We generate entangled fields to illuminate a room-temperature object at a distance of 1 m in a free-space detection setup. We implement a digital phase-conjugate receiver based on linear quadrature measurements that outperforms a symmetric classical noise radar in the same conditions, despite the entanglement-breaking signal path. Starting from experimental data, we also simulate the case of perfect idler photon number detection, which results in a quantum advantage compared with the relative classical benchmark. Our results highlight the opportunities and challenges in the way toward a first room-temperature application of microwave quantum circuits.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:05Z","ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_id":"7913","file_name":"2020_ScienceAdvances_Barzanjeh.pdf","file_size":795822,"date_created":"2020-06-02T09:18:36Z","access_level":"open_access","checksum":"16fa61cc1951b444ee74c07188cda9da","relation":"main_file","date_updated":"2020-07-14T12:48:05Z","content_type":"application/pdf","creator":"dernst"}],"intvolume":"         6","external_id":{"pmid":["32548249"],"arxiv":["1908.03058"],"isi":["000531171100045"]},"issue":"19","oa_version":"Published Version","status":"public","_id":"7910","citation":{"ista":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. 2020. Microwave quantum illumination using a digital receiver. Science Advances. 6(19), eabb0451.","ama":"Barzanjeh S, Pirandola S, Vitali D, Fink JM. Microwave quantum illumination using a digital receiver. <i>Science Advances</i>. 2020;6(19). doi:<a href=\"https://doi.org/10.1126/sciadv.abb0451\">10.1126/sciadv.abb0451</a>","ieee":"S. Barzanjeh, S. Pirandola, D. Vitali, and J. M. Fink, “Microwave quantum illumination using a digital receiver,” <i>Science Advances</i>, vol. 6, no. 19. AAAS, 2020.","apa":"Barzanjeh, S., Pirandola, S., Vitali, D., &#38; Fink, J. M. (2020). Microwave quantum illumination using a digital receiver. <i>Science Advances</i>. AAAS. <a href=\"https://doi.org/10.1126/sciadv.abb0451\">https://doi.org/10.1126/sciadv.abb0451</a>","chicago":"Barzanjeh, Shabir, S. Pirandola, D Vitali, and Johannes M Fink. “Microwave Quantum Illumination Using a Digital Receiver.” <i>Science Advances</i>. AAAS, 2020. <a href=\"https://doi.org/10.1126/sciadv.abb0451\">https://doi.org/10.1126/sciadv.abb0451</a>.","short":"S. Barzanjeh, S. Pirandola, D. Vitali, J.M. Fink, Science Advances 6 (2020).","mla":"Barzanjeh, Shabir, et al. “Microwave Quantum Illumination Using a Digital Receiver.” <i>Science Advances</i>, vol. 6, no. 19, eabb0451, AAAS, 2020, doi:<a href=\"https://doi.org/10.1126/sciadv.abb0451\">10.1126/sciadv.abb0451</a>."},"year":"2020","publisher":"AAAS","arxiv":1,"day":"06","isi":1,"doi":"10.1126/sciadv.abb0451","type":"journal_article","publication_identifier":{"eissn":["2375-2548"]},"pmid":1,"title":"Microwave quantum illumination using a digital receiver","oa":1,"article_number":"eabb0451","scopus_import":"1","corr_author":"1","author":[{"orcid":"0000-0003-0415-1423","first_name":"Shabir","last_name":"Barzanjeh","id":"2D25E1F6-F248-11E8-B48F-1D18A9856A87","full_name":"Barzanjeh, Shabir"},{"first_name":"S.","full_name":"Pirandola, S.","last_name":"Pirandola"},{"full_name":"Vitali, D","last_name":"Vitali","first_name":"D"},{"orcid":"0000-0001-8112-028X","first_name":"Johannes M","full_name":"Fink, Johannes M","id":"4B591CBA-F248-11E8-B48F-1D18A9856A87","last_name":"Fink"}],"publication":"Science Advances","date_created":"2020-05-31T22:00:49Z","article_processing_charge":"No","quality_controlled":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/scientists-demonstrate-quantum-radar-prototype/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"status":"public","id":"9001","relation":"later_version"}]},"project":[{"call_identifier":"H2020","_id":"26336814-B435-11E9-9278-68D0E5697425","name":"A Fiber Optic Transceiver for Superconducting Qubits","grant_number":"758053"},{"name":"Quantum readout techniques and technologies","_id":"237CBA6C-32DE-11EA-91FC-C7463DDC885E","call_identifier":"H2020","grant_number":"862644"},{"name":"Microwave-to-Optical Quantum Link: Quantum Teleportation and Quantum Illumination with cavity Optomechanics","_id":"258047B6-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","grant_number":"707438"},{"call_identifier":"H2020","_id":"257EB838-B435-11E9-9278-68D0E5697425","name":"Hybrid Optomechanical Technologies","grant_number":"732894"},{"name":"QUANTUM INFORMATION SYSTEMS BEYOND CLASSICAL CAPABILITIES / P5- Integration of Superconducting Quantum Circuits","_id":"bdb108fd-d553-11ed-ba76-83dc74a9864f","grant_number":"F07105"}],"language":[{"iso":"eng"}],"department":[{"_id":"JoFi"}],"volume":6,"publication_status":"published","month":"05"},{"tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"fulldoi":"https://doi.org/10.1103/physrevresearch.2.023154","article_type":"original","date_published":"2020-05-11T00:00:00Z","has_accepted_license":"1","ddc":["530"],"date_updated":"2024-10-21T06:02:23Z","ec_funded":1,"abstract":[{"lang":"eng","text":"We explore the time evolution of two impurities in a trapped one-dimensional Bose gas that follows a change of the boson-impurity interaction. We study the induced impurity-impurity interactions and their effect on the quench dynamics. In particular, we report on the size of the impurity cloud, the impurity-impurity entanglement, and the impurity-impurity correlation function. The presented numerical simulations are based upon the variational multilayer multiconfiguration time-dependent Hartree method for bosons. To analyze and quantify induced impurity-impurity correlations, we employ an effective two-body Hamiltonian with a contact interaction. We show that the effective model consistent with the mean-field attraction of two heavy impurities explains qualitatively our results for weak interactions. Our findings suggest that the quench dynamics in cold-atom systems can be a tool for studying impurity-impurity correlations."}],"file_date_updated":"2020-07-14T12:48:05Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","intvolume":"         2","file":[{"file_id":"7926","file_name":"2020_PhysRevResearch_Mistakidis.pdf","date_created":"2020-06-04T13:51:59Z","file_size":1741098,"access_level":"open_access","checksum":"e1c362fe094d6b246b3cd4a49722e78b","relation":"main_file","date_updated":"2020-07-14T12:48:05Z","content_type":"application/pdf","creator":"dernst"}],"oa_version":"Published Version","status":"public","_id":"7919","publisher":"American Physical Society","citation":{"ieee":"S. I. Mistakidis, A. Volosniev, and P. Schmelcher, “Induced correlations between impurities in a one-dimensional quenched Bose gas,” <i>Physical Review Research</i>, vol. 2. American Physical Society, 2020.","apa":"Mistakidis, S. I., Volosniev, A., &#38; Schmelcher, P. (2020). Induced correlations between impurities in a one-dimensional quenched Bose gas. <i>Physical Review Research</i>. American Physical Society. <a href=\"https://doi.org/10.1103/physrevresearch.2.023154\">https://doi.org/10.1103/physrevresearch.2.023154</a>","ista":"Mistakidis SI, Volosniev A, Schmelcher P. 2020. Induced correlations between impurities in a one-dimensional quenched Bose gas. Physical Review Research. 2, 023154.","ama":"Mistakidis SI, Volosniev A, Schmelcher P. Induced correlations between impurities in a one-dimensional quenched Bose gas. <i>Physical Review Research</i>. 2020;2. doi:<a href=\"https://doi.org/10.1103/physrevresearch.2.023154\">10.1103/physrevresearch.2.023154</a>","short":"S.I. Mistakidis, A. Volosniev, P. Schmelcher, Physical Review Research 2 (2020).","mla":"Mistakidis, S. I., et al. “Induced Correlations between Impurities in a One-Dimensional Quenched Bose Gas.” <i>Physical Review Research</i>, vol. 2, 023154, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/physrevresearch.2.023154\">10.1103/physrevresearch.2.023154</a>.","chicago":"Mistakidis, S. I., Artem Volosniev, and P. Schmelcher. “Induced Correlations between Impurities in a One-Dimensional Quenched Bose Gas.” <i>Physical Review Research</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/physrevresearch.2.023154\">https://doi.org/10.1103/physrevresearch.2.023154</a>."},"year":"2020","day":"11","type":"journal_article","doi":"10.1103/physrevresearch.2.023154","oa":1,"title":"Induced correlations between impurities in a one-dimensional quenched Bose gas","publication_identifier":{"issn":["2643-1564"]},"article_number":"023154 ","scopus_import":"1","author":[{"first_name":"S. I.","full_name":"Mistakidis, S. I.","last_name":"Mistakidis"},{"first_name":"Artem","orcid":"0000-0003-0393-5525","full_name":"Volosniev, Artem","id":"37D278BC-F248-11E8-B48F-1D18A9856A87","last_name":"Volosniev"},{"first_name":"P.","last_name":"Schmelcher","full_name":"Schmelcher, P."}],"publication":"Physical Review Research","article_processing_charge":"No","date_created":"2020-06-03T11:30:10Z","quality_controlled":"1","project":[{"call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425","name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411"}],"publication_status":"published","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"volume":2,"month":"05"},{"abstract":[{"lang":"eng","text":"In the course of sample preparation for Next Generation Sequencing (NGS), DNA is fragmented by various methods. Fragmentation shows a persistent bias with regard to the cleavage rates of various dinucleotides. With the exception of CpG dinucleotides the previously described biases were consistent with results of the DNA cleavage in solution. Here we computed cleavage rates of all dinucleotides including the methylated CpG and unmethylated CpG dinucleotides using data of the Whole Genome Sequencing datasets of the 1000 Genomes project. We found that the cleavage rate of CpG is significantly higher for the methylated CpG dinucleotides. Using this information, we developed a classifier for distinguishing cancer and healthy tissues based on their CpG islands statuses of the fragmentation. A simple Support Vector Machine classifier based on this algorithm shows an accuracy of 84%. The proposed method allows the detection of epigenetic markers purely based on mechanochemical DNA fragmentation, which can be detected by a simple analysis of the NGS sequencing data."}],"file_date_updated":"2020-07-14T12:48:05Z","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","date_updated":"2026-04-03T09:26:06Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)"},"article_type":"original","fulldoi":"https://doi.org/10.1038/s41598-020-65406-1","date_published":"2020-05-25T00:00:00Z","has_accepted_license":"1","ddc":["570"],"publisher":"Springer Nature","citation":{"mla":"Uroshlev, Leonid A., et al. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” <i>Scientific Reports</i>, vol. 10, 8635, Springer Nature, 2020, doi:<a href=\"https://doi.org/10.1038/s41598-020-65406-1\">10.1038/s41598-020-65406-1</a>.","short":"L.A. Uroshlev, E.T. Abdullaev, I.R. Umarova, I.A. Il’Icheva, L.A. Panchenko, R.V. Polozov, F. Kondrashov, Y.D. Nechipurenko, S.L. Grokhovsky, Scientific Reports 10 (2020).","chicago":"Uroshlev, Leonid A., Eldar T. Abdullaev, Iren R. Umarova, Irina A. Il’Icheva, Larisa A. Panchenko, Robert V. Polozov, Fyodor Kondrashov, Yury D. Nechipurenko, and Sergei L. Grokhovsky. “A Method for Identification of the Methylation Level of CpG Islands from NGS Data.” <i>Scientific Reports</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41598-020-65406-1\">https://doi.org/10.1038/s41598-020-65406-1</a>.","apa":"Uroshlev, L. A., Abdullaev, E. T., Umarova, I. R., Il’Icheva, I. A., Panchenko, L. A., Polozov, R. V., … Grokhovsky, S. L. (2020). A method for identification of the methylation level of CpG islands from NGS data. <i>Scientific Reports</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41598-020-65406-1\">https://doi.org/10.1038/s41598-020-65406-1</a>","ieee":"L. A. Uroshlev <i>et al.</i>, “A method for identification of the methylation level of CpG islands from NGS data,” <i>Scientific Reports</i>, vol. 10. Springer Nature, 2020.","ama":"Uroshlev LA, Abdullaev ET, Umarova IR, et al. A method for identification of the methylation level of CpG islands from NGS data. <i>Scientific Reports</i>. 2020;10. doi:<a href=\"https://doi.org/10.1038/s41598-020-65406-1\">10.1038/s41598-020-65406-1</a>","ista":"Uroshlev LA, Abdullaev ET, Umarova IR, Il’Icheva IA, Panchenko LA, Polozov RV, Kondrashov F, Nechipurenko YD, Grokhovsky SL. 2020. A method for identification of the methylation level of CpG islands from NGS data. Scientific Reports. 10, 8635."},"year":"2020","isi":1,"day":"25","oa_version":"Published Version","_id":"7931","status":"public","intvolume":"        10","file":[{"file_name":"2020_ScientificReports_Uroshlev.pdf","file_size":1001724,"date_created":"2020-06-08T06:27:32Z","file_id":"7947","date_updated":"2020-07-14T12:48:05Z","content_type":"application/pdf","creator":"dernst","access_level":"open_access","checksum":"099e51611a5b7ca04244d03b2faddf33","relation":"main_file"}],"external_id":{"isi":["000560774200007"],"pmid":["32451390"]},"author":[{"first_name":"Leonid A.","last_name":"Uroshlev","full_name":"Uroshlev, Leonid A."},{"last_name":"Abdullaev","full_name":"Abdullaev, Eldar T.","first_name":"Eldar T."},{"last_name":"Umarova","full_name":"Umarova, Iren R.","first_name":"Iren R."},{"full_name":"Il’Icheva, Irina A.","last_name":"Il’Icheva","first_name":"Irina A."},{"last_name":"Panchenko","full_name":"Panchenko, Larisa A.","first_name":"Larisa A."},{"first_name":"Robert V.","full_name":"Polozov, Robert V.","last_name":"Polozov"},{"orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87","last_name":"Kondrashov","full_name":"Kondrashov, Fyodor"},{"first_name":"Yury D.","last_name":"Nechipurenko","full_name":"Nechipurenko, Yury D."},{"first_name":"Sergei L.","full_name":"Grokhovsky, Sergei L.","last_name":"Grokhovsky"}],"publication":"Scientific Reports","scopus_import":"1","article_number":"8635","type":"journal_article","doi":"10.1038/s41598-020-65406-1","oa":1,"title":"A method for identification of the methylation level of CpG islands from NGS data","publication_identifier":{"eissn":["2045-2322"]},"pmid":1,"month":"05","publication_status":"published","language":[{"iso":"eng"}],"department":[{"_id":"FyKo"}],"volume":10,"quality_controlled":"1","article_processing_charge":"No","date_created":"2020-06-07T22:00:51Z"},{"scopus_import":"1","author":[{"full_name":"Xu, Duo","id":"3454D55E-F248-11E8-B48F-1D18A9856A87","last_name":"Xu","first_name":"Duo"},{"first_name":"Atul","orcid":"0000-0002-3072-5999","full_name":"Varshney, Atul","last_name":"Varshney","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-0179-9737","first_name":"Xingyu","last_name":"Ma","id":"34BADBA6-F248-11E8-B48F-1D18A9856A87","full_name":"Ma, Xingyu"},{"first_name":"Baofang","full_name":"Song, Baofang","last_name":"Song"},{"first_name":"Michael","orcid":"0000-0003-4844-6311","last_name":"Riedl","id":"3BE60946-F248-11E8-B48F-1D18A9856A87","full_name":"Riedl, Michael"},{"full_name":"Avila, Marc","last_name":"Avila","first_name":"Marc"},{"full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","first_name":"Björn","orcid":"0000-0003-2057-2754"}],"publication":"Proceedings of the National Academy of Sciences of the United States of America","type":"journal_article","doi":"10.1073/pnas.1913716117","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.11190"}],"oa":1,"title":"Nonlinear hydrodynamic instability and turbulence in pulsatile flow","publication_identifier":{"issn":["0027-8424"],"eissn":["1091-6490"]},"pmid":1,"publication_status":"published","department":[{"_id":"BjHo"}],"language":[{"iso":"eng"}],"volume":117,"page":"11233-11239","month":"05","article_processing_charge":"No","date_created":"2020-06-07T22:00:51Z","quality_controlled":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/blood-flows-more-turbulent-than-previously-expected/","description":"News on IST Homepage","relation":"press_release"}],"record":[{"relation":"dissertation_contains","id":"12726","status":"public"},{"status":"public","relation":"dissertation_contains","id":"14530"}]},"project":[{"call_identifier":"FWF","name":"Instabilities in pulsating pipe flow in complex fluids","_id":"238B8092-32DE-11EA-91FC-C7463DDC885E","grant_number":"I04188"},{"call_identifier":"H2020","name":"ISTplus - Postdoctoral Fellowships","_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411"}],"date_updated":"2026-04-07T13:29:13Z","abstract":[{"lang":"eng","text":"Pulsating flows through tubular geometries are laminar provided that velocities are moderate. This in particular is also believed to apply to cardiovascular flows where inertial forces are typically too low to sustain turbulence. On the other hand, flow instabilities and fluctuating shear stresses are held responsible for a variety of cardiovascular diseases. Here we report a nonlinear instability mechanism for pulsating pipe flow that gives rise to bursts of turbulence at low flow rates. Geometrical distortions of small, yet finite, amplitude are found to excite a state consisting of helical vortices during flow deceleration. The resulting flow pattern grows rapidly in magnitude, breaks down into turbulence, and eventually returns to laminar when the flow accelerates. This scenario causes shear stress fluctuations and flow reversal during each pulsation cycle. Such unsteady conditions can adversely affect blood vessels and have been shown to promote inflammation and dysfunction of the shear stress-sensitive endothelial cell layer."}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","fulldoi":"https://doi.org/10.1073/pnas.1913716117","article_type":"original","date_published":"2020-05-26T00:00:00Z","oa_version":"Preprint","_id":"7932","status":"public","publisher":"National Academy of Sciences","citation":{"ama":"Xu D, Varshney A, Ma X, et al. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. 2020;117(21):11233-11239. doi:<a href=\"https://doi.org/10.1073/pnas.1913716117\">10.1073/pnas.1913716117</a>","ista":"Xu D, Varshney A, Ma X, Song B, Riedl M, Avila M, Hof B. 2020. Nonlinear hydrodynamic instability and turbulence in pulsatile flow. Proceedings of the National Academy of Sciences of the United States of America. 117(21), 11233–11239.","ieee":"D. Xu <i>et al.</i>, “Nonlinear hydrodynamic instability and turbulence in pulsatile flow,” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 21. National Academy of Sciences, pp. 11233–11239, 2020.","apa":"Xu, D., Varshney, A., Ma, X., Song, B., Riedl, M., Avila, M., &#38; Hof, B. (2020). Nonlinear hydrodynamic instability and turbulence in pulsatile flow. <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences. <a href=\"https://doi.org/10.1073/pnas.1913716117\">https://doi.org/10.1073/pnas.1913716117</a>","chicago":"Xu, Duo, Atul Varshney, Xingyu Ma, Baofang Song, Michael Riedl, Marc Avila, and Björn Hof. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>. National Academy of Sciences, 2020. <a href=\"https://doi.org/10.1073/pnas.1913716117\">https://doi.org/10.1073/pnas.1913716117</a>.","short":"D. Xu, A. Varshney, X. Ma, B. Song, M. Riedl, M. Avila, B. Hof, Proceedings of the National Academy of Sciences of the United States of America 117 (2020) 11233–11239.","mla":"Xu, Duo, et al. “Nonlinear Hydrodynamic Instability and Turbulence in Pulsatile Flow.” <i>Proceedings of the National Academy of Sciences of the United States of America</i>, vol. 117, no. 21, National Academy of Sciences, 2020, pp. 11233–39, doi:<a href=\"https://doi.org/10.1073/pnas.1913716117\">10.1073/pnas.1913716117</a>."},"year":"2020","isi":1,"day":"26","arxiv":1,"intvolume":"       117","issue":"21","external_id":{"isi":["000536797100014"],"arxiv":["2005.11190"],"pmid":["32393637"]}},{"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","ec_funded":1,"abstract":[{"text":"We study a mobile quantum impurity, possessing internal rotational degrees of freedom, confined to a ring in the presence of a many-particle bosonic bath. By considering the recently introduced rotating polaron problem, we define the Hamiltonian and examine the energy spectrum. The weak-coupling regime is studied by means of a variational ansatz in the truncated Fock space. The corresponding spectrum indicates that there emerges a coupling between the internal and orbital angular momenta of the impurity as a consequence of the phonon exchange. We interpret the coupling as a phonon-mediated spin-orbit coupling and quantify it by using a correlation function between the internal and the orbital angular momentum operators. The strong-coupling regime is investigated within the Pekar approach, and it is shown that the correlation function of the ground state shows a kink at a critical coupling, that is explained by a sharp transition from the noninteracting state to the states that exhibit strong interaction with the surroundings. The results might find applications in such fields as spintronics or topological insulators where spin-orbit coupling is of crucial importance.","lang":"eng"}],"date_updated":"2026-04-07T11:52:53Z","date_published":"2020-05-01T00:00:00Z","article_type":"original","fulldoi":"https://doi.org/10.1103/PhysRevB.101.184104","isi":1,"day":"01","arxiv":1,"publisher":"American Physical Society","citation":{"ieee":"M. Maslov, M. Lemeshko, and E. Yakaboylu, “Synthetic spin-orbit coupling mediated by a bosonic environment,” <i>Physical Review B</i>, vol. 101, no. 18. American Physical Society, 2020.","apa":"Maslov, M., Lemeshko, M., &#38; Yakaboylu, E. (2020). Synthetic spin-orbit coupling mediated by a bosonic environment. <i>Physical Review B</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">https://doi.org/10.1103/PhysRevB.101.184104</a>","ista":"Maslov M, Lemeshko M, Yakaboylu E. 2020. Synthetic spin-orbit coupling mediated by a bosonic environment. Physical Review B. 101(18), 184104.","ama":"Maslov M, Lemeshko M, Yakaboylu E. Synthetic spin-orbit coupling mediated by a bosonic environment. <i>Physical Review B</i>. 2020;101(18). doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">10.1103/PhysRevB.101.184104</a>","mla":"Maslov, Mikhail, et al. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” <i>Physical Review B</i>, vol. 101, no. 18, 184104, American Physical Society, 2020, doi:<a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">10.1103/PhysRevB.101.184104</a>.","short":"M. Maslov, M. Lemeshko, E. Yakaboylu, Physical Review B 101 (2020).","chicago":"Maslov, Mikhail, Mikhail Lemeshko, and Enderalp Yakaboylu. “Synthetic Spin-Orbit Coupling Mediated by a Bosonic Environment.” <i>Physical Review B</i>. American Physical Society, 2020. <a href=\"https://doi.org/10.1103/PhysRevB.101.184104\">https://doi.org/10.1103/PhysRevB.101.184104</a>."},"year":"2020","_id":"7933","status":"public","oa_version":"Preprint","issue":"18","external_id":{"isi":["000530754700003"],"arxiv":["1912.03092"]},"intvolume":"       101","publication":"Physical Review B","author":[{"first_name":"Mikhail","orcid":"0000-0003-4074-2570","full_name":"Maslov, Mikhail","id":"2E65BB0E-F248-11E8-B48F-1D18A9856A87","last_name":"Maslov"},{"orcid":"0000-0002-6990-7802","first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail"},{"full_name":"Yakaboylu, Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","orcid":"0000-0001-5973-0874","first_name":"Enderalp"}],"scopus_import":"1","article_number":"184104 ","title":"Synthetic spin-orbit coupling mediated by a bosonic environment","oa":1,"publication_identifier":{"eissn":["2469-9969"],"issn":["2469-9950"]},"type":"journal_article","doi":"10.1103/PhysRevB.101.184104","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1912.03092"}],"month":"05","publication_status":"published","department":[{"_id":"MiLe"}],"language":[{"iso":"eng"}],"volume":101,"project":[{"name":"Quantum rotations in the presence of a many-body environment","_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P29902"},{"grant_number":"801770","call_identifier":"H2020","name":"Angulon: physics and applications of a new quasiparticle","_id":"2688CF98-B435-11E9-9278-68D0E5697425"}],"quality_controlled":"1","related_material":{"record":[{"status":"public","id":"19048","relation":"dissertation_contains"}]},"article_processing_charge":"No","date_created":"2020-06-07T22:00:52Z"},{"month":"03","department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"publication_status":"published","quality_controlled":"1","related_material":{"record":[{"status":"deleted","id":"8331","relation":"dissertation_contains"},{"relation":"dissertation_contains","id":"8390","status":"public"}]},"date_created":"2020-06-07T22:00:53Z","article_processing_charge":"No","author":[{"full_name":"Royer, Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87","last_name":"Royer","orcid":"0000-0002-8407-0705","first_name":"Amélie"},{"orcid":"0000-0001-8622-7887","first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph"}],"publication":"IEEE Winter Conference on Applications of Computer Vision","scopus_import":1,"conference":{"end_date":"2020-03-05","name":"WACV: Winter Conference on Applications of Computer Vision","location":" Snowmass Village, CO, United States","start_date":"2020-03-01"},"article_number":"1716-1725","doi":"10.1109/WACV45572.2020.9093288","main_file_link":[{"url":"https://arxiv.org/abs/2004.12623","open_access":"1"}],"type":"conference","publication_identifier":{"isbn":["9781728165530"]},"oa":1,"title":"Localizing grouped instances for efficient detection in low-resource scenarios","citation":{"chicago":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” In <i>IEEE Winter Conference on Applications of Computer Vision</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/WACV45572.2020.9093288\">https://doi.org/10.1109/WACV45572.2020.9093288</a>.","short":"A. Royer, C. Lampert, in:, IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","mla":"Royer, Amélie, and Christoph Lampert. “Localizing Grouped Instances for Efficient Detection in Low-Resource Scenarios.” <i>IEEE Winter Conference on Applications of Computer Vision</i>, 1716–1725, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/WACV45572.2020.9093288\">10.1109/WACV45572.2020.9093288</a>.","ama":"Royer A, Lampert C. Localizing grouped instances for efficient detection in low-resource scenarios. In: <i>IEEE Winter Conference on Applications of Computer Vision</i>. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/WACV45572.2020.9093288\">10.1109/WACV45572.2020.9093288</a>","ista":"Royer A, Lampert C. 2020. Localizing grouped instances for efficient detection in low-resource scenarios. IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 1716–1725.","apa":"Royer, A., &#38; Lampert, C. (2020). Localizing grouped instances for efficient detection in low-resource scenarios. In <i>IEEE Winter Conference on Applications of Computer Vision</i>.  Snowmass Village, CO, United States: IEEE. <a href=\"https://doi.org/10.1109/WACV45572.2020.9093288\">https://doi.org/10.1109/WACV45572.2020.9093288</a>","ieee":"A. Royer and C. Lampert, “Localizing grouped instances for efficient detection in low-resource scenarios,” in <i>IEEE Winter Conference on Applications of Computer Vision</i>,  Snowmass Village, CO, United States, 2020."},"year":"2020","publisher":"IEEE","arxiv":1,"day":"01","oa_version":"Preprint","status":"public","_id":"7936","external_id":{"arxiv":["2004.12623"]},"abstract":[{"lang":"eng","text":"State-of-the-art detection systems are generally evaluated on their ability to exhaustively retrieve objects densely distributed in the image, across a wide variety of appearances and semantic categories. Orthogonal to this, many real-life object detection applications, for example in remote sensing, instead require dealing with large images that contain only a few small objects of a single class, scattered heterogeneously across the space. In addition, they are often subject to strict computational constraints, such as limited battery capacity and computing power.To tackle these more practical scenarios, we propose a novel flexible detection scheme that efficiently adapts to variable object sizes and densities: We rely on a sequence of detection stages, each of which has the ability to predict groups of objects as well as individuals. Similar to a detection cascade, this multi-stage architecture spares computational effort by discarding large irrelevant regions of the image early during the detection process. The ability to group objects provides further computational and memory savings, as it allows working with lower image resolutions in early stages, where groups are more easily detected than individuals, as they are more salient. We report experimental results on two aerial image datasets, and show that the proposed method is as accurate yet computationally more efficient than standard single-shot detectors, consistently across three different backbone architectures."}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2026-04-08T07:26:43Z","fulldoi":"https://doi.org/10.1109/WACV45572.2020.9093288","date_published":"2020-03-01T00:00:00Z"},{"publication_status":"published","department":[{"_id":"ChLa"}],"language":[{"iso":"eng"}],"month":"03","article_processing_charge":"No","date_created":"2020-06-07T22:00:53Z","quality_controlled":"1","related_material":{"record":[{"status":"deleted","id":"8331","relation":"dissertation_contains"},{"status":"public","id":"8390","relation":"dissertation_contains"}]},"conference":{"name":"WACV: Winter Conference on Applications of Computer Vision","end_date":"2020-03-05","location":"Snowmass Village, CO, United States","start_date":"2020-03-01"},"scopus_import":"1","publication":"2020 IEEE Winter Conference on Applications of Computer Vision","author":[{"orcid":"0000-0002-8407-0705","first_name":"Amélie","full_name":"Royer, Amélie","id":"3811D890-F248-11E8-B48F-1D18A9856A87","last_name":"Royer"},{"id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","last_name":"Lampert","full_name":"Lampert, Christoph","orcid":"0000-0001-8622-7887","first_name":"Christoph"}],"oa":1,"title":"A flexible selection scheme for minimum-effort transfer learning","publication_identifier":{"isbn":["9781728165530"]},"type":"conference","doi":"10.1109/WACV45572.2020.9093635","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/2008.11995"}],"article_number":"2180-2189","_id":"7937","status":"public","oa_version":"Preprint","isi":1,"arxiv":1,"day":"01","publisher":"IEEE","year":"2020","citation":{"ama":"Royer A, Lampert C. A flexible selection scheme for minimum-effort transfer learning. In: <i>2020 IEEE Winter Conference on Applications of Computer Vision</i>. IEEE; 2020. doi:<a href=\"https://doi.org/10.1109/WACV45572.2020.9093635\">10.1109/WACV45572.2020.9093635</a>","ista":"Royer A, Lampert C. 2020. A flexible selection scheme for minimum-effort transfer learning. 2020 IEEE Winter Conference on Applications of Computer Vision. WACV: Winter Conference on Applications of Computer Vision, 2180–2189.","apa":"Royer, A., &#38; Lampert, C. (2020). A flexible selection scheme for minimum-effort transfer learning. In <i>2020 IEEE Winter Conference on Applications of Computer Vision</i>. Snowmass Village, CO, United States: IEEE. <a href=\"https://doi.org/10.1109/WACV45572.2020.9093635\">https://doi.org/10.1109/WACV45572.2020.9093635</a>","ieee":"A. Royer and C. Lampert, “A flexible selection scheme for minimum-effort transfer learning,” in <i>2020 IEEE Winter Conference on Applications of Computer Vision</i>, Snowmass Village, CO, United States, 2020.","chicago":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” In <i>2020 IEEE Winter Conference on Applications of Computer Vision</i>. IEEE, 2020. <a href=\"https://doi.org/10.1109/WACV45572.2020.9093635\">https://doi.org/10.1109/WACV45572.2020.9093635</a>.","short":"A. Royer, C. Lampert, in:, 2020 IEEE Winter Conference on Applications of Computer Vision, IEEE, 2020.","mla":"Royer, Amélie, and Christoph Lampert. “A Flexible Selection Scheme for Minimum-Effort Transfer Learning.” <i>2020 IEEE Winter Conference on Applications of Computer Vision</i>, 2180–2189, IEEE, 2020, doi:<a href=\"https://doi.org/10.1109/WACV45572.2020.9093635\">10.1109/WACV45572.2020.9093635</a>."},"external_id":{"isi":["000578444802027"],"arxiv":["2008.11995"]},"date_updated":"2026-04-08T07:26:44Z","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","abstract":[{"text":"Fine-tuning is a popular way of exploiting knowledge contained in a pre-trained convolutional network for a new visual recognition task. However, the orthogonal setting of transferring knowledge from a pretrained network to a visually different yet semantically close source is rarely considered: This commonly happens with real-life data, which is not necessarily as clean as the training source (noise, geometric transformations, different modalities, etc.).To tackle such scenarios, we introduce a new, generalized form of fine-tuning, called flex-tuning, in which any individual unit (e.g. layer) of a network can be tuned, and the most promising one is chosen automatically. In order to make the method appealing for practical use, we propose two lightweight and faster selection procedures that prove to be good approximations in practice. We study these selection criteria empirically across a variety of domain shifts and data scarcity scenarios, and show that fine-tuning individual units, despite its simplicity, yields very good results as an adaptation technique. As it turns out, in contrast to common practice, rather than the last fully-connected unit it is best to tune an intermediate or early one in many domain- shift scenarios, which is accurately detected by flex-tuning.","lang":"eng"}],"date_published":"2020-03-01T00:00:00Z","fulldoi":"https://doi.org/10.1109/WACV45572.2020.9093635"},{"scopus_import":"1","publication":"Transformation Groups","author":[{"full_name":"Yang, Yaping","id":"360D8648-F248-11E8-B48F-1D18A9856A87","last_name":"Yang","first_name":"Yaping"},{"first_name":"Gufang","id":"2BC2AC5E-F248-11E8-B48F-1D18A9856A87","last_name":"Zhao","full_name":"Zhao, Gufang"}],"title":"The PBW theorem for affine Yangians","oa":1,"publication_identifier":{"issn":["1083-4362"],"eissn":["1531-586X"]},"type":"journal_article","doi":"10.1007/s00031-020-09572-6","main_file_link":[{"url":"https://arxiv.org/abs/1804.04375","open_access":"1"}],"page":"1371-1385","publication_status":"published","volume":25,"language":[{"iso":"eng"}],"department":[{"_id":"TaHa"}],"month":"12","article_processing_charge":"No","date_created":"2020-06-07T22:00:55Z","project":[{"call_identifier":"FP7","name":"Arithmetic and physics of Higgs moduli spaces","_id":"25E549F4-B435-11E9-9278-68D0E5697425","grant_number":"320593"}],"quality_controlled":"1","date_updated":"2025-07-10T11:54:50Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"We prove that the Yangian associated to an untwisted symmetric affine Kac–Moody Lie algebra is isomorphic to the Drinfeld double of a shuffle algebra. The latter is constructed in [YZ14] as an algebraic formalism of cohomological Hall algebras. As a consequence, we obtain the Poincare–Birkhoff–Witt (PBW) theorem for this class of affine Yangians. Another independent proof of the PBW theorem is given recently by Guay, Regelskis, and Wendlandt [GRW18]."}],"ec_funded":1,"date_published":"2020-12-01T00:00:00Z","article_type":"original","fulldoi":"https://doi.org/10.1007/s00031-020-09572-6","_id":"7940","status":"public","oa_version":"Preprint","isi":1,"arxiv":1,"day":"01","publisher":"Springer Nature","citation":{"ama":"Yang Y, Zhao G. The PBW theorem for affine Yangians. <i>Transformation Groups</i>. 2020;25:1371-1385. doi:<a href=\"https://doi.org/10.1007/s00031-020-09572-6\">10.1007/s00031-020-09572-6</a>","ista":"Yang Y, Zhao G. 2020. The PBW theorem for affine Yangians. Transformation Groups. 25, 1371–1385.","ieee":"Y. Yang and G. Zhao, “The PBW theorem for affine Yangians,” <i>Transformation Groups</i>, vol. 25. Springer Nature, pp. 1371–1385, 2020.","apa":"Yang, Y., &#38; Zhao, G. (2020). The PBW theorem for affine Yangians. <i>Transformation Groups</i>. Springer Nature. <a href=\"https://doi.org/10.1007/s00031-020-09572-6\">https://doi.org/10.1007/s00031-020-09572-6</a>","chicago":"Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” <i>Transformation Groups</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1007/s00031-020-09572-6\">https://doi.org/10.1007/s00031-020-09572-6</a>.","short":"Y. Yang, G. Zhao, Transformation Groups 25 (2020) 1371–1385.","mla":"Yang, Yaping, and Gufang Zhao. “The PBW Theorem for Affine Yangians.” <i>Transformation Groups</i>, vol. 25, Springer Nature, 2020, pp. 1371–85, doi:<a href=\"https://doi.org/10.1007/s00031-020-09572-6\">10.1007/s00031-020-09572-6</a>."},"year":"2020","acknowledgement":"Gufang Zhao is affiliated to IST Austria, Hausel group until July of 2018. Supported by the Advanced Grant Arithmetic and Physics of Higgs moduli spaces No. 320593 of the European Research Council.","external_id":{"isi":["000534874300003"],"arxiv":["1804.04375"]},"intvolume":"        25"},{"_id":"7942","status":"public","oa_version":"Preprint","arxiv":1,"day":"01","isi":1,"acknowledgement":"M.H., Y.-T.H. and S.E.S. acknowledge support from the Royal Society, the Winton Programme for the Physics of Sustainability, EPSRC (studentship, grant no. EP/P024947/1 and EPSRC Strategic Equipment grant no. EP/M000524/1) and the European Research Council (grant no. 772891). S.E.S. acknowledges support from the Leverhulme Trust by way of the award of a Philip Leverhulme Prize. H.Z., J.W. and Z.Z. acknowledge support from the National Key Research and Development Program of China (grant no. 2016YFA0401704). A portion of this work was performed at the National High Magnetic Field Laboratory, which is supported by the National Science Foundation Cooperative Agreement no. DMR-1644779, the state of Florida and the US Department of Energy. Work performed by M.K.C., R.D.M. and N.H. was supported by the US DOE BES ‘Science of 100 T’ programme.","year":"2020","citation":{"chicago":"Hartstein, Máté, Yu Te Hsu, Kimberly A Modic, Juan Porras, Toshinao Loew, Matthieu Le Tacon, Huakun Zuo, et al. “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” <i>Nature Physics</i>. Springer Nature, 2020. <a href=\"https://doi.org/10.1038/s41567-020-0910-0\">https://doi.org/10.1038/s41567-020-0910-0</a>.","short":"M. Hartstein, Y.T. Hsu, K.A. Modic, J. Porras, T. Loew, M.L. Tacon, H. Zuo, J. Wang, Z. Zhu, M.K. Chan, R.D. Mcdonald, G.G. Lonzarich, B. Keimer, S.E. Sebastian, N. Harrison, Nature Physics 16 (2020) 841–847.","mla":"Hartstein, Máté, et al. “Hard Antinodal Gap Revealed by Quantum Oscillations in the Pseudogap Regime of Underdoped High-Tc Superconductors.” <i>Nature Physics</i>, vol. 16, Springer Nature, 2020, pp. 841–47, doi:<a href=\"https://doi.org/10.1038/s41567-020-0910-0\">10.1038/s41567-020-0910-0</a>.","ista":"Hartstein M, Hsu YT, Modic KA, Porras J, Loew T, Tacon ML, Zuo H, Wang J, Zhu Z, Chan MK, Mcdonald RD, Lonzarich GG, Keimer B, Sebastian SE, Harrison N. 2020. Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. Nature Physics. 16, 841–847.","ama":"Hartstein M, Hsu YT, Modic KA, et al. Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. <i>Nature Physics</i>. 2020;16:841-847. doi:<a href=\"https://doi.org/10.1038/s41567-020-0910-0\">10.1038/s41567-020-0910-0</a>","apa":"Hartstein, M., Hsu, Y. T., Modic, K. A., Porras, J., Loew, T., Tacon, M. L., … Harrison, N. (2020). Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors. <i>Nature Physics</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41567-020-0910-0\">https://doi.org/10.1038/s41567-020-0910-0</a>","ieee":"M. Hartstein <i>et al.</i>, “Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors,” <i>Nature Physics</i>, vol. 16. Springer Nature, pp. 841–847, 2020."},"publisher":"Springer Nature","external_id":{"isi":["000535464400005"],"arxiv":["2005.14123"]},"intvolume":"        16","date_updated":"2025-07-10T11:54:52Z","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","abstract":[{"lang":"eng","text":"An understanding of the missing antinodal electronic excitations in the pseudogap state is essential for uncovering the physics of the underdoped cuprate high-temperature superconductors1,2,3,4,5,6. The majority of high-temperature experiments performed thus far, however, have been unable to discern whether the antinodal states are rendered unobservable due to their damping or whether they vanish due to their gapping7,8,9,10,11,12,13,14,15,16,17,18. Here, we distinguish between these two scenarios by using quantum oscillations to examine whether the small Fermi surface pocket, found to occupy only 2% of the Brillouin zone in the underdoped cuprates19,20,21,22,23,24, exists in isolation against a majority of completely gapped density of states spanning the antinodes, or whether it is thermodynamically coupled to a background of ungapped antinodal states. We find that quantum oscillations associated with the small Fermi surface pocket exhibit a signature sawtooth waveform characteristic of an isolated two-dimensional Fermi surface pocket25,26,27,28,29,30,31,32. This finding reveals that the antinodal states are destroyed by a hard gap that extends over the majority of the Brillouin zone, placing strong constraints on a drastic underlying origin of quasiparticle disappearance over almost the entire Brillouin zone in the pseudogap regime7,8,9,10,11,12,13,14,15,16,17,18."}],"date_published":"2020-08-01T00:00:00Z","article_type":"letter_note","fulldoi":"https://doi.org/10.1038/s41567-020-0910-0","page":"841-847","department":[{"_id":"KiMo"}],"volume":16,"language":[{"iso":"eng"}],"publication_status":"published","month":"08","date_created":"2020-06-07T22:00:56Z","article_processing_charge":"No","quality_controlled":"1","related_material":{"record":[{"status":"public","id":"9708","relation":"research_data"}]},"scopus_import":"1","publication":"Nature Physics","author":[{"first_name":"Máté","last_name":"Hartstein","full_name":"Hartstein, Máté"},{"first_name":"Yu Te","last_name":"Hsu","full_name":"Hsu, Yu Te"},{"orcid":"0000-0001-9760-3147","first_name":"Kimberly A","last_name":"Modic","id":"13C26AC0-EB69-11E9-87C6-5F3BE6697425","full_name":"Modic, Kimberly A"},{"first_name":"Juan","full_name":"Porras, Juan","last_name":"Porras"},{"last_name":"Loew","full_name":"Loew, Toshinao","first_name":"Toshinao"},{"first_name":"Matthieu Le","last_name":"Tacon","full_name":"Tacon, Matthieu Le"},{"first_name":"Huakun","full_name":"Zuo, Huakun","last_name":"Zuo"},{"first_name":"Jinhua","full_name":"Wang, Jinhua","last_name":"Wang"},{"full_name":"Zhu, Zengwei","last_name":"Zhu","first_name":"Zengwei"},{"full_name":"Chan, Mun K.","last_name":"Chan","first_name":"Mun K."},{"first_name":"Ross D.","full_name":"Mcdonald, Ross D.","last_name":"Mcdonald"},{"first_name":"Gilbert G.","full_name":"Lonzarich, Gilbert G.","last_name":"Lonzarich"},{"full_name":"Keimer, Bernhard","last_name":"Keimer","first_name":"Bernhard"},{"first_name":"Suchitra E.","last_name":"Sebastian","full_name":"Sebastian, Suchitra E."},{"first_name":"Neil","full_name":"Harrison, Neil","last_name":"Harrison"}],"publication_identifier":{"eissn":["1745-2481"],"issn":["1745-2473"]},"title":"Hard antinodal gap revealed by quantum oscillations in the pseudogap regime of underdoped high-Tc superconductors","oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2005.14123"}],"doi":"10.1038/s41567-020-0910-0","type":"journal_article"},{"file":[{"file_name":"THESIS_Zuzka_Masarova.pdf","file_size":13661779,"date_created":"2020-06-08T00:34:00Z","file_id":"7945","date_updated":"2020-07-14T12:48:05Z","content_type":"application/pdf","creator":"zmasarov","access_level":"open_access","checksum":"df688bc5a82b50baee0b99d25fc7b7f0","relation":"main_file"},{"file_id":"7946","file_size":32184006,"date_created":"2020-06-08T00:35:30Z","file_name":"THESIS_Zuzka_Masarova_SOURCE_FILES.zip","checksum":"45341a35b8f5529c74010b7af43ac188","access_level":"closed","relation":"source_file","creator":"zmasarov","content_type":"application/zip","date_updated":"2020-07-14T12:48:05Z"}],"day":"09","supervisor":[{"first_name":"Uli","orcid":"0000-0002-1494-0568","full_name":"Wagner, Uli","last_name":"Wagner","id":"36690CA2-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-9823-6833","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","last_name":"Edelsbrunner"}],"citation":{"mla":"Masárová, Zuzana. <i>Reconfiguration Problems</i>. Institute of Science and Technology Austria, 2020, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7944\">10.15479/AT:ISTA:7944</a>.","short":"Z. Masárová, Reconfiguration Problems, Institute of Science and Technology Austria, 2020.","chicago":"Masárová, Zuzana. “Reconfiguration Problems.” Institute of Science and Technology Austria, 2020. <a href=\"https://doi.org/10.15479/AT:ISTA:7944\">https://doi.org/10.15479/AT:ISTA:7944</a>.","ieee":"Z. Masárová, “Reconfiguration problems,” Institute of Science and Technology Austria, 2020.","apa":"Masárová, Z. (2020). <i>Reconfiguration problems</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:7944\">https://doi.org/10.15479/AT:ISTA:7944</a>","ama":"Masárová Z. Reconfiguration problems. 2020. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:7944\">10.15479/AT:ISTA:7944</a>","ista":"Masárová Z. 2020. Reconfiguration problems. Institute of Science and Technology Austria."},"year":"2020","publisher":"Institute of Science and Technology Austria","_id":"7944","status":"public","oa_version":"Published Version","OA_place":"publisher","ddc":["516","514"],"has_accepted_license":"1","date_published":"2020-06-09T00:00:00Z","fulldoi":"https://doi.org/10.15479/AT:ISTA:7944","keyword":["reconfiguration","reconfiguration graph","triangulations","flip","constrained triangulations","shellability","piecewise-linear balls","token swapping","trees","coloured weighted token swapping"],"tmp":{"name":"Creative Commons Attribution-ShareAlike 4.0 International Public License (CC BY-SA 4.0)","short":"CC BY-SA (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","image":"/images/cc_by_sa.png"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","abstract":[{"text":"This thesis considers two examples of reconfiguration problems: flipping edges in edge-labelled triangulations of planar point sets and swapping labelled tokens placed on vertices of a graph. In both cases the studied structures – all the triangulations of a given point set or all token placements on a given graph – can be thought of as vertices of the so-called reconfiguration graph, in which two vertices are adjacent if the corresponding structures differ by a single elementary operation – by a flip of a diagonal in a triangulation or by a swap of tokens on adjacent vertices, respectively. We study the reconfiguration of one instance of a structure into another via (shortest) paths in the reconfiguration graph.\r\n\r\nFor triangulations of point sets in which each edge has a unique label and a flip transfers the label from the removed edge to the new edge, we prove a polynomial-time testable condition, called the Orbit Theorem, that characterizes when two triangulations of the same point set lie in the same connected component of the reconfiguration graph. The condition was first conjectured by Bose, Lubiw, Pathak and Verdonschot. We additionally provide a polynomial time algorithm that computes a reconfiguring flip sequence, if it exists. Our proof of the Orbit Theorem uses topological properties of a certain high-dimensional cell complex that has the usual reconfiguration graph as its 1-skeleton.\r\n\r\nIn the context of token swapping on a tree graph, we make partial progress on the problem of finding shortest reconfiguration sequences. We disprove the so-called Happy Leaf Conjecture and demonstrate the importance of swapping tokens that are already placed at the correct vertices. We also prove that a generalization of the problem to weighted coloured token swapping is NP-hard on trees but solvable in polynomial time on paths and stars.","lang":"eng"}],"file_date_updated":"2020-07-14T12:48:05Z","date_updated":"2026-04-08T07:23:01Z","alternative_title":["ISTA Thesis"],"degree_awarded":"PhD","related_material":{"record":[{"id":"7950","relation":"part_of_dissertation","status":"public"},{"status":"public","relation":"part_of_dissertation","id":"5986"}]},"date_created":"2020-06-08T00:49:46Z","article_processing_charge":"No","month":"06","license":"https://creativecommons.org/licenses/by-sa/4.0/","page":"160","department":[{"_id":"HeEd"},{"_id":"UlWa"}],"language":[{"iso":"eng"}],"publication_status":"published","publication_identifier":{"isbn":["978-3-99078-005-3"],"issn":["2663-337X"]},"oa":1,"title":"Reconfiguration problems","doi":"10.15479/AT:ISTA:7944","type":"dissertation","author":[{"first_name":"Zuzana","orcid":"0000-0002-6660-1322","id":"45CFE238-F248-11E8-B48F-1D18A9856A87","last_name":"Masárová","full_name":"Masárová, Zuzana"}],"corr_author":"1"}]