[{"isi":1,"license":"https://creativecommons.org/licenses/by/4.0/","doi":"10.1007/978-3-319-96145-3_5","publication_status":"published","oa_version":"Published Version","day":"18","language":[{"iso":"eng"}],"_id":"160","ddc":["000"],"abstract":[{"text":"We present layered concurrent programs, a compact and expressive notation for specifying refinement proofs of concurrent programs. A layered concurrent program specifies a sequence of connected concurrent programs, from most concrete to most abstract, such that common parts of different programs are written exactly once. These programs are expressed in the ordinary syntax of imperative concurrent programs using gated atomic actions, sequencing, choice, and (recursive) procedure calls. Each concurrent program is automatically extracted from the layered program. We reduce refinement to the safety of a sequence of concurrent checker programs, one each to justify the connection between every two consecutive concurrent programs. These checker programs are also automatically extracted from the layered program. Layered concurrent programs have been implemented in the CIVL verifier which has been successfully used for the verification of several complex concurrent programs.","lang":"eng"}],"oa":1,"title":"Layered Concurrent Programs","department":[{"_id":"ToHe"}],"status":"public","date_created":"2018-12-11T11:44:57Z","conference":{"name":"CAV: Computer Aided Verification","start_date":"2018-07-14","location":"Oxford, UK","end_date":"2018-07-17"},"publist_id":"7761","article_processing_charge":"No","page":"79 - 102","month":"07","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","year":"2018","type":"conference","date_updated":"2026-04-08T07:23:52Z","citation":{"short":"B. Kragl, S. Qadeer, in:, Springer, 2018, pp. 79–102.","apa":"Kragl, B., &#38; Qadeer, S. (2018). Layered Concurrent Programs (Vol. 10981, pp. 79–102). Presented at the CAV: Computer Aided Verification, Oxford, UK: Springer. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>","chicago":"Kragl, Bernhard, and Shaz Qadeer. “Layered Concurrent Programs,” 10981:79–102. Springer, 2018. <a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">https://doi.org/10.1007/978-3-319-96145-3_5</a>.","ista":"Kragl B, Qadeer S. 2018. Layered Concurrent Programs. CAV: Computer Aided Verification, LNCS, vol. 10981, 79–102.","ieee":"B. Kragl and S. Qadeer, “Layered Concurrent Programs,” presented at the CAV: Computer Aided Verification, Oxford, UK, 2018, vol. 10981, pp. 79–102.","mla":"Kragl, Bernhard, and Shaz Qadeer. <i>Layered Concurrent Programs</i>. Vol. 10981, Springer, 2018, pp. 79–102, doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>.","ama":"Kragl B, Qadeer S. Layered Concurrent Programs. In: Vol 10981. Springer; 2018:79-102. doi:<a href=\"https://doi.org/10.1007/978-3-319-96145-3_5\">10.1007/978-3-319-96145-3_5</a>"},"external_id":{"isi":["000491481600005"]},"alternative_title":["LNCS"],"publisher":"Springer","has_accepted_license":"1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8332"}]},"project":[{"name":"Formal methods for the design and analysis of complex systems","grant_number":"Z211","call_identifier":"FWF","_id":"25F42A32-B435-11E9-9278-68D0E5697425"},{"call_identifier":"FWF","_id":"25832EC2-B435-11E9-9278-68D0E5697425","grant_number":"S 11407_N23","name":"Rigorous Systems Engineering"}],"intvolume":"     10981","file_date_updated":"2020-07-14T12:45:04Z","volume":10981,"author":[{"id":"320FC952-F248-11E8-B48F-1D18A9856A87","first_name":"Bernhard","full_name":"Kragl, Bernhard","last_name":"Kragl","orcid":"0000-0001-7745-9117"},{"first_name":"Shaz","full_name":"Qadeer, Shaz","last_name":"Qadeer"}],"file":[{"creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:45:04Z","access_level":"open_access","file_id":"5705","date_created":"2018-12-17T12:52:12Z","file_name":"2018_LNCS_Kragl.pdf","file_size":1603844,"relation":"main_file","checksum":"c64fff560fe5a7532ec10626ad1c215e"}],"date_published":"2018-07-18T00:00:00Z"},{"ddc":["570"],"_id":"161","language":[{"iso":"eng"}],"day":"30","oa_version":"Published Version","oa":1,"abstract":[{"lang":"eng","text":"Which properties of metabolic networks can be derived solely from stoichiometry? Predictive results have been obtained by flux balance analysis (FBA), by postulating that cells set metabolic fluxes to maximize growth rate. Here we consider a generalization of FBA to single-cell level using maximum entropy modeling, which we extend and test experimentally. Specifically, we define for Escherichia coli metabolism a flux distribution that yields the experimental growth rate: the model, containing FBA as a limit, provides a better match to measured fluxes and it makes a wide range of predictions: on flux variability, regulation, and correlations; on the relative importance of stoichiometry vs. optimization; on scaling relations for growth rate distributions. We validate the latter here with single-cell data at different sub-inhibitory antibiotic concentrations. The model quantifies growth optimization as emerging from the interplay of competitive dynamics in the population and regulation of metabolism at the level of single cells."}],"isi":1,"publication_status":"published","doi":"10.1038/s41467-018-05417-9","article_number":"2988","article_processing_charge":"No","ec_funded":1,"publist_id":"7760","issue":"1","status":"public","department":[{"_id":"GaTk"},{"_id":"CaGu"}],"title":"Statistical mechanics for metabolic networks during steady state growth","date_created":"2018-12-11T11:44:57Z","external_id":{"isi":["000440149300021"]},"citation":{"short":"D. De Martino, A.A. Mc, T. Bergmiller, C.C. Guet, G. Tkačik, Nature Communications 9 (2018).","apa":"De Martino, D., Mc, A. A., Bergmiller, T., Guet, C. C., &#38; Tkačik, G. (2018). Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>","ista":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. 2018. Statistical mechanics for metabolic networks during steady state growth. Nature Communications. 9(1), 2988.","ieee":"D. De Martino, A. A. Mc, T. Bergmiller, C. C. Guet, and G. Tkačik, “Statistical mechanics for metabolic networks during steady state growth,” <i>Nature Communications</i>, vol. 9, no. 1. Springer Nature, 2018.","chicago":"De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gašper Tkačik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41467-018-05417-9\">https://doi.org/10.1038/s41467-018-05417-9</a>.","ama":"De Martino D, Mc AA, Bergmiller T, Guet CC, Tkačik G. Statistical mechanics for metabolic networks during steady state growth. <i>Nature Communications</i>. 2018;9(1). doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>","mla":"De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” <i>Nature Communications</i>, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41467-018-05417-9\">10.1038/s41467-018-05417-9</a>."},"date_updated":"2025-04-15T06:50:08Z","type":"journal_article","year":"2018","publisher":"Springer Nature","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","month":"07","scopus_import":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"author":[{"full_name":"De Martino, Daniele","last_name":"De Martino","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele"},{"last_name":"Mc","full_name":"Mc, Andersson Anna","first_name":"Andersson Anna"},{"last_name":"Bergmiller","full_name":"Bergmiller, Tobias","orcid":"0000-0001-5396-4346","first_name":"Tobias","id":"2C471CFA-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0001-6220-2052","last_name":"Guet","full_name":"Guet, Calin C","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","full_name":"Tkacik, Gasper","first_name":"Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"}],"file_date_updated":"2020-07-14T12:45:06Z","volume":9,"intvolume":"         9","date_published":"2018-07-30T00:00:00Z","file":[{"creator":"dernst","content_type":"application/pdf","date_updated":"2020-07-14T12:45:06Z","access_level":"open_access","file_id":"5728","date_created":"2018-12-17T16:44:28Z","file_name":"2018_NatureComm_DeMartino.pdf","file_size":1043205,"relation":"main_file","checksum":"3ba7ab27b27723c7dcf633e8fc1f8f18"}],"publication":"Nature Communications","related_material":{"record":[{"status":"public","id":"5587","relation":"popular_science"}]},"has_accepted_license":"1","project":[{"grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"},{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]},{"publisher":"eLife Sciences Publications","year":"2018","type":"journal_article","external_id":{"isi":["000436227500001"]},"citation":{"short":"M. Kaucka, J. Petersen, M. Tesarova, B. Szarowska, M. Kastriti, M. Xie, A. Kicheva, K. Annusver, M. Kasper, O. Symmons, L. Pan, F. Spitz, J. Kaiser, M. Hovorakova, T. Zikmund, K. Sunadome, M.P. Matise, H. Wang, U. Marklund, H. Abdo, P. Ernfors, P. Maire, M. Wurmser, A.S. Chagin, K. Fried, I. Adameyko, ELife 7 (2018).","apa":"Kaucka, M., Petersen, J., Tesarova, M., Szarowska, B., Kastriti, M., Xie, M., … Adameyko, I. (2018). Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>","chicago":"Kaucka, Marketa, Julian Petersen, Marketa Tesarova, Bara Szarowska, Maria Kastriti, Meng Xie, Anna Kicheva, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>. eLife Sciences Publications, 2018. <a href=\"https://doi.org/10.7554/eLife.34465\">https://doi.org/10.7554/eLife.34465</a>.","ieee":"M. Kaucka <i>et al.</i>, “Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage,” <i>eLife</i>, vol. 7. eLife Sciences Publications, 2018.","ista":"Kaucka M, Petersen J, Tesarova M, Szarowska B, Kastriti M, Xie M, Kicheva A, Annusver K, Kasper M, Symmons O, Pan L, Spitz F, Kaiser J, Hovorakova M, Zikmund T, Sunadome K, Matise MP, Wang H, Marklund U, Abdo H, Ernfors P, Maire P, Wurmser M, Chagin AS, Fried K, Adameyko I. 2018. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. eLife. 7, e34465.","mla":"Kaucka, Marketa, et al. “Signals from the Brain and Olfactory Epithelium Control Shaping of the Mammalian Nasal Capsule Cartilage.” <i>ELife</i>, vol. 7, e34465, eLife Sciences Publications, 2018, doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>.","ama":"Kaucka M, Petersen J, Tesarova M, et al. Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage. <i>eLife</i>. 2018;7. doi:<a href=\"https://doi.org/10.7554/eLife.34465\">10.7554/eLife.34465</a>"},"date_updated":"2025-04-14T07:27:30Z","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":"1","month":"06","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","file":[{"checksum":"da2378cdcf6b5461dcde194e4d608343","relation":"main_file","file_size":9816484,"file_name":"2018_eLife_Kaucka.pdf","date_created":"2018-12-17T16:41:58Z","file_id":"5727","access_level":"open_access","date_updated":"2020-07-14T12:45:07Z","content_type":"application/pdf","creator":"dernst"}],"date_published":"2018-06-13T00:00:00Z","intvolume":"         7","volume":7,"file_date_updated":"2020-07-14T12:45:07Z","author":[{"first_name":"Marketa","full_name":"Kaucka, Marketa","last_name":"Kaucka"},{"first_name":"Julian","last_name":"Petersen","full_name":"Petersen, Julian"},{"first_name":"Marketa","last_name":"Tesarova","full_name":"Tesarova, Marketa"},{"first_name":"Bara","last_name":"Szarowska","full_name":"Szarowska, Bara"},{"first_name":"Maria","last_name":"Kastriti","full_name":"Kastriti, Maria"},{"full_name":"Xie, Meng","last_name":"Xie","first_name":"Meng"},{"first_name":"Anna","id":"3959A2A0-F248-11E8-B48F-1D18A9856A87","last_name":"Kicheva","full_name":"Kicheva, Anna","orcid":"0000-0003-4509-4998"},{"full_name":"Annusver, Karl","last_name":"Annusver","first_name":"Karl"},{"last_name":"Kasper","full_name":"Kasper, Maria","first_name":"Maria"},{"last_name":"Symmons","full_name":"Symmons, Orsolya","first_name":"Orsolya"},{"full_name":"Pan, Leslie","last_name":"Pan","first_name":"Leslie"},{"first_name":"Francois","full_name":"Spitz, Francois","last_name":"Spitz"},{"last_name":"Kaiser","full_name":"Kaiser, Jozef","first_name":"Jozef"},{"first_name":"Maria","last_name":"Hovorakova","full_name":"Hovorakova, Maria"},{"full_name":"Zikmund, Tomas","last_name":"Zikmund","first_name":"Tomas"},{"first_name":"Kazunori","full_name":"Sunadome, Kazunori","last_name":"Sunadome"},{"first_name":"Michael P","full_name":"Matise, Michael P","last_name":"Matise"},{"last_name":"Wang","full_name":"Wang, Hui","first_name":"Hui"},{"first_name":"Ulrika","full_name":"Marklund, Ulrika","last_name":"Marklund"},{"first_name":"Hind","last_name":"Abdo","full_name":"Abdo, Hind"},{"last_name":"Ernfors","full_name":"Ernfors, Patrik","first_name":"Patrik"},{"full_name":"Maire, Pascal","last_name":"Maire","first_name":"Pascal"},{"first_name":"Maud","last_name":"Wurmser","full_name":"Wurmser, Maud"},{"first_name":"Andrei S","full_name":"Chagin, Andrei S","last_name":"Chagin"},{"first_name":"Kaj","full_name":"Fried, Kaj","last_name":"Fried"},{"full_name":"Adameyko, Igor","last_name":"Adameyko","first_name":"Igor"}],"project":[{"name":"Coordination of Patterning And Growth In the Spinal Cord","grant_number":"680037","call_identifier":"H2020","_id":"B6FC0238-B512-11E9-945C-1524E6697425"}],"has_accepted_license":"1","related_material":{"record":[{"relation":"research_data","id":"9838","status":"public"}]},"publication":"eLife","oa":1,"abstract":[{"text":"Facial shape is the basis for facial recognition and categorization. Facial features reflect the underlying geometry of the skeletal structures. Here, we reveal that cartilaginous nasal capsule (corresponding to upper jaw and face) is shaped by signals generated by neural structures: brain and olfactory epithelium. Brain-derived Sonic Hedgehog (SHH) enables the induction of nasal septum and posterior nasal capsule, whereas the formation of a capsule roof is controlled by signals from the olfactory epithelium. Unexpectedly, the cartilage of the nasal capsule turned out to be important for shaping membranous facial bones during development. This suggests that conserved neurosensory structures could benefit from protection and have evolved signals inducing cranial cartilages encasing them. Experiments with mutant mice revealed that the genomic regulatory regions controlling production of SHH in the nervous system contribute to facial cartilage morphogenesis, which might be a mechanism responsible for the adaptive evolution of animal faces and snouts.","lang":"eng"}],"oa_version":"Published Version","day":"13","language":[{"iso":"eng"}],"_id":"162","ddc":["571"],"doi":"10.7554/eLife.34465","publication_status":"published","isi":1,"article_processing_charge":"No","article_number":"e34465","status":"public","department":[{"_id":"AnKi"}],"title":"Signals from the brain and olfactory epithelium control shaping of the mammalian nasal capsule cartilage","date_created":"2018-12-11T11:44:57Z","publist_id":"7759","ec_funded":1},{"article_processing_charge":"No","article_type":"original","page":"903-921","title":"Agitation modules: Flexible means to accelerate automated freeze substitution","department":[{"_id":"RySh"},{"_id":"EM-Fac"}],"date_created":"2018-12-11T11:44:57Z","status":"public","issue":"12","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"01","_id":"163","ddc":["570"],"abstract":[{"lang":"eng","text":"For ultrafast fixation of biological samples to avoid artifacts, high-pressure freezing (HPF) followed by freeze substitution (FS) is preferred over chemical fixation at room temperature. After HPF, samples are maintained at low temperature during dehydration and fixation, while avoiding damaging recrystallization. This is a notoriously slow process. McDonald and Webb demonstrated, in 2011, that sample agitation during FS dramatically reduces the necessary time. Then, in 2015, we (H.G. and S.R.) introduced an agitation module into the cryochamber of an automated FS unit and demonstrated that the preparation of algae could be shortened from days to a couple of hours. We argued that variability in the processing, reproducibility, and safety issues are better addressed using automated FS units. For dissemination, we started low-cost manufacturing of agitation modules for two of the most widely used FS units, the Automatic Freeze Substitution Systems, AFS(1) and AFS2, from Leica Microsystems, using three dimensional (3D)-printing of the major components. To test them, several labs independently used the modules on a wide variety of specimens that had previously been processed by manual agitation, or without agitation. We demonstrate that automated processing with sample agitation saves time, increases flexibility with respect to sample requirements and protocols, and produces data of at least as good quality as other approaches."}],"oa":1,"isi":1,"pmid":1,"doi":"10.1369/0022155418786698","publication_status":"published","main_file_link":[{"url":"https://doi.org/10.1369/0022155418786698","open_access":"1"}],"intvolume":"        66","volume":66,"author":[{"first_name":"Siegfried","full_name":"Reipert, Siegfried","last_name":"Reipert"},{"last_name":"Goldammer","full_name":"Goldammer, Helmuth","first_name":"Helmuth"},{"full_name":"Richardson, Christine","last_name":"Richardson","first_name":"Christine"},{"last_name":"Goldberg","full_name":"Goldberg, Martin","first_name":"Martin"},{"last_name":"Hawkins","full_name":"Hawkins, Timothy","first_name":"Timothy"},{"first_name":"Elena","id":"3C054040-F248-11E8-B48F-1D18A9856A87","last_name":"Hollergschwandtner","full_name":"Hollergschwandtner, Elena"},{"first_name":"Walter","id":"3F99E422-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-9735-5315","last_name":"Kaufmann","full_name":"Kaufmann, Walter"},{"first_name":"Sebastian","full_name":"Antreich, Sebastian","last_name":"Antreich"},{"full_name":"Stierhof, York","last_name":"Stierhof","first_name":"York"}],"date_published":"2018-12-01T00:00:00Z","publication_identifier":{"issn":["0022-1554"]},"publication":"Journal of Histochemistry and Cytochemistry","year":"2018","type":"journal_article","citation":{"short":"S. Reipert, H. Goldammer, C. Richardson, M. Goldberg, T. Hawkins, E. Saeckl, W. Kaufmann, S. Antreich, Y. Stierhof, Journal of Histochemistry and Cytochemistry 66 (2018) 903–921.","apa":"Reipert, S., Goldammer, H., Richardson, C., Goldberg, M., Hawkins, T., Saeckl, E., … Stierhof, Y. (2018). Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>","ieee":"S. Reipert <i>et al.</i>, “Agitation modules: Flexible means to accelerate automated freeze substitution,” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12. SAGE Publications, pp. 903–921, 2018.","ista":"Reipert S, Goldammer H, Richardson C, Goldberg M, Hawkins T, Saeckl E, Kaufmann W, Antreich S, Stierhof Y. 2018. Agitation modules: Flexible means to accelerate automated freeze substitution. Journal of Histochemistry and Cytochemistry. 66(12), 903–921.","chicago":"Reipert, Siegfried, Helmuth Goldammer, Christine Richardson, Martin Goldberg, Timothy Hawkins, Elena Saeckl, Walter Kaufmann, Sebastian Antreich, and York Stierhof. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>. SAGE Publications, 2018. <a href=\"https://doi.org/10.1369/0022155418786698\">https://doi.org/10.1369/0022155418786698</a>.","ama":"Reipert S, Goldammer H, Richardson C, et al. Agitation modules: Flexible means to accelerate automated freeze substitution. <i>Journal of Histochemistry and Cytochemistry</i>. 2018;66(12):903-921. doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>","mla":"Reipert, Siegfried, et al. “Agitation Modules: Flexible Means to Accelerate Automated Freeze Substitution.” <i>Journal of Histochemistry and Cytochemistry</i>, vol. 66, no. 12, SAGE Publications, 2018, pp. 903–21, doi:<a href=\"https://doi.org/10.1369/0022155418786698\">10.1369/0022155418786698</a>."},"external_id":{"pmid":["29969056"],"isi":["000452277700005"]},"date_updated":"2026-06-18T17:50:00Z","publisher":"SAGE Publications","month":"12","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","scopus_import":"1"},{"date_created":"2018-12-11T11:44:11Z","department":[{"_id":"BjHo"}],"status":"public","title":"Drag enhancement and drag reduction in viscoelastic flow","issue":"10","publist_id":"8038","ec_funded":1,"article_processing_charge":"No","article_number":"103302 ","publication_status":"published","doi":"10.1103/PhysRevFluids.3.103302","isi":1,"oa":1,"abstract":[{"lang":"eng","text":"Creeping flow of polymeric fluid without inertia exhibits elastic instabilities and elastic turbulence accompanied by drag enhancement due to elastic stress produced by flow-stretched polymers. However, in inertia-dominated flow at high Re and low fluid elasticity El, a reduction in turbulent frictional drag is caused by an intricate competition between inertial and elastic stresses. Here we explore the effect of inertia on the stability of viscoelastic flow in a broad range of control parameters El and (Re,Wi). We present the stability diagram of observed flow regimes in Wi-Re coordinates and find that the instabilities' onsets show an unexpectedly nonmonotonic dependence on El. Further, three distinct regions in the diagram are identified based on El. Strikingly, for high-elasticity fluids we discover a complete relaminarization of flow at Reynolds number in the range of 1 to 10, different from a well-known turbulent drag reduction. These counterintuitive effects may be explained by a finite polymer extensibility and a suppression of vorticity at high Wi. Our results call for further theoretical and numerical development to uncover the role of inertial effect on elastic turbulence in a viscoelastic flow."}],"_id":"17","ddc":["532"],"oa_version":"Published Version","day":"15","language":[{"iso":"eng"}],"project":[{"name":"ISTplus - Postdoctoral Fellowships","grant_number":"754411","call_identifier":"H2020","_id":"260C2330-B435-11E9-9278-68D0E5697425"}],"publication":"Physical Review Fluids","has_accepted_license":"1","date_published":"2018-10-15T00:00:00Z","file":[{"content_type":"application/pdf","creator":"system","date_updated":"2020-07-14T12:45:12Z","file_id":"4800","date_created":"2018-12-12T10:10:14Z","access_level":"open_access","file_name":"IST-2018-1061-v1+1_PhysRevFluids.3.103302.pdf","file_size":1409040,"checksum":"e1445be33e8165114e96246275600750","relation":"main_file"}],"author":[{"last_name":"Varshney","full_name":"Varshney, Atul","orcid":"0000-0002-3072-5999","first_name":"Atul","id":"2A2006B2-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Victor","full_name":"Steinberg, Victor","last_name":"Steinberg"}],"intvolume":"         3","volume":3,"file_date_updated":"2020-07-14T12:45:12Z","scopus_import":"1","month":"10","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","publisher":"American Physical Society","pubrep_id":"1061","external_id":{"isi":["000447311500001"]},"citation":{"apa":"Varshney, A., &#38; Steinberg, V. (2018). Drag enhancement and drag reduction in viscoelastic flow. <i>Physical Review Fluids</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">https://doi.org/10.1103/PhysRevFluids.3.103302</a>","short":"A. Varshney, V. Steinberg, Physical Review Fluids 3 (2018).","ama":"Varshney A, Steinberg V. Drag enhancement and drag reduction in viscoelastic flow. <i>Physical Review Fluids</i>. 2018;3(10). doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">10.1103/PhysRevFluids.3.103302</a>","mla":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” <i>Physical Review Fluids</i>, vol. 3, no. 10, 103302, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">10.1103/PhysRevFluids.3.103302</a>.","ista":"Varshney A, Steinberg V. 2018. Drag enhancement and drag reduction in viscoelastic flow. Physical Review Fluids. 3(10), 103302.","ieee":"A. Varshney and V. Steinberg, “Drag enhancement and drag reduction in viscoelastic flow,” <i>Physical Review Fluids</i>, vol. 3, no. 10. American Physical Society, 2018.","chicago":"Varshney, Atul, and Victor Steinberg. “Drag Enhancement and Drag Reduction in Viscoelastic Flow.” <i>Physical Review Fluids</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevFluids.3.103302\">https://doi.org/10.1103/PhysRevFluids.3.103302</a>."},"date_updated":"2025-04-14T07:43:59Z","year":"2018","type":"journal_article"},{"publication_status":"published","doi":"10.4230/LIPIcs.SoCG.2018.39","oa":1,"abstract":[{"lang":"eng","text":"We resolve in the affirmative conjectures of A. Skopenkov and Repovš (1998), and M. Skopenkov (2003) generalizing the classical Hanani-Tutte theorem to the setting of approximating maps of graphs on 2-dimensional surfaces by embeddings. Our proof of this result is constructive and almost immediately implies an efficient algorithm for testing whether a given piecewise linear map of a graph in a surface is approximable by an embedding. More precisely, an instance of this problem consists of (i) a graph G whose vertices are partitioned into clusters and whose inter-cluster edges are partitioned into bundles, and (ii) a region R of a 2-dimensional compact surface M given as the union of a set of pairwise disjoint discs corresponding to the clusters and a set of pairwise disjoint &quot;pipes&quot; corresponding to the bundles, connecting certain pairs of these discs. We are to decide whether G can be embedded inside M so that the vertices in every cluster are drawn in the corresponding disc, the edges in every bundle pass only through its corresponding pipe, and every edge crosses the boundary of each disc at most once."}],"_id":"185","ddc":["510"],"oa_version":"Published Version","day":"01","language":[{"iso":"eng"}],"date_created":"2018-12-11T11:45:04Z","conference":{"name":"SoCG: Symposium on Computational Geometry","location":"Budapest, Hungary","start_date":"2018-06-11","end_date":"2018-06-14"},"department":[{"_id":"UlWa"}],"title":"Hanani-Tutte for approximating maps of graphs","status":"public","publist_id":"7735","article_number":"39","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"scopus_import":1,"month":"01","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"date_updated":"2021-01-12T06:53:36Z","citation":{"short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","apa":"Fulek, R., &#38; Kynčl, J. (2018). Hanani-Tutte for approximating maps of graphs (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">https://doi.org/10.4230/LIPIcs.SoCG.2018.39</a>","chicago":"Fulek, Radoslav, and Jan Kynčl. “Hanani-Tutte for Approximating Maps of Graphs,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">https://doi.org/10.4230/LIPIcs.SoCG.2018.39</a>.","ista":"Fulek R, Kynčl J. 2018. Hanani-Tutte for approximating maps of graphs. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 39.","ieee":"R. Fulek and J. Kynčl, “Hanani-Tutte for approximating maps of graphs,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","mla":"Fulek, Radoslav, and Jan Kynčl. <i>Hanani-Tutte for Approximating Maps of Graphs</i>. Vol. 99, 39, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">10.4230/LIPIcs.SoCG.2018.39</a>.","ama":"Fulek R, Kynčl J. Hanani-Tutte for approximating maps of graphs. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.39\">10.4230/LIPIcs.SoCG.2018.39</a>"},"year":"2018","type":"conference","project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","call_identifier":"FWF","_id":"261FA626-B435-11E9-9278-68D0E5697425"}],"publication_identifier":{"isbn":["978-3-95977-066-8"]},"has_accepted_license":"1","date_published":"2018-01-01T00:00:00Z","file":[{"content_type":"application/pdf","creator":"dernst","date_updated":"2020-07-14T12:45:19Z","file_size":718857,"checksum":"f1b94f1a75b37c414a1f61d59fb2cd4c","relation":"main_file","date_created":"2018-12-17T12:33:52Z","file_id":"5701","access_level":"open_access","file_name":"2018_LIPIcs_Fulek.pdf"}],"author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"full_name":"Kynčl, Jan","last_name":"Kynčl","first_name":"Jan"}],"intvolume":"        99","volume":99,"file_date_updated":"2020-07-14T12:45:19Z"},{"author":[{"first_name":"Radoslav","id":"39F3FFE4-F248-11E8-B48F-1D18A9856A87","last_name":"Fulek","full_name":"Fulek, Radoslav","orcid":"0000-0001-8485-1774"},{"last_name":"Kynčl","full_name":"Kynčl, Jan","first_name":"Jan"}],"volume":99,"intvolume":"        99","date_published":"2018-06-11T00:00:00Z","related_material":{"record":[{"id":"11593","relation":"later_version","status":"public"}]},"project":[{"name":"Eliminating intersections in drawings of graphs","grant_number":"M02281","_id":"261FA626-B435-11E9-9278-68D0E5697425","call_identifier":"FWF"}],"citation":{"apa":"Fulek, R., &#38; Kynčl, J. (2018). The ℤ2-Genus of Kuratowski minors (Vol. 99, p. 40.1-40.14). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>","short":"R. Fulek, J. Kynčl, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14.","ama":"Fulek R, Kynčl J. The ℤ2-Genus of Kuratowski minors. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:40.1-40.14. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>","mla":"Fulek, Radoslav, and Jan Kynčl. <i>The ℤ2-Genus of Kuratowski Minors</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 40.1-40.14, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">10.4230/LIPIcs.SoCG.2018.40</a>.","ista":"Fulek R, Kynčl J. 2018. The ℤ2-Genus of Kuratowski minors. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 40.1-40.14.","ieee":"R. Fulek and J. Kynčl, “The ℤ2-Genus of Kuratowski minors,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 40.1-40.14.","chicago":"Fulek, Radoslav, and Jan Kynčl. “The ℤ2-Genus of Kuratowski Minors,” 99:40.1-40.14. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.40\">https://doi.org/10.4230/LIPIcs.SoCG.2018.40</a>."},"date_updated":"2025-04-14T13:52:37Z","external_id":{"arxiv":["1803.05085"]},"type":"conference","year":"2018","alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","arxiv":1,"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","scopus_import":"1","article_processing_charge":"No","page":"40.1 - 40.14","publist_id":"7734","conference":{"end_date":"2018-06-14","start_date":"2018-06-11","location":"Budapest, Hungary","name":"SoCG: Symposium on Computational Geometry"},"title":"The ℤ2-Genus of Kuratowski minors","date_created":"2018-12-11T11:45:05Z","status":"public","department":[{"_id":"UlWa"}],"_id":"186","language":[{"iso":"eng"}],"day":"11","oa_version":"Submitted Version","oa":1,"abstract":[{"text":"A drawing of a graph on a surface is independently even if every pair of nonadjacent edges in the drawing crosses an even number of times. The ℤ2-genus of a graph G is the minimum g such that G has an independently even drawing on the orientable surface of genus g. An unpublished result by Robertson and Seymour implies that for every t, every graph of sufficiently large genus contains as a minor a projective t × t grid or one of the following so-called t-Kuratowski graphs: K3, t, or t copies of K5 or K3,3 sharing at most 2 common vertices. We show that the ℤ2-genus of graphs in these families is unbounded in t; in fact, equal to their genus. Together, this implies that the genus of a graph is bounded from above by a function of its ℤ2-genus, solving a problem posed by Schaefer and Štefankovič, and giving an approximate version of the Hanani-Tutte theorem on orientable surfaces.","lang":"eng"}],"main_file_link":[{"url":"https://arxiv.org/abs/1803.05085","open_access":"1"}],"publication_status":"published","doi":"10.4230/LIPIcs.SoCG.2018.40"},{"abstract":[{"lang":"eng","text":"Given a locally finite X ⊆ ℝd and a radius r ≥ 0, the k-fold cover of X and r consists of all points in ℝd that have k or more points of X within distance r. We consider two filtrations - one in scale obtained by fixing k and increasing r, and the other in depth obtained by fixing r and decreasing k - and we compute the persistence diagrams of both. While standard methods suffice for the filtration in scale, we need novel geometric and topological concepts for the filtration in depth. In particular, we introduce a rhomboid tiling in ℝd+1 whose horizontal integer slices are the order-k Delaunay mosaics of X, and construct a zigzag module from Delaunay mosaics that is isomorphic to the persistence module of the multi-covers. "}],"oa":1,"ddc":["516"],"_id":"187","day":"11","language":[{"iso":"eng"}],"oa_version":"Published Version","publication_status":"published","doi":"10.4230/LIPIcs.SoCG.2018.34","article_number":"34","publist_id":"7732","conference":{"location":"Budapest, Hungary","start_date":"2018-06-11","end_date":"2018-06-14","name":"SoCG: Symposium on Computational Geometry"},"date_created":"2018-12-11T11:45:05Z","title":"The multi-cover persistence of Euclidean balls","status":"public","department":[{"_id":"HeEd"}],"alternative_title":["LIPIcs"],"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","date_updated":"2026-04-08T07:01:29Z","citation":{"short":"H. Edelsbrunner, G.F. Osang, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018.","apa":"Edelsbrunner, H., &#38; Osang, G. F. (2018). The multi-cover persistence of Euclidean balls (Vol. 99). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>","chicago":"Edelsbrunner, Herbert, and Georg F Osang. “The Multi-Cover Persistence of Euclidean Balls,” Vol. 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">https://doi.org/10.4230/LIPIcs.SoCG.2018.34</a>.","ieee":"H. Edelsbrunner and G. F. Osang, “The multi-cover persistence of Euclidean balls,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99.","ista":"Edelsbrunner H, Osang GF. 2018. The multi-cover persistence of Euclidean balls. SoCG: Symposium on Computational Geometry, LIPIcs, vol. 99, 34.","mla":"Edelsbrunner, Herbert, and Georg F. Osang. <i>The Multi-Cover Persistence of Euclidean Balls</i>. Vol. 99, 34, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>.","ama":"Edelsbrunner H, Osang GF. The multi-cover persistence of Euclidean balls. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.34\">10.4230/LIPIcs.SoCG.2018.34</a>"},"type":"conference","year":"2018","scopus_import":1,"acknowledgement":"This work is partially supported by the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund (FWF).","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"06","date_published":"2018-06-11T00:00:00Z","file":[{"file_name":"2018_LIPIcs_Edelsbrunner_Osang.pdf","file_id":"5738","date_created":"2018-12-18T09:27:22Z","access_level":"open_access","checksum":"d8c0533ad0018eb4ed1077475eb8fc18","relation":"main_file","file_size":528018,"date_updated":"2020-07-14T12:45:19Z","content_type":"application/pdf","creator":"dernst"}],"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","orcid":"0000-0002-9823-6833","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner"},{"last_name":"Osang","full_name":"Osang, Georg F","orcid":"0000-0002-8882-5116","first_name":"Georg F","id":"464B40D6-F248-11E8-B48F-1D18A9856A87"}],"volume":99,"file_date_updated":"2020-07-14T12:45:19Z","intvolume":"        99","project":[{"name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35","call_identifier":"FWF","_id":"2561EBF4-B435-11E9-9278-68D0E5697425"}],"related_material":{"record":[{"id":"9317","relation":"later_version","status":"public"},{"status":"public","id":"9056","relation":"dissertation_contains"}]},"has_accepted_license":"1"},{"page":"35:1 - 35:13","date_created":"2018-12-11T11:45:05Z","conference":{"name":"SoCG: Symposium on Computational Geometry","end_date":"2018-06-14","location":"Budapest, Hungary","start_date":"2018-06-11"},"department":[{"_id":"HeEd"}],"title":"Smallest enclosing spheres and Chernoff points in Bregman geometry","status":"public","publist_id":"7733","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"11","ddc":["000"],"_id":"188","oa":1,"abstract":[{"text":"Smallest enclosing spheres of finite point sets are central to methods in topological data analysis. Focusing on Bregman divergences to measure dissimilarity, we prove bounds on the location of the center of a smallest enclosing sphere. These bounds depend on the range of radii for which Bregman balls are convex.","lang":"eng"}],"doi":"10.4230/LIPIcs.SoCG.2018.35","publication_status":"published","intvolume":"        99","file_date_updated":"2020-07-14T12:45:20Z","volume":99,"author":[{"id":"3FB178DA-F248-11E8-B48F-1D18A9856A87","first_name":"Herbert","full_name":"Edelsbrunner, Herbert","last_name":"Edelsbrunner","orcid":"0000-0002-9823-6833"},{"full_name":"Virk, Ziga","last_name":"Virk","first_name":"Ziga"},{"last_name":"Wagner","full_name":"Wagner, Hubert","first_name":"Hubert","id":"379CA8B8-F248-11E8-B48F-1D18A9856A87"}],"file":[{"checksum":"7509403803b3ac1aee94bbc2ad293d21","relation":"main_file","file_size":489080,"file_name":"2018_LIPIcs_Edelsbrunner.pdf","file_id":"5724","date_created":"2018-12-17T16:31:31Z","access_level":"open_access","date_updated":"2020-07-14T12:45:20Z","content_type":"application/pdf","creator":"dernst"}],"date_published":"2018-06-11T00:00:00Z","has_accepted_license":"1","project":[{"_id":"2561EBF4-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Persistence and stability of geometric complexes","grant_number":"I02979-N35"}],"year":"2018","type":"conference","date_updated":"2021-01-12T06:53:48Z","citation":{"short":"H. Edelsbrunner, Z. Virk, H. Wagner, in:, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13.","apa":"Edelsbrunner, H., Virk, Z., &#38; Wagner, H. (2018). Smallest enclosing spheres and Chernoff points in Bregman geometry (Vol. 99, p. 35:1-35:13). Presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary: Schloss Dagstuhl - Leibniz-Zentrum für Informatik. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>","ieee":"H. Edelsbrunner, Z. Virk, and H. Wagner, “Smallest enclosing spheres and Chernoff points in Bregman geometry,” presented at the SoCG: Symposium on Computational Geometry, Budapest, Hungary, 2018, vol. 99, p. 35:1-35:13.","ista":"Edelsbrunner H, Virk Z, Wagner H. 2018. Smallest enclosing spheres and Chernoff points in Bregman geometry. SoCG: Symposium on Computational Geometry, Leibniz International Proceedings in Information, LIPIcs, vol. 99, 35:1-35:13.","chicago":"Edelsbrunner, Herbert, Ziga Virk, and Hubert Wagner. “Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry,” 99:35:1-35:13. Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018. <a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">https://doi.org/10.4230/LIPIcs.SoCG.2018.35</a>.","ama":"Edelsbrunner H, Virk Z, Wagner H. Smallest enclosing spheres and Chernoff points in Bregman geometry. In: Vol 99. Schloss Dagstuhl - Leibniz-Zentrum für Informatik; 2018:35:1-35:13. doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>","mla":"Edelsbrunner, Herbert, et al. <i>Smallest Enclosing Spheres and Chernoff Points in Bregman Geometry</i>. Vol. 99, Schloss Dagstuhl - Leibniz-Zentrum für Informatik, 2018, p. 35:1-35:13, doi:<a href=\"https://doi.org/10.4230/LIPIcs.SoCG.2018.35\">10.4230/LIPIcs.SoCG.2018.35</a>."},"publisher":"Schloss Dagstuhl - Leibniz-Zentrum für Informatik","alternative_title":["Leibniz International Proceedings in Information, LIPIcs"],"month":"06","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"This research is partially supported by the Office of Naval Research, through grant no. N62909-18-1-2038, and the DFG Collaborative Research Center TRR 109, ‘Discretization in Geometry and Dynamics’, through grant no. I02979-N35 of the Austrian Science Fund","scopus_import":1},{"scopus_import":"1","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","month":"08","publisher":"Oxford University Press","type":"journal_article","year":"2018","external_id":{"pmid":["30169679"],"isi":["000452567200006"]},"citation":{"chicago":"Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>. Oxford University Press, 2018. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>.","ieee":"A. Palmer, R. P. Chait, and R. Kishony, “Nonoptimal gene expression creates latent potential for antibiotic resistance,” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11. Oxford University Press, pp. 2669–2684, 2018.","ista":"Palmer A, Chait RP, Kishony R. 2018. Nonoptimal gene expression creates latent potential for antibiotic resistance. Molecular Biology and Evolution. 35(11), 2669–2684.","mla":"Palmer, Adam, et al. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.” <i>Molecular Biology and Evolution</i>, vol. 35, no. 11, Oxford University Press, 2018, pp. 2669–84, doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>.","ama":"Palmer A, Chait RP, Kishony R. Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. 2018;35(11):2669-2684. doi:<a href=\"https://doi.org/10.1093/molbev/msy163\">10.1093/molbev/msy163</a>","short":"A. Palmer, R.P. Chait, R. Kishony, Molecular Biology and Evolution 35 (2018) 2669–2684.","apa":"Palmer, A., Chait, R. P., &#38; Kishony, R. (2018). Nonoptimal gene expression creates latent potential for antibiotic resistance. <i>Molecular Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/molbev/msy163\">https://doi.org/10.1093/molbev/msy163</a>"},"date_updated":"2023-10-17T11:51:06Z","publication_identifier":{"issn":["0737-4038"]},"publication":"Molecular Biology and Evolution","date_published":"2018-08-28T00:00:00Z","volume":35,"intvolume":"        35","author":[{"first_name":"Adam","last_name":"Palmer","full_name":"Palmer, Adam"},{"orcid":"0000-0003-0876-3187","last_name":"Chait","full_name":"Chait, Remy P","first_name":"Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"doi":"10.1093/molbev/msy163","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pubmed/30169679"}],"publication_status":"published","pmid":1,"isi":1,"oa":1,"abstract":[{"text":"Bacteria regulate genes to survive antibiotic stress, but regulation can be far from perfect. When regulation is not optimal, mutations that change gene expression can contribute to antibiotic resistance. It is not systematically understood to what extent natural gene regulation is or is not optimal for distinct antibiotics, and how changes in expression of specific genes quantitatively affect antibiotic resistance. Here we discover a simple quantitative relation between fitness, gene expression, and antibiotic potency, which rationalizes our observation that a multitude of genes and even innate antibiotic defense mechanisms have expression that is critically nonoptimal under antibiotic treatment. First, we developed a pooled-strain drug-diffusion assay and screened Escherichia coli overexpression and knockout libraries, finding that resistance to a range of 31 antibiotics could result from changing expression of a large and functionally diverse set of genes, in a primarily but not exclusively drug-specific manner. Second, by synthetically controlling the expression of single-drug and multidrug resistance genes, we observed that their fitness-expression functions changed dramatically under antibiotic treatment in accordance with a log-sensitivity relation. Thus, because many genes are nonoptimally expressed under antibiotic treatment, many regulatory mutations can contribute to resistance by altering expression and by activating latent defenses.","lang":"eng"}],"day":"28","language":[{"iso":"eng"}],"oa_version":"Submitted Version","_id":"19","issue":"11","publist_id":"8036","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_created":"2018-12-11T11:44:11Z","title":"Nonoptimal gene expression creates latent potential for antibiotic resistance","status":"public","page":"2669 - 2684","article_processing_charge":"No","article_type":"original"},{"isi":1,"pmid":1,"doi":"10.1002/jez.b.22824","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://onlinelibrary.wiley.com/doi/am-pdf/10.1002/jez.b.22824"}],"oa_version":"Submitted Version","day":"11","language":[{"iso":"eng"}],"_id":"190","oa":1,"abstract":[{"lang":"eng","text":"The German cockroach, Blattella germanica, is a worldwide pest that infests buildings, including homes, restaurants, and hospitals, often living in unsanitary conditions. As a disease vector and producer of allergens, this species has major health and economic impacts on humans. Factors contributing to the success of the German cockroach include its resistance to a broad range of insecticides, immunity to many pathogens, and its ability, as an extreme generalist omnivore, to survive on most food sources. The recently published genome shows that B. germanica has an exceptionally high number of protein coding genes. In this study, we investigate the functions of the 93 significantly expanded gene families with the aim to better understand the success of B. germanica as a major pest despite such inhospitable conditions. We find major expansions in gene families with functions related to the detoxification of insecticides and allelochemicals, defense against pathogens, digestion, sensory perception, and gene regulation. These expansions might have allowed B. germanica to develop multiple resistance mechanisms to insecticides and pathogens, and enabled a broad, flexible diet, thus explaining its success in unsanitary conditions and under recurrent chemical control. The findings and resources presented here provide insights for better understanding molecular mechanisms that will facilitate more effective cockroach control."}],"status":"public","department":[{"_id":"BeVi"}],"date_created":"2018-12-11T11:45:06Z","title":"Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest","publist_id":"7730","article_processing_charge":"No","article_type":"original","page":"254-264","month":"07","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","scopus_import":"1","year":"2018","type":"journal_article","external_id":{"pmid":["29998472"],"isi":["000443231000002"]},"date_updated":"2023-09-11T13:59:54Z","citation":{"ista":"Harrison M, Arning N, Kremer L, Ylla G, Belles X, Bornberg Bauer E, Huylmans AK, Jongepier E, Puilachs M, Richards S, Schal C. 2018. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution. 330, 254–264.","ieee":"M. Harrison <i>et al.</i>, “Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest,” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330. Wiley, pp. 254–264, 2018.","chicago":"Harrison, Mark, Nicolas Arning, Lucas Kremer, Guillem Ylla, Xavier Belles, Erich Bornberg Bauer, Ann K Huylmans, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley, 2018. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>.","ama":"Harrison M, Arning N, Kremer L, et al. Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. 2018;330:254-264. doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>","mla":"Harrison, Mark, et al. “Expansions of Key Protein Families in the German Cockroach Highlight the Molecular Basis of Its Remarkable Success as a Global Indoor Pest.” <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>, vol. 330, Wiley, 2018, pp. 254–64, doi:<a href=\"https://doi.org/10.1002/jez.b.22824\">10.1002/jez.b.22824</a>.","short":"M. Harrison, N. Arning, L. Kremer, G. Ylla, X. Belles, E. Bornberg Bauer, A.K. Huylmans, E. Jongepier, M. Puilachs, S. Richards, C. Schal, Journal of Experimental Zoology Part B: Molecular and Developmental Evolution 330 (2018) 254–264.","apa":"Harrison, M., Arning, N., Kremer, L., Ylla, G., Belles, X., Bornberg Bauer, E., … Schal, C. (2018). Expansions of key protein families in the German cockroach highlight the molecular basis of its remarkable success as a global indoor pest. <i>Journal of Experimental Zoology Part B: Molecular and Developmental Evolution</i>. Wiley. <a href=\"https://doi.org/10.1002/jez.b.22824\">https://doi.org/10.1002/jez.b.22824</a>"},"publisher":"Wiley","publication":"Journal of Experimental Zoology Part B: Molecular and Developmental Evolution","intvolume":"       330","volume":330,"author":[{"last_name":"Harrison","full_name":"Harrison, Mark","first_name":"Mark"},{"full_name":"Arning, Nicolas","last_name":"Arning","first_name":"Nicolas"},{"last_name":"Kremer","full_name":"Kremer, Lucas","first_name":"Lucas"},{"full_name":"Ylla, Guillem","last_name":"Ylla","first_name":"Guillem"},{"first_name":"Xavier","last_name":"Belles","full_name":"Belles, Xavier"},{"last_name":"Bornberg Bauer","full_name":"Bornberg Bauer, Erich","first_name":"Erich"},{"last_name":"Huylmans","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961","first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Jongepier, Evelien","last_name":"Jongepier","first_name":"Evelien"},{"first_name":"Maria","last_name":"Puilachs","full_name":"Puilachs, Maria"},{"first_name":"Stephen","last_name":"Richards","full_name":"Richards, Stephen"},{"first_name":"Coby","last_name":"Schal","full_name":"Schal, Coby"}],"date_published":"2018-07-11T00:00:00Z"},{"date_published":"2018-06-25T00:00:00Z","intvolume":"         4","volume":4,"author":[{"orcid":"0000-0002-9767-8699","full_name":"Fendrych, Matyas","last_name":"Fendrych","id":"43905548-F248-11E8-B48F-1D18A9856A87","first_name":"Matyas"},{"last_name":"Akhmanova","full_name":"Akhmanova, Maria","orcid":"0000-0003-1522-3162","first_name":"Maria","id":"3425EC26-F248-11E8-B48F-1D18A9856A87"},{"id":"4515C308-F248-11E8-B48F-1D18A9856A87","first_name":"Jack","orcid":"0000-0001-5145-4609","full_name":"Merrin, Jack","last_name":"Merrin"},{"last_name":"Glanc","full_name":"Glanc, Matous","first_name":"Matous"},{"full_name":"Hagihara, Shinya","last_name":"Hagihara","first_name":"Shinya"},{"full_name":"Takahashi, Koji","last_name":"Takahashi","first_name":"Koji"},{"first_name":"Naoyuki","last_name":"Uchida","full_name":"Uchida, Naoyuki"},{"last_name":"Torii","full_name":"Torii, Keiko U","first_name":"Keiko U"},{"orcid":"0000-0002-8302-7596","last_name":"Friml","full_name":"Friml, Jirí","first_name":"Jirí","id":"4159519E-F248-11E8-B48F-1D18A9856A87"}],"related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-mechanism-for-the-plant-hormone-auxin-discovered/","relation":"press_release","description":"News on IST Homepage"}]},"publication":"Nature Plants","publisher":"Springer Nature","year":"2018","type":"journal_article","external_id":{"isi":["000443221200017"],"pmid":["29942048"]},"citation":{"short":"M. Fendrych, M. Akhmanova, J. Merrin, M. Glanc, S. Hagihara, K. Takahashi, N. Uchida, K.U. Torii, J. Friml, Nature Plants 4 (2018) 453–459.","apa":"Fendrych, M., Akhmanova, M., Merrin, J., Glanc, M., Hagihara, S., Takahashi, K., … Friml, J. (2018). Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>","chicago":"Fendrych, Matyas, Maria Akhmanova, Jack Merrin, Matous Glanc, Shinya Hagihara, Koji Takahashi, Naoyuki Uchida, Keiko U Torii, and Jiří Friml. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41477-018-0190-1\">https://doi.org/10.1038/s41477-018-0190-1</a>.","ista":"Fendrych M, Akhmanova M, Merrin J, Glanc M, Hagihara S, Takahashi K, Uchida N, Torii KU, Friml J. 2018. Rapid and reversible root growth inhibition by TIR1 auxin signalling. Nature Plants. 4(7), 453–459.","ieee":"M. Fendrych <i>et al.</i>, “Rapid and reversible root growth inhibition by TIR1 auxin signalling,” <i>Nature Plants</i>, vol. 4, no. 7. Springer Nature, pp. 453–459, 2018.","mla":"Fendrych, Matyas, et al. “Rapid and Reversible Root Growth Inhibition by TIR1 Auxin Signalling.” <i>Nature Plants</i>, vol. 4, no. 7, Springer Nature, 2018, pp. 453–59, doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>.","ama":"Fendrych M, Akhmanova M, Merrin J, et al. Rapid and reversible root growth inhibition by TIR1 auxin signalling. <i>Nature Plants</i>. 2018;4(7):453-459. doi:<a href=\"https://doi.org/10.1038/s41477-018-0190-1\">10.1038/s41477-018-0190-1</a>"},"date_updated":"2023-09-15T12:11:03Z","scopus_import":"1","month":"06","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","page":"453 - 459","article_processing_charge":"No","article_type":"original","date_created":"2018-12-11T11:45:07Z","status":"public","title":"Rapid and reversible root growth inhibition by TIR1 auxin signalling","department":[{"_id":"JiFr"},{"_id":"DaSi"},{"_id":"NanoFab"}],"publist_id":"7728","issue":"7","abstract":[{"lang":"eng","text":"The phytohormone auxin is the information carrier in a plethora of developmental and physiological processes in plants(1). It has been firmly established that canonical, nuclear auxin signalling acts through regulation of gene transcription(2). Here, we combined microfluidics, live imaging, genetic engineering and computational modelling to reanalyse the classical case of root growth inhibition(3) by auxin. We show that Arabidopsis roots react to addition and removal of auxin by extremely rapid adaptation of growth rate. This process requires intracellular auxin perception but not transcriptional reprogramming. The formation of the canonical TIR1/AFB-Aux/IAA co-receptor complex is required for the growth regulation, hinting to a novel, non-transcriptional branch of this signalling pathway. Our results challenge the current understanding of root growth regulation by auxin and suggest another, presumably non-transcriptional, signalling output of the canonical auxin pathway."}],"oa":1,"oa_version":"Submitted Version","day":"25","language":[{"iso":"eng"}],"_id":"192","doi":"10.1038/s41477-018-0190-1","publication_status":"published","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pubmed/29942048","open_access":"1"}],"isi":1,"pmid":1},{"publisher":"ACM","year":"2018","type":"conference","date_updated":"2024-11-04T13:52:29Z","external_id":{"isi":["000516620100005"]},"citation":{"chicago":"Alwen, Joel F, Peter Gazi, Chethan Kamath Hosdurg, Karen Klein, Georg F Osang, Krzysztof Z Pietrzak, Lenoid Reyzin, Michal Rolinek, and Michal Rybar. “On the Memory Hardness of Data Independent Password Hashing Functions.” In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, 51–65. ACM, 2018. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>.","ista":"Alwen JF, Gazi P, Kamath Hosdurg C, Klein K, Osang GF, Pietrzak KZ, Reyzin L, Rolinek M, Rybar M. 2018. On the memory hardness of data independent password hashing functions. Proceedings of the 2018 on Asia Conference on Computer and Communication Security. ASIACCS: Asia Conference on Computer and Communications Security , 51–65.","ieee":"J. F. Alwen <i>et al.</i>, “On the memory hardness of data independent password hashing functions,” in <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, Incheon, Republic of Korea, 2018, pp. 51–65.","mla":"Alwen, Joel F., et al. “On the Memory Hardness of Data Independent Password Hashing Functions.” <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>, ACM, 2018, pp. 51–65, doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>.","ama":"Alwen JF, Gazi P, Kamath Hosdurg C, et al. On the memory hardness of data independent password hashing functions. In: <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i>. ACM; 2018:51-65. doi:<a href=\"https://doi.org/10.1145/3196494.3196534\">10.1145/3196494.3196534</a>","short":"J.F. Alwen, P. Gazi, C. Kamath Hosdurg, K. Klein, G.F. Osang, K.Z. Pietrzak, L. Reyzin, M. Rolinek, M. Rybar, in:, Proceedings of the 2018 on Asia Conference on Computer and Communication Security, ACM, 2018, pp. 51–65.","apa":"Alwen, J. F., Gazi, P., Kamath Hosdurg, C., Klein, K., Osang, G. F., Pietrzak, K. Z., … Rybar, M. (2018). On the memory hardness of data independent password hashing functions. In <i>Proceedings of the 2018 on Asia Conference on Computer and Communication Security</i> (pp. 51–65). Incheon, Republic of Korea: ACM. <a href=\"https://doi.org/10.1145/3196494.3196534\">https://doi.org/10.1145/3196494.3196534</a>"},"acknowledgement":"Leonid Reyzin was supported in part by IST Austria and by US NSF grants 1012910, 1012798, and 1422965; this research was performed while he was visiting IST Austria.","scopus_import":"1","month":"06","quality_controlled":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_published":"2018-06-01T00:00:00Z","author":[{"first_name":"Joel F","id":"2A8DFA8C-F248-11E8-B48F-1D18A9856A87","last_name":"Alwen","full_name":"Alwen, Joel F"},{"last_name":"Gazi","full_name":"Gazi, Peter","first_name":"Peter"},{"id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan","full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg"},{"full_name":"Klein, Karen","last_name":"Klein","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"orcid":"0000-0002-8882-5116","full_name":"Osang, Georg F","last_name":"Osang","id":"464B40D6-F248-11E8-B48F-1D18A9856A87","first_name":"Georg F"},{"id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","first_name":"Krzysztof Z","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"},{"full_name":"Reyzin, Lenoid","last_name":"Reyzin","first_name":"Lenoid"},{"last_name":"Rolinek","full_name":"Rolinek, Michal","first_name":"Michal","id":"3CB3BC06-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Rybar, Michal","last_name":"Rybar","id":"2B3E3DE8-F248-11E8-B48F-1D18A9856A87","first_name":"Michal"}],"project":[{"_id":"25FBA906-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Discrete Optimization in Computer Vision: Theory and Practice","grant_number":"616160"},{"name":"Teaching Old Crypto New Tricks","grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020"}],"publication":"Proceedings of the 2018 on Asia Conference on Computer and Communication Security","oa":1,"abstract":[{"lang":"eng","text":"We show attacks on five data-independent memory-hard functions (iMHF) that were submitted to the password hashing competition (PHC). Informally, an MHF is a function which cannot be evaluated on dedicated hardware, like ASICs, at significantly lower hardware and/or energy cost than evaluating a single instance on a standard single-core architecture. Data-independent means the memory access pattern of the function is independent of the input; this makes iMHFs harder to construct than data-dependent ones, but the latter can be attacked by various side-channel attacks. Following [Alwen-Blocki'16], we capture the evaluation of an iMHF as a directed acyclic graph (DAG). The cumulative parallel pebbling complexity of this DAG is a measure for the hardware cost of evaluating the iMHF on an ASIC. Ideally, one would like the complexity of a DAG underlying an iMHF to be as close to quadratic in the number of nodes of the graph as possible. Instead, we show that (the DAGs underlying) the following iMHFs are far from this bound: Rig.v2, TwoCats and Gambit each having an exponent no more than 1.75. Moreover, we show that the complexity of the iMHF modes of the PHC finalists Pomelo and Lyra2 have exponents at most 1.83 and 1.67 respectively. To show this we investigate a combinatorial property of each underlying DAG (called its depth-robustness. By establishing upper bounds on this property we are then able to apply the general technique of [Alwen-Block'16] for analyzing the hardware costs of an iMHF."}],"oa_version":"Submitted Version","language":[{"iso":"eng"}],"day":"01","_id":"193","doi":"10.1145/3196494.3196534","main_file_link":[{"url":"https://eprint.iacr.org/2016/783","open_access":"1"}],"publication_status":"published","isi":1,"page":"51 - 65","article_processing_charge":"No","date_created":"2018-12-11T11:45:07Z","conference":{"name":"ASIACCS: Asia Conference on Computer and Communications Security ","location":"Incheon, Republic of Korea","start_date":"2018-06-04","end_date":"2018-06-08"},"title":"On the memory hardness of data independent password hashing functions","status":"public","department":[{"_id":"KrPi"},{"_id":"HeEd"},{"_id":"VlKo"}],"publist_id":"7723","ec_funded":1},{"type":"journal_article","year":"2018","external_id":{"isi":["000449359700035"],"pmid":["29939785"]},"date_updated":"2026-06-18T18:15:11Z","citation":{"chicago":"Liutkeviciute, Zita, Esther Gil Mansilla, Thomas Eder, Barbara E Casillas Perez, Maria Giulia Di Giglio, Edin Muratspahić, Florian Grebien, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” <i>The FASEB Journal</i>. FASEB, 2018. <a href=\"https://doi.org/10.1096/fj.201800443\">https://doi.org/10.1096/fj.201800443</a>.","ieee":"Z. Liutkeviciute <i>et al.</i>, “Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity,” <i>The FASEB Journal</i>, vol. 32, no. 12. FASEB, pp. 6808–6821, 2018.","ista":"Liutkeviciute Z, Gil Mansilla E, Eder T, Casillas Perez BE, Giulia Di Giglio M, Muratspahić E, Grebien F, Rattei T, Muttenthaler M, Cremer S, Gruber C. 2018. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. The FASEB Journal. 32(12), 6808–6821.","mla":"Liutkeviciute, Zita, et al. “Oxytocin-like Signaling in Ants Influences Metabolic Gene Expression and Locomotor Activity.” <i>The FASEB Journal</i>, vol. 32, no. 12, FASEB, 2018, pp. 6808–21, doi:<a href=\"https://doi.org/10.1096/fj.201800443\">10.1096/fj.201800443</a>.","ama":"Liutkeviciute Z, Gil Mansilla E, Eder T, et al. Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. <i>The FASEB Journal</i>. 2018;32(12):6808-6821. doi:<a href=\"https://doi.org/10.1096/fj.201800443\">10.1096/fj.201800443</a>","short":"Z. Liutkeviciute, E. Gil Mansilla, T. Eder, B.E. Casillas Perez, M. Giulia Di Giglio, E. Muratspahić, F. Grebien, T. Rattei, M. Muttenthaler, S. Cremer, C. Gruber, The FASEB Journal 32 (2018) 6808–6821.","apa":"Liutkeviciute, Z., Gil Mansilla, E., Eder, T., Casillas Perez, B. E., Giulia Di Giglio, M., Muratspahić, E., … Gruber, C. (2018). Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity. <i>The FASEB Journal</i>. FASEB. <a href=\"https://doi.org/10.1096/fj.201800443\">https://doi.org/10.1096/fj.201800443</a>"},"publisher":"FASEB","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","month":"11","scopus_import":"1","volume":32,"intvolume":"        32","author":[{"first_name":"Zita","last_name":"Liutkeviciute","full_name":"Liutkeviciute, Zita"},{"first_name":"Esther","last_name":"Gil Mansilla","full_name":"Gil Mansilla, Esther"},{"first_name":"Thomas","full_name":"Eder, Thomas","last_name":"Eder"},{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez"},{"first_name":"Maria","full_name":"Giulia Di Giglio, Maria","last_name":"Giulia Di Giglio"},{"first_name":"Edin","last_name":"Muratspahić","full_name":"Muratspahić, Edin"},{"last_name":"Grebien","full_name":"Grebien, Florian","first_name":"Florian"},{"last_name":"Rattei","full_name":"Rattei, Thomas","first_name":"Thomas"},{"first_name":"Markus","last_name":"Muttenthaler","full_name":"Muttenthaler, Markus"},{"orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia"},{"full_name":"Gruber, Christian","last_name":"Gruber","first_name":"Christian"}],"date_published":"2018-11-29T00:00:00Z","publication_identifier":{"issn":["0892-6638"]},"publication":"The FASEB Journal","project":[{"_id":"25E3D34E-B435-11E9-9278-68D0E5697425","name":"Individual function and social role of oxytocin-like neuropeptides in ants"}],"day":"29","language":[{"iso":"eng"}],"oa_version":"Published Version","_id":"194","ddc":["570"],"oa":1,"abstract":[{"text":"Ants are emerging model systems to study cellular signaling because distinct castes possess different physiologic phenotypes within the same colony. Here we studied the functionality of inotocin signaling, an insect ortholog of mammalian oxytocin (OT), which was recently discovered in ants. In Lasius ants, we determined that specialization within the colony, seasonal factors, and physiologic conditions down-regulated the expression of the OT-like signaling system. Given this natural variation, we interrogated its function using RNAi knockdowns. Next-generation RNA sequencing of OT-like precursor knock-down ants highlighted its role in the regulation of genes involved in metabolism. Knock-down ants exhibited higher walking activity and increased self-grooming in the brood chamber. We propose that OT-like signaling in ants is important for regulating metabolic processes and locomotion.","lang":"eng"}],"pmid":1,"isi":1,"doi":"10.1096/fj.201800443","main_file_link":[{"open_access":"1","url":" https://doi.org/10.1096/fj.201800443"}],"publication_status":"published","article_processing_charge":"No","article_type":"original","page":"6808-6821","issue":"12","publist_id":"7721","department":[{"_id":"SyCr"}],"status":"public","title":"Oxytocin-like signaling in ants influences metabolic gene expression and locomotor activity","date_created":"2018-12-11T11:45:08Z"},{"page":"689-703","article_type":"original","article_processing_charge":"No","date_created":"2025-04-05T10:51:16Z","status":"public","title":"Rational right triangles of a given area","issue":"8","OA_type":"green","abstract":[{"text":"Starting from any given rational-sided, right triangle, for example, the (3,4,5)-triangle with area 6, we use Euclidean geometry to show that there are infinitely many other rational-sided, right triangles of the same area. We show further that the set of all such triangles of a given area is finitely generated under our geometric construction. Such areas are known as “congruent numbers” and have a rich history in which all the results in this article have been proved and far more. Yet, as far as we can tell, this seems to be the first exploration using this kind of geometric technique.","lang":"eng"}],"oa":1,"_id":"19494","oa_version":"Preprint","language":[{"iso":"eng"}],"day":"28","OA_place":"repository","publication_status":"published","main_file_link":[{"open_access":"1","url":"https://doi.org/10.48550/arXiv.1706.05919"}],"doi":"10.1080/00029890.2018.1495491","date_published":"2018-09-28T00:00:00Z","author":[{"orcid":"0000-0001-8467-4106","last_name":"Chan","full_name":"Chan, Yik Tung","first_name":"Yik Tung","id":"c4c0afc8-9262-11ed-9231-d8b0bc743af1"}],"intvolume":"       125","volume":125,"publication":"The American Mathematical Monthly","publication_identifier":{"issn":["0002-9890"],"eissn":["1930-0972"]},"arxiv":1,"publisher":"Taylor & Francis","external_id":{"arxiv":["1706.05919"]},"date_updated":"2025-07-10T11:51:49Z","citation":{"short":"S. Chan, The American Mathematical Monthly 125 (2018) 689–703.","apa":"Chan, S. (2018). Rational right triangles of a given area. <i>The American Mathematical Monthly</i>. Taylor &#38; Francis. <a href=\"https://doi.org/10.1080/00029890.2018.1495491\">https://doi.org/10.1080/00029890.2018.1495491</a>","ieee":"S. Chan, “Rational right triangles of a given area,” <i>The American Mathematical Monthly</i>, vol. 125, no. 8. Taylor &#38; Francis, pp. 689–703, 2018.","ista":"Chan S. 2018. Rational right triangles of a given area. The American Mathematical Monthly. 125(8), 689–703.","chicago":"Chan, Stephanie. “Rational Right Triangles of a given Area.” <i>The American Mathematical Monthly</i>. Taylor &#38; Francis, 2018. <a href=\"https://doi.org/10.1080/00029890.2018.1495491\">https://doi.org/10.1080/00029890.2018.1495491</a>.","ama":"Chan S. Rational right triangles of a given area. <i>The American Mathematical Monthly</i>. 2018;125(8):689-703. doi:<a href=\"https://doi.org/10.1080/00029890.2018.1495491\">10.1080/00029890.2018.1495491</a>","mla":"Chan, Stephanie. “Rational Right Triangles of a given Area.” <i>The American Mathematical Monthly</i>, vol. 125, no. 8, Taylor &#38; Francis, 2018, pp. 689–703, doi:<a href=\"https://doi.org/10.1080/00029890.2018.1495491\">10.1080/00029890.2018.1495491</a>."},"year":"2018","type":"journal_article","scopus_import":"1","extern":"1","month":"09","quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"},{"issue":"4","date_created":"2018-12-11T11:45:08Z","department":[{"_id":"MiLe"}],"status":"public","title":"Anyonic statistics of quantum impurities in two dimensions","corr_author":"1","ec_funded":1,"article_number":"045402","article_processing_charge":"No","doi":"10.1103/PhysRevB.98.045402","main_file_link":[{"url":"https://arxiv.org/abs/1712.00308","open_access":"1"}],"publication_status":"published","isi":1,"abstract":[{"text":"We demonstrate that identical impurities immersed in a two-dimensional many-particle bath can be viewed as flux-tube-charged-particle composites described by fractional statistics. In particular, we find that the bath manifests itself as an external magnetic flux tube with respect to the impurities, and hence the time-reversal symmetry is broken for the effective Hamiltonian describing the impurities. The emerging flux tube acts as a statistical gauge field after a certain critical coupling. This critical coupling corresponds to the intersection point between the quasiparticle state and the phonon wing, where the angular momentum is transferred from the impurity to the bath. This amounts to a novel configuration with emerging anyons. The proposed setup paves the way to realizing anyons using electrons interacting with superfluid helium or lattice phonons, as well as using atomic impurities in ultracold gases.","lang":"eng"}],"oa":1,"language":[{"iso":"eng"}],"day":"15","oa_version":"Submitted Version","_id":"195","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"26031614-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Quantum rotations in the presence of a many-body environment","grant_number":"P29902"}],"publication":"Physical Review B - Condensed Matter and Materials Physics","date_published":"2018-07-15T00:00:00Z","volume":98,"intvolume":"        98","author":[{"first_name":"Enderalp","id":"38CB71F6-F248-11E8-B48F-1D18A9856A87","last_name":"Yakaboylu","full_name":"Yakaboylu, Enderalp","orcid":"0000-0001-5973-0874"},{"first_name":"Mikhail","id":"37CB05FA-F248-11E8-B48F-1D18A9856A87","last_name":"Lemeshko","full_name":"Lemeshko, Mikhail","orcid":"0000-0002-6990-7802"}],"scopus_import":"1","user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","quality_controlled":"1","month":"07","publisher":"American Physical Society","arxiv":1,"type":"journal_article","year":"2018","citation":{"ama":"Yakaboylu E, Lemeshko M. Anyonic statistics of quantum impurities in two dimensions. <i>Physical Review B - Condensed Matter and Materials Physics</i>. 2018;98(4). doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">10.1103/PhysRevB.98.045402</a>","mla":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 98, no. 4, 045402, American Physical Society, 2018, doi:<a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">10.1103/PhysRevB.98.045402</a>.","ista":"Yakaboylu E, Lemeshko M. 2018. Anyonic statistics of quantum impurities in two dimensions. Physical Review B - Condensed Matter and Materials Physics. 98(4), 045402.","ieee":"E. Yakaboylu and M. Lemeshko, “Anyonic statistics of quantum impurities in two dimensions,” <i>Physical Review B - Condensed Matter and Materials Physics</i>, vol. 98, no. 4. American Physical Society, 2018.","chicago":"Yakaboylu, Enderalp, and Mikhail Lemeshko. “Anyonic Statistics of Quantum Impurities in Two Dimensions.” <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society, 2018. <a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">https://doi.org/10.1103/PhysRevB.98.045402</a>.","apa":"Yakaboylu, E., &#38; Lemeshko, M. (2018). Anyonic statistics of quantum impurities in two dimensions. <i>Physical Review B - Condensed Matter and Materials Physics</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevB.98.045402\">https://doi.org/10.1103/PhysRevB.98.045402</a>","short":"E. Yakaboylu, M. Lemeshko, Physical Review B - Condensed Matter and Materials Physics 98 (2018)."},"external_id":{"arxiv":["1712.00308"],"isi":["000436939100007"]},"date_updated":"2025-04-15T06:50:28Z"},{"year":"2018","type":"journal_article","external_id":{"pmid":["30455989 "]},"date_updated":"2025-07-10T11:51:52Z","citation":{"ama":"Bulatov E, Sayarova R, Mingaleeva R, et al. Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors. <i>Cell Death Discovery</i>. 2018;4. doi:<a href=\"https://doi.org/10.1038/s41420-018-0120-z\">10.1038/s41420-018-0120-z</a>","mla":"Bulatov, Emil, et al. “Isatin-Schiff Base-Copper (II) Complex Induces Cell Death in P53-Positive Tumors.” <i>Cell Death Discovery</i>, vol. 4, 103, Springer Nature, 2018, doi:<a href=\"https://doi.org/10.1038/s41420-018-0120-z\">10.1038/s41420-018-0120-z</a>.","ista":"Bulatov E, Sayarova R, Mingaleeva R, Miftakhova R, Gomzikova M, Ignatev I, Petukhov A, Davidovich P, Rizvanov A, Barlev NA. 2018. Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors. Cell Death Discovery. 4, 103.","ieee":"E. Bulatov <i>et al.</i>, “Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors,” <i>Cell Death Discovery</i>, vol. 4. Springer Nature, 2018.","chicago":"Bulatov, Emil, Regina Sayarova, Rimma Mingaleeva, Regina Miftakhova, Marina Gomzikova, Iurii Ignatev, Alexey Petukhov, Pavel Davidovich, Albert Rizvanov, and Nickolai A. Barlev. “Isatin-Schiff Base-Copper (II) Complex Induces Cell Death in P53-Positive Tumors.” <i>Cell Death Discovery</i>. Springer Nature, 2018. <a href=\"https://doi.org/10.1038/s41420-018-0120-z\">https://doi.org/10.1038/s41420-018-0120-z</a>.","apa":"Bulatov, E., Sayarova, R., Mingaleeva, R., Miftakhova, R., Gomzikova, M., Ignatev, I., … Barlev, N. A. (2018). Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors. <i>Cell Death Discovery</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41420-018-0120-z\">https://doi.org/10.1038/s41420-018-0120-z</a>","short":"E. Bulatov, R. Sayarova, R. Mingaleeva, R. Miftakhova, M. Gomzikova, I. Ignatev, A. Petukhov, P. Davidovich, A. Rizvanov, N.A. Barlev, Cell Death Discovery 4 (2018)."},"publisher":"Springer Nature","month":"11","quality_controlled":"1","DOAJ_listed":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","extern":"1","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"intvolume":"         4","volume":4,"author":[{"first_name":"Emil","last_name":"Bulatov","full_name":"Bulatov, Emil"},{"first_name":"Regina","last_name":"Sayarova","full_name":"Sayarova, Regina"},{"first_name":"Rimma","full_name":"Mingaleeva, Rimma","last_name":"Mingaleeva"},{"first_name":"Regina","full_name":"Miftakhova, Regina","last_name":"Miftakhova"},{"last_name":"Gomzikova","full_name":"Gomzikova, Marina","first_name":"Marina"},{"full_name":"Ignatev, Iurii","last_name":"Ignatev","id":"2ac71786-dc7d-11ea-9b2f-c5ad4b9faff6","first_name":"Iurii"},{"first_name":"Alexey","last_name":"Petukhov","full_name":"Petukhov, Alexey"},{"first_name":"Pavel","full_name":"Davidovich, Pavel","last_name":"Davidovich"},{"first_name":"Albert","last_name":"Rizvanov","full_name":"Rizvanov, Albert"},{"last_name":"Barlev","full_name":"Barlev, Nickolai A.","first_name":"Nickolai A."}],"date_published":"2018-11-13T00:00:00Z","publication_identifier":{"issn":["2058-7716"]},"has_accepted_license":"1","publication":"Cell Death Discovery","oa_version":"Published Version","language":[{"iso":"eng"}],"day":"13","OA_place":"publisher","_id":"19544","ddc":["570"],"oa":1,"abstract":[{"lang":"eng","text":"Medicinal bioinorganic chemistry is a thriving field of drug research for cancer treatment. Transition metal complexes coordinated to essential biological scaffolds represent a highly promising class of compounds for design of novel target-specific therapeutics. We report here the biological evaluation of a novel Isatin-Schiff base derivative and its Cu(II) complex in several tumor cell lines by assessing their effects on cellular metabolism, real-time cell proliferation and induction of apoptosis. Further, the impact of compounds on the p53 protein and expression of its target genes, including MDM2, p21/CDKN1A, and PUMA was evaluated. Results obtained in this study provide further evidence in support of our prior data suggesting the p53-mediated mechanism of action for Isatin-Schiff base derivatives and their complexes and also shed light on potential use of these compounds for stimulation of apoptosis in breast cancer cells via activation of the pro-apoptotic PUMA gene."}],"OA_type":"gold","pmid":1,"doi":"10.1038/s41420-018-0120-z","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1038/s41420-018-0120-z"}],"publication_status":"published","article_number":"103","article_processing_charge":"Yes","article_type":"original","date_created":"2025-04-11T01:31:42Z","status":"public","title":"Isatin-Schiff base-copper (II) complex induces cell death in p53-positive tumors","department":[{"_id":"GradSch"},{"_id":"LoSw"}]},{"ec_funded":1,"corr_author":"1","publist_id":"7718","date_created":"2018-12-11T11:45:09Z","status":"public","department":[{"_id":"ChLa"}],"title":"Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images","article_processing_charge":"No","page":"113","supervisor":[{"first_name":"Christoph","id":"40C20FD2-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-8622-7887","last_name":"Lampert","full_name":"Lampert, Christoph"}],"publication_status":"published","doi":"10.15479/AT:ISTA:th_1021","_id":"197","ddc":["004"],"OA_place":"publisher","day":"25","language":[{"iso":"eng"}],"oa_version":"Published Version","abstract":[{"lang":"eng","text":"Modern computer vision systems heavily rely on statistical machine learning models, which typically require large amounts of labeled data to be learned reliably. Moreover, very recently computer vision research widely adopted techniques for representation learning, which further increase the demand for labeled data. However, for many important practical problems there is relatively small amount of labeled data available, so it is problematic to leverage full potential of the representation learning methods. One way to overcome this obstacle is to invest substantial resources into producing large labelled datasets. Unfortunately, this can be prohibitively expensive in practice. In this thesis we focus on the alternative way of tackling the aforementioned issue. We concentrate on methods, which make use of weakly-labeled or even unlabeled data. Specifically, the first half of the thesis is dedicated to the semantic image segmentation task. We develop a technique, which achieves competitive segmentation performance and only requires annotations in a form of global image-level labels instead of dense segmentation masks. Subsequently, we present a new methodology, which further improves segmentation performance by leveraging tiny additional feedback from a human annotator. By using our methods practitioners can greatly reduce the amount of data annotation effort, which is required to learn modern image segmentation models. In the second half of the thesis we focus on methods for learning from unlabeled visual data. We study a family of autoregressive models for modeling structure of natural images and discuss potential applications of these models. Moreover, we conduct in-depth study of one of these applications, where we develop the state-of-the-art model for the probabilistic image colorization task."}],"oa":1,"has_accepted_license":"1","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","project":[{"_id":"2532554C-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"308036","name":"Lifelong Learning of Visual Scene Understanding"}],"author":[{"id":"2D157DB6-F248-11E8-B48F-1D18A9856A87","first_name":"Alexander","full_name":"Kolesnikov, Alexander","last_name":"Kolesnikov"}],"file_date_updated":"2020-07-14T12:45:22Z","date_published":"2018-05-25T00:00:00Z","file":[{"date_updated":"2020-07-14T12:45:22Z","content_type":"application/pdf","creator":"system","checksum":"bc678e02468d8ebc39dc7267dfb0a1c4","relation":"main_file","file_size":12918758,"file_name":"IST-2018-1021-v1+1_thesis-unsigned-pdfa.pdf","file_id":"5113","date_created":"2018-12-12T10:14:57Z","access_level":"open_access"},{"content_type":"application/zip","creator":"dernst","date_updated":"2020-07-14T12:45:22Z","file_id":"6225","date_created":"2019-04-05T09:34:49Z","access_level":"closed","file_name":"2018_Thesis_Kolesnikov_source.zip","file_size":55973760,"checksum":"bc66973b086da5a043f1162dcfb1fde4","relation":"source_file"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","month":"05","acknowledgement":"I also gratefully acknowledge the support of NVIDIA Corporation with the donation of the GPUs used for this research.","citation":{"short":"A. Kolesnikov, Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images, Institute of Science and Technology Austria, 2018.","apa":"Kolesnikov, A. (2018). <i>Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">https://doi.org/10.15479/AT:ISTA:th_1021</a>","chicago":"Kolesnikov, Alexander. “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images.” Institute of Science and Technology Austria, 2018. <a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">https://doi.org/10.15479/AT:ISTA:th_1021</a>.","ista":"Kolesnikov A. 2018. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. Institute of Science and Technology Austria.","ieee":"A. Kolesnikov, “Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images,” Institute of Science and Technology Austria, 2018.","mla":"Kolesnikov, Alexander. <i>Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images</i>. Institute of Science and Technology Austria, 2018, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">10.15479/AT:ISTA:th_1021</a>.","ama":"Kolesnikov A. Weakly-Supervised Segmentation and Unsupervised Modeling of Natural Images. 2018. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:th_1021\">10.15479/AT:ISTA:th_1021</a>"},"date_updated":"2026-04-08T14:05:16Z","pubrep_id":"1021","type":"dissertation","year":"2018","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria"},{"publisher":"MDPI","citation":{"chicago":"Mosienko, Valentina, Seyed Rasooli-Nejad, Kasumi Kishi, Matt De Both, David Jane, Matt J. Huentelman, Sergey Kasparov, and Anja G. Teschemacher. “Putative Receptors Underpinning L-Lactate Signalling in Locus Coeruleus.” <i>Neuroglia</i>. MDPI, 2018. <a href=\"https://doi.org/10.3390/neuroglia1020025\">https://doi.org/10.3390/neuroglia1020025</a>.","ieee":"V. Mosienko <i>et al.</i>, “Putative receptors underpinning L-Lactate signalling in locus coeruleus,” <i>Neuroglia</i>, vol. 1, no. 2. MDPI, pp. 365–380, 2018.","ista":"Mosienko V, Rasooli-Nejad S, Kishi K, De Both M, Jane D, Huentelman MJ, Kasparov S, Teschemacher AG. 2018. Putative receptors underpinning L-Lactate signalling in locus coeruleus. Neuroglia. 1(2), 365–380.","mla":"Mosienko, Valentina, et al. “Putative Receptors Underpinning L-Lactate Signalling in Locus Coeruleus.” <i>Neuroglia</i>, vol. 1, no. 2, MDPI, 2018, pp. 365–80, doi:<a href=\"https://doi.org/10.3390/neuroglia1020025\">10.3390/neuroglia1020025</a>.","ama":"Mosienko V, Rasooli-Nejad S, Kishi K, et al. Putative receptors underpinning L-Lactate signalling in locus coeruleus. <i>Neuroglia</i>. 2018;1(2):365-380. doi:<a href=\"https://doi.org/10.3390/neuroglia1020025\">10.3390/neuroglia1020025</a>","short":"V. Mosienko, S. Rasooli-Nejad, K. Kishi, M. De Both, D. Jane, M.J. Huentelman, S. Kasparov, A.G. Teschemacher, Neuroglia 1 (2018) 365–380.","apa":"Mosienko, V., Rasooli-Nejad, S., Kishi, K., De Both, M., Jane, D., Huentelman, M. J., … Teschemacher, A. G. (2018). Putative receptors underpinning L-Lactate signalling in locus coeruleus. <i>Neuroglia</i>. MDPI. <a href=\"https://doi.org/10.3390/neuroglia1020025\">https://doi.org/10.3390/neuroglia1020025</a>"},"date_updated":"2025-05-19T08:28:40Z","type":"journal_article","year":"2018","scopus_import":"1","acknowledgement":"This work was supported by grants from BBSRC BB/L019396/1, and MRC MR/L020661/1. David Kleinfeld for his gift of CNiFER cells, Lesley Arberry for expert technical support, Andrew Herman for support with FACS sorting.","tmp":{"image":"/images/cc_by.png","short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"quality_controlled":"1","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","DOAJ_listed":"1","month":"12","date_published":"2018-12-01T00:00:00Z","file":[{"creator":"dernst","content_type":"application/pdf","success":1,"date_updated":"2025-05-19T08:20:19Z","file_size":1909402,"relation":"main_file","checksum":"cadb56618f72edf4703b6a9855e84baa","access_level":"open_access","file_id":"19711","date_created":"2025-05-19T08:20:19Z","file_name":"2018_Neuroglia_Mosienko.pdf"}],"author":[{"first_name":"Valentina","last_name":"Mosienko","full_name":"Mosienko, Valentina"},{"last_name":"Rasooli-Nejad","full_name":"Rasooli-Nejad, Seyed","first_name":"Seyed"},{"id":"3065DFC4-F248-11E8-B48F-1D18A9856A87","first_name":"Kasumi","full_name":"Kishi, Kasumi","last_name":"Kishi"},{"full_name":"De Both, Matt","last_name":"De Both","first_name":"Matt"},{"first_name":"David","full_name":"Jane, David","last_name":"Jane"},{"full_name":"Huentelman, Matt J.","last_name":"Huentelman","first_name":"Matt J."},{"first_name":"Sergey","full_name":"Kasparov, Sergey","last_name":"Kasparov"},{"first_name":"Anja G.","full_name":"Teschemacher, Anja G.","last_name":"Teschemacher"}],"volume":1,"file_date_updated":"2025-05-19T08:20:19Z","intvolume":"         1","publication":"Neuroglia","has_accepted_license":"1","publication_identifier":{"eissn":["2571-6980"]},"OA_type":"gold","oa":1,"abstract":[{"lang":"eng","text":"The importance of astrocytic l-lactate (LL) for normal functioning of neural circuits such as those regulating learning/memory, sleep/wake state, autonomic homeostasis, or emotional behaviour is being increasingly recognised. l-Lactate can act on neurones as a metabolic or redox substrate, but transmembrane receptor targets are also emerging. A comparative review of the hydroxy-carboxylic acid receptor (HCA1, formerly known as GPR81), Olfactory Receptor Family 51 Subfamily E Member 2 (OR51E2), and orphan receptor GPR4 highlights differences in their LL sensitivity, pharmacology, intracellular coupling, and localisation in the brain. In addition, a putative Gs-coupled receptor on noradrenergic neurones, LLRx, which we previously postulated, remains to be identified. Next-generation sequencing revealed several orphan receptors expressed in locus coeruleus neurones. Screening of a selection of these suggests additional LL-sensitive receptors: GPR180 which inhibits and GPR137 which activates intracellular cyclic AMP signalling in response to LL in a heterologous expression system. To further characterise binding of LL at LLRx, we carried out a structure–activity relationship study which demonstrates that carboxyl and 2-hydroxyl moieties of LL are essential for triggering d-lactate-sensitive noradrenaline release in locus coeruleus, and that the size of the LL binding pocket is limited towards the methyl group position. The evidence accumulating to date suggests that LL acts via multiple receptor targets to modulate distinct brain functions."}],"_id":"19706","ddc":["570"],"OA_place":"publisher","language":[{"iso":"eng"}],"day":"01","oa_version":"Published Version","publication_status":"published","doi":"10.3390/neuroglia1020025","page":"365-380","article_type":"original","article_processing_charge":"Yes","issue":"2","department":[{"_id":"AnKi"}],"date_created":"2025-05-18T22:02:51Z","title":"Putative receptors underpinning L-Lactate signalling in locus coeruleus","status":"public"},{"oa_version":"Preprint","language":[{"iso":"eng"}],"day":"01","_id":"435","abstract":[{"lang":"eng","text":"It is shown that two fundamentally different phenomena, the bound states in continuum and the spectral singularity (or time-reversed spectral singularity), can occur simultaneously. This can be achieved in a rectangular core dielectric waveguide with an embedded active (or absorbing) layer. In such a system a two-dimensional bound state in a continuum is created in the plane of a waveguide cross section, and it is emitted or absorbed along the waveguide core. The idea can be used for experimental implementation of a laser or a coherent-perfect-absorber for a photonic bound state that resides in a continuous spectrum."}],"oa":1,"isi":1,"doi":"10.1364/OL.43.000607","main_file_link":[{"url":"https://arxiv.org/abs/1711.01986","open_access":"1"}],"publication_status":"published","article_processing_charge":"No","page":"607 - 610","ec_funded":1,"status":"public","date_created":"2018-12-11T11:46:27Z","title":"Coherent-perfect-absorber and laser for bound states in a continuum","department":[{"_id":"MiLe"}],"publist_id":"7388","issue":"3","corr_author":"1","year":"2018","type":"journal_article","citation":{"short":"B. Midya, V. Konotop, Optics Letters 43 (2018) 607–610.","apa":"Midya, B., &#38; Konotop, V. (2018). Coherent-perfect-absorber and laser for bound states in a continuum. <i>Optics Letters</i>. Optica Publishing Group. <a href=\"https://doi.org/10.1364/OL.43.000607\">https://doi.org/10.1364/OL.43.000607</a>","chicago":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” <i>Optics Letters</i>. Optica Publishing Group, 2018. <a href=\"https://doi.org/10.1364/OL.43.000607\">https://doi.org/10.1364/OL.43.000607</a>.","ieee":"B. Midya and V. Konotop, “Coherent-perfect-absorber and laser for bound states in a continuum,” <i>Optics Letters</i>, vol. 43, no. 3. Optica Publishing Group, pp. 607–610, 2018.","ista":"Midya B, Konotop V. 2018. Coherent-perfect-absorber and laser for bound states in a continuum. Optics Letters. 43(3), 607–610.","mla":"Midya, Bikashkali, and Vladimir Konotop. “Coherent-Perfect-Absorber and Laser for Bound States in a Continuum.” <i>Optics Letters</i>, vol. 43, no. 3, Optica Publishing Group, 2018, pp. 607–10, doi:<a href=\"https://doi.org/10.1364/OL.43.000607\">10.1364/OL.43.000607</a>.","ama":"Midya B, Konotop V. Coherent-perfect-absorber and laser for bound states in a continuum. <i>Optics Letters</i>. 2018;43(3):607-610. doi:<a href=\"https://doi.org/10.1364/OL.43.000607\">10.1364/OL.43.000607</a>"},"date_updated":"2025-06-03T11:21:56Z","external_id":{"arxiv":["1711.01986"],"isi":["000423776600066"]},"arxiv":1,"publisher":"Optica Publishing Group","month":"02","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","quality_controlled":"1","scopus_import":"1","acknowledgement":"Seventh Framework Programme (FP7) People: Marie-Curie Actions (PEOPLE) (291734). B. M. acknowledges the financial support by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/ 2007-2013) under REA.","intvolume":"        43","volume":43,"author":[{"first_name":"Bikashkali","id":"456187FC-F248-11E8-B48F-1D18A9856A87","last_name":"Midya","full_name":"Midya, Bikashkali"},{"last_name":"Konotop","full_name":"Konotop, Vladimir","first_name":"Vladimir"}],"date_published":"2018-02-01T00:00:00Z","publication":"Optics Letters","project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7"}]}]