[{"quality_controlled":"1","day":"01","arxiv":1,"intvolume":"       141","date_published":"2019-11-01T00:00:00Z","citation":{"short":"J. Kühnen, D. Scarselli, B. Hof, Journal of Fluids Engineering 141 (2019).","ama":"Kühnen J, Scarselli D, Hof B. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. <i>Journal of Fluids Engineering</i>. 2019;141(11). doi:<a href=\"https://doi.org/10.1115/1.4043494\">10.1115/1.4043494</a>","ista":"Kühnen J, Scarselli D, Hof B. 2019. Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. Journal of Fluids Engineering. 141(11), 111105.","apa":"Kühnen, J., Scarselli, D., &#38; Hof, B. (2019). Relaminarization of pipe flow by means of 3D-printed shaped honeycombs. <i>Journal of Fluids Engineering</i>. ASME. <a href=\"https://doi.org/10.1115/1.4043494\">https://doi.org/10.1115/1.4043494</a>","ieee":"J. Kühnen, D. Scarselli, and B. Hof, “Relaminarization of pipe flow by means of 3D-printed shaped honeycombs,” <i>Journal of Fluids Engineering</i>, vol. 141, no. 11. ASME, 2019.","chicago":"Kühnen, Jakob, Davide Scarselli, and Björn Hof. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” <i>Journal of Fluids Engineering</i>. ASME, 2019. <a href=\"https://doi.org/10.1115/1.4043494\">https://doi.org/10.1115/1.4043494</a>.","mla":"Kühnen, Jakob, et al. “Relaminarization of Pipe Flow by Means of 3D-Printed Shaped Honeycombs.” <i>Journal of Fluids Engineering</i>, vol. 141, no. 11, 111105, ASME, 2019, doi:<a href=\"https://doi.org/10.1115/1.4043494\">10.1115/1.4043494</a>."},"department":[{"_id":"BjHo"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"ASME","issue":"11","article_processing_charge":"No","publication_identifier":{"issn":["0098-2202"],"eissn":["1528-901X"]},"article_number":"111105","acknowledged_ssus":[{"_id":"M-Shop"}],"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1809.07625","open_access":"1"}],"doi":"10.1115/1.4043494","oa":1,"date_updated":"2026-05-15T22:30:53Z","publication_status":"published","month":"11","author":[{"id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen","first_name":"Jakob","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob"},{"id":"40315C30-F248-11E8-B48F-1D18A9856A87","last_name":"Scarselli","full_name":"Scarselli, Davide","first_name":"Davide","orcid":"0000-0001-5227-4271"},{"full_name":"Hof, Björn","orcid":"0000-0003-2057-2754","first_name":"Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"publication":"Journal of Fluids Engineering","_id":"6486","title":"Relaminarization of pipe flow by means of 3D-printed shaped honeycombs","scopus_import":"1","status":"public","article_type":"original","related_material":{"record":[{"id":"7258","relation":"dissertation_contains","status":"public"}]},"external_id":{"isi":["000487748600005"],"arxiv":["1809.07625"]},"date_created":"2019-05-26T21:59:13Z","oa_version":"Preprint","abstract":[{"text":"Based on a novel control scheme, where a steady modification of the streamwise velocity profile leads to complete relaminarization of initially fully turbulent pipe flow, we investigate the applicability and usefulness of custom-shaped honeycombs for such control. The custom-shaped honeycombs are used as stationary flow management devices which generate specific modifications of the streamwise velocity profile. Stereoscopic particle image velocimetry and pressure drop measurements are used to investigate and capture the development of the relaminarizing flow downstream these devices. We compare the performance of straight (constant length across the radius of the pipe) honeycombs with custom-shaped ones (variable length across the radius) and try to determine the optimal shape for maximal relaminarization at minimal pressure loss. The optimally modified streamwise velocity profile is found to be M-shaped, and the maximum attainable Reynolds number for total relaminarization is found to be of the order of 10,000. Consequently, the respective reduction in skin friction downstream of the device is almost by a factor of 5. The break-even point, where the additional pressure drop caused by the device is balanced by the savings due to relaminarization and a net gain is obtained, corresponds to a downstream stretch of distances as low as approximately 100 pipe diameters of laminar flow.","lang":"eng"}],"ec_funded":1,"isi":1,"project":[{"grant_number":"306589","_id":"25152F3A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin"}],"volume":141,"year":"2019"},{"title":"Relaminarising pipe flow by wall movement","scopus_import":"1","status":"public","language":[{"iso":"eng"}],"publication":"Journal of Fluid Mechanics","_id":"6228","author":[{"orcid":"0000-0001-5227-4271","first_name":"Davide","full_name":"Scarselli, Davide","last_name":"Scarselli","id":"40315C30-F248-11E8-B48F-1D18A9856A87"},{"id":"3A47AE32-F248-11E8-B48F-1D18A9856A87","last_name":"Kühnen","first_name":"Jakob","orcid":"0000-0003-4312-0179","full_name":"Kühnen, Jakob"},{"last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn"}],"month":"05","date_updated":"2026-05-15T22:30:53Z","publication_status":"published","project":[{"grant_number":"306589","call_identifier":"FP7","name":"Decoding the complexity of turbulence at its origin","_id":"25152F3A-B435-11E9-9278-68D0E5697425"},{"_id":"25104D44-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Eliminating turbulence in oil pipelines","grant_number":"737549"}],"volume":867,"isi":1,"year":"2019","page":"934-948","ec_funded":1,"abstract":[{"lang":"eng","text":"Following  the  recent  observation  that  turbulent  pipe  flow  can  be  relaminarised  bya  relatively  simple  modification  of  the  mean  velocity  profile,  we  here  carry  out  aquantitative  experimental  investigation  of  this  phenomenon.  Our  study  confirms  thata  flat  velocity  profile  leads  to  a  collapse  of  turbulence  and  in  order  to  achieve  theblunted  profile  shape,  we  employ  a  moving  pipe  segment  that  is  briefly  and  rapidlyshifted  in  the  streamwise  direction.  The  relaminarisation  threshold  and  the  minimumshift  length  and  speeds  are  determined  as  a  function  of  Reynolds  number.  Althoughturbulence  is  still  active  after  the  acceleration  phase,  the  modulated  profile  possessesa  severely  decreased  lift-up  potential  as  measured  by  transient  growth.  As  shown,this  results  in  an  exponential  decay  of  fluctuations  and  the  flow  relaminarises.  Whilethis  method  can  be  easily  applied  at  low  to  moderate  flow  speeds,  the  minimumstreamwise  length  over  which  the  acceleration  needs  to  act  increases  linearly  with  theReynolds  number."}],"oa_version":"Preprint","external_id":{"arxiv":["1807.05357"],"isi":["000462606100001"]},"date_created":"2019-04-07T21:59:14Z","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"7258"}],"link":[{"relation":"supplementary_material","url":"https://doi.org/10.1017/jfm.2019.191"}]},"article_processing_charge":"No","publication_identifier":{"issn":["0022-1120"],"eissn":["1469-7645"]},"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"BjHo"}],"citation":{"ista":"Scarselli D, Kühnen J, Hof B. 2019. Relaminarising pipe flow by wall movement. Journal of Fluid Mechanics. 867, 934–948.","apa":"Scarselli, D., Kühnen, J., &#38; Hof, B. (2019). Relaminarising pipe flow by wall movement. <i>Journal of Fluid Mechanics</i>. Cambridge University Press. <a href=\"https://doi.org/10.1017/jfm.2019.191\">https://doi.org/10.1017/jfm.2019.191</a>","chicago":"Scarselli, Davide, Jakob Kühnen, and Björn Hof. “Relaminarising Pipe Flow by Wall Movement.” <i>Journal of Fluid Mechanics</i>. Cambridge University Press, 2019. <a href=\"https://doi.org/10.1017/jfm.2019.191\">https://doi.org/10.1017/jfm.2019.191</a>.","ieee":"D. Scarselli, J. Kühnen, and B. Hof, “Relaminarising pipe flow by wall movement,” <i>Journal of Fluid Mechanics</i>, vol. 867. Cambridge University Press, pp. 934–948, 2019.","mla":"Scarselli, Davide, et al. “Relaminarising Pipe Flow by Wall Movement.” <i>Journal of Fluid Mechanics</i>, vol. 867, Cambridge University Press, 2019, pp. 934–48, doi:<a href=\"https://doi.org/10.1017/jfm.2019.191\">10.1017/jfm.2019.191</a>.","short":"D. Scarselli, J. Kühnen, B. Hof, Journal of Fluid Mechanics 867 (2019) 934–948.","ama":"Scarselli D, Kühnen J, Hof B. Relaminarising pipe flow by wall movement. <i>Journal of Fluid Mechanics</i>. 2019;867:934-948. doi:<a href=\"https://doi.org/10.1017/jfm.2019.191\">10.1017/jfm.2019.191</a>"},"publisher":"Cambridge University Press","intvolume":"       867","date_published":"2019-05-25T00:00:00Z","quality_controlled":"1","arxiv":1,"day":"25","doi":"10.1017/jfm.2019.191","oa":1,"type":"journal_article","main_file_link":[{"url":"https://arxiv.org/abs/1807.05357","open_access":"1"}]},{"project":[{"grant_number":"742985","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","call_identifier":"H2020","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"isi":1,"volume":180,"year":"2019","page":"1152-1165","abstract":[{"text":"Polar auxin transport plays a pivotal role in plant growth and development. PIN auxin efflux carriers regulate directional auxin movement by establishing local auxin maxima, minima, and gradients that drive multiple developmental processes and responses to environmental signals. Auxin has been proposed to modulate its own transport by regulating subcellular PIN trafficking via processes such as clathrin-mediated PIN endocytosis and constitutive recycling. Here, we further investigated the mechanisms by which auxin affects PIN trafficking by screening auxin analogs and identified pinstatic acid (PISA) as a positive modulator of polar auxin transport in Arabidopsis thaliana. PISA had an auxin-like effect on hypocotyl elongation and adventitious root formation via positive regulation of auxin transport. PISA did not activate SCFTIR1/AFB signaling and yet induced PIN accumulation at the cell surface by inhibiting PIN internalization from the plasma membrane. This work demonstrates PISA to be a promising chemical tool to dissect the regulatory mechanisms behind subcellular PIN trafficking and auxin transport.","lang":"eng"}],"ec_funded":1,"oa_version":"Published Version","external_id":{"isi":["000470086100045"],"pmid":["30936248"]},"related_material":{"record":[{"relation":"dissertation_contains","id":"11626","status":"public"},{"status":"public","id":"8822","relation":"dissertation_contains"}]},"date_created":"2019-04-09T08:38:20Z","title":"Pinstatic acid promotes auxin transport by inhibiting PIN internalization","scopus_import":"1","status":"public","article_type":"original","publication":"Plant Physiology","language":[{"iso":"eng"}],"_id":"6260","month":"06","author":[{"last_name":"Oochi","full_name":"Oochi, A","first_name":"A"},{"full_name":"Hajny, Jakub","first_name":"Jakub","orcid":"0000-0003-2140-7195","id":"4800CC20-F248-11E8-B48F-1D18A9856A87","last_name":"Hajny"},{"first_name":"K","full_name":"Fukui, K","last_name":"Fukui"},{"last_name":"Nakao","full_name":"Nakao, Y","first_name":"Y"},{"id":"35A03822-F248-11E8-B48F-1D18A9856A87","last_name":"Gallei","first_name":"Michelle C","orcid":"0000-0003-1286-7368","full_name":"Gallei, Michelle C"},{"last_name":"Quareshy","full_name":"Quareshy, M","first_name":"M"},{"last_name":"Takahashi","full_name":"Takahashi, K","first_name":"K"},{"last_name":"Kinoshita","full_name":"Kinoshita, T","first_name":"T"},{"first_name":"SR","full_name":"Harborough, SR","last_name":"Harborough"},{"full_name":"Kepinski, S","first_name":"S","last_name":"Kepinski"},{"first_name":"H","full_name":"Kasahara, H","last_name":"Kasahara"},{"last_name":"Napier","full_name":"Napier, RM","first_name":"RM"},{"first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","last_name":"Friml"},{"first_name":"KI","full_name":"Hayashi, KI","last_name":"Hayashi"}],"date_updated":"2026-05-15T22:30:55Z","publication_status":"published","doi":"10.1104/pp.19.00201","oa":1,"pmid":1,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1104/pp.19.00201"}],"acknowledgement":"We thank Dr. H. Fukaki (University of Kobe), Dr. R. Offringa (Leiden University), Dr. Jianwei Pan (Zhejiang Normal University), and Dr. M. Estelle (University of California at San Diego) for providing mutants and transgenic line seeds.\r\nThis work was supported by the Ministry of Education, Culture, Sports, Science, and Technology (Grant-in-Aid for Scientific Research no. JP25114518 to K.H.), the Biotechnology and Biological Sciences Research Council (award no. BB/L009366/1 to R.N. and S.K.), and the European Union’s Horizon2020 program (European Research Council grant agreement no. 742985 to J.F.).","article_processing_charge":"No","publication_identifier":{"issn":["0032-0889"],"eissn":["1532-2548"]},"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","department":[{"_id":"JiFr"}],"citation":{"ama":"Oochi A, Hajny J, Fukui K, et al. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. <i>Plant Physiology</i>. 2019;180(2):1152-1165. doi:<a href=\"https://doi.org/10.1104/pp.19.00201\">10.1104/pp.19.00201</a>","short":"A. Oochi, J. Hajny, K. Fukui, Y. Nakao, M.C. Gallei, M. Quareshy, K. Takahashi, T. Kinoshita, S. Harborough, S. Kepinski, H. Kasahara, R. Napier, J. Friml, K. Hayashi, Plant Physiology 180 (2019) 1152–1165.","mla":"Oochi, A., et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” <i>Plant Physiology</i>, vol. 180, no. 2, ASPB, 2019, pp. 1152–65, doi:<a href=\"https://doi.org/10.1104/pp.19.00201\">10.1104/pp.19.00201</a>.","ista":"Oochi A, Hajny J, Fukui K, Nakao Y, Gallei MC, Quareshy M, Takahashi K, Kinoshita T, Harborough S, Kepinski S, Kasahara H, Napier R, Friml J, Hayashi K. 2019. Pinstatic acid promotes auxin transport by inhibiting PIN internalization. Plant Physiology. 180(2), 1152–1165.","apa":"Oochi, A., Hajny, J., Fukui, K., Nakao, Y., Gallei, M. C., Quareshy, M., … Hayashi, K. (2019). Pinstatic acid promotes auxin transport by inhibiting PIN internalization. <i>Plant Physiology</i>. ASPB. <a href=\"https://doi.org/10.1104/pp.19.00201\">https://doi.org/10.1104/pp.19.00201</a>","chicago":"Oochi, A, Jakub Hajny, K Fukui, Y Nakao, Michelle C Gallei, M Quareshy, K Takahashi, et al. “Pinstatic Acid Promotes Auxin Transport by Inhibiting PIN Internalization.” <i>Plant Physiology</i>. ASPB, 2019. <a href=\"https://doi.org/10.1104/pp.19.00201\">https://doi.org/10.1104/pp.19.00201</a>.","ieee":"A. Oochi <i>et al.</i>, “Pinstatic acid promotes auxin transport by inhibiting PIN internalization,” <i>Plant Physiology</i>, vol. 180, no. 2. ASPB, pp. 1152–1165, 2019."},"issue":"2","publisher":"ASPB","intvolume":"       180","date_published":"2019-06-01T00:00:00Z","quality_controlled":"1","day":"01"},{"language":[{"iso":"eng"}],"_id":"6435","title":"Collective defenses of garden ants against a fungal pathogen","status":"public","file":[{"access_level":"open_access","content_type":"application/pdf","embargo":"2020-05-08","relation":"main_file","file_name":"tesisDoctoradoBC.pdf","creator":"casillas","file_id":"6438","date_created":"2019-05-13T09:16:20Z","date_updated":"2021-02-11T11:17:15Z","checksum":"6daf2d2086111aa8fd3fbc919a3e2833","file_size":3895187},{"date_updated":"2020-07-14T12:47:30Z","embargo_to":"open_access","date_created":"2019-05-13T09:16:20Z","checksum":"3d221aaff7559a7060230a1ff610594f","file_size":7365118,"file_name":"tesisDoctoradoBC.zip","relation":"source_file","content_type":"application/zip","access_level":"closed","file_id":"6439","creator":"casillas"}],"date_updated":"2026-04-08T14:02:12Z","publication_status":"published","ddc":["570","006","578","592"],"author":[{"first_name":"Barbara E","full_name":"Casillas Perez, Barbara E","id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","last_name":"Casillas Perez"}],"month":"05","page":"183","abstract":[{"text":"Social insect colonies tend to have numerous members which function together like a single organism in such harmony that the term ``super-organism'' is often used. In this analogy the reproductive caste is analogous to the primordial germ\r\ncells of a metazoan, while the sterile worker caste corresponds to somatic cells. The worker castes, like tissues, are\r\nin charge of all functions of a living being, besides reproduction. The establishment of new super-organismal units\r\n(i.e. new colonies) is accomplished by the co-dependent castes. The term oftentimes goes beyond a metaphor. We invoke it when we speak about the metabolic rate, thermoregulation, nutrient regulation and gas exchange of a social insect colony. Furthermore, we assert that the super-organism has an immune system, and benefits from ``social immunity''.\r\n\r\nSocial immunity was first summoned by evolutionary biologists to resolve the apparent discrepancy between the expected high frequency of disease outbreak amongst numerous, closely related tightly-interacting hosts, living in stable and microbially-rich environments, against the exceptionally scarce epidemic accounts in natural populations. Social\r\nimmunity comprises a multi-layer assembly of behaviours which have evolved to effectively keep the pathogenic enemies of a colony at bay. The field of social immunity has drawn interest, as it becomes increasingly urgent to stop\r\nthe collapse of pollinator species and curb the growth of invasive pests. In the past decade, several mechanisms of\r\nsocial immune responses have been dissected, but many more questions remain open.\r\n\r\nI present my work in two experimental chapters. In the first, I use invasive garden ants (*Lasius neglectus*) to study how pathogen load and its distribution among nestmates affect the grooming response of the group. Any given group of ants will carry out the same total grooming work, but will direct their grooming effort towards individuals\r\ncarrying a relatively higher spore load. Contrary to expectation, the highest risk of transmission does not stem from grooming highly contaminated ants, but instead, we suggest that the grooming response likely minimizes spore loss to the environment, reducing contamination from inadvertent pickup from the substrate.\r\n\r\nThe second is a comparative developmental approach. I follow black garden ant queens (*Lasius niger*) and their colonies from mating flight, through hibernation for a year. Colonies which grow fast from the start, have a lower chance of survival through hibernation, and those which survive grow at a lower pace later. This is true for colonies of naive\r\nand challenged queens. Early pathogen exposure of the queens changes colony dynamics in an unexpected way: colonies from exposed queens are more likely to grow slowly and recover in numbers only after they survive hibernation.\r\n\r\nIn addition to the two experimental chapters, this thesis includes a co-authored published review on organisational\r\nimmunity, where we enlist the experimental evidence and theoretical framework on which this hypothesis is built,\r\nidentify the caveats and underline how the field is ripe to overcome them. In a final chapter, I describe my part in\r\ntwo collaborative efforts, one to develop an image-based tracker, and the second to develop a classifier for ant\r\nbehaviour.","lang":"eng"}],"ec_funded":1,"project":[{"_id":"2649B4DE-B435-11E9-9278-68D0E5697425","name":"Epidemics in ant societies on a chip","call_identifier":"H2020","grant_number":"771402"}],"year":"2019","date_created":"2019-05-13T08:58:35Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"1999"}]},"oa_version":"Published Version","degree_awarded":"PhD","department":[{"_id":"SyCr"}],"citation":{"ama":"Casillas Perez BE. Collective defenses of garden ants against a fungal pathogen. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>","short":"B.E. Casillas Perez, Collective Defenses of Garden Ants against a Fungal Pathogen, Institute of Science and Technology Austria, 2019.","mla":"Casillas Perez, Barbara E. <i>Collective Defenses of Garden Ants against a Fungal Pathogen</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6435\">10.15479/AT:ISTA:6435</a>.","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","chicago":"Casillas Perez, Barbara E. “Collective Defenses of Garden Ants against a Fungal Pathogen.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019.","apa":"Casillas Perez, B. E. (2019). <i>Collective defenses of garden ants against a fungal pathogen</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6435\">https://doi.org/10.15479/AT:ISTA:6435</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","article_processing_charge":"No","supervisor":[{"orcid":"0000-0002-2193-3868","first_name":"Sylvia M","full_name":"Cremer, Sylvia M","last_name":"Cremer","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87"}],"publication_identifier":{"issn":["2663-337X"]},"day":"07","OA_place":"publisher","date_published":"2019-05-07T00:00:00Z","file_date_updated":"2021-02-11T11:17:15Z","type":"dissertation","doi":"10.15479/AT:ISTA:6435","oa":1,"keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"has_accepted_license":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"corr_author":"1"},{"OA_place":"publisher","date_published":"2019-09-09T00:00:00Z","day":"09","supervisor":[{"full_name":"Csicsvari, Jozsef L","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari"}],"article_processing_charge":"No","publication_identifier":{"isbn":["978-3-99078-003-9"],"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"JoCs"}],"citation":{"mla":"Rangel Guerrero, Dámaris K. <i>The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6849\">10.15479/AT:ISTA:6849</a>.","ista":"Rangel Guerrero DK. 2019. The role of CCK-interneurons in regulating hippocampal network dynamics. Institute of Science and Technology Austria.","apa":"Rangel Guerrero, D. K. (2019). <i>The role of CCK-interneurons in regulating hippocampal network dynamics</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6849\">https://doi.org/10.15479/AT:ISTA:6849</a>","ieee":"D. K. Rangel Guerrero, “The role of CCK-interneurons in regulating hippocampal network dynamics,” Institute of Science and Technology Austria, 2019.","chicago":"Rangel Guerrero, Dámaris K. “The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6849\">https://doi.org/10.15479/AT:ISTA:6849</a>.","ama":"Rangel Guerrero DK. The role of CCK-interneurons in regulating hippocampal network dynamics. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6849\">10.15479/AT:ISTA:6849</a>","short":"D.K. Rangel Guerrero, The Role of CCK-Interneurons in Regulating Hippocampal Network Dynamics, Institute of Science and Technology Austria, 2019."},"alternative_title":["ISTA Thesis"],"acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"M-Shop"}],"corr_author":"1","has_accepted_license":"1","doi":"10.15479/AT:ISTA:6849","oa":1,"type":"dissertation","file_date_updated":"2021-02-10T23:30:09Z","month":"09","author":[{"full_name":"Rangel Guerrero, Dámaris K","orcid":"0000-0002-8602-4374","first_name":"Dámaris K","last_name":"Rangel Guerrero","id":"4871BCE6-F248-11E8-B48F-1D18A9856A87"}],"publication_status":"published","date_updated":"2026-04-08T13:56:53Z","ddc":["570"],"status":"public","file":[{"creator":"drangel","file_id":"6865","file_name":"Thesis_Damaris_Rangel_source.docx","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","checksum":"244dc4f74dbfc94f414156092298831f","file_size":18253100,"date_updated":"2021-02-10T23:30:09Z","date_created":"2019-09-09T13:09:45Z","embargo_to":"open_access"},{"file_size":2160109,"checksum":"59c73be40eeaa1c4db24067270151555","date_created":"2019-09-09T13:09:52Z","date_updated":"2020-09-11T22:30:04Z","request_a_copy":0,"file_id":"6866","creator":"drangel","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2020-09-10","file_name":"Thesis_Damaris_Rangel_pdfa.pdf"}],"title":"The role of CCK-interneurons in regulating hippocampal network dynamics","language":[{"iso":"eng"}],"_id":"6849","oa_version":"Published Version","related_material":{"record":[{"id":"5914","relation":"part_of_dissertation","status":"public"}]},"date_created":"2019-09-06T06:54:16Z","year":"2019","page":"97","abstract":[{"text":"Brain function is mediated by complex dynamical interactions between excitatory and inhibitory cell types. The Cholecystokinin-expressing inhibitory cells (CCK-interneurons) are one of the least studied types, despite being suspected to play important roles in cognitive processes. We studied the network effects of optogenetic silencing of CCK-interneurons in the CA1 hippocampal area during exploration and sleep states. The cell firing pattern in response to light pulses allowed us to classify the recorded neurons in 5 classes, including disinhibited and non-responsive pyramidal cell and interneurons, and the inhibited interneurons corresponding to the CCK group. The light application, which inhibited the activity of CCK interneurons triggered wider changes in the firing dynamics of cells. We observed rate changes (i.e. remapping) of pyramidal cells during the exploration session in which the light was applied relative to the previous control session that was not restricted neither in time nor space to the light delivery. Also, the disinhibited pyramidal cells had higher increase in bursting than in single spike firing rate as a result of CCK silencing. In addition, the firing activity patterns during exploratory periods were more weakly reactivated in sleep for those periods in which CCK-interneuron were silenced than in the unaffected periods. Furthermore, light pulses during sleep disrupted the reactivation of recent waking patterns. Hence, silencing CCK neurons during exploration suppressed the reactivation of waking firing patterns in sleep and CCK interneuron activity was also required during sleep for the normal reactivation of waking patterns. These findings demonstrate the involvement of CCK cells in reactivation-related memory consolidation. An important part of our analysis was to test the relationship of the identified CCKinterneurons to brain oscillations. Our findings showed that these cells exhibited different oscillatory behaviour during anaesthesia and natural waking and sleep conditions. We showed that: 1) Contrary to the past studies performed under anaesthesia, the identified CCKinterneurons fired on the descending portion of the theta phase in waking exploration. 2) CCKinterneuron preferred phases around the trough of gamma oscillations. 3) Contrary to anaesthesia conditions, the average firing rate of the CCK-interneurons increased around the peak activity of the sharp-wave ripple (SWR) events in natural sleep, which is congruent with new reports about their functional connectivity. We also found that light driven CCK-interneuron silencing altered the dynamics on the CA1 network oscillatory activity: 1) Pyramidal cells negatively shifted their preferred theta phases when the light was applied, while interneurons responses were less consistent. 2) As a population, pyramidal cells negatively shifted their preferred activity during gamma oscillations, albeit we did not find gamma modulation differences related to the light application when pyramidal cells were subdivided into the disinhibited and unaffected groups. 3) During the peak of SWR events, all but the CCK-interneurons had a reduction in their relative firing rate change during the light application as compared to the change observed at SWR initiation. Finally, regarding to the place field activity of the recorded pyramidal neurons, we showed that the disinhibited pyramidal cells had reduced place field similarity, coherence and spatial information, but only during the light application. The mechanisms behind such observed behaviours might involve eCB signalling and plastic changes in CCK-interneuron synapses. In conclusion, the observed changes related to the light-mediated silencing of CCKinterneurons have unravelled characteristics of this interneuron subpopulation that might change the understanding not only of their particular network interactions, but also of the current theories about the emergence of certain cognitive processes such as place coding needed for navigation or hippocampus-dependent memory consolidation. ","lang":"eng"}]},{"intvolume":"       573","date_published":"2019-09-12T00:00:00Z","quality_controlled":"1","day":"12","article_processing_charge":"No","publication_identifier":{"eissn":["1476-4687"],"issn":["0028-0836"]},"citation":{"chicago":"Kampjut, Domen, and Leonid A Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1519-2\">https://doi.org/10.1038/s41586-019-1519-2</a>.","apa":"Kampjut, D., &#38; Sazanov, L. A. (2019). Structure and mechanism of mitochondrial proton-translocating transhydrogenase. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1519-2\">https://doi.org/10.1038/s41586-019-1519-2</a>","ieee":"D. Kampjut and L. A. Sazanov, “Structure and mechanism of mitochondrial proton-translocating transhydrogenase,” <i>Nature</i>, vol. 573, no. 7773. Springer Nature, pp. 291–295, 2019.","ista":"Kampjut D, Sazanov LA. 2019. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. Nature. 573(7773), 291–295.","mla":"Kampjut, Domen, and Leonid A. Sazanov. “Structure and Mechanism of Mitochondrial Proton-Translocating Transhydrogenase.” <i>Nature</i>, vol. 573, no. 7773, Springer Nature, 2019, pp. 291–295, doi:<a href=\"https://doi.org/10.1038/s41586-019-1519-2\">10.1038/s41586-019-1519-2</a>.","short":"D. Kampjut, L.A. Sazanov, Nature 573 (2019) 291–295.","ama":"Kampjut D, Sazanov LA. Structure and mechanism of mitochondrial proton-translocating transhydrogenase. <i>Nature</i>. 2019;573(7773):291–295. doi:<a href=\"https://doi.org/10.1038/s41586-019-1519-2\">10.1038/s41586-019-1519-2</a>"},"department":[{"_id":"LeSa"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","issue":"7773","publisher":"Springer Nature","acknowledged_ssus":[{"_id":"ScienComp"}],"has_accepted_license":"1","acknowledgement":" We thank R. Thompson, G. Effantin and V.-V. Hodirnau for their assistance with collecting NADP+, NADPH and apo datasets, respectively. Data processing was performed at the IST high-performance computing cluster.\r\nThis project has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie Grant Agreement no. 665385.","doi":"10.1038/s41586-019-1519-2","oa":1,"file_date_updated":"2020-11-26T16:33:44Z","pmid":1,"type":"journal_article","month":"09","author":[{"id":"37233050-F248-11E8-B48F-1D18A9856A87","last_name":"Kampjut","full_name":"Kampjut, Domen","first_name":"Domen","orcid":"0000-0002-6018-3422"},{"id":"338D39FE-F248-11E8-B48F-1D18A9856A87","last_name":"Sazanov","first_name":"Leonid A","orcid":"0000-0002-0977-7989","full_name":"Sazanov, Leonid A"}],"date_updated":"2026-05-15T22:30:58Z","publication_status":"published","ddc":["572"],"title":"Structure and mechanism of mitochondrial proton-translocating transhydrogenase","status":"public","file":[{"checksum":"52728cda5210a3e9b74cc204e8aed3d5","file_size":3066206,"date_updated":"2020-11-26T16:33:44Z","date_created":"2020-11-26T16:33:44Z","success":1,"file_id":"8821","creator":"lsazanov","file_name":"Manuscript_final_acc_withFigs_SI_opt_red.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf"}],"scopus_import":"1","article_type":"letter_note","publication":"Nature","language":[{"iso":"eng"}],"_id":"6848","oa_version":"Submitted Version","external_id":{"pmid":["31462775"],"isi":["000485415400061"]},"date_created":"2019-09-04T06:21:41Z","related_material":{"link":[{"description":"News on IST Website","url":"https://ist.ac.at/en/news/high-end-microscopy-reveals-structure-and-function-of-crucial-metabolic-enzyme/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","id":"8340","status":"public"}]},"volume":573,"project":[{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","name":"International IST Doctoral Program","call_identifier":"H2020"}],"isi":1,"year":"2019","page":"291–295","ec_funded":1,"abstract":[{"lang":"eng","text":"Proton-translocating transhydrogenase (also known as nicotinamide nucleotide transhydrogenase (NNT)) is found in the plasma membranes of bacteria and the inner mitochondrial membranes of eukaryotes. NNT catalyses the transfer of a hydride between NADH and NADP+, coupled to the translocation of one proton across the membrane. Its main physiological function is the generation of NADPH, which is a substrate in anabolic reactions and a regulator of oxidative status; however, NNT may also fine-tune the Krebs cycle1,2. NNT deficiency causes familial glucocorticoid deficiency in humans and metabolic abnormalities in mice, similar to those observed in type II diabetes3,4. The catalytic mechanism of NNT has been proposed to involve a rotation of around 180° of the entire NADP(H)-binding domain that alternately participates in hydride transfer and proton-channel gating. However, owing to the lack of high-resolution structures of intact NNT, the details of this process remain unclear5,6. Here we present the cryo-electron microscopy structure of intact mammalian NNT in different conformational states. We show how the NADP(H)-binding domain opens the proton channel to the opposite sides of the membrane, and we provide structures of these two states. We also describe the catalytically important interfaces and linkers between the membrane and the soluble domains and their roles in nucleotide exchange. These structures enable us to propose a revised mechanism for a coupling process in NNT that is consistent with a large body of previous biochemical work. Our results are relevant to the development of currently unavailable NNT inhibitors, which may have therapeutic potential in ischaemia reperfusion injury, metabolic syndrome and some cancers7,8,9."}]},{"file":[{"file_name":"Supplementary_movie_1.avi","relation":"main_file","access_level":"open_access","content_type":"video/x-msvideo","embargo":"2020-02-11","file_id":"6270","creator":"dernst","date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-09T14:35:18Z","file_size":5402078,"checksum":"c958f27dd752712886e7e2638b847a3c"},{"checksum":"8786fdc29c62987c0aad3c866a4d3691","file_size":5927736,"date_created":"2019-04-09T14:35:18Z","date_updated":"2021-02-11T23:30:15Z","file_id":"6271","creator":"dernst","relation":"main_file","content_type":"video/x-msvideo","access_level":"open_access","embargo":"2020-02-11","file_name":"3.7_supplementary_movie_10.avi"},{"file_name":"3.7_supplementary_movie_9.avi","embargo":"2020-02-11","content_type":"video/x-msvideo","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"6272","date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-09T14:35:18Z","checksum":"25f784c5159d6f4d966b2f9b371ebaf6","file_size":9570210},{"embargo":"2020-02-11","content_type":"video/x-msvideo","access_level":"open_access","relation":"main_file","file_name":"3.7_supplementary_movie_8.avi","creator":"dernst","file_id":"6273","date_created":"2019-04-09T14:35:18Z","date_updated":"2021-02-11T23:30:15Z","file_size":2827360,"checksum":"917069272a7a08d1f38224d5e12765d6"},{"date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-09T14:35:18Z","file_size":5771410,"checksum":"81e74f5ca0ad70050504f18192236dc0","file_name":"3.7_supplementary_movie_7.avi","content_type":"video/x-msvideo","embargo":"2020-02-11","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"6274"},{"file_name":"3.7_supplementary_movie_6.avi","relation":"main_file","embargo":"2020-02-11","access_level":"open_access","content_type":"video/x-msvideo","file_id":"6275","creator":"dernst","date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-09T14:35:18Z","checksum":"47eb37b27a2930252713924307ea8c6f","file_size":1113486},{"file_name":"3.7_supplementary_movie_5.avi","embargo":"2020-02-11","content_type":"video/x-msvideo","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"6276","date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-09T14:35:18Z","checksum":"f68f66721041ce84e331959c9a5779c3","file_size":1057232},{"date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-09T14:35:23Z","file_size":127472916,"checksum":"67c01cefab51b363c5e214fe4cd671f3","file_name":"3.7_supplementary_movie_3.avi","content_type":"video/x-msvideo","embargo":"2020-02-11","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"6277"},{"date_created":"2019-04-09T14:35:19Z","date_updated":"2021-02-11T23:30:15Z","file_size":3181238,"checksum":"e5a397edbee05b8821e2b19b3c1a9260","embargo":"2020-02-11","content_type":"video/x-msvideo","access_level":"open_access","relation":"main_file","file_name":"3.7_supplementary_movie_4.avi","creator":"dernst","file_id":"6278"},{"file_size":5970952,"checksum":"32d92b2a9277f956fdb0b42351d07c0b","date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-09T14:35:19Z","file_id":"6279","creator":"dernst","file_name":"3.7_supplementary_movie_2.avi","relation":"main_file","embargo":"2020-02-11","content_type":"video/x-msvideo","access_level":"open_access"},{"date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-09T14:35:21Z","file_size":39835236,"checksum":"efe7001f5d9a8c61e631e12d5f324ade","file_name":"3.7_Supplementary_movie_1.avi","content_type":"video/x-msvideo","embargo":"2020-02-11","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"6280"},{"file_size":3696740,"checksum":"eeb0a5603c6449c5f34eacd5ff0b3a16","date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-09T14:35:21Z","creator":"dernst","file_id":"6281","file_name":"2.5_Suppl_Movie_4_AP2A1_TagRFP.avi","embargo":"2020-02-11","content_type":"video/x-msvideo","access_level":"open_access","relation":"main_file"},{"checksum":"8e7c00ef6223bf0e177deb168338af13","file_size":6741232,"date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-09T14:35:21Z","creator":"dernst","file_id":"6282","file_name":"2.5_Suppl_Movie_3_TPLATE_GFP.avi","content_type":"video/x-msvideo","access_level":"open_access","embargo":"2020-02-11","relation":"main_file"},{"relation":"main_file","content_type":"video/x-msvideo","access_level":"open_access","embargo":"2020-02-11","file_name":"2.5_Suppl_Movie_2_CLC_GFP.avi","file_id":"6283","creator":"dernst","date_created":"2019-04-09T14:35:22Z","date_updated":"2021-02-11T23:30:15Z","checksum":"3636006a7cb709a7543d6581e359b28d","file_size":2445946},{"file_name":"2.5_Suppl_Movie_1_CLC_GFPxAxl1_mcherry.avi","content_type":"video/x-msvideo","embargo":"2020-02-11","access_level":"open_access","relation":"main_file","creator":"dernst","file_id":"6284","date_updated":"2021-02-11T23:30:15Z","date_created":"2019-04-09T14:35:22Z","file_size":58594,"checksum":"39ca5519a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endocytosis, post-endocytic trafficking and their regulatory controls in plants ","language":[{"iso":"eng"}],"_id":"6269","author":[{"id":"44BF24D0-F248-11E8-B48F-1D18A9856A87","last_name":"Narasimhan","full_name":"Narasimhan, Madhumitha","first_name":"Madhumitha","orcid":"0000-0002-8600-0671"}],"month":"02","publication_status":"published","date_updated":"2026-04-08T14:00:24Z","ddc":["575"],"year":"2019","page":"138","abstract":[{"text":"Clathrin-Mediated Endocytosis (CME) is an aspect of cellular trafficking that is constantly regulated for mediating developmental and physiological responses. The main aim of my thesis is to decipher the basic mechanisms of CME and post-endocytic trafficking in the whole multicellular organ systems of Arabidopsis. The first chapter of my thesis describes the search for new components involved in CME. Tandem affinity purification was conducted using CLC and its interacting partners were identified. Amongst the identified proteins were the Auxilin-likes1 and 2 (Axl1/2), putative uncoating factors, for which we made a full functional analysis. Over-expression of Axl1/2 causes extreme modifications in the dynamics of the machinery proteins and inhibition of endocytosis altogether. However the loss of function of the axl1/2 did not present any cellular or physiological phenotype, meaning Auxilin-likes do not form the major uncoating machinery. The second chapter of my thesis describes the establishment/utilisation of techniques to capture the dynamicity and the complexity of CME and post-endocytic trafficking. We have studied the development of endocytic pits at the PM – specifically, the mode of membrane remodeling during pit development and the role of actin in it, given plant cells possess high turgor pressure. Utilizing the improved z-resolution of TIRF and VAEM techniques, we captured the time-lapse of the endocytic events at the plasma membrane; and using particle detection software, we quantitatively analysed all the endocytic trajectories in an unbiased way to obtain the endocytic rate of the system. This together with the direct analysis of cargo internalisation from the PM provided an estimate on the endocytic potential of the cell. We also developed a methodology for ultrastructural analysis of different populations of Clathrin-Coated Structures (CCSs) in both PM and endomembranes in unroofed protoplasts. Structural analysis, together with the intensity profile of CCSs at the PM show that the mode of CCP development at the PM follows ‘Constant curvature model’; meaning that clathrin polymerisation energy is a major contributing factor of membrane remodeling. In addition, other analyses clearly show that actin is not required for membrane remodeling during invagination or any other step of CCP development, despite the prevalent high turgor pressure. However, actin is essential in orchestrating the post-endocytic trafficking of CCVs facilitating the EE formation. We also observed that the uncoating process post-endocytosis is not immediate; an alternative mechanism of uncoating – Sequential multi-step process – functions in the cell. Finally we also looked at one of the important physiological stimuli modulating the process – hormone, auxin. auxin has been known to influence CME before. We have made a detailed study on the concentration-time based effect of auxin on the machinery proteins, CCP development, and the specificity of cargoes endocytosed. To this end, we saw no general effect of auxin on CME at earlier time points. However, very low concentration of IAA, such as 50nM, accelerates endocytosis of specifically PIN2 through CME. Such a tight regulatory control with high specificity to PIN2 could be essential in modulating its polarity. ","lang":"eng"}],"oa_version":"Published Version","related_material":{"record":[{"id":"412","relation":"part_of_dissertation","status":"public"}]},"date_created":"2019-04-09T14:37:06Z","article_processing_charge":"No","supervisor":[{"last_name":"Friml","id":"4159519E-F248-11E8-B48F-1D18A9856A87","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596","first_name":"Jiří"}],"publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"JiFr"}],"alternative_title":["ISTA Thesis"],"citation":{"ista":"Narasimhan M. 2019. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . Institute of Science and Technology Austria.","chicago":"Narasimhan, Madhumitha. “Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants .” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:th1075\">https://doi.org/10.15479/at:ista:th1075</a>.","apa":"Narasimhan, M. (2019). <i>Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants </i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:th1075\">https://doi.org/10.15479/at:ista:th1075</a>","ieee":"M. Narasimhan, “Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants ,” Institute of Science and Technology Austria, 2019.","mla":"Narasimhan, Madhumitha. <i>Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants </i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:th1075\">10.15479/at:ista:th1075</a>.","short":"M. Narasimhan, Clathrin-Mediated Endocytosis, Post-Endocytic Trafficking and Their Regulatory Controls in Plants , Institute of Science and Technology Austria, 2019.","ama":"Narasimhan M. Clathrin-Mediated endocytosis, post-endocytic trafficking and their regulatory controls in plants . 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:th1075\">10.15479/at:ista:th1075</a>"},"OA_place":"publisher","date_published":"2019-02-04T00:00:00Z","day":"04","doi":"10.15479/at:ista:th1075","oa":1,"type":"dissertation","file_date_updated":"2021-02-11T23:30:15Z","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"EM-Fac"}],"tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1"},{"file_date_updated":"2024-04-10T22:30:48Z","type":"dissertation","doi":"10.15479/AT:ISTA:6825","oa":1,"has_accepted_license":"1","corr_author":"1","degree_awarded":"PhD","department":[{"_id":"JoCs"},{"_id":"GradSch"}],"citation":{"ista":"Käfer K. 2019. The hippocampus and medial prefrontal cortex during flexible behavior. Institute of Science and Technology Austria.","chicago":"Käfer, Karola. “The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6825\">https://doi.org/10.15479/AT:ISTA:6825</a>.","apa":"Käfer, K. (2019). <i>The hippocampus and medial prefrontal cortex during flexible behavior</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6825\">https://doi.org/10.15479/AT:ISTA:6825</a>","ieee":"K. Käfer, “The hippocampus and medial prefrontal cortex during flexible behavior,” Institute of Science and Technology Austria, 2019.","mla":"Käfer, Karola. <i>The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6825\">10.15479/AT:ISTA:6825</a>.","short":"K. Käfer, The Hippocampus and Medial Prefrontal Cortex during Flexible Behavior, Institute of Science and Technology Austria, 2019.","ama":"Käfer K. The hippocampus and medial prefrontal cortex during flexible behavior. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6825\">10.15479/AT:ISTA:6825</a>"},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"publisher":"Institute of Science and Technology Austria","supervisor":[{"last_name":"Csicsvari","id":"3FA14672-F248-11E8-B48F-1D18A9856A87","full_name":"Csicsvari, Jozsef L","orcid":"0000-0002-5193-4036","first_name":"Jozsef L"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"day":"24","OA_place":"publisher","date_published":"2019-08-24T00:00:00Z","page":"89","abstract":[{"lang":"eng","text":"The solving of complex tasks requires the functions of more than one brain area and their interaction. Whilst spatial navigation and memory is dependent on the hippocampus, flexible behavior relies on the medial prefrontal cortex (mPFC). To further examine the roles of the hippocampus and mPFC, we recorded their neural activity during a task that depends on both of these brain regions.\r\nWith tetrodes, we recorded the extracellular activity of dorsal hippocampal CA1 (HPC) and mPFC neurons in Long-Evans rats performing a rule-switching task on the plus-maze. The plus-maze task had a spatial component since it required navigation along one of the two start arms and at the maze center a choice between one of the two goal arms. Which goal contained a reward depended on the rule currently in place. After an uncued rule change the animal had to abandon the old strategy and switch to the new rule, testing cognitive flexibility. Investigating the coordination of activity between the HPC and mPFC allows determination during which task stages their interaction is required. Additionally, comparing neural activity patterns in these two brain regions allows delineation of the specialized functions of the HPC and mPFC in this task. We analyzed neural activity in the HPC and mPFC in terms of oscillatory interactions, rule coding and replay.\r\nWe found that theta coherence between the HPC and mPFC is increased at the center and goals of the maze, both when the rule was stable or has changed. Similar results were found for locking of HPC and mPFC neurons to HPC theta oscillations. However, no differences in HPC-mPFC theta coordination were observed between the spatially- and cue-guided rule. Phase locking of HPC and mPFC neurons to HPC gamma oscillations was not modulated by\r\nmaze position or rule type. We found that the HPC coded for the two different rules with cofiring relationships between\r\ncell pairs. However, we could not find conclusive evidence for rule coding in the mPFC. Spatially-selective firing in the mPFC generalized between the two start and two goal arms. With Bayesian positional decoding, we found that the mPFC reactivated non-local positions during awake immobility periods. Replay of these non-local positions could represent entire behavioral trajectories resembling trajectory replay of the HPC. Furthermore, mPFC\r\ntrajectory-replay at the goal positively correlated with rule-switching performance. \r\nFinally, HPC and mPFC trajectory replay occurred independently of each other. These results show that the mPFC can replay ordered patterns of activity during awake immobility, possibly underlying its role in flexible behavior. "}],"year":"2019","date_created":"2019-08-21T15:00:57Z","related_material":{"record":[{"id":"5949","relation":"part_of_dissertation","status":"public"}]},"oa_version":"Published Version","language":[{"iso":"eng"}],"_id":"6825","title":"The hippocampus and medial prefrontal cortex during flexible behavior","status":"public","file":[{"date_updated":"2020-09-06T22:30:03Z","date_created":"2019-09-03T08:07:13Z","file_size":3205202,"checksum":"2664420e332a33338568f4f3bfc59287","file_name":"Thesis_Kaefer_PDFA.pdf","content_type":"application/pdf","access_level":"open_access","embargo":"2020-09-05","relation":"main_file","creator":"kkaefer","file_id":"6846","request_a_copy":0},{"file_name":"Thesis_Kaefer.zip","access_level":"closed","content_type":"application/zip","relation":"source_file","creator":"kkaefer","file_id":"6847","date_updated":"2024-04-10T22:30:48Z","date_created":"2019-09-03T08:07:17Z","embargo_to":"open_access","file_size":2506835,"checksum":"9a154eab6f07aa590a3d2651dc0d926a"}],"date_updated":"2026-04-08T13:56:14Z","publication_status":"published","ddc":["570"],"author":[{"full_name":"Käfer, Karola","first_name":"Karola","last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"}],"month":"08"},{"project":[{"name":"Design principles underlying genetic switch architecture","_id":"251EE76E-B435-11E9-9278-68D0E5697425","grant_number":"24573"}],"year":"2019","abstract":[{"lang":"eng","text":"Decades of studies have revealed the mechanisms of gene regulation in molecular detail. We make use of such well-described regulatory systems to explore how the molecular mechanisms of protein-protein and protein-DNA interactions shape the dynamics and evolution of gene regulation. \r\n\r\ni) We uncover how the biophysics of protein-DNA binding determines the potential of regulatory networks to evolve and adapt, which can be captured using a simple mathematical model. \r\nii) The evolution of regulatory connections can lead to a significant amount of crosstalk between binding proteins. We explore the effect of crosstalk on gene expression from a target promoter, which seems to be modulated through binding competition at non-specific DNA sites. \r\niii) We investigate how the very same biophysical characteristics as in i) can generate significant fitness costs for cells through global crosstalk, meaning non-specific DNA binding across the genomic background. \r\niv) Binding competition between proteins at a target promoter is a prevailing regulatory feature due to the prevalence of co-regulation at bacterial promoters. However, the dynamics of these systems are not always straightforward to determine even if the molecular mechanisms of regulation are known. A detailed model of the biophysical interactions reveals that interference between the regulatory proteins can constitute a new, generic form of system memory that records the history of the input signals at the promoter. \r\n\r\nWe demonstrate how the biophysics of protein-DNA binding can be harnessed to investigate the principles that shape and ultimately limit cellular gene regulation. These results provide a basis for studies of higher-level functionality, which arises from the underlying regulation.   \r\n"}],"page":"152","oa_version":"Published Version","related_material":{"record":[{"id":"67","relation":"part_of_dissertation","status":"public"},{"relation":"popular_science","id":"5585","status":"public"}]},"date_created":"2019-05-03T11:55:51Z","title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","status":"public","file":[{"date_created":"2019-05-03T11:54:52Z","date_updated":"2021-02-11T11:17:13Z","checksum":"c0085d47c58c9cbcab1b0a783480f6da","file_size":12597663,"relation":"main_file","content_type":"application/pdf","access_level":"open_access","embargo":"2020-05-02","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","file_id":"6373","creator":"cigler"},{"date_created":"2019-05-03T11:54:54Z","embargo_to":"open_access","date_updated":"2020-07-14T12:47:28Z","file_size":34644426,"checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx","creator":"cigler","file_id":"6374"}],"_id":"6371","language":[{"iso":"eng"}],"author":[{"last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87","full_name":"Igler, Claudia","orcid":"0000-0001-7777-546X","first_name":"Claudia"}],"month":"05","ddc":["576","579"],"date_updated":"2026-04-08T13:56:27Z","publication_status":"published","oa":1,"doi":"10.15479/AT:ISTA:6371","file_date_updated":"2021-02-11T11:17:13Z","type":"dissertation","corr_author":"1","has_accepted_license":"1","keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"publication_identifier":{"issn":["2663-337X"]},"supervisor":[{"full_name":"Guet, Calin C","orcid":"0000-0001-6220-2052","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"article_processing_charge":"No","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"ista":"Igler C. 2019. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. Institute of Science and Technology Austria.","chicago":"Igler, Claudia. “On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>.","ieee":"C. Igler, “On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation,” Institute of Science and Technology Austria, 2019.","apa":"Igler, C. (2019). <i>On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6371\">https://doi.org/10.15479/AT:ISTA:6371</a>","mla":"Igler, Claudia. <i>On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>.","short":"C. Igler, On the Nature of Gene Regulatory Design - The Biophysics of Transcription Factor Binding Shapes Gene Regulation, Institute of Science and Technology Austria, 2019.","ama":"Igler C. On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6371\">10.15479/AT:ISTA:6371</a>"},"alternative_title":["ISTA Thesis"],"department":[{"_id":"CaGu"}],"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","date_published":"2019-05-03T00:00:00Z","OA_place":"publisher","day":"03"},{"intvolume":"        29","date_published":"2019-09-01T00:00:00Z","quality_controlled":"1","day":"01","article_processing_charge":"Yes (via OA deal)","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","department":[{"_id":"JoCs"}],"citation":{"apa":"Käfer, K., Malagon-Vina, H., Dickerson, D., O’Neill, J., Trossbach, S. V., Korth, C., &#38; Csicsvari, J. L. (2019). Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. <i>Hippocampus</i>. Wiley. <a href=\"https://doi.org/10.1002/hipo.23076\">https://doi.org/10.1002/hipo.23076</a>","chicago":"Käfer, Karola, Hugo Malagon-Vina, Desiree Dickerson, Joseph O’Neill, Svenja V. Trossbach, Carsten Korth, and Jozsef L Csicsvari. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” <i>Hippocampus</i>. Wiley, 2019. <a href=\"https://doi.org/10.1002/hipo.23076\">https://doi.org/10.1002/hipo.23076</a>.","ieee":"K. Käfer <i>et al.</i>, “Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization,” <i>Hippocampus</i>, vol. 29, no. 9. Wiley, pp. 802–816, 2019.","ista":"Käfer K, Malagon-Vina H, Dickerson D, O’Neill J, Trossbach SV, Korth C, Csicsvari JL. 2019. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. Hippocampus. 29(9), 802–816.","mla":"Käfer, Karola, et al. “Disrupted-in-Schizophrenia 1 Overexpression Disrupts Hippocampal Coding and Oscillatory Synchronization.” <i>Hippocampus</i>, vol. 29, no. 9, Wiley, 2019, pp. 802–16, doi:<a href=\"https://doi.org/10.1002/hipo.23076\">10.1002/hipo.23076</a>.","short":"K. Käfer, H. Malagon-Vina, D. Dickerson, J. O’Neill, S.V. Trossbach, C. Korth, J.L. Csicsvari, Hippocampus 29 (2019) 802–816.","ama":"Käfer K, Malagon-Vina H, Dickerson D, et al. Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization. <i>Hippocampus</i>. 2019;29(9):802-816. doi:<a href=\"https://doi.org/10.1002/hipo.23076\">10.1002/hipo.23076</a>"},"publisher":"Wiley","issue":"9","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"has_accepted_license":"1","doi":"10.1002/hipo.23076","oa":1,"file_date_updated":"2020-07-14T12:47:13Z","type":"journal_article","author":[{"full_name":"Käfer, Karola","first_name":"Karola","last_name":"Käfer","id":"2DAA49AA-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Hugo","full_name":"Malagon-Vina, Hugo","last_name":"Malagon-Vina"},{"full_name":"Dickerson, Desiree","first_name":"Desiree","last_name":"Dickerson","id":"444EB89E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"O'Neill","full_name":"O'Neill, Joseph","first_name":"Joseph"},{"full_name":"Trossbach, Svenja V.","first_name":"Svenja V.","last_name":"Trossbach"},{"last_name":"Korth","full_name":"Korth, Carsten","first_name":"Carsten"},{"id":"3FA14672-F248-11E8-B48F-1D18A9856A87","last_name":"Csicsvari","first_name":"Jozsef L","orcid":"0000-0002-5193-4036","full_name":"Csicsvari, Jozsef L"}],"month":"09","date_updated":"2026-05-15T22:30:59Z","publication_status":"published","ddc":["570"],"title":"Disrupted-in-schizophrenia 1 overexpression disrupts hippocampal coding and oscillatory synchronization","status":"public","scopus_import":"1","file":[{"date_created":"2019-02-11T10:42:51Z","date_updated":"2020-07-14T12:47:13Z","file_size":2132893,"checksum":"5e8de271ca04aef92a5de42d6aac4404","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_Hippocampus_Kaefer.pdf","file_id":"5950","creator":"dernst"}],"article_type":"original","publication":"Hippocampus","language":[{"iso":"eng"}],"_id":"5949","oa_version":"Published Version","external_id":{"isi":["000480635400003"]},"related_material":{"record":[{"id":"6825","relation":"dissertation_contains","status":"public"}]},"date_created":"2019-02-10T22:59:18Z","project":[{"call_identifier":"FP7","name":"inter-and intracellular signalling in schizophrenia","_id":"257BBB4C-B435-11E9-9278-68D0E5697425","grant_number":"607616"}],"volume":29,"isi":1,"year":"2019","page":"802-816","ec_funded":1,"abstract":[{"text":"Aberrant proteostasis of protein aggregation may lead to behavior disorders including chronic mental illnesses (CMI). Furthermore, the neuronal activity alterations that underlie CMI are not well understood. We recorded the local field potential and single-unit activity of the hippocampal CA1 region in vivo in rats transgenically overexpressing the Disrupted-in-Schizophrenia 1 (DISC1) gene (tgDISC1), modeling sporadic CMI. These tgDISC1 rats have previously been shown to exhibit DISC1 protein aggregation, disturbances in the dopaminergic system and attention-related deficits. Recordings were performed during exploration of familiar and novel open field environments and during sleep, allowing investigation of neuronal abnormalities in unconstrained behavior. Compared to controls, tgDISC1 place cells exhibited smaller place fields and decreased speed-modulation of their firing rates, demonstrating altered spatial coding and deficits in encoding location-independent sensory inputs. Oscillation analyses showed that tgDISC1 pyramidal neurons had higher theta phase locking strength during novelty, limiting their phase coding ability. However, their mean theta phases were more variable at the population level, reducing oscillatory network synchronization. Finally, tgDISC1 pyramidal neurons showed a lack of novelty-induced shift in their preferred theta and gamma firing phases, indicating deficits in coding of novel environments with oscillatory firing. By combining single cell and neuronal population analyses, we link DISC1 protein pathology with abnormal hippocampal neural coding and network synchrony, and thereby gain a more comprehensive understanding of CMI mechanisms.","lang":"eng"}]},{"related_material":{"record":[{"status":"public","id":"402","relation":"part_of_dissertation"},{"id":"664","relation":"part_of_dissertation","status":"public"}]},"date_created":"2019-10-14T16:54:52Z","oa_version":"Published Version","page":"142","abstract":[{"lang":"eng","text":"Lymph nodes  are es s ential organs  of the immune  s ys tem where adaptive immune responses originate, and consist of various leukocyte populations and a stromal backbone. Fibroblastic reticular  cells (FRCs) are  the  main  stromal  cells and  form  a sponge-like extracellular matrix network,   called  conduits ,  which  they   thems elves   enwrap   and  contract.  Lymph,  containing  s oluble  antigens ,  arrive in  lymph  nodes  via afferent lymphatic  vessels that  connect  to  the  s ubcaps ular  s inus   and  conduit  network.  According  to  the  current  paradigm,  the  conduit  network   dis tributes   afferent  lymph  through   lymph  nodes   and  thus   provides   acces s   for  immune  cells to lymph-borne  antigens. An  elas tic  caps ule  s urrounds   the  organ  and  confines   the immune  cells and  FRC  network.   Lymph   nodes   are  completely  packed  with  lymphocytes   and  lymphocyte  numbers  directly  dictates  the size  of  the  organ.  Although  lymphocytes   cons tantly  enter  and  leave  the  lymph  node,  its   s ize  remains   remarkedly   s table  under  homeostatic conditions. It is only partly known  how the cellularity and s ize of the lymph node is regulated and  how  the  lymph  node  is able to swell in inflammation.  The role of the FRC network   in  lymph  node   s welling  and  trans fer  of  fluids   are  inves tigated in  this   thes is.  Furthermore,   we  s tudied  what  trafficking  routes   are  us ed  by  cancer  cells   in  lymph  nodes   to  form  distal metastases.We examined the role of a mechanical feedback in regulation of lymph  node swelling. Using parallel plate compression  and UV-las er  cutting  experiments   we  dis s ected  the  mechanical  force dynamics  of the whole lymph  node, and individually for FRCs  and the  caps ule. Physical forces   generated  by  packed  lymphocytes   directly  affect  the  tens ion  on  the  FRC  network  and  capsule,  which  increases  its  resistance  to   swelling.  This  implies  a  feedback  mechanism  between   tis s ue   pres s ure   and   ability   of   lymphocytes    to   enter   the   organ.   Following   inflammation,  the  lymph  node  swells ∼10 fold in two weeks . Yet, what  is  the role  for tens ion on  the  FRC  network   and  caps ule,  and  how  are  lymphocytes   able  to  enter  in  conditions  that resist swelling remain open ques tions . We s how that tens ion on the FRC network is  important to  limit  the  swelling  rate  of  the  organ  so  that  the  FRC  network  can  grow  in  a  coordinated  fashion. This is illustrated by interfering with FRC contractility, which leads to faster swelling rates  and a dis organized FRC network  in the inflamed lymph  node. Growth  of the FRC network  in  turn  is   expected  to  releas e  tens ion  on  thes e  s tructures   and  lowers   the  res is tance  to  swelling, thereby allowing more lymphocytes to enter the organ and drive more swelling. Halt of  swelling coincides   with  a  thickening  of  the  caps ule,  which  forms   a  thick  res is tant  band  around  the organ and lowers  tens ion on the FRC network  to form a new force equilibrium.The  FRC  and  conduit   network   are  further   believed  to  be  a  privileged  s ite  of  s oluble  information  within  the  lymph  node,  although  many  details   remain  uns olved.  We  s how  by  3D  ultra-recons truction   that  FRCs   and  antigen  pres enting  cells   cover  the  s urface  of  conduit  s ys tem for more  than 99% and we dis cus s  the implications  for s oluble information  exchangeat the conduit level.Finally, there  is an ongoing debate in the cancer field whether and how cancer cells  in lymph nodes   s eed  dis tal  metas tas es .  We  s how  that  cancer  cells   infus ed  into  the  lymph  node  can  utilize trafficking routes of immune  cells and  rapidly  migrate  to  blood  vessels. Once  in  the  blood circulation,  these cells are able to form  metastases in distal tissues."}],"year":"2019","publication_status":"published","date_updated":"2026-04-08T14:01:50Z","ddc":["570"],"month":"10","author":[{"full_name":"Assen, Frank P","orcid":"0000-0003-3470-6119","first_name":"Frank P","last_name":"Assen","id":"3A8E7F24-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"_id":"6947","file":[{"date_created":"2019-11-06T12:30:02Z","embargo_to":"open_access","date_updated":"2020-11-07T23:30:03Z","file_size":214172667,"checksum":"53a739752a500f84d0f8ec953cbbd0b6","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","file_name":"PhDthesis_FrankAssen_revised2.docx","creator":"fassen","file_id":"6990"},{"file_size":83637532,"checksum":"8c156b65d9347bb599623a4b09f15d15","date_created":"2019-11-06T12:30:57Z","date_updated":"2020-11-07T23:30:03Z","file_id":"6991","creator":"fassen","relation":"main_file","access_level":"open_access","content_type":"application/pdf","embargo":"2020-11-06","file_name":"PhDthesis_FrankAssen_revised2.pdf"}],"status":"public","title":"Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking","has_accepted_license":"1","corr_author":"1","acknowledged_ssus":[{"_id":"Bio"},{"_id":"PreCl"},{"_id":"EM-Fac"}],"type":"dissertation","file_date_updated":"2020-11-07T23:30:03Z","doi":"10.15479/AT:ISTA:6947","oa":1,"day":"09","OA_place":"publisher","date_published":"2019-10-09T00:00:00Z","degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","citation":{"mla":"Assen, Frank P. <i>Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>.","chicago":"Assen, Frank P. “Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>.","apa":"Assen, F. P. (2019). <i>Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6947\">https://doi.org/10.15479/AT:ISTA:6947</a>","ieee":"F. P. Assen, “Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking,” Institute of Science and Technology Austria, 2019.","ista":"Assen FP. 2019. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. Institute of Science and Technology Austria.","ama":"Assen FP. Lymph node mechanics: Deciphering the interplay between stroma contractility, morphology and lymphocyte trafficking. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6947\">10.15479/AT:ISTA:6947</a>","short":"F.P. Assen, Lymph Node Mechanics: Deciphering the Interplay between Stroma Contractility, Morphology and Lymphocyte Trafficking, Institute of Science and Technology Austria, 2019."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"MiSi"}],"alternative_title":["ISTA Thesis"],"supervisor":[{"id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","full_name":"Sixt, Michael K","first_name":"Michael K","orcid":"0000-0002-6620-9179"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]}},{"year":"2019","volume":8,"isi":1,"project":[{"name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells","_id":"253CDE40-B435-11E9-9278-68D0E5697425","grant_number":"24283"},{"grant_number":"P29638","name":"The role of Drosophila TNF alpha in immune cell invasion","call_identifier":"FWF","_id":"253B6E48-B435-11E9-9278-68D0E5697425"},{"name":"Investigating the role of transporters in invasive migration through junctions","call_identifier":"FP7","_id":"2536F660-B435-11E9-9278-68D0E5697425","grant_number":"334077"},{"grant_number":"329540","_id":"25388084-B435-11E9-9278-68D0E5697425","name":"Breaking barriers: Investigating the junctional and mechanobiological changes underlying the ability of Drosophila immune cells to invade an epithelium","call_identifier":"FP7"},{"call_identifier":"H2020","name":"International IST Doctoral Program","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","grant_number":"665385"}],"ec_funded":1,"abstract":[{"lang":"eng","text":"Aberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify a key conserved regulator that orchestrates O-glycosylation on a protein subset to activate a program governing migration steps important for both development and cancer metastasis."}],"oa_version":"Published Version","date_created":"2019-03-28T13:37:45Z","external_id":{"isi":["000462530200001"]},"related_material":{"link":[{"description":"News on IST Homepage","relation":"press_release","url":"https://ist.ac.at/en/news/new-gene-potentially-involved-in-metastasis-identified/"}],"record":[{"relation":"dissertation_contains","id":"6530"},{"id":"8983","relation":"dissertation_contains","status":"public"},{"id":"6546","relation":"dissertation_contains","status":"public"}]},"scopus_import":"1","file":[{"file_name":"2019_eLife_Valoskova.pdf","relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_id":"6188","creator":"dernst","date_updated":"2020-07-14T12:47:23Z","date_created":"2019-03-28T14:00:41Z","checksum":"cc0d1a512559d52e7e7cb0e9b9854b40","file_size":4496017}],"status":"public","title":"A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion","_id":"6187","publication":"eLife","language":[{"iso":"eng"}],"author":[{"id":"46F146FC-F248-11E8-B48F-1D18A9856A87","last_name":"Valosková","first_name":"Katarina","orcid":"0000-0002-7926-0221","full_name":"Valosková, Katarina"},{"first_name":"Julia","full_name":"Biebl, Julia","last_name":"Biebl","id":"3CCBB46E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Roblek, Marko","orcid":"0000-0001-9588-1389","first_name":"Marko","last_name":"Roblek","id":"3047D808-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Shamsi","orcid":"0000-0001-6981-6938","full_name":"Emtenani, Shamsi","id":"49D32318-F248-11E8-B48F-1D18A9856A87","last_name":"Emtenani"},{"last_name":"György","id":"3BCEDBE0-F248-11E8-B48F-1D18A9856A87","full_name":"György, Attila","orcid":"0000-0002-1819-198X","first_name":"Attila"},{"last_name":"Misova","id":"495A3C32-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-2427-6856","first_name":"Michaela","full_name":"Misova, Michaela"},{"id":"2F064CFE-F248-11E8-B48F-1D18A9856A87","last_name":"Ratheesh","first_name":"Aparna","orcid":"0000-0001-7190-0776","full_name":"Ratheesh, Aparna"},{"first_name":"Patricia","orcid":"0000-0003-1681-508X","full_name":"Dos Reis Rodrigues, Patricia","id":"26E95904-5160-11E9-9C0B-C5B0DC97E90F","last_name":"Dos Reis Rodrigues"},{"first_name":"Katerina","full_name":"Shkarina, Katerina","last_name":"Shkarina"},{"full_name":"Larsen, Ida Signe Bohse","first_name":"Ida Signe Bohse","last_name":"Larsen"},{"last_name":"Vakhrushev","first_name":"Sergey Y","full_name":"Vakhrushev, Sergey Y"},{"full_name":"Clausen, Henrik","first_name":"Henrik","last_name":"Clausen"},{"full_name":"Siekhaus, Daria E","first_name":"Daria E","orcid":"0000-0001-8323-8353","id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus"}],"month":"03","ddc":["570"],"publication_status":"published","date_updated":"2026-05-15T22:31:01Z","oa":1,"doi":"10.7554/elife.41801","type":"journal_article","file_date_updated":"2020-07-14T12:47:23Z","acknowledged_ssus":[{"_id":"LifeSc"}],"has_accepted_license":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","short":"CC BY (4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_number":"e41801","publication_identifier":{"issn":["2050-084X"]},"article_processing_charge":"No","publisher":"eLife Sciences Publications","citation":{"mla":"Valosková, Katarina, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” <i>ELife</i>, vol. 8, e41801, eLife Sciences Publications, 2019, doi:<a href=\"https://doi.org/10.7554/elife.41801\">10.7554/elife.41801</a>.","apa":"Valosková, K., Bicher, J., Roblek, M., Emtenani, S., György, A., Misova, M., … Siekhaus, D. E. (2019). A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. <i>ELife</i>. eLife Sciences Publications. <a href=\"https://doi.org/10.7554/elife.41801\">https://doi.org/10.7554/elife.41801</a>","chicago":"Valosková, Katarina, Julia Bicher, Marko Roblek, Shamsi Emtenani, Attila György, Michaela Misova, Aparna Ratheesh, et al. “A Conserved Major Facilitator Superfamily Member Orchestrates a Subset of O-Glycosylation to Aid Macrophage Tissue Invasion.” <i>ELife</i>. eLife Sciences Publications, 2019. <a href=\"https://doi.org/10.7554/elife.41801\">https://doi.org/10.7554/elife.41801</a>.","ieee":"K. Valosková <i>et al.</i>, “A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion,” <i>eLife</i>, vol. 8. eLife Sciences Publications, 2019.","ista":"Valosková K, Bicher J, Roblek M, Emtenani S, György A, Misova M, Ratheesh A, Dos Reis Rodrigues P, Shkarina K, Larsen ISB, Vakhrushev SY, Clausen H, Siekhaus DE. 2019. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. eLife. 8, e41801.","ama":"Valosková K, Bicher J, Roblek M, et al. A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion. <i>eLife</i>. 2019;8. doi:<a href=\"https://doi.org/10.7554/elife.41801\">10.7554/elife.41801</a>","short":"K. Valosková, J. Bicher, M. Roblek, S. Emtenani, A. György, M. Misova, A. Ratheesh, P. Dos Reis Rodrigues, K. Shkarina, I.S.B. Larsen, S.Y. Vakhrushev, H. Clausen, D.E. Siekhaus, ELife 8 (2019)."},"department":[{"_id":"DaSi"}],"user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","date_published":"2019-03-26T00:00:00Z","intvolume":"         8","day":"26","quality_controlled":"1"},{"year":"2019","project":[{"grant_number":"24283","name":"Examination of the role of a MFS transporter in the migration of Drosophila immune cells","_id":"253CDE40-B435-11E9-9278-68D0E5697425"}],"page":"141","abstract":[{"lang":"eng","text":"Invasive migration plays a crucial role not only during development and homeostasis but also in pathological states, such as tumor metastasis. Drosophila macrophage migration into the extended germband is an interesting system to study invasive migration. It carries similarities to immune cell transmigration and cancer cell invasion, therefore studying this process could also bring new understanding of invasion in higher organisms. In our work, we uncover a highly conserved member of the major facilitator family that plays a role in tissue invasion through regulation of glycosylation on a subgroup of proteins and/or by aiding the precise timing of DN-Cadherin downregulation. \r\n\r\nAberrant display of the truncated core1 O-glycan T-antigen is a common feature of human cancer cells that correlates with metastasis. Here we show that T-antigen in Drosophila melanogaster macrophages is involved in their developmentally programmed tissue invasion. Higher macrophage T-antigen levels require an atypical major facilitator superfamily (MFS) member that we named Minerva which enables macrophage dissemination and invasion. We characterize for the first time the T and Tn glycoform O-glycoproteome of the Drosophila melanogaster embryo, and determine that Minerva increases the presence of T-antigen on proteins in pathways previously linked to cancer, most strongly on the sulfhydryl oxidase Qsox1 which we show is required for macrophage tissue entry. Minerva’s vertebrate ortholog, MFSD1, rescues the minerva mutant’s migration and T-antigen glycosylation defects. We thus identify \r\na key conserved regulator that orchestrates O-glycosylation on a protein subset to activate \r\na program governing migration steps important for both development and cancer metastasis. \r\n"}],"oa_version":"Published Version","date_created":"2019-06-07T12:49:19Z","related_material":{"record":[{"status":"public","id":"544","relation":"part_of_dissertation"},{"relation":"part_of_dissertation","id":"6187","status":"public"}]},"file":[{"file_name":"Katarina Valoskova_PhD thesis_final version.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","creator":"khribikova","file_id":"6549","date_updated":"2020-07-14T12:47:33Z","date_created":"2019-06-07T13:00:04Z","embargo_to":"open_access","file_size":14110626,"checksum":"68949c2d96210b45b981a23e9c9cd93c"},{"date_updated":"2021-02-11T11:17:14Z","date_created":"2019-06-07T13:00:08Z","file_size":10054156,"checksum":"555329cd76e196c96f5278c480ee2e6e","file_name":"Katarina Valoskova_PhD thesis_final version.pdf","relation":"main_file","embargo":"2020-06-07","content_type":"application/pdf","access_level":"open_access","file_id":"6550","creator":"khribikova"}],"status":"public","title":"The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration","language":[{"iso":"eng"}],"_id":"6546","author":[{"full_name":"Valosková, Katarina","orcid":"0000-0002-7926-0221","first_name":"Katarina","last_name":"Valosková","id":"46F146FC-F248-11E8-B48F-1D18A9856A87"}],"month":"06","publication_status":"published","date_updated":"2026-04-08T13:58:36Z","ddc":["570"],"doi":"10.15479/AT:ISTA:6546","oa":1,"type":"dissertation","file_date_updated":"2021-02-11T11:17:14Z","acknowledged_ssus":[{"_id":"Bio"}],"corr_author":"1","has_accepted_license":"1","supervisor":[{"id":"3D224B9E-F248-11E8-B48F-1D18A9856A87","last_name":"Siekhaus","first_name":"Daria E","orcid":"0000-0001-8323-8353","full_name":"Siekhaus, Daria E"}],"article_processing_charge":"No","publication_identifier":{"issn":["2663-337X"]},"degree_awarded":"PhD","publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"citation":{"mla":"Valosková, Katarina. <i>The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6546\">10.15479/AT:ISTA:6546</a>.","apa":"Valosková, K. (2019). <i>The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6546\">https://doi.org/10.15479/AT:ISTA:6546</a>","chicago":"Valosková, Katarina. “The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6546\">https://doi.org/10.15479/AT:ISTA:6546</a>.","ieee":"K. Valosková, “The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration,” Institute of Science and Technology Austria, 2019.","ista":"Valosková K. 2019. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. Institute of Science and Technology Austria.","ama":"Valosková K. The role of a highly conserved major facilitator superfamily member in Drosophila embryonic macrophage migration. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6546\">10.15479/AT:ISTA:6546</a>","short":"K. Valosková, The Role of a Highly Conserved Major Facilitator Superfamily Member in Drosophila Embryonic Macrophage Migration, Institute of Science and Technology Austria, 2019."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"DaSi"}],"OA_place":"publisher","date_published":"2019-06-07T00:00:00Z","day":"07"},{"file_date_updated":"2021-02-11T11:17:15Z","type":"dissertation","oa":1,"doi":"10.15479/AT:ISTA:6363","has_accepted_license":"1","corr_author":"1","department":[{"_id":"PeJo"}],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","alternative_title":["ISTA Thesis"],"citation":{"short":"C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria, 2019.","ama":"Espinoza Martinez C. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6363\">10.15479/AT:ISTA:6363</a>","chicago":"Espinoza Martinez, Claudia . “Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6363\">https://doi.org/10.15479/AT:ISTA:6363</a>.","apa":"Espinoza Martinez, C. (2019). <i>Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6363\">https://doi.org/10.15479/AT:ISTA:6363</a>","ieee":"C. Espinoza Martinez, “Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits,” Institute of Science and Technology Austria, 2019.","ista":"Espinoza Martinez C. 2019. Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits. Institute of Science and Technology Austria.","mla":"Espinoza Martinez, Claudia. <i>Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6363\">10.15479/AT:ISTA:6363</a>."},"publisher":"Institute of Science and Technology Austria","degree_awarded":"PhD","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-000-8"]},"article_processing_charge":"No","supervisor":[{"full_name":"Jonas, Peter M","first_name":"Peter M","orcid":"0000-0001-5001-4804","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","last_name":"Jonas"}],"day":"30","date_published":"2019-04-30T00:00:00Z","OA_place":"publisher","abstract":[{"text":"Distinguishing  between  similar  experiences  is  achieved  by  the  brain  in  a  process called  pattern  separation.  In  the  hippocampus,  pattern  separation  reduces  the interference of memories and increases the storage capacity by decorrelating similar inputs  patterns  of  neuronal  activity  into  non-overlapping output  firing  patterns. Winners-take-all  (WTA)  mechanism  is  a  theoretical  model  for  pattern  separation  in which  a  \"winner\"  cell  suppresses  the  activity  of  the  neighboring  neurons  through feedback inhibition. However, if the network properties of the dentate gyrus support WTA as a biologically conceivable model remains unknown. Here, we showed that the connectivity rules of PV+interneurons and their synaptic properties are optimizedfor efficient pattern separation. We found using multiple whole-cell in vitrorecordings that PV+interneurons mainly connect to granule cells (GC) through lateral inhibition, a form of  feedback  inhibition  in  which  a  GC  inhibits  other  GCs  but  not  itself  through  the activation of PV+interneurons. Thus, lateral inhibition between GC–PV+interneurons was ~10 times more abundant than recurrent connections. Furthermore, the GC–PV+interneuron  connectivity  was  more  spatially  confined  but  less  abundant  than  PV+interneurons–GC  connectivity,  leading  to  an  asymmetrical  distribution  of  excitatory and inhibitory connectivity. Our network model of the dentate gyrus with incorporated real connectivity rules efficiently decorrelates neuronal activity patterns using WTA as the  primary  mechanism.  This  process  relied  on  lateral  inhibition,  fast-signaling properties  of  PV+interneurons  and  the  asymmetrical  distribution  of  excitatory  and inhibitory connectivity. Finally, we found that silencing the activity of PV+interneurons in  vivoleads  to  acute  deficits  in  discrimination  between  similar  environments, suggesting  that  PV+interneuron  networks  are  necessary  for  behavioral  relevant computations.  Our   results   demonstrate   that   PV+interneurons  possess  unique connectivity  and  fast  signaling  properties  that confer  to  the  dentate  gyrus  network properties that allow the emergence of pattern separation. Thus, our results contribute to the knowledge of how specific forms of network organization underlie sophisticated types of information processing. \r\n","lang":"eng"}],"page":"140","year":"2019","date_created":"2019-04-30T11:56:10Z","related_material":{"record":[{"status":"public","relation":"part_of_dissertation","id":"21"}]},"oa_version":"Published Version","_id":"6363","language":[{"iso":"eng"}],"title":"Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits","status":"public","file":[{"file_size":13966891,"checksum":"77c6c05cfe8b58c8abcf1b854375d084","date_created":"2019-05-07T16:00:39Z","date_updated":"2021-02-11T11:17:15Z","creator":"cespinoza","file_id":"6389","access_level":"open_access","content_type":"application/pdf","embargo":"2020-05-09","relation":"main_file","file_name":"Espinozathesis_all2.pdf"},{"file_size":11159900,"checksum":"f6aa819f127691a2b0fc21c76eb09746","date_updated":"2020-07-14T12:47:28Z","embargo_to":"open_access","date_created":"2019-05-07T16:00:48Z","file_id":"6390","creator":"cespinoza","file_name":"Espinoza_Thesis.docx","relation":"source_file","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed"}],"ddc":["570"],"date_updated":"2026-04-08T13:57:19Z","publication_status":"published","author":[{"orcid":"0000-0003-4710-2082","first_name":"Claudia ","full_name":"Espinoza Martinez, Claudia ","last_name":"Espinoza Martinez","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87"}],"month":"04"},{"oa_version":"Published Version","related_material":{"record":[{"relation":"old_edition","id":"6266","status":"public"}]},"date_created":"2019-11-27T09:07:14Z","year":"2019","abstract":[{"lang":"eng","text":"A major challenge in neuroscience research is to dissect the circuits that orchestrate behavior in health and disease. Proteins from a wide range of non-mammalian species, such as microbial opsins, have been successfully transplanted to specific neuronal targets to override their natural communication patterns. The goal of our work is to manipulate synaptic communication in a manner that closely incorporates the functional intricacies of synapses by preserving temporal encoding (i.e. the firing pattern of the presynaptic neuron) and connectivity (i.e. target specific synapses rather than specific neurons). Our strategy to achieve this goal builds on the use of non-mammalian transplants to create a synthetic synapse. The mode of modulation comes from pre-synaptic uptake of a synthetic neurotransmitter (SN) into synaptic vesicles by means of a genetically targeted transporter selective for the SN. Upon natural vesicular release, exposure of the SN to the synaptic cleft will modify the post-synaptic potential through an orthogonal ligand gated ion channel. To achieve this goal we have functionally characterized a mixed cationic methionine-gated ion channel from Arabidopsis thaliana, designed a method to functionally characterize a synthetic transporter in isolated synaptic vesicles without the need for transgenic animals, identified and extracted multiple prokaryotic uptake systems that are substrate specific for methionine (Met), and established a primary/cell line co-culture system that would allow future combinatorial testing of this orthogonal transmitter-transporter-channel trifecta.\r\nSynthetic synapses will provide a unique opportunity to manipulate synaptic communication while maintaining the electrophysiological integrity of the pre-synaptic cell. In this way, information may be preserved that was generated in upstream circuits and that could be essential for concerted function and information processing."}],"page":"95","author":[{"full_name":"Mckenzie, Catherine","first_name":"Catherine","last_name":"Mckenzie","id":"3EEDE19A-F248-11E8-B48F-1D18A9856A87"}],"month":"06","ddc":["571","573"],"publication_status":"published","date_updated":"2026-05-15T22:31:06Z","file":[{"file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.docx","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","access_level":"closed","relation":"source_file","creator":"dernst","file_id":"7133","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-11-27T09:06:10Z","file_size":5054633,"checksum":"34d0fe0f6e0af97b5937205a3e350423"},{"file_size":3231837,"checksum":"140dfb5e3df7edca34f4b6fcc55d876f","date_updated":"2020-07-14T12:47:50Z","date_created":"2019-11-27T09:06:10Z","creator":"dernst","file_id":"7134","file_name":"McKenzie PhD Thesis August 2018 - Corrected Final.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file"}],"status":"public","title":"Design and characterization of methods and biological components to realize synthetic neurotransmission","_id":"7132","language":[{"iso":"eng"}],"corr_author":"1","has_accepted_license":"1","oa":1,"doi":"10.15479/at:ista:7132","type":"dissertation","file_date_updated":"2020-07-14T12:47:50Z","date_published":"2019-06-27T00:00:00Z","OA_place":"publisher","day":"27","publication_identifier":{"issn":["2663-337X"]},"article_processing_charge":"No","supervisor":[{"id":"33BA6C30-F248-11E8-B48F-1D18A9856A87","last_name":"Janovjak","first_name":"Harald L","orcid":"0000-0002-8023-9315","full_name":"Janovjak, Harald L"}],"publisher":"Institute of Science and Technology Austria","alternative_title":["ISTA Thesis"],"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"HaJa"}],"citation":{"ama":"Mckenzie C. Design and characterization of methods and biological components to realize synthetic neurotransmission. 2019. doi:<a href=\"https://doi.org/10.15479/at:ista:7132\">10.15479/at:ista:7132</a>","short":"C. Mckenzie, Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission, Institute of Science and Technology Austria, 2019.","mla":"Mckenzie, Catherine. <i>Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission</i>. Institute of Science and Technology Austria, 2019, doi:<a href=\"https://doi.org/10.15479/at:ista:7132\">10.15479/at:ista:7132</a>.","ista":"Mckenzie C. 2019. Design and characterization of methods and biological components to realize synthetic neurotransmission. Institute of Science and Technology Austria.","apa":"Mckenzie, C. (2019). <i>Design and characterization of methods and biological components to realize synthetic neurotransmission</i>. Institute of Science and Technology Austria. <a href=\"https://doi.org/10.15479/at:ista:7132\">https://doi.org/10.15479/at:ista:7132</a>","ieee":"C. Mckenzie, “Design and characterization of methods and biological components to realize synthetic neurotransmission,” Institute of Science and Technology Austria, 2019.","chicago":"Mckenzie, Catherine. “Design and Characterization of Methods and Biological Components to Realize Synthetic Neurotransmission.” Institute of Science and Technology Austria, 2019. <a href=\"https://doi.org/10.15479/at:ista:7132\">https://doi.org/10.15479/at:ista:7132</a>."},"degree_awarded":"PhD"},{"article_number":"114502","oa":1,"doi":"10.1103/PhysRevLett.122.114502","main_file_link":[{"url":"https://arxiv.org/abs/1809.06358","open_access":"1"}],"pmid":1,"type":"journal_article","date_published":"2019-03-22T00:00:00Z","intvolume":"       122","arxiv":1,"day":"22","quality_controlled":"1","publication_identifier":{"eissn":["1079-7114"],"issn":["0031-9007"]},"article_processing_charge":"No","citation":{"mla":"Agrawal, Nishchal, et al. “Transition to Turbulence in Particle Laden Flows.” <i>Physical Review Letters</i>, vol. 122, no. 11, 114502, American Physical Society, 2019, doi:<a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">10.1103/PhysRevLett.122.114502</a>.","apa":"Agrawal, N., Choueiri, G. H., &#38; Hof, B. (2019). Transition to turbulence in particle laden flows. <i>Physical Review Letters</i>. American Physical Society. <a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">https://doi.org/10.1103/PhysRevLett.122.114502</a>","ieee":"N. Agrawal, G. H. Choueiri, and B. Hof, “Transition to turbulence in particle laden flows,” <i>Physical Review Letters</i>, vol. 122, no. 11. American Physical Society, 2019.","chicago":"Agrawal, Nishchal, George H Choueiri, and Björn Hof. “Transition to Turbulence in Particle Laden Flows.” <i>Physical Review Letters</i>. American Physical Society, 2019. <a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">https://doi.org/10.1103/PhysRevLett.122.114502</a>.","ista":"Agrawal N, Choueiri GH, Hof B. 2019. Transition to turbulence in particle laden flows. Physical Review Letters. 122(11), 114502.","ama":"Agrawal N, Choueiri GH, Hof B. Transition to turbulence in particle laden flows. <i>Physical Review Letters</i>. 2019;122(11). doi:<a href=\"https://doi.org/10.1103/PhysRevLett.122.114502\">10.1103/PhysRevLett.122.114502</a>","short":"N. Agrawal, G.H. Choueiri, B. Hof, Physical Review Letters 122 (2019)."},"user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","department":[{"_id":"BjHo"}],"issue":"11","publisher":"American Physical Society","oa_version":"Preprint","date_created":"2019-03-31T21:59:12Z","related_material":{"record":[{"relation":"dissertation_contains","id":"9728","status":"public"}]},"external_id":{"pmid":["30951357"],"arxiv":["1809.06358"],"isi":["000461922000006"]},"volume":122,"isi":1,"year":"2019","abstract":[{"lang":"eng","text":"Suspended particles can alter the properties of fluids and in particular also affect the transition fromlaminar to turbulent flow. An earlier study [Mataset al.,Phys. Rev. Lett.90, 014501 (2003)] reported howthe subcritical (i.e., hysteretic) transition to turbulent puffs is affected by the addition of particles. Here weshow that in addition to this known transition, with increasing concentration a supercritical (i.e.,continuous) transition to a globally fluctuating state is found. At the same time the Newtonian-typetransition to puffs is delayed to larger Reynolds numbers. At even higher concentration only the globallyfluctuating state is found. The dynamics of particle laden flows are hence determined by two competinginstabilities that give rise to three flow regimes: Newtonian-type turbulence at low, a particle inducedglobally fluctuating state at high, and a coexistence state at intermediate concentrations."}],"author":[{"last_name":"Agrawal","id":"469E6004-F248-11E8-B48F-1D18A9856A87","full_name":"Agrawal, Nishchal","first_name":"Nishchal"},{"full_name":"Choueiri, George H","first_name":"George H","last_name":"Choueiri","id":"448BD5BC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0003-2057-2754","first_name":"Björn","full_name":"Hof, Björn","last_name":"Hof","id":"3A374330-F248-11E8-B48F-1D18A9856A87"}],"month":"03","date_updated":"2026-05-15T22:31:10Z","publication_status":"published","title":"Transition to turbulence in particle laden flows","status":"public","scopus_import":"1","_id":"6189","language":[{"iso":"eng"}],"publication":"Physical Review Letters"},{"oa_version":"Published Version","related_material":{"record":[{"status":"public","id":"7902","relation":"part_of_dissertation"}]},"external_id":{"pmid":["31487522"],"isi":["000484400200002"]},"date_created":"2019-08-25T22:00:50Z","year":"2019","isi":1,"volume":103,"page":"750-752","month":"09","author":[{"first_name":"Ximena","full_name":"Contreras, Ximena","last_name":"Contreras","id":"475990FE-F248-11E8-B48F-1D18A9856A87"},{"id":"37B36620-F248-11E8-B48F-1D18A9856A87","last_name":"Hippenmeyer","full_name":"Hippenmeyer, Simon","first_name":"Simon","orcid":"0000-0003-2279-1061"}],"publication_status":"published","date_updated":"2026-05-15T22:31:12Z","scopus_import":"1","status":"public","title":"Memo1 tiles the radial glial cell grid","article_type":"letter_note","publication":"Neuron","language":[{"iso":"eng"}],"_id":"6830","doi":"10.1016/j.neuron.2019.08.021","oa":1,"pmid":1,"type":"journal_article","main_file_link":[{"open_access":"1","url":"https://doi.org/10.1016/j.neuron.2019.08.021"}],"intvolume":"       103","date_published":"2019-09-04T00:00:00Z","quality_controlled":"1","day":"04","article_processing_charge":"No","publication_identifier":{"issn":["0896-6273"],"eissn":["1097-4199"]},"publisher":"Elsevier","issue":"5","user_id":"ba8df636-2132-11f1-aed0-ed93e2281fdd","citation":{"mla":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” <i>Neuron</i>, vol. 103, no. 5, Elsevier, 2019, pp. 750–52, doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">10.1016/j.neuron.2019.08.021</a>.","chicago":"Contreras, Ximena, and Simon Hippenmeyer. “Memo1 Tiles the Radial Glial Cell Grid.” <i>Neuron</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">https://doi.org/10.1016/j.neuron.2019.08.021</a>.","ieee":"X. Contreras and S. Hippenmeyer, “Memo1 tiles the radial glial cell grid,” <i>Neuron</i>, vol. 103, no. 5. Elsevier, pp. 750–752, 2019.","apa":"Contreras, X., &#38; Hippenmeyer, S. (2019). Memo1 tiles the radial glial cell grid. <i>Neuron</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">https://doi.org/10.1016/j.neuron.2019.08.021</a>","ista":"Contreras X, Hippenmeyer S. 2019. Memo1 tiles the radial glial cell grid. Neuron. 103(5), 750–752.","ama":"Contreras X, Hippenmeyer S. Memo1 tiles the radial glial cell grid. <i>Neuron</i>. 2019;103(5):750-752. doi:<a href=\"https://doi.org/10.1016/j.neuron.2019.08.021\">10.1016/j.neuron.2019.08.021</a>","short":"X. Contreras, S. Hippenmeyer, Neuron 103 (2019) 750–752."},"department":[{"_id":"SiHi"}]},{"intvolume":"         3","date_published":"2019-10-01T00:00:00Z","quality_controlled":"1","day":"01","arxiv":1,"article_processing_charge":"No","publisher":"ACM","user_id":"8b945eb4-e2f2-11eb-945a-df72226e66a9","citation":{"apa":"Huang, M., Fu, H., Chatterjee, K., &#38; Goharshady, A. K. (2019). Modular verification for almost-sure termination of probabilistic programs. In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i> (Vol. 3). Athens, Greece: ACM. <a href=\"https://doi.org/10.1145/3360555\">https://doi.org/10.1145/3360555</a>","chicago":"Huang, Mingzhang, Hongfei Fu, Krishnendu Chatterjee, and Amir Kafshdar Goharshady. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” In <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>, Vol. 3. ACM, 2019. <a href=\"https://doi.org/10.1145/3360555\">https://doi.org/10.1145/3360555</a>.","ieee":"M. Huang, H. Fu, K. Chatterjee, and A. K. Goharshady, “Modular verification for almost-sure termination of probabilistic programs,” in <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>, Athens, Greece, 2019, vol. 3.","ista":"Huang M, Fu H, Chatterjee K, Goharshady AK. 2019. Modular verification for almost-sure termination of probabilistic programs. Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications . OOPSLA: Object-oriented Programming, Systems, Languages and Applications vol. 3, 129.","mla":"Huang, Mingzhang, et al. “Modular Verification for Almost-Sure Termination of Probabilistic Programs.” <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>, vol. 3, 129, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3360555\">10.1145/3360555</a>.","short":"M. Huang, H. Fu, K. Chatterjee, A.K. Goharshady, in:, Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications , ACM, 2019.","ama":"Huang M, Fu H, Chatterjee K, Goharshady AK. Modular verification for almost-sure termination of probabilistic programs. In: <i>Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications </i>. Vol 3. ACM; 2019. doi:<a href=\"https://doi.org/10.1145/3360555\">10.1145/3360555</a>"},"department":[{"_id":"KrCh"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial 4.0 International (CC BY-NC 4.0)","short":"CC BY-NC (4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc/4.0/legalcode","image":"/images/cc_by_nc.png"},"article_number":"129","has_accepted_license":"1","doi":"10.1145/3360555","oa":1,"type":"conference","file_date_updated":"2020-07-14T12:47:40Z","conference":{"name":"OOPSLA: Object-oriented Programming, Systems, Languages and Applications","start_date":"2019-10-23","location":"Athens, Greece","end_date":"2019-10-25"},"month":"10","author":[{"last_name":"Huang","full_name":"Huang, Mingzhang","first_name":"Mingzhang"},{"full_name":"Fu, Hongfei","first_name":"Hongfei","last_name":"Fu"},{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","full_name":"Chatterjee, Krishnendu","orcid":"0000-0002-4561-241X","first_name":"Krishnendu"},{"full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584","id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady"}],"publication_status":"published","date_updated":"2026-05-15T22:31:16Z","ddc":["000"],"scopus_import":"1","file":[{"date_created":"2019-08-12T15:40:57Z","date_updated":"2020-07-14T12:47:40Z","checksum":"3482d8ace6fb4991eb7810e3b70f1b9f","file_size":1024643,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"oopsla-2019.pdf","file_id":"6807","creator":"akafshda"},{"file_name":"2019_ACM_Huang.pdf","access_level":"open_access","content_type":"application/pdf","relation":"main_file","creator":"dernst","file_id":"7821","date_updated":"2020-07-14T12:47:40Z","date_created":"2020-05-12T15:15:14Z","file_size":538579,"checksum":"4e5a6fb2b59a75222a4e8335a5a60eac"}],"status":"public","title":"Modular verification for almost-sure termination of probabilistic programs","language":[{"iso":"eng"}],"publication":"Proceedings of the 34th ACM International Conference on Object-Oriented Programming, Systems, Languages, and Applications ","_id":"6780","oa_version":"Published Version","related_material":{"record":[{"relation":"dissertation_contains","id":"8934","status":"public"}]},"date_created":"2019-08-09T09:54:20Z","external_id":{"arxiv":["1901.06087"]},"year":"2019","project":[{"grant_number":"ICT15-003","_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification"},{"grant_number":"S11407","name":"Game Theory","call_identifier":"FWF","_id":"25863FF4-B435-11E9-9278-68D0E5697425"},{"name":"Quantitative Graph Games: Theory and Applications","call_identifier":"FP7","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"267066CE-B435-11E9-9278-68D0E5697425","name":"Quantitative Analysis of Probabilistic Systems with a focus on Crypto-Currencies"},{"_id":"266EEEC0-B435-11E9-9278-68D0E5697425","name":"Quantitative Game-theoretic Analysis of Blockchain Applications and Smart Contracts"}],"volume":3,"abstract":[{"lang":"eng","text":"In this work, we consider the almost-sure termination problem for probabilistic programs that asks whether a\r\ngiven probabilistic program terminates with probability 1. Scalable approaches for program analysis often\r\nrely on modularity as their theoretical basis. In non-probabilistic programs, the classical variant rule (V-rule)\r\nof Floyd-Hoare logic provides the foundation for modular analysis. Extension of this rule to almost-sure\r\ntermination of probabilistic programs is quite tricky, and a probabilistic variant was proposed in [16]. While the\r\nproposed probabilistic variant cautiously addresses the key issue of integrability, we show that the proposed\r\nmodular rule is still not sound for almost-sure termination of probabilistic programs.\r\nBesides establishing unsoundness of the previous rule, our contributions are as follows: First, we present a\r\nsound modular rule for almost-sure termination of probabilistic programs. Our approach is based on a novel\r\nnotion of descent supermartingales. Second, for algorithmic approaches, we consider descent supermartingales\r\nthat are linear and show that they can be synthesized in polynomial time. Finally, we present experimental\r\nresults on a variety of benchmarks and several natural examples that model various types of nested while\r\nloops in probabilistic programs and demonstrate that our approach is able to efficiently prove their almost-sure\r\ntermination property"}],"ec_funded":1},{"publisher":"ACM","department":[{"_id":"KrCh"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","citation":{"short":"K. Chatterjee, A.K. Goharshady, E.K. Goharshady, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 400–408.","ama":"Chatterjee K, Goharshady AK, Goharshady EK. The treewidth of smart contracts. In: <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>. Vol Part F147772. ACM; 2019:400-408. doi:<a href=\"https://doi.org/10.1145/3297280.3297322\">10.1145/3297280.3297322</a>","apa":"Chatterjee, K., Goharshady, A. K., &#38; Goharshady, E. K. (2019). The treewidth of smart contracts. In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i> (Vol. Part F147772, pp. 400–408). Limassol, Cyprus: ACM. <a href=\"https://doi.org/10.1145/3297280.3297322\">https://doi.org/10.1145/3297280.3297322</a>","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Ehsan Kafshdar Goharshady. “The Treewidth of Smart Contracts.” In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Part F147772:400–408. ACM, 2019. <a href=\"https://doi.org/10.1145/3297280.3297322\">https://doi.org/10.1145/3297280.3297322</a>.","ieee":"K. Chatterjee, A. K. Goharshady, and E. K. Goharshady, “The treewidth of smart contracts,” in <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Limassol, Cyprus, 2019, vol. Part F147772, pp. 400–408.","ista":"Chatterjee K, Goharshady AK, Goharshady EK. 2019. The treewidth of smart contracts. Proceedings of the 34th ACM Symposium on Applied Computing. SAC: Symposium on Applied Computing vol. Part F147772, 400–408.","mla":"Chatterjee, Krishnendu, et al. “The Treewidth of Smart Contracts.” <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, vol. Part F147772, ACM, 2019, pp. 400–08, doi:<a href=\"https://doi.org/10.1145/3297280.3297322\">10.1145/3297280.3297322</a>."},"publication_identifier":{"isbn":["9781450359337"]},"pubrep_id":"1070","article_processing_charge":"No","day":"01","quality_controlled":"1","date_published":"2019-04-01T00:00:00Z","conference":{"end_date":"2019-04-12","location":"Limassol, Cyprus","start_date":"2019-04-08","name":"SAC: Symposium on Applied Computing"},"type":"conference","file_date_updated":"2020-07-14T12:47:32Z","oa":1,"doi":"10.1145/3297280.3297322","has_accepted_license":"1","corr_author":"1","_id":"6490","publication":"Proceedings of the 34th ACM Symposium on Applied Computing","language":[{"iso":"eng"}],"status":"public","scopus_import":"1","file":[{"checksum":"dddc20f6d9881f23b8755eb720ec9d6f","file_size":6937138,"date_updated":"2020-07-14T12:47:32Z","date_created":"2020-05-14T09:50:11Z","creator":"dernst","file_id":"7827","file_name":"2019_ACM_Chatterjee.pdf","content_type":"application/pdf","access_level":"open_access","relation":"main_file"}],"title":"The treewidth of smart contracts","ddc":["000"],"publication_status":"published","date_updated":"2026-05-15T22:31:15Z","month":"04","author":[{"last_name":"Chatterjee","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","first_name":"Krishnendu","full_name":"Chatterjee, Krishnendu"},{"id":"391365CE-F248-11E8-B48F-1D18A9856A87","last_name":"Goharshady","full_name":"Goharshady, Amir Kafshdar","first_name":"Amir Kafshdar","orcid":"0000-0003-1702-6584"},{"first_name":"Ehsan Kafshdar","full_name":"Goharshady, Ehsan Kafshdar","last_name":"Goharshady"}],"abstract":[{"lang":"eng","text":"Smart contracts are programs that are stored and executed on the Blockchain and can receive, manage and transfer money (cryptocurrency units). Two important problems regarding smart contracts are formal analysis and compiler optimization. Formal analysis is extremely important, because smart contracts hold funds worth billions of dollars and their code is immutable after deployment. Hence, an undetected bug can cause significant financial losses. Compiler optimization is also crucial, because every action of a smart contract has to be executed by every node in the Blockchain network. Therefore, optimizations in compiling smart contracts can lead to significant savings in computation, time and energy.\r\n\r\nTwo classical approaches in program analysis and compiler optimization are intraprocedural and interprocedural analysis. In intraprocedural analysis, each function is analyzed separately, while interprocedural analysis considers the entire program. In both cases, the analyses are usually reduced to graph problems over the control flow graph (CFG) of the program. These graph problems are often computationally expensive. Hence, there has been ample research on exploiting structural properties of CFGs for efficient algorithms. One such well-studied property is the treewidth, which is a measure of tree-likeness of graphs. It is known that intraprocedural CFGs of structured programs have treewidth at most 6, whereas the interprocedural treewidth cannot be bounded. This result has been used as a basis for many efficient intraprocedural analyses.\r\n\r\nIn this paper, we explore the idea of exploiting the treewidth of smart contracts for formal analysis and compiler optimization. First, similar to classical programs, we show that the intraprocedural treewidth of structured Solidity and Vyper smart contracts is at most 9. Second, for global analysis, we prove that the interprocedural treewidth of structured smart contracts is bounded by 10 and, in sharp contrast with classical programs, treewidth-based algorithms can be easily applied for interprocedural analysis. Finally, we supplement our theoretical results with experiments using a tool we implemented for computing treewidth of smart contracts and show that the treewidth is much lower in practice. We use 36,764 real-world Ethereum smart contracts as benchmarks and find that they have an average treewidth of at most 3.35 for the intraprocedural case and 3.65 for the interprocedural case.\r\n"}],"page":"400-408","year":"2019","isi":1,"volume":"Part F147772","date_created":"2019-05-26T21:59:15Z","external_id":{"isi":["000474685800052"]},"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"oa_version":"Submitted Version"},{"title":"Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving","status":"public","scopus_import":"1","file":[{"date_created":"2019-05-06T12:09:27Z","date_updated":"2020-07-14T12:47:29Z","checksum":"fbfbcd5a0c7a743862bfc3045539a614","file_size":1023934,"relation":"main_file","access_level":"open_access","content_type":"application/pdf","file_name":"2019_ACM_Chatterjee.pdf","file_id":"6379","creator":"dernst"}],"publication":"Proceedings of the 34th ACM Symposium on Applied Computing","language":[{"iso":"eng"}],"_id":"6378","author":[{"first_name":"Krishnendu","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","last_name":"Chatterjee"},{"last_name":"Goharshady","id":"391365CE-F248-11E8-B48F-1D18A9856A87","full_name":"Goharshady, Amir Kafshdar","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar"},{"first_name":"Arash","full_name":"Pourdamghani, Arash","last_name":"Pourdamghani"}],"month":"04","date_updated":"2026-05-15T22:31:16Z","publication_status":"published","ddc":["004"],"isi":1,"volume":"Part F147772","project":[{"call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications","_id":"2581B60A-B435-11E9-9278-68D0E5697425","grant_number":"279307"},{"_id":"25892FC0-B435-11E9-9278-68D0E5697425","name":"Efficient Algorithms for Computer Aided Verification","grant_number":"ICT15-003"},{"_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering","grant_number":"S 11407_N23"}],"year":"2019","page":"374-381","abstract":[{"text":"In today's cryptocurrencies, Hashcash proof of work is the most commonly-adopted approach to mining. In Hashcash, when a miner decides to add a block to the chain, she has to solve the difficult computational puzzle of inverting a hash function. While Hashcash has been successfully adopted in both Bitcoin and Ethereum, it has attracted significant and harsh criticism due to its massive waste of electricity, its carbon footprint and environmental effects, and the inherent lack of usefulness in inverting a hash function. Various other mining protocols have been suggested, including proof of stake, in which a miner's chance of adding the next block is proportional to her current balance. However, such protocols lead to a higher entry cost for new miners who might not still have any stake in the cryptocurrency, and can in the worst case lead to an oligopoly, where the rich have complete control over mining. In this paper, we propose Hybrid Mining: a new mining protocol that combines solving real-world useful problems with Hashcash. Our protocol allows new miners to join the network by taking part in Hashcash mining without having to own an initial stake. It also allows nodes of the network to submit hard computational problems whose solutions are of interest in the real world, e.g.~protein folding problems. Then, miners can choose to compete in solving these problems, in lieu of Hashcash, for adding a new block. Hence, Hybrid Mining incentivizes miners to solve useful problems, such as hard computational problems arising in biology, in a distributed manner. It also gives researchers in other areas an easy-to-use tool to outsource their hard computations to the blockchain network, which has enormous computational power, by paying a reward to the miner who solves the problem for them. Moreover, our protocol provides strong security guarantees and is at least as resilient to double spending as Bitcoin.","lang":"eng"}],"ec_funded":1,"oa_version":"Submitted Version","external_id":{"isi":["000474685800049"]},"date_created":"2019-05-06T12:11:36Z","related_material":{"record":[{"id":"8934","relation":"dissertation_contains","status":"public"}]},"article_processing_charge":"No","pubrep_id":"1069","publication_identifier":{"isbn":["9781450359337"]},"department":[{"_id":"KrCh"}],"citation":{"ama":"Chatterjee K, Goharshady AK, Pourdamghani A. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In: <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>. Vol Part F147772. ACM; 2019:374-381. doi:<a href=\"https://doi.org/10.1145/3297280.3297319\">10.1145/3297280.3297319</a>","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381.","mla":"Chatterjee, Krishnendu, et al. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, vol. Part F147772, ACM, 2019, pp. 374–81, doi:<a href=\"https://doi.org/10.1145/3297280.3297319\">10.1145/3297280.3297319</a>.","apa":"Chatterjee, K., Goharshady, A. K., &#38; Pourdamghani, A. (2019). Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i> (Vol. Part F147772, pp. 374–381). Limassol, Cyprus: ACM. <a href=\"https://doi.org/10.1145/3297280.3297319\">https://doi.org/10.1145/3297280.3297319</a>","ieee":"K. Chatterjee, A. K. Goharshady, and A. Pourdamghani, “Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving,” in <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Limassol, Cyprus, 2019, vol. Part F147772, pp. 374–381.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, and Arash Pourdamghani. “Hybrid Mining: Exploiting Blockchain’s Computational Power for Distributed Problem Solving.” In <i>Proceedings of the 34th ACM Symposium on Applied Computing</i>, Part F147772:374–81. ACM, 2019. <a href=\"https://doi.org/10.1145/3297280.3297319\">https://doi.org/10.1145/3297280.3297319</a>.","ista":"Chatterjee K, Goharshady AK, Pourdamghani A. 2019. Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving. Proceedings of the 34th ACM Symposium on Applied Computing. ACM Symposium on Applied Computing vol. Part F147772, 374–381."},"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","publisher":"ACM","date_published":"2019-04-01T00:00:00Z","quality_controlled":"1","day":"01","doi":"10.1145/3297280.3297319","oa":1,"file_date_updated":"2020-07-14T12:47:29Z","type":"conference","conference":{"name":"ACM Symposium on Applied Computing","start_date":"2019-04-08","location":"Limassol, Cyprus","end_date":"2019-04-12"},"has_accepted_license":"1"}]