[{"publication_status":"published","external_id":{"isi":["000464950700053"],"arxiv":["1808.10608"]},"issue":"7752","_id":"6348","oa_version":"Preprint","type":"journal_article","publisher":"Springer Nature","department":[{"_id":"JoFi"}],"month":"04","year":"2019","publication_identifier":{"eissn":["14764687"],"issn":["00280836"]},"isi":1,"scopus_import":"1","main_file_link":[{"url":"https://arxiv.org/abs/1808.10608","open_access":"1"}],"related_material":{"link":[{"relation":"erratum","url":"https://doi.org/10.1038/s41586-019-1220-5"}]},"abstract":[{"text":"High-speed optical telecommunication is enabled by wavelength-division multiplexing, whereby hundreds of individually stabilized lasers encode information within a single-mode optical fibre. Higher bandwidths require higher total optical power, but the power sent into the fibre is limited by optical nonlinearities within the fibre, and energy consumption by the light sources starts to become a substantial cost factor1. Optical frequency combs have been suggested to remedy this problem by generating numerous discrete, equidistant laser lines within a monolithic device; however, at present their stability and coherence allow them to operate only within small parameter ranges2,3,4. Here we show that a broadband frequency comb realized through the electro-optic effect within a high-quality whispering-gallery-mode resonator can operate at low microwave and optical powers. Unlike the usual third-order Kerr nonlinear optical frequency combs, our combs rely on the second-order nonlinear effect, which is much more efficient. Our result uses a fixed microwave signal that is mixed with an optical-pump signal to generate a coherent frequency comb with a precisely determined carrier separation. The resonant enhancement enables us to work with microwave powers that are three orders of magnitude lower than those in commercially available devices. We emphasize the practical relevance of our results to high rates of data communication. To circumvent the limitations imposed by nonlinear effects in optical communication fibres, one has to solve two problems: to provide a compact and fully integrated, yet high-quality and coherent, frequency comb generator; and to calculate nonlinear signal propagation in real time5. We report a solution to the first problem.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-25T10:15:25Z","status":"public","author":[{"first_name":"Alfredo R","id":"3B82B0F8-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6249-5860","full_name":"Rueda Sanchez, Alfredo R","last_name":"Rueda Sanchez"},{"first_name":"Florian","last_name":"Sedlmeir","full_name":"Sedlmeir, Florian"},{"last_name":"Kumari","full_name":"Kumari, Madhuri","first_name":"Madhuri"},{"first_name":"Gerd","last_name":"Leuchs","full_name":"Leuchs, Gerd"},{"first_name":"Harald G.L.","last_name":"Schwefel","full_name":"Schwefel, Harald G.L."}],"arxiv":1,"quality_controlled":"1","citation":{"apa":"Rueda Sanchez, A. R., Sedlmeir, F., Kumari, M., Leuchs, G., &#38; Schwefel, H. G. L. (2019). Resonant electro-optic frequency comb. <i>Nature</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41586-019-1110-x\">https://doi.org/10.1038/s41586-019-1110-x</a>","chicago":"Rueda Sanchez, Alfredo R, Florian Sedlmeir, Madhuri Kumari, Gerd Leuchs, and Harald G.L. Schwefel. “Resonant Electro-Optic Frequency Comb.” <i>Nature</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41586-019-1110-x\">https://doi.org/10.1038/s41586-019-1110-x</a>.","mla":"Rueda Sanchez, Alfredo R., et al. “Resonant Electro-Optic Frequency Comb.” <i>Nature</i>, vol. 568, no. 7752, Springer Nature, 2019, pp. 378–81, doi:<a href=\"https://doi.org/10.1038/s41586-019-1110-x\">10.1038/s41586-019-1110-x</a>.","ama":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. Resonant electro-optic frequency comb. <i>Nature</i>. 2019;568(7752):378-381. doi:<a href=\"https://doi.org/10.1038/s41586-019-1110-x\">10.1038/s41586-019-1110-x</a>","ieee":"A. R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, and H. G. L. Schwefel, “Resonant electro-optic frequency comb,” <i>Nature</i>, vol. 568, no. 7752. Springer Nature, pp. 378–381, 2019.","short":"A.R. Rueda Sanchez, F. Sedlmeir, M. Kumari, G. Leuchs, H.G.L. Schwefel, Nature 568 (2019) 378–381.","ista":"Rueda Sanchez AR, Sedlmeir F, Kumari M, Leuchs G, Schwefel HGL. 2019. Resonant electro-optic frequency comb. Nature. 568(7752), 378–381."},"date_created":"2019-04-28T21:59:13Z","oa":1,"title":"Resonant electro-optic frequency comb","page":"378-381","date_published":"2019-04-18T00:00:00Z","intvolume":"       568","day":"18","publication":"Nature","volume":568,"article_processing_charge":"No","doi":"10.1038/s41586-019-1110-x"},{"has_accepted_license":"1","intvolume":"       177","date_published":"2019-05-02T00:00:00Z","day":"02","publication":"Cell","volume":177,"pmid":1,"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"article_processing_charge":"No","ec_funded":1,"doi":"10.1016/j.cell.2019.04.015","file_date_updated":"2020-07-14T12:47:28Z","citation":{"short":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, J. Friml, Cell 177 (2019) 957–969.e13.","ista":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. 2019. Re-activation of stem cell pathways for pattern restoration in plant wound healing. Cell. 177(4), 957–969.e13.","ieee":"P. Marhavá, L. Hörmayer, S. Yoshida, P. Marhavý, E. Benková, and J. Friml, “Re-activation of stem cell pathways for pattern restoration in plant wound healing,” <i>Cell</i>, vol. 177, no. 4. Elsevier, p. 957–969.e13, 2019.","ama":"Marhavá P, Hörmayer L, Yoshida S, Marhavý P, Benková E, Friml J. Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. 2019;177(4):957-969.e13. doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>","chicago":"Marhavá, Petra, Lukas Hörmayer, Saiko Yoshida, Peter Marhavý, Eva Benková, and Jiří Friml. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>.","apa":"Marhavá, P., Hörmayer, L., Yoshida, S., Marhavý, P., Benková, E., &#38; Friml, J. (2019). Re-activation of stem cell pathways for pattern restoration in plant wound healing. <i>Cell</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">https://doi.org/10.1016/j.cell.2019.04.015</a>","mla":"Marhavá, Petra, et al. “Re-Activation of Stem Cell Pathways for Pattern Restoration in Plant Wound Healing.” <i>Cell</i>, vol. 177, no. 4, Elsevier, 2019, p. 957–969.e13, doi:<a href=\"https://doi.org/10.1016/j.cell.2019.04.015\">10.1016/j.cell.2019.04.015</a>."},"date_created":"2019-04-28T21:59:14Z","acknowledged_ssus":[{"_id":"Bio"}],"quality_controlled":"1","oa":1,"title":"Re-activation of stem cell pathways for pattern restoration in plant wound healing","page":"957-969.e13","related_material":{"link":[{"description":"News on IST Homepage","url":"https://ist.ac.at/en/news/specialized-plant-cells-regain-stem-cell-features-to-heal-wounds/","relation":"press_release"}],"record":[{"relation":"dissertation_contains","status":"public","id":"9992"}]},"abstract":[{"text":"A process of restorative patterning in plant roots correctly replaces eliminated cells to heal local injuries despite the absence of cell migration, which underpins wound healing in animals. \r\n\r\nPatterning in plants relies on oriented cell divisions and acquisition of specific cell identities. Plants regularly endure wounds caused by abiotic or biotic environmental stimuli and have developed extraordinary abilities to restore their tissues after injuries. Here, we provide insight into a mechanism of restorative patterning that repairs tissues after wounding. Laser-assisted elimination of different cells in Arabidopsis root combined with live-imaging tracking during vertical growth allowed analysis of the regeneration processes in vivo. Specifically, the cells adjacent to the inner side of the injury re-activated their stem cell transcriptional programs. They accelerated their progression through cell cycle, coordinately changed the cell division orientation, and ultimately acquired de novo the correct cell fates to replace missing cells. These observations highlight existence of unknown intercellular positional signaling and demonstrate the capability of specified cells to re-acquire stem cell programs as a crucial part of the plant-specific mechanism of wound healing.","lang":"eng"}],"scopus_import":"1","date_updated":"2024-03-25T23:30:06Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"status":"public","author":[{"id":"44E59624-F248-11E8-B48F-1D18A9856A87","first_name":"Petra","full_name":"Marhavá, Petra","last_name":"Marhavá"},{"full_name":"Hörmayer, Lukas","last_name":"Hörmayer","orcid":"0000-0001-8295-2926","first_name":"Lukas","id":"2EEE7A2A-F248-11E8-B48F-1D18A9856A87"},{"id":"2E46069C-F248-11E8-B48F-1D18A9856A87","first_name":"Saiko","full_name":"Yoshida, Saiko","last_name":"Yoshida"},{"last_name":"Marhavy","full_name":"Marhavy, Peter","orcid":"0000-0001-5227-5741","first_name":"Peter","id":"3F45B078-F248-11E8-B48F-1D18A9856A87"},{"id":"38F4F166-F248-11E8-B48F-1D18A9856A87","first_name":"Eva","orcid":"0000-0002-8510-9739","full_name":"Benková, Eva","last_name":"Benková"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"}],"file":[{"content_type":"application/pdf","access_level":"open_access","date_updated":"2020-07-14T12:47:28Z","checksum":"4ceba04a96a74f5092ec3ce2c579a0c7","file_size":10272032,"date_created":"2019-05-13T06:12:45Z","file_name":"2019_Cell_Marhava.pdf","creator":"dernst","file_id":"6411","relation":"main_file"}],"ddc":["570"],"oa_version":"Published Version","type":"journal_article","publication_status":"published","external_id":{"isi":["000466843000015"],"pmid":["31051107"]},"_id":"6351","issue":"4","publisher":"Elsevier","department":[{"_id":"JiFr"},{"_id":"EvBe"}],"publication_identifier":{"issn":["00928674"],"eissn":["10974172"]},"isi":1,"project":[{"grant_number":"742985","call_identifier":"H2020","name":"Tracing Evolution of Auxin Transport and Polarity in Plants","_id":"261099A6-B435-11E9-9278-68D0E5697425"}],"month":"05","year":"2019"},{"author":[{"full_name":"Temnov, Andrey Alexandrovich","last_name":"Temnov","first_name":"Andrey Alexandrovich"},{"first_name":"Konstantin Arkadevich","full_name":"Rogov, Konstantin Arkadevich","last_name":"Rogov"},{"first_name":"Alla Nikolaevna","full_name":"Sklifas, Alla Nikolaevna","last_name":"Sklifas"},{"last_name":"Klychnikova","full_name":"Klychnikova, Elena Valerievna","first_name":"Elena Valerievna"},{"first_name":"Markus","full_name":"Hartl, Markus","last_name":"Hartl"},{"first_name":"Kristina","full_name":"Djinovic-Carugo, Kristina","last_name":"Djinovic-Carugo"},{"full_name":"Charnagalov, Alexej","last_name":"Charnagalov","id":"49F06DBA-F248-11E8-B48F-1D18A9856A87","first_name":"Alexej"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-08-25T10:14:26Z","scopus_import":"1","abstract":[{"text":"Chronic overuse of common pharmaceuticals, e.g. acetaminophen (paracetamol), often leads to the development of acute liver failure (ALF). This study aimed to elucidate the effect of cultured mesenchymal stem cells (MSCs) proteome on the onset of liver damage and regeneration dynamics in animals with ALF induced by acetaminophen, to test the liver protective efficacy of MSCs proteome depending on the oxygen tension in cell culture, and to blueprint protein components responsible for the effect. Protein compositions prepared from MSCs cultured in mild hypoxic (5% and 10%  O2) and normal (21%  O2) conditions were used to treat ALF induced in mice by injection of acetaminophen. To test the effect of reduced oxygen tension in cell culture on resulting MSCs proteome content we applied a combination of high performance liquid chromatography and mass-spectrometry (LC–MS/MS) for the identification of proteins in lysates of MSCs cultured at different  O2 levels. The treatment of acetaminophen-administered animals with proteins released from cultured MSCs resulted in the inhibition of inflammatory reactions in damaged liver; the area of hepatocyte necrosis being reduced in the first 24 h. Compositions obtained from MSCs cultured at lower O2 level were shown to be more potent than a composition prepared from normoxic cells. A comparative characterization of protein pattern and identification of individual components done by a cytokine assay and proteomics analysis of protein compositions revealed that even moderate hypoxia produces discrete changes in the expression of various subsets of proteins responsible for intracellular respiration and cell signaling. The application of proteins prepared from MSCs grown in vitro at reduced oxygen tension significantly accelerates healing process in damaged liver tissue. The proteomics data obtained for different preparations offer new information about the potential candidates in the MSCs protein repertoire sensitive to oxygen tension in culture medium, which can be involved in the generalized mechanisms the cells use to respond to acute liver failure.","lang":"eng"}],"month":"04","year":"2019","isi":1,"publication_identifier":{"eissn":["15734978"],"issn":["03014851"]},"department":[{"_id":"LeSa"}],"publisher":"Springer","_id":"6352","publication_status":"published","external_id":{"isi":["000470332600049"]},"type":"journal_article","oa_version":"Published Version","file":[{"file_name":"2019_MolecularBioReport_Temnov.pdf","relation":"main_file","file_id":"6362","creator":"dernst","date_updated":"2020-07-14T12:47:28Z","access_level":"open_access","content_type":"application/pdf","date_created":"2019-04-30T09:52:36Z","file_size":1948014,"checksum":"45bf040bbce1cea274f6013fa18ba21b"}],"ddc":["570"],"file_date_updated":"2020-07-14T12:47:28Z","doi":"10.1007/s11033-019-04765-z","article_processing_charge":"Yes (via OA deal)","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"acknowledgement":"The studies were supported by the Austrian Federal Ministry of Economy, Family and Youth through the initiative “Laura Bassi Centres of Expertise” funding the Center of Optimized Structural Stud-ies, grant No. 253275","publication":"Molecular Biology Reports","day":"12","date_published":"2019-04-12T00:00:00Z","has_accepted_license":"1","title":"Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure","oa":1,"quality_controlled":"1","date_created":"2019-04-28T21:59:14Z","citation":{"short":"A.A. Temnov, K.A. Rogov, A.N. Sklifas, E.V. Klychnikova, M. Hartl, K. Djinovic-Carugo, A. Charnagalov, Molecular Biology Reports (2019).","ieee":"A. A. Temnov <i>et al.</i>, “Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure,” <i>Molecular Biology Reports</i>. Springer, 2019.","ista":"Temnov AA, Rogov KA, Sklifas AN, Klychnikova EV, Hartl M, Djinovic-Carugo K, Charnagalov A. 2019. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. Molecular Biology Reports.","ama":"Temnov AA, Rogov KA, Sklifas AN, et al. Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. <i>Molecular Biology Reports</i>. 2019. doi:<a href=\"https://doi.org/10.1007/s11033-019-04765-z\">10.1007/s11033-019-04765-z</a>","mla":"Temnov, Andrey Alexandrovich, et al. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” <i>Molecular Biology Reports</i>, Springer, 2019, doi:<a href=\"https://doi.org/10.1007/s11033-019-04765-z\">10.1007/s11033-019-04765-z</a>.","chicago":"Temnov, Andrey Alexandrovich, Konstantin Arkadevich Rogov, Alla Nikolaevna Sklifas, Elena Valerievna Klychnikova, Markus Hartl, Kristina Djinovic-Carugo, and Alexej Charnagalov. “Protective Properties of the Cultured Stem Cell Proteome Studied in an Animal Model of Acetaminophen-Induced Acute Liver Failure.” <i>Molecular Biology Reports</i>. Springer, 2019. <a href=\"https://doi.org/10.1007/s11033-019-04765-z\">https://doi.org/10.1007/s11033-019-04765-z</a>.","apa":"Temnov, A. A., Rogov, K. A., Sklifas, A. N., Klychnikova, E. V., Hartl, M., Djinovic-Carugo, K., &#38; Charnagalov, A. (2019). Protective properties of the cultured stem cell proteome studied in an animal model of acetaminophen-induced acute liver failure. <i>Molecular Biology Reports</i>. Springer. <a href=\"https://doi.org/10.1007/s11033-019-04765-z\">https://doi.org/10.1007/s11033-019-04765-z</a>"}},{"file_date_updated":"2021-02-11T11:17:15Z","doi":"10.15479/AT:ISTA:6363","article_processing_charge":"No","day":"30","date_published":"2019-04-30T00:00:00Z","has_accepted_license":"1","degree_awarded":"PhD","page":"140","title":"Parvalbumin+ interneurons enable efficient pattern separation in hippocampal microcircuits","oa":1,"date_created":"2019-04-30T11:56:10Z","citation":{"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>","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.","short":"C. Espinoza Martinez, Parvalbumin+ Interneurons Enable Efficient Pattern Separation in Hippocampal Microcircuits, Institute of Science and Technology Austria, 2019.","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>","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>.","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>."},"status":"public","author":[{"last_name":"Espinoza Martinez","full_name":"Espinoza Martinez, Claudia ","orcid":"0000-0003-4710-2082","first_name":"Claudia ","id":"31FFEE2E-F248-11E8-B48F-1D18A9856A87"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-15T12:03:48Z","related_material":{"record":[{"id":"21","relation":"part_of_dissertation","status":"public"}]},"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"}],"month":"04","year":"2019","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-000-8"]},"department":[{"_id":"PeJo"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Peter M","id":"353C1B58-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-5001-4804","full_name":"Jonas, Peter M","last_name":"Jonas"}],"alternative_title":["ISTA Thesis"],"publication_status":"published","_id":"6363","file":[{"relation":"main_file","creator":"cespinoza","file_id":"6389","file_name":"Espinozathesis_all2.pdf","date_created":"2019-05-07T16:00:39Z","checksum":"77c6c05cfe8b58c8abcf1b854375d084","file_size":13966891,"date_updated":"2021-02-11T11:17:15Z","content_type":"application/pdf","embargo":"2020-05-09","access_level":"open_access"},{"date_updated":"2020-07-14T12:47:28Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","embargo_to":"open_access","date_created":"2019-05-07T16:00:48Z","file_size":11159900,"checksum":"f6aa819f127691a2b0fc21c76eb09746","file_name":"Espinoza_Thesis.docx","relation":"source_file","file_id":"6390","creator":"cespinoza"}],"ddc":["570"],"oa_version":"Published Version","type":"dissertation"},{"scopus_import":"1","abstract":[{"lang":"eng","text":"Plants have a remarkable capacity to adjust their growth and development to elevated ambient temperatures. Increased elongation growth of roots, hypocotyls and petioles in warm temperatures are hallmarks of seedling thermomorphogenesis. In the last decade, significant progress has been made to identify the molecular signaling components regulating these growth responses. Increased ambient temperature utilizes diverse components of the light sensing and signal transduction network to trigger growth adjustments. However, it remains unknown whether temperature sensing and responses are universal processes that occur uniformly in all plant organs. Alternatively, temperature sensing may be confined to specific tissues or organs, which would require a systemic signal that mediates responses in distal parts of the plant. Here we show that Arabidopsis (Arabidopsis thaliana) seedlings show organ-specific transcriptome responses to elevated temperatures, and that thermomorphogenesis involves both autonomous and organ-interdependent temperature sensing and signaling. Seedling roots can sense and respond to temperature in a shoot-independent manner, whereas shoot temperature responses require both local and systemic processes. The induction of cell elongation in hypocotyls requires temperature sensing in cotyledons, followed by generation of a mobile auxin signal. Subsequently, auxin travels to the hypocotyl where it triggers local brassinosteroid-induced cell elongation in seedling stems, which depends upon a distinct, permissive temperature sensor in the hypocotyl."}],"main_file_link":[{"url":"www.doi.org/10.1104/pp.18.01377","open_access":"1"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","language":[{"iso":"eng"}],"date_updated":"2023-09-05T12:25:19Z","author":[{"full_name":"Bellstaedt, Julia","last_name":"Bellstaedt","first_name":"Julia"},{"first_name":"Jana","full_name":"Trenner, Jana","last_name":"Trenner"},{"full_name":"Lippmann, Rebecca","last_name":"Lippmann","first_name":"Rebecca"},{"full_name":"Poeschl, Yvonne","last_name":"Poeschl","first_name":"Yvonne"},{"last_name":"Zhang","full_name":"Zhang, Xixi","orcid":"0000-0001-7048-4627","id":"61A66458-47E9-11EA-85BA-8AEAAF14E49A","first_name":"Xixi"},{"first_name":"Jiří","id":"4159519E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8302-7596","full_name":"Friml, Jiří","last_name":"Friml"},{"last_name":"Quint","full_name":"Quint, Marcel","first_name":"Marcel"},{"last_name":"Delker","full_name":"Delker, Carolin","first_name":"Carolin"}],"status":"public","issue":"2","_id":"6366","publication_status":"published","external_id":{"isi":["000470086100019"],"pmid":["31000634"]},"oa_version":"Published Version","type":"journal_article","publisher":"ASPB","article_type":"original","department":[{"_id":"JiFr"}],"month":"06","year":"2019","isi":1,"publication_identifier":{"eissn":["1532-2548"],"issn":["0032-0889"]},"date_published":"2019-06-01T00:00:00Z","intvolume":"       180","pmid":1,"volume":180,"publication":"Plant Physiology","day":"01","article_processing_charge":"No","doi":"10.1104/pp.18.01377","quality_controlled":"1","citation":{"mla":"Bellstaedt, Julia, et al. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” <i>Plant Physiology</i>, vol. 180, no. 2, ASPB, 2019, pp. 757–66, doi:<a href=\"https://doi.org/10.1104/pp.18.01377\">10.1104/pp.18.01377</a>.","apa":"Bellstaedt, J., Trenner, J., Lippmann, R., Poeschl, Y., Zhang, X., Friml, J., … Delker, C. (2019). A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. <i>Plant Physiology</i>. ASPB. <a href=\"https://doi.org/10.1104/pp.18.01377\">https://doi.org/10.1104/pp.18.01377</a>","chicago":"Bellstaedt, Julia, Jana Trenner, Rebecca Lippmann, Yvonne Poeschl, Xixi Zhang, Jiří Friml, Marcel Quint, and Carolin Delker. “A Mobile Auxin Signal Connects Temperature Sensing in Cotyledons with Growth Responses in Hypocotyls.” <i>Plant Physiology</i>. ASPB, 2019. <a href=\"https://doi.org/10.1104/pp.18.01377\">https://doi.org/10.1104/pp.18.01377</a>.","ama":"Bellstaedt J, Trenner J, Lippmann R, et al. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. <i>Plant Physiology</i>. 2019;180(2):757-766. doi:<a href=\"https://doi.org/10.1104/pp.18.01377\">10.1104/pp.18.01377</a>","short":"J. Bellstaedt, J. Trenner, R. Lippmann, Y. Poeschl, X. Zhang, J. Friml, M. Quint, C. Delker, Plant Physiology 180 (2019) 757–766.","ieee":"J. Bellstaedt <i>et al.</i>, “A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls,” <i>Plant Physiology</i>, vol. 180, no. 2. ASPB, pp. 757–766, 2019.","ista":"Bellstaedt J, Trenner J, Lippmann R, Poeschl Y, Zhang X, Friml J, Quint M, Delker C. 2019. A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls. Plant Physiology. 180(2), 757–766."},"date_created":"2019-04-30T15:24:22Z","oa":1,"title":"A mobile auxin signal connects temperature sensing in cotyledons with growth responses in hypocotyls","page":"757-766"},{"day":"03","degree_awarded":"PhD","has_accepted_license":"1","date_published":"2019-05-03T00:00:00Z","doi":"10.15479/AT:ISTA:6371","file_date_updated":"2021-02-11T11:17:13Z","article_processing_charge":"No","oa":1,"date_created":"2019-05-03T11:55:51Z","citation":{"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.","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.","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>","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>.","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>."},"page":"152","title":"On the nature of gene regulatory design - The biophysics of transcription factor binding shapes gene regulation","date_updated":"2024-02-21T13:45:52Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"id":"67","relation":"part_of_dissertation","status":"public"},{"relation":"popular_science","status":"public","id":"5585"}]},"keyword":["gene regulation","biophysics","transcription factor binding","bacteria"],"abstract":[{"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","lang":"eng"}],"status":"public","author":[{"full_name":"Igler, Claudia","last_name":"Igler","id":"46613666-F248-11E8-B48F-1D18A9856A87","first_name":"Claudia"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"full_name":"Guet, Calin C","last_name":"Guet","orcid":"0000-0001-6220-2052","first_name":"Calin C","id":"47F8433E-F248-11E8-B48F-1D18A9856A87"}],"type":"dissertation","ddc":["576","579"],"file":[{"access_level":"open_access","embargo":"2020-05-02","content_type":"application/pdf","date_updated":"2021-02-11T11:17:13Z","checksum":"c0085d47c58c9cbcab1b0a783480f6da","file_size":12597663,"date_created":"2019-05-03T11:54:52Z","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.pdf","file_id":"6373","creator":"cigler","relation":"main_file"},{"embargo_to":"open_access","date_created":"2019-05-03T11:54:54Z","file_size":34644426,"checksum":"2eac954de1c8bbf7e6fb35ed0221ae8c","date_updated":"2020-07-14T12:47:28Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","relation":"source_file","file_id":"6374","creator":"cigler","file_name":"IglerClaudia_OntheNatureofGeneRegulatoryDesign.docx"}],"oa_version":"Published Version","publication_status":"published","alternative_title":["ISTA Thesis"],"_id":"6371","publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"24573","_id":"251EE76E-B435-11E9-9278-68D0E5697425","name":"Design principles underlying genetic switch architecture (DOC Fellowship)"}],"month":"05","year":"2019","department":[{"_id":"CaGu"}]},{"author":[{"full_name":"Dejonghe, Wim","last_name":"Dejonghe","first_name":"Wim"},{"last_name":"Sharma","full_name":"Sharma, Isha","first_name":"Isha"},{"last_name":"Denoo","full_name":"Denoo, Bram","first_name":"Bram"},{"last_name":"De Munck","full_name":"De Munck, Steven","first_name":"Steven"},{"full_name":"Lu, Qing","last_name":"Lu","first_name":"Qing"},{"first_name":"Kiril","last_name":"Mishev","full_name":"Mishev, Kiril"},{"last_name":"Bulut","full_name":"Bulut, Haydar","first_name":"Haydar"},{"last_name":"Mylle","full_name":"Mylle, Evelien","first_name":"Evelien"},{"last_name":"De Rycke","full_name":"De Rycke, Riet","first_name":"Riet"},{"id":"3407EB18-F248-11E8-B48F-1D18A9856A87","first_name":"Mina K","last_name":"Vasileva","full_name":"Vasileva, Mina K"},{"first_name":"Daniel V.","last_name":"Savatin","full_name":"Savatin, Daniel V."},{"last_name":"Nerinckx","full_name":"Nerinckx, Wim","first_name":"Wim"},{"last_name":"Staes","full_name":"Staes, An","first_name":"An"},{"full_name":"Drozdzecki, Andrzej","last_name":"Drozdzecki","first_name":"Andrzej"},{"first_name":"Dominique","last_name":"Audenaert","full_name":"Audenaert, Dominique"},{"first_name":"Klaas","full_name":"Yperman, Klaas","last_name":"Yperman"},{"first_name":"Annemieke","last_name":"Madder","full_name":"Madder, Annemieke"},{"id":"4159519E-F248-11E8-B48F-1D18A9856A87","first_name":"Jiří","last_name":"Friml","full_name":"Friml, Jiří","orcid":"0000-0002-8302-7596"},{"last_name":"Van Damme","full_name":"Van Damme, Daniël","first_name":"Daniël"},{"first_name":"Kris","last_name":"Gevaert","full_name":"Gevaert, Kris"},{"first_name":"Volker","full_name":"Haucke, Volker","last_name":"Haucke"},{"first_name":"Savvas N.","last_name":"Savvides","full_name":"Savvides, Savvas N."},{"first_name":"Johan","last_name":"Winne","full_name":"Winne, Johan"},{"first_name":"Eugenia","full_name":"Russinova, Eugenia","last_name":"Russinova"}],"status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"date_updated":"2023-09-07T12:54:35Z","scopus_import":"1","abstract":[{"lang":"eng","text":"Clathrin-mediated endocytosis (CME) is a highly conserved and essential cellular process in eukaryotic cells, but its dynamic and vital nature makes it challenging to study using classical genetics tools. In contrast, although small molecules can acutely and reversibly perturb CME, the few chemical CME inhibitors that have been applied to plants are either ineffective or show undesirable side effects. Here, we identify the previously described endosidin9 (ES9) as an inhibitor of clathrin heavy chain (CHC) function in both Arabidopsis and human cells through affinity-based target isolation, in vitro binding studies and X-ray crystallography. Moreover, we present a chemically improved ES9 analog, ES9-17, which lacks the undesirable side effects of ES9 while retaining the ability to target CHC. ES9 and ES9-17 have expanded the chemical toolbox used to probe CHC function, and present chemical scaffolds for further design of more specific and potent CHC inhibitors across different systems."}],"related_material":{"record":[{"relation":"dissertation_contains","status":"public","id":"7172"}]},"month":"06","year":"2019","isi":1,"publication_identifier":{"issn":["15524450"],"eissn":["15524469"]},"article_type":"original","department":[{"_id":"JiFr"}],"publisher":"Springer Nature","_id":"6377","issue":"6","publication_status":"published","external_id":{"isi":["000468195600018"]},"type":"journal_article","oa_version":"None","doi":"10.1038/s41589-019-0262-1","article_processing_charge":"No","volume":15,"day":"01","publication":"Nature Chemical Biology","date_published":"2019-06-01T00:00:00Z","intvolume":"        15","page":"641–649","title":"Disruption of endocytosis through chemical inhibition of clathrin heavy chain function","quality_controlled":"1","date_created":"2019-05-05T21:59:11Z","citation":{"ama":"Dejonghe W, Sharma I, Denoo B, et al. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. <i>Nature Chemical Biology</i>. 2019;15(6):641–649. doi:<a href=\"https://doi.org/10.1038/s41589-019-0262-1\">10.1038/s41589-019-0262-1</a>","short":"W. Dejonghe, I. Sharma, B. Denoo, S. De Munck, Q. Lu, K. Mishev, H. Bulut, E. Mylle, R. De Rycke, M.K. Vasileva, D.V. Savatin, W. Nerinckx, A. Staes, A. Drozdzecki, D. Audenaert, K. Yperman, A. Madder, J. Friml, D. Van Damme, K. Gevaert, V. Haucke, S.N. Savvides, J. Winne, E. Russinova, Nature Chemical Biology 15 (2019) 641–649.","ista":"Dejonghe W, Sharma I, Denoo B, De Munck S, Lu Q, Mishev K, Bulut H, Mylle E, De Rycke R, Vasileva MK, Savatin DV, Nerinckx W, Staes A, Drozdzecki A, Audenaert D, Yperman K, Madder A, Friml J, Van Damme D, Gevaert K, Haucke V, Savvides SN, Winne J, Russinova E. 2019. Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. Nature Chemical Biology. 15(6), 641–649.","ieee":"W. Dejonghe <i>et al.</i>, “Disruption of endocytosis through chemical inhibition of clathrin heavy chain function,” <i>Nature Chemical Biology</i>, vol. 15, no. 6. Springer Nature, pp. 641–649, 2019.","mla":"Dejonghe, Wim, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” <i>Nature Chemical Biology</i>, vol. 15, no. 6, Springer Nature, 2019, pp. 641–649, doi:<a href=\"https://doi.org/10.1038/s41589-019-0262-1\">10.1038/s41589-019-0262-1</a>.","apa":"Dejonghe, W., Sharma, I., Denoo, B., De Munck, S., Lu, Q., Mishev, K., … Russinova, E. (2019). Disruption of endocytosis through chemical inhibition of clathrin heavy chain function. <i>Nature Chemical Biology</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41589-019-0262-1\">https://doi.org/10.1038/s41589-019-0262-1</a>","chicago":"Dejonghe, Wim, Isha Sharma, Bram Denoo, Steven De Munck, Qing Lu, Kiril Mishev, Haydar Bulut, et al. “Disruption of Endocytosis through Chemical Inhibition of Clathrin Heavy Chain Function.” <i>Nature Chemical Biology</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41589-019-0262-1\">https://doi.org/10.1038/s41589-019-0262-1</a>."}},{"date_updated":"2025-06-02T08:53:46Z","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","abstract":[{"lang":"eng","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."}],"related_material":{"record":[{"id":"8934","status":"public","relation":"dissertation_contains"}]},"scopus_import":"1","author":[{"orcid":"0000-0002-4561-241X","last_name":"Chatterjee","full_name":"Chatterjee, Krishnendu","first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady","orcid":"0000-0003-1702-6584","first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Pourdamghani","full_name":"Pourdamghani, Arash","first_name":"Arash"}],"status":"public","pubrep_id":"1069","publisher":"ACM","file":[{"date_updated":"2020-07-14T12:47:29Z","access_level":"open_access","content_type":"application/pdf","date_created":"2019-05-06T12:09:27Z","file_size":1023934,"checksum":"fbfbcd5a0c7a743862bfc3045539a614","file_name":"2019_ACM_Chatterjee.pdf","relation":"main_file","file_id":"6379","creator":"dernst"}],"type":"conference","oa_version":"Submitted Version","ddc":["004"],"_id":"6378","external_id":{"isi":["000474685800049"]},"publication_status":"published","isi":1,"publication_identifier":{"isbn":["9781450359337"]},"month":"04","year":"2019","project":[{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"},{"name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425","grant_number":"ICT15-003"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Rigorous Systems Engineering"}],"department":[{"_id":"KrCh"}],"volume":"Part F147772","day":"01","publication":"Proceedings of the 34th ACM Symposium on Applied Computing","has_accepted_license":"1","date_published":"2019-04-01T00:00:00Z","doi":"10.1145/3297280.3297319","file_date_updated":"2020-07-14T12:47:29Z","article_processing_charge":"No","ec_funded":1,"oa":1,"date_created":"2019-05-06T12:11:36Z","citation":{"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>.","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>","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>.","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.","short":"K. Chatterjee, A.K. Goharshady, A. Pourdamghani, in:, Proceedings of the 34th ACM Symposium on Applied Computing, ACM, 2019, pp. 374–381.","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.","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>"},"conference":{"start_date":"2019-04-08","name":"ACM Symposium on Applied Computing","location":"Limassol, Cyprus","end_date":"2019-04-12"},"quality_controlled":"1","page":"374-381","title":"Hybrid Mining: Exploiting blockchain’s computational power for distributed problem solving"},{"status":"public","author":[{"first_name":"Krishnendu","id":"2E5DCA20-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-4561-241X","full_name":"Chatterjee, Krishnendu","last_name":"Chatterjee"},{"first_name":"Amir Kafshdar","id":"391365CE-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-1702-6584","full_name":"Goharshady, Amir Kafshdar","last_name":"Goharshady"},{"first_name":"Nastaran","full_name":"Okati, Nastaran","last_name":"Okati"},{"id":"49704004-F248-11E8-B48F-1D18A9856A87","first_name":"Andreas","full_name":"Pavlogiannis, Andreas","last_name":"Pavlogiannis","orcid":"0000-0002-8943-0722"}],"related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"8934"}]},"abstract":[{"lang":"eng","text":"There is a huge gap between the speeds of modern caches and main memories, and therefore cache misses account for a considerable loss of efficiency in programs. The predominant technique to address this issue has been Data Packing: data elements that are frequently accessed within time proximity are packed into the same cache block, thereby minimizing accesses to the main memory. We consider the algorithmic problem of Data Packing on a two-level memory system. Given a reference sequence R of accesses to data elements, the task is to partition the elements into cache blocks such that the number of cache misses on R is minimized. The problem is notoriously difficult: it is NP-hard even when the cache has size 1, and is hard to approximate for any cache size larger than 4. Therefore, all existing techniques for Data Packing are based on heuristics and lack theoretical guarantees. In this work, we present the first positive theoretical results for Data Packing, along with new and stronger negative results. We consider the problem under the lens of the underlying access hypergraphs, which are hypergraphs of affinities between the data elements, where the order of an access hypergraph corresponds to the size of the affinity group. We study the problem parameterized by the treewidth of access hypergraphs, which is a standard notion in graph theory to measure the closeness of a graph to a tree. Our main results are as follows: We show there is a number q* depending on the cache parameters such that (a) if the access hypergraph of order q* has constant treewidth, then there is a linear-time algorithm for Data Packing; (b)the Data Packing problem remains NP-hard even if the access hypergraph of order q*-1 has constant treewidth. Thus, we establish a fine-grained dichotomy depending on a single parameter, namely, the highest order among access hypegraphs that have constant treewidth; and establish the optimal value q* of this parameter. Finally, we present an experimental evaluation of a prototype implementation of our algorithm. Our results demonstrate that, in practice, access hypergraphs of many commonly-used algorithms have small treewidth. We compare our approach with several state-of-the-art heuristic-based algorithms and show that our algorithm leads to significantly fewer cache-misses. "}],"language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2024-03-25T23:30:18Z","department":[{"_id":"KrCh"}],"project":[{"grant_number":"ICT15-003","name":"Efficient Algorithms for Computer Aided Verification","_id":"25892FC0-B435-11E9-9278-68D0E5697425"},{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"grant_number":"279307","_id":"2581B60A-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Quantitative Graph Games: Theory and Applications"}],"month":"01","year":"2019","publication_identifier":{"issn":["2475-1421"]},"publication_status":"published","_id":"6380","issue":"POPL","oa_version":"Published Version","ddc":["004"],"file":[{"date_updated":"2020-07-14T12:47:29Z","access_level":"open_access","content_type":"application/pdf","date_created":"2019-05-06T12:23:11Z","file_size":1294962,"checksum":"c157752f96877b36685ad7063ada4524","file_name":"2019_ACM_POPL_Chatterjee.pdf","relation":"main_file","file_id":"6381","creator":"dernst"}],"type":"journal_article","publisher":"ACM","pubrep_id":"1056","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"file_date_updated":"2020-07-14T12:47:29Z","doi":"10.1145/3290366","date_published":"2019-01-01T00:00:00Z","has_accepted_license":"1","intvolume":"         3","day":"01","publication":"Proceedings of the ACM on Programming Languages","volume":3,"title":"Efficient parameterized algorithms for data packing","quality_controlled":"1","date_created":"2019-05-06T12:18:17Z","citation":{"mla":"Chatterjee, Krishnendu, et al. “Efficient Parameterized Algorithms for Data Packing.” <i>Proceedings of the ACM on Programming Languages</i>, vol. 3, no. POPL, 53, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3290366\">10.1145/3290366</a>.","chicago":"Chatterjee, Krishnendu, Amir Kafshdar Goharshady, Nastaran Okati, and Andreas Pavlogiannis. “Efficient Parameterized Algorithms for Data Packing.” <i>Proceedings of the ACM on Programming Languages</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3290366\">https://doi.org/10.1145/3290366</a>.","apa":"Chatterjee, K., Goharshady, A. K., Okati, N., &#38; Pavlogiannis, A. (2019). Efficient parameterized algorithms for data packing. <i>Proceedings of the ACM on Programming Languages</i>. ACM. <a href=\"https://doi.org/10.1145/3290366\">https://doi.org/10.1145/3290366</a>","short":"K. Chatterjee, A.K. Goharshady, N. Okati, A. Pavlogiannis, Proceedings of the ACM on Programming Languages 3 (2019).","ieee":"K. Chatterjee, A. K. Goharshady, N. Okati, and A. Pavlogiannis, “Efficient parameterized algorithms for data packing,” <i>Proceedings of the ACM on Programming Languages</i>, vol. 3, no. POPL. ACM, 2019.","ista":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. 2019. Efficient parameterized algorithms for data packing. Proceedings of the ACM on Programming Languages. 3(POPL), 53.","ama":"Chatterjee K, Goharshady AK, Okati N, Pavlogiannis A. Efficient parameterized algorithms for data packing. <i>Proceedings of the ACM on Programming Languages</i>. 2019;3(POPL). doi:<a href=\"https://doi.org/10.1145/3290366\">10.1145/3290366</a>"},"oa":1,"article_number":"53"},{"year":"2019","month":"05","publication_identifier":{"issn":["2663-337X"],"isbn":["978-3-99078-001-5"]},"department":[{"_id":"ToBo"}],"supervisor":[{"id":"3E6DB97A-F248-11E8-B48F-1D18A9856A87","first_name":"Mark Tobias","orcid":"0000-0003-4398-476X","full_name":"Bollenbach, Mark Tobias","last_name":"Bollenbach"}],"publisher":"IST Austria","_id":"6392","alternative_title":["IST Austria Thesis"],"publication_status":"published","ddc":["570"],"type":"dissertation","oa_version":"Published Version","file":[{"checksum":"829bda074444857c7935171237bb7c0c","file_size":43740796,"embargo_to":"open_access","date_created":"2019-05-10T13:51:49Z","access_level":"closed","content_type":"application/vnd.openxmlformats-officedocument.wordprocessingml.document","date_updated":"2020-07-14T12:47:29Z","file_id":"6409","creator":"mlukacisin","relation":"hidden","file_name":"Thesis_Draft_v3.4Final.docx"},{"creator":"mlukacisin","file_id":"6410","relation":"main_file","file_name":"Thesis_Draft_v3.4FinalA.pdf","checksum":"56cb5e97f5f8fc41692401b53832d8e0","file_size":35228388,"date_created":"2019-05-10T14:13:42Z","content_type":"application/pdf","access_level":"open_access","embargo":"2020-04-17","date_updated":"2021-02-11T11:17:16Z"}],"author":[{"first_name":"Martin","id":"298FFE8C-F248-11E8-B48F-1D18A9856A87","last_name":"Lukacisin","full_name":"Lukacisin, Martin","orcid":"0000-0001-6549-4177"}],"status":"public","language":[{"iso":"eng"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","date_updated":"2023-09-22T09:19:41Z","extern":"1","abstract":[{"lang":"eng","text":"The regulation of gene expression is one of the most fundamental processes in living systems. In recent years, thanks to advances in sequencing technology and automation, it has become possible to study gene expression quantitatively, genome-wide and in high-throughput. This leads to the possibility of exploring changes in gene expression in the context of many external perturbations and their combinations, and thus of characterising the basic principles governing gene regulation. In this thesis, I present quantitative experimental approaches to studying transcriptional and protein level changes in response to combinatorial drug treatment, as well as a theoretical data-driven approach to analysing thermodynamic principles guiding transcription of protein coding genes.  \r\nIn the first part of this work, I present a novel methodological framework for quantifying gene expression changes in drug combinations, termed isogrowth profiling. External perturbations through small molecule drugs influence the growth rate of the cell, leading to wide-ranging changes in cellular physiology and gene expression. This confounds the gene expression changes specifically elicited by the particular drug. Combinatorial perturbations, owing to the increased stress they exert, influence the growth rate even more strongly and hence suffer the convolution problem to a greater extent when measuring gene expression changes. Isogrowth profiling is a way to experimentally abstract non-specific, growth rate related changes, by performing the measurement using varying ratios of two drugs at such concentrations that the overall inhibition rate is constant. Using a robotic setup for automated high-throughput re-dilution culture of Saccharomyces cerevisiae, the budding yeast, I investigate all pairwise interactions of four small molecule drugs through sequencing RNA along a growth isobole. Through principal component analysis, I demonstrate here that isogrowth profiling can uncover drug-specific as well as drug-interaction-specific gene expression changes. I show that drug-interaction-specific gene expression changes can be used for prediction of higher-order drug interactions. I propose a simplified generalised framework of isogrowth profiling, with few measurements needed for each drug pair, enabling the broad application of isogrowth profiling to high-throughput screening of inhibitors of cellular growth and beyond. Such high-throughput screenings of gene expression changes specific to pairwise drug interactions will be instrumental for predicting the higher-order interactions of the drugs.\r\n\r\nIn the second part of this work, I extend isogrowth profiling to single-cell measurements of gene expression, characterising population heterogeneity in the budding yeast in response to combinatorial drug perturbation while controlling for non-specific growth rate effects. Through flow cytometry of strains with protein products fused to green fluorescent protein, I discover multiple proteins with bi-modally distributed expression levels in the population in response to drug treatment. I characterize more closely the effect of an ionic stressor, lithium chloride, and find that it inhibits the splicing of mRNA, most strongly affecting ribosomal protein transcripts and leading to a bi-stable behaviour of a small ribosomal subunit protein Rps22B. Time-lapse microscopy of a microfluidic culture system revealed that the induced Rps22B heterogeneity leads to preferential survival of Rps22B-low cells after long starvation, but to preferential proliferation of Rps22B-high cells after short starvation. Overall, this suggests that yeast cells might use splicing of ribosomal genes for bet-hedging in fluctuating environments. I give specific examples of how further exploration of cellular heterogeneity in yeast in response to external perturbation has the potential to reveal yet-undiscovered gene regulation circuitry.\r\n\r\nIn the last part of this thesis, a re-analysis of a published sequencing dataset of nascent elongating transcripts is used to characterise the thermodynamic constraints for RNA polymerase II (RNAP) elongation. Population-level data on RNAP position throughout the transcribed genome with single nucleotide resolution are used to infer the sequence specific thermodynamic determinants of RNAP pausing and backtracking. This analysis reveals that the basepairing strength of the eight nucleotide-long RNA:DNA duplex relative to the basepairing strength of the same sequence when in DNA:DNA duplex, and the change in this quantity during RNA polymerase movement, is the key determinant of RNAP pausing. This is true for RNAP pausing while elongating, but also of RNAP pausing while backtracking and of the backtracking length. The quantitative dependence of RNAP pausing on basepairing energetics is used to infer the increase in pausing due to transcriptional mismatches, leading to a hypothesis that pervasive RNA polymerase II pausing is due to basepairing energetics, as an evolutionary cost for increased RNA polymerase II fidelity.\r\n\r\nThis work advances our understanding of the general principles governing gene expression, with the goal of making computational predictions of single-cell gene expression responses to combinatorial perturbations based on the individual perturbations possible. This ability would substantially facilitate the design of drug combination treatments and, in the long term, lead to our increased ability to more generally design targeted manipulations to any biological system. "}],"related_material":{"record":[{"id":"1029","relation":"part_of_dissertation","status":"public"}]},"page":"103","title":"Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory","oa":1,"date_created":"2019-05-09T19:53:00Z","citation":{"chicago":"Lukacisin, Martin. “Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory.” IST Austria, 2019. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>.","apa":"Lukacisin, M. (2019). <i>Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory</i>. IST Austria. <a href=\"https://doi.org/10.15479/AT:ISTA:6392\">https://doi.org/10.15479/AT:ISTA:6392</a>","mla":"Lukacisin, Martin. <i>Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory</i>. IST Austria, 2019, doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>.","ieee":"M. Lukacisin, “Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory,” IST Austria, 2019.","short":"M. Lukacisin, Quantitative Investigation of Gene Expression Principles through Combinatorial Drug Perturbation and Theory, IST Austria, 2019.","ista":"Lukacisin M. 2019. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. IST Austria.","ama":"Lukacisin M. Quantitative investigation of gene expression principles through combinatorial drug perturbation and theory. 2019. doi:<a href=\"https://doi.org/10.15479/AT:ISTA:6392\">10.15479/AT:ISTA:6392</a>"},"acknowledged_ssus":[{"_id":"LifeSc"},{"_id":"M-Shop"},{"_id":"Bio"}],"file_date_updated":"2021-02-11T11:17:16Z","doi":"10.15479/AT:ISTA:6392","day":"09","date_published":"2019-05-09T00:00:00Z","has_accepted_license":"1"},{"scopus_import":"1","abstract":[{"text":"Polycomb group (PcG) proteins play critical roles in the epigenetic inheritance of cell fate. The Polycomb Repressive Complexes PRC1 and PRC2 catalyse distinct chromatin modifications to enforce gene silencing, but how transcriptional repression is propagated through mitotic cell divisions remains a key unresolved question. Using reversible tethering of PcG proteins to ectopic sites in mouse embryonic stem cells, here we show that PRC1 can trigger transcriptional repression and Polycomb-dependent chromatin modifications. We find that canonical PRC1 (cPRC1), but not variant PRC1, maintains gene silencing through cell division upon reversal of tethering. Propagation of gene repression is sustained by cis-acting histone modifications, PRC2-mediated H3K27me3 and cPRC1-mediated H2AK119ub1, promoting a sequence-independent feedback mechanism for PcG protein recruitment. Thus, the distinct PRC1 complexes present in vertebrates can differentially regulate epigenetic maintenance of gene silencing, potentially enabling dynamic heritable responses to complex stimuli. Our findings reveal how PcG repression is potentially inherited in vertebrates.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-25T10:31:56Z","author":[{"last_name":"Moussa","full_name":"Moussa, Hagar F.","first_name":"Hagar F."},{"first_name":"Daniel","last_name":"Bsteh","full_name":"Bsteh, Daniel"},{"full_name":"Yelagandula, Ramesh","last_name":"Yelagandula","first_name":"Ramesh"},{"last_name":"Pribitzer","full_name":"Pribitzer, Carina","first_name":"Carina"},{"first_name":"Karin","full_name":"Stecher, Karin","last_name":"Stecher"},{"last_name":"Bartalska","full_name":"Bartalska, Katarina","first_name":"Katarina","id":"4D883232-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Luca","last_name":"Michetti","full_name":"Michetti, Luca"},{"full_name":"Wang, Jingkui","last_name":"Wang","first_name":"Jingkui"},{"first_name":"Jorge A.","last_name":"Zepeda-Martinez","full_name":"Zepeda-Martinez, Jorge A."},{"first_name":"Ulrich","full_name":"Elling, Ulrich","last_name":"Elling"},{"last_name":"Stuckey","full_name":"Stuckey, Jacob I.","first_name":"Jacob I."},{"first_name":"Lindsey I.","full_name":"James, Lindsey I.","last_name":"James"},{"last_name":"Frye","full_name":"Frye, Stephen V.","first_name":"Stephen V."},{"first_name":"Oliver","last_name":"Bell","full_name":"Bell, Oliver"}],"status":"public","_id":"6412","issue":"1","publication_status":"published","external_id":{"isi":["000466118700002"]},"type":"journal_article","oa_version":"Published Version","file":[{"file_id":"6448","creator":"dernst","relation":"main_file","file_name":"2019_NatureComm_Moussa.pdf","checksum":"6550a328335396c856db4cbdda7d2994","file_size":1223647,"date_created":"2019-05-14T08:45:51Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:29Z"}],"ddc":["570"],"publisher":"Springer Nature","department":[{"_id":"SaSi"}],"month":"04","year":"2019","isi":1,"publication_identifier":{"eissn":["20411723"]},"date_published":"2019-04-29T00:00:00Z","has_accepted_license":"1","intvolume":"        10","volume":10,"day":"29","publication":"Nature Communications","article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"file_date_updated":"2020-07-14T12:47:29Z","doi":"10.1038/s41467-019-09628-6","quality_controlled":"1","citation":{"chicago":"Moussa, Hagar F., Daniel Bsteh, Ramesh Yelagandula, Carina Pribitzer, Karin Stecher, Katarina Bartalska, Luca Michetti, et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” <i>Nature Communications</i>. Springer Nature, 2019. <a href=\"https://doi.org/10.1038/s41467-019-09628-6\">https://doi.org/10.1038/s41467-019-09628-6</a>.","apa":"Moussa, H. F., Bsteh, D., Yelagandula, R., Pribitzer, C., Stecher, K., Bartalska, K., … Bell, O. (2019). Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. <i>Nature Communications</i>. Springer Nature. <a href=\"https://doi.org/10.1038/s41467-019-09628-6\">https://doi.org/10.1038/s41467-019-09628-6</a>","mla":"Moussa, Hagar F., et al. “Canonical PRC1 Controls Sequence-Independent Propagation of Polycomb-Mediated Gene Silencing.” <i>Nature Communications</i>, vol. 10, no. 1, 1931, Springer Nature, 2019, doi:<a href=\"https://doi.org/10.1038/s41467-019-09628-6\">10.1038/s41467-019-09628-6</a>.","short":"H.F. Moussa, D. Bsteh, R. Yelagandula, C. Pribitzer, K. Stecher, K. Bartalska, L. Michetti, J. Wang, J.A. Zepeda-Martinez, U. Elling, J.I. Stuckey, L.I. James, S.V. Frye, O. Bell, Nature Communications 10 (2019).","ieee":"H. F. Moussa <i>et al.</i>, “Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing,” <i>Nature Communications</i>, vol. 10, no. 1. Springer Nature, 2019.","ista":"Moussa HF, Bsteh D, Yelagandula R, Pribitzer C, Stecher K, Bartalska K, Michetti L, Wang J, Zepeda-Martinez JA, Elling U, Stuckey JI, James LI, Frye SV, Bell O. 2019. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. Nature Communications. 10(1), 1931.","ama":"Moussa HF, Bsteh D, Yelagandula R, et al. Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing. <i>Nature Communications</i>. 2019;10(1). doi:<a href=\"https://doi.org/10.1038/s41467-019-09628-6\">10.1038/s41467-019-09628-6</a>"},"date_created":"2019-05-13T07:58:35Z","article_number":"1931","oa":1,"title":"Canonical PRC1 controls sequence-independent propagation of Polycomb-mediated gene silencing"},{"_id":"6413","external_id":{"isi":["000474496000002"],"arxiv":["1902.07351"]},"publication_status":"published","oa_version":"Preprint","type":"journal_article","publisher":"Elsevier","article_type":"original","department":[{"_id":"BjHo"}],"year":"2019","month":"08","isi":1,"publication_identifier":{"issn":["03019322"]},"scopus_import":"1","abstract":[{"lang":"eng","text":"Phase-field methods have long been used to model the flow of immiscible fluids. Their ability to naturally capture interface topological changes is widely recognized, but their accuracy in simulating flows of real fluids in practical geometries is not established. We here quantitatively investigate the convergence of the phase-field method to the sharp-interface limit with simulations of two-phase pipe flow. We focus on core-annular flows, in which a highly viscous fluid is lubricated by a less viscous fluid, and validate our simulations with an analytic laminar solution, a formal linear stability analysis and also in the fully nonlinear regime. We demonstrate the ability of the phase-field method to accurately deal with non-rectangular geometry, strong advection, unsteady fluctuations and large viscosity contrast. We argue that phase-field methods are very promising for quantitatively studying moderately turbulent flows, especially at high concentrations of the disperse phase."}],"main_file_link":[{"url":"https://arxiv.org/abs/1902.07351","open_access":"1"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-25T10:19:55Z","author":[{"first_name":"Baofang","full_name":"Song, Baofang","last_name":"Song"},{"full_name":"Plana, Carlos","last_name":"Plana","first_name":"Carlos"},{"first_name":"Jose M","id":"40770848-F248-11E8-B48F-1D18A9856A87","last_name":"Lopez Alonso","full_name":"Lopez Alonso, Jose M","orcid":"0000-0002-0384-2022"},{"last_name":"Avila","full_name":"Avila, Marc","first_name":"Marc"}],"status":"public","quality_controlled":"1","arxiv":1,"citation":{"ama":"Song B, Plana C, Lopez Alonso JM, Avila M. Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. 2019;117:14-24. doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>","short":"B. Song, C. Plana, J.M. Lopez Alonso, M. Avila, International Journal of Multiphase Flow 117 (2019) 14–24.","ieee":"B. Song, C. Plana, J. M. Lopez Alonso, and M. Avila, “Phase-field simulation of core-annular pipe flow,” <i>International Journal of Multiphase Flow</i>, vol. 117. Elsevier, pp. 14–24, 2019.","ista":"Song B, Plana C, Lopez Alonso JM, Avila M. 2019. Phase-field simulation of core-annular pipe flow. International Journal of Multiphase Flow. 117, 14–24.","apa":"Song, B., Plana, C., Lopez Alonso, J. M., &#38; Avila, M. (2019). Phase-field simulation of core-annular pipe flow. <i>International Journal of Multiphase Flow</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>","chicago":"Song, Baofang, Carlos Plana, Jose M Lopez Alonso, and Marc Avila. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027</a>.","mla":"Song, Baofang, et al. “Phase-Field Simulation of Core-Annular Pipe Flow.” <i>International Journal of Multiphase Flow</i>, vol. 117, Elsevier, 2019, pp. 14–24, doi:<a href=\"https://doi.org/10.1016/j.ijmultiphaseflow.2019.04.027\">10.1016/j.ijmultiphaseflow.2019.04.027</a>."},"date_created":"2019-05-13T07:58:35Z","oa":1,"title":"Phase-field simulation of core-annular pipe flow","page":"14-24","date_published":"2019-08-01T00:00:00Z","intvolume":"       117","volume":117,"day":"01","publication":"International Journal of Multiphase Flow","article_processing_charge":"No","doi":"10.1016/j.ijmultiphaseflow.2019.04.027"},{"article_processing_charge":"No","author":[{"id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","first_name":"Sylvia","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia","last_name":"Cremer"}],"status":"public","doi":"10.1016/j.cois.2019.03.011","date_published":"2019-06-01T00:00:00Z","scopus_import":"1","abstract":[{"text":"Ant invasions are often harmful to native species communities. Their pathogens and host disease defense mechanisms may be one component of their devastating success. First, they can introduce harmful diseases to their competitors in the introduced range, to which they themselves are tolerant. Second, their supercolonial social structure of huge multi-queen nest networks means that they will harbor a broad pathogen spectrum and high pathogen load while remaining resilient, unlike the smaller, territorial colonies of the native species. Thus, it is likely that invasive ants act as a disease reservoir, promoting their competitive advantage and invasive success.","lang":"eng"}],"intvolume":"        33","language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-25T10:31:31Z","volume":33,"publication":"Current Opinion in Insect Science","day":"01","title":"Pathogens and disease defense of invasive ants","department":[{"_id":"SyCr"}],"month":"06","year":"2019","page":"63-68","isi":1,"publication_identifier":{"issn":["22145745"],"eissn":["22145753"]},"_id":"6415","quality_controlled":"1","publication_status":"published","external_id":{"isi":["000477666000012"]},"citation":{"ista":"Cremer S. 2019. Pathogens and disease defense of invasive ants. Current Opinion in Insect Science. 33, 63–68.","ieee":"S. Cremer, “Pathogens and disease defense of invasive ants,” <i>Current Opinion in Insect Science</i>, vol. 33. Elsevier, pp. 63–68, 2019.","short":"S. Cremer, Current Opinion in Insect Science 33 (2019) 63–68.","ama":"Cremer S. Pathogens and disease defense of invasive ants. <i>Current Opinion in Insect Science</i>. 2019;33:63-68. doi:<a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">10.1016/j.cois.2019.03.011</a>","mla":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current Opinion in Insect Science</i>, vol. 33, Elsevier, 2019, pp. 63–68, doi:<a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">10.1016/j.cois.2019.03.011</a>.","chicago":"Cremer, Sylvia. “Pathogens and Disease Defense of Invasive Ants.” <i>Current Opinion in Insect Science</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">https://doi.org/10.1016/j.cois.2019.03.011</a>.","apa":"Cremer, S. (2019). Pathogens and disease defense of invasive ants. <i>Current Opinion in Insect Science</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.cois.2019.03.011\">https://doi.org/10.1016/j.cois.2019.03.011</a>"},"date_created":"2019-05-13T07:58:36Z","type":"journal_article","oa_version":"None","publisher":"Elsevier"},{"page":"1033-1044","title":"Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome","oa":1,"citation":{"ama":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome biology and evolution</i>. 2019;11(4):1033-1044. doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>","ieee":"A. K. Huylmans, M. A. Toups, A. Macon, W. J. Gammerdinger, and B. Vicoso, “Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome,” <i>Genome biology and evolution</i>, vol. 11, no. 4. Oxford University Press, pp. 1033–1044, 2019.","ista":"Huylmans AK, Toups MA, Macon A, Gammerdinger WJ, Vicoso B. 2019. Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. Genome biology and evolution. 11(4), 1033–1044.","short":"A.K. Huylmans, M.A. Toups, A. Macon, W.J. Gammerdinger, B. Vicoso, Genome Biology and Evolution 11 (2019) 1033–1044.","apa":"Huylmans, A. K., Toups, M. A., Macon, A., Gammerdinger, W. J., &#38; Vicoso, B. (2019). Sex-biased gene expression and dosage compensation on the Artemia franciscana Z-chromosome. <i>Genome Biology and Evolution</i>. Oxford University Press. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>","chicago":"Huylmans, Ann K, Melissa A Toups, Ariana Macon, William J Gammerdinger, and Beatriz Vicoso. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>. Oxford University Press, 2019. <a href=\"https://doi.org/10.1093/gbe/evz053\">https://doi.org/10.1093/gbe/evz053</a>.","mla":"Huylmans, Ann K., et al. “Sex-Biased Gene Expression and Dosage Compensation on the Artemia Franciscana Z-Chromosome.” <i>Genome Biology and Evolution</i>, vol. 11, no. 4, Oxford University Press, 2019, pp. 1033–44, doi:<a href=\"https://doi.org/10.1093/gbe/evz053\">10.1093/gbe/evz053</a>."},"date_created":"2019-05-13T07:58:38Z","acknowledged_ssus":[{"_id":"ScienComp"}],"quality_controlled":"1","doi":"10.1093/gbe/evz053","file_date_updated":"2020-07-14T12:47:29Z","ec_funded":1,"article_processing_charge":"No","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"volume":11,"day":"01","publication":"Genome biology and evolution","has_accepted_license":"1","intvolume":"        11","date_published":"2019-04-01T00:00:00Z","isi":1,"publication_identifier":{"eissn":["1759-6653"]},"month":"04","year":"2019","project":[{"call_identifier":"H2020","name":"Prevalence and Influence of Sexual Antagonism on Genome Evolution","_id":"250BDE62-B435-11E9-9278-68D0E5697425","grant_number":"715257"}],"department":[{"_id":"BeVi"}],"publisher":"Oxford University Press","ddc":["570"],"type":"journal_article","oa_version":"Published Version","file":[{"checksum":"7d0ede297b6741f3dc89cd59017c7642","file_size":1256303,"date_created":"2019-05-14T08:29:38Z","access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:29Z","file_id":"6446","creator":"dernst","relation":"main_file","file_name":"2019_GBE_Huylmans.pdf"}],"issue":"4","_id":"6418","external_id":{"isi":["000476569800003"]},"publication_status":"published","author":[{"first_name":"Ann K","id":"4C0A3874-F248-11E8-B48F-1D18A9856A87","last_name":"Huylmans","full_name":"Huylmans, Ann K","orcid":"0000-0001-8871-4961"},{"orcid":"0000-0002-9752-7380","last_name":"Toups","full_name":"Toups, Melissa A","first_name":"Melissa A","id":"4E099E4E-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Macon","full_name":"Macon, Ariana","id":"2A0848E2-F248-11E8-B48F-1D18A9856A87","first_name":"Ariana"},{"last_name":"Gammerdinger","full_name":"Gammerdinger, William J","orcid":"0000-0001-9638-1220","first_name":"William J","id":"3A7E01BC-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-4579-8306","full_name":"Vicoso, Beatriz","last_name":"Vicoso","id":"49E1C5C6-F248-11E8-B48F-1D18A9856A87","first_name":"Beatriz"}],"status":"public","date_updated":"2024-02-21T12:45:41Z","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","language":[{"iso":"eng"}],"abstract":[{"lang":"eng","text":"Males and females of Artemia franciscana, a crustacean commonly used in the aquarium trade, are highly dimorphic. Sex is determined by a pair of ZW chromosomes, but the nature and extent of differentiation of these chromosomes is unknown. Here, we characterize the Z chromosome by detecting genomic regions that show lower genomic coverage in female than in male samples, and regions that harbor an excess of female-specific SNPs. We detect many Z-specific genes, which no longer have homologs on the W, but also Z-linked genes that appear to have diverged very recently from their existing W-linked homolog. We assess patterns of male and female expression in two tissues with extensive morphological dimorphism, gonads, and heads. In agreement with their morphology, sex-biased expression is common in both tissues. Interestingly, the Z chromosome is not enriched for sex-biased genes, and seems to in fact have a mechanism of dosage compensation that leads to equal expression in males and in females. Both of these patterns are contrary to most ZW systems studied so far, making A. franciscana an excellent model for investigating the interplay between the evolution of sexual dimorphism and dosage compensation, as well as Z chromosome evolution in general."}],"related_material":{"record":[{"relation":"popular_science","status":"public","id":"6060"}]},"scopus_import":"1"},{"status":"public","author":[{"id":"3184041C-F248-11E8-B48F-1D18A9856A87","first_name":"Victoria","full_name":"Pokusaeva, Victoria","last_name":"Pokusaeva","orcid":"0000-0001-7660-444X"},{"first_name":"Dinara R.","last_name":"Usmanova","full_name":"Usmanova, Dinara R."},{"last_name":"Putintseva","full_name":"Putintseva, Ekaterina V.","first_name":"Ekaterina V."},{"first_name":"Lorena","full_name":"Espinar, Lorena","last_name":"Espinar"},{"first_name":"Karen","id":"39A7BF80-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5375-6341","last_name":"Sarkisyan","full_name":"Sarkisyan, Karen"},{"full_name":"Mishin, Alexander S.","last_name":"Mishin","first_name":"Alexander S."},{"last_name":"Bogatyreva","full_name":"Bogatyreva, Natalya S.","first_name":"Natalya S."},{"full_name":"Ivankov, Dmitry","last_name":"Ivankov","id":"49FF1036-F248-11E8-B48F-1D18A9856A87","first_name":"Dmitry"},{"first_name":"Arseniy","id":"430D2C90-F248-11E8-B48F-1D18A9856A87","last_name":"Akopyan","full_name":"Akopyan, Arseniy","orcid":"0000-0002-2548-617X"},{"last_name":"Avvakumov","full_name":"Avvakumov, Sergey","id":"3827DAC8-F248-11E8-B48F-1D18A9856A87","first_name":"Sergey"},{"last_name":"Povolotskaya","full_name":"Povolotskaya, Inna S.","first_name":"Inna S."},{"full_name":"Filion, Guillaume J.","last_name":"Filion","first_name":"Guillaume J."},{"first_name":"Lucas B.","last_name":"Carey","full_name":"Carey, Lucas B."},{"last_name":"Kondrashov","full_name":"Kondrashov, Fyodor","orcid":"0000-0001-8243-4694","first_name":"Fyodor","id":"44FDEF62-F248-11E8-B48F-1D18A9856A87"}],"scopus_import":"1","related_material":{"record":[{"id":"9789","status":"public","relation":"research_data"},{"id":"9790","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9797"}]},"abstract":[{"lang":"eng","text":"Characterizing the fitness landscape, a representation of fitness for a large set of genotypes, is key to understanding how genetic information is interpreted to create functional organisms. Here we determined the evolutionarily-relevant segment of the fitness landscape of His3, a gene coding for an enzyme in the histidine synthesis pathway, focusing on combinations of amino acid states found at orthologous sites of extant species. Just 15% of amino acids found in yeast His3 orthologues were always neutral while the impact on fitness of the remaining 85% depended on the genetic background. Furthermore, at 67% of sites, amino acid replacements were under sign epistasis, having both strongly positive and negative effect in different genetic backgrounds. 46% of sites were under reciprocal sign epistasis. The fitness impact of amino acid replacements was influenced by only a few genetic backgrounds but involved interaction of multiple sites, shaping a rugged fitness landscape in which many of the shortest paths between highly fit genotypes are inaccessible."}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-25T10:30:37Z","department":[{"_id":"FyKo"}],"project":[{"grant_number":"665385","name":"International IST Doctoral Program","call_identifier":"H2020","_id":"2564DBCA-B435-11E9-9278-68D0E5697425"}],"year":"2019","month":"04","publication_identifier":{"eissn":["15537404"]},"isi":1,"external_id":{"isi":["000466866000029"]},"publication_status":"published","issue":"4","_id":"6419","type":"journal_article","ddc":["570"],"file":[{"access_level":"open_access","content_type":"application/pdf","date_updated":"2020-07-14T12:47:30Z","file_size":3726017,"checksum":"cf3889c8a8a16053dacf9c3776cbe217","date_created":"2019-05-14T08:26:08Z","file_name":"2019_PLOSGenetics_Pokusaeva.pdf","file_id":"6445","creator":"dernst","relation":"main_file"}],"oa_version":"Published Version","publisher":"Public Library of Science","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"ec_funded":1,"article_processing_charge":"No","file_date_updated":"2020-07-14T12:47:30Z","doi":"10.1371/journal.pgen.1008079","date_published":"2019-04-10T00:00:00Z","has_accepted_license":"1","intvolume":"        15","publication":"PLoS Genetics","day":"10","volume":15,"title":"An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape","quality_controlled":"1","citation":{"short":"V. Pokusaeva, D.R. Usmanova, E.V. Putintseva, L. Espinar, K. Sarkisyan, A.S. Mishin, N.S. Bogatyreva, D. Ivankov, A. Akopyan, S. Avvakumov, I.S. Povolotskaya, G.J. Filion, L.B. Carey, F. Kondrashov, PLoS Genetics 15 (2019).","ista":"Pokusaeva V, Usmanova DR, Putintseva EV, Espinar L, Sarkisyan K, Mishin AS, Bogatyreva NS, Ivankov D, Akopyan A, Avvakumov S, Povolotskaya IS, Filion GJ, Carey LB, Kondrashov F. 2019. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. PLoS Genetics. 15(4), e1008079.","ieee":"V. Pokusaeva <i>et al.</i>, “An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape,” <i>PLoS Genetics</i>, vol. 15, no. 4. Public Library of Science, 2019.","ama":"Pokusaeva V, Usmanova DR, Putintseva EV, et al. An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. <i>PLoS Genetics</i>. 2019;15(4). doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079\">10.1371/journal.pgen.1008079</a>","chicago":"Pokusaeva, Victoria, Dinara R. Usmanova, Ekaterina V. Putintseva, Lorena Espinar, Karen Sarkisyan, Alexander S. Mishin, Natalya S. Bogatyreva, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” <i>PLoS Genetics</i>. Public Library of Science, 2019. <a href=\"https://doi.org/10.1371/journal.pgen.1008079\">https://doi.org/10.1371/journal.pgen.1008079</a>.","apa":"Pokusaeva, V., Usmanova, D. R., Putintseva, E. V., Espinar, L., Sarkisyan, K., Mishin, A. S., … Kondrashov, F. (2019). An experimental assay of the interactions of amino acids from orthologous sequences shaping a complex fitness landscape. <i>PLoS Genetics</i>. Public Library of Science. <a href=\"https://doi.org/10.1371/journal.pgen.1008079\">https://doi.org/10.1371/journal.pgen.1008079</a>","mla":"Pokusaeva, Victoria, et al. “An Experimental Assay of the Interactions of Amino Acids from Orthologous Sequences Shaping a Complex Fitness Landscape.” <i>PLoS Genetics</i>, vol. 15, no. 4, e1008079, Public Library of Science, 2019, doi:<a href=\"https://doi.org/10.1371/journal.pgen.1008079\">10.1371/journal.pgen.1008079</a>."},"date_created":"2019-05-13T07:58:38Z","oa":1,"article_number":"e1008079"},{"oa":1,"conference":{"end_date":"2019-04-18","location":"Montreal, Canada","start_date":"2019-04-16","name":"HSCC: Hybrid Systems Computation and Control"},"quality_controlled":"1","date_created":"2019-05-13T08:13:46Z","citation":{"ama":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. Interface-aware signal temporal logic. In: <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>. ACM; 2019:57-66. doi:<a href=\"https://doi.org/10.1145/3302504.3311800\">10.1145/3302504.3311800</a>","short":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, J. Kapinski, in:, Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control, ACM, 2019, pp. 57–66.","ieee":"T. Ferrere, D. Nickovic, A. Donzé, H. Ito, and J. Kapinski, “Interface-aware signal temporal logic,” in <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>, Montreal, Canada, 2019, pp. 57–66.","ista":"Ferrere T, Nickovic D, Donzé A, Ito H, Kapinski J. 2019. Interface-aware signal temporal logic. Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control. HSCC: Hybrid Systems Computation and Control, 57–66.","apa":"Ferrere, T., Nickovic, D., Donzé, A., Ito, H., &#38; Kapinski, J. (2019). Interface-aware signal temporal logic. In <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i> (pp. 57–66). Montreal, Canada: ACM. <a href=\"https://doi.org/10.1145/3302504.3311800\">https://doi.org/10.1145/3302504.3311800</a>","chicago":"Ferrere, Thomas, Dejan Nickovic, Alexandre Donzé, Hisahiro Ito, and James Kapinski. “Interface-Aware Signal Temporal Logic.” In <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>, 57–66. ACM, 2019. <a href=\"https://doi.org/10.1145/3302504.3311800\">https://doi.org/10.1145/3302504.3311800</a>.","mla":"Ferrere, Thomas, et al. “Interface-Aware Signal Temporal Logic.” <i>Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control</i>, ACM, 2019, pp. 57–66, doi:<a href=\"https://doi.org/10.1145/3302504.3311800\">10.1145/3302504.3311800</a>."},"page":"57-66","title":"Interface-aware signal temporal logic","publication":"Proceedings of the 2019 22nd ACM International Conference on Hybrid Systems: Computation and Control","day":"16","date_published":"2019-04-16T00:00:00Z","has_accepted_license":"1","file_date_updated":"2020-10-08T17:25:45Z","doi":"10.1145/3302504.3311800","article_processing_charge":"No","publisher":"ACM","_id":"6428","publication_status":"published","external_id":{"isi":["000516713900007"]},"file":[{"file_name":"2019_ACM_Ferrere.pdf","relation":"main_file","file_id":"8633","creator":"dernst","date_updated":"2020-10-08T17:25:45Z","access_level":"open_access","content_type":"application/pdf","date_created":"2020-10-08T17:25:45Z","checksum":"b8e967081e051d1c55ca5d18fb187890","file_size":1055421,"success":1}],"ddc":["000"],"oa_version":"Submitted Version","type":"conference","year":"2019","month":"04","project":[{"grant_number":"S 11407_N23","_id":"25832EC2-B435-11E9-9278-68D0E5697425","name":"Rigorous Systems Engineering","call_identifier":"FWF"},{"call_identifier":"FWF","name":"The Wittgenstein Prize","_id":"25F42A32-B435-11E9-9278-68D0E5697425","grant_number":"Z211"}],"isi":1,"publication_identifier":{"isbn":["9781450362825"]},"department":[{"_id":"ToHe"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-25T10:19:23Z","scopus_import":"1","abstract":[{"text":"Safety and security are major concerns in the development of Cyber-Physical Systems (CPS). Signal temporal logic (STL) was proposedas a language to specify and monitor the correctness of CPS relativeto formalized requirements. Incorporating STL into a developmentprocess enables designers to automatically monitor and diagnosetraces, compute robustness estimates based on requirements, andperform requirement falsification, leading to productivity gains inverification and validation activities; however, in its current formSTL is agnostic to the input/output classification of signals, andthis negatively impacts the relevance of the analysis results.In this paper we propose to make the interface explicit in theSTL language by introducing input/output signal declarations. Wethen define new measures of input vacuity and output robustnessthat better reflect the nature of the system and the specification in-tent. The resulting framework, which we call interface-aware signaltemporal logic (IA-STL), aids verification and validation activities.We demonstrate the benefits of IA-STL on several CPS analysisactivities: (1) robustness-driven sensitivity analysis, (2) falsificationand (3) fault localization. We describe an implementation of our en-hancement to STL and associated notions of robustness and vacuityin a prototype extension of Breach, a MATLAB®/Simulink®toolboxfor CPS verification and validation. We explore these methodologi-cal improvements and evaluate our results on two examples fromthe automotive domain: a benchmark powertrain control systemand a hydrogen fuel cell system.","lang":"eng"}],"author":[{"first_name":"Thomas","id":"40960E6E-F248-11E8-B48F-1D18A9856A87","last_name":"Ferrere","full_name":"Ferrere, Thomas","orcid":"0000-0001-5199-3143"},{"last_name":"Nickovic","full_name":"Nickovic, Dejan","id":"41BCEE5C-F248-11E8-B48F-1D18A9856A87","first_name":"Dejan"},{"first_name":"Alexandre","full_name":"Donzé, Alexandre","last_name":"Donzé"},{"last_name":"Ito","full_name":"Ito, Hisahiro","first_name":"Hisahiro"},{"first_name":"James","full_name":"Kapinski, James","last_name":"Kapinski"}],"status":"public"},{"page":"317-346","title":"Adaptively secure proxy re-encryption","oa":1,"citation":{"short":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, K.Z. Pietrzak, in:, Springer Nature, 2019, pp. 317–346.","ista":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. 2019. Adaptively secure proxy re-encryption. PKC: Public-Key Cryptograhy, LNCS, vol. 11443, 317–346.","ieee":"G. Fuchsbauer, C. Kamath Hosdurg, K. Klein, and K. Z. Pietrzak, “Adaptively secure proxy re-encryption,” presented at the PKC: Public-Key Cryptograhy, Beijing, China, 2019, vol. 11443, pp. 317–346.","ama":"Fuchsbauer G, Kamath Hosdurg C, Klein K, Pietrzak KZ. Adaptively secure proxy re-encryption. In: Vol 11443. Springer Nature; 2019:317-346. doi:<a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">10.1007/978-3-030-17259-6_11</a>","chicago":"Fuchsbauer, Georg, Chethan Kamath Hosdurg, Karen Klein, and Krzysztof Z Pietrzak. “Adaptively Secure Proxy Re-Encryption,” 11443:317–46. Springer Nature, 2019. <a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">https://doi.org/10.1007/978-3-030-17259-6_11</a>.","apa":"Fuchsbauer, G., Kamath Hosdurg, C., Klein, K., &#38; Pietrzak, K. Z. (2019). Adaptively secure proxy re-encryption (Vol. 11443, pp. 317–346). Presented at the PKC: Public-Key Cryptograhy, Beijing, China: Springer Nature. <a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">https://doi.org/10.1007/978-3-030-17259-6_11</a>","mla":"Fuchsbauer, Georg, et al. <i>Adaptively Secure Proxy Re-Encryption</i>. Vol. 11443, Springer Nature, 2019, pp. 317–46, doi:<a href=\"https://doi.org/10.1007/978-3-030-17259-6_11\">10.1007/978-3-030-17259-6_11</a>."},"date_created":"2019-05-13T08:13:46Z","quality_controlled":"1","conference":{"end_date":"2019-04-17","location":"Beijing, China","name":"PKC: Public-Key Cryptograhy","start_date":"2019-04-14"},"doi":"10.1007/978-3-030-17259-6_11","article_processing_charge":"No","ec_funded":1,"day":"06","volume":11443,"intvolume":"     11443","date_published":"2019-04-06T00:00:00Z","publication_identifier":{"isbn":["9783030172589"],"issn":["03029743"],"eissn":["16113349"]},"project":[{"grant_number":"682815","_id":"258AA5B2-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"Teaching Old Crypto New Tricks"}],"year":"2019","month":"04","department":[{"_id":"KrPi"}],"publisher":"Springer Nature","oa_version":"Preprint","type":"conference","alternative_title":["LNCS"],"publication_status":"published","_id":"6430","status":"public","author":[{"last_name":"Fuchsbauer","full_name":"Fuchsbauer, Georg","first_name":"Georg","id":"46B4C3EE-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Kamath Hosdurg, Chethan","last_name":"Kamath Hosdurg","id":"4BD3F30E-F248-11E8-B48F-1D18A9856A87","first_name":"Chethan"},{"last_name":"Klein","full_name":"Klein, Karen","id":"3E83A2F8-F248-11E8-B48F-1D18A9856A87","first_name":"Karen"},{"first_name":"Krzysztof Z","id":"3E04A7AA-F248-11E8-B48F-1D18A9856A87","full_name":"Pietrzak, Krzysztof Z","last_name":"Pietrzak","orcid":"0000-0002-9139-1654"}],"date_updated":"2023-09-08T11:33:20Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"status":"public","relation":"dissertation_contains","id":"10035"}]},"main_file_link":[{"open_access":"1","url":"https://eprint.iacr.org/2018/426"}],"abstract":[{"lang":"eng","text":"A proxy re-encryption (PRE) scheme is a public-key encryption scheme that allows the holder of a key pk to derive a re-encryption key for any other key 𝑝𝑘′. This re-encryption key lets anyone transform ciphertexts under pk into ciphertexts under 𝑝𝑘′ without having to know the underlying message, while transformations from 𝑝𝑘′ to pk should not be possible (unidirectional). Security is defined in a multi-user setting against an adversary that gets the users’ public keys and can ask for re-encryption keys and can corrupt users by requesting their secret keys. Any ciphertext that the adversary cannot trivially decrypt given the obtained secret and re-encryption keys should be secure.\r\n\r\nAll existing security proofs for PRE only show selective security, where the adversary must first declare the users it wants to corrupt. This can be lifted to more meaningful adaptive security by guessing the set of corrupted users among the n users, which loses a factor exponential in  Open image in new window , rendering the result meaningless already for moderate Open image in new window .\r\n\r\nJafargholi et al. (CRYPTO’17) proposed a framework that in some cases allows to give adaptive security proofs for schemes which were previously only known to be selectively secure, while avoiding the exponential loss that results from guessing the adaptive choices made by an adversary. We apply their framework to PREs that satisfy some natural additional properties. Concretely, we give a more fine-grained reduction for several unidirectional PREs, proving adaptive security at a much smaller loss. The loss depends on the graph of users whose edges represent the re-encryption keys queried by the adversary. For trees and chains the loss is quasi-polynomial in the size and for general graphs it is exponential in their depth and indegree (instead of their size as for previous reductions). Fortunately, trees and low-depth graphs cover many, if not most, interesting applications.\r\n\r\nOur results apply e.g. to the bilinear-map based PRE schemes by Ateniese et al. (NDSS’05 and CT-RSA’09), Gentry’s FHE-based scheme (STOC’09) and the LWE-based scheme by Chandran et al. (PKC’14)."}],"scopus_import":"1"},{"day":"07","has_accepted_license":"1","degree_awarded":"PhD","date_published":"2019-05-07T00:00:00Z","doi":"10.15479/AT:ISTA:6435","file_date_updated":"2021-02-11T11:17:15Z","ec_funded":1,"article_processing_charge":"No","oa":1,"citation":{"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>.","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>","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>.","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.","ista":"Casillas Perez BE. 2019. Collective defenses of garden ants against a fungal pathogen. Institute of Science and Technology Austria.","ieee":"B. E. Casillas Perez, “Collective defenses of garden ants against a fungal pathogen,” Institute of Science and Technology Austria, 2019."},"date_created":"2019-05-13T08:58:35Z","acknowledged_ssus":[{"_id":"Bio"},{"_id":"ScienComp"},{"_id":"M-Shop"},{"_id":"LifeSc"}],"page":"183","title":"Collective defenses of garden ants against a fungal pathogen","date_updated":"2023-09-07T12:57:04Z","language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","related_material":{"record":[{"relation":"part_of_dissertation","status":"public","id":"1999"}]},"keyword":["Social Immunity","Sanitary care","Social Insects","Organisational Immunity","Colony development","Multi-target tracking"],"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"}],"status":"public","author":[{"id":"351ED2AA-F248-11E8-B48F-1D18A9856A87","first_name":"Barbara E","full_name":"Casillas Perez, Barbara E","last_name":"Casillas Perez"}],"publisher":"Institute of Science and Technology Austria","supervisor":[{"first_name":"Sylvia M","id":"2F64EC8C-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-2193-3868","full_name":"Cremer, Sylvia M","last_name":"Cremer"}],"oa_version":"Published Version","type":"dissertation","ddc":["570","006","578","592"],"file":[{"date_created":"2019-05-13T09:16:20Z","file_size":3895187,"checksum":"6daf2d2086111aa8fd3fbc919a3e2833","date_updated":"2021-02-11T11:17:15Z","content_type":"application/pdf","embargo":"2020-05-08","access_level":"open_access","relation":"main_file","creator":"casillas","file_id":"6438","file_name":"tesisDoctoradoBC.pdf"},{"file_name":"tesisDoctoradoBC.zip","relation":"source_file","creator":"casillas","file_id":"6439","date_updated":"2020-07-14T12:47:30Z","content_type":"application/zip","access_level":"closed","date_created":"2019-05-13T09:16:20Z","embargo_to":"open_access","checksum":"3d221aaff7559a7060230a1ff610594f","file_size":7365118}],"publication_status":"published","alternative_title":["ISTA Thesis"],"_id":"6435","publication_identifier":{"issn":["2663-337X"]},"project":[{"grant_number":"771402","call_identifier":"H2020","name":"Epidemics in ant societies on a chip","_id":"2649B4DE-B435-11E9-9278-68D0E5697425"}],"month":"05","year":"2019","department":[{"_id":"SyCr"}]},{"title":"Fundamental solutions for water wave animation","oa":1,"article_number":"130","quality_controlled":"1","date_created":"2019-05-14T07:04:06Z","acknowledged_ssus":[{"_id":"ScienComp"}],"citation":{"ama":"Schreck C, Hafner C, Wojtan C. Fundamental solutions for water wave animation. <i>ACM Transactions on Graphics</i>. 2019;38(4). doi:<a href=\"https://doi.org/10.1145/3306346.3323002\">10.1145/3306346.3323002</a>","short":"C. Schreck, C. Hafner, C. Wojtan, ACM Transactions on Graphics 38 (2019).","ieee":"C. Schreck, C. Hafner, and C. Wojtan, “Fundamental solutions for water wave animation,” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4. ACM, 2019.","ista":"Schreck C, Hafner C, Wojtan C. 2019. Fundamental solutions for water wave animation. ACM Transactions on Graphics. 38(4), 130.","apa":"Schreck, C., Hafner, C., &#38; Wojtan, C. (2019). Fundamental solutions for water wave animation. <i>ACM Transactions on Graphics</i>. ACM. <a href=\"https://doi.org/10.1145/3306346.3323002\">https://doi.org/10.1145/3306346.3323002</a>","chicago":"Schreck, Camille, Christian Hafner, and Chris Wojtan. “Fundamental Solutions for Water Wave Animation.” <i>ACM Transactions on Graphics</i>. ACM, 2019. <a href=\"https://doi.org/10.1145/3306346.3323002\">https://doi.org/10.1145/3306346.3323002</a>.","mla":"Schreck, Camille, et al. “Fundamental Solutions for Water Wave Animation.” <i>ACM Transactions on Graphics</i>, vol. 38, no. 4, 130, ACM, 2019, doi:<a href=\"https://doi.org/10.1145/3306346.3323002\">10.1145/3306346.3323002</a>."},"file_date_updated":"2020-07-14T12:47:30Z","doi":"10.1145/3306346.3323002","ec_funded":1,"article_processing_charge":"No","publication":"ACM Transactions on Graphics","day":"01","volume":38,"date_published":"2019-07-01T00:00:00Z","intvolume":"        38","has_accepted_license":"1","project":[{"_id":"2533E772-B435-11E9-9278-68D0E5697425","name":"Efficient Simulation of Natural Phenomena at Extremely Large Scales","call_identifier":"H2020","grant_number":"638176"},{"_id":"24F9549A-B435-11E9-9278-68D0E5697425","name":"MATERIALIZABLE: Intelligent fabrication-oriented Computational Design and Modeling","call_identifier":"H2020","grant_number":"715767"},{"grant_number":"665385","_id":"2564DBCA-B435-11E9-9278-68D0E5697425","call_identifier":"H2020","name":"International IST Doctoral Program"}],"month":"07","year":"2019","isi":1,"department":[{"_id":"ChWo"}],"publisher":"ACM","publication_status":"published","external_id":{"isi":["000475740600104"]},"_id":"6442","issue":"4","ddc":["000","005"],"file":[{"relation":"main_file","file_id":"6443","creator":"dernst","file_name":"2019_ACM_Schreck.pdf","date_created":"2019-05-14T07:03:55Z","checksum":"1b737dfe3e051aba8f3f4ab1dceda673","file_size":44328918,"date_updated":"2020-07-14T12:47:30Z","access_level":"open_access","content_type":"application/pdf"}],"oa_version":"Submitted Version","type":"journal_article","status":"public","author":[{"first_name":"Camille","id":"2B14B676-F248-11E8-B48F-1D18A9856A87","full_name":"Schreck, Camille","last_name":"Schreck"},{"first_name":"Christian","id":"400429CC-F248-11E8-B48F-1D18A9856A87","full_name":"Hafner, Christian","last_name":"Hafner"},{"orcid":"0000-0001-6646-5546","full_name":"Wojtan, Christopher J","last_name":"Wojtan","id":"3C61F1D2-F248-11E8-B48F-1D18A9856A87","first_name":"Christopher J"}],"language":[{"iso":"eng"}],"user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","date_updated":"2023-08-25T10:18:46Z","scopus_import":"1","related_material":{"link":[{"url":"https://ist.ac.at/en/news/new-method-makes-realistic-water-wave-animations-more-efficient/","relation":"press_release","description":"News on IST Homepage"}]},"abstract":[{"lang":"eng","text":"This paper investigates the use of fundamental solutions for animating detailed linear water surface waves. We first propose an analytical solution for efficiently animating circular ripples in closed form. We then show how to adapt the method of fundamental solutions (MFS) to create ambient waves interacting with complex obstacles. Subsequently, we present a novel wavelet-based discretization which outperforms the state of the art MFS approach for simulating time-varying water surface waves with moving obstacles. Our results feature high-resolution spatial details, interactions with complex boundaries, and large open ocean domains. Our method compares favorably with previous work as well as known analytical solutions. We also present comparisons between our method and real world examples."}]},{"title":"EGFR controls hair shaft differentiation in a p53-independent manner","page":"243-256","quality_controlled":"1","citation":{"chicago":"Amberg, Nicole, Panagiota A. Sotiropoulou, Gerwin Heller, Beate M. Lichtenberger, Martin Holcmann, Bahar Camurdanoglu, Temenuschka Baykuscheva-Gentscheva, Cedric Blanpain, and Maria Sibilia. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” <i>IScience</i>. Elsevier, 2019. <a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">https://doi.org/10.1016/j.isci.2019.04.018</a>.","apa":"Amberg, N., Sotiropoulou, P. A., Heller, G., Lichtenberger, B. M., Holcmann, M., Camurdanoglu, B., … Sibilia, M. (2019). EGFR controls hair shaft differentiation in a p53-independent manner. <i>IScience</i>. Elsevier. <a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">https://doi.org/10.1016/j.isci.2019.04.018</a>","mla":"Amberg, Nicole, et al. “EGFR Controls Hair Shaft Differentiation in a P53-Independent Manner.” <i>IScience</i>, vol. 15, Elsevier, 2019, pp. 243–56, doi:<a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">10.1016/j.isci.2019.04.018</a>.","ista":"Amberg N, Sotiropoulou PA, Heller G, Lichtenberger BM, Holcmann M, Camurdanoglu B, Baykuscheva-Gentscheva T, Blanpain C, Sibilia M. 2019. EGFR controls hair shaft differentiation in a p53-independent manner. iScience. 15, 243–256.","ieee":"N. Amberg <i>et al.</i>, “EGFR controls hair shaft differentiation in a p53-independent manner,” <i>iScience</i>, vol. 15. Elsevier, pp. 243–256, 2019.","short":"N. Amberg, P.A. Sotiropoulou, G. Heller, B.M. Lichtenberger, M. Holcmann, B. Camurdanoglu, T. Baykuscheva-Gentscheva, C. Blanpain, M. Sibilia, IScience 15 (2019) 243–256.","ama":"Amberg N, Sotiropoulou PA, Heller G, et al. EGFR controls hair shaft differentiation in a p53-independent manner. <i>iScience</i>. 2019;15:243-256. doi:<a href=\"https://doi.org/10.1016/j.isci.2019.04.018\">10.1016/j.isci.2019.04.018</a>"},"date_created":"2019-05-14T11:47:40Z","oa":1,"article_processing_charge":"No","tmp":{"image":"/images/cc_by_nc_nd.png","name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)"},"file_date_updated":"2020-07-14T12:47:30Z","doi":"10.1016/j.isci.2019.04.018","date_published":"2019-05-31T00:00:00Z","has_accepted_license":"1","intvolume":"        15","volume":15,"publication":"iScience","day":"31","department":[{"_id":"SiHi"}],"month":"05","year":"2019","isi":1,"publication_identifier":{"issn":["2589-0042"]},"_id":"6451","publication_status":"published","external_id":{"isi":["000470104600022"]},"type":"journal_article","file":[{"file_name":"2019_iScience_Amberg.pdf","relation":"main_file","creator":"dernst","file_id":"6452","date_updated":"2020-07-14T12:47:30Z","content_type":"application/pdf","access_level":"open_access","date_created":"2019-05-14T11:51:51Z","checksum":"a9ad2296726c9474ad5860c9c2f53622","file_size":8365970}],"oa_version":"Published Version","ddc":["570"],"publisher":"Elsevier","author":[{"orcid":"0000-0002-3183-8207","last_name":"Amberg","full_name":"Amberg, Nicole","id":"4CD6AAC6-F248-11E8-B48F-1D18A9856A87","first_name":"Nicole"},{"first_name":"Panagiota A.","last_name":"Sotiropoulou","full_name":"Sotiropoulou, Panagiota A."},{"full_name":"Heller, Gerwin","last_name":"Heller","first_name":"Gerwin"},{"last_name":"Lichtenberger","full_name":"Lichtenberger, Beate M.","first_name":"Beate M."},{"last_name":"Holcmann","full_name":"Holcmann, Martin","first_name":"Martin"},{"last_name":"Camurdanoglu","full_name":"Camurdanoglu, Bahar","first_name":"Bahar"},{"first_name":"Temenuschka","full_name":"Baykuscheva-Gentscheva, Temenuschka","last_name":"Baykuscheva-Gentscheva"},{"first_name":"Cedric","full_name":"Blanpain, Cedric","last_name":"Blanpain"},{"full_name":"Sibilia, Maria","last_name":"Sibilia","first_name":"Maria"}],"status":"public","abstract":[{"text":"Epidermal growth factor receptor (EGFR) signaling controls skin development and homeostasis inmice and humans, and its deficiency causes severe skin inflammation, which might affect epidermalstem cell behavior. Here, we describe the inflammation-independent effects of EGFR deficiency dur-ing skin morphogenesis and in adult hair follicle stem cells. Expression and alternative splicing analysisof RNA sequencing data from interfollicular epidermis and outer root sheath indicate that EGFR con-trols genes involved in epidermal differentiation and also in centrosome function, DNA damage, cellcycle, and apoptosis. Genetic experiments employingp53deletion in EGFR-deficient epidermis revealthat EGFR signaling exhibitsp53-dependent functions in proliferative epidermal compartments, aswell asp53-independent functions in differentiated hair shaft keratinocytes. Loss of EGFR leads toabsence of LEF1 protein specifically in the innermost epithelial hair layers, resulting in disorganizationof medulla cells. Thus, our results uncover important spatial and temporal features of cell-autonomousEGFR functions in the epidermis.","lang":"eng"}],"language":[{"iso":"eng"}],"user_id":"c635000d-4b10-11ee-a964-aac5a93f6ac1","date_updated":"2023-09-08T11:38:04Z"}]